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

December 31, 2022

More Professors Should Start Companies #1: Autonomy

Filed under: Uncategorized — James @ 12:41 pm

One of the great things about academia is that is gives smart and motivated people without the social skills to do well in corporate world a way to be engaged and contribute to society.

I don’t do well with bosses. The one exception I ever ran into was my grad school mentor who was wildly known as somebody who gave grad students an enormous amount of freedom and autonomy. To the point that about half the students who joined his lab struggled with feeling directionless and to graduate in even seven years. The other half of students to join his lab seem to have loved and and gone on to be extremely successful professors and leaders in industry. Every other person I’ve worked for I’ve butted heads with consistently. Getting older I’ve gotten better at “managing up” but I still don’t enjoy it.

One of the great things about being a professor — especially a tenured professor — is that we can spend a lot of time feeling like we don’t have a boss. My poor department head (whose priorities I don’t agree with but who is a perfectly decent human being) has something like 70 direct reports most of whom she cannot hire or fire. Academia is a good place for people who don’t do well taking orders … but launching your own company is even better.

Do you know how long it took me to get a raise for my amazing lab manager in my academic lab? Four months. At least ten meetings with three different people. Biweekly follow up e-mails. Multiple appeal forms and reworking of position descriptions while crossing my fingers and doing my best to combat the bitterness I see setting in to an enthusiastic and motivated scientist who can’t understand why it’s taking me so long to follow through on the raise we’d discussed months ago. Responsibility without authority sucks. A lot.

Do you know how long it took me to get a raise for an outstanding plant breeder in one of my companies? Three minutes. Me to co-founder: “We should really raise $X’s pay, he’s taken on so much extra work this year.” co-founder to me: “I agree. How about $Y,000?” “Sounds good. I’ll e-mail our HR contractor.”

The same relative ratio of work applies to buying a piece of equipment. Or renting new space as your team grows. Or paying an invoice. Or hiring a new person. In academia I typically have to fight through layers of people whose job it is to make sure I don’t do the wrong thing and get the university in trouble. At the startup we just decide, it happens, and if we make a mistake we deal with the consequences.

Of course the power to give your team raises doesn’t matter if we don’t have money to pay that new higher salary. Securing the money to be able to do stuff is a big thing both professors and founders put a lot of their time and effort into. But that’s a discussion for part two.

December 19, 2022

The Paspalum Genome

Filed under: agriculture,biology,genomics,Plants — James @ 4:41 pm

A paper eight years in the making and sixteen months in review. A real credit to Guangchao. I don’t think it ever would have come out without his dedication above and beyond what anyone could expect from a postdoc – James.

A team of researchers, led by Dr. Guangchao Sun and Prof. James Schnable of the University of Nebraska just published the genome of paspalum (Paspalum vaginatum) alongside evidence that paspalum may employ some tricks that could help its relative, corn, grow better with less fertilizer. 

Illustration of a paspalum vaginatum inflorescence.
A flowering paspalum plant growing in the University of Nebraska’s Beadle
Center greenhouses.

The Nebraska team, in collaboration with researchers from the Department of Energy’s Joint Genome Institute, the University of Georgia, and the HudsonAlpha Institute for Biotechnology, wanted to use the new genome sequenced this resilient grass to understand what makes the grass so much more stress tolerant that closely related crops, including corn and sorghum.

Using comparative transcriptomic and metabolomic analyses of paspalum, corn, and sorghum under optimal and stress conditions they identified a specific metabolic pathway — trehalose — that was being produced in paspalum, but not in corn and sorghum, in response to stress. 

The team used a strategy called chemical genetics to convince corn plants to also start producing and accumulating trehalose and showed that these corn plants grew faster and larger in conditions without enough fertilizer than corn plants without extra trehalose. Finally, the team used a combination of experiments to show that the reason these corn plants were able to grow more with less fertilizer was because of a process called autophagy, essentially a recycling program within plant cells that breaks down old, damaged, and unneeded proteins into spare parts that can be used to make new proteins. 

Guangchao Sun working with Aime Valentin Nishimwe measure nitrogen stressed plants in the Schnable lab at the University of Nebraska-Lincoln
Dr. Guangchao Sun working with Aime Valentin Nishimwe to collect data from
plants grown without enough nitrogen fertilizer.

“I’m so excited to see this story come out,” said Prof. Schnable, who is currently taking leave from the University of Nebraska while working at Google. “Paspalum is vegetatively propagated which means we cannot just save seeds, we always have to keep living plants for our research. There was a period where no one remembered to water the paspalum plant for a couple of months. But the plant was completely fine. In fact it usually grows so fast it’ll try to invade the pots of neighboring plants and the greenhouse manager has to yell at me or folks in my lab to come down and trim it. With this genome sequence and all the great work Guangchao Sun and the team have done, we finally are starting to understand just what makes this plant so

Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nature Communications 13, 773 (2022) doi: 10.1038/s41467-022-35507-8

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