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

February 16, 2010

Newer Tighter CoGe-MaizeGDB demo

Filed under: Computers and Coding,research stories — Tags: , , — James @ 1:08 am

I invested in a new video capture program that lets me record voice overs in real time. There are a few more ums and uhhs but my voice and the action on screen are in much better sync, and I don’t find myself rushing to keep up with the movements of my own mouse or trying to fill apparently dead time while nothing happens on screen. The new video is also two minutes and fifteen seconds shorter, dropping below the psychologically important 5 minute barrier, above which watching a video starts to feel a lot more like work, and I get to show off two new features (visually flagged tandems, and predictions of where a gene would have been before it was lost) that we’re still in the process of rolling out.

Sorry to harp on the same topic a second time, this video is just SO MUCH BETTER than the previous one and I needed to show it off. 😉

February 15, 2010

The Color of Corn and Cultural Values

Filed under: Feeding the world,food,Plant breeding — Tags: , , , , — James @ 8:49 am

MAT_kinase has sparked an interesting discussion about the associations people have with corn of different colors. I’d previously heard that yellow corn (where pre-vitamin A carotenoids are produced in the kernels) isn’t popular in Africa, with the reason usually being given as its association with American food aid.* If yellow corn comes predominantely from food aid, it eventually becomes associated with being poor and/or starving, so that when people have a choice they eat other varieties of corn. I can’t find where I read it, but I vividly remember reading an interview with a woman who talked about the shame of eating yellow food-aid corn, knowing that it had originally been intended to feed livestock in the US, not people.

MAT points out another more pragmatic reason yellow corn may not be favored in Africa that I hadn’t heard of before. Apparently the extra carotenoids make yellow corn more susceptiable to spoilage than white corn varieties, a very pertenent issue in areas without access to the kinds of storage facilities we take for granted in American agriculture.

Jeremy at the Agricultural Biodiversity Weblog picked up the torch, highlighting a number of their own previous posts relevant to the discussion, including one by fellow blogger Luigi that relates the reaction of his own wife, originally from Kenya, on ordering polenta** at a restuarant and receiving a yellow dish.

Fortunately breeds of corn that contain even more beta carotene (the carotenoid most easily converted into vitamin A by our bodies) aren’t even yellow all the time. Although I wasn’t able to find a freely available picture, sometimes they’re ORANGE.*** While it turns out the correlation between color and beta carotene content isn’t perfect****, there’s still reason to hope varieties bred for the highest pre-vitamin A content will end up a striking orange color. For a visual examples of how orange corn can get, check out check out Dr. Rocheford’s lab website.

Will the distinction between orange and yellow***** be enough to get over the Africa’s lack of enthusiasm for yellow corn? Will the benefits of a diet with more vitamin A be enough to outweight the issues with yellow corn going “off” if stored improperly? I certainly hope the answers to both these questions are yes, but we won’t know for sure until we try. And there are some hopeful signs. For example this segment in a story from NPR: (more…)

February 13, 2010

Plant Links of the Day: Diverse Citrus, Extinct Cucurbits, and more

Filed under: Link Posts,Plants — Tags: , — James @ 9:27 am

When I woke up (which yes, was only a couple hours ago, but remember I’m on pacific time) I found a whole bunch of interesting plant links waiting in my RSS reader, and I thought I’d pass along a few to you guys.

Keith Robinson writing over at Omics! Omics! posted Celebrating Citrus where he catelogs some of the diversity available to him from local grocery stores before pointing out a citrus review article that suggests all that diversity can be traced back to only three wild species and wraps it up by pointing out the project to sequence the sweet orange genome.

Imagine if you could have a whole series of clementine-like fruits, with the size & easy peeling characteristics but with the whole range of other citrus flavors and colors genetically grafted in — cara cara clementines and blood clementines and ruby red clementines and perhaps even sweet lemontines and key clemenlimes.

Highly recommended.

The Biogeography of Darwin’s Gourd is a post I discovered through research blogging (speaking of which I should really write another entry that meets their standards some day). The gourd of the title is Sicyos villosus, a cucurbit (the group of plants that includes squashes, melons, and pumpkins) collected by Darwin from one of the islands in the Galapagos the better part of two centuries ago … and never again recorded by science. At this point the dried sample collected by Darwin may be the only existence the species ever lived:

The analysis of the cucurbit’s DNA, extracted from the seed samples taken by Darwin, revealed that S. villosus is closest in relation to cucurbits in North America and Mexico. The species probably diverged roughly 4 mya, when the Galapagos were still geologically young. Dispersal was not human in origin, meaning long distance from the mainland, potentially from its spiny fruits stuck to birds, the authors suggest.

How cool is it that we can learn so much from a single sample of a species that has otherwise vanished from the earth?

Finally, by way of DailyKos, comes a pointer to this valentine’s day themed article, clearly written for the non-scientist, where a summary written by me seems superfluous given the title: Sex, Drugs, and Paleo-botany! And yes, the exclamation point is in the original title as well.

February 12, 2010

Easy DNA extractions (with pineapple!)

Filed under: teaching — Tags: , — James @ 2:00 pm

First wet lab work I've done in more than a month. Also how often do you see a bottle actually LABELLED as "Strawberry DNA extraction"?

It’s actually quite easy* to extract visible quantities of DNA from fruits and vegetables using nothing less common than dish soap and rubbing alcohol. For our class we chose strawberries, but I also heard of people using kiwis and bananas to great success.

Of course it takes a mere second for someone to say “I don’t eat food with genes in it” and 15 minutes to prove them wrong by extracting DNA from an (organically grown) banana, but that imbalance between the time and effort it takes to repeat piece of false information and the time it takes to refute that same misinformation isn’t going to change. It is something anyone in the habit of going up against misconceptions with nothing but demonstrable facts on their side has to get used to.

The demonstration itself went pretty smoothly. Unfortunately, since it’s a hundred student lecture, we had to do most of the preparation beforehand, so I don’t think most of them realized just how easy DNA extractions can be.

*Note that this recipe calls for the use of meat tenderizer to break down some of the remaining proteins in the solution before extracting DNA, and points out that pineapple juice will make an acceptable alternative (as it also contains enzymes that break down proteins.) I mention this only to reiterate my point, as if you hadn’t heard it before, that pineapples are one of the most awesome fruits known to mankind.

February 11, 2010

Why to Celebrate the Publication of the Brachypodium Genome

Brachypodium distachyon (photo courtesy of Devin O'Conner)

Sorry this is late going up. -James

This morning Nature officially published the paper* describing the sequence of the Brachypodium distachyon genome. This publication brings the number of grass genomes available for comparative analysis to four. In celebration I’m going to list four reasons to be excited about the publication of this genome.

The location of Brachypodium within the grass family tree.

Brachy (as I will refer to the species from here on) is a member of the Pooideae a sub-family of grasses from which no sequenced grasses have come. For the work we do in my lab this is exciting because it adds more depth to our analysis of changes in the grass genomes. The more distantly related grasses we can compare at the whole genome level, the better we can infer what the ancestral species that gave rise to all the grasses might have been like at a genome level. The most we know, or can make educated guesses about that species, the better position we are in to say what changed along the evolutionary paths leading to grasses like maize, rice, and sorghum. The choice of the Pooideae wasn’t at random, or even because of the sub-family’s distant relationship to other sequenced grasses. (more…)

February 10, 2010

The top ten instutitions attending the 52nd Maize Meeting this March

Filed under: Fun With Numbers — Tags: — James @ 11:54 am

As determined by the domain names of 402 e-mail addresses that were recently revealed.

  1. Cornell University
  2. Google <– gmail.com was the second most common domain name among these e-mail addresses.
  3. Cold Spring Harbor
  4. University of Guelph
  5. Iowa State University
  6. University of California-Berkeley
  7. University of Florida
  8. UMR de Génétique Végétale du Moulon*
  9. (8) Purdue University*
  10. Syngenta

Overall a total of 134 organizations (or at least domain names) were represented in the list of e-mail addresses of attendees in my possession. If I could dig up historical data it’d be interesting to see how the rankings change over time.

Doing this sort of analysis very quickly (generating the data for this post took ~4 minutes, I timed myself) is one of the fringe benefits of learning even a little about programming.

Official 52nd Maize Meeting website.

(You see what happens when a guy has too much caffeine and then has a chunk of time too short to get any real work done?!)

*These two institutions are tied for number of attendees

February 9, 2010

India and Bt Brinjal/Eggplant

Filed under: agriculture,Feeding the world,Politics — Tags: , , , — James @ 8:32 pm

India has delayed the introduction of their insect resistant eggplants.

Read about it in:

MaizeGDB and CoGe: A Beautiful Friendship

Editor’s note: I have a new shorter, better, tutorial, here.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you. (more…)

February 8, 2010

The Taste of Tomatoes + Tomato Mutagenesis

Filed under: agriculture,Feeding the world,Genetics,Plants — Tags: , , , — James @ 4:21 pm

An anonymous indian tomato vendor in Chennai, Tamal Nadu. photo mckaysavage, flickr (click to see photo in it's original context)

First, since I didn’t explicitly state it in my previous post, the paper on the longer lasting tomatoes developed by India’s National Institute for Plant Genome Research didn’t report any data on how the RNAi knock-down tomatoes actually taste.* The tomatoes are nearly twice as firm as tomatoes in which these genes are NOT knocked down, so it’s possible they’d seem unpleasantly crunchy, I don’t know how doubling the firmness of a tomato translates into the feeling when a person bites into one.

On the other hand, if the tomatoes do turn out to be tasty and delicious, it’s quite possible the trait could be replicated without genetic engineering. And if that turns out to be true, it’s absolutely the approach anyone developing longer lasting farmers to Indian farmers, or farmers anywhere, should take (for why I’m saying this, check out the bit in bold further into this post). (more…)

February 7, 2010

Biofortified Also Covers Indian Tomatoes

Filed under: Site Business — James @ 8:28 pm

Check out Anastasia’s write up here, check it out! Especially if you’d like a better explanation of the synthetic micro-RNA technique used to knock down the tomato genes targeted in the paper.

My own write up from yesterday also just became my first submission to Research Blogging. My approval from the site just came through this afternoon (a real person had to check out this site and decide if I was serious enough to be allowed to submit posts!). Not sure how often I’ll be writing up Research Blogging worthy entries as they do require a much greater investment of time than my usual content, and I’m pretty sure my 500 word entries get read a lot more than my 1500 word ones anyway, but there are a couple of genome evolution papers that I’d love to talk about in detail when I have the time.

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