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

October 24, 2009

Microbial Art

Filed under: biology,Link Posts — James @ 5:45 pm

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

October 22, 2009

Agriculture in Popular Culture: CSI Miami

Filed under: biology,Entertainment — Tags: — James @ 7:54 pm

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 ┬áreal 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…)

October 14, 2009

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.

October 13, 2009

Potato Genome!

Filed under: biology,Plants,research stories — Tags: , , , , , — James @ 7:26 pm
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Photo from graibeard

Sort of anyway. What was released was a pre-publication scaffold of the genome. A final, published, version might include more primary sequence data, will have fewer gaps, and most importantly of all, people will be able publish their own work which draws on the potato genome.

Overall I have mixed feelings on the current practice of releasing genome sequences prior to publication. As someone who does comparative genomics, having access to more genomes is great, but the agreements they’re released under severely limit how they can be used in publications prior to the publication of the genome paper itself (which can be a LONG time).

Within the grasses four genomes are available (Maize(corn), Sorghum, Rice and Brachypodium) however only two of them, Rice and Sorghum, are published. Any paper making use of whole genome analysis of all four cannot be published before the Maize and Brachy papers come out (hopefully before the end of this year!).

That said having even a rough draft of the potato genome is cool. Potato is a great plant for a lot of reasons. Potatoes are the fourth staple crop (behind only rice, maize and wheat) that provided enough food for people to build civilizations and probably the most important non-grass crop in the world. Currently there are no GMO-potatoes on the market, as I mentioned here. Domesticated potatoes are tetraploid and rarely breed true (their offspring aren’t much like the parents).* And I still owe it a post of its own.

Another reason to be interested in potatoes are is the family tree of the species. Potato can claim tomatoes, eggplant, and deadly nightshade as close relatives.** That whole group of species belongs to a different branch of the family tree of plants (the Asterids) from the early non-grass genomes (Arabidopsis, Papaya, and Grape) which were all in a group called the Rosids. These two groups are responsible for a lot of the diversity of species within the Eudicots*** so it’s good we are starting to starting to see Asterid genomes.

*Potatoes grown from seed not sharing many characteristics with their parents is why most cultivation of potatoes is done by planting pieces of potatoes instead of seed. The plant that sprouts out of a potato is genetically identical to the plant that grew the potato. It’s a clone. Apples actually face a similar issue with apple seeds not being much like their parents. That’s why breeds of apples are propagated by grafting. A breeder cuts off a piece of a branch from one tree and carefully connects it to the stem of an unrelated apple tree. If the graft is done properly the branch will grow, flower, and produce fruit just as it would normally. So all apples of the same variety (say Gala, Macintosh, or my new favorite Cripps Pink) are clones of each other.

**The obvious family resemblance to deadly nightshade was one of the reasons Europeans originally believed tomatoes and potatoes to be toxic when they were introduced from the Americas.

***For a sense of how Eudicots fit into the family tree of all plants, check out Phylogeny of Pineapple, a further explanation of awesomeness

October 8, 2009

Superweeds

Filed under: agriculture,biology — James @ 5:46 pm

I’m sure everyone reading this has heard the term ‘superweed.’ These are the terrible new creations that will, or in some cases have, been created by herbicide resistant crops. What makes them so super and terrible? They’re resistant to the same herbicide as the herbicide resistant crop they grow among. Treating crops with herbicides selects for herbicide resistance crops in the same way treating infections with antibiotics selects for antibiotic resistant bacteria. Taking antibiotic drugs kills all the bacteria susceptible to the antibiotic. That means any individual bacterium which can survive the treatment is much more likely to reproduce and thrive now that all its competitors were killed by the drug. In the same way, spraying fields with an herbicide, while good at killing off weeds, also gives a big selective advantage to any weeds that carry traits which allow them to survive the spray. Thusly are the superweeds born. Why isn’t that the end of the world? Read on the find out.

(more…)

October 6, 2009

Practice Talk

Filed under: biology,Campus Life — James @ 7:05 pm

For my teaching assistant training class we have to give half hour presentations. I just finished mine and I’m SO glad I held my own against the person who went before me. He had the advantage of talking about ecology, which usually is better at engaging the audience, and has a polished powerpoint presentation. My talk was basically an expanded version of Phylogeny of Pineapple, a further explanation of awesomeness.

People seemed genuinely engaged and the feedback after the talk was positive. Whenever phylogeny and genomics can go up against biodiversity and ecosystem services, and not be humiliatingly crushed is a victory for all of us.

No offense to ecologists, you guy do exciting research and I love getting the chance to sit in on your talks, it’s just nice when we plant biologists can get attention too.

September 29, 2009

DNA Sequencing Technology

Filed under: biology — James @ 6:46 pm

John Timmer has started a cool post on sequencing technology over at arstechnica. The writing seems like it would be quite accessible to someone without much biology or chemistry background. Sunday’s post is focused on Sanger sequencing which is the classical technique and still used by people working with one or a few genes at a time. There’s a whole new set of technologies that are now (or soon will be) used to tackle large scale projects like sequencing whole genomes and I assume that’s he will talk about in part 2.

The principles behind sanger sequencing are quite old but it’s a great example of the huge difference optimization and specialization can make. Back in the day, grad students and technicians poured their own gels, ran their own reactions with radioactive reagents and then ran the reactions out and interpreted a couple of hundred base pairs of dna sequence from the pattern of bands which appeared.

By the time I first needed to sequence something, I put my DNA in a little test tube (microfuge tube) with a little bit of the same DNA primer I’d used to amplify my sequence and walked it down two stories and across the hallway to drop it off in the sequencing lab. The technology had come so far that now a single technician loaded dozens of samples, dropped off from all over campus, into a giant machine, and a few hours later sequences data 4-5 times longer than back in the bad old days, was e-mailed back to all the researchers whose samples had been in that run. No radioactivity. No problems with gels and most importantly, so many fewer hours spent by researchers.

The ABI 3700 was a sequencing machine that represented the peak of those trends. It could sequence 96 samples at once and run up to eight times per day. Assuming 1 kb of sequence per sample, which is about the maximum of sanger sequencing, that means each machine could produce ~750 kilobases* of sequence data per day.

Two of the new sequencing technologies you may have heard about are 454 sequencing and solexa sequencing. A single machine using the 454 sequencing technique can generate as much sequence per day as 1,300 of the ABI 3700 machines. A Solexa sequencer can generate 4 times a much sequence as a 454 sequencer, four billion individual A’s T’s C’s or G’s. The only downsides are shorter read lengths (somewhat shorter for 454, and much shorter for solexa), and the fact sanger sequencing is the only technology that can start at specified point on the DNA molecule (specified by a primer.)

Very cool technologies and when Dr. Timmer posts part two which addresses these new techologies I’ll be sure to link to that one as well.

If you’re interested in how the new sequencing technologies stack up against each other PolITgenomics has a great reference chart.

*A kilobase is one thousand A’s T’s C’s or G’s of DNA

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