Posts Tagged ‘lab’

Home Straight

Apr 4th, 2009

The end of my PhD is rapidly approaching, and suddenly it no longer seems some distant event. By the time Christmas comes around I very much hope to be out of the lab, and to have a good chunk of my thesis written up. However all of this means getting the lab work finished, or at least in a state in which it is possible to write up.

As things stand at the moment that goal has yet to be achieved, and there as still a few key experiments that need to be completed. The past week I gave the first run through of one such experiment, and am currently in the ‘debugging’ phase, in which I try to work out exactly where everything has been going wrong. Its one of those tasks which is okay in the short term, and can even be quite satisfying, but which gets demoralising if it runs on too long.

Fridays result was initially a bit confusing, until I realised that what it was actually telling me is that an earlier result was the misleading one. Fortunately everything is still in order, and it hopefully means that I’ll be able to address some of my problems on Monday. The rest of the problems however still need further scrutiny.

All this meant that I was in the lab this morning preparing materials for use on Monday. I have already decided that I’ll try and make the most of weekends between now and September, although that doesn’t quite mean pulling a 10/7. Don’t get me wrong, I’ve been no stranger to the lab at weekends, but previously I have tended to use them to facilitate the weeks work, rather than as working days in and of themselves.

The annoyance of temperature sensitive mutants

Jun 10th, 2007

More news from the lab and this time its me ranting about the behaviour of my cells.
When investigating the function of a particular gene one tactic geneticists have availible to them is to break the gene and see what happens. One way of achieving this is to ‘knock it out,’ to entirely remove the gene from the genome, or otherwise inactivate it. This allows you to study the phenotype (Characteristics) of the resultant cells to try and work out what the gene was probably doing. However in some cases the gene is very important indeed, and the resultant phenotype is merely ‘dead’ which makes it very difficult to actually do anything with the cells, and impossible to get enough to actually characterise them. Dead isn’t a very usefull phenotype, we want to know exactly what type of dead they are.
One way of overcoming this hurdle is through what is known as a conditional mutant. As the name suggests, this is a mutated version of a gene which only shows its abberent behaviour under certain ‘restrictive’ conditions. One of the most common forms of conditional mutant is the temperature sensitive mutant, which only shows its ‘dead’ phenotype at higher temperatures. Thus most work is conducted at a lower temperature and then the cells are shifted to a higher temperature for testing.
The only problem is that even at the cooler temperature temperature-sensitive mutants are rarely wild-type (normal) and are usually at a slight disadvantage, showing slower growth than normal cells. Now as any student of Darwin will realise we have a bit of a problem. Genomes mutate with a low background frequency which is nethertheless high enough to cause problems, as any mutations that help rescue the slight disadvantages will be selected for, either by outcompetition in liquid culture, or by selection bias (which is basically me selecting the bigest colonies on my plates). Unfortunately sometimes these new mutations also help to make the cells grow better at the higher, normally restrictive temperature, and better than dead happens to be alive.
Now this is very annoying to me, as I want my cells to be dead at the restrictive temperature. For one it identifies where my mutant gene is, and for another is important for other experiements in which I try and make them not dead through other means (largely by making other mutations, or introducing other genes). But seing as I do most my growth at the colder permissive temperature there is no way of telling if my cells have reverted untill I shift them to the higher temperature, at which point they are dead and of no use to me. Fortunately it is possible to replica plate cells, in which a plat of cells is transfered onto velvet, and then ‘copied’ onto two seperate plates, one of which is kept at the restrictive temperature and the other the permissive. This allows me to make sure I choose cells which grow on one plate but not the other.
Unfortunately I am finding that selection is something which must be maintained almost constantly, and even then revertants still seem to slip through the cracks. It seems sometimes you only realise that something has gone wrong when things grow when they shouldn’t have done.
[tags]genetics, pombe, science, phd, mutants[/tags]

Previously: Welcome Back

Dec 12th, 2005

I got hacked, a couple of times actually. The first guy modified this page, the second took control a bit more noticeably. I’ve decided to leave this message here, rather than tracking down the original, as a lesson to myself.

Just hope I’ve patched the vulnerability.

Edit: Oh sod it. I decided to track down the original, and have quoted it below. I even corrected a few of the spelling errors.

After a long period of downtime my blog is finally back online, this time running under different software. Unfortunately the old blog died when my webhost went bankrupt, but through the wonders of Google I have again be able to save the content. I’ll probably just chuck the best of it in a static archive page.

For those of you who don’t know a lot has happened since the last time I posted here the main of which is my graduation and subsequent removal to Edinburgh. Here I’m studying in my Masters year of a four year combined PhD/Masters. I have just recently finished my first mini-project, a ten week lab research project in which not only did I get some decent and novel results but I also wasted several thousand pounds in simple mistakes. The biologists among you will find my addition of DNase to a transcription reaction amusing, the rest of you will be lost.

On Friday we had the unit Christmas party, complete with ceilidh, which proved very exhausting. Naturally, for someone tho has only been to one ceilidh before, I was at a complete loss for half the dances, but thankfully I was not alone in this. We all get another crack at it on Burns Night, so expect lots of grumblings about sore limbs around then. This event also signaled the beginning of the Christmas season in terms of events going on and somehow I seem to have been tied in to about four Christmas dinners, two of which have already happened. I also fear further dinners when I get hope, completely destroying my somewhat naive plans to have my overdraft cleared by January. Still, once Christmas is out the way I should get it paid off fairly quickly. I don’t like being in the red, even when it is interest free. Still, as a general trend income is greater than expenditure at the moment so things shouldn’t be be getting any worse.

My new lab project is working with yeast again, although this time is is S.Pombe, S.cervevisiae’s less famous brother. At the moment things are a bit slow as I’m having to get everything up and ready for the experiment proper, which will probably begin after Christmas. The aim is to over-express a particular gene, making the cells sick in the process. Following this I will over express lots of other genes and look for rescue, that is a gene that can make the sick cells healthy again. In doing so I should hopefully discover what the first gene does, as well as possibly identifying some new genes which have previously been uncharacterized. If it works it should be all very exciting and may mean that I get a chance to name a few genes.