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

June 22, 2010


Filed under: Uncategorized — James @ 3:34 pm

I’m officially PhD-candidate James. 😀

June 15, 2010

Grain built cities, millstones liberated them

Filed under: Uncategorized — James @ 6:27 pm

Excerpt from a fascinating talk (go and read the whole transcript!):

There’s only one way to feed a city, at least historically, and that’s to feed it with grains—rice, wheat, maize, barley, sorghum, etc.. …

And what do you need in terms of grains? For most of history—really, until about 150 years ago—most people in most cities, except for the very wealthy, lived almost exclusively on grains. They got about ninety percent of their calories from grains.

That meant that for every single person in a city you had to have 2 lbs of grains a day, turned into something that people could eat. …

Depending on how good you are, it takes somewhere between fifty minutes and an hour to do enough maize for tortillas for one person. That means for a family of five someone is going to be spending four or five hours a day doing nothing but grind. It’s very exhausting, grinding.

It’s particularly fascinating when she gets into why milling came later to mexico (has too do with the consistency and nutrition of corn that’s ground while dry vs corn that’s ground wet). I wish I had time to say more on this subject, but I’m only one week out from my qualifying exam and falling to pieces mentally (which I’m told is all a part of the process).

h/t The Agricultural Biodiversity Weblog

June 3, 2010


Filed under: Uncategorized — James @ 8:23 pm

So this was not the week to embark on an epic tale of transposons. Just got back from lab and I’m completely beat. The last two installments of transposon week are really cool stories and I want to do them justice. Will try to have them up as soon as I can manage.

Transposon Mutagenesis

Filed under: biology,genomics — James @ 12:30 am

In yesterday’s Transposon Week post, I discussed how transposons can spread through a species by without providing any benefit to the animals, plants, fungus, or micro-organisms that host them.

Adding a little extra useless DNA doesn’t help an organism survive, but it also doesn’t cause serious harm. But in yesterday’s post I completely avoided one serious question:

When new copies of a transposon get inserted across the genome, what happens to the DNA they land in? For what matter, what kind of DNA do transposons land in in the first place?

The answer to the second question is that different kinds of transposons each have their favorite places to land in the genome. Some transposons like to land in centromeres. Some transposons like to land in other transposons. Some transposons like to land near genes.

Then there are transposons like Mutator. Mutator is a maize/corn transposon that really likes to insert itself into genes. Transposons that usually land in other parts of the genome are also sometimes found in genes.

When a transposon lands in a gene, whether because that’s where it likes to insert or simply by accident, the gene stops working. Depending on which gene has to misfortune to interrupted by a transposon, the effects can range from so-subtle-we-can’t-even-detect-them to so lethal the organism dies before we get a chance to study it. In between are a whole range of effects. From severe developmental mutants, to gorgeous and apparently random streaks of color in flowers, to the spotted corn kernels which were my first introduction to the world of transposons.* (**)

Transposons are always breaking genes. The deadliest mutations disappear from the population as quickly as their appear. More subtle mutations can linger on for generations given rise to all sorts of genetic disorders. And keep in mind many genes can be broken with no visible effect at all. Anything you eat from asparagus to zuccini has the potential to contain genes broken by transposons. And depending on the gene, you’d probably never even know it.

Sorry to put this post up so late (it’s technically already Thursday) and in such a poor shape. I had some craziness in lab today and was waiting (unfortunately without any luck) to hear back about some more interesting stories I could tell about the Mutator transposon.

*To be fair, the last two are actually caused by transposons jumping OUT of genes allowing them to resume their normal function. The original mutations caused by transposons inserting into genes were to break the biochemical pathways used by Dahlia’s to make red pigment in their petals and by corn to produce purple pigment (anthocyanin) in its kernels.

**I really wish there was a good source of freely usable pictures things like transposon sectors in flowers and corn kernels. I can usually find pictures of normal plants on Flickr with creative common licenses. But I really want to be able to show you guys the cool mutants that make genetics so exciting.

June 1, 2010

Transposons: The Difference Between Junk DNA and Selfish DNA

Filed under: biology,evolution,genomics — Tags: — James @ 3:47 pm

Tranposons are one of those really cool features of genomes that never really seem to make the jump into the public eye. Most people at least have some conception of what a gene is. It’s a piece of DNA that contains the instructions for making a protein plays some role in the cell. A lot of other people can recall hearing an off-hand statistic only some tiny fraction of the human genome is made up of genes, with the rest being “junk DNA”. The question of why most of our genomes have no apparent function is why there’s a slow trickle of scientific research that gets picked up in the popular press as “scientistists discover junk DNA not junk after all!”.

But the reason most of genetics-genomics people aren’t in a huge rush to discover the hidden function behind most of this “junk DNA” is because we KNOW what most of it does and where it comes from. It’s not junk, it’s selfish DNA. <– although there’s certainly lots of cool stuff remaining to be discovered in the much smaller fractions of genomes we can’t classify at all. (more…)

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