Crowd sourcing genetics: Ash die back on Facebook

Sometimes I am astounded by the sheer volume of data that we create in science nowadays. Where a few years ago we were sequencing individual genes, made up of a few thousand letters, now with a single Illumina run we can generate terabytes of data.

But what to do with that data? A lot of genomics at the moment is concerned with targeted resequencing, and bulk segregant analysis. Producing genome #1 is a lot of hard work, and doesn’t tell us all that much. Producing genomes #2 to #10 for the same species tells us a lot more: Why does wheat cultivar 1 have a higher yield than wheat cultivar 2? Why is apple variety 1 susceptible to a disease when apple variety 2 is not? 

Round Up #6

Unlike its predecessors, this round up doesn’t feature on a Friday. It features on a day when I’ve struggled to concentrate ever since I got in to work. I don’t want to launch into a full length blog when I’m not achieving anything else (what can I say, my Mum never let me go to Brownies if I hadn’t been at school either…) but equally having all of these tabs open is probably preventing me from achieving anything else.

So, without further ado and in no particular order:

• Tamsin Edwards writes a thoughtful piece in the Guardian about whether scientists should air their political viewpoints
• Scientists at Bristol University discover that the four kinds of virus causing Dengue Fever may be quite different to one another
• Six Turkish academics have been charged with terrorism after what appears to amount to nothing more than secularism
• Scientists from the United Arab Emirates have identified a mutation that gives plants reduced susceptibility to two fungal pathogens, Botrytis cinerea and Alternaria brassicicola.
• In case you missed it, scientists produced the world’s first synthetically grown beef burger this week. New Scientist unpacks the story.
• Groups in Australia and New Zealand have identified a potential new insectide, produced by bacteria. Along the way they showed that the bacteria keep this toxin in a special vesicle, allowing it to build up to high levels without damaging the micro-organism.

A juicy candidate: GM oranges take on citrus greening

The story of GM oranges begins in pretty much the same way that every other GM story begins nowadays: an unstoppable disease. The fastest developments all start with a fungus or virus or bacteria that is wiping out a major crop. This time, it’s Huanglongbing or citrus greening as caused by Candidatus Liberibacter, a bacterium carried by psyllids (like aphids, but… not).

In 2005 this long-dreaded disease reached the citrus orchards of Florida, sparking a state-wide campaign of insecticide spraying and preventative chopping down of trees. The problem is that, being spread by a parasite, keeping infected trees away from each other isn’t enough. Just like how people can’t be protected from malaria just by keeping them away from malarial patients, as long as psyllids can make it from infected trees to uninfected trees the disease continues to spread.

Whenever a devestating disease appears, the first port of call is to find a source of immunity. Ug99 is a name known and feared by people in my line of business: a variety of wheat stem rust (originating in Uganda in 1999 – go figure) that wiped out huge parts of the African wheat harvest. When it began rampaging across Africa and Europe in 2006 the first port of call was to find a naturally resistant variety of wheat that could be used to breed with other elite cultivars. A variety of einkorn wheat (a diploid wheat) from Turkey was found to contain a gene Sr35 that conferred resistance. (Well, sort of. Technically they found a QTL. And then the gene earlier this year. I’ll talk about that another time.)

Only there was no resistant variety of citrus tree to be found anywhere. The only option it seemed was to search further afield: Early contenders included one from a bacteriophage (i.e. a virus that kills bacteria), but concerns that people would react more strongly to an organism modified with genes from a virus put that one to bed. Similar fears about a well-performing tree with a gene from pig put that one on the back burner too. An alternative was a gene from spinach, and in 2010 this was finally trialled.

Sunday’s New York Times carried this lovely piece about the fight to win both regulatory approval and consumer acceptance of the new GM orange trees, which will hopefully be available for juice production in the next 5 years.

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C Saintenac, W Zhang, A Salcedo et al (2013) Science
“Identification of Wheat Gene Sr35That Confers Resistance to Ug99 Stem Rust Race Group”
Science DOI: 10.1126/science.1239022

GMO company launches GMO Answers

Today could well be a day for GM blogging I feel. As a start, GM giant Monsanto has launched a new website called GMO Answers.

GMO Answers is an initiative committed to responding to your questions about how food is grown. Its goal is to make information about GMOs in food and agriculture easier to access and understand.

I’m skeptical about how far they’ll get with this. I imagine it’s going to take a lot of moderation and they’ll be fielding a lot of angry comments from the anti-GM brigade, but I really hope there’ll be the chance for some sensible dialogue on there as well.

Monsanto pulls out of Europe

In a move surprising to nobody, Monsanto (the agri-super-giant responsible for ‘Roundup Ready’ maize and soy) has pulled its GM research out of Europe for the time being, citing the legislation that makes it next-to-impossible to get anything approved on this side of the pond.  This comes not long after BASF Plant Science, the  German agri-business responsible for one of two GM crops grown in the EU (Amflora high-starch potato) moved its base to the US due to anti-GM feeling in the EU.

The path from developing a new crop to getting it approved in Europe involves regulation by the European Food Safety Authority (EFSA), followed by a proposal by the European Commission and subsequent voting by all of the EU member states. Although the EFSA has approved eight crops in the past decade, the European Commission hasn’t allowed them to be commerically grown, due to anti-GM feeling in some of the member states. Among the crops still waiting to be approved are three maize cultivars, and a soy bean, which are all produced by Monsanto. Three of these are to be abandoned – Monsanto will only continue to pursue one variety of GM maize (MON810), which is already grown in the EU but is up for re-approval soon.  The other companies waiting for approval (duPont Pioneer and Syngenta) are still waiting. 

 

Finding the misery molecule? More like imaging a candidate

Depression, like just about every other mental disease, is a strange and mysterious beast. We’ve reached the stage where most people finally understand that it’s really an illness, really a physical problem, not something can be controlled. We know that there are myriad drugs that can help: citalopram, sertraline, paroxetine, fluoxetine…  But we still can’t reach out and touch it. We still can’t predict it. There’s still not a physical test that you can do. An assay that proves that no, this person isn’t just lazy or melancholy or antisocial: they are depressed.

The headlines

Over the weekend, the news outlets got a bit excited at the prospect that scientists had finally discovered “the molecule responsible for causing feelings of depression” (Independent), “the brain’s most miserable molecule” (The Sunday Times) “the little bastard molecule that causes depression” (msn), “The Thing Responsible for Depression” (Jezebel).

And the science

I wish I could say I’m as excited as they are, but of course the science is never as simple as this. The actual paper released is a slog to say the least, and more Physics than Biology, but I’ll give it a go. 

Giant viruses shake up the status quo

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). 

I smell a rat, and it isn’t in the pig sty

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. 

The Ramen Diaries Part 9: The Thesis Plan Appears

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. 

Adventures in protein land part 2: Cytosolic protein extraction

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!