A quick microbiology primer before we begin, for the uninitiated or those who don’t have a 14 year old in their lives to ask.
Microbe is a catch-all terms that we use to describe microscopic organisms. These may or may not be pathogenic (disease-causing). They include, but are not limited to:
- Bacteria (like E. coli and S. aureus, which cause food poisoning)
- Fungi (like athlete’s foot and brewer’s yeast)
- Protists (like Plasmodium, which causes malaria and Naegleria, which you might have seen in an episode of House)
We probably shouldn’t include viruses (like the common cold) or prions (like variant CJD) in there because they’re not really classified as organisms: they’re not alive, simply inert particles that harness other living things to replicate themselves. As my year 8s would tell you, they don’t do MRS NERG (movement, reproduction, sensitivity, nutrition, excretion, respiration or growth). Continue reading
One of the things that I find most disappointing in any debate is the realisation that somewhere along the line somebody knows that what they are saying is not true. It’s the reason that I get angry at comments from the Catholic church about the ineffectiveness of using condoms against HIV, and it’s the reason that I get pretty frustrated by large parts of the anti-GM lobby too.
We’ve all heard claims that GM foods aren’t safe because they aren’t properly tested yet, or they haven’t been independently validated by scientists with nothing to be gained from their success. In 2013 there are around 600 peer-reviewed journal articles documenting the safety of genetically modified groups. Of these, around a third were funded by independent organisations. Around 3 billion GM meals have been eaten (since the vast majority of American soy and maize is now GM) without a single human health law suit. This is not to say that the case is closed and there’s nothing left to be learned, just that the public perception about these things is remarkably skewed. Continue reading
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?
So this is going to be more like a lab book entry than anything else, but I’m finally starting to get my head around some of this protein malarkey and figured I should write it down in multiple places! Continue reading
Posted in Biology, In the lab, Protein, Science
Tagged biology, chemicals, Everyday lab, grad school, in the lab, protein, proteomics, ramen, science.
No full length post here, just a suggestion that you all go to read Mark Lynas*’ fantastic deconstruction of various anti-GMO arguments. Obviously none of the arguments mean ‘go grow GM across the world immediately!’ but he gives some lovely detailed responses to the inconsistency in various people’s thinking (e.g. how objecting to Monsanto creating a monopoly on corn should not lead to trashing open source disease tolerant papaya in Africa) and explanations of how environmental groups are doing things that simply aren’t good for the environment.
It’s long, but a very good read.
Following a decade and a half of scientific and field research, I think we can now say with very high confidence that the key tenets of the anti-GMO case were not just wrong in points of fact but in large parts the precise opposite of the truth.
This is why I use the term conspiracy theory. Populist ideas about conspiracies do not arise spontaneously in a political and historic vacuum. They result when powerful ideological narratives collide with major world events, rare occasions where even a tiny number of dedicated activists can create a lasting change in public consciousness.
The anti-GMO campaign has also undoubtedly led to unnecessary deaths. The best documented example, which is laid out in detail by Robert Paarlberg in his book ‘Starved for Science’, is the refusal of the Zambian government to allow its starving population to eat imported GMO corn during a severe famine in 2002.
Full link is here
*Mark Lynas as in the authors of Six Degrees, a pop science book about how the world would change as average global temperature increased by 1 degree, 2 degrees, 3 degrees etc… It’s basically a huge meta study of primary literature and very enjoyable. Apparently he’s good at writing about GM too – who knew?
Posted in Biology, Genetics, Science
Tagged activists, biology, conspiracy, crops, food security, genetics, GM, Mark Lynas, other blogs, science, science communication, science journalism
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