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Food Nostalgia

Mar 10th, 2010
by James.
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James McWilliams, writing at the nytimes, makes the point that the idealizing the diets of generations past has been going on for at least 150 years. Michael Pollan’s rule: “Don’t eat anything your great-grandmother wouldn’t recognize as food” loses some of its effectiveness when you picture all four* of your great grandmothers (who were probably alive in the era of the world wars) idealizing the diets of diet of civil war era american, and so on.

h/t to Greed, Green, and Grains.

GG&G is well worth checking out in its own right. On this particular subject Michael Roberts, the blog’s author, makes the point that just because nostalgia for the foods of the past isn’t a new development, doesn’t mean there aren’t real problems with the food we eat today.

There are real problems with the ways we produce and consume food in this country. (And a whole separate set of problems in other parts of the world.) But by over-idealizing the food our great grandparents ate we’re looking for the answers to today’s problems in the past, when the real answers to the problems we face can be found (you guessed it) in the future.

Which is not to say we can’t learn from the mistakes and successes of the past. I just don’t think it’d be a good trade to exchange my diet for that of my great grandmother (any of the four).

*Four great-grandmothers (eight great-grandparents!), but consider that if we go back ten generations (perhaps an average of 250 years) we’re each descended from over 1000 people. (1024 assuming your family tree was completely free of inter-marriage).

Posted in: Link Posts.

Wow!

Mar 9th, 2010
by James.
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Who could have predicted maize geneticists would be so interested in maize genes? The entry I posted last night on Purple plant1 and Colored aleurone1 easily received more traffic in its first day on the site (it’s still got a long way to go before it catches long term readership attractors like water chestnuts and the NIPGR tomatoes), than any entry since the heady days of the maize genome release back in November.

The relationships of the four grass species with sequenced genomes. The branches are NOT to scale with how long ago the species split apart. Green stars represent whole genome duplications. The most important one to notice in the one in the ancestry of maize/corn. That duplication means that every region in sorghum, rice, or brachypodium is equivalent to two different places in the maize genome, one descended from each of the two copies of the genome that existed after the duplication.

And this morning the dataset I drew that example from, 464 classical maize genes mapped onto the maize genome assembly plus syntenic orthologs in up to four grass species: sorghum, rice, brachypodium, and the other region of the maize genome created by the maize whole genome duplication (technically syntenic homeologs since we started in maize to begin with, by the principle is the same), went out to the maize genetics community (thank you MaizeGDB!).

A postdoc in our lab tells me more people have visited CoGe today than any day on record (and we hit that mark before noon!).

Anyway, thank you guys, it’s great to feel appreciated!

Posted in: Campus Life, Genetics, biology, genomics.
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Scientific Posters

Mar 8th, 2010
by James.
3 comments

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)

Posted in: Campus Life.
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Two classical maize genes, synteny, and the mystery of the missing gene

Mar 8th, 2010
by James.
6 comments

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). Continue reading →

Posted in: Genetics, Plants, biology, genomics.
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The Hair Shirt Fallacy

Mar 7th, 2010
by James.
3 comments

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. Continue reading →

Posted in: Politics.

Oliva Judson’s Salute to Grasses

Mar 3rd, 2010
by James.
1 comment

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.

Posted in: Genetics, Plants, biology, evolution.
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The Most Studied Genes of Maize (and why we love kernel phenotypes)

Mar 2nd, 2010
by James.
3 comments

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.

Posted in: Genetics, Plant breeding, Plants.
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Corn Smut

Feb 27th, 2010
by James.
9 comments

Corn Smut photo: oceandesetoiles, flickr (click to see photo in its original context)

And no that doesn’t mean corn pornography*. Corn smut, or Ustilago maydis, is a fungus that infects corn plants. It’s an old acquantance from my days working in the field. We always used to tell the new hires that corn smut was a rare delicacy in some countries (as we’d been told ourselves), but this was in the days before iPhones so until recently I never actually checked on this bit of received wisdom.

Turns out this particular bit of knowledge was true:

The immature galls, gathered two to three weeks after an ear of corn is infected, still retain moisture and, when cooked, have a flavor described as mushroom-like, sweet, savory, woody, and earthy.

More corn smut. Photo: moskatexugo, flickr (click to see photo in its original context)

I haven’t been able to figure out what the trade off in nutrition is between the ear of corn that is produced by a normal plant and the fungal galls that can be harvested from a plant infected with corn smut. I’d imagine corn smut provides more (and more complete) protein than an ear of corn (assuming corn smut is nutritionally similar to mushrooms.) But what’s the comparison in number of calories? The fungus is certainly sold at a higher price pound for pound.

My renewed interest in corn smut comes courtesy of a new paper** that came out in PLoS Biology describing how the fungus steals energy from infected corn plants without triggering the corn’s usual anti-fungal defenses. It’s an interesting read, you can check out the paper itself since PLoS Biology is open access, or Diane Kelley’s summary at “Science Made Cool.”

I’d seen a number of talks recently about another fungal parasite, powdery mildew in Arabidopsis, but somehow it’s much easier to focus on this stuff now that I can connect it back to corn. Even mammalian systems can be interesting*** once the make that connection.

*Please PLEASE don’t let that phrase start showing up in the search terms people use to find my site!

**Wahl R, Wippel K, Goos S, Kämper J, Sauer N (2010) A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis. PLoS Biol 8(2): e1000303. doi:10.1371/journal.pbio.1000303

***The talk I’m practicing for Monday actually uses an example of a pheromone receptor in new world monkeys that was lost 23 million years ago in old world monkeys (including us humans).

Posted in: Plants, food.
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The Sacrifices People Make For Science

Feb 26th, 2010
by James.
1 comment

Just to give you a sense what Macro Island looks like. photo: John Walker, flickr. (click photo to see in original context)

My heart bleeds for those poor scientists forced to spend the week at Marco Island for the Advances in Genome Biology and Technology conference. Not only do they have to put up with temperatures in the 60s (~20 C) and views like the one attached, but consider the grueling workload they labor under even after the sun goes down. (Excerpt from coverage by the Daily Scan):

The real marathon, though, came Thursday night with an increasingly competitive host of vendors vying to throw the best party. As far as Daily Scan can remember, you’d have to go back to the heady days of 2002 or so to see this conference with such participation from vendors, who have to be especially creative now that there’s no exhibit hall. Life Technologies and Caliper hosted parties showing off their new instruments, while Complete Genomics and Ion Torrent offered plenty of opportunity to schmooze with fellow attendees. Friday night we’re expecting fireworks (not the metaphorical kind) from Pacific Biosciences.

Posted in: Campus Life.

One MORE reason pineapples are awesome

Feb 26th, 2010
by James.
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Pineapple plant. photo: CameliaTWU, flickr (click photo to see in original context)

Pineapples use CAM photosynthesis. Normally plants have to open tiny holes in their leaves (called stomata) during the day to let in carbon dioxide that they use during photosynthesis. The problem they face is that when they’re letting carbon-dioxide in, plants also let water out.

CAM plants get around this water loss by collecting all their carbon dioxide at night (when it’s not as hot so they lose less water when they open their stomata) and storing it within their leaves until they need it during the day. This allows them to be much more efficient with water than normal plants (ones carry out plain old vanilla C3 photosynthesis.*)

Why do pineapple plants need to be so frugal when it comes to water? The fact that pineapples are native to paraguay and southern brazil is repeated across the internet, but as you can imagine, that description covers a wide range of climates and habitats some of which are much drier than others. Clearly more research on the subject is called for on my part.

The fact that pineapples do CAM photosynthesis came up in a discussion with another guy in my lab where we discussed the fact that pineapples would make an excellent comparison for grass genomes** and have a reasonably small genome at ~500 megabases***, half the size of the recently published soybean and sorghum genomes and less than a quarter the size of the maize genome.

With all these new third generation sequencing technologies coming out in 2010, hopefully someone will sequence the pineapple genome. If not, maybe the cost of sequencing will drop enough while I’m in grad school that I can sequence the genome myself ( a guy can dream).

For more on my long running admiration for pineapple (second only to my appreciation of corn itself):

Why Pineapples are Awesome.

Phylogeny of Pineapple, an further explanation of awesomeness.

*Let the record reflect that corn does C4 photosynthesis, which another awesome variation on the standard system of photosynthesis.

**In addition to both pineapple  and grasses being monocots, they’re in the same order of plants, Poales, as grasses. The first non-grass monocot to be sequenced will almost certainly be the banana (in fact the process as already begun), but while bananas are monocots they belong to a different order Zingiberales (which includes spice plants like ginger, cardamom, and tumeric).

***526 Megabases as cited in Patterson AH, Freeling M, Sasaki, T “Grains of Knowledge” Genome Research 10.1101/gr.3725905

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