NRPS – Delfibactin project

by Ilia

1. delfibactin:

• export from biocompartiments: unspecific outer membrane transporter (so delfibactin gets into medium)
• synthesis: pathway known, e.coli strain for production (maybe not clone DelC)

2. NRPS: introduction

• modular enzymes: 3 modular domains (together 110 kDa)
• steps: adenylation, acylation, condensation

3. software: input

• match amino acid to known A-domain substrates
• recognize easy modification (in amino acids) for which substrate you need it
• method: substructure based algorithm for searching and predicting substrate specifity
• it works in a R-package
• 10 amino acids are important for the substrate specifity

4. biobrick library

• there is no standard for the Biobricks of NRPS

GHB

by Flo and Nils

1. Jugend forscht: done a test (we do not understand how it works)

• not reached the supervisor yet
• she didn't win anything
• detect it via Spectrometry

2. 3 ideas for integrating the receptor

• artifiial membranes are not an option (you can't predict how the protein is located)
• in vitro expression of GPCRs (takes too long)
• Luciferase activity under directt ligand-dependent control of muscarinic acetylcholine receptor

=> measurments possible (very sensitive: represses glowing a little bit, a bit more... but never completely) (integrate it is fast, but the mutagenesis takes a long time)

Artificial yeast-cells for sensing Insulin-level and producing/distribute the Insulin

by Flo

• presentation of the idea and past igem projects regarding this theme
• semipermeable biocapsules (with cells inside)
• the cells (yeast , bacillus subtilis, e.coli... ) for producing insulin if it is necessary
• there exists a famous lab for synthetic biology which works on insulin production

Software Project

by Julia, Konrad and Hanna

• parameters for statistical analysis and how they correlate (like teammembers, advisors, organsims, score regarding a scoring funtion)
• graphics: basically histograms

work for the next weeks

1. software project

• look on the focus of the team!
• better definition of the parameters
• estimate the cost of an IGEM project (there exists something for the nature paper... just looking at the methods etc...)
• already made something with these parameters
• clustering for example, not only directed
• software project should be finished before the lab phase: end of June/ July

2. Gold Project

• working on this project: Nils, Ilia, Julia, Ralf, Hanna
• find stuff we have to order and send Dominik an email => done!
• talk to companies (interested, is it done already and how, are there established assays)
• find succesful examples

3. general information

• we have to register and then apply for the team. LogIn
• send an email for getting the contact details (parameters which here already used)

Agenda for next meeting (29.04.2013 at 5 pm)

1. results of pilot project (delfibactin in the lab)
2. present a project plan (goals, time etc.)
3. update on the software project. How to proceed etc.