Quiet

Haven't blogged for a week. I could say that I haven't had time, but that's probably not right, I just haven't been bothered. I think I check twitter so often now that I forget about blogging. Haven't really been up to much. Went to see Slumdog Millionaire last week which was very good. Got a bit of a man-cold after that but I seem to be over the worst of that. Had a spontaneous night out on Friday which was cool. Not had one of those for quite a while. Screwed up an experiment on Monday big time, wasted 24 hours, maybe about £100 worth of reagents, and felt really stupid. Some rude words were said at 18:00 on Monday in our lab!

Quick blog

Feel really tired today, no idea why, had plenty sleep last night, had cup of tea before I left the flat (the last time I felt like my brain was slowed like this, I realised I'd not had a cup of tea in the morning!). Perhaps best if I don't sit at the computer too much today. Write up lab book, plan luminometric assays for next week.

Going to the cinema tonight to see Slumdog Millionaire, hope I don't fall asleep.

Twitter seems to be broke this morning. There need to be an addon for chrome to have twitter active in the corner like twitterfox. Harumph! Maybe I should download the latest Google firefox addon which seems to make Firefox more like Chrome. I like the simplicity of chrome. I guess the addons will get there.

Right, secondary antibody!

Snow Snow Everywhere!

Yes, it is finally snowing like crazy here. Funny how the rest of the country gets it first before North Scotland. Still, I can stay in tomorrow and don't have to go anywhere. Can't think of much more to say. Finally started writing this chapter section that my boss wants us to write, only 400 or so words but it's a start. Otherwise my work has been a bit frustrating this week. Dot blots still not working, thought we have some thoughts as to what to do next to see if it's ever going to work, I only have a month and a bit left on this project!

Mmm what a dull blog.

My present work, in a nutshell

A Negative Feedback Loop Operating at the level of Translation in Yeast

Translation termination in Saccharomyces cerevisiae requires the essential protein eRF1 (eukaryotic release factor 1). eRF1 has a tRNA-like structure and interacts specifically with any of the three possible stop codons. This allows the release of the newly synthesised peptide from the ribosomal complex. Therefore eRF1 is crucial for determining the correct length of proteins in yeast.

We have identified four nonsense mutations in the eRF1 gene SUP45, which allow cell viability, despite correctly translated eRF1 being essential. This is due to negative feedback at the translational level. Truncated eRF1 produced from a nonsense mutation will not be able to terminate translation correctly, including termination at a nonsense mutation site. Consequently there is read-through of the nonsense mutation, resulting in increased amounts of full-length functional eRF1, which in turn will terminate efficiently at nonsense mutations producing increased amounts of truncated eRF1.

We are modelling this system not only as an elegant example of feedback, but also as there are biological examples of such negative feedback loops. For example; the bacterial release factor RF2 which recognises UGA and UAA stop codons, negatively regulates itself due to a premature UGA stop codon. Pausing at this stop codon (due to inefficient termination) causes a +1 frameshift and translation of the full-length RF2.

Initial results have concentrated on elucidating parameters for the model. E.g., numbers of release factor molecules per S. cerevisiae cell, half-life of proteins, and proportion of read-through of nonsense mutations.

We aim to perturb the system biologically as well as mathematically by regulating the amount of eRF1 or suppressor tRNAs for example. This will give us information on how robust the system is as well as being able to validate the model with experimental results. 

Almost a week

Yes, it's almost a week since I last blogged.

Presentation for tomorrow's lab meeting is taking longer than I'd hoped.

I had quite a successful and productive weekend though. Called Tiscali and got the broadband fixed, an issue with login spontaneously changing it seems. When we were looking for a broadband provider, many people said that Tiscali had rubbish tech support, but I thought they were great.

Got the RAM sorted on my computer. Apparently 1GB and 512 KB DIMMS don't like being interspersed with each other. Put them all next to each other and everything is fine, 3GB switch in the boot.ini file and everything.

Pulled my graphics card out to discover I have a PCIex16 slot not a PCI-X slot as my diagnostic programme reckoned. Which is nice because it means I can get a 1GB GeForce something or other for just under £50. But not from Dabs, as they will only deliver to the address that the credit card is registered to, they want me to be in, £9 during the week and £14 on Saturday!!! In the words of a New York gangster: Forget about it!

Had to replace the booting hard drive in Abi's computer with a different one so that I could format it and put a new Windows on. Then I could slave the old hard drive, and all the files are still there and useable. We just couldn't boot windows off it. So that works fine now.

And I bought some new jeans! Must be the busiest weekend I've had in ages.

Right, more presentation.