Dundee Life Sciences Centre
After designing the systems for antibiotic screening, our team set up a meeting at the Dundee School of Life Sciences with Dr Paul Andrews to investigate the considerations we’d need to take if our system were to be used under real life conditions. This is an important aspect of the project, as it ensures that the systems we devised were realistic and have the potential to be useful. This visit was an exciting opportunity to develop our understanding of modern day screening techniques and to see them in a practical setting. After discussing the system we had devised, Paul was able to give us feedback on alternative approaches to increase the applicability in real life setting. He advised us that when we were to carry out the planned experiments, we would have to culture the bacterial populations in clear media to ensure that the media had no influence on fluorescence readings. In response to this, we chose to grow our populations of E.Coli in M9 minimal media. Initially, growth was stunted in these conditions, when compared to the bacteria that had previously been growing in LB. To alleviate these issues, the successfully transformed cultures were allowed to proliferate in LB, before being transferred to M9 media. Once the bacteria had adapted to these conditions, it was then possible to record the fluorescence.
In addition to this, we discussed the potential use of bioluminescence rather than fluorescence, as a more direct visualisation of the outcome of the experiment. However, after researching more into this possibility, it became clear that this type of signal would not be suitable, as we required a split system to detect cell lysis. Furthermore, using bioluminescence would most likely complicate our experiment further as bioluminescence needs an energy source to function and as it is outside the cell that manufactured it, we would need to provide such energy source.
Prof. Harry De Koning
Another part of our integrated human practices involved a meeting with Prof Harry De Koning from The University of Glasgow. At the time of the meeting we were looking into improving our experimental methods in the Biofilm experiment. This involved researching a plate which would allow for simple manipulation of grown biofilm. We looked into a plate from MBEC Assay’s called the Biofilm Inoculator which is a specialized set of pins that can be placed into a 96 well plate. The idea behind this was that the biofilm could grow on the pin and then be removed from the media potentially avoiding a wash (one of the main issues with current methods of biofilm detection). He suggested that if we could find an appropriate fluorescent protein it could be possible to take the pins directly out of the media and place into a acidic solution which would dissolve the biofilm releasing the binding protein and fluorescent protein if they had previously attached to the pin. This plate could then be neutralised if necessary and then put directly into a plate reader. Not only would this reduce the number of washes (increasing the efficiency of detection) it would also allow for the experiment to be run multiple times at once to increase precision of the results.
After researching this we discovered it would be possible however it was likely we would have to use a chemical fluorophore rather than a protein due to the low pH required to dissolve the biofilm. Therefore this method is not in line with iGEM’s aim of genetic engineering so though possible we ruled it out. He also mentioned Fret Detection as a method to carry out the experiment and after research we determined that it was too late to make such a dramatic change to our experiment especially when our advisors do not specialise in this area. It may be something to look into next year however and could provide a further improvement over the method we are currently developing.
If we were successful in constructing this new system someone in a position like Harry Dekoning could potentially use it in their own research. Therefore, this meeting and his suggestions to develop our experimental method provide a direct way for our project to impact the community it is intended for.
In order to gauge the success of iGEM as vehicle for student learning, we will implement a series of surveys which compare the impact of traditional laboratory assistant positions (summer internships during which undergraduates perform small projects related to the research and under the supervision of teaching staff at the university) to iGEM (which by contrast is entirely student-driven, with advice and assistance from staff when necessary).
There will be one survey directly after completing the summer, one survey upon graduation, and one survey a year after graduation, in order to assess the longevity of the impact of both kinds of research experience. The surveys will be anonymous but linked together using the matriculation numbers of the participating students.
The aim of these surveys is to quantify the differences in the techniques learned and the leadership and planning skills developed in each of these related experiences. In order for us to successfully disseminate the surveys, they passed rigorous consideration from the ethics committees of both the School of Psychology and Neuroscience and the School of Biology.
After the surveys have been completed, we also plan to hold a focus group led by an independent third party (such as a member of staff or the School President of Biology) to compare in real time the differences between the responses of students who had staff-directed research assistant positions with those of iGEM participants. We plan to use these comments and those from the surveys to modify our practices for teams in years to come. Possible suggestions might include different ways of brainstorming for our project topic, a different timeline for the research and implementation components of the project, a designated person whose responsibility is fundraising, etc.