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Team:Purdue/Notebook
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== Monday, May 15 == | == Monday, May 15 == | ||
| - | + | === List of useful contacts on the google doc, including DowAgro === | |
| + | === Begin to list the different devices/constructs that will be used in our project=== | ||
| + | ==== Attachment (adhesion)==== | ||
| + | ===== Filtration ===== | ||
| + | * Modularize the sequence so we can test individually (e.g. but GFP, RFP, YFP at the end of each segment – construct silica binding protein first with constitutive promoter/repressible promoter to produce promoter and make sure it does what you think it should) | ||
| + | * Investigate multiple silica binding protein (surface protein – silica binding peptide);must choose several top candidates for each element. | ||
| + | ==== Hierarchy ==== | ||
| + | ==== Perfecting the FFL ==== | ||
| + | * And (low affinity, not dimer), Or (high affinity) | ||
| + | * [[Media:schematic.jpg| Schematic Diagram]] | ||
| - | + | ==== Modeling and Experimental ==== | |
| - | + | * Communication in terms of data (e.g. kinetic parameters) | |
| - | + | * Review Characterization Data Sheets (look in the DropBox for an uploaded link from Sean ) | |
| - | + | * Strong integration of modeling translates to a strong performance in the competition. | |
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| - | + | == List of things we need == | |
| + | * Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy)may have the needed cells) | ||
| + | * Antibiotics (AMP, tetracycline) | ||
| + | * Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease ) | ||
| + | * Parts (available in the registry) | ||
| + | ** Constitutive promoter (orthogonal t7 promoter) | ||
| + | ** Signaling Promoters (investigate the precedent for construction FFL) | ||
| + | ** RBS –(B0034) | ||
| + | *** Thermodynamic models for designing RBSs, etc (Voights model) | ||
| + | ** Terminators | ||
| + | ** Proteins Transcription Factors | ||
== Monday, May 21 == | == Monday, May 21 == | ||
Revision as of 19:11, 29 May 2012
| Home | Team | Official Team Profile | Project | Parts Submitted to the Registry | Modeling | Notebook | Safety | Attributions |
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You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.
Contents |
Monday, May 15
List of useful contacts on the google doc, including DowAgro
Begin to list the different devices/constructs that will be used in our project
Attachment (adhesion)
Filtration
- Modularize the sequence so we can test individually (e.g. but GFP, RFP, YFP at the end of each segment – construct silica binding protein first with constitutive promoter/repressible promoter to produce promoter and make sure it does what you think it should)
- Investigate multiple silica binding protein (surface protein – silica binding peptide);must choose several top candidates for each element.
Hierarchy
Perfecting the FFL
- And (low affinity, not dimer), Or (high affinity)
- Schematic Diagram
Modeling and Experimental
- Communication in terms of data (e.g. kinetic parameters)
- Review Characterization Data Sheets (look in the DropBox for an uploaded link from Sean )
- Strong integration of modeling translates to a strong performance in the competition.
List of things we need
- Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy)may have the needed cells)
- Antibiotics (AMP, tetracycline)
- Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease )
- Parts (available in the registry)
- Constitutive promoter (orthogonal t7 promoter)
- Signaling Promoters (investigate the precedent for construction FFL)
- RBS –(B0034)
- Thermodynamic models for designing RBSs, etc (Voights model)
- Terminators
- Proteins Transcription Factors
Monday, May 21
- We're all looking forward to an exciting iGEM summer! Our SURF students have just arrived and are gradually being introduced to synthetic biology and iGEM.
- Sean gave a crash course on synthetic biology to Mrudula, Rachel, Amanda and August. The powerpoint is available here, compiled by our wonderful graduate mentor, Janie.
Tuesday, May 22
- First Journal Club Meeting - Identified the reducible elements of our system
- Detailed outline of the project to the SURF students
- What is the advantage of using this entire process? Is not it kind of roundabout?
For the NEXT MEETING Tuesday 29th May :
- Identify, in these teams:
a. What Adhesion system we want to use (Amanda, Peter, Mrudula)
b. Which silica-binding system we want to use (Rachel, August)
c. Control Elements (Max, Mrudula, Rachel, Sean)
d. Find strain auxotrophic for RSC (gene which breaks down arabinose) (Jim)
Announcements:
- Be ready to explain your assigned element of the project (starting generally and moving more specifically)
- Read the introductory/background elements of the thesis that Dr. Rickus will put in the dropbox General Announcements
- Be ready to work the BioBuilder HighSchool Teacher iGEM workshop during the week of June 4th – June 8th (more details to come)
- Everyone is welcome to visit Drs. Rickus and Clase’s lab group meeting on Thursday at 12PM
Tuesday, May 29
Overview of small group presentations
Adhesion Proteins – Amanda, Mrudula, and Peter
- Ag43 : [University of Queensland 2009] PROS: makes chains instead of aggregates, works well in flow, in the registry, abiotic adherence CONS: not concomitant
- TibA: PROS: modular, concomitant, auto-transport CONS: not in the registry
- AIDA-1: PROS: binds Ag43 and self, in registry, higher shear tolerance CONS: only expressed in certain cells, blocked by Fimbriae (due to length)
- FimA-H: [Michigan 2010] PROS: forms chains, compatible w/ E. coli, shear resistant, grows in constant flow, binds well to glycoproteins CONS: inhibits function of other proteins
- Curli: [Lyons 2011] PROS: well characterized in registry, amyloid fibers CONS: inhibits Ag43 and AIDA-1
Decision:
- primary: AIDA-1 [order from registry and improve bad sequencing or re-synthesize] ====
- secondary (if AIDA-1 proves unfeasible): TibA [with goal of characterizing part, must synthesize]
Silica Binding Proteins – Rachel and August
- INP – Silicatein [MN 2011] – PROS: CONS: very large, no data on viability, not biobrick compatible.
- OmpA-Silicatein alpha fusion – PROS: shorter than INP-Silicatein, active in neutral pH, no illegal sites, known to work CONS: must construct fusion peptide vector NOTES: optimum at low temperatures [OmpA - K103006]
- R5 peptide: PROS: active at neutral pH, small, has been used in E. coli CONS: part of a larger protein (no silaffin post-translational modifications), contains EcoRI site
Modeling the Network Motif - Max, Mrudula, Rachel, and Sean
- Modeled the simplified system
- Matlab and MathCad Model
- Need concrete entry parameters for more robust models
For Next week:
- Construct your parts in DNA 2.0 and anything in registry start detailing
