Really quite knackered

We moved house last weekend, that is we moved to our first ever house last weekend. Picked up the keys on Friday. Hired a van on Saturday, and several friends helped us move all of the large furniture that require the van. Promised to pay them in beer and pizza, except that they all left, and Abi and I didn't have our pizza until about midnight!

Sunday, more moving, smaller boxes this time that could fit into a car. Abi's Mum and Dad helped, celebrated with some bubbly that evening.

Monday, more boxes, helped by Abi's Dad.

Tuesday, I went back to work, but Abi and her Dad kept moving stuff, including all of our Froesch boxes from the garage in Dyce. Went to Spice of Life for a curry in the evening.

Wednesday, both of us at work, moved the last of the little bits out of the flat in the evening, again with the help of Abi's Mum and Dad.  The amount of stuff we have is beyond a joke, I've no idea how it all fitted in that tiny flat.

Thursday, cleaned the flat. Out there until 22:00. 3 Mince pies (of the small Christmas variety) for tea! In bed by about 23:30

Friday, up at 06:00 again. Finishing work early to do a last check of the flat before we hand the keys back. Then we will only live in Inverurie. Yeay!

No  unpacking or anything tonight, I'm knackered!

eeeek!

So we've had an offer accepted on a house! It seems as though the mortgage application is going OK, that is our FA (Financial Advisor not Football Association!) hasn't told us of any brick walls hit yet. This all seems very grown up. Walking around the area when we went to view the house it struck us how very suburban it all was. Can we really live there? Will we really not be awoken at 03:00 in the morning by pissed people shouting/wanting there keys back because they have to go to work in the morning? No more suspicious exchanges of money under our living room window? I've almost got used to Chavs shouting at the top of their voices down the street! Mmmm maybe not.

I think marriage and buying a house are meant to be two huge life events. Of course marriage was a massive life event, but it was easy. I love my wife very much, and I wanted nothing more than to marry her. Buying a house is a massive financial commitment though. I'm sure Abi will still love me if I don't have a job, or am very ill for a long time. However, there are more serious financial repercussions to these situations when you have mortgage repayments to make!

Anyway, I'm jabbering on (mmmm, interesting. google. It seems the spell check in Chrome likes the spelling of "jabbering" but not google! Go figure). Too much for the two people who read this blog. So I shall end with a quote I read on the Guardian website today: "Tesco: Never will you seen such a hive of scum and villainy!"

Rain

Man it rained yesterday! Serious flooding on a lot of roads, and some people from Elgin were being evacuated from their homes!

I was still able to make it to work though. Not that I've had much to do. Cells have grown really slow, they should be ready by about 17:00, at which point I'm going home, I'll do the Luciferase assay on Monday.

Weekend! I hope that we will get out cycling on one of the days if it doesn't rain all weekend. Abi is desperate to go out on her new bike, she's buying lots of accessories as well. I'm sure I could do with some new tyres, and I might like some body geometry handlebar grips.

Well since I can't do any lab work for the next fours hours I'll try and fight with GIMP again (GNU Image Manipulation Programme) to try and superimpose my GFP image with that of the yeast cells.

Phones

I guess in these days of mobile web phones, I should be able to Blog
from my phone.

10 Year Old

So apparently Blogger is 10 years old now, seems like that should be worth a blog.

Went out to Inverurie to see another house this evening. Quite a nice semi detached, but quite lacking in storage space. Can't decide if we need to slim down our inventory or try and find a house with lots of storage space!

The trains out were rubbish again. Got to Dyce and the doors were buggered, so we were stuck there for 15 min as they were fixed (with some reversing and bumping of the rear carriages into the front carriages!).

I'm sure I was going to write about other things, but I can't remember now. I'm sure I will remember when I have shut the computer down.

Goodnight.

Loch Tay 2009

We just had a great weekend down in Perthshire. Abi's Uncle/Auntie/cousins and associated husbands/children hire a cottage for a week in Lawers (about half way along Loch Tay), and we were invited out for a couple of days.
Booked into our B&B in Killin (very nice, super breakfasts) and headed up to the cottage for a lovely BBQ, no rain and very few midges!
On Friday Sandy (Uncle) Abi and I climbed Beinn Ghlas (see photo of obligatory summit shot). Weather wasn't great on the way up, drizzle, a bit more serious rain, and then walking in cloud for most of the rest of the time (hence the lovely view behind us in the photo). Naturally, when we got back down to the car park, the sky cleared and the sun came out.
But then the weather stayed great. The next day Abi and I hired bikes from the Outdoor Shop in Killin and cycled along the Sustrans National Cycle Network Route 7. Had a great time, particularly on the long slope down towards Lochearnhead. But not on the way back up, these were the most uncomfortable saddles I had ever ridden on! We were both still bruised in saddle-straddling places on Sunday! Sunburnt, sore but happy, we really should get out more. All in all a great long 4-day weekend (more of these please), always good to catch up with the other Mavor side of the family.
Back to work now, at least the boss is away for another week!

Michael Owen

I can't believe Michael Owen has signed for Man Utd!

Cooler today, only 25°C in the lab which is workable in. Still, this is the 5th day in a row that I have worn shorts, that's surely unprecedented in Aberdeen. Lovely weather at the weekend, great for sitting inside and watching Star Wars films. We did have a BBQ and sit out in the Kemnay sunshine for 2 hours. 

Quite a busy day today, which is nice, trying in vain to see the boss, but he's always busy. Not a very interesting post.

Terribly Vexed

So having got sequencing results back today, it seems as though I've not been working with the reagents I thought I was. Apparently sup45-18 is actually sup45-28 and vice versa! Both strains, and plasmids! Basically, I'm gonna have to repeat a bunch of experiments. Bugger.

On a happier note the lab is cooler today, only 26.5°C rather than the 29.5°C of yesterday.

Looking forward to the weekend. A friend who has recently bought a 42" LCD tv is having a Star Wars watching day. That is Episodes 4, 5, and 6, proper Star Wars. So I must go home and bake a cheesecake tonight, as we are providing dessert for the BBQ. Mmmm, probably just cursed the weather, still, what's a BBQ in Scotland without rain!

Scorchio

To quote from a certain sketch show. Google weather says that it is 29°C in Cults. It feels hotter in the lab. The 30°C incubators are beeping because they can't maintain their temperature. This is a day to skive off early and sit in the park (the boss is away anyway). Must drink more water or I'll feel rubbish later on.

Keine lust!

Haven't blogged for ages. Busy at work, but I can't be bothered today.

Started new project. Haven't finished last one! But we have submitted a review article, which was nice. What wasn't nice was testing the online submission procedure on Friday at 18:00 with a test.doc file with the word "test" in it, only to find out that once "submit" it pressed, no matter how much the site says you will be able to review the manuscript before submission, you can't!

So we submitted the test.doc to RNA journal, edited by a guy who won the joint Nobel Prize for chemistry in 1989! Oops! Ah well, the proper manuscript got submitted eventually.

Ooo. My timer will go off in a minute, I'll actually have to do some work!

Warwick

So, I was down in Warwick for a conference at the end of last week. I do confess, I didn't really know where Warwick was! Not far from Coventry, which in turn is not far from Birmingham it would seem.

Translation UK 2009 was the conference. Quite interesting really, the highlight (terrifying moment) was me giving a 12 min presentation. I think it went OK, I felt quite nervous, though since there was probably about 150 people there, I think that's fair enough. Especially given that some of them have been doing this kind of work for far longer than me.

Abi's birthday tomorrow, I hope she has a good day. She'll only be in work for a few hours, and is having lunch with a friend, so it can't be all bad. Then we're going out for dinner in the evening. Funny how I seem to get more excited by Abi's birthday and giving her presents now, rather than my birthday and getting presents! Am I getting old, is this one of the lesser known consequences of old age?

Mmm trying to install Age of Empires III on Abi's PC and it just came up with and error message! Followed by the obigatory error box with "OK" as the only option to click, when it quite clearly isn't OK.

Maybe I should go and concentrate on that now!!

Happy Wednesday

Today I am happy, because after two weeks of frustration, my yeasty cells seem to be growing fine, as they should, and I have finished one of my assays for this week, and it is only lunchtime! This means I may actually have some sort of results to present at this conference in Warwick next week.

It also means I will be able to leave work on time today, and perhaps go to the cinema with Abi, if there's anything worth seeing (saw Watchmen last week).

Mum, Dad, and sister came to visit over the weekend. It was Mum's birthday, so there was plenty of eating and drinking done, which is always nice. It's always great to see them, even if it is for such a short time. But then there's only so much you can do in Aberdeen if you stay for as long as a week! I shall see them again in a month when it is my sister's 30th birthday. I can't really believe she is going to be 30! Not that I can really believe that I'm over 30.

Last month of project

It's going to be a busy month. Lots of experiments to do, and we're hoping to get three publications out of this project. Which is quite impressive for an 18 month project. I can see that I will be in late quite a lot this month. If the yeasty cultures don't grow as fast as I expect, I really just need to stay at work until they do grow so that I can do these experiments.

Still, holiday at the end of it. We'll be going away to a cottage in Aberdour (just north of Edinburgh) for a week. It's not that fantastic a place, but the cottage looks nice, and we're going with at least 6 other friends, so that would make the holiday no matter where we were going. We'll just be able to chill out for a week and arse about, talk rubbish as usual.

After that we will go down the road to my parent's, as it will be my sister's 30th birthday. My goodness. 30!

Oh, and we'll be going to Norway some time in June, or is it July? Crap, it's not even in my calendar! I guess we should book some travel so I know when it is!

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.

Nothing Kinda much

Nothing much to say, and that's a text from my wife saying she's on the way to Sainsbury's! So time to leave work and go shopping!

Quick blog

Nothing much to blog about. Busy kinda day. Fire alarm in the building went off at 11:30 which was nice. Got to stand outside in the cold for 20 min and not know why. Fire brigade turned up after about 15 min. Rapid response or what? Maybe they were finishing watching something on TV before they came out.

17:30 so I'm going home now.

Wii-kend

Had tremendous fun at the weekend at a friends flat playing lots of Wii Force Unleashed, and Star Wars Lego, both of which are tremendous fun. Being able to force grip an enemy and then throw your lightsaber at them and impaling them was particularly satisfying! I only found that the cable that connected the controller to the nunchuck was too short, as I kept whipping myself while doing force repel. All Nintendo need to produce now is a glove to be worn on the non-lightsaber hand that could detect the movements in the hand for force chock, push or lightning, now that would be really cool!

Quite day at work really. Forgot that we have a Systems Biology away day tomorrow, so I can't really plan anything today to finish tomorrow. So I've spent the day reading papers and planning experiments. Going to an open lecture tonight at Waterstones about science in society, and the public's understanding of science. I hope it will be quite interesting. Then hopefully I can catch the end of Liverpool vs Everton.

Friday

Busy day. Lab meeting this morning. Quick lunch, then 24 protein extracts to make followed by 10 yeast transformations.

Now I need to get out of here so that I can go and catch the train to Elgin at 17:18. Weekend in Lossie playing Force unleashed and watch DVDs with friends. Cool.

With the highs come the lows

Well, after I was really happy that I got my final clone on Tuesday, it was only natural that yesterday would be crappy. Western blot was completely blank, not even the positive control worked this time! Ah well, onwards! Growth experiment today, 7 hours worth, Schön! This is only the third time I have done this total, I hope I get some worthwhile samples out of it this time.

RAM story so far: having switched out the two new RAM modules I found that the computer is happy with one of them, but not the other (the one hard up against the video card). I guess I should contact crucial, see what they say, and whether it's likely that they sent me bad RAM. At least I can play Star Wars Battlefront at the moment!

Right, need to go and right up my lab book for meeting tomorrow.

Sequencing

Yeay, I have finally got my inserts into my pAC98 plasmid (geeky science talk eh?). I started all this on 21.08.08, and finally today I got the sequencing results back for my final construct SAL4-18, the final and most awkward of the 8 constructs. The other 7 clones were not nearly as bad, with successful clones being #1 or #2, perhaps #7 in a screen for the correct plasmid. But good old SAL4-18 waited until clone #27! I can do some proper experiments now!

Well that's the most exciting thing that has happened today!

09.01.09 Blog

First week back at work seems to have gone fast and slow at the same time. Each day has gone by quite fast as I have been quite busy, but at the same time, the week has seemed long, and so I feel that I have got lots done. It will just round the week off nicely if my sequencing results come back this afternoon with the correct sequence for pAC98 SAL4-18 in the correct orientation!

So to the weekend. Off down to Glasgow tomorrow at the chirpy time of 07:30! We are going for a Chinese lunch to celebrate joint birthdays for one of my wife's cousins and her Mum (so Auntie). Cousin is 30, Auntie is 60. It should be a good weekend as they are all really great people, it just sucks that we have to get up so early on a day off!

Bit off late night shopping last night, reasonably successful. Wife bought clothes, I got new headphones for mp3 player, and train tickets for going up to Elgin next weekend (visit friends to play Force Unleashed on their Wii! Their idea not ours!). We then had an impromptu dinner at a wee Italian restaurant, very nice. Pizza and Calzone (not both mine!) and some wine. Not particularly cheap, but then it's not very often that just the two of us go out for dinner.

Put new memory into computer last night, I have a lovely 3GB of RAM now. It was a bit of a fiddle as usual. I really love the way in the instructions of how to install memory it tells you to push down with even pressure until it clicks into place with a clear diagram of someone with their hands directly over the module pushing easily. Of course in reality there is no such space, just wires everywhere that poke in the wrong place, one of the clips hard up against the graphics card so it wouldn't open fully, and absolutely no space to manouver at all unless you have hand the size of a three-year old! Still we did it, and then after my computer decided it needed to reboot itself twice, it worked.

Anyway, some of that work. Western blot, transformation, plates to pour (which I should go and do now instead of blogging!), and hopefully sequencing to check. Mmmm quite busy!

Wednesday

Western blot, plates out of incubator and reading papers. Not a particularly action packed day. So I'll sing a song instead.

O let the sun beat down upon my head, stars fill my dreams,

I am a traveller of both time and space, to be where I have been.

Kashmir, Led Zeppelin

New Year

...and first day back at work. Actually the day went really quickly, and after not really looking forward to the first day back, I had forgotten that I actually really enjoy my job. Still really happy that we got the grant at the end of last year!

So I got straight back into things, from where I left off. Hopefully I'll be able to get a goodly amount of stuff done this week before the Honours students start in the lab next week! Looks like I'll be closely supervising one of them so I should really discuss with the boss what we're going to do with them!

Mmmm earphones on mp3 player seem to be getting a bit bust. I guess they've had a good stint, looks like I'll have to fork out for some new ones.