Postscript

And time runs out. Finished my studentship a few weeks ago, moved to a new town, started a new job, but more about that later. By finished I mean that there were some unforeseen complications, and I didn't get to do everything that we initially planned. If only I had a few more weeks..

That said, I'd still like to think that we managed to achieve something - at the very least we now have a siRNA construct that seems to knock down rat AKAP2 pretty effectively. Plus, I've learnt a great deal in terms of specific techniques as well as some less obvious (but no less important) skills. I've started my placement year in a pharmaceutical company, and although the sort of work here is completely different, I feel that because of this studentship I'm more confident in a laboratory environment.

I've also started thinking more about what I'm doing - why I'm doing each step, and also the ultimate goal of the experiment. Maybe it's just me or the education system I had to go through, but I used to (and still occasionally have the tendency to) just accept whatever I'm told without much independent thought. Even in undergraduate practical sessions, it's too easy to just follow the instruction 'recipe' that's often provided. I've experienced firsthand that research isn't always as neat and clear cut as I'd expected; you can think of possible results, but even those don't always work out. What makes it all worthwhile are the moments when something does go right. Then you're hooked. PhD, maybe?

"If at first you don't succeed, try, try again. Then again, there's always skydiving."

Someone, sometime, in the lab.

Warning: Rant ahead

I'm annoyed. Seems like my cell cultures got infested with bacteria. Again. It has to be the new media that I made up - I didn't realise I was meant to filter sterilise the serum before adding it to the media. Obvious, really, if you think about it. But well, I guess I didn't. What really got to me is that after the first bacterial assault on my poor defenseless cells, I incubated some of the media overnight with LB, and it was still clear the next day. I figured it was just me having done something stupid, e.g. sneeze on my cells, and it was safe to use the aforementioned (and henceforth damned) bottle of media - big mistake.. (oh, and on a random tangent, apparently it's possible to give your cells a yeast infection just by breathing on them after a night out drinking). Man.. as if I'm not already behind schedule with this project. Just hope I'll have something to show at the end of this.

So much for the best laid schemes of mice and men.

A month later

I can't believe it's been a month - 8 weeks seemed so much longer then. And just when I've started to get my bearings too.. Ok, down to business. As it was advertised, this project relates to "the molecular basis for learning and memory". More specifically we're looking at an A Kinase Anchoring Protein (AKAP2) that may be important in neuronal signalling, as explained below:

"The enhancement of neurotransmitter release from synapses in the brain by protein kinase A (PKA) is an important regulatory mechanism that is involved in learning. The project will test the hypothesis that the targeting and not just the catalytic activity of PKA is important for regulating neurotransmitter release. Plasmids designed to silence the expression of a synaptic PKA anchoring protein (AKAP2) will be constructed and then validated in heterologous cells. The plasmids will then be introduced into cultured neurons to assess the role of PKA anchoring in living synapses."

Simple enough concept, huh? Knock down AKAP2 with siRNA, then see if it affects neurotransmitter release. It's only in this last week where I've gotten preliminary (and fortunately encouraging) results. There's still much to be done though! I'll try to keep this site more updated than it is now..

In case you were wondering, yes, things are still going wrong, and odd results pop up every now and then. Still making mistakes, still learning, still enjoying myself.

The curious incident of the melted gel

“Start at the beginning and continue on until you reach the end. Then stop.”

The King in Lewis Carroll's Alice's Adventures in Wonderland

Or your gel melts. Or your stain focuses into a mysterious spot on the gel, not once, but twice. Or for some other inexplicable and unforeseeable reason, things go wrong. We do manage to solve these problems, but the fact is that they happen even when you do things exactly by the book. (By the way, when I say 'we' I mean Gareth and Chris, his postdoc).

And then there are times when it's down to simple human error. I've messed up seemingly simple procedures more times than I would like to admit. There was the one time when I mistakenly added loading buffer to my whole stock of purified plasmid vectors when I still needed them for ligation. Sigh. Wash, rinse, repeat.

More than a week's gone by now since I started this studentship, and I've been thoroughly enjoying it, don't get me wrong. Mistakes, well, they're a part of life, and we learn from them - that's why I applied for this studentship in the first place. Plus, for every mistake you make, chances are you're doing so many more things right.

To those of you reading this, it'd be great to hear about your experiences (especially the other students). I'm sure we could all use a little encouragement here!

A tube full of joy...

You know you're a science geek when, this:

Or something like this:

leaves you feeling happy and satisfied with the day's work. Over the last couple of days, I've done a number of midipreps to purify plasmid DNA from transformed bacterial cultures; some successful, some not quite so - but that's another story (in case the title didn't give it away, this post is about happy things only). So, after a couple of steps involving centrifugation, cell lysis, filtration, washing, and DNA precipitation, you elute off your plasmids into an Eppendorf tube not unlike the ones in the first picture (which was shamelessly stolen via the wondrous technology that is the internet).

The problem with plasmids, and many other things in molecular biology for that matter, is that you can't distinguish a tube containing a gene conferring the ability to move at light speed and the strength to rub superman's face in the dirt, from another filled with good old sugar solution. This is where the second picture comes in - agarose gels which let you know that your clear, colourless solution actually contains what you were expecting (in my case, pSUPER.GFP plasmids). Or confirm your worst fears that your sample only has the power to induce diabetes if you drink enough of it.

My conclusion? None, really, except maybe to get used to the fact that tubes, bands on gels, and other seemingly inconsequential items will become your source of satisfaction should you go into biological research.

Collect £200

Where better to start than right at 'go'? With not a single hour of previous experience, I have much to be grateful about. My thanks to Gareth and the Biochemical Society, who have so generously allowed me this chance to get a taste of what research in a working lab is like.

Maybe a little preamble would be useful.. I'm a biology undergraduate student at York, currently involved in a studentship between my 2nd and 3rd years looking at one of the components of cell signalling (more details to follow in a later post, maybe?). The plan is that I'll be documenting experiences/thoughts/etc. over these 8 weeks and Gareth will be commenting from a supervisor's point of view. All this blogging stuff is rather new to me, so any comments, questions and suggestions are most welcome! On second thought, do leave a comment - at least then I can get an idea of the (limited) readership of this blog.

p.s. I actually started in the lab last week, so the first few posts may be backdated, heh.