Geoffrey Thomson

@jrossibarra My institution uses this sbatch (slurm) wrapper for running arrays of job submissions. I think it's neat. github.com/ycrc/dsq

About to take the helm of the HPC core at UC Davis. One goal is to make things easier for users & increase usage. So help me out. What are things you like about how HPC runs at your institution? What are things you wish were different? If you could use HPC but don't, why not?

@pmoyniha @ATinyGreenCell If organism A and B are in the Plaza or Zoonomia databases you can just use them. Otherwise the OrthoFinder program is straightforward to use to identify orthologs for large numbers of genes.

Is there anyone out there that can point me towards a simple way to take a list of genes (over 1000) from organism A and list the orthologs in organism B?

Congrats to Qingqing and the rest of the team! Check out our new paper showing plants can sense two seasons simultaneously to control growth and flowering. science.org/doi/10.1126/sc…

@triplettlr I didn't realise this was a reference that translated to America

How is everyone enjoying Aptos

@ATinyGreenCell also onlinelibrary.wiley.com/doi/full/10.11…

@ATinyGreenCell I recommend looking into the fruit development literature then. The authors usually focus on the fruit which develop but often document floral phenotypes along the way. For example, maxapress.com/article/doi/10…

Ah crap if this doesn't exist I may have to write it. Surely the individual species level comparisons exist as disparate papers but a wide review seems a bit absent from the narrative. Would be a good writing exercise even if it does exist...

@ATinyGreenCell ncbi.nlm.nih.gov/pmc/articles/P…

@ATinyGreenCell These seem good: nph.onlinelibrary.wiley.com/doi/10.1111/np…

Maybe the core problem isn't who is, as Thorp describes "performing the hard intellectual labor of choosing, from the mass of research, those discoveries that deserve publication in a top journal" but that they are doing this at all.

Does anyone know the record for the Arabidopsis plant with the most independent T-DNA insertions? Has someone made a octuple mutant by crossing or something?

Another year with no funding for plant biology from the #MarsdenFund

@ATinyGreenCell Welcome to the Nutmeg state. You are welcome to stop off in New Haven if you are passing through

I've made it to the Ford of Harts. A great tree stands before me. A gilded spire glints in the distance. >

@gmopundit Absolutely, introduce double strand breaks in DNA and such outcomes are bound to occur

@GojThomson But at least some types of irradiation mutagenesis have similar actions

Agro is frequently used in Plant Sci to create transgenic plants. Yet, beyond expressing the genes on the T-DNA, how many pause to consider the effects of transgene insertion into the genome of a plant? We review this here: doi.org/10.1111/tpj.16… #Plants #TDNA #Agrobacterium

@ChenxinLi2 Personally, i find it unsatisfactory that the field seems content with such variable outcomes. We are far from genetic "engineering" 😜

@ChenxinLi2 Yes, that is why independent lines are essential! However remember the ida-2 mutant has a 11.8 Mb translocation no one noticed for 14 years, and the disruption of BSM causing the lethality in the abp1-1 allele was not detected for 15 years

it is important to recognize that a high level of genomic disruption is inherent to the creation of transgenic plants. This is not an argument against their use, but I believe that we need to be upfront about the potential consequences of this technology

I think few plant scientists realize that 10–20% of transgenic plants have some sort of chromosomal translocation. Thus while there is a lot of discussion around the precision of contemporary gene editing tools ...

@jlsteenwyk @M_L_Carpenter @OmicsOmicsBlog @CantataBio I have also used @CantataBio and am very happy with the service

@M_L_Carpenter @OmicsOmicsBlog @CantataBio We have to follow each other for DMs to open. Will message you when possible :)

Does anyone know of a sequencing service for gDNA isolation, long-read sequencing, and Hi-C sequencing?

Had a BLAST at the 2023 @MCDB_Yale retreat 🤩. Alongside my brilliant fellow Postdocs, @cintiasagawa and @GojThomson, we had the privilege of showcasing our incredible Citrus project, which aims to combat the #citrusgreening disease using gene editing.🍊