Summer 2012 SynBio Project (Davidson and MWSU)

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

• Erich Baker Proposal: Media:Erich_Baker_proposal.docx This proposal deals with Phytochromes and Light Sensitive Channel Proteins
• 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
  

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 are possible sources of error?

Cellular Automata

• [1] General CA intoduction
• [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