Dan Kliebenstein
@spicybotrytis.bsky.social
Dogs, Horses and Gardening, with a side of research on complexity and metabolic warfare in plants
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.
Shouldn't that claim require the reverse, lots of reps, etc.
November 21, 2025 at 6:24 PM
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.
Shouldn't that claim require the reverse, lots of reps, etc.
Reposted by Dan Kliebenstein
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
Convergence and constraint in glucosinolate evolution across the Brassicaceae
Studying a glucosinolate enzyme across the Brassicaceae shows evolution of plant specialized metabolism involves independent gene losses, distal duplicatio
doi.org
November 21, 2025 at 6:08 PM
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?
November 15, 2025 at 9:57 PM
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?
Reposted by Dan Kliebenstein
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
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
Convergence and constraint in glucosinolate evolution across the Brassicaceae
Studying a glucosinolate enzyme across the Brassicaceae shows evolution of plant specialized metabolism involves independent gene losses, distal duplicatio
academic.oup.com
November 13, 2025 at 4:01 PM
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
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
November 12, 2025 at 2:28 AM
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.
November 9, 2025 at 12:35 AM
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?
Or how Mendelian genetics does not inherently make causal arguments?
Or how polygenic traits follow Mendelian rules?
November 7, 2025 at 11:44 PM
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?
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.
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.
October 29, 2025 at 5:03 PM
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.
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.
October 26, 2025 at 4:25 AM
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.
- 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.
October 22, 2025 at 11:30 PM
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.
- 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.
Admittedly the Maui coconut porter is a guilty exception.
October 19, 2025 at 9:42 PM
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.
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.
October 19, 2025 at 5:12 PM
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?
October 19, 2025 at 4:45 PM
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.
October 17, 2025 at 11:00 PM
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.
October 17, 2025 at 9:47 PM
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?
Does anyone have good literature on a anthocyanin biosynthetic mutant having a stress sensitivity phenotype in the wild beyond UV-B?
October 17, 2025 at 5:33 PM
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?
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.
PS - Yes, I should not be teaching writing classes.
October 15, 2025 at 8:00 PM
@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.
PS - Yes, I should not be teaching writing classes.
Reposted by Dan Kliebenstein
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 :)
October 11, 2025 at 4:18 PM
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.
October 11, 2025 at 2:38 PM
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)
a dachshund wearing a cowboy hat and a blue shirt says party time
ALT: a dachshund wearing a cowboy hat and a blue shirt says party time
media.tenor.com
October 10, 2025 at 7:54 PM
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.
October 10, 2025 at 12:15 AM
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.
Reposted by Dan Kliebenstein
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
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
October 9, 2025 at 7:58 AM
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
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.
I.e. because plants are autotrophic, they are sessile.
October 7, 2025 at 10:13 PM
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.
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
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
October 7, 2025 at 9:50 PM
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
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
October 5, 2025 at 10:52 PM
Breakfast in bed with new season butternut. A happy Mastiff