Tag Archive for 'postdoc'

New beginnings…

Published on July 8, 2010 in Daily titbits, Observations and Philosophies. 2 Comments Tags: , , .

I have been remiss, once again taking a protracted break from this blog. I was essentially forced, by economic factors beyond my control, into taking quarter of this year off work. I used this time to re-assess, travel, reflect and generally think about myself and my own directions; time I’ve not taken since 1999, which was careless of me. Whether I can consider myself rested enough within three months is neither here nor there, for I am back, or at least I will be back, but in a somewhat modified form.

One of the big problems with maintaining a science blog where I wander through a range of subject matter is that it does rather take my eyes away from my day job, and you only need read a few science blogs to realise the the day job of a jobbing postdoc is rather full of teaching, supervision, research, reading, writing and banging ones head against a wall. Thus, whilst I was increasingly thankful for this distraction in my last research position, I have recently joined a new research team who are doing some interesting and meaningful work; I will be taking the advice of Daniel McArthur of Genetic Future who at Science Online London 2009 said that one way to succeed at both blogging and your day job is to fuse the two. To that end, this is what I will be doing, obviously not giving the game of our own research away, that would be silly, but instead talking about the field in general.

So what field? Well, my new position sees me returning to my roots; I started out in Staphylococcal molecular genetics a decade ago and spent my most formative doctoral training years working in a rather academic aspect of horizontal gene transfer. It was then, and still is (though not for long) a highly under-studied area of research that couldn’t possibly be more important with what we are coming to understand about the nature of antibiotic resistance, evolutionary microbiology and the human microbiome. I am now working in an area that brings together several recurring themes of interest for me: evolution, horizontal gene transfer, bacteria (Staphylococcus aureus to be precise) and antibiotics research, specifically the evolution of bacterial fitness.

This is exciting times for me, and I can’t tell you how many fantastic papers I’ve already discovered from my period of absence in this field; people have been busy, and I intend to talk about it. However, much of what I have to say won’t necessary be in this blog, for I will be moving. This blog will remain of course, as part of my efforts to regale you with edifying titbits.

As for where I will be moving to, well I now have a blog over at the Nature Network, called ‘The Gene Gym‘.

I will not be closing this blog down, it will be a repository for all those science stories and titbits that don’t fit in with my Gene Gym remit.

Thanks for reading.

 

 

A dichotomy of research…..

Published on February 21, 2009 in Rants and Science. 0 Comments Tags: , , , , , .

[ratings]

I AM a juggler by profession, but it is not balls that I juggle; instead, I juggle variables.

I currently work on basic technologies research. This does not mean to say that my research is basic, rather it means that the technologies that we are trying to develop are at a fundamental, or grass-roots, level. As such, some might call such research ground-breaking; though I hasten to add that this term is more considered in it’s metaphorical context. If any of you have ever had to dig in a new garden, or have led the way in deep snow on a mountain, then you’ll have some idea of what breaking new ground is all about. It is hard, unrelenting and there is no lateral movement, you either move forward into new ground, or you back-step until you get to base camp and set off in a new direction.

I am working on a biochemical reaction (a reaction involving biomolecules such as proteins and DNA) that has been shown to work in solution, in a tube. Other people have shown this, and I have shown it. However, interesting as this reaction is, we want to go further with it and have it work on a solid gold surface. Why? Well, ultimately we would like to be able to control the reaction by using an electric field, to turn it on or off, or better still control the precise level of its activity.

Having a biological system that works at the flick of a switch seems like a pretty cool idea, right? You’re sitting in a small, dusty village in central Africa or central South America. You’ve taken a load of blood and saliva samples that you intend to test for certain antibodies, or for the presence of current bacterial or viral diseases. It’s hot, there is no power and it took you a week of travel to get there. You are worried that your samples will degrade before you can get into a position to test them, and if you are especially well funded, you will have brought a whole portable lab with you, at great cost, and at great loss if it breaks on route.

What if, instead of the above hassle, you take out the small box you brought with you, in which there are several foil-wrapped packets containing plastic cassettes about the size of your thumb, but considerably flatter. What if you could inject the blood or saliva sample in at one end of the cassette, wait a minute and at the other end one of several LEDs light up. The combination of LEDs will tell you what the cassette has detected. Inside the cassette are small flow-channels that each contain different biomolecules that have all been painstakingly developed to function in this capacity. Simple, potentially very cheap, a laboratory on a chip.

Furthermore, you flick a switch on the cassette, which makes the juice from the small battery alternate from just powering the LEDs to instead put an electric field through the flow-cells; you can now conduct a second set of reactions using biomolecules that had been inactive until that point. TWO labs on a chip! Lab on a chip technology already exists, but there is much further for it to go, and this requires basic technologies research.

Ideally we would have a chip that could perform logic functions, so rather than it just detecting molecule A and it saying “hey man, you’ve got some molecule A here”, or likewise with molecule B; perhaps if molecule A and molecule B are both present, then this indicates something more serious, which is indicated by the presence of molecule C. Rather than you wasting time, and another chip, going back and testing the blood sample again for molecule C, the chip can detect both A AND B in combination, and in doing so will have activated another internal component that is able to then detect C. However, if the chip detects only B, NOT A, then this could indicate something else, so it triggers something that can detect this something else, perhaps molecule D. See? A logical chip.

Well, returning from the realms of near-future science fiction, in order to achieve any of the above in my basic technologies research, there are several variables we (meaning I) need to juggle, and this is where the fun pain starts:
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