Tag Archives: scientists

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.  Continue reading

100 genomes of 100 year olds for $100 000

On June 26th 2000 the consortium of researchers working on the Human Genome Project announced they had created their first ‘working draft’ of the human genome sequence. It had taken a decade to achieve, with groups in at least 5 countries collaborating, cost $3 billion and provided 7-fold coverage (i.e. on average, for any single point on the genome they had seven sequences).

Twelve years have gone by, and you might think that we would be busy sequencing other things. (Well, we sort of are: bonobosbananas…) But actually we’re still looking at human DNA. We might know what humans look like at a molecular level ‘on average’: but on average doesn’t tell you why some people are more prone to cancer, or why some people are more likely to get Alzheimers, or why some people can taste PROP. It doesn’t tell you why some people can live to 100 either, in spite of having genes that make them prone to clotting disorders or dementia or heart disease.

The competition

In 2006, non-profit organisation X-prize announced that they would give a $10 million prize to the company that could sequence (and assemble) the entire genomes of 100 centenarians at a cost of less than $1000 per genome in 30 days. With an unprecedented level of accuracy. Given the HGP cost around $3 billion to complete, that’s quite an ask!

The general idea is that by comparing these genomes, particular area of interest might ‘pop out’ as being associated with longevity. 100 people is actually a pretty small sample size, but it’s a starting point and may identify several candidate genes that can then be studied by other (cheaper!) methods.

The first entrant

For the first time, technology has progressed to a place where achieving the aims of the X prize really is a viable possibility. The Ion Proton sequencer (which, with a bit of luck, we’ll be buying soon-ish – squee!) might just be up to the job, and as of this week its inventors are the first company to actually sign up to the challenge. There’s still almost a year left for other companies to get on board, but Illumina (makers of the GA II and the new-to-the-market HiSeq) have already come out and said that they don’t plan to participate. Oxford Nanopore and Complete Genomics are still not making any decisions about whether or not to enter: presumably because they’re waiting  to see what state their technology is in 10 months from now.

As per the good old $1000 dollar genome, $10 000 analysis script, most of the time isn’t actually going to be spent sequencing the genomes. The vast majority of the 30 days will be spent in assembling the sequencing fragments into longer strings that match the known order of genes in the human chromosomes: the biggest time-constraint for the competitors is getting the sequencing done as fast as possible to leave the four whole weeks for genome assembly. We’ve been hearing for a while now that the $1000 dollar genome is right around the corner, so it’s exciting to see Ion Torrent putting their money where their mouth is. Come next October we can see whether they’re right.

 

Friday Roundup

Here are a few odds and ends that have caught my eye over the last day or two to finish the week with.

The 523Mb draft genome for banana, Musa acuminata, has been released (more on that later) in a paper in Nature by D’Hont et al  and with it this awesome Venn Diagram comparing the genes that are homologous between banana and some other important plants. (Arabidopsis is the model species for all plants – the equivalent of a lab mouse; Brachypodium is the model for grasses; Oryza is rice).

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Science: it’s a girl thing. We are nerdy and that is okay.

This week the EU Commission launched a campaign called Science: It’s a girl thing designed to encourage girls to  become scientists. It involved some nice shorts of female scientists talking about who they are and what they do.

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On engaging with the public, and why we do science

This morning I read a fantastic piece by @ScientistsMags about science engagement, which so completely echoed my own sentiments I just had to link to it. Quite apart from the fact that I think we need more women in science and greater scientific literacy amongst the general public, there is another reason why I really like talking to sixth formers and school pupils about science; and even teaching undergrads. Every time I explain my research, I understand it a little bit better myself.

Excerpt:

You would think that a scientist would love nothing more than to talk about their work. They do, usually to another scientist. The general public is an afterthought or not even considered. … I do believe that if you can’t explain it simply, you don’t understand it well enough, and so did Richard Feynman.

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A quick round up

It’s been a busy few days, and in the meantime lots of other people (who may be more articulate than I am right now) have done some great coverage of the Take the Flour Back protest, and GM stuff in general. I kinda want to get out of my little Rothamsted loop and talk about something else, so here are some links to articles and blog pieces I enjoyed.

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Someone is WRONG on the internet (More on GM…)

This is me this lunch time:

Faced with a day of experiments that don’t require poking every 15 minutes, an inability to order anything due to some delightful fluke of our ordering system, no teaching commitments because my undergrads had their exam this morning, and no social engagements, you might expect that I would be spending a peaceful half hour sat on a polystyrene box outside my office enjoying the sun. (That’s not actually a joke… photos to follow).

Sadly, not.

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