I had a meeting with my supervisor for my fourth year project. He alternated between saying "I have no expectations of you, don't worry" and "you have the scope to get more out of this than just a project" and "this is part of something I'm being funded for" but "I have no expectations"...

...so yes, I am worried, actually! I'd prefer if he told me what his expectations were so I could try to live up to them. Oh well. I'm sure it will be fine.

Arrays and networks and brains, oh my :D

I don't have time to write about it properly, but this paper - the new transcriptome study of autism-spectrum brains, from Nature, makes me really excited. Comparing gene expression in a high throughput way, using microarrays - creating networks and identifying significant modules - using genome-wide association study data to back up your conclusions - this is awesome. This is the point of an entire module of my course this year! (1)

More to the point, this is kinda the point of the systems biology course I'm going to be doing next year. This is what I want to be doing. I haven't had a chance to look at the paper more critically yet, but I really hope it stands up to thorough analyses and follow-up work, because I think it showcases perfectly what new technologies and systems-level approaches can do. I hope that I'll see more of this kind of integrative study in future!

And now, back to the cave of revision... See you in two weeks!

(1) "Human genetics, genomics, and systems biology". Yeaaaahhh. I need to reference this paper in the exam!

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Reference:
'Transcriptomic analysis of autistic brain reveals convergent molecular pathology', Irina Voineagu, Xinchen Wang, Patrick Johnston, Jennifer K. Lowe, Yuan Tian, Steve Horvath, Jonathan Mill, Rita M. Cantor, Benjamin J. Blencowe & Daniel H. Geschwind, Nature (2011), doi:10.1038/nature10110

Aspirations

Yesterday, I gave a tour of the department to a thirteen year old and her mother. When I was thirteen, I wanted to be a costume designer for films (blame Lord of the Rings).

No, the girl wasn’t some kind of prodigy (although she did seem pretty smart). Her mum just emailed the head of the department, saying her daughter was interested in science and the university, and they were going to be in the area, so could they come and have a look? And he passed it on, and I volunteered. I was impressed, to be honest, that the girl had that much of an idea of what she wanted to do and was keen enough to want to find out more, which is why I offered to show her around. That, and it was a good break from revising, and it was a chance to practice talking about science to non-experts.

Blood groups and bruises

Fig 1: I has a bruise.

I went to give blood last Thursday. Giving blood is something I feel quite strongly about, so I try to go as often as I can. Sadly I hadn't been in about a year - but I persuaded a friend to come and donate, too, so I felt less guilty! Unfortunately this time, for me, it didn't go too smoothly. I didn't actually manage to give blood, because the needle went in wrong. Hence the bruise. So I'm going back in a couple of weeks.

After you first give blood, you are sent a donor card, which tells you your blood type. I'm O+ - this was a bit of a surprise to me, as both my parents are A+! A quick Google cleared up why: the A blood group is inherited dominantly, so it's possible for someone to carry one copy of a gene that produces the A antigen, and one copy that doesn't, and still have the A blood group (they are heterozygous). So, both of my parents must carry an A allele and an O allele. (Blood types have actually been used to clear up paternity disputes, before more detailed genetic information was easily available.)

But what do these A, O (and B) things actually mean?

Baking is science for hungry people! :D

Term is over, my lab project is over (well, the part that involves being in the lab is at least, if not the write-up) - and so to celebrate, I made C .elegans cake!

Fig 1: Caaaaaaake. Photo by me.

Worms! Everywhere!

I now have my very own box in the freezer in my project lab. (It has a bright green name sticker on it, because I feel I should keep up my reputation for liking shiny things :P) I feel like I belong there, finally!

Okay, that's an overstatement, but it does feel like my project is finally starting to go somewhere. So far I, and the other girl doing her third year project in the same lab, have spent five weeks doing Western blots over and over again, with various different protocols and equipment and extracts, and to a certain extent it felt like going around in circles. Now, however, we finally have a set up that works well, and tomorrow, perhaps, touch wood, we will have some results.

C. elegans - an adult and a couple that have just hatched. Source.

How to import a new citation style in LyX

This post is for my own future reference, and for the use of any other users of LyX for Windows, because there seems to be very little documentation out there that doesn't assume a lot of prior knowledge.

I had an extended essay to write over the Christmas holidays: 3000-5000 words, roughly 10% of my final grade, and most relevantly, it needed proper references, and LOTS of them. The guidelines stated citations should use the style found in the journal Cell - Harvard-style referencing, which I personally hate, never mind. The default citation style in LyX is bracketed numbers, like so [1]. It took me some trial and error and far too much time to figure out how to change this, so hopefully this will save other people some bother.