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From 2012.igem.org

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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 1 Monday, May 15 2 Monday, May 21 3 Tuesday, May 22 4 Tuesday, May 29 4.1 Overview of small group presentations 4.1.1 Adhesion Proteins – Amanda, Mrudula, and Peter 4.1.1.1 Decision: 4.1.2 Silica Binding Proteins – Rachel and August 4.1.3 Modeling the Network Motif - Max, Mrudula, Rachel, and Sean 4.2 For Next week:

Monday, May 15

1. List of useful contacts on the google doc, including DowAgro

2. Begin to list the different devices/constructs that will be used in our project

       a.  	Attachment (adhesion)
       b.	Filtration
              i.	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)
              ii.	Investigate multiple silica binding protein (surface protein – silica binding peptide);
                       must choose several top candidates for each element and 
       c.	Hierarchy
       d.	Perfecting the FFL
              i.	And (low affinity, not dimer), Or (high affinity)

3. Modeling and Experimental

      a.	Communication in terms of data (e.g.  kinetic parameters)
      b.	Review Characterization Data Sheets (look in the DropBox for an uploaded link from Sean )
      c.	Strong integration of modeling translates to a strong performance in the competition
	

4. List of things we need

      a.	Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy) 
                may have the needed cells)
      b.	Antibiotics (AMP, tetracycline, 
      c.	Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease )
      d.	Parts (available in the registry)
               i.	Constitutive promoter (orthogonal t7 promoter)
               ii.	Signaling Promoters (investigate the precedent for construction FFL)
      e.	RBS –(B0034)
               i.	Thermodynamic models for designing RBSs, etc (Voights model)
      f.	Terminators
      g.	Proteins Transcription Factors

Schematic Diagram

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