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

Revision as of 19:47, 4 June 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

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.

-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

• [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

Peptides

• Pep-1 can carry large amounts of cargo across cell membrane
• Pep-1 has no anti-microbial activity against E. coli, see page 121
• [6]General Manual for CPP After opening, click on the PDF General Manual for detailed information concerning Cellular Permeating Peptides, and products of the like.
• General info on Pep-1
• Very clear, easy to read, discussion on how CPPs work, and more specific info on Pep-1, look in Chapter 1 to start
• Pep-1 is a synthetic peptide
• Pep-1 fusion protein made in E. coli
• Targeting proteins to E. coli periplasmic space (GFP)
• 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 [[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

• Degradation Tags with Gfp protein reporters - research paper

• [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)

• http://partsregistry.org/PBAD_Promoter_Family

C-Dog Section

Degradation Tag Section

Selection Modules

Bad-ish genes/proteins

• Toxicity of rat insulin gene on E.coli
• SacB gene with sucrose and E.coli
• Hda-mediated homeostasis in E.coli
• Lon protease from M.smegmatis
• SinI enzyme has moderate growth-inhibition in E.coli
• Excess violecein production toxic to E.coli
• ToxN inhibits growth of E.coli
• Eukaryotic membrane proteins toxic to E.coli
• HbpA proteins moderately toxic to E.coli
• Alpha-luffin and E.coli
• BBG29 gene from 'Borrelia'

Good genes/proteins

• Tet-resistance in E.coli
• Database of Antibiotic Resistance Genes

CRISPR process

• Background on CRISPR and steps in adaptation process
• Envelope stress trigger for CRISPR response - and background info on E.coli Cascade complex
• CRISPR database - to compare and find
• CRISPR immune system in Sulfolobales
• CRISPR System protects Microbes against Phages, Plasmids
• Impact on Small Repeat Sequences on Bacterial Genome Evolution
• Structural Basis for CRISPR RNA-guided DNA recognition by Cascade
• Structures of the RNA-guided surveillance complex from a bacterial immune system -figures of Subnanometer structures of Cascade
• 2011 iGEM team- CRISPR/Cas and GFP
• Diversity of CRISPR loci in E.coli
• Guild of 45 CRISPR-associated protein families
• CRISPR Interference Directs Strand Specific Spacer Acquisition
• CRISPR interference: RNA-directed Adaptive Immunity in Bacteria and Archaea
• Mature crRNA length measured by ruler mechanism
• 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
• The CRISPR System: small RNA-guided defense in bacteria and archaea

Regulated Biosynthesis Pathways

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

Aptamers

• Use of riboswitch in Bacteria

Gas-Phase Communication

• Biopixel Paper
• ArcAB system in V. fischeri Includes promoter sequences
• ArcAB system in E. Coli
• ArcAB system Responses to Hydrogen Peroxide in E. coli
• Visual Diagram of ArcAB System in E. Coli
• Amino Acid Sequence for ArcA in E. Coli
• Amino Acid Sequence for ArcB in E. Coli
• Amino Acid Sequence for ArcA in V. Fischeri
• Blast Amino Acid Sequence Comparison for ArcA in E. coli and V. fischeri
• Blast Amino Acid Sequence Comparison for ArcB in E. coli and V. fischeri
• Potential Promoters that ArcA Might Bind To in E. Coli
• More Potential Promoters that ArcA Might Bind To in E. Coli-fad regulon
• List of Operons Repressed or Activated by ArcA in E. coli
• Sequence of focAP2 promoter-activated by ArcA
• Sequence of cydAP1 promoter-activated by ArcA
• Sequence of icdAp1 promoter-repressed by ArcA
• CydAB Activated in E. Coli
• Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis
• ArcAB system and how it works-sort of
• Specifics of how ArcB works/its composition
• How ArcAB functions as resistance to reactive oxygen stress/hydrogen peroxide
• ArcAB and the cydAB promoter with the H-NS protein

Light

• Review of types and mechanisms of light-gated ion channels (2006)
• Channelrhodopsins
• Halorhodopsin (NpHR)
• p. 117: ChR2 doesn't express in E. coli?
• Halorhodopsin can be expressed in E. coli: HsHR
• Retinal necessary for functional PR in E. coli
• Function of PR in nature and in E. coli
• pH inducible promoters
  • pH inducible promoter system pSM10
  • Media:pH inducible promoter.pdf pSM-10
  • High pH induced proteins
  • cadA promoter sequence (low pH induced)
    • rest of cadA promoter sequence
  • E. coli maintain a relatively constant intracellular pH (pumps sense extracellular pH)
  • TnaA promoter (high pH)

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 [15]
  • General
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • [16] Gene Regulatory Network wikipedia page
    • [17] long dissertation on modeling GRNs
    • Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
  • Process Calculus
    • [18] 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
    • [19] Boolean Network wiki page; elementary CA are special cases of Boolean networks
    • Boolean modeling of GRNs
    • 'The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response
    • Or-Not Logic Gate with E.Coli
  • Dynamical Systems
    • Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast
    • 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
  • Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
  • Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions

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

Communication

• Bacterial Conjugation
  • Conjugative transfer of antibiotic resistance
  • Molecular basis for control of conjugation
  • Contour length of F-pili
  • Male-Specific Bacteriophages to inhibit mating

Neural Networks

• [35]
• [36] Neural networks in plain English; seems to be a basic of how to programming guide for them as well
• [37] Paper on neural networks in bacteria

General

• Workshop Summary of Applications of Synthetic Biology