Jen Herman 🌪️

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

(💩💩)^3 = 💩💩💩💩💩💩💩💩

These days I read the strains & media/growth conditions before I even peak at results

New in JB: Weiss, Tamayo et al. describe a very cool microbial interaction wherein Enterococcus faecalis, an opportunist found in the inflamed gut, impacts phase-variation noted by chaining & rough colony morphology of C. diff.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

No one ever noticed me, but I was super fast and deadly.

Realized today - beyond conference interaction network (which I can only go to 1 or 2 (max!)/yr - there is a whole other online interaction ntwk that I did not know about for almost 15 yrs! Not know what to feel; like slow kid when everyone's picking teams at recess, I guess.Dodgeball champion btw

Happy birthday to one of my favourite haters, Charles Darwin

Big news from our lab: we can now stably edit the genome of a parasitic plant! Transgene-free, genome-edited P. japonicum in one generation! This will transform how we study #parasiticplants and other hard-to-transform plants.
www.biorxiv.org/content/10.6...

Buff-tip moths look like twigs!

Our new paper is out on the cell wall UDP-sugar nucleotide pathways in Candida & their potential as antifungal drug targets. doi.org/10.1016/j.tc...
@mrccmm.bsky.social @youngecmm.bsky.social @ecmmcandidaiv.bsky.social @ishamycology.bsky.social @youngisham.bsky.social @bsmm-meeting.bsky.social

Medium bad decision = spirit animal

A ligand-binding sensor domain got a tiny insertion from cytochrome c, which contained a heme-binding motif, and now it is a nitric oxide sensor. As simple as that: www.biorxiv.org/content/10.6...

Strategy to generate a DMS plasmid library for Your Favorite Gene (YFG) using short, degenerate libraries. 1. Segmentation of YFG into sub-fragments, each fragment corresponding to a DNA region to be synthesized. The same approach can be applied to promoter and terminator regions, if desired. 2. Example of a pool of degenerate oligonucleotides (oPool) derived from one YFG fragment associated with DNA barcodes. Each oPool contains: (i) ~40 bp of homology upstream of the YFG fragment of interest, (ii) the YFG fragment sequence with a single NNK codon, (iii) BsaI cloning sites, (iv) a DNA barcode composed of codon-position specific regions and six degenerate nucleotides (N), and (v) a conserved i7 primer binding site (PBS_i7) present in all oPools and used for rapid and efficient sequencing library preparation. Current oligonucleotide synthesis technologies allow for a total of nine degenerate positions per fragment: three are used for the degenerate codon (NNK), and six for the barcode. A complete list of all oPool sequences and their detailed composition is provided in S1 Table. 3. Protocol for constructing YFG DMS plasmid library from oPools using two cloning steps that maintain the physical barcode-mutation association. The libraries of oPools are cloned into the plasmid template by Gibson cloning. Following this step, for each fragment, a necessary short-read sequencing using PBS_i5 (included in the 5′ sequencing primer) and PBS_i7 is performed to associate each barcode with its corresponding mutation and to assess both barcode diversity per mutation and mutation coverage for the whole fragment. The ultimate step consists in Golden Gate cloning of the missing 3′ gene fragment between the degenerate fragment and the barcode. An additional short-read sequencing step of the barcodes can be performed to make sure that coverage and diversity have been maintained. Figure created in BioRender.

#DeepMutationalScanning (DMS) experiments are limited by gene size due to library complexity & costs. @christianlandry.bsky.social &co develop an efficient & cost-effective barcoded cloning strategy for plasmid-based DMS libraries that enables study of large genes @plosbiology.org 🧪 plos.io/4abhyUf

I'm part of a node. A very small, non-carcinogenic node

!!! 💪

*IN

Sincere.I can look only run 5 min before my reptile brain kicks: WOT ARE YOU DOING?!? STOP FFS

A mile is amazing!

👆

Wait... You run?

Moderna says FDA refuses its application for new mRNA flu vaccine The U.S. Food and Drug Administration is refusing to consider Moderna’s application for a new flu vaccine made with mRNA technology.

It is absolutely outrageous that Moderna’s flu vaccine was met with a “refusal-to-file” even after their approved their protocol with FDA and carried out the trial as agreed. This vaccine works better in older adults than the current flu vaccines.

apnews.com/article/mode...

Sometimes you meet someone & they seem abrasive but end up being great friends

And sometimes the abrasive ones are just rotty

Is there a way to tell the difference?

One criterion I judge people by (fair or not) is how they treat people they have nothing to gain from. If you can't acknowledge the person that removes the trash from your office, I figure you have drank so much self-importance kool-aid there's no hope. RIP

Please share: we're hiring a new tenure-track faculty member to our Department of Genetics at Albert Einstein College of Medicine.

faculty-einstein.icims.com/jobs/17847/a...

I used to love computer it was my friend. Now I have hate in my heart

A high-throughput biocatalytic platform for screening isomeric kainoid natural products Shepherd and Ramachandra et al. present a fast, chromatography-free method for resolving isomeric products from engineered enzymes. This platform enables large-scale screening and identifies improved ...

Hey all, excited to share this collab w/
@shaunmckinnie.bsky.social
TL;DR we combined our expertise to develop and validate a MALDI-tims platform for screening the production of isomeric small molecules (~212 Da) directly from E coli colonies in high throughput
www.cell.com/cell-reports...

Mugshot of Rosa Parks holding prisoner number placard that reads: 7053

Today in #BlackHistoryMonth, 2/4/1913 #Rosa Parks was born. 1955 refused to move to the back of the bus in a planned #directaction against #JimCrow, sparking Montgomery Bus #Boycott. Later in her life, she became a supporter of the Black Power Movement and an anti-Apartheid activist.

New in JB: Jorgenson reviews recent advances in cell envelope assembly via the lens of the essential lipid carrier undecaprenyl phosphate and with an eye on targets of novel Abx development.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

@poojag96.bsky.social work on the bioenergetics of spore germination is now published- Pooja had a really nice summary that I've put below but essentially we think the role of bioenergetics in spore germination has been completely overlooked!

www.pnas.org/doi/10.1073/...

A pore-forming antiphage defence is activated by oligomeric phage proteins - Nature Bacteria use diverse defence systems against phages, including a 164-residue prophage-encoded protein, Rip1, which senses conserved phage assembly rings to form membrane pores that block virion matura...

Here is ANOTHER one- this one uses its ring to form a pore after interacting with phage ring proteins. Whereas system above activates an RNA-degrading nuclease. From Norris and Maxwell labs www.nature.com/articles/s41...