With 9 months left on the clock before I have to submit, it’s time for the bakingbiologist to start writing. Given I haven’t exactly finished lab work this is a slightly terrifying prospect, but two weeks ago I took to it with gusto on the instruction of my supervisor. It turns out that ‘You should start writing’ is actually supervisor-speak for “We should have a meeting about how one writes a thesis and what I expect from you” and cheerfully producing a first draft of Chapter 1 is liable to lead to cross words rather than exclamations of joy, but more on that another time.
This week’s most valuable lesson is: Before you start writing a thesis, write a thesis plan! For one thing, it allows you to defend your structural choices and talk about figures before you’ve put in two weeks of solid work, and when you’re not feeling protective about the work because you haven’t already done it. Continue reading
Before we start, you need to read this: Partly because my punch line is going to hang on you being familiar with the metaphor, and partly because if you’re here, then basically you need it in your life.
It would be safe to say that my PhD has not been plain sailing. I’m not sure that anybody’s doctorate actually goes smoothly and pleasantly at all times, but I genuinely believe that – as the lovely Jenny Rohn from LabLit.com said yesterday – if you can survive this then you can survive anything. So how do you? Survive, I mean. I’ve talked about making your PhD easier by being organised from the start, and finding a support network and by not letting yourself get dragged down. But what about when you’re completely at rock bottom? What about when it’s time to do or die?
There’s a new PhD student in our lab, and I’ve been trying to sort her out with a list of useful tools and websites. I figured that there are probably plenty of other newbies in the field who are fumbling their way around as I did when I started and could benefit from access to my bookmarks bar, so here goes:
When you first start dealing with sequence you may find it useful to know there are tools for converting all sequence types (e.g. FASTA) to RAW format, which is what you’ll need sequence in for lots of alignment softare to use (I genuinely did it by hand a few times before I found that). Also there are obviously tools for reverse transcribing sequence and translating nucleotides into protein sequence.
BLAST (Basic Local Alignment Search Tool) is the ‘search for a gene or a protein’ database that everybody uses across all fields. Use it to find out what an unknown transcript sequence codes for, or how similar it is to the same gene in other species. (Use BLAST-N for nucleotide sequences, BLAST-P for protein to protein, and X for searching for one with the other)
Cereals DB is the wheat-only search engine as maintained by the university of Bristol. Search for 454 genomic sequence (from the University of Liverpool) – e.g. if you’re building a genomic contig to match your cDNA sequence; ESTs – i.e. a summary of where your gene might be expressed or SNPs (although this doesn’t yet tell you which varieties the SNPs are between).
Once you have some sequence, until you get your hands on proper alignment software (this is assuming you’re using <50 sequences – we’re not talking Next Gen data here) like Chromas, DNAman or Sequencher (the latest version does Next Gen but I’m still on 4.10) Clustal W2 is a handy alignment tool. (You’ll need all sequences going in the same direction, so use the reverse transcribe tool above). It works for protein transcripts too.
To find out a bit more about the function of a protein (e.g. what domains it has) use InterPro Scan (which searches other databases like Panther)
For comparative genomics you should be aware of Gramene which allows you to search genomic data for a bunch of plants together. That links to the European Nucleotide Archive, which covers similar ground to the BLAST database and the PlantsDB databases, hosted at MIPS, for if you’re interesting in things other than wheat.
You can get access to the shotgun sequencing data from the IWGSC consortium for particular chromosomes, although you need to request access and get a password. This is useful for mapping your gene of interest.
Has anybody got others that I’ve missed?
Posted in Biology, Genetics, Grad school, Science
Tagged alignment, bioinformatics, BLAST, genetics, genomics, protein, SNPs, wheat
I’m not a protein biologist.
I wouldn’t usually describe myself as a geneticist either, unless trying to clarify what it is that I spend my time doing, in the same way that for years I would describe myself as playing the violin rather than as a violinist, because that seemed to indicate some level of skill that I didn’t feel I yet had.
But I’m definitely not a protein biologist, because I did no protein work as an undergrad, and I didn’t sign up to do a protein based PhD, and there’s only one post doc in the lab who has the first clue about proteins and – while she is possibly the most helpful post doc ever to cross my academic path – there’s only so much help someone can give you when you don’t know what questions to ask.
Yet in spite of this, I appear to be in a situation where doing protein work is inevitable. A few months ago I learned about PAGE gels and Coomassie blue staining and Western blots. Now, I must actually start extracting protein from real live plants, as opposed to my nice-n-easy-burst-like-a-bubble-E. coli. It turns out that this is rather more complicated than I had hoped. Continue reading
Posted in Biology, Grad school, Protein, Science
Tagged biology, chemicals, Everyday lab, grad school, in the lab, protein, proteomics, ramen, science
After a week off with flu, there’s just no avoiding it. Today I have to get back in the lab and do my first ever protein extractions from a plant. I have a protocol, that I am assured works, and no reason to suspect it doesn’t. And I have been sat here for 54 minutes doing admin instead of even going to the greenhouse to get my plants. Looks like the stage fright is back. Le sigh….
When I started this blog, it was supposed to be a news blog: me getting to grips with and explaining new papers that I found interesting. Recently I’ve been thoroughly uninspired, but trying not to resort to writing more opinion pieces about how to survive Grad school (even if that does seem to be what I do best).
Nevertheless, it’s been over 2 weeks since my last post, and while demonstrating yesterday, a familiar itch beginning to niggle. Whereas in previous years I’ve done a more-than-normal amount of tutoring and demonstrating, this year I’ve only covering a small handful of lab classes, one of which is Introductory Genetics. The class is pretty simple. Students are given a variety of mutant Arabidopsis that they have to phenotype, in addition to the F1 and F2 of back crosses to the wild type and crosses between mutants. They are trying to find out whether the mutations are single gene traits; dominants or recessive; and whether multiple mutants are caused by mutations in the same or different lines.
This is the third year I have demonstrated for this class, and the previous year I marked the open book exam that students take at the end, without having demonstrated for the practical, so I’m probably more familiar with the class than anybody except for the professor teaching it. Along the way I have had to do a fair amount of mental gymnastics, but I’ve also picked up on a few of the most common misconceptions that students hold. I actually clearly remember as a first year undergraduate being confused by the term “wild type” because nobody had explained to me that this was a technological term for the working copy of a gene: I thought it meant the type of gene that animals had in the wild. Which is fine, until you start thinking about mouse or Drosophila genetics! Continue reading
Posted in Biology, Genetics, Grad school, In the lab, Science
Tagged Arabidopsis, biology, genetics, lab, mutant, science, tales from the teaching lab, teaching
Occasionally, I have the realisation that I am not entirely sane. Not in a catastrophic hearing-voices type way, but when I talk to myself and then remember that this is not normal. This morning I arrived at the sports centre to discover that circuits wasn’t on, and I would just have to go run in the gym instead. Upon finding my mp3 player in the bottom of my bag, and realising that I had in fact remembered to put it on hold (therefore meaning there was enough battery to get me through a 40 minute hill slog) I smiled and mentally called myself a good girl . Continue reading