#ASPBPlantCellTuesday #ICYMI

#ASPBPlantCellTuesday #ICYMI

Bummed to see corn plants drawn so clearly wrong. The tassel does not magically turn into an ear on the top of the plant. Not a great look for a plant journal.

Interesting how I keep seeing papers say that QTL mapping of enzyme variation to metabolite to insect herbivory and tritrophic interactions hasn't been done before. #secmet

What if generalist pathogens aren't brute killers but poly-specialist perfectionists, optimizing to each host.

Settled for a long winters nap.

What are everyone's favorite papers showing that individual plant TFs function to coordinate primary and specialized metabolism? Rather than solely regulating a specialized metabolite. #secmet

An atmospheric holidays.

Every time a scientist says "my area of expertise takes years of training but I can learn the rest from a book" a chatGPT agent gets its wings. Every single gd time.

Reupping this perennial #MPMI question, has an apoplastic Superoxide dismutase been cloned and proven to take RBOHD O2-• into H2O2? Or are all the models still assuming?

Every time a scientist says "my area of expertise takes years of training but I can learn the rest from a book" a chatGPT agent gets its wings. Every single gd time.

Maybe the best way to really affect the companies suggesting genetics to design your kid .. Pass legislation making those companies legally and financially responsible for any and all known and unknown pleiotropies and epistatic interactions. Nothing better than unknown and unlimited liability.

An interesting aspect of transcriptomics on plant-pathogen interactions. The data exists to say that plant hormones don't have synergistic or antagonistic interactions, instead it is a property of the output gene. For example, there are lots of genes in the datasets showing SA-JA synergism. #MPMI

Elli Cryan, coadvised by @spicybotrytis.bsky.social and I, giving her exit seminar next week! Zoom link in the alt text

Interesting phenomena in pop and evo genetics, when you have loci or even sequences associated with a trait, that is considered generalizable information. Once you know the actual function of these genes their perceived generalizability inherently decreases. Even if the only change is knowing fnxn.

Last of the years pomegranates preparing for their starring role as a Christmas aperitif.

So if one wants to claim there are no RNA diffs between two genotypes, is it appropriate to use only technical replicates, only three samples per genotype, a higher than normal q threshold and a log2 threshold to call difference? Shouldn't that claim require the reverse, lots of reps, etc.

Convergence and constraint in glucosinolate evolution across the Brassicaceae (Amanda Agosto Ramos, Kevin A Bird, Annanya Jain, Gabriel Philip Sumo, Odinaka Okegbe, Lucy Holland, Daniel J Kliebenstein) doi.org/10.1093/plce... #PlantScience @aspbofficial

If one supports raising college football ticket prices to afford a better quarterback or O’line, I assume they think higher tuition is acceptable for a better university?

Happy to see this paper from my time with @spicybotrytis.bsky.social out in @theplantcell.bsky.social! Amanda, a fantastic PhD student with Dan, led this "phylo-functional" work & uncovered complex duplication & loss of a glucosinolate gene across the Brassicaceae affecting enantiomeric specificity

Camera picking up a smidge of northern lights in Davis

There are lots of answers out there that are beautiful because the truth of the system is beautiful. If I find one of these beautiful facts, it doesn’t make me brilliant. Just right place and right time. True scientific heroes acknowledge that fact.

How many other people teaching Genetics go into how Mendelian genetics concepts do not need DNA to be true? Or how Mendelian genetics does not inherently make causal arguments? Or how polygenic traits follow Mendelian rules?

Enzyme/GO overlap note of the week. Plant Glutathione-S-transferases might have more biosynthetic functions than ROS detoxification functions. Also, CYP450s are listed as redox genes but are almost all biosynthetic. So if you see ROS/Redox terms, take a glance to make sure it isn't biosynthesis.

I wonder how Ross Douthat from @nytimes.com is thinking his oped on current foreign policy success is aging? After only a week.

In plant-pathogen or plant-microbe interactions what is the proper null. - there is specific coevolution of any pathogen/microbe such that it was at least partly adapted to the host isolated. -the host of isolation may have not effected the pathogen in the slightest.

Why can’t an American brewery understand how simple is super tasty. No need for bourbon barrels, peanut butter, imperial, espresso, etc. just a solid brown/dark beer. Perfect fall yardwork break. Admittedly the Maui coconut porter is a guilty exception.

It is official, I am fully my maternal grandmother. The African violet is supposedly a cutting from hers.

So theoretical question, if one can shift a trait from oligo to polygenic simply by removing a large effect allele from the population, is there a real difference or is it just human desire to define?

Waiting for Ross Douthat at @nytimes.com to write an article about how the pope is wrong and that unrepentant violence and aggression against anyone is perfectly appropriate for a Catholic to support. While being pedantic about and around everything.

MPMI Terminology question - What simple phrasing would you use differentiate a plant response that happens to all members of a pathogen species versus the same plants response that is limited to one or a few pathogen genotypes in the species.

I'm thinking I should make this a weekly post - Does anyone have good literature on a anthocyanin biosynthetic mutant having a stress sensitivity phenotype in the wild beyond UV-B?

@planteditors.bsky.social, any good suggestions on how to erase writing from ones head? I'm teaching a couple of writing classes and realizing I can't erase the previous document from my head efficiently enough to pay full attention to the next. PS - Yes, I should not be teaching writing classes.

What makes me really happy is that someone as experienced as yourself continues to see the value of professional editors in helping improve the writing :)

Half of this years squash crop. All volunteer due to megafauna dispersal.

After having @planteditors.bsky.social look through a paper and only suggest a single wording change within the main text. Only took 24 years to get there. (Gotta love that caveat)

Host-pathogen cotranscriptome papers are really intricate to write as you have genes that are host influenced, pathogen influenced and interaction influenced in both the host and the pathogen.

Our article "Guns in Rosettes: The Arabidopsis chemical weapons arsenal" is finally published @plantphys.bsky.social! You can download the #OpenAccess PDF here: doi.org/10.1093/plph... But real connoisseurs of #AntimicrobialCompounds will want to get the vinyl boxset: #PlantScience #PlantImmunity

Thinking of the standard senntence saying “because plants are sessile they …”. Is the direction arrow correct? Or is sessile not a cause but a consequence? I.e. because plants are autotrophic, they are sessile.

If you were the predicting sort, how much of a plants metabolism would be in the following four categories? Primary Anabolism Primary Catabolism Specialized Anabolism Specialized Catabolism Feel free to define "how much" by gene #, enzyme #, flux fraction, etc. And your own 1 v 2 defn. #secmet

Breakfast in bed with new season butternut. A happy Mastiff

An interesting part of Brassica/Glucosinolate. There is so much myrosinase that the glucosinolates 1/2 life in herbivory is on the order of seconds. For any receptor signal to matter it has to cause significant effects in less time than seconds onlinelibrary.wiley.com/doi/10.1111/.... #secmet

Anyone have any literature on how yeast or other fungi detect plant phytohormones? I know they respond to them but am struggling with the search terms to find the genes that allow fungi to respond to plant compounds.

Fantastic PhD opportunity to join myself, Nicola Patron and @lichmanlab.bsky.social in uncovering the biosynthesis and function of lettuce sesquiterpene lactones. 4-year fully-funded combining molecular & engineering biology, & plant pathology. Deadline Nov 25th www.findaphd.com/phds/project...

Just an outrageous amount of structural variation in pennycress. While not yet reproductively isolated, its likely these shredded pericentromeres contribute to some reproductive incompatibilities.

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Having a 17 hand Gelding who likes to lean on fences means weekends are a bit of exercise.

NSF GRFP solicitation is out. www.nsf.gov/funding/oppo... • Have completed less than one academic year in a graduate degree program (according to the institution’s academic calendar; non-degree coursework must be clearly identified in the transcript and does not count toward this limit).

Colt; Why are we up so early? I had another hour of sleeping. Me; have genetics to teach at 8AM Colt; ha ha ha, who did you irritate? Me; eat your alfalfa. Colt; ha ha ha, munch munch munch

Fun review of Arabidopsis anti-pathogen metabolism with @somssich.bsky.social and @tonnigrubeandersen.bsky.social. Started to make a complete catalogue and had to focus. Even with all this knowledge, we still haven't studied most Arabidopsis enzymes or metabolites doi.org/10.1093/plph...