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

March 8, 2010

Scientific Posters

Filed under: Campus Life — Tags: , , — James @ 11:29 pm

I’m involved in the designing of two posters my lab will be taking to the maize meeting in a weeks time. What are scientific posters?

A cross between a very short paper and a very short, on demand, research seminar, a poster is a dozen square feet of scientific data. We grad students cobble together some figures describing the data we’ve painstakingly acquired though months of long days and nights in lab*, hang our poster a scientific conference and spend hours hovering nearby, ready to explain our research to anyone who seems even marginally interested.

Probably the most important role of posters is that designing them gets us thinking about the questions our research (what we actually do all day) is really trying to answer and how to communicate our results to people who don’t specialize in those exact same questions. A trap that I often catch myself falling into.

As for the value of posters as a real method of scientific communication… it’s best not to set your expectations too high:

The best general advice I can give a first-time poster constructor is to describe the circumstances in which a poster will eventually be viewed: a hot, congested room filled with people who are there primarily to socialize, not to look at posters. Because poster sessions are often concurrent with the “wine and beer” mixer, chaos is further increased by hundreds of uninhibited graduate students staggering around hitting on each other. It’s not a pretty sight.

And it gets worse: meeting organizers will invariably sandwich your poster between two posters that are infinitely more entertaining, such as “Teaching house cats to perform cold fusion” and “Mating preferences in extraordinarily adorable red pandas.”

Words that were comforting to read when I first started stressing out about never having put together a scientific poster before. (And just to be clear, I’m not saying posters can’t be very effective methods of communicating science, only that the worst case scenario for a poster is that it gets ignored. The worst case scenario for a paper is it comes back with a rejection notice and horrible reviews, and the absolute worst case scenario for a scientific talk is, I suppose, heckling followed by a mass walk out. My point is, by comparison, designing a poster should be a low stress activity.)

That said, I think we’ve got some interesting data to present, so if you’re going to be at the maize meeting next week and are willing to risk my inexperience with designing scientific posters, be sure to stop by poster #31 or #39.

The two posters discuss, respectively, the way extra copies of genes are lost from the genomes of plants following how genome duplications, and a project where we’ve identified equivalent genes between up to five grass genomes (which would be quite the trick since only four grass species have sequenced genomes, but since maize has its own whole genome duplication we count it twice) based on the conserved order of genes along chromosomes (synteny).

*At least that’s usually what ends up on posters. I can’t wait to find out what interesting stuff ends up on the Biofortified poster (#167)

Two classical maize genes, synteny, and the mystery of the missing gene

Filed under: biology,Genetics,genomics,Plants — Tags: , , , , , , — James @ 12:50 pm

Colored aleurone1 and Purple plant1 are both genes with long histories in maize research and are involved in the regulation of anthocyanin biosynthesis.The mutant version of purple plant1 does exactly what it sounds like. (In the proper genetic background) it has plants producing anthocyanin (a purple plant pigment) everywhere, resulting in purple plants. The mutant form of colored aleurone1 was identified from a mutant that changed the color of individual corn kernels. Guess which of these two classic maize mutants made it into the top 15 most published on genes in maize, and which fell barely short.

Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth). (more…)

March 7, 2010

The Hair Shirt Fallacy

Filed under: Politics — James @ 8:07 pm

Kids are told to eat their vegetables because, even though they taste bad, because vegetables are good for them. They are told they can’t have ice cream every night, even though it tastes good, because ice cream is bad for them. The danger arrises when people generalize that rule, that if it’s pleasant it’s bad for you, and if you don’t like it it must be good for you. (more…)

March 3, 2010

Oliva Judson’s Salute to Grasses

Filed under: biology,evolution,Genetics,Plants — Tags: , , , , — James @ 2:33 pm

People who can actually get the general public interested in science are almost as rare as hen’s teeth.* One of those gifted scientist-communicators is Olivia Judson, an english evolutionary biologist who sometimes writes a column for the nytimes and published an interesting/hilarious pop-science book titled: Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex.**

I mention all this to explain why I was so excited to learn that her post this week sings the praises of a group of species near and dear to my heart, the grasses. The whole post is definitely worth a read. Even if you don’t learn something you didn’t already know, read it as a source of inspiration for telling OTHER people how cool grasses are. And the closing is truly excellent:

We usually talk of our domestication of grasses, and the ways in which we have evolved them: we have made plants with bigger, more nutritious seeds that don’t fall to the ground, for example.But their effect on us has been far more profound. Our domestication of grasses, 10,000 years ago or so, allowed the building of the first cities, and marks the start of civilization as we know it. Grasses thus enabled the flowering of a new kind of evolution, a kind not seen before in the history of life: the evolution of human culture.

Some of the comments are heart warming to read as well, although a bunch of people have fallen prey to the maize/corn confusion. (Explained in detail here)

*Speaking of cool science that most of the general public doesn’t know about: We’ve known for more than four years that mutations of the gene talpid2 in chickens cause chicken embyros to develop teeth, something we thought birds had lost the ability to do 60-80 million years ago (around the same time grass was bursting onto the world stage.) Don’t worry too much about getting bitten by a sabertoothed turkey, the toothed embryos have other problems that mean they don’t survive.

**There’s also a three-part video series based on the book that I can best describe as … odd.

March 2, 2010

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Filed under: Genetics,Plant breeding,Plants — Tags: , , , , , — James @ 12:41 pm

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

  • A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
  • Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
  • They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
  • While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
  • That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

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