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biology

Biological Control of Western Corn Rootworms

Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

This post discusses the paper Degenhardt, J et al. (2009) “Restoring a maize root signal that attracts insect-killing nematodes to control a major pest”

The Western Corn Rootworm (which as you can see from the picture to the right are not actually worms) is estimated to cost farmers in the US alone one billion dollars a year in lost yield and pest control measures. The newly hatched larva begin feeding on root hairs and as they get bigger start attacking the main roots of a corn plant. The damage to the roots from the feeding itself is exacerbated by the open wounds becoming infected. The loss of roots both stresses the plant and reduces yield by decreasing the plant’s supply of nutrients and water, but also makes it much more vulnerable to lodging (getting blown down by a gust of wind). Oh, and did I mention the adults like to feed on the corn plant’s reproductive tissues, decreasing yield even further?

Rootworms are one of the pests controlled by plants genetically engineered to express BT a protein taken from organic agriculture. Without it, the 1 billion dollar price tag for rootworm damage and control would be even higher. But this isn’t an article about bt, it’s an article about how some corn already knows how to call for help when rootworms attack.

Rootworm larva may feast on the roots of maize, but they are in turn eaten by some species of nematodes.* And it turns out some kinds of corn know how to attract nematodes, and when they’re under attack by rootworms they do just that. The nematodes get a delicious meal of rootworms and the corn plant gets to keep more of its roots intact.

How do corn plants attract their, unintentional, nematode defenders? (more…)

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Figure from my Research Proposal

“My budget…triples the number of National Science Foundation graduate research fellowships.  This program was created as part of the space race five decades ago. In the decades since, it’s remained largely the same size –- even as the numbers of students who seek these fellowships has skyrocketed.  We ought to be supporting these young people who are pursuing scientific careers, not putting obstacles in their path.” – President Obama

I’m still feeling brain dead after the final push for submitting.

Speaking of NSF, here’s the one figure I managed to shoehorn into my research proposal.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy. As usual click the picture to see it fullsized

If you’d like you can even click here to be able to play around with the figure yourself using the CoGe interface. Now I’ve got to try to explain what this figure is about. (more…)

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It is Done

NSF fellowship application complete and submitted with just under an hour and a half to spare before the deadline. More inside. (more…)

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Bruce Sterling and Kim Stanley Robinson on Climate Change

This post was followed up by More on Why Science Isn’t a Perfect Fit with the Left or the Right

Bruce Sterling writes science fiction cyber-punk. Kim Stanley Robinson writes enormous science fiction trilogies. One on terraforming mars (Red Mars, Green Mars, and Blue Mars) that I read when I was younger and space mad. He’s also put out a more recent trilogy (40 Signs of Rain, 50 Degrees Below, and 60 Days and Counting) which I haven’t had a chance to read yet, but I’m told is quite good, and that at least the first book presents an accurate and depressing picture of the process for funding NSF grant proposals. Not something I want to think about I’m ~24 hours from submitting my own.

Kim Stanley Robinson recently did an interview for his new book Galileo’s Dream (you can find the whole text here). It’s a great read, although there’s plenty of stuff I disagree with.

One thing happening is that the Republican Party in the USA has decided to fight the idea of climate change (polls and studies show the shift over the first decade of this century, in terms of the leadership turning against it and the rank and file following), which is like the Catholic Church denying the Earth went around the sun in Galileo’s time; a big mistake they are going to crawl away from later and pretend never happened. And here the damage could be worse, because we need to act now.

What’s been set up and is playing out now is a huge world historical battle between science and capitalism. Science is insisting more emphatically every day that this is a real and present danger. Capitalism is saying it isn’t, because if it were true it would mean more government control of economies, more social justice (as a climate stabilization technique) and so on. These are the two big players in our civilization, so I say, be aware, watch the heavyweights go at it, and back science every chance you get. I speak to all fellow leftists around the world: science is now a leftism, and thank God; but capitalism is very, very strong. So it’s a dangerous moment. People who like their history dramatic and non-utopian should be pleased.

Reading the answer to this question made me feel a little weird about Mr. Robinson’s claiming of science for one side of the political debate (and also not a big fan science vs. capitalism, the climate change debate is more about the split between short and long term planning). Science isn’t a side in the political process, it’s a set of knowledge and tools that are openly available to all and political movements are free to either accept them, or, as sadly seems more common, toss them aside. Which is why Bruce Sterling’s response cracked me up: (more…)

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Sugar Belle Citrus and Patents

Mandarin Orange (Not a Sugar Belle)

Mandarin Orange (Not a Sugar Belle) from dungodung on flickr

We’ve been talking about grains and genetic engineering strait for a few days, so I thought it’d be the perfect time to put up a story about conventionally bred citrus. The University of Florida put out a press release about a new mandarin orange breed developed by Fred Gmitter, called Sugar Belle. The fruit is of course described as delicious and it may well be, I can’t say one way or the other. Importantly to a different group of people (producers rather than consumers of citrus fruit), the fruit matures 4-6 weeks earlier than other varieties of mandarin, making the harvest better timed to cater to the demand for citrus around Christmas.

Fred has been developing the breed since 1985, when he found the tree Sugar Belle was bred from in the experimental plot of another plant breeder who’d just retired. That’s twenty-four years of research and development. 1985 is the year “new coke” was released. Soviet and Western forces still faced off against each other across the Berlin Wall. If Sugar Belle was a person, it’d already be old enough to be in grad school right now.

The lesson here (one of them) is that it takes a long time to breed fruit trees.

But that’s not the only interesting thing about this story. (more…)

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Predictable Spinning of Squash

I dont have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

I don't have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

What could be a more fitting topic for a Halloween post than cucurbits, the family of plants that (in addition to crops like watermelon and cucumber) include squash and pumpkins? Yeah, I know it’s a stretch.

A week ago a paper came out in PNAS (the proceedings of the national academy of sciences. A very prestigious journal, one step down from Science or Nature), that showed when an artificially inserted gene in squashes that provided virus resistance was introgressed into a wild related species it actually made them less fit. Short version: the wild squash also suffer from the virus which attacked domesticated squash but are also attacked by beetles, and the beetles prefer to eat squash without the virus. Tomorrow’s Table has a much better and more complete explanation of the research.

In that post the very first commenter predicted the result, that in this particular case a transgene (like most genes involved in domestication) was beneficial for farmers but not for wild plants, would be spun into “another failure for GMOs” when the real message is “we were worried about pollen drift, but in this case it turns out we didn’t have to be.”

He was right. (more…)

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Banana Biology

When I was giving my lecture to on phylogeny and tetraploidies, I found out not everyone knows why bananas don’t have seeds.

The reason the bananas we eat don’t have seeds is that they are all sterile. A long time ago the Cavendish bananas first came into being when a tetraploid banana (that is a plant that has four copies of every chromosome instead of the normal two) mated with a normal diploid banana. The result, a banana with three copies of every chromosome couldn’t mate or produce seeds. One of the steps in making reproductive cells (the analog of human sperm and egg cells) is the even dividing of a plant’s chromosomes into two reproductive cells.* Normal diploid cells can easily divide into two cells (one copy of each chromosome in each cell), tetraploid plants can divide the same way (two copies of each chromosome in each cell). Hexaploid, three copies in each and so on. Odd numbers of chromosomes don’t work. The plants can’t successfully make the cells it needs to reproduce, if it can’t reproduce it can’t make seeds, and that is why bananas (or seedless watermelons) don’t have seeds. (more…)

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Microbial Art

Check out some of the gorgeous art people can make in petri dishes.

Clearly the people who create these have far steadier hands than I do when it comes to smearing out colonies.

by Niall Hamilton

by Niall Hamilton

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Agriculture in Popular Culture: CSI Miami

Sorry for missing my daily post yesterday. Still trying to get over whatever I caught last week.

Last week, 13.3 million people watched CSI Miami in prime-time. That’s more people than live in the state Illinois. It doesn’t consider reruns, Tivo recordings, or piracy.** So to the untrained eye (mine), it seems likely the show is making enough money to hire a scientific consultant or two. Clearly the untrained eye is wrong and budgets are so tight that that the expense of finding someone who’d taken intro biology anytime in the past fifteen years was far too much. As demonstrated in this weeks episode “Bad Seed.”

Before I continue, let me say first of all I’m not one of CSI:Miami’s regular viewers. They don’t have to worry about losing me as a fan. I never was one. Second, I don’t get angry when shows like Fringe or the SyFy (<–that’s really how they spell their name now) Channel’s disaster and/or monster movie of the week completely mangle science. They are, and acknowledge themselves to be, science fiction. Shows based on fictional science. On the other hand, shows such as the CSI and Law&Order families set fictional stories in what, we are supposed to believe is, the  real world. As such, the burden on them to get their facts straight is much stronger.

A burden the writers of CSI Miami clearly can’t be bothered to live up to. (Oh, if it wasn’t obvious already, spoilers ahead). (more…)

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Potato Breeding

Unfortunately the purple potatoes aren't a Cornell Breed

Unfortunately these purple potatoes aren't one of the Cornell breeds

A lot of people may not share my enthusiasm for the potato genome, hopefully you all enjoy eating potatoes. The stereotype of potatoes is lots of boring sameness one identical to the next.* Reality, as usual, is much more complicated. Tens of thousands of cultivars can still be found in the South American regions where potatoes were first domesticated. In America, breeders are constantly working to bring in desirable traits from those (often really cool looking) breeds and even wild relatives of the potato. They face both genetic barriers (species barriers are bad enough normally, but trying to introgress genes across a tetraploidy can be a mess) and consumer acceptance ones.

This was driven home in a story at the NYtimes about Cornell potato breeders who have developed breeds which grow much better in upstate New York, but run into problems because the potatoes look and taste different than the couple of varieties of potatoes consumers and restaurants are used to (most notably Idaho grown Russet Burbanks**). Cornell Extension has been working on overcoming that barrier providing the potatoes to restaurants and, in what I think is a genius move, culinary schools throughout the region.

If you happen to visit New York farmers markets take a moment to ask sellers about the breeds of potatoes they have for sale.*** The potatoes covered in the story are Salem, Eva (both white potatoes), Lehigh, Keuka Gold (yellow breeds), Adirondack Blue and Adirondack Red (both of which are just the color you’d expect from the name.) Purple potatoes in particular just look really cool, see image above.

*There was a saying about accepting differences that I vaguely remember from a childhood TV show, something along the lines of “People aren’t the same like potatoes, and that’s a good thing because potatoes are boring.”

**The Russett Burbank was developed by a truck gardener outside of New York City called Luther Burbank in the 1800s who was initially inspired to become involved in plant breeding by Charles Darwin’s 1868 The Variation of Animals and Plants Under Domestication. He later moved to California where he became famous plant breeder and, among other things championed the practice of grafting (connecting a cutting from one plant (usually a tree) to the stem of another, which, if done properly grows the two together and the cutting will grow flower and produce fruit like it would normally) a practice at the time condemned as unnatural. <– This info from Mendel in the Kitchen by Nina Fedoroff and Nancy Brown a great resource

***In fact, whenever you’re buying directly from a farmer, if you get a chance, ask about the breed of whatever you’re buying. More often than you’d expect there’s an interesting story about why he or she is growing that particular breed and where it came from.

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