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

March 6, 2017

Some thoughts on open science and the power of defaults

Filed under: Uncategorized — James @ 12:15 pm

Tomorrow I’m driving out to St. Louis for four back-to-back related meetings. Genomes to Fields, Corn Breeding, MaizeGDB, and Maize Genetics Conference.

For the 3rd year in a row the Maize Genetics Conference is going to operate under an “opt in” social media policy. Unless people explicitly opt in, attendees are forbidden from discussing talks or posters on social media (presumably this include blogs). Seven years ago, at my second maize genetics conference ever, I would have been in violation of this policy (if it had existed at the time) because I wrote these two posts. I know one of the authors well and he’s never expressed any concern over that post, and, while I’ve only met the second author in passing, I’m guessing she wasn’t bothered by my post since she cited it in her masters defense announcement.

In principle opt-in and opt-out should give identical results, but we know from a number of natural experiments that this is not the case, and that changing between these two can be used as a small nudge to produce socially desirable outcomes. (more…)

August 31, 2015

A worrying trend

Filed under: Uncategorized — James @ 10:59 am

Worrying_Trend

August 24, 2015

There are undergrad EVERYWHERE!

Filed under: Uncategorized — James @ 9:00 am

Which I suppose is not an unexpected development on the first day of classes for the fall semester. But it holds a special something this year. This semester for the first time as an actual assistant professor… I have to teach. First lecture tomorrow. Wish me luck, because I’m going to need as much of it as I can get.

My previous teaching experience was heavily weighted towards being a TA in multiple “science for non-majors” courses, which could have been a lot of fun. Unfortunately, each course had a reputation as an easy-A which attracted students who had absolutely no interest in the material.

Tomorrow should go a lot better than that. Much smaller class, specifically for the major, teaching material I developed myself. … fingers crossed….

August 20, 2015

Mini-Foxtail Millet

Filed under: Uncategorized — James @ 9:51 am

It’s even smaller than mini-maize!

Developed by Xianmin Diao at CAAS and growing just outside of Beijing, China

Developed by Xianmin Diao at CAAS and growing just outside of Beijing, China

 

And here are the wonderful group on researchers who work on Setaria italica (foxtail millet) at the Chinese Academy of Agricultural Sciences.

IMG_0592

Just got back from a two week visit to China that let me catch up with a lot of old friends and collaborators as well as hopefully making a few important new connections.

Five cities (Shanghai, Tai’an, Wuhan, Chengdu, and CAAS) and seven presentations in fourteen days. And classes start on Monday.

July 28, 2015

The race between foxtail millet and green foxtail continues

Filed under: Uncategorized — James @ 3:03 pm

At 32 days after planting, the wild species (Setaria viridis, A10.1, green foxtail) takes a commanding lead in life cycle over the domesticated crop (Setaria italica, foxtail millet).

 

Domesticated foxtail millet on the left, wild green foxtail on the right. Both 32 days after planting.

Domesticated foxtail millet on the left, wild green foxtail on the right. Both 32 days after planting.

But don’t despair, you fans of working with domesticated species: Foxtail millet still have a good chance of taking the lead in the generations per year game. After they are harvested seeds from that green foxtail plant won’t be ready to germinate for months, while the foxtail millet seeds can be planted as soon as they are mature enough to harvest.

July 19, 2015

Narrowing in on Setaria viridis

Filed under: Uncategorized — James @ 11:31 pm

So I’m now confident the Setaria photo in the last post was yellow foxtail (Setaria pumila). One of the key diagnostic criteria is the larger spikelets of yellow foxtail relative to green foxtail (Setaria viridis), which sounds fine on paper, but you need a reference point to compare against. Now I have one. This is either Setaria viridis or Setaria faberi* but either way you can see the much smaller spikelets than yellow foxtail.

Setaria viridis or Setaria faberi. Setaria faberi is an allotetraploid formed by a cross between Setaria viridis and a closely related species.

Setaria viridis or Setaria faberi. Setaria faberi is an allotetraploid formed by a cross between Setaria viridis and a closely related species.

Setaria pumila (yellow foxtail).

Setaria pumila (yellow foxtail). Click to zoom.

*From the description of Setaria faberi “Characteristic foxtail-like seedhead that droops when mature and leaves with many hairs on the upper leaf surface, which helps to distinguish this weed from both Green Foxtail (Setaria viridis) and Yellow Foxtail (Setaria glauca**). Giant foxtail may be identified by the presence of many short hairs on the upper surface of the leaf blades, unlike the other foxtails.”

Source: Division of Plant Biology, University of Missouri: http://weedid.missouri.edu/weedinfo.cfm?weed_id=256

 

July 17, 2015

Procrastinating by making figures (part #1)

Filed under: Uncategorized — James @ 3:44 pm

Part #1 of a likely infinite part series.

Today’s innovation was figuring out how to manually set the exposure/AEB setting on the camera so images didn’t look frightening washed out when photographed against a traditional black background.

So here’s today’s procrastination figure:

Post-anthesis Setaria italica (foxtail millet)

Post-anthesis Setaria italica (foxtail millet)

Of course we really should compare to the wild progenitor, Seteria viridis (Green foxtail). Unfortunately, our Setaria viridis isn’t flowering the greenhouse yet. Fortunately, my tomatillo batch at home is prone to weeds. Unfortunately, I’m not enough of a botanist to code this plant out beyond the genus level. The image below is either Setaria viridis (the direct progenitor of Setaria italica), or (according to the list of grasses native to Nebraska) it could be Setaria faberi, Setaria pumila or Setaria verticillata. I’m reasonably confident it isn’t S. faberi or S. verticillata but S. pumila (Yellow foxtail) is a real possibility. Actually, the more I read about it the more I think this is Setaria pumila given the largish spikelets and tan color of the bristles.

Either Setaria viridis (green foxtail) or Setaria pumila (yellow foxtail). Actually, the more I read about it the more I think this is Setaria pumila.

Either Setaria viridis (green foxtail) or Setaria pumila (yellow foxtail). But probably yellow foxtail…

Study of the S. viridis clade also needs to include S. pumila (Poir.) Roem. & Schult., a common weed that often grows in mixed populations with S. viridis and its relatives. Although it appears to be of African origin (Rominger, 2003) and is not closely related to S. viridis in phylogenies (Doust et al., 2007; Kellogg et al., 2009), the ecological preferences of S. pumila are similar to S. faberi and S. viridis (hereafter collectively the “S. viridis clade”).*

So just a tiny bit of DNA sequencing would answer my question once and for all….

In the meantime, I’ll just have to wait for our validated S. viridis plants to flower. Currently twenty one days after planting.

Foxtail millet (Setaria italica genotype Yugu1) on the left hand side and green foxtail (Setaria viridis genotype A10) on the right hand side. Both plants are 21 days old. Note that Yugu1 is significantly taller but unbranched, but the A10 accessopm of green foxtail has already started producing tillers.

Foxtail millet (Setaria italica genotype Yugu1) on the left hand side and green foxtail (Setaria viridis genotype A10) on the right hand side. Both plants are 21 days old. Note that Yugu1 is significantly taller but unbranched, but the A10 accession of green foxtail has already started producing tillers.

 

*Daniel J. Layton and Elizabeth A. Kellogg “Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives” Am. J. Bot. March 2014 101:539557 doi: 10.3732/ajb.1300428

July 14, 2015

Fun Grass Inflorescence Pictures

Filed under: Uncategorized — James @ 11:48 am

Remember how similar grass species look prior to flowering? Flowering is a whole different story. Here’s a couple of nice pictures we took in lab this week now that we’re no longer constrained by the use of cell phone cameras. (Click to zoom in to a ridiculously high resolution.)

Dichanthelium oligosanthes is a wild species. We're collaborating with the Studer lab at UIUC in some comparative biology on the species. So few seeds per inflorescence! (At least we're lucky enough that each plant produces a lot of these infloresences, or building up a significant reserve of seeds would really be impossible.)

Dichanthelium oligosanthes is a wild species. We’re collaborating with the Studer lab at UIUC in some comparative biology on the species. So few seeds per inflorescence! (At least we’re lucky enough that each plant produces a lot of these infloresences, or building up a significant reserve of seeds would really be impossible.)

Japanese_millet_head

Japanese millet inflorescence. Lots of big seeds forming here. If you click and zoom in to the maximum resolution, you’ll be able to see the anthers hanging out of many of the individual spikelets.

If I am lucky our Paspalum vaginatum will flower sometime in September. Until them I’ll continue to use this blurry iPhone photo.

Paspalum vaginatum flower. September 2013

Paspalum vaginatum flowers. September 2013

June 24, 2015

Depressing predictions about the future

Filed under: Uncategorized — James @ 8:15 am

Now for something not directly related to plant biology:

After 300 years of breathtaking innovation, people aren’t massively unemployed or indentured by machines. But to suggest how this could change, some economists have pointed to the defunct career of the second-most-important [Editors note: Animal] species in U.S. economic history: the horse.

For many centuries, people created technologies that made the horse more productive and more valuable—like plows for agriculture and swords for battle. One might have assumed that the continuing advance of complementary technologies would make the animal ever more essential to farming and fighting, historically perhaps the two most consequential human activities. Instead came inventions that made the horse obsolete—the tractor, the car, and the tank. After tractors rolled onto American farms in the early 20th century, the population of horses and mules began to decline steeply, falling nearly 50 percent by the 1930s and 90 percent by the 1950s.

Source: http://www.theatlantic.com/magazine/archive/2015/07/world-without-work/395294/

The whole article is quite long, but made for an interesting read. For further thoughts in this area, check out the Plant Money “Will Your Job Be Done By a Machine” calculator. Plant biologists apparently aren’t common enough to be listed, but the odds for the biology-related fields* are low enough I’m not ready to run for the hills just yet … despite the fact that robots like this one are now being field tested in labs back in California.

*Animal Scientists are at 6.1%, Microbiologists are at 1.2 % and Medical Scientists are at 0.5%, so

June 23, 2015

Updated albino corn

Filed under: Uncategorized — James @ 9:26 am

A few days later, that albino corn plant I was complaining about has matured a lot.

 

Albino corn 10 DAP

Albino corn 10 DAP

One of the grad students has decided to transplant it and see how long it will manage to survive in the complete absence of photosynthesis.

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