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.

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. 

Essential response to anti-GM from Mark Lynas

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?

Useful Resources (for Wheat Genetics Researchers)

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?

Rusty Research: Fighting Bread’s Biggest Bad-guy

This has been a bad year for farmers: last year’s wet summer and then the cold winter that just won’t end have scuppered one harvest and probably knocked this year’s right down too. Even when conditions are more ideal than they have been this year, farmers and breeders fight an uphill battle trying to prevent a significant proportion of the crop being lost to various pathogens. When it comes to wheat that means rust: black rust, brown rust and yellow rust. Where it strikes, yield losses are likely to be around 20% in susceptible varieties, and the problem is getting much worse. Most resistance to black rust (Puccinia triticina) is caused by a single gene, which a new resistant kind of rust (Ug99) managed to overcome in much the same way as MRSA became resistant to methicillin in our hospitals.

Close-up of wheat leaf rust (”Puccinia triticinia”) on wheat. Photo by James Kolmer. http://www.ars.usda.gov/is/graphics/photos/jun06/d519-1.htm Image Number D519-1 PD-USGov-USDA-ARS

Now scientists from Norwich, Cambridge and the USA are trying to find out how some kinds of a similar disease, yellow rust, (Puccinia striiformis or PST) are able to overcome the plant’s natural defences and infect. 

Salvaging the salty small holdings

When people interested in food security aren’t busy worrying about plateauing crop yields, they tend to be worrying about how much agricultural land we’re losing. We already use so much of the world for growing food crops (around a third) that there’s very little spare land left, and some of the techniques we use for growing crops lead to the land we already have being lost. When crops are grown in an area with insufficient rainfall they must be irrigated (i.e. watered). But all standing water, even if it doesn’t come from the sea, contains small traces of salts: just look at the label on a bottle of Evian. This means that over time, the land becomes saltier or salinised and since plants don’t like salty soil they struggle to grow there.