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

April 3, 2017

A new chapter

Filed under: Feeding the world,Site Business — James @ 2:38 pm

Whatever anyone tells you, remember to play to your greatest strengths, not your weaknesses.

March 14, 2010

And the list gets better!

Filed under: genomics,Site Business — James @ 4:02 pm

Based on e-mails and responses to my previous post I’ve made the following additions to the sequenced plant genomes page:

  • Added an entry on Columbine, a member of an early diverging group of eudicots. As far as I can tell this sequence is currently unreleased, but from the JGI website it looks like the initial assembly is already complete, so if you know of a way for people to get ahold of that let me know.
  • Added an entry on the Castor Bean. The sequencing group has released a 4x coverage genome assembly. (The castor bean is the source of the deadly toxin ricin, and is not grown in the US, we import our castor oil from other countries.)
  • Split the entry on Arabidopsis into “Arabidopsis species and allies“. This gives the Arabidopsis lyrata its own heading, and will be important since there are another 7 species from the Arabidopsis genus and its close relatives in the JGI sequencing pipeline.
  • Added an entry on v2 of the date palm genome generated by Weill Cornell Medical College in Qatar. This definitely should still be considered an “in progress” genome, but at least until the banana genome comes out it’s the best non-grass monocot genome available.
  • Added an entry on the genome of Physcomitrella patens, which, as a moss, is the descendant of an evolutionary lineage that split from all the other genomes I’ve listed on the page around 450 million years ago.
  • Added the recently announced sunflower genome project to the list of planned, in-progress, and private genome efforts. (Apparently the genome of the cultivated sunflower is more 3 gigabases. Bigger than corn!) That’ll be a cool genome to see when it comes out.
  • Added information on the woodland strawberry genome project, which aims to have an assembled genome of Fragaria vesca by sometime this year. You may remember the woodland strawberry genome from the mix up back in January.
  • Added the various groups that have announced they have private genome sequences of the oil palm genome to the same section.

Particular thanks to Greg, Jeff, and Eric whose suggestions where behind most of these additions.

Completely unrelated, you may have noticed I switched the RSS feed back to full length entries. I recently tried out Google Reader (I’m way behind the times I know), and it is SO MUCH nicer to see the full entries there than have to click through from a brief summary. The downside, as I know from previous experiences, is that when I send out the full entries by RSS I get a lot less traffic.

I don’t earn any income from traffic to this site, but it is a nice feeling to know people are reading and enjoying something I wrote, and I have no way of tracking how many people (if any) read an article from the RSS feed.

Anyway I’ll keep sending out full entries for at least the next week (I expect I’ll be too busy to worry about ego stroking traffic statistics until at least a week from Tuesday.)

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.

January 15, 2010

It’s Been Two Years!

Filed under: Site Business — James @ 9:44 am

…since my first entry. I wish I could call it a lengthy piece of insightful writing, but sadly, it is not.

With two years of data I can say that there’s a hint of an annual pattern to my writting with greatest number of entries being written in the final months of the calandar year and the least during the summer months. But two 1-year datasets isn’t nearly enough to prove a trend, simply suggest one.

It’s been a lot of fun to become more engaged in the online community the past couple of years,particularly the last six months or so as this site slowly transitioned from a cool new computational toy to mess around with, to a way of communicating with friends and family, to (what I now like to imagine is) a place that’s telling interesting stories about plant genetics to people, some of whom I’ve never met, who might not have come across it otherwise.

When considering what ancient quotes to dig up from the archieves for this entry, there really wasn’t much contest. From Another Day of 10,000 Interviews (talking about part of my visit to Berkeley to interview for the graduate program I later joined):

This time I have seven[interviews]. Three with faculty, and four with the labs of absent professors. And I can honestly say that I walked out of each interview very excited about the science in that lab. … the grad students here at Berkelely seem happy.

And from Wrap up in Berkeley (the same visit):

I still can’t get used to palm trees. I’ve seen them in movies, but then again, I’ve seen velociraptors in movies too, and in my mind they both have about equal business showing up in the real world where people go about their daily business.

January 13, 2010

No strawberry genome ::sniff::

Filed under: Site Business — James @ 12:26 am

From the article on the genome at scienceblog.com:

Contrary to the information posted in the article on January 11, 2010, the strawberry genome sequence has not been completed or released.

The news release above was a premature and highly inaccurate dissemination from the USDA. The strawberry genome has not been published, it has not been released, and analysis is not complete.

The genome of diploid strawberry (Fragaria vesca) will be sequenced and released in 2010. The effort was led by an international consortium representing over 40 institutions and the efforts of countless researchers. Details can be found at strawberry.vbi.vt.edu.

A formal presentation of the current state of the draft sequence was presented by Dr. Vladimir Shulaev at the Plant Animal Genome Conference in San Diego on December 9th, 2010 (editor’s note: as pointed out in the comments this was almost certainly intended to read January 9th, 2010). This presentation was potentially misinterpreted as a formal announcement, and a conversation with a scientist on the project laced the above article with inaccurate interpretations.

The draft sequence will be published shortly after complete analysis and peer review. The above article is not accurate in many facets and should not in any way be considered representative of the scientific efforts of the Strawberry Genome Sequencing Consortium.

The work was also supported by many organizations in addition to Roche, with substantial financial and other commitments from sources including (but absolutely not limited to) Virginia Tech, IASMA Research Center (Italy) University of Florida, Driscoll’s Strawberry Associates, Plant and Food Research (New Zealand) and the USDA.

A formal retraction of the initial press release is being pursued.

Kevin M. Folta
University of Florida, on behalf of Dr. Vladimir Shulaev and the Strawberry Genome Sequencing Consortium

From the outside it is hard to know exactly what happened but clearly SOMEONE jumped the gun and the internet echo chamber, of which I’m apparently now a component, swung into motion.

My apologies go out to everyone involved in the strawberry genome sequencing project, and anyone who was reading about the woodland strawberry genome here who got as excited as I did about the possibilities.

I’d still be fascinated to load a pre-release version of the strawberry genome into CoGe when/if it becomes available. And speaking as someone who has done gene annotation work previously on an newly sequenced genome CoGe is a GREAT tool to have  when one is sanity checking gene models and contig assembly.

January 12, 2010

Ideas on why plant genomes rule?

Filed under: Site Business — James @ 1:11 pm

I’m considering starting a series on several ways that plant genomes can take more punishment than mammalian genomes and survive. Right now I can think of:

-Methylation knockouts

-Telomerase knockouts (for a few generations) and tissue culture for decades

-Whole genome duplications/and aneuploidy

Can you think of any other examples of things plant genomes can survive better than animal genomes? (Or counter examples of things that are horrible for plants but that animal genomes can shrug off without ill effects?).

I’m not asking anyone to do my research for me, I’ll track down the papers for myself. But in finding research results, like many things, knowning they’re there to be found is half the battle.

December 31, 2009

Year End Wrap Up

Filed under: Site Business — Tags: — James @ 3:46 pm

Happy New Year’s Eve! (or New Year’s Day, I know I have at least a few readers in the eastern hemisphere)

I figured the last day of the year would be a fun time to look back as some of the posts from earlier in the year. I was originally going to do a top five most popular entries of the year but first of all, the list is dominated by my coverage of the maize genome and even if I condense that inside a single item, the list would still be dominated by recent entries (the result of a take off in readership over the past six months, thank you guys!) so instead I picked some entries I particularly enjoyed writing.


December 19, 2009

Lack of Daily Updates

Filed under: Site Business — James @ 1:48 am

Just a quick update. I’ve been trying to keep a couple too many balls in the air, with the result that I have, unambigiously, ended my stretch of daily updates (and basically dropped off the face of the internet).

Anyway, to any loyal readers, I intend to return to daily updates either after Christmas or at the start of the new year. I’ve proven I can do it. It’s just a matter of making the time.

November 26, 2009

Happy Thanksgiving!

Filed under: food,Link Posts,Site Business — Tags: , — James @ 9:59 am

In recognitions of the huge feasts many of us are or soon will be sitting down to, let us take a moment to think about the very fact that vast range of different foods human beings can eat might be the very reason we out competed other hominids (specifically neaderthals) with more specialized diets. Our ability and willingness to eat almost anything may have been the crucial edge we needed.

Picture a small, warm valley in Northern Europe that supported enough deer, wild cattle and sheep to support a band of neanderthals. If they reproduced too much (or another band of neanderthals moved in), the now-unsustainable harvest of prey would force them to disperse to better hunting grounds, and in time, with relaxed predation, the prey would likely repopulate the valley.

But if a band of humans moved in, they may not only help over-harvest the big game, but also refuse to leave when the game ran out. Maybe there’s still good year-round living to be made on rabbits, seeds, fish, grubs and berries. And while they’re out gathering, they’d certainly help themselves to any of the (now rare) big game that they came across.

Read more in MAT Kinase’s exciting post on the subject over at The Scientist Gardener.

In addition to the many other things I am grateful for, from my amazing family, to being able to work on such interesting science surrounded by such wonderful fellow researchers, and all the many other things that aren’t of any interest if you don’t know me personally, I am grateful for a digestive system that can handle fungus and the milk produced by other species to feed their own young, and insects, and grains, and fruits, and vegetables (including some vegetables that are just glorified leaves), and, of course, delicious turkey.

Edit: I’m also very thankful for readers of this site, and the fellow authors I’ve discovered through my writing here, too numerous to name. It’s good to know I’m not alone in my attempt to bring the public and science back together.

Edit 2: I also just realized this is my 250th post in 22 months writing on this site!

November 25, 2009


Filed under: Site Business — Tags: , — James @ 1:02 am

So I’m about to depart on what promises to be a 14 plus hour journey back to the land of corn (maize), porkburgers, and possibly snow. This couldn’t be coming at a worse time in the submission process for the paper my lab is trying to get out the door. Never before have I so closely mapped out my travel times and when I’ll have internet access. I kind of like it. I’ll be out of town until Monday and if I’m pulling long hours on the computer instead of seeing friends and family it’s going to be in pursuit of publication not internet fame and fortune. Anyway I’ve got a few ideas about content over the thanksgiving holiday but I’m afraid I can’t promise many 200+ word updates. Here’s wishing everyone a happy Thanksgiving tomorrow.

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