GcatWiki - User contributions [en]

File:Summer Work CRISPR final.pptx

2012-07-25T16:01:44Z

Cavrana:

Summer 2012 Outcomes

2012-07-25T16:01:30Z

2012-06-12T14:07:57Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
*[http://mic.sgmjournals.org/content/155/3/733.long '''Short motif sequences determine the targets of the prokaryotic CRISPR defense system''']
**[http://mic.sgmjournals.org/content/155/3/733/suppl/DC1 '''Supplementary data to 'Short motif sequences paper'''']
*[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011126#pone-0011126-g001 '''The Small, Slow, and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
***[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=ba9d9a34-c144-454b-bee9-2dc462b75a0a%40sessionmgr112&vid=2&hid=109 Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia ecoli cadBA operon]
***[http://jb.asm.org/content/174/2/530.full.pdf Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH.]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-12T13:39:13Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
*[http://mic.sgmjournals.org/content/155/3/733.long '''Short motif sequences determine the targets of the prokaryotic CRISPR defense system''']
**[http://mic.sgmjournals.org/content/155/3/733/suppl/DC1 '''Supplementary data to 'Short motif sequences paper'''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
***[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=ba9d9a34-c144-454b-bee9-2dc462b75a0a%40sessionmgr112&vid=2&hid=109 Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia ecoli cadBA operon]
***[http://jb.asm.org/content/174/2/530.full.pdf Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH.]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-12T13:38:54Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
*[http://mic.sgmjournals.org/content/155/3/733.long '''Short motif sequences determine the targets of the prokaryotic CRISPR defense system''']
**[http://mic.sgmjournals.org/content/155/3/733/suppl/DC1 '''Supplementary data to Short motif sequences paper''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
***[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=ba9d9a34-c144-454b-bee9-2dc462b75a0a%40sessionmgr112&vid=2&hid=109 Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia ecoli cadBA operon]
***[http://jb.asm.org/content/174/2/530.full.pdf Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH.]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-12T13:38:36Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
*[http://mic.sgmjournals.org/content/155/3/733.long '''Short motif sequences determine the targets of the prokaryotic CRISPR defense system''']
**[http://mic.sgmjournals.org/content/155/3/733/suppl/DC1 '''Supplementary data to Short motif sequences paper'''
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
***[http://ehis.ebscohost.com/ehost/pdfviewer/pdfviewer?sid=ba9d9a34-c144-454b-bee9-2dc462b75a0a%40sessionmgr112&vid=2&hid=109 Altered pH and lysine signalling mutants of cadC, a gene encoding a membrane-bound transcriptional activator of the Escherichia ecoli cadBA operon]
***[http://jb.asm.org/content/174/2/530.full.pdf Identification of elements involved in transcriptional regulation of the Escherichia coli cad operon by external pH.]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-12T13:11:01Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
*[http://mic.sgmjournals.org/content/155/3/733.long '''Short motif sequences determine the targets of the prokaryotic CRISPR defense system''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Synergy Machine Protocol

2012-06-08T18:54:30Z

Cavrana:

Synergy Machine Protocol
#All Wells should contain 200 microliters of cells in broth.
##Be sure to include wells containing broth with no cells- for negative control.
#Open Gen 5 software
#Click on Existing protocol OR move to step 3
#Click on Create New Protocol
#Select Standard Protocol type
#Click on Procedure
#Under Shake, select Orbital Shake for 3 seconds
#Under Read, select Fluorescence from drop down menu
##Enter Emission and Excitation wavelengths
###If you are reading more than one type of fluorescence, click the appropriate number of types above the wavelength values.
##For RFP, select 585 nm (excitation) and 615 nm (emission) for optimal reading (with 100 gain)
##For GFP, select 485 (excitation) and 515 (emission) for optimal reading (with 100 gain)
##If GFP and RFP are combined in the same well, use a different method.
###Use the wavelengths of 460nm (excitation) and 490 nm(emission) for GFP, and 585 nm(excitation) and 615 nm (emission) for RFP, to minimize noise/interference. However, some of the GFP reading will be from bleeding over of RFP.
#Under Read, select Absorbance from the drop down menu and enter 590 nm
#Once those values have been submitted, drag tasks into proper order. First Shake, then read Fluorescence, then read Absorbance.
##If you are measuring GFP and RFP, measure GFP before RFP.
#Click OK, and from the banner menu, select File, New Task, then Read Now (selecting the procedure you created)
#Place the well inside the machine, and Click OK when ready.
#After the machine has run, you can export the data to Excel using the Excel button on the banner of the window that pops up.
#Note- if only a few wells give a value of OVRFLW, try lowering the gain from 100 to 95 or 90 (or lower if necessary). Enter the value on the page with the wavelengths for fluorescence. If all wells give a value of OVRFLW, this means the wavelengths are too close together. Try increasing the difference between the excitation and emission wavelengths.
#[[File:Optimal GFP.PNG]]
## 485 nm/515 nm (100 gain) are the optimal exitation/emission wavelengths for use with GFP.
#[[File:CaptureRFP.PNG]]
##585 nm/615 nm (100 gain) are the optimal excitation/emission wavelengths for use with RFP, as they resulted in the highest fluorescence readings.
#[[File:Fake_GFP.PNG]]
##460 nm (excitation) and 490 nm (emission) are the optimal wavelengths to use with GFP and RFP in the same well, in order to minimize noise/interference from RFP at GFP wavelengths.

File:Fake GFP.PNG

2012-06-08T18:53:59Z

Cavrana:

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-08T18:22:24Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
**[http://nar.oxfordjournals.org/content/suppl/2012/02/25/gks216.DC1 '''Supplementary data''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-08T01:21:16Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[http://jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-08T01:20:59Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

[http://django.gibthon.org/]Tool for using Gibson Assembly 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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
*[jb.asm.org/content/192/23/6291.full.pdf '''The Escherichia coli CRISPR System Protects from lambda Lysogenization, Lysogens, and Prophage Induction''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image:Pathway ygcf2.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-07T19:32:00Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

==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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image: Desktop.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-07T19:31:19Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

==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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
*[[Media:Supplemental information to Essential Features paper.pdf]]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819186/ '''The CRISPR System: small RNA-guided defense in bacteria and archaea''']
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858662/ '''Screen for synthetic riboswitches reveals mechanistic insights into their function''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00100 '''Sequence of cydAP1 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']
*[http://jb.asm.org/content/192/3/746.full.pdf '''ArcAB system and how it works-sort of''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179413/ '''Specifics of how ArcB works/its composition''']
*[http://www.biomedcentral.com/content/pdf/1471-2180-9-183.pdf '''How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide''']
*[http://www.ncbi.nlm.nih.gov/pubmed/11123679 '''ArcAB and the cydAB promoter with the H-NS protein''']
*[http://jb.asm.org/content/186/7/2085.full.pdf '''The Effects of D-lactate on ArcB in Aerobic and Anaerobic Conditions''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95567/ '''Intracellular Concentration of Hydrogen Peroxide and Catalase in E. coli''']

==Light==
*light-gated ion channels/pumps
**[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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
**[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
***[http://www.ncbi.nlm.nih.gov/nuccore/48994873?report=graph rest of cadA promoter sequence]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]
***[http://www.ecogene.org/geneInfo.php?eg_id=EG11276 rest of TnaA promoter sequence]
*[http://www.jbc.org/content/276/39/36508.long luciferin regeneration]


Blue Light Regulated Promoter YgcF

*Articles/ References:
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/?tool=pubmed] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
**[http://www.ncbi.nlm.nih.gov/pubmed/16533062] Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF)
**[http://partsregistry.org/Part:BBa_K238013] Group: iGEM09_KULeuven (2009-08-02)

*Proposed Pathway:
**[[Image: Desktop.jpg|200px|thumb|left|alt=text|Relationship to Selection Module]] 

 
*Parts to Build:
**K238013
**gnl|ECOLI|G6603
**gnl|ECOLI|G6602

==Maths==

*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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

*'''Neural Networks'''
**[http://axon.cs.byu.edu/papers/smith_2010biot.pdf]
**[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
**[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

*'''Fuzzy Logic/Modeling'''
**[http://en.wikipedia.org/wiki/Soft_computing] Soft Computing (general field)
**[http://books.google.es/books/about/Fuzzy_Rule_Based_Modeling_with_Applicati.html?hl=es&id=YkB_wfN7GBkC] A whole book on fuzzy rule based modeling
**[http://www.ncbi.nlm.nih.gov/pubmed/16233352] Fuzzy modeling and control of biological processes
**[http://www.biomedcentral.com/1752-0509/1/13 Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery]
**[http://jfuzzylogic.sourceforge.net/html/index.html] FCL Java package
**[http://www.newelectronics.co.uk/electronics-technology/cover-story-whats-all-this-noise-about/31678/] Noise-based logic
**[http://ocw.mit.edu/courses/health-sciences-and-technology/hst-951j-medical-decision-support-spring-2003/lecture-notes/lecture4.pdf] Fuzzy sets overview slides (MIT)

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

2012-06-06T18:26:13Z

Cavrana:

File:Capture.PNG

2012-06-06T18:25:26Z

Cavrana:

Synergy Machine Protocol

2012-06-06T17:39:44Z

Cavrana:

Synergy Machine Protocol

2012-06-05T21:07:21Z

Cavrana:

Synergy Machine Protocol

2012-06-05T21:06:57Z

Cavrana:

Synergy Machine Protocol
#1. Open Gen 5 software
#2. Click on Existing protocol OR move to step 3
#3. Click on Create New Protocol
#4. Select Standard Protocol type
#5. Click on Procedure
#6. Under Shake, select Orbital Shake for 3 seconds
#7. Under Read, select Fluorescence from drop down menu
##a. Enter Emission and Excitation wavelengths
###i. If you are reading more than one type of fluorescence, click the appropriate number of types above the wavelength values.
##b. For RFP, select 585 nm (excitation) and 615 nm (emission) for optimal reading (with 100 gain)
##c. For GFP, select ___ (excitation) and ___ (emission) for optimal reading (with 100 gain)
#8. Under Read, select Absorbance from the drop down menu and enter 590 nm
#9. Once those values have been submitted, drag tasks into proper order. First Shake, then read Fluorescence, then read Absorbance.
##a. If you are measuring GFP and RFP, measure GFP before RFP.
#10. Click OK, and from the banner menu, select File, New Task, then Read Now (selecting the procedure you created)
#11. Place the well inside the machine, and Click OK when ready.
#12. After the machine has run, you can export the data to Excel using the Excel button on the banner of the window that pops up.

Synergy Machine Protocol

2012-06-05T21:04:59Z

Cavrana: Created page with 'Synergy Machine Protocol 1. Open Gen 5 software 2. Click on Existing protocol OR move to step 3 3. Click on Create New Protocol 4. Select Standard Protocol type 5. Click on Pro…'

Synergy Machine Protocol
1. Open Gen 5 software
2. Click on Existing protocol OR move to step 3
3. Click on Create New Protocol
4. Select Standard Protocol type
5. Click on Procedure
6. Under Shake, select Orbital Shake for 3 seconds
7. Under Read, select Fluorescence from drop down menu
a. Enter Emission and Excitation wavelengths
i. If you are reading more than one type of fluorescence, click the appropriate number of types above the wavelength values.
b. For RFP, select 585 nm (excitation) and 615 nm (emission) for optimal reading (with 100 gain)
c. For GFP, select ___ (excitation) and ___ (emission) for optimal reading (with 100 gain)
8. Under Read, select Absorbance from the drop down menu and enter 590 nm
9. Once those values have been submitted, drag tasks into proper order. First Shake, then read Fluorescence, then read Absorbance.
a. If you are measuring GFP and RFP, measure GFP before RFP.
10. Click OK, and from the banner menu, select File, New Task, then Read Now (selecting the procedure you created)
11. Place the well inside the machine, and Click OK when ready.
12. After the machine has run, you can export the data to Excel using the Excel button on the banner of the window that pops up.

Davidson Protocols

2012-06-05T21:04:08Z

2012-06-01T19:10:58Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

==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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Background on CRISPR and steps in adaptation process''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]
*[[Media:Essential features and rational design of CRISPR RNAs that function with the Cas RAMP Module complex to cleave RNAs.pdf]]
'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. Coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']

==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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
*[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]

{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}

==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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

Communication
*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]
*[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
*[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

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

Summer 2012 SynBio Project (Davidson and MWSU)

2012-06-01T15:38:30Z

Cavrana: /* 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==

[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

[http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/prop_exonucleases_endonucleases.asp#.T8eBVLD-_h4] Properties of Exonuclease

==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''']
'''CRISPR process'''
*[http://nar.oxfordjournals.org/content/early/2012/03/08/nar.gks216.long '''Background on CRISPR and steps in adaptation process''']
*[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07482.x/full '''Envelope stress trigger for CRISPR response'''] - and background info on E.coli Cascade complex
*[http://crispr.u-psud.fr/ '''CRISPR database - to compare and find''']
*[http://www.biochemsoctrans.org/bst/039/0051/bst0390051.htm '''CRISPR immune system in Sulfolobales''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&ved=0CFAQFjAA&url=http%3A%2F%2Fwww.asm.org%2Fasm%2Ffiles%2FccLibraryFiles%2FFilename%2F000000004866%2Fznw00509000224.pdf&ei=94LHT7qaPISI8QTYoNGnDw&usg=AFQjCNFrr_J74_27CeXeiqoUuZv_IlS0VA '''CRISPR System protects Microbes against Phages, Plasmids''']
*[http://gbe.oxfordjournals.org/content/3/959.long#ref-2 '''Impact on Small Repeat Sequences on Bacterial Genome Evolution''']
*[http://www.nature.com/nsmb/journal/v18/n5/full/nsmb.2019.html '''Structural Basis for CRISPR RNA-guided DNA recognition by Cascade''']
*[http://www.nature.com/nature/journal/v477/n7365/full/nature10402.html '''Structures of the RNA-guided surveillance complex from a bacterial immune system '''] -figures of Subnanometer structures of Cascade
*[http://2011.igem.org/Team:USC/Project '''2011 iGEM team- CRISPR/Cas and GFP''']
*[http://mic.sgmjournals.org/content/156/5/1351.full.pdf+html '''Diversity of CRISPR loci in E.coli''']
*[http://www.ploscompbiol.org/article/fetchObjectAttachment.action;jsessionid=C9354D14BE928C01B1A00C4DD72328D6?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.0010060&representation=PDF '''Guild of 45 CRISPR-associated protein families''']
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338789/ '''CRISPR Interference Directs Strand Specific Spacer Acquisition''']
*[http://people.bu.edu/mfk/crispr.pdf '''CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea''']
*[http://www.pnas.org/content/early/2011/12/06/1112832108.full.pdf '''Mature crRNA length measured by ruler mechanism''']
*[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=2&ved=0CEkQFjAB&url=http%3A%2F%2Fwww.annualreviews.org%2Fdoi%2Fpdf%2F10.1146%2Fannurev-genet-110410-132430&ei=ZN_IT9rYKImK8QS10cyTDw&usg=AFQjCNGSjKz7D2ovE5zHsIN08_79Ep2uHw '''CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation''']
*[[Media:CRISPR-based adaptive immune systems-terns.pdf]]
*[[Media:Evolution and Classification of the CRISPR-Cas systems- Makarova.pdf]]

'''Regulated Biosynthesis Pathways'''

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

'''Aptamers'''
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988590/pdf/1537-10.pdf '''Use of riboswitch in Bacteria''']

==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://biocyc.org/ECOLI/new-image?type=PATHWAY&object=PWY0-1505 '''Visual Diagram of ArcAB System 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://akongo.psb.ugent.be/ECOLI/NEW-IMAGE?type=OPERON&object=TU00378 '''Sequence of focAP2 promoter-activated by ArcA''']
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00107 '''Sequence of icdAp1 promoter-repressed by ArcA''']
*[http://www.ncbi.nlm.nih.gov/pubmed/9302022 '''CydAB Activated in E. Coli''']
*[http://ac.els-cdn.com/S1097276510000286/1-s2.0-S1097276510000286-main.pdf?_tid=fdf03f53d6749a0fc705cfb757f09864&acdnat=1338478651_a66723fcc34b19db282a2833d80eb547 '''Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis''']

==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.ncbi.nlm.nih.gov/pmc/articles/PMC103662/pdf/1472-6793-2-5.pdf Retinal necessary for functional PR in E. coli]
*[http://www.lbl.gov/Science-Articles/Archive/PBD-proteorhodopsin.html Function of PR in nature and in E. coli]
*pH inducible promoters
**[http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1994.tb47400.x/abstract pH inducible promoter system pSM10]
**[[Media:pH inducible promoter.pdf]] pSM-10
**[http://www.freepatentsonline.com/article/Science-Progress/125489472.html High pH induced proteins]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00467 cadA promoter sequence (low pH induced)]
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373043/pdf/microrev00059-0007.pdf E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)]
**[http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00085 TnaA promoter (high pH)]

{| border="1" class="wikitable"
|-
! Pump !! [http://pubs.acs.org/doi/pdf/10.1021/bi011788g phR] !! [https://wiki.ornl.gov/sites/carboncapture/Shared%20Documents/Background%20Materials/Membranes/A.%20Kocer2.pdf MscL] !! [http://pubs.acs.org/doi/pdf/10.1021/bi201876p NpHR] !! [http://www.jbc.org/content/262/19/9271.full.pdf e-BO/e-BR/h-BR] !! [http://www.pnas.org/content/104/7/2408.full.pdf PR]
|-
| '''wavelength''' || max absorbance at 578-599 || open with 366 nm, close with visible light (>466 nm) || 578 nm (with NaCl in media) || 550-560 nm || ~525 nm
|-
| '''particles that can travel through it''' || Chloride ions || non-selective, 3-nm diameter || anions || protons || protons
|-
| '''pump/channel?''' || pump || channel || pump || pump || pump
|-
| '''type of protein'''|| halorhodopsin || n/a || halorhodopsin || BR=bacteriorhodopsin, BO=bacterio-opsin || proteorhodopsin
|-
| '''direction''' || into cell || n/a || into cell || into cell || out of cell
|}

==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''']
**[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29061/ '''Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions''']

*'''Agent Based Models/Complex Adaptive Systems'''
**[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
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&sqi=2&ved=0CHsQFjAJ&url=http%3A%2F%2Fwww.mcs.anl.gov%2F~leyffer%2Flistn%2Fslides-06%2FMacalNorth.pdf&ei=CHbHT93JI4ym8gSMgenADw&usg=AFQjCNGLaH7dMit3DpX2F6lJxa5t3T8jvQ&sig2=E5QCbTVem3fCwtBJhZmH5A] Good slide-show covering ideas of ABM
**[http://www.santafe.edu/search/results/?query=agent-based] Sante Fe Institute Agent-Based Modeling links
**[http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFUQFjAB&url=http%3A%2F%2Fwww.cs.unicam.it%2Fmerelli%2FNY.pdf&ei=EX3HT6v5I4G-9QTXvfWoDw&usg=AFQjCNEyzeC0iH0fmy7liKTbzTADGfWJpQ&sig2=OZ45qoI5jl1dF1kxa380iA] Slideshow on modeling intercell stuff via AMB
*'''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 1964 study that used analog computers to model a bacterial cell
**[http://www.cs.columbia.edu/~simha/hdcacase.pdf] Paper on combined use of analog and digital computation
**[http://books.google.com/books?id=TZHpu9i8viAC&printsec=frontcover#v=onepage&q&f=false] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit

Communication
*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]
*[http://www.ai-junkie.com/ann/evolved/nnt1.html] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
*[http://jb.asm.org/content/187/1/26.full] Paper on neural networks in bacteria

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