GcatWiki - User contributions [en]

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:10:38Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC454214/] '''gene-specific promoter element is required for optimal expression of the histone H1 gene in S-phase.'''

*[http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.57.030502.090913] '''Multiple Sigma Factors'''

'''Promoters Section'''

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)'''

*http://partsregistry.org/PBAD_Promoter_Family

'''C-Dog Section'''

*

*

'''Degradation Tag Section'''

*

*

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:08:42Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC454214/] '''gene-specific promoter element is required for optimal expression of the histone H1 gene in S-phase.'''
'''Promoters Section'''

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)'''

*http://partsregistry.org/PBAD_Promoter_Family

'''C-Dog Section'''

*

*

'''Degradation Tag Section'''

*

*

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:07:16Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

'''Promoters Section'''

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)'''

*http://partsregistry.org/PBAD_Promoter_Family

'''C-Dog Section'''

*

*

'''Degradation Tag Section'''

*

*

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:06:14Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

'''Promoters Section'''

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)'''

*

'''C-Dog Section'''

*

*

'''Degradation Tag Section'''

*

*

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:04:57Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts--all inclusive and in regards to any and all parts that are listed, or wish to be listed'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

Promoters Section

*['''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

*

C-Dog Section

*

*

Degradation Tag Section

*

*

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:01:26Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:00:50Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
**'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:00:32Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
**[http://www.sciencedirect.com/science/article/pii/0022519364900189] Abstract of a 1968 study that used analog computers to model a bacterial cell

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:00:17Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T20:00:02Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:59:08Z

Jmorton3:

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Research Papers, Articles & Manuscripts'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:56:09Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''
== Articles, Papers & Manuscripts ==
'''

*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

*'''6 possible promoters for project 3 constitutive, 3 inducible - (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:54:19Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Articles, Papers & Manuscripts'''

**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/ '''Degradation Tags with Gfp protein reporters - research paper''']

**['''6 possible promoters for project (3 constitutive, 3 inducible (Word file not yet saved on wiki)''']

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:52:02Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
*'''Articles, Papers & Manuscripts'''

**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] '''Degradation Tags with Gfp protein reporters - research paper'''

[6 possible promoters for project (3 constitutive, 3 inducible)] "Word file not yet saved on wiki"

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:50:59Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Articles, Papers & Manuscripts'''

**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] Degradation Tags with Gfp protein reporters - research paper

[6 possible promoters for project (3 constitutive, 3 inducible)] "Word file not yet saved on wiki"

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:50:01Z

Jmorton3: /* Library of Parts */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==
'''Articles, Papers & Manuscripts'''
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] Degradation Tags with Gfp protein reporters - research paper

[6 possible promoters for project (3 constitutive, 3 inducible)] "Word file not yet saved on wiki"

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:43:00Z

Jmorton3: /* Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library of Parts==

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] Degradation Tags with Gfp protein reporters - research paper

[6 possible promoters for project (3 constitutive, 3 inducible)] "Word file not yet saved on wiki"

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:42:35Z

Jmorton3: /* Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library==

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] Degradation Tags with Gfp protein reporters - research paper

[6 possible promoters for project (3 constitutive, 3 inducible)] "Word file not yet saved on wiki"

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
**[http://jb.asm.org/content/187/1/175.full '''BBG29 gene from 'Borrelia'''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
**[http://www.analogmuseum.org/english/] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:25:28Z

Jmorton3: /* Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library==

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] Degradation Tags with Gfp protein reporters - research paper

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:25:11Z

Jmorton3: /* Assembly */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library==

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:24:19Z

Jmorton3: /* Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library==

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:22:28Z

Jmorton3:

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Library==

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T19:20:28Z

Jmorton3: /* Assembly and Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

[http://www.cambridgeigem.org/RFC57.pdf]Assembly of BioBricks by the Gibson Method

==Selection Modules==
*'''Bad-ish genes/proteins'''
**[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
**[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
**[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
**[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
**[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
**[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
**[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']
**[http://ajpcell.physiology.org/content/281/3/C733.full '''Eukaryotic membrane proteins toxic to E.coli''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98520/ '''HbpA proteins moderately toxic to E.coli''']
**[http://abbs.oxfordjournals.org/content/42/8/585.long '''Alpha-luffin and E.coli''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']
**[http://ardb.cbcb.umd.edu/ '''Database of Antibiotic Resistance Genes''']

'''Regulated Biosynthesis Pathways'''

http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]
*[http://www.ncbi.nlm.nih.gov/pubmed/21925140 Halorhodopsin can be expressed in E. coli: HsHR]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli: e-BO, e-BR]
*[https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf Using mechanosensitive channel of large conductance in E. coli as light-sensitive channel]
*[http://pubs.acs.org/doi/pdf/10.1021/bi201876p More detail on expressing NpHR/halorhodopsin in E. coli]
*[http://pubs.acs.org/doi/pdf/10.1021/bi011788g halorhodopsin in E. coli: phR]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
*'''Flux Balance Analysis'''
**[http://www.sciencedirect.com/science/article/pii/S0006349502739039 '''Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli''']
*'''Agent Based Models/Chaos'''
**[http://cscs.umich.edu/~crshalizi/weblog/556.html] Set of lecture slides on chaos, including one on ABMs.
**[http://edge.org/conversation/beyond-reductionism-reinventing-the-sacred] Stuart Kauffman on emergence
*'''Real Computing/Complexity'''
**[http://stellar.mit.edu/S/course/6/sp12/6.045/materials.html] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
**[http://arxiv.org/abs/quant-ph/0502072] Review of physical computing by the same researcher
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
**[http://hrl.harvard.edu/analog/] Harvard analog computing
**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
**[http://www.google.com/url?sa=t&rct=j&q=computing%20on%20the%20reals&source=web&cd=2&ved=0CFMQFjAB&url=http%3A%2F%2Fwww-2.cs.cmu.edu%2F~lblum%2FPAPERS%2FTuringMeetsNewton.pdf&ei=hlvGT9SLAoKy8QTq64nPBg&usg=AFQjCNE20AT9tGoGAZBrzaUSjxSeey1o9g] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas

Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
**[http://www.weizmann.ac.il/mcb/UriAlon/Network_motifs_in_coli/ColiNet-1.1/regInterFullFiltered.html '''List of Operons Repressed or Activated by ArcA in E. coli''']
**http://cat.inist.fr/?aModele=afficheN&cpsidt=6828850

*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T15:07:39Z

Jmorton3: /* Assembly and Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly and Library==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

==Selection Module==
*[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
*[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
*[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
*[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
*[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
*[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
*[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T15:07:13Z

Jmorton3: /* Assembly and Library */

<center>'''Summer 2012 Synthetic Biology Project: MWSU and Davidson College'''</center> 
# [[Davidson Protocols]] 
# [[MWSU_protocols]] 
# [http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
# [[Laboratory_Notebooks]] 
# [[Golden Gate]] 

== Student Proposals from Ind. Studies==
* Erich Baker Proposal: [[Media:Erich_Baker_proposal.docx]] This proposal deals with Phytochromes and Light Sensitive Channel Proteins

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms.
As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design.
-Caleb Carr

* Ben Clarkson Proposal: [[Media:Ben_Clarkson_proposal.docx]]
* Duke DeLoache Proposal: [[Media:Duke_DeLoache_Proposal.docx]]
* Becca Evans Proposal: [[Media:Becca_Evans_proposal.docx]]
* Ellen Johnson Proposal: [[Media:Ellen_Johnson_proposal.docx]]

 

== PPT Presentations ==

* This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. 
[[Media:Reports_on_Circuits.pptx]]

* This PPT contains slides summarizing some of the best and most complicated papers from Week 11. 
[[Media:Week_11.pptx]]

== Papers ==

''Methods Papers''
* '''DNA assembly for synthetic biology: from parts to pathways and beyond''' 
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis, Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

*[http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].

* Everyone should watch this 5 minute video on [http://www.nature.com/nmeth/video/moy2010/index.html optogenetics]. Combine that video with the 2010 champoinship iGEM invention of [http://2010.igem.org/Team:Cambridge E. glowi].

''Older Lab Papers''
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. 
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.] 
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. 
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.] 
Journal of Biological Engineering. Vol. 3:11

*'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''. 
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] 
Interdisciplinary Bio Central. Vol. 3, article no. 10. 
[http://www.bio.davidson.edu/courses/genomics/2008/DeLoache/TimeDelayedAmpRDiffusionWithTimes.avi Time Delayed Growth Movie]

''Network Papers''
* [http://www.sciencemag.org/content/309/5743/2010.full.pdf '''Noise in Gene Expression: Origins, Consequences, and Control'''] 
Jonathan M. Raser and Erin K. O’Shea 
Science. Vol. 309, page 2010 

Please post pdf.
 

* [http://www.sciencemag.org/content/333/6047/1244.full.pdf '''Synthetic Biology: Integrated Gene Circuits'''] 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244. 

Please post pdf.
 

* [http://www.sciencemag.org/content/298/5594/824.full.pdf '''Network Motifs: Simple Building Blocks of Complex Networks'''] 
R. Milo, S. Shen-Orr, et al 
Science. Vol. 298, page 824. 

Please post pdf.
 

* [http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf '''Controllability of complex networks'''] 
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si 
Nature. 2011. Vol. 473, page 167. 

Please post pdf.
 

''Ethics Papers''
* [http://www.nature.com/news/2010/100616/pdf/465867a.pdf '''Talking the Talk'''] 
Colin Mcilswain 
Nature. Vol 465, page 867.

* [http://www.jbioleng.org/content/5/1/9/ Word selection affects perceptions of synthetic biology.] Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others).
-Eddie Miles

* Read "Moral" ethics paper on synthetic biology. [[Media:Moral.pdf]]

* Read "Future" ethics paper on synthetic biology. [[Media:Future.pdf]]

== Questions to Consider About Network Pathways ==

* Are they naturally occurring or synthetic?

* Do they involve screening or selection?

* Are they anabolic or catabolic?

* How many steps are in each pathway?

* How can they relate to cell fitness?

* What specific challenges would need to be addressed if we worked with the pathway?

[[Network Pathways Chart]]

==Cellular Automata==
*[http://cscs.umich.edu/~crshalizi/notabene/cellular-automata.html] General CA introduction
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton], [http://mathworld.wolfram.com/ElementaryCellularAutomaton.html] Elementary Cellular Automata
*[http://www.gmilburn.ca/2008/12/02/elementary-cellular-automata/] Good explanation of how elementary CAs work
*[http://en.wikipedia.org/wiki/Elementary_cellular_automaton] Rule 110

*[http://2008.igem.org/Team:Groningen '''iGEM Team Groningen''']
*[http://2009.igem.org/Team:LCG-UNAM-Mexico:CA '''iGEM Team IPN-UNAM Mexico''']
*[http://2011.igem.org/Team:MIT '''MIT 2011 iGEM Tissue Design''']
*[http://eudl.eu/pdf/10.4108/ICST.BIONETICS2007.2410 '''In Vivo Cellular Automata''']
*[http://www.taborlab.rice.edu/pdf/tabor_cell_2009.pdf '''Edge Detection PDF''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715369/pdf/1754-1611-3-10.pdf '''Patterning of E. coli''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700907/pdf/zpq10135.pdf '''Tunable Bacterial Band-Pass Filter''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387235/pdf/msb200824.pdf '''E. coli Predator-Prey Ecosystem''']
*[http://scholar.google.com/scholar_url?hl=en&q=http://www.plantsci.cam.ac.uk/Haseloff/teaching/iGEM/page229/downloads-5/downloads-11/files/Basu2005.pdf&sa=X&scisig=AAGBfm0_84Y23OGW3GgGOCerPyXGOSxd0A&oi=scholarr '''Multicellular System for Programmed Pattern Formation''']

==Peptides==
*[http://onlinelibrary.wiley.com/doi/10.1002/psc.1340/abstract '''Pep-1 can carry large amounts of cargo across cell membrane''']
*[http://jac.oxfordjournals.org/content/63/1/115.full.pdf+html '''Pep-1 has no anti-microbial activity against E. coli, see page 121''']
*[http://www.jenabioscience.com/cms/en/1/catalog/1271_internalization_cocktails.html]'''General Manual for CPP''' After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
*[http://www.anaspec.com/products/product.asp?id=48181 '''General info on Pep-1''']
*[http://repositorio.ul.pt/bitstream/10451/1605/1/17865_ulsd_re_143_PhDThesis_STHenriques.pdf '''Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start''']
*[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=45aaa8ea-e974-43b2-9fb1-a0fa30a0777e%40sessionmgr113&vid=2&hid=120 '''Pep-1 is a synthetic peptide''']
* [http://bmbreports.org/jbmb/jbmb_files/%5B39-5%5D0609282325_642.pdf '''Pep-1 fusion protein made in E. coli''']
* [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2001.02253.x/abstract '''Targeting proteins to E. coli periplasmic space (GFP)''']
* [http://www.biomedcentral.com/content/pdf/1475-2859-3-4.pdf '''Review of targeting proteins to periplasm''']

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles
[[http://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1B5IPKio2nb1G1c3hNf&search_mode=CitedFullRecord&isickref=WOS:000229493800001]]

==Assembly and Library==

[http://2010.igem.org/Team:Cambridge/Gibson/Introduction]iGEM Introduction to Gibson Assembly

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318.pdf]Enzymatic assembly of DNA molecules up to several hundred kilobases

[http://www.synbio.org.uk/gibson/resources/Gibson2009_nmeth.1318-S1.pdf] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

==Selection Module==
*[http://www.ncbi.nlm.nih.gov/pubmed?term=Toxicity%20of%20an%20overproduced%20foreign%20gene%20product%20in%20Escherichia%20coli%20and%20its%20use%20in%20plasmid%20vectors%20for%20the%20selection%20of%20transcription%20terminators '''Toxicity of rat insulin gene on E.coli''']
*[http://arep.med.harvard.edu/labgc/pko3.html '''SacB gene with sucrose and E.coli''']
*[http://genesdev.cshlp.org/content/20/15/2121.long '''Hda-mediated homeostasis in E.coli''']
*[http://pubs.acs.org/doi/full/10.1021/bi971732f '''Lon protease from M.smegmatis''']
*[http://www.microbialcellfactories.com/content/11/1/11 '''SinI enzyme has moderate growth-inhibition in E.coli''']
*[http://www.jbioleng.org/content/5/1/10 '''Excess violecein production toxic to E.coli''']
*[http://www.pnas.org/content/106/3/894.full.pdf '''ToxN inhibits growth of E.coli''']

==Light==
*[http://pubs.acs.org/doi/pdf/10.1021/bi0618058 Review of types and mechanisms of light-gated ion channels (2006)]
*[http://en.wikipedia.org/wiki/Channelrhodopsin Channelrhodopsins]
*[http://en.wikipedia.org/wiki/Halorhodopsin Halorhodopsin (NpHR)]
*[http://syntheticneurobiology.org/PDFs/11.01.chow.pdf p. 117: ChR2 doesn't express in E. coli?]

==Other Ideas==

*Networks (Modeling Focused)
**Field might be kind of saturated; it seems like a lot of work has been done.
***But not with netLogo. How could that work?
**RePast: another ABM suite that might be mroe suited to networks [http://repast.sourceforge.net/]
**'''General'''
***[http://www.nature.com/ng/journal/v31/n1/full/ng881.html '''Network motifs in the transcriptional regulation network of Escherichia coli''']
***[http://en.wikipedia.org/wiki/Gene_regulatory_network] Gene Regulatory Network wikipedia page
***[http://si2.epfl.ch/~demichel/graduates/theses/garg.pdf] long dissertation on modeling GRNs
***[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050008 '''Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles''']
**'''Process Calculus'''
***[http://en.wikipedia.org/wiki/Process_calculus] Process Calculus wikipedia page
***[[http://www.google.com/url?sa=t&rct=j&q=bioambients&source=web&cd=1&ved=0CFIQFjAA&url=http%3A%2F%2Flucacardelli.name%2FPapers%2FBioAmbients%2520An%2520Abstraction%2520for%2520Biological%2520Compartments.pdf&ei=7ai_T86aEYqi8QSwpInMCw&usg=AFQjCNEpF2xX4oheiDUWTIR6Q6ERuYmnkA&cad=rja '''BioAmbients: An abstraction for biological compartments'''] Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
**'''Boolean Networks'''
***[http://en.wikipedia.org/wiki/Boolean_network] Boolean Network wiki page; elementary CA are special cases of Boolean networks
***[http://www.phys.psu.edu/~ralbert/pdf/springer_final.pdf '''Boolean modeling of GRNs''']
***[http://w02.biomedcentral.com/1752-0509/2/21 '''The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response'']
***[http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/c1mb05094j '''Or-Not Logic Gate with E.Coli''']
**'''Dynamical Systems'''
***[http://www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdf '''Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast''']
***[http://www.springerlink.com/content/q247r247r28nkl86/ '''A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast''']
Communication
*Gas-Phase Communication
**[http://biocircuits.ucsd.edu/lev/papers/Prindle_Nature2012.pdf '''Biopixel Paper''']
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2007.05809.x/pdf '''ArcAB system in V. fischeri'''] Includes promoter sequences
**[http://www.sciencemag.org/content/292/5525/2314.full.html '''ArcAB system in E. Coli''']
**[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''ArcAB system Responses to Hydrogen Peroxide in E. coli''']
**[http://www.uniprot.org/uniprot/P0A9Q1 '''Amino Acid Sequence for ArcA in E. Coli''']
**[http://www.uniprot.org/uniprot/P0AEC3 '''Amino Acid Sequence for ArcB in E. Coli''']
**[http://www.uniprot.org/uniprot/B5FAK4 '''Amino Acid Sequence for ArcA in V. Fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri''']
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi '''Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri''']
**[http://jb.asm.org/content/178/21/6238.full.pdf+html '''Potential Promoters that ArcA Might Bind To in E. Coli''']
**[http://mic.sgmjournals.org/content/152/8/2207.long '''More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon''']
*Bacterial Conjugation
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829062/?tool=pubmed '''Conjugative transfer of antibiotic resistance''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655123/?tool=pubmed '''Molecular basis for control of conjugation''']
**[http://pubs.rsc.org/en/Content/ArticleLanding/2010/IB/b917761b '''Contour length of F-pili''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105745/?tool=pubmed '''Male-Specific Bacteriophages to inhibit mating''']
'''Neural Networks'''
*[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]

General
*[http://www.ncbi.nlm.nih.gov/books/NBK84445/ '''Workshop Summary of Applications of Synthetic Biology''']

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-29T18:40:04Z

Jmorton3: /* Peptides */

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-29T18:39:35Z

Jmorton3: /* Peptides */

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-29T18:37:42Z

Jmorton3: /* Peptides */

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-29T18:31:57Z

Jmorton3: /* Peptides */

Melanin Search Page

2011-07-05T17:13:53Z

Jmorton3:

This folder is a random collection of things pertaining to the color melanin and how it can be obtained for use as a single gene in e-coli--for use as a indicator. Some sites maybe listed below as a simple book mark for later reference, but may not be beneficial in the long run.

[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC526845/] This article shows melanin being used as marker and was taken from Streptomyces.

[http://www.jic.ac.uk/science/molmicro/Strept.html] A little back ground information of Streptomyces Coelicolor.

[http://scholar.google.com/scholar?q=streptomyces+coelicolor+%2B+melanin&hl=en&as_sdt=0&as_vis=1&oi=scholart] Google Scholar search.

[http://2009.igem.org/Team:Cambridge/Project/ME01] Team Cambridge's melanin 2009

[http://ghr.nlm.nih.gov/gene/TYR] Tyrosinase Defined

[http://www.sciencedirect.com/science/article/pii/S0141022905003546] Expression of the melA gene from Rhizobium etli CFN42 in Escherichia coli and characterization of the encoded tyrosinase

[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=347834&lvl=3&lin=f&keep=1&srchmode=1&unlock] NCBI R. etli CFN42

[http://gtps.ddbj.nig.ac.jp/single/index.php?chid=Retl_CFN42:p42d] Gene Trek in Prokaryote Space

Melanin Search Page

2011-06-29T16:49:35Z

Jmorton3:

Melanin Search Page

2011-06-29T16:04:21Z

Jmorton3:

Melanin Search Page

2011-06-29T14:43:39Z

Jmorton3:

Melanin Search Page

2011-06-29T14:24:19Z

Jmorton3:

Melanin Search Page

2011-06-27T16:52:06Z

Jmorton3:

Melanin Search Page

2011-06-27T16:45:23Z

Jmorton3:

Melanin Search Page

2011-06-27T16:39:17Z

Jmorton3:

Melanin Search Page

2011-06-27T16:37:33Z

Jmorton3: Created page with 'This folder is a random collection of things pertaining to the color melanin and how it can be obtained for use as a single gene in e-coli--for use as a marker. Some sites maybe …'

This folder is a random collection of things pertaining to the color melanin and how it can be obtained for use as a single gene in e-coli--for use as a marker. Some sites maybe listed below as a simple book mark for later reference, but may not be beneficial in the long run.

Missouri Western/Davidson SynBio 2011

2011-06-27T16:31:58Z

Jmorton3:

This space will be used starting May, 2011 for brainstorming and a shared whiteboard space. 

[[Davidson Protocols]] 
[[MWSU_protocols]] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
[[Laboratory_Notebooks]] 
[[Data Folder 2010]] 
[[DNA computing]] 
[[Golden Gate]] 
[[HPP Status]] 
[[HPP Oligos 6-9-11]] 
[[Set Covering Problem]] 
[[T7RNAp information page.]] 
[[Melanin Search Page]]

Missouri Western/Davidson SynBio 2011

2011-06-27T16:31:29Z

Jmorton3:

Missouri Western/Davidson SynBio 2011

2011-06-27T16:31:12Z

Jmorton3:

T7RNAp information page.

2011-06-21T16:15:52Z

Jmorton3:

[http://www.bio.davidson.edu/courses/genomics/lab/proteomics/t7rnapframe.html] 3D computer model of T7RNAp in elongation phase. Found on Davidson's website.

[http://www.nature.com/emboj/journal/v17/n14/full/7591110a.html] Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme

[http://academic.brooklyn.cuny.edu/chem/zhuang/Nicolas/structur.htm] Structural characterization of T7 RNAp

[http://www.euchromatin.net/Durniak01.html] Structure of Transcribing T7 RNAp. If you scroll down the page you find structural diagrams of T7 RNA in the initiation, intermediate, and elongation complexes.

T7RNAp information page.

2011-06-21T16:11:47Z

Jmorton3: