Discussion on current ideas 

BMC drug delivery mechanism, using E-coli to release a drug and act as a ‘smart bomb’  

Was discussed about creating a Bio yoghurt and using BMC to deliver to the gut however was decided that this may not be a commercially viable option as it is being done already using bacteria not BMC. 

Instead it was suggested a simple BMC could be created that contains an antimicrobial peptide.  This would be ingested and the BMC would not be broken down through digestion, protecting the peptide, until it reached the gut where it would naturally be degraded and the antimicrobial peptide released. 

Mark Sheppard suggested creating this type of BMC would be one of the more simple ideas.  Using that as a base a more complex approach could be added to the project.   

If we went with the antimicrobial peptide idea we would need to think of the following; 

Which peptide would we want to use? 

Which organism do we want to target 

What’s the selling point/ novelty of the project? 

Another idea suggested was in the area of Biofuels.  Trying to increase higher yields of Biofuels.  The industry is struggling to produce shorter chains and possibly we could create them using e-coli bacteria. 

This suggestion however was dismissed due to the fact there are better adapted organisms than E-coli such as clostridium already carrying out such work making this idea difficult to pitch to the judges. 

Odours and perfumes was an additional idea bought to the table.  

- MIT in 2006 engineered E-coli to produce banana and mint fragrances at different points of its life cycle.   

- It is suggested we could try and improve existing bio bricks to create perfumes and fragrances that did not work in the past .  

- Ways that we could pitch our fragrance idea to the judges could be;  

- new smells/ novel smells 

- Environmentally friendly – less waste products, renewable source 

- Cheaper to produce than what is on the current market  

- High quality  

Roles within the team

Quick discussion on roles within the team took place and initial roles that have been decided upon are; 

- Taylor and Alex- working on the Wiki 

- Brogan- Working on the lab diary  

- What has been done in the labs? 

This week competent cells were made and transformations on the cells were started.  

It was suggested to test the competent cells with the diluted plasmid cells and kit 

Need to calculate the CFU (colony forming unit)/ plasmid mg- there is a spreadsheet on the igem webpage to help with this.  

Current Events and General points 

1. Sheffield meeting on the 18/07/2014 starts 1pm.  Need 1 or 2 members of the team to go up to Sheffield and provide a short 2 minute presentation of what out project is about.   

2. Funding opportunity from ERASynBio 

3. Next week both Mark and Lisa will be back with the team so it is important to fill in Lisa with what has been happening so she can get up to speed.   

When creating these need to think about the following: 

-Melting temperatures of all the primers are similar 

-They don’t form a self-complementary structure 

-Can the primers self-associate? 

When designing the primers there is online software that can be used  

Was suggested about using light activating promoters and we can change between different fragrances using different light.  This was thought to be a good on-going idea but we need to get the basics sorted out first. 

Also was suggested about thinking about how we could use diffusion calculations to help our project. 

The Teams Wiki 

The Wiki is being worked on by Alex and Taylor, and was decided we should aim for a simple minimalistic approach to the Wiki (the Google effect).  

Was also suggested to stick to creating a wiki rather than a webpage as it is more unusual and may help us to stand out more.   

15.07.14

Notices:

-The lab form has been completed and sent off to iGEM 

-The next safety form is due on Monday 21/7- Alex said he would look over it. 

-Sheffield trip is on Friday 18/07 and Alex and Ellie will be representing the team, need to take lots of photos and try to make connections with other teams. 

Project Work:

Currently got 5 sequences can realistically only afford to sequence 2 genes. £600 maximum budget has been put on the sequences by Wei-Feng. 

So we need to decide on the 2 genes that we are going to synthesize.   

Was strongly urged that we order the sequence in vector form as it will be much easier to handle.  Extra restriction sites need to be added so that the Gibson assembly method can still be used if needed to be. 

Need to also decide on the strain of Ecoli that we want to use, current thoughts that top 10 should be ok and K12 should be sufficient.  

Tasks needed for next week:

-Logo design for the poster and Sheffield presentation needs to be sorted 

-Feedback from the Sheffield meet up 

-Look for recording equipment to help make videos to go on the wiki 

-Need to make a start on the Wiki; upload all files onto the one drive so that it is easy to load everything up onto the Wiki once it is running. 

-Everyone check the sequence that we are sending off 

-Need to carry on with the mini prep and run a gel for the GFP to see if it is present in our extracted cells.

Deadlines:

Safety form draft deadline was met however needs to be improved upon before it can be resubmitted.  It was suggested that we think about how the project would need dsaftey in industry and how safety would have to be adapted for industry. 

15th August the team roster and project description are due in. 

General: 

We did not receive any funding from the ERASynBio  

London YSB 2.0 is on 1/09/14 and 2/09/14 need to have a poster and presentsation prepared.  On the poster our designed Bio brick and sequence needs to be displayed.  Also was suggested that Rosie and Matt would like to present the presentation.   

Everyone does not need to attend both days of the meeting it is up to individuals. 

Travel and accommodation to USA is being sorted out this weekby Wei-Feng.  The team need to send off an email to him with name and DOB as stated on the passport. 

Lab Safety. This week after a visit from Martin Carden it has been highlighted that we need to follow safety rules in the lab. There needs to be two or more people in the lab at all times.  Supervisors for the group are; WFX, Ben or Morena. 

WIKI- Need to get a move on with the wiki as we want to be able to direct people towards the wiki so they can further understand our project.  Taylor and Alex are going to be working on the wiki next week. 

Paris team collaboration- A skype meeting has been set up for Tuesday evening.  Discussion was held about what we want to collaborate about, it was decided to keep our first meeting undetailed and get a sense of what they would like from us and if they seem happy to work with us. 

Givaudan emailed back and are happy to help us, we need to decide again what we would like from them and email them back. WFX suggested we talk with Lee asshe may have some good advice.   

It was discussed about using an odourless Ecoli however Gary Robinson suggested that it would be unnecessary. 

Zingiberene has been ordered and it should take 8-10 days to arrive.   

This week had problems photographing our gels WFX suggested that we need to save them as a JPEG not a TIFF and that if you alter the contrast then should be able to see something.   

By next week:

-Have all components grown up for limonene  

-Attempt the double digests, for this need to find a digest protocol  

-Have a think about computational questions  

-Have made progress with the Wiki 

-Remember to keep growing up new transformed colonies, use single colonies.

YSB sign up deadline has passed all of the team need to make sure they have signed up or need to tell wfx and he can email the organiser.

Wiki is looking good and Taylor is making good progress, just need to start adding lab notes on and make team profiles.

Boston is still not booked but the University has all our details and should go through by the end of this week.

Presentation for YSB has been started and a draft shown today, feedback has been given and a second run through to be given in a few weeks' time.

A draft of the Poster for YSB needs to be given at the next meeting.

Emailed France team back and have set up a Gmail account so we can swap information between teams

We have replied to Givaudan asking if we can arrange a meeting with them to ask questions about the fragrance industry and see an industrial take on our project. We also asked if they would be willing to supply us with any fragrance compounds so that we can use it as a control to test against our own.

Computational questions- discussion about computational questions was held these are the suggested ideas that were put forward.

- Observing the difference in yield/flux between the mono-terpenes and the sesqui-terpenes

Was suggested that we look at the Edinburgh team from 2008 who made limonene and see what they did

This week the team have been working on limonene and the aim by next week is to have it working as a bio brick

Also this week we want to practise the techniques we will be using on Zingiberene. So using limonene work on PCR and ligation techniques.

With limonene having problems doing a gel extraction of the RBS and promoter, they are small and keep running off the gel. It was suggested that instead we PCR the RBS and Promoter so there is a higher concentration and it will be easier to see on the gel. Also to run the gel for less time.

19.08.2014

Final Safety Form is due on the 1/09/2014 Taylor has volunteered to do the final draft and get it submitted

Title and Abstract needs to be finalised and submitted by the 30/08/2014. Currently there is a draft submitted just need to change the title and modify the abstract.

Need to have poster A1 size draft in by next Tuesday so can into the printers by Thursday/Friday.

Presentation needs to be finalised so it can be practised next week. Rosie and Matt are both Talking. We have been given number one presentation position.

Need to sort out train times to get to London and organise if we are going to stay in the arranged accommodation

Need to reply To the German team about their meet up and politely decline as we are going to the London meet up.

Need to sort out the Jamboree registration- see If there is a way we can register as a group so we don't have to do it individually.

Medway Research Festival is on the 10/09/14 need to come up with ideas of what to do. Suggested that we can use the poster from the YSB2.0.

Current areas of interest to look into are flux of our system, enabling us to see areas where high flux control is and enabling us to make possible changes.

Went over the powerpoint for YSB and feedback was given to Rosie and Matt so that changes can be made to improve.

26.08.2014

Abstract and title still need to be looked over need to add our tag line- Sweet scents. Nothing cheesy. onto the title.

Safety form still needs to be completed, it was suggested that it could be given over to Alex to get done.

Registration for the Jamboree has been completed, so everyone flying out to Boston is registered.

An Insurance form and occupational health form for the trip needs to be filled out by everyone going to Boston, Wfx will send around the form that needs to be completed.

Also everyone needs to remember to fill out the esta for going to the US.

Wiki looks the same as last week

Claire has written a bit about our project and has uploaded it onto the one drive.

Matt and Taylor have looked at the Edinburgh Wiki and they didn't find much out about their computational work.

Need to do more research into flux control ect

Had a proper presentation run through and feedback was provided for Rosie and Matt, general consensus was that it was good just a few more additional changes could be made.

09.09.2014

Review the check-in form before the 1st of October

Discussion and comments post- YSB2.0 conference in London about other teams and presentations.

Analysis and preparation of the questionnaire to be distributed in the Medway Science Fair (10/10/2014)

Tips on writing up iGEM results on wiki – use of 3rd person

Possible collaborations with other teams in terms of modelling-e.g. SDU-Denmark igem team which were also present during YSB 2.0

Outreach. The dates for presenting in Langdons Girls High school is beginning of October

Check the shipping form for the submission of the biobrick (R-Linalool)

Target the assembly of the biobricks

Retry PCR of the liberalized backbones: tet + cam+amp

Arrival of Zingeberene Synthase this week – PCR to have a stock

We have to move to the labs upstairs.

16.09.2014

We have been asked to go into Simon Langton Girls School on the 10th October to give a talk about our project and synthetic Biology.

On the 1/10/14 we have to give a 15-20 minute presentation with the summer school students about our project.

Also run a single digest on RBS and promoter containing the plasmid and then put these onto a gel. Again just to confirm that they are there.

Taylor has obtained Km values for R-linalool and Zingiberene.

We hope to be able to able to set up a system that allows us to change parameters such as concentration of substrates and enzymes in order to see how this affects flux of the system.

Suggested methods were shearing cells, French press and chemically breaking cells.

We need to also think about how we could collect the fragrance. Suggested methods were gas chromatography but it was pointed out that this would be expensive on an industrial scale.

More research needs to be done in this area before Boston.