Difference between revisions of "Summer 2012 SynBio Project (Davidson and MWSU)"

Revision as of 16:00, 25 May 2012

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

Based on discussions we have had this week at Missouri Western in regards to the new project... We have been closely examining the proposals that have been put forth on potential pathways and methods we might use. An important factor that was brought up in our discussions has been how to categorize and choose a pathway or pathways to use. Depending on what we choose we will have to use screening or selection as a method for determining the relative efficiency of changes in the pathway. The one that we would like to use the most is selection because it may be the most strait forward approach.

-David 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

• data sheets for standardized parts.

• 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

• Noise in Gene Expression: Origins, Consequences, and Control
  

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

Please post pdf.

• Synthetic Biology: Integrated Gene Circuits
  

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

Please post pdf.

• Network Motifs: Simple Building Blocks of Complex Networks
  

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

Please post 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

• Talking the Talk
  

Colin Mcilswain
Nature. Vol 465, page 867.

• Word selection affects perceptions of synthetic biology. Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.

• 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 long are they?

• How can they relate to cell fitness?

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

Cellular Automata

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

• iGEM Team Groningen
• iGEM Team IPN-UNAM Mexico
• MIT 2011 iGEM Tissue Design
• In Vivo Cellular Automata
• Edge Detection PDF
• Patterning of E. coli
• Tunable Bacterial Band-Pass Filter
• E. coli Predator-Prey Ecosystem
• Multicellular System for Programmed Pattern Formation

Other Ideas

• Networks
  • General
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • [6] Gene Regulatory Network wikipedia page
    • [7] long dissertation on modeling GRNs
    • Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
  • Process Calculus
    • [8] Process Calculus wikipedia page
    • [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
    • [9] Boolean Network wiki page; elementary CA are special cases of Boolean networks
    • [www.phys.psu.edu/~ralbert/pdf/springer_final.pdf Boolean modeling of GRNs]
    • 'The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response

• • Dynamical Systems

[www.cs.nmsu.edu/~joemsong/publications/Song2008-DDS.pdfDiscrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast]

• General
  • Workshop Summary of Applications of Synthetic Biology