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Team:Calgary/23 July 2009
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| - | + | Modelling report and plan of attack | |
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| - | + | We touched on that briefly today but had to put that on hold to discuss lab work. We’re planning to put together something that includes a description of what we’re planning to look at (Hill equation, static/dynamic behaviour, response time, population mean and range), why it’s useful and how we plan to collect the data to develop the model or quantify that aspect of characterisation. | |
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| + | Making the introduction less superficial | ||
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| + | We all know that I’m making a lot of vague claims in the introduction (ie, why coordinated behaviour could be useful in degrading biofilms). These need to be substantiated by something specific and credible. I will address that as much as I can within the next few hours. Other areas of concern include a lacklustre description and comparison of the AHL and AI-2 signalling pathways that needs to be improved (ie, why do we want AI-2 beyond my favourite example of enabling a quorum-based logic gate? I need to mention specific cases where the AHL system does not function while AI-2 does, which can be found in the literature); poor formatting of names that need to be italicised or not (genes vs proteins); a more rigorous description of how and why bacteria use quorum sensing in nature; a better introduction to LuxOD47A, where it came from, how it was developed and in what specific experiment it was used in. This list is by no means exhaustive and I’m sure that more will come up once I address the issues that I’ve mentioned. | ||
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| + | Materials and methods and results writing | ||
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| + | We discussed this in our paper meeting today. I was still somewhat in thesis mode and I wasn’t sure how much detail to include because I thought that we were just writing this for the wiki. As mentioned in the meeting today, I’ll make it less cumbersome, assume some prior knowledge of technologies such as PCR, and use the descriptions that I wrote for the typed edition of my notebook. | ||
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| + | I’m still a little uncertain about the results too – I haven’t focussed on it that much yet because I’ve been caught up in the previous sections. From what I understand, since I don’t have any functional validations (if my cells glowed, I would worry), the sequencing results really are the verification that something happened. I’ll also include my very last gel, which includes the DNA ladder, a negative control, LuxOD47A BBk, LuxOD47A BBk + B0015, and J13002 + Lux… + B0015. This displays everything that we’re contributing to the registry; has a good negative control; and distinct size differences that help validate the results. I’ll have a better sense of whether to include more detail as the section takes form – we had talked about including a gel for every stage of the process, but if I can embody all 3 Registry contributions in one, it would be the least cumbersome to just use that. | ||
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Revision as of 07:04, 21 August 2009
UNIVERSITY OF CALGARY
