2 February 2011

The first four recruited iGEM team members met at Med Campus, namely Ezio, Sasha, Richard and Natasia. We discussed further recruiting of members from the Science, Humanities and Engineering faculties. Marco gave us advice on ways in which to work best together. He also told us that we should aim to start lab work earlier than the team of last year.

3 February 2011 (Karl and Natasia)

After being recruited on the iGEM team, I met with Karl who is my supervisor for the project for the year. He and I discussed a few ideas for the project. He recommended that I read Jay Keasling's articles. Some of the ideas we discussed was a way of hydrolysing hormones present in water using bacteria. We also discussed perhaps a project looking at the ability to stop conjugation in bacteria.

7 February 2011 (Karl and Natasia)

We discussed the Jay Keasling articles I had read. The one which was most interesting was the one on the production of an antimalarial precursor. We also discussed a project idea to aid in the treatment of acid mine drainage.

9 February 2011 (Karl, Brad, Richard and Natasia)

Richard and Brad met with Karl for the first time. Brad said he would create the wiki for the team as well as being involved in the modeling and process control. Richard, also an engineer, will too be involved in the process control and modeling as well as aid us in the chemical engineering aspect of the project.

11 Feburary 2011 (Meeting at the PiG)

The team members who were able to attend this meeting were Sasha, Ezio, Richard and Natasia. Michelle from last year's team was also there. We spoke about recruiting a fourth biologist. We also discussed fundraising ideas as well as the direction of the project (whether it would be industrial or medical in nature).

16 February 2011 (Pizza at Primi)

At the meeting at Primi Piatti, we officially welcomed Gloria onto our team. She is the fourth biologist on the team and is doing her honours in microbiology at Wits. We used the time at the restaurant to get to know each other better as well as to discuss some ways of ensuring the group works well together. We discussed our goals in the project and were advised by those involved in last year's iGEM Wits team to ensure we include all team members in all aspects of the project as this will ensure enthusiasm throughout the project. We also discussed our goals for the project and what we wish to achieve in the competition. We are all very excited about the project and motivated to do well.

21 February 2011 (Industry Challenge)

We met with Dr Cluett, who is involved in the beverage industry. He outlined some of the issues faced in the industry. Of primary concern is the formation of biofilms within pipes and tanks. We discussed this further and agreed to do research. Another issue raised was that of tracking and tracing in the food/beverage industry as part of quality control of the product. After the meeting, the group members brainstormed on ways in which biofilms could be sensed andn then controlled.

25 February 2011

At this meeting, various members of the group had the chance to present their own ideas to the entire team. The feasibility and the challenges associated with each idea were discussed, resulting in the development of the idea through group input. It was decided that all the basic ideas had potential, but they required a lot more background research for the idea to be developed further. Some of the ideas that were presented involved strategies to remove biofilms, which is a big challenge in industrial processes. The strategies included: 1) using bacteria as a Trojan horse to deliver a detergent that is carried in a carbon nanotube into the core of the biofilm to disrupt it and 2) mechanisms to induce the differential expression of highly negatively charged peptides, on the surface of early colonisers of the biofilm, so that they will be repelled from the surface into the surrounding solution. Another idea that was mentioned was that of a smart drug delivery system which detects pathophysiological stimuli and reacts by releasing the appropriate therapeutic.

2 March 2011

Today, the team came together to meet with two industry experts, that is Dr Marco Weinberg and Vincent Rathbone. Dr. Weinberg, a medical scientist at the Antiviral Gene Therapy Research Unit at the University of the Witwatersrand, and a supervisor of the iGEM team, introduced the group to the concept of gene therapy and its use as a powerful molecular tool in treating diseases. He highlighted the need for the development of controlled and targeted therapeutics that would not just treat the symptoms, but rather provide a once off cure. He also provided some very interesting examples of gene therapy that got the team quite excited. Afterwards, Vincent Rathbone who is a scientist employed by Anglo Gold Ashanti, presented to the team the various challenges that are associated with the mining industry. He spoke of occupational hygiene problems and process related issues. These included the spread of TB in the work environment and the inefficiency of the systems that are currently employed to deliver cooled water underground. The latter was the focus of debate as the team proposed and discussed various ideas that could deal with the problem. After the meeting, the team met up privately and discussed brainstorming techniques to increase the output of feasible ideas. It was decided that it would be beneficial for the team to have brainstorming workshops, where the entire team would assemble, and discuss and research ideas together. This would enable team members to contribute to each other’s ideas and also allow the group to spend more time together and bond as a unit.

17 March 2011

The team discussed some of the ideas for the project. Two of these were in the fields of gene therapy and biofilm degradation. The team evaluated the pros and cons of each of these ideas as well as the methodology that would be required for each. We spoke about getting the team together for a social event to get to know each other better. We also spoke about our strategies for the interface of the Wiki. We discussed that we should upload photos of the teams' involvement in the project every step of the way.

11 April 2011

Student team members presented individual ideas, which were then discussed among the rest of the group. The main idea discussed was the bacterial granulation idea which involves inducing granulation to make it a reliable technology. We discussed to which applications this technology could be applied. We also discussed deadlines for a final idea for the project. The deadline set was the end of May.

15 April 2011 (Brainstorming)

Ezio,Gloria, Sasha, Richard and Natasia got together at med campus to brainstorm more new ideas. We discussed the bacterial granulation idea and in particular its application to water treatment. We also discussed the potential use of a colour reporter system to indicate when the bacteria had degraded the molecule in the water we wish to remove although the molecule to degrade was not decided upon. A potential molecule would be a hormone that is a pollutant in some water systems in America and South Africa alike.

18 April 2011

The team got together under Prof. Marco Weinberg's supervision to give feedback about the ideas that were researched over the weekend. Everyone was given a specific area to research before the next meeting. The engineers were sent a paper on biofilms and mathematical modelling. The biologists went away to look deeper into specific target areas for the biofilm eradication idea. Gloria chose to gain more insight into developing a new diagnostics tool/test.

22 April 2011

Richard, Ezio, Gloria and Natasia and Sasha met to discuss various aspects of the project. We discussed various ideas on the project. Some of the team members then went out for lunch to learn more about one another and have some fun.

29 April 2011

The team met at Med Campus where Brad and Natasia started working on the wiki. The team also discussed the project ideas. The main idea discussed was the use of bacterial chemotaxis to allow a bacterium to move towards a source, and once the source is found, to move back to the start. This idea was then finalized as our idea for the iGEM competition. Each team member then agreed to research different aspects of the project.

3 May 2011

The team met at med campus to discuss various aspects of the iGEM competition. The community outreach aspect of the project was discussed where Gloria and Sasha were put in charge. Potential projects would be a science cafe, a collaberation with SciBono, educating school children on synthetic biology as well as assessing the impact of our project on society. We also discussed the modelling for the project to ensure that our machine works optimally. Brad and Richard were put in charge of this aspect of the project. We discussed the development of the wiki. Over the weekend, Natasia sourced a computer programmer who would be willing to do the wiki for us. He began the process over the weekend creating a working site with a high level of functionality. Team members contributed ideas for the site. One idea was to have a quiz or game for visitors of the site to enjoy. Next we discussed the funding for the iGEM project. Sasha and Natasia were put in charge of this area of the project. We discussed our fund raising strategies and decided that we should construct a brosure to present to potential sponsors. We discussed the biology of the project next. We handed out an information sheet to all team members to summarize the chemotaxis in ''E. coli''. We discussed what aptamers we will use and agreed to research potential promoters for the construct. In the wrap up of the meeting, we decided on some deadlines. We agreed that the machine construct should be ready by 16 May where we will present our final idea to those involved in the project as well as to the CSIR, one of our sponsors.

4 May 2011

The biologists met to discuss the aptamers we will be using as well as the promoters. We agreed that we will definitely use theophylline. We agreed to continue doing research on the various other options we had for the second riboswitch.

6 May 2011

Natasia had a meeting with a connection in the corporate industry about the approach we should have with the funding. She was able to source the CSI handbook which contains a list of companies and their respective funding areas. She received many tips and hints on the construction of the document to go to potential contributers to the team's travel and research expenses.

7 May 2011

The biologists met at Med Campus to discuss the biology of the project. The complete genetic circuit was not determined by this due date so the date was extended by a week. The one riboswitch that will be used will contain an aptamer sensitive to theophylline but the other one is not decided yet. The most promising option discussed was tetracycline. The system needs to be sensitive to a particular concentration of antibiotic. Thus, a toggle switch was proposed to allow the circuit to switch positive chemotaxis to switch off at a specific concentration of the antibiotic. This is a crucial element in the genetic circuit and the team committed to spending time ensuring it will work correctly. We also discussed the use of modelling for each step of the circuit.

9 May 2011

Sasha and Natasia met to discuss the biology of the project as well as to discuss potetial donors to the iGEM project. They discussed the promoter which will be necessary to respond only to a particular concentration of the chosen antibiotic. They spoke to Marco about some of the promoter ideas and developed a toggle switch for this. Sasha and Natasia also met with Michelle to ask her for some advice since she did the fund raising for the iGEM team last year. Natasia and Sasha went through the CSI handbook searching for companies who are interested in investing in tertiary research and agreed to send out the documents to the companies as soon as possible. They proposed an A5 brochure which would summarize the official document. We agreed to approach Karl for any advice on this.

10 May 2011

Natasia met with Karl to show him the updated genetic circuit and to ask his advice on approaching potential sponsors. He aided us in the construction of an A5 pamphlet to accompany official documents to go to the donors. He also spoke to her about the rules and regulations regarding the employment of vendors through Wits.

10 May 2011

Ezio, Sasha and Gloria drove to CSIR Pretoria accompanied by Marco and Michelle to meet with Dr Musa Mhlanga. In addition to being the competency area manager of synthetic biology and research group leader of the gene expression and biophysics group at the CSIR, Dr Musa Mhlanga is a highly regarded team Advisor. At CSIR, the team presented the idea and the proposed genetic circuit to Dr Mhlanga. Dr Mhlanga brought to the teams attention, potential problems with the genetic circuit, gave the team advice and made suggestions. All that Dr Mhlanga said was noted and for the team it was back to the drawing board.

16 May 2011

Sasha and Natasia met with the staff at the Wits fundraising office to understand the ways in which to approach potential donors to this project. We agreed to meet on Thursday (19 May) to go through a list of companies whose focuses for corporate social investment are aligned with our project.

19 May

Sasha and Natasia met with Tsepiso, who works at the fundraising office and is finding suitable donors for our project. She proposed a number of potentials, comprising of biotechnology, pharmaceutical and health care companies. She agreed to clear this list with her director and hand over the verified list to us on Wednesday (25 May). At this point Sasha and Natasia will begin to approach these companies.

20 May

A team meeting took place in the microbiology common room where the team tackled a few issues. First was the organisation of an event to educate the public, students and the press on synthetic biology. We agreed for this event to take place on 17 August at the university. We agreed to do a presentation on this day which would deal with synthetic biology as a whole and to introduce our idea to South Africa! We also agreed to contact SciBono for a potential collaboration with them which would enable us to reach far wider and share our knowledge on synthetic biology with the broader public.

Next Brad was asked to design the look and feel of the Wiki as well as to design a logo for our project which will appear on all of our team apparel and on the website.

On the biological aspect of the project, we were advised by Karl to take on separate responsibilities for instance, be in charge of creating particular buffers so that they are always produced by the same individual in the same way. We agreed to start preparing plates for the bacteria next week (23-27 May). We also spoke about the modelling that needs to be done for the project. Brad and Richard are in charge of this section of the project but we all showed great interest in understanding how the models will be produced and the benefits of their application.

The team agreed to go away and think of potential applications of this project. We have, thus far, focused our attention on applying this synthetic biology project on searching for colon cancer. There are potential applications in the mining and wastewater treatment areas as well.