Summer 2012 SynBio Project (Davidson and MWSU)

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Summer 2012 Synthetic Biology Project: MWSU and Davidson College


  1. Davidson Protocols
  2. MWSU_protocols
  3. GCAT-alog Freezer Stocks
  4. Laboratory_Notebooks
  5. Golden Gate


Student Proposals from Ind. Studies

-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



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

Tom Ellis, Tom Adieac and Geoff S. Baldwin
Integr. Biol., 2011, 3, 109–118

  • Everyone should watch this 5 minute video on optogenetics. Combine that video with the 2010 champoinship iGEM invention of E. glowi.


Older Lab Papers

  • Engineering bacteria to solve the Burnt Pancake Problem.

Haynes, Karmella, et al.
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

  • Solving a Hamiltonian Path Problem with a Bacterial Computer.

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.

Brianna Pearson*, Kin H. Lau* et al.
Interdisciplinary Bio Central. Vol. 3, article no. 10.
Time Delayed Growth Movie


Network Papers

Jonathan M. Raser and Erin K. O’Shea
Science. Vol. 309, page 2010

Please post pdf.

Nagarajan Nandagopal and Michael B. Elowitz
Science. Vol. 333, page 1244.

Please post pdf.

R. Milo, S. Shen-Orr, et al
Science. Vol. 298, page 824.

Please post pdf.

Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si
Nature. 2011. Vol. 473, page 167.

Please post pdf.


Ethics Papers

Colin Mcilswain
Nature. Vol 465, page 867.

-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

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

  • [1] General CA introduction
  • [2], [3] Elementary Cellular Automata
  • [4] Good explanation of how elementary CAs work
  • [5] Rule 110

Peptides

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles [[7]]

Assembly

[8]iGEM Introduction to Gibson Assembly

[9]Enzymatic assembly of DNA molecules up to several hundred kilobases

[10] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[11]Assembly of BioBricks by the Gibson Method

[12] 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

  • [13] gene-specific promoter element is required for optimal expression of the histone H1 gene in S-phase.
  • [14] Multiple Sigma Factors

Promoters Section

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

C-Dog Section

Degradation Tag Section

Selection Modules

Bad-ish genes/proteins

Good genes/proteins

CRISPR process

Regulated Biosynthesis Pathways

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

Aptamers

Gas-Phase Communication

Light

Pump phR MscL NpHR e-BO/e-BR/h-BR 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

Blue Light Regulated Promoter YgcF

  • Articles:
    • [15] The BLUF-EAL protein YgcF acts as a direct anti-repressor in a blue-light response of E.coli
    • [16] 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)

Other Ideas

  • Agent Based Models/Complex Adaptive Systems
    • [22] Set of lecture slides on chaos, including one on ABMs.
    • [23] Stuart Kauffman on emergence
    • [24] Good slide-show covering ideas of ABM
    • [25] Sante Fe Institute Agent-Based Modeling links
    • [26] Slideshow on modeling intercell stuff via AMB
  • Real Computing/Complexity
    • [27] Lecture transcripts from two MIT courses on compleity by a very smart guy in the field
    • [28] Review of physical computing by the same researcher
    • [29] Part of a textbook on computation theory
    • [30] Harvard analog computing
    • [31] Free draft of Princeton text on computational complexity
    • [32] Paper written by one of the authors of Complexity and Real Computation that contains the same basic ideas
    • [33] An analog computer museum and information site run by a Dr. Bernd Ulmann, who did his doctoral thesis on analog computing
    • [34] Abstract of a 1964 study that used analog computers to model a bacterial cell
    • [35] Paper on combined use of analog and digital computation
    • [36] First 28 pages of Neural Networks and Analog Computing: Beyond the Turing Limit


Communication

Neural Networks

  • [37]
  • [38] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
  • [39] Paper on neural networks in bacteria

General

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