James and the Giant Corn

“Back in my day,” countless middle aged professors have said, “if you cloned a gene in grad school, that was it, you were done and graduated.”

Well times change, and cloning a gene isn’t quite as hard as it used to be. But don’t let the nostalgia a lot of old school geneticsts give off fool you into thinking identifying the gene responsible for some interesting mutant phenotype isn’t still a big deal.

Here are the three most recent papers I can think of off the top of my head reporting the cloning of maize mutants:

People have been studying the genetics of maize pretty much since the word “genetics” entered the english language at the beginning of the 20th century and the community is full of people, myself included, who can trace their academic lineage back through generations of maize geneticsts to the founder of the field himself R. A. Emerson himself. Each generation laboring for decades (often in the blazing sun and sucking mud of cornfields that are about as far as possible from the air conditions labs and white lab coats that the word “geneticist” usual brings to mind) to increase our community’s understanding of this crazy plant and left a legacy of hundreds of genes whose functions do not need to be inferred by BLAST searches, conserved domains or expression patterns, but have been individually studied and quantified by talents scientists through years of field work and wet-lab experimentation.

The Classical Maize Gene list is an attempt to capture as much of that knowledge as possible and make it accessible and useful to the new generation of genomic researchers — who spend a lot more time in air conditioned comfort than our predecessors in the maize community (although I imagine I’d still get thoroughly laughed at if I showed up to work in a white labcoat).

With the announced release of a new version of the maize genome and maize gene models in august, it’s time for me to update the list again. But I need your help. If there are maize genes which have been cloned, but are missing from the current list (available here), please let me know using the “Contact Me” form at the top of this page and pass this appeal on to others you know who studies (or has studied in the past) maize.

From an article on wired:

So-called nanocellulose fibers rival Kevlar in strength but are renewable, and the researchers believe they could be widely used within a couple of years. … Pineapple may be the most promising source of nanocellulose.

Clearly we have no choice, to secure future production of incredibly light/strong/renewable/biodegradable plastics, the time has come to sequence the pineapple genome.

::cough cough::

It’s kind of dusty in here…

Hi all, I know this site has been pretty dead for a long time. I hadn’t stopped writing, but a lot of that writing was re-directed into a series of scientific papers, now published. My plan is to post a series of postson these papers, but I’ve had a lot of plans to start writing again, and most of them have come to nothing, so until that happens: (more…)

If you’re going to be at PAG too and find yourself bored during the poster presentation sessions on Monday, I’m be standing next to P230 “Fractionation Of A Tetraploidy Preceding The Diversification Of The Grasses.” (Please forgive the two “estimated”‘s in the first sentence of the abstract.)

Sometimes people on the internet have a hard time believing that yes, I do study plants, but no, it has absolutely no direct connection to genetic engineering one way or the other. Hopefully this abstract makes it abundantly clear that my research is exactly that. Fascinating but without direct commercial implications. The main bearing my research has on genetic engineering is that, using comparative genomics, I have the chance to see for myself the really crazy stuff that “natural” plants have been doing to their own genomes for millions of years.

After starring at enough dying corpses of genes and weird frankenstein amalgamations of exons from multiple old genes (annotation errors? real biological innovation?) it’s even harder to understand the mindset that a single introduced gene will likely to throw the entire system out of whack (and do so without condemning the plant to that great waste bin of all failed evolutionary innovation: inability to thrive and reproduce.)

Anyway, talk about tangents! The point is: if you’re not going to PAG, I hope you have a great weekend, if you are, hope to see you there.

I would urge anyone who reads this site to pop over to the Washington Post to read George Will’s column today on government funding for research. It starts off slowly but gets powerful fast. The arguments for why and how investments in basic research drive long term economics growth have all been made before, however one of the lessons I hope everyone takes away from his column is that even cutting research funding COMPLETELY won’t do anything to help with the long term problems in the federal budget:

Annual federal spending on mathematics, the physical sciences and engineering now equals only the increase in health-care costs every nine weeks. [Emphasis retained from the original]

The other statistic that’s going to stick in my head going forward is the percent of people graduating from college in the US who majored in the natural sciences or engineering. Less than one in six. In South Korea, more than 1 in 3 college students graduate with such a major. In China, the statistic is close to 1 in 2.

A lot of the stats he used came from a report called “Rising Above the Gathering Storm, Revisited” which you can download as a free PDF. The original report, which came out five years ago, focused mostly on the physical sciences because at the time funding for biosciences (as a whole) were doing comparatively well after a sustained increase in the budget of the National Institutes of Health*. The updated report makes it clear that since then:

However, shortly after the “doubling” in the health sciences was achieved, the funding for that activity was permitted to erode once again—the exception being a major one-time, two-year funding infusion as part of the American Recovery and Reinvestment Act.

Many of the findings of the Academies’ study regarding the physical sciences, mathematics and engineering now pertain to the biological sciences as well.

To really visualize what federal research funding looks like as a part of the federal budget, we turn to PhDComics inspire graph “Two Cents on the Dollar“:

*The National Institutes of Health fund research in some way related to human health or disease. National Science Foundation funded bioscience (where the money that plays for research in the REST of bioscience — including plant biology — comes from) is only 2% as much as the budget of NIH (going of the Jorge Cham’s numbers).

From a behind the scenes explanation of how the strawberry genome (and the strawberry genome paper which is quite a different kind of project) came to be:

Dr. Tom Davis from University of New Hampshire submitted the letter of intent for the January 13, 2006 deadline, days before the Plant Animal Genome meeting in San Diego. At the Rosaceae Executive Committee annual meeting on Jan. 15 Tom announced that he had submitted the letter.  … Tom was convinced to withdraw his strawberry sequencing proposal, differing to the eventual DOE-JGI support of peach.

…

At PAG in San Diego, 2008, Vladimir Shulaev and Richard Veilleux from Virginia Tech attended the Rosaceae Executive Committee meeting.   Vladimir announced that Virginia Tech had thrown support behind the idea of genome sequencing- both some financial support as well as technical and facility support.  This was the seed that was needed.  The discussion had a pure “pass-the-hat” flavor to it.  Nobody had big funds, but Vlad and Richard had a big idea.  That proved to eliminate the first major barrier to a complete sequence.

…

Luckily some enthusiasm was found at PAG 2010.  Vladimir presented the genome work at a major symposium.  It looked awfully sweet on the big screen and many of us felt a sense of prime time.  It was energizing. Todd Mockler, Todd Michael and Tom Davis met.  Later that night we had a strategy-n-pizza meeting with all of those present in the consortium.

The whole thing is a fascinating read, especially if you’ve never had a chance to hear about the politics and organization that go into sequencing a plant genome. But the point I’m making with the quotes I’ve pulled from the article is that P.A.G. seems to be the meeting for people from across the community to come together to plan and work on these large collaborations.

This year I’m most going to be there to take in the sights and find out what approaches other people are using since there aren’t a lot of other labs at my home institution that carry out related kinds of research, but it’s exciting to think that someday I might get to be involved in the back door wheeling and dealing that makes large collaborative science work!

Also, reading how the strawberry genome took from 10 months from its first rejection in February to its final publication yesterday helps put my own self pity about (not nearly as data rich) a manuscript I’ve been trying to get published since June into perspective.

Weird enough that suggestions like this make it into the scientific literature:

Given the large number of new genes with different GC structures in grasses, perhaps the lineage was initiated by a wide hybridization event with another species that had genes with a high GC content, followed by selective gene retention and loss to create today’s Poaceae. The wide hybridization, while most likely to have involved a plant species, could have been prokaryotic or algal and, a prokaryotic origin could explain the higher proportion of intronless Poaceae-specific genes (1).

The above text comes from a paper published just two years ago (one year before the publication of the maize genome) describing the sequence of thousands of maize genes. It’s a wild claim — hybridizing with a prokaryote (bacteria) or algae not the wide cross part — and one I personally don’t think is very likely. But the reason people can make it with a straight face is because grasses are so different from everything that came before them, and so successful.

Grasses look and act almost nothing like the species they’re related to — the grass family belongs to the same order (the next organizational step up) as pineapples. They’re flowering plants but have either discarded things as basic to flowers as petals or modified them into something completely unrecognizable (the petals and sepals of other flowering plants might have become the lemmas, paleas, and/or lodicules of grasses).  Grasses have also reversed course from most flowering plants that depend on birds or insects to carry pollen from one plant to another and gone back to good old wind pollination. Yet, without the necessity of appealing to different pollinators to drive speciation, the grass family still encompasses more than ten-thousand species. And in the 50 or so million years or so since the major grass families split from each other, they have reshaped a whole quarter of the earth’s surface (2) creating whole new ecosystems (grasslands) that never existed before.

1. Nickolai N Alexandrov et al., “Insights into corn genes derived from large-scale cDNA sequencing,” Plant Molecular Biology 69, no. 1 (January 2009): 179-194.
2. H. L. Shantz, “The Place of Grasslands in the Earth’s Cover,” Ecology 35, no. 2 (April 1954): 143-145.