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Newcastle University/5 June 2008
From 2008.igem.org
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Minutes
Minute Taker: Nina Nielson
Action Plan for next week
Group
• Design a flyer/poster.
• Look at which parts have been identified already. If some of the parts that we are using haven’t been added to the repository yet, the group should put them on.
• Add iGem calendar of events to our calendar on our wiki.
• We need to research safety of our application. Do we understand the implications? Ask Jan for some tips, cosh form etc..
• We also need to ask Jan if he actually has the strains of bacteria we are going to be using. Thus we need to define the strains that we have been looking at for him.
• Look at cell-cell signalling article on iGem page.
• Do Hibernet tutorial]
• Do cellML tutorial and start modelling parts.
• Compare interfaces with User stories.
Megan
• Research the comC rather than vncR/S TCS in S. pneumoniae (or another suitable two component system).
• Continue adding to Java.doc.
• Investigate more parts for the chosen peptides.
• Finish designing the architecture for her database.
• Practise using JBDC
Nina
• Find all associated parts for PlcR/PapR (Blast the peptide).
• Email Jan about making sensor-fluorescent protein biobricks, strains of bacteria, and safety information . • Investigate potential for using Bacillus anthracis as well as Bacillus cereus. Find associate parts for this species too.
• Practise using JBDC
Mark
• Finish registering to iGem 2008
• Meeting with Jen to discuss EA on Tuesday – develop his own action points for EA.
• Construct architecture
Time: 14:30 – 17:20
Attendees
Neil Wipat – Supervisor
Jen Hallinan – Supervisor
Matthew Pocock - Supervisor
Morgan Taschuk – Project 5
Mark Wappett – Project 3
Megan Aylward – Project 1
Nina Nielsen – Project 2
Meeting Content
Agenda 1: Update on Biosensor
Students briefly discuss the bioinformatic analyses for S. aureus, S. pneumoniae, B. cereus, L. monocytogene that they have carried out this week.
Mark explains that the autoinducer peptide released by S. aureus is unique to the species.
Megan mentions that she has had difficulties locating the repressor of the vncR/S two component system (TCS). It is then suggested that an alternative TCS is exploited (since there are 12 others to choose from in S. pneumoniae). Megan suggests the comC two component system. This was ruled out earlier since it was thought to be too similar to other species.
Nina explains that she has found a promoter (pxylA), repressor (Spo0A) and other components of the PlcR/PapR TCS and that the pentapeptide released by B. cereus is unique to the species.
Mark comments on difficulties he has faced with L. monocytogene. The lisK/R system has no autoinducer system discovered. He is concerned that the common arg system is too similar although it has a unique HK. Neil approved that this feature was suitable enough to use.
Neil suggests using other Bacillus species such as Bacillus anthracis. Mark previously searched for a unique two component system and peptide but struggled. The group decides another attempt could be useful.
Neil then also suggests producing sensor BioBricks linked directly to fluorescent proteins to show that the system works. This can be done with each of the species. Jan should be emailed to help design these.
Nina offered to email Jan and research this. She should also inquire the combination of fluorescent protein outputs that are distinguishable to allow more sensors to be sensed.
Making the biobricks would also qualify the team for the awards.
Agenda 2: Teacher’s Meeting in Paris
Jen attended the iGem teachers’ meeting in Paris last weekend and summarized it. Talks were given by Randy Rettberg and Tom Knight. Jen showed us an example of an exercise.
Once a basic part has been added, the process is similarly repeated to add a composite part. (run of basic parts)
Adding parts exercise example (pt53) >add a part >add a basic part now //use the next number available (easier than assigning ranges of numbers each). >Write a short description of the part: pt53 >Write a long description of the part: tumour protein p53 – Guardian of the genome. >Source: Genbank //write where you found the part in the source >Sequence: Paste the sequence in this box
An advantage of adding the sequence is that the repository annotates it, for example indicating restriction sites such as Xbal and Pst.
Jen also mentions that BioBricks are written in XML format which could be particularly useful for us since we will all be using cellML.
Agenda 3: Mini-talks
Students give 10 minute presentations on individual project progress for the supervisors to assess their presentation skills.
Matt gave some general comments • When introducing the bug, give some interesting facts about it. Such as what infections it is responsible for etc…
• Show alignments of the cleaved peptides to show they are unique. Only Mark did this.
• Nina stop leaning on chairs and tables and standing on one leg. Try to stand still and sound believable.
• Mark stop saying like and er and um. Try and replace this with taking a breath.
• All of the students should also try and point at the screen.
• Jen said in general, the talks are much better than the proposal presentations
• Neil says try and sound enthusiastic and happy. Be American!
Agenda 4: Architecture
Nina expressed her problems with installing TortoiseSVN. Matt suggested uninstalling what she has installed and to shut down the system and reinstall with Morgan’s supervision.
Matt explained the architecture will consist of three top level directories (one each) which will be siblings with Morgan’s workbench.
The package will have a java.import function to import stuff to the URL. This ensures the same code isn’t written.
Within the package.
Nina draws the layout of the package (guided by Matt).
Matt suggests to look at Hibernet – object relational mapping, for an example of JDBC. Megan and Nina should definitely look at the Hibernet tutorial with access (on windows).
There is a link on the java exercises set by Morgan on the wiki.
Megan goes through some of the classes that she would incorporate
PartR
getTypes();
getAllPartsID()
getPartTypeID(partType)
getModel(partID)
List <Part types> List<All Parts> List<Part types> cellML
Both Nina and Mark should attempt this exercise. The team should then compare the interfaces with user stories.
AOB
• Neil and Jen are away next week
• Neil emphasises importance of finishing a week earlier since DNA synthesis takes approx. 3 weeks, not 2 weeks. • Edinburgh rendez vous is on the 15/16th July not June.
• CellML tutorial talk 06/06/08 9.30 am by Neil.
• A writing group should be set up – group references shared since a lot of overlap.
