James and the Giant Corn Genetics: Studying the Source Code of Nature

March 31, 2010

BBC on drought tolerant maize/corn

Filed under: agriculture,Feeding the world,Link Posts — Tags: , , , , — James @ 8:31 am

There’s a new episode of BBC’s Discovery: Feeling the World out this morning. It’s only 26 minutes long, and the full piece is definitely worth a listen, but if you don’t have 26 minutes, the meat of the post can be summarized in 8 minutes:

3:20-7:54: Introducing the subject, developing drought tolerant varieties of maize in Africa, and the fact that the researchers working on it as using conventional breeding, marker assisted breeding and a genetically engineered trait Monsanto. When battling starvation, you use any tool that comes to hand.

18:40-21:20: This part is almost hard to listen to. You can hear the raw emotion in the researcher’s voice as the reporter keeps trying to make genetic engineering sound, at best, like a last resort. Couldn’t they just try irrigating more crop land she suggests?

25:10-end. Conclusion. I also thought this part was very powerful.

A few complaints: (more…)

March 30, 2010

What is the Joint Genome Institute?

Filed under: Uncategorized — James @ 8:49 am

They’ve produced an incredibly slick video to answer that question for the general public.

Of course now I want a video like this to introduce my own research…

March 26, 2010

The two genomes of maize

Filed under: genomics — Tags: , , — James @ 12:24 pm

I recently go back from the maize meeting. I mentioned before that big part of the reason to do poster presentations is to get comfortable discussing ones research with people who haven’t specialized in the exact same subject. In my case, my poster got a fair bit of interest which was great. (Although I was surprised which parts people were most interested in.) But there were also a couple of concepts I had a lot of trouble getting across.

It’s too late to do me any good at the maize meeting, but I have created the figure I think I needed to explain those ideas. Too late for the maize meeting, but maybe I can squeeze it into my qualifying exam proposal. Or maybe the next time I get a chance to give a talk on campus. Let’s just not get into how much of my morning I spent putting this together, and pretend it was a good investment of my time ok? (more…)

Marriage vs The PhD

Filed under: Uncategorized — James @ 9:45 am

If you have been associated with academia for any length of time you probably already read PhD comics, but anyone who doesn’t read it already should definitely check out today’s comic “Marriage v The PhD”

March 23, 2010

Paintings of the last supper reflect growing abundance of food.

Filed under: Link Posts — James @ 8:35 am

“The last thousand years have witnessed dramatic increases in the production, availability, safety, abundance and affordability of food…. We think that as art imitates life, these changes have been reflected in paintings of history’s most famous dinner.” – Brian Wansink (Cornell University)

Read more at Discoblog. Note that these results are normalized to head size, so I suppose the alternative explanation is painters have started giving their subjects smaller heads over the past 1000 years.

March 22, 2010

Regarding Scientists…

Filed under: Uncategorized — James @ 6:22 pm

Finally, let me speak up for scientists. In my experience, the vast majority of scientists are honest, sometimes slightly nerdish people who are grateful to be able to work on something about which they have a passionate interest. Scientists can be arrogant: but overall they do not deceive themselves, or the public.

From an article written by Philip Strange. I’m not sure about slightly nerdy, but there is a lot of variation even among people studying science, and I’m probably at the nerdy end of the spectrum.

Getting back in the saddle

Filed under: Recreational Travel — James @ 11:41 am

I got back from the maize meeting in Italy last night to find my DSL connection at home was dead again. I’m now at work and think I’m pretty much caught up with the backlog of internet related stuff that accumulated during my absence. So if you e-mailed me, tweeted at me, or commented on a post sometime in the last week, please accept my apologies for not getting back to you before now.

And if you still haven’t heard back from me, please try getting in touch again.

Random thoughts from my travels:

  • Carrying a 40 inch long poster case 1/3 of the way around the earth and back again certainly gives me a new appreciation for the training old fashioned riflemen (whose rifles were much longer than my poster) must have had.
  • Travelling with three other Americans makes other countries seem a lot less foreign. We talked among ourselves in english, and while the language barrier meant we never asked for directions, as a group of four men we wouldn’t have been living up to our stereotype by asking for directions even if we’d been able to. Walk even 100 feet away and the awareness of being in a strange land (and not speaking a word of the native language), suddenly sinks in.
  • German airports list departing flights by time of departure, not the name of the destination city. (It look an embarrassingly long moment to realize flights weren’t simply listed at random.)

March 20, 2010

Gene Annotation Won’t Kill You

Filed under: Uncategorized — James @ 3:43 pm

I just got out of a meeting about how we’re going to improve the annotations of the maize genome. It’s got me riled up.

But first, what is gene annotation (in twenty words or less): (more…)

Transcriptome Sequencing!

Filed under: Uncategorized — James @ 1:16 am

One of the themes, looking over the abstracts and talks for this year’s maize meeting before I leave is that a year from now we can expect to have much more detailed information about where genes are expressed in corn, and at what levels. One of the great dividends of the dropping cost and increasing speed of short read sequencing.

At this meeting alone we’ll be hearing about the incredibly detailed leaf transcriptome[1] (which seperates out expression of four developmental zones of the leaf, plus uses laser capture to look at the expression of genes the bundle sheath and mesophyll cells within the maize leaf seperately). And at least two posters on the subject also caught my eye (although there may be a lot more that involve profiling expression using high throughput sequencing). Two groups based at Oregon State and Stanford are in the process of sequencing the transcriptomes of the male and female gametophytes* of maize[2], and a group based primarily at Cold Spring Harbor is in the proccess of sequencing the transcriptome of developing ears (the kind covered in corn kernels, not the kind you hear out of)[3]. Both of these transcriptomes actually represents a number of seperate data sets from different tissue types and/or developmental stages.

All these datasets makes me wish the Fort Lauderdale Accords** applied to expression data in addition to genome sequences themselves, but since it doesn’t, I’ll happily oooh and awww over other people’s cool data.

A special thanks to Andrea Eveland’s abstract for introducing me to units that can actually quantify the wa expression is measured in these studies RPKM (Reads Per Kilobase of exon per Million reads).

*Plants practice alteration of generations, switching between diploid (two copies of the genome, one from each parent) and haploid (only a single copies of their genome) multicellular forms of life. In flowering plants, the kind we spend most of our time with, the haploid generation is almost vestigial, but it still exists. Plant pollen contains an entire male haploid plant (the male gametophyte), which has been reduced to a mere three cells (two which are sperm cells). The female gametophytes of flowering plants are only a little larger, at seven cells. In other plants, the gametophyte can exist as a free living life form visible to the naked eye.

**The agreement that allows genome sequence data to be released to the whole community before the people who sequenced that genome have published their paper.

[1] Pinghua Li et al. “Characterization of the maize leaf transcriptome through ultra high-throughput sequencing” Talk #14 2010 Maize Meeting (Presented by Thomas Brutnell)

[2] Rex A. Cole et al. “Analysis of the Maize Gametophytic Transcriptomes” Poster #27 2010 Maize Meeting (Presented by Matt Evans)

[3] Andrea L. Eveland et al. “Transcriptome sequencing and expression profiling during maize inflorescence development.” Poster #113 2010 Maize Meeting

March 19, 2010

Helitron Capture Creating New Genes?

Filed under: biology,Genetics — James @ 1:15 am

One of the things that has made annotating genes in the maize genome so difficult (there are currently two sets of gene models one with only 32,000 genes, which is low estimate, and the other with 100,000 is far too many) is the presence of large numbers of gene fragments that have been captured and duplicated by a class of transposon called helitrons (yes I know that sounds like a character from Transformers).

The helitron captured fragments are copied from real genes (often multiple pieces are captured from different genes) which is why many gene annotation programs (trained to recongize the difference between genes and non-coding DNA) will identify the fragments being genes themselves.

What if some of those fragments actually are genes? By combining pieces from completely different genes, helitrons could be a whole new source of crazy new genes that natural selection could act upon.

That is the question the authors of this poster are trying to get at, by identifying more helitron fragments and checking to see if those fragments were actually expressed in the genome.

Allison Barbaglia et al. “Accessing the transcriptional activity of Helitron-captured genes of maize” Poster #243 2010 Maize Meeting

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