Team:Newcastle/Meetings/14 April 2010

Informal meeting - 14 April 2010

• Room: Walton Library; Start: 11 am
• Chair: Phil, Minutes: Richard, Computer: Alan
• Agenda

Roll call and apologies

• Apologies: Steve, Absent: Rachel, Zoltan, Late: Alan,

Approval of agenda and minutes

• Both last informal and formal meetings approved

Brief summary of previous meeting

1. Graphic designer or civil engineer needed from Anil and Jen
2. Testing strength of concrete
3. Email to Chris Voigt - will draft bullet points in formal meeting after everyone has read the spider silk paper
4. Give advance notice of absence at meetings
5. Anil and Jen to look at Bug'seye view flowchart.

Previous action points (7 April)

• Bug’s eye view flowchart
  • Da and Harsh confirmed they understood the .ppt

Update on research

1. Jannetta explained her research project and she is trying to come up with ways that it could be used in iGEM, e.g. searching for parts (biobricks) to make spidersilk proteins. Alan: FTSc needed for bacteria to become strands, knock this gene out.
2. Draft email to Colin and Chris
   • Richard outlined content
3. Logo/T-shirts
   • New design by Younus

Funding

Time line discussion

All up to date apart from logo

What next?

• Big picture overview

Other business

• Deena is a Civil Engineer at Newcastle interested in the project. Ask Jen about interview, funding, progress etc.

Items for next agenda

1. Harsh to email sponsor letter to iGEM team for approval
2. Ask Niel and Jen or previous iGEM team members about rules for about sponsor involvement/ interests in the project
3. Harsh mentionned that Anil said that it is easier to transform E.coli, and will transfer genes from E.coli to Bacillus. Need to confirm with Anil and Jen if this is the procedure we will be using.
4. Jannetta and Richard need to go through kill switch research so can feed back at formal meeting
5. Everyone to ensure he has read the Voigt spidersilk paper before formal meeting so that we can list bullet points for an email
6. Formal meeting - put up backgrounds to logo on display for voting
7. Younus to email an alternative logo design Jannetta will transfer to Inkscape.

Next informal meeting

• All to be arranged at formal meeting

Formal Meeting - 14 April 2010

• Room: Claremont tower 922; Start: 3 pm
• Chair: Phil, Minutes: Richard, Computer: Alan
• Agenda

Roll call and apologies

1. Present: Phil, Jen, Jem, Jannetta, Zoltan, Younus, Harsh, Da, Richard
2. Apologies: Steve, Absent: Rachel, Late: Matt,

Brief summary of previous formal meeting

1. Research feedback
2. 2 weeks for Bug’s eye flow chart to insert our ideas.
3. Email to Voigt and Harwood
4. Civil engineering advisor, will lead to recruitment of interested students
5. Logo - Jannetta doing work on this
6. Tutorials
7. Update standing agenda - Steve hasn’t done this
8. Bullet points for email to Voigt

Matters arising (from last meeting)

1. Email Steven reminder
2. Advance notice to everybody if not able to be present
3. Individual bug's eye view
4. Draft invitation email to Colin Harwood
5. Read spider silk paper

Approval of previous minutes

• Yes with minor modification. Registration for iGEM was completed last week.

Approval of agenda

• Approved

Tutorial - Sin operon

1. Evolutionary design of a stochastic switch for synthetic genetic circuits
2. Sin operon - Control of sporulation/cell phasing/biofilm/ flaggella formation
3. SinI/SinR
4. Components of biofilm (SinR tetramer inhibits biofilm formation, activates flaggellum formation)
5. SinI reduces rate of tetramer formation by forming a dimer with SinR.
6. S08
7. Cytoscape - drawing networks
8. Modelling Stochastic switch
9. Voigt + Kobashyi model
10. Run simulation - does it form a biofilm or flagellum? Develop switch that would predict correct 60 % of the time.
11. Pull out kinetic parameters from literature.
12. Cell designer. Capasi - no graphical interface, but more powerful. Can write Java code and call Capasi from it more specific activities. SBML shorthand. Differential equations to SBML

Research Feedback

1. Properties of concrete and surface tension (Zoltan and Steven)
2. Microinjection (Zoltan and Steven)
   • Zoltan to answer specific questions
     • soaking up of water into crack through pores
     • how big are the microcracks (presumably greater than size of pores)
     • crack distribution
3. Genetics Homologous recombination plasmid chromosome (Harsh and Rachel)
   • Jen confirmed that will need to to plasmid work in E.coli first because it will not be stable in Bacillus. As long as use correct vector, should work in Bacillus though.
4. Nutrients (Harsh and Rachel)
5. Sporulation, germination and secretion control (Alan and Da)
6. Quorum sensing (Younus and Phil)
   • Do we use existing quorum sensing funtionality or engineer in an additional one? Jen: yes could probably ‘piggy-back’ off existing system. Jem: additional system - to pick up on subtilin signal rather than engineering into the Sin system and causing unexpected effects. (Gold award: improving an existing biobrick).
7. Kill switch (Richard and Jannetta)
8. Linear DNA (Richard)
   • Produced model for exonucleases, structures resistant to these and their disruption by 5’ gap produces by DNA replication. To produce model for simple eating away by exonucleases.
9. Glue, CaCO3 and spider silk (Zoltan and Jannetta)
   • Zoltan and Jannetta will do some more research on the glue.
10. Other points
    • Can knock out genes so that BS becomes filamentous at the correct point.
    • SOS system in BS to make cells fillamentous (homologue of E.coli solA).
    • Jem: recommends that we choose exactly which bonding agent we are using (spidersilk, CaCO3, glue) - Voigt will be able to advise whether can be done in BS or E.coli (rather than Salmonella). Over-expression of urease to precipitate CaCO3. Jem: spidersilk is very difficult cloning!
    • We dont want to lyse rods - may need stochastic switch to determine which cells become rods and which are single-celled, lyse and bond the whole together.
    • Jen - can only have 6 people in lab at a time.
    • Newcastle will host event for all UK iGEM teams. Need to think of an activity.
    • Jannetta request: can go into more detail about interpreting results from models. Possibly as a later tutorial

Action points

1. Bug's eye view flowchart (Richard)
   • Not discussed in detail
2. Email to Colin Harwood
   • Approved by team, waiting for final approval by Anil
3. Logo/T-shirts
   • Finalised logo colours
4. Tutorials
   • Matt would like to see an animation or similar about what exactly our project does. Matt deliver Flash tutorial (in a fortnight 30 mins)
   • Tutorials next week - Anil Modelling 2.
5. Registration Fee
6. Wiki transfer
7. Travel plans
   • Flights
   • Accomodation
8. Funding
9. Modelling
10. What's needed (what’s next?)
11. Advisors/ New members
12. Time line discussion
    • up to date (excluding overdue logo)

Update of standing agenda

• Steve failed to complete this in time

Other business

Action points for next agenda

1. Do Bug's eye flowchart.
2. Anil: to look at Colin Harwood email. Richard to email to Anil for approval.
3. All: transfer our individual profiles to wiki
4. All: external wiki put up exam dates
5. Steve: update standing agenda again

Next meeting

• Chair (Da), Minutes (Phil), Computer (Harsh)
• Advance apologies from Richard and Zoltan (Wed)
• No informal meeting. All agreed.