GcatWiki - User contributions [en]

Summer 2012 SynBio Project (Davidson and MWSU)

2012-05-30T18:43:13Z

Ccarr: /* Other Ideas */

<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

[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''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']

'''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]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli]
*[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]

==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

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)

2012-05-30T18:41:45Z

Ccarr: /* Selection Modules */

<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

[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''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']

'''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]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli]
*[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]

==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

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''']
*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)

2012-05-30T18:41:26Z

Ccarr: /* Selection Modules */

<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

[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''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']

'''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]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli]
*[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]

==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

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''']
*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)

2012-05-30T18:40:55Z

Ccarr: /* Selection Modules */

<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

[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''']
*'''Good genes/proteins'''
**[http://aac.asm.org/content/48/3/1066 '''Tet-resistance in E.coli''']

'''Regulated Biosynthesis Pathways'''

==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]
*[http://www.jbc.org/content/262/19/9271.full.pdf Expression of light-gated proton pumps in E. coli]
*[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]

==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

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''']
*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)

2012-05-24T22:20:02Z

Ccarr: /* Student Proposals from Ind. Studies */

Synthetic Biology Network Research

2012-02-17T23:48:14Z

Ccarr: /* MWSU */

This page is designed as a community page for students at MWSU and Davidson College who are using synthetic biology to learn more about graph theory and network topology.

==Davidson College==
Our first meeting will be on Thursday, January 19, 2012. We will meet at 11 am (the common hour) in the Think Tank in the back of Belk computer lab.

'''Grading'''
* Weekly Journals (your own paper summary and those of others) = 30% final grade
* Weekly Presentations = 30% final grade
* Research Proposal by teams = 40% final grade

You must keep hard copies of your weekly journal entries in a 3-ring binder. We will grade these periodically during the semester. You will also keep copies of your papers, any drawings of ideas you have, protocols used in lab, etc.

'''Scheduling with [http://doodle.com/xkssebxsv4g3rwxk Doodle]'''

[[WEEK ONE (January 17 - 20)]]

[[WEEK TWO (January 23 - 27)]]

[[WEEK THREE (January 30 - February 3)]]

[[WEEK FOUR (February 6 - 10)]] '''WET LAB WEEK'''

[[WEEK FIVE (February 13 - 17)]]

[[WEEK SIX (February 20 - 24)]] 
Synthetic Seminar 4:30 pm Feb. 23 in '''VAC classroom''' and '''lunch''' with [http://haynes.lab.asu.edu/index.html speaker Dr. Karmella Haynes] at Arizona State University

[[WEEK SEVEN (February 27 - March 2)]]

[[WEEK EIGHT (March 5 - 9)]] '''SPRING BREAK'''

[[WEEK NINE (March 12 - 16)]]

[[WEEK TEN (March 19 - 23)]]

[[WEEK ELEVEN (March 26 - 30)]]

[[WEEK TWELVE (April 2 - 6)]]

[[WEEK THIRTEEN (April 9 - 13)]] '''INCLUDES EASTER BREAK''' 
Genomics Seminar 4:30 pm April. 11 in '''Dana 146''' and '''lunch''' with [http://guolab.uncc.edu/members/jguo4 speaker Dr. Jun-tao Gua] at UNCC Bioinformatics

[[WEEK FOURTEEN (April 16 - 20)]] 
Genomics Seminar 4:30 pm April 18 in '''Dana 146''' and '''lunch''' with [http://pediatrics.duke.edu/faculty/details/0554303 speaker Dr. Sallie Permar PhD, MD (& Davidson alumna)] at Duke University

[[WEEK FIFTEEN (April 23 - 27)]]

[[WEEK SIXTEEN (April 30 - May 4)]]

[[WEEK SEVENTEEN (May 7 - 9)]] '''READING DAY May 10'''

Over the next 14 weeks, we will read a series of papers. We have chosen some to help us get started, but as the semester progresses, you will take the lead in identifying papers. Some of these papers will be easy for you, but others will be more difficult. We will work as a group to understand what is going on. In all cases, we will use these papers to help us frame a research project that will be conducted this summer by 8 Davidson students.

We will need to become experts in the [http://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit magnetosome] produced by bacteria. We will need to identify key papers to understand what is known so far. We also need to understand what UW-Seattle iGEM2011 did with this project.

<center>'''Some possible papers'''</center>
* '''The creativity crisis'''. 
Po Bronson and Ashley Merryman 
Newsweek. July 19, 2010. page 44.

* '''Synthetic Biology Moving into the Clinic''' 
Warren C. Ruder,* Ting Lu,* James J. Collins 
Science. Vol. 333. page 1248.

* '''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

* '''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,*ab Tom Adieac and Geoff S. Baldwin] 
Integr. Biol., 2011, 3, 109–118

* '''Information Transduction Capacity of Noisy Biochemical Signaling Networks''' 
Raymond Cheong, Alex Rhee, Chiaochun Joanne Wang, Ilya Nemenman, Andre Levchenko 
Science. Vol. 334, page 354.

* '''Synthetic Biology: Regulating Industry Uses of New Biotechnologies''' 
Brent Erickson, Rina Singh, Paul Winters 
Science. Vol. 333, page 1254.

* '''Synthetic Biology: Integrated Gene Circuits''' 
Nagarajan Nandagopal and Michael B. Elowitz 
Science. Vol. 333, page 1244.

* '''Community Structure in Time-Dependent, Multiscale, and Multiplex Networks''' 
Peter J. Mucha, Thomas Richardson, Kevin Macon, Mason A. Porter, and Jukka-Pekka Onnela 
Science. Vol. 328. page 876-878.

* '''Stochastic Pulse Regulation in Bacterial Stress Response''' 
James C. W. Locke,* Jonathan W. Young,* Michelle Fontes, María Jesús Hernández Jiménez, Michael B. Elowitz 
Science. Vol. 334. page 366.

* '''Synthetic biology: applications come of age''' 
Ahmad S. Khalil* and James J. Collins 
Nature Review Genetics. Vol. 11. page 367.

* '''A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria''' 
Christopher T. Lefèvre, et al. 
Science. Vol. 334. page 1720.

* '''Five hard truths for synthetic biology'''. 
Roberta Kwok 
Nature. Vol. 463. page 288.

* '''Controllability of complex networks''' 
Yang-Yu Liu1,2, Jean-Jacques Slotine3,4 & Albert-La ́szlo ́ Baraba ́si 
Nature. Vol. 473. page 167.

==MWSU==
2-17-2012

'''"Networks and confusion"'''

I have been attempting to work through the current tentative idea for our approach to network projects. I was originally confused by the idea that we would optimize an entire genome via varying RBC's, promoters, degradation tags, etc, and that we could call that a network. To make sense of the general idea of a network that we could design and eventually "train" to function, I went back to the start of what makes a network a network.

A network is a specified pathway that via interaction with a stimulus produces/degrades/builds/reacts. Antibiotic resistance is a reaction to a stimulus, but generally only uses one gene to create resistance. Whereas a metabolic pathway can use a small number to many different "nodes" or parts to the system to produce a single overall reaction in response to the stimulus.

I had an idea, this is a generalized idea, is in no way complete, but should be used as the jumping-off point. It is this: Evolution, via phenotype variation, has created the myriad of reporters and selection tools we use currently in our labs to determine if our bacteria are behaving the way we want them to. In the evolution of the various types of antibiotics we have discovered and utilize to kill bacterium, so too have those bacteria evolved to resist these killers. Looking at the scope of the interaction that a bacterium community would have to undergo in order to build a resistance to an antibiotic, one can see that it isn't likely a quick thing. however, may antibiotics are similar in function, and the resistance we encode many of our projects with are similar in their DNA construct and function as well.

'''Generalized proposal using antibiotic resistance as the stand-in for network function:'''''Italic text''

Using a bacterial strain resistant to a specific antibiotic, we add the "tools" for said bacteria to become resistant to a different but similar antibiotic by chopping up the DNA that would give them resistance and adding them to the genome of the aforementioned bacteria. Basically, we would be smashing and then giving a Rubik's cube to blind bacteria, and ordering them to put it together or we allow the new antibiotic to shoot them. We then politely poke and prod them to get to work by reassembling, chopping, and trying out new ways to use these pieces. Along the way, we use the phenotypic variation (which is inherent in all organisms) of these bacteria to train some of them (hopefully the ones that at least got part of the puzzle correct) to reach the end of a "stepwise" pathway and put the Rubik's cube back together. This pathway, keeping in mind the phenotype variation of these bacteria, doesn't have to be A-B-C-END. They might start with small a, or a triangle that strongly resembles an A, but still something similar enough to deliver the end result: resistance to a new antibiotic. This will almost assuredly be a poly-divergent pathway from start to finish. Much like many people are tall and many are small, but some of the small and the tall have dark hair or light hair, we would use the variation of our bacteria to get them from ~A through to the END. It wouldn't matter how they got to the end, even if they take shortcuts, as long as they get there, all they have to do is tell us how they did it.

Long and short, we give them the tools to solve a problem or to build a pathway, and see if they can get it right. At this stage, there are no restrictions on this idea as it is still in its infancy.

-Caleb Carr

Synthetic Biology Network Research

2012-02-17T23:43:28Z

Ccarr: /* MWSU */