Nick Pokorzynski

Long-term control of Salmonella after transient T3SS-2 inhibition https://www.biorxiv.org/content/10.1101/2025.10.30.685576v1

If you want to understand Jim Watson’s legacy, I think this passage from Lewontin’s “The Triple Helix” helps:

Office sign means it’s official, and it’s got my go-to Salmonella-infected macrophage cartoon on it.

Grant submitted/tossed into the abyss. Pray for me.

Georges Canguilhem, “A Vital Rationalist”

Please share: I'm hiring a postdoctoral scholar to investigate molecular mechanisms governing Salmonella cell envelope homeostasis inside mammalian host cells. Come join a great microbiology community @oregonstate.edu in beautiful Corvallis, OR!

Appy here: hr.oregonstate.edu/open-postdoc...

Anybody out there using the Bio-rad TransBlot Turbo system? Do you like it? Have you compared to the iBlot platform? Pros, cons? Welcoming all strongly opinionated immunoblot snobs in the replies below 👇

My only criticism of One Battle After Another is that they got the molecular biology wrong

Our lab website is live, check it out: pokorzynski-lab.squarespace.com

Conservation and evolution of the programmed ribosomal frameshift in prfB across the bacterial domain | mBio Translation termination is catalyzed by one of two release factors in bacteria, RF1 or RF2. It has been known for decades that RF2 levels in Escherichia coli are regulated by a programmed ribosomal frameshift within the prfB gene that encodes RF2. We ...

Latest from the lab! Analysis of everyone’s favorite regulatory mechanism in bacteria — the RF2 programmed frameshift! Likely present in the ancestor of bacteria, use of this mechanism is influenced by stop codon usage! Big congrats to @cassidyprints.bsky.social
journals.asm.org/doi/10.1128/...

A metabolic diagram illustrating various ways the HPr protein interacts with other proteins to affect metabolism.

The B. subtilis histidine-containing phosphocarrier protein (HPr) supports PTS-sugar import, interacts with GAPDH, and helps mediate carbon catabolite repression (CCR). Here, a mutant HPr protein is shown to alleviate metabolic intoxication in a cpgA mutant.
journals.asm.org/doi/10.1128/...

Chlamydia iron starvation links nutritional immunity to pathogen recognition Nutritional immunity is an antimicrobial strategy that evolved to starve pathogens of essential nutrients, with death as the desired outcome. Here, we report that transient iron starvation of the obli...

Cool to see this out in the world - a project that I helped start in the Carabeo lab before I left for Yale: iron starvation enables recognition of intracellular Chlamydia due to dysregulated peptidoglycan remodeling. Congrats to 1st author Monisha Alla!

www.biorxiv.org/content/10.1...

200 days in, checking in on HHMI funding opportunities:

Freeman Hrabowski Scholars Program - not accepting applications

Gilliam Fellows Program - not accepting applications

Hanna H. Gray Fellows Program - not accepting applications

Investigator Program - not accepting applications

Mechanistic study of a low-power bacterial maintenance state using high-throughput electrochemistry Anaerobic phenazine cycling by an opportunistic bacterial pathogen supports a low-power, non-growth metabolism that lends itself to quantitative and mechanistic study of maintenance physiology.

Dianne Newman: beautiful demonstration of maintenance metabolism in #Psuedomonas, which uses PCN redox cycling to support PMF during anaerobic growth #Phages2025

www.cell.com/cell/abstrac...

Super excited to share our paper online 🚨today🚨 in Cell Host & Microbe‬! Xiaomei Ren @xiaomeiren.bsky.social and Mason Clark @rmasonclark.bsky.social‬ co-led discovery of ecological factors for Acinetobacter baumannii carriage in the gut, a reservoir for pathogen spread. 🎉

tinyurl.com/443kfefk

Microbial metal physiology: ions to ecosystems Nature Reviews Microbiology - Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review,...

Metal ions are universally required for life, and many of the foundational principles of metal homeostasis have emerged from studies of microbial systems. In this review, I provide a introductory overview targeted to those new to the field.
#MicroSky #Metals

rdcu.be/eycU2

If this all sounds like a calculated plan to reduce the size of the federally funding biomedical research enterprise, I believe that is exactly what is it.

The notion that this "facilitates efficient management" of grants and the appropriation is, to use an official NIH term, horseshit.

/fin

NIH staff are being required to fully fund ~ 50% of their grants. This means that all 4 years of an award will be paid out of this appropriation. This will help them get the appropriated funds spent, but will mean they can only fund (1/2 + 1/4*1/2) = 5/8 has many grants as they would have otherwise.

Probably also worth pointing out that when you look at highly “productive” scientific operations, the main thing you find is an increase in human contribution (eg, more scientists) not some streamlined procedure to arrive at groundbreaking findings. I’m not sure we can escape that fact!

In other words, if we imagine an “efficient” science, we necessarily have to imagine a science that spends less time at the bench, less time mired in figuring out unexpected results, and less time arriving at truly novel outcomes. This ultimately compromises the potential - and efficacy - of science

Rooting science in practical activity - rather than say, good ideas (replace with good experiments!) - reveals why improving the “efficiency” of science is a lost cause. The only real efficiency to be gained would ultimately diminish the *practice* of science, and thus its creative potential.

Agreed and in addition: the essence of creativity is practical activity. That is, the real human interaction with nature/the environment/the object is what produces creativity. This is why AI is so *barren* - its substrate is preexisting information, not the creative frontier of knowledge.

a graph of the cumulative binomial probability of 1 or more hits given a number of trials and a 5%, 10% or 20% per-trial rate

Time to revisit the probability of at least one NIH grant award given relevant success rates. It has been ~20% overall success in recent completed FY. Many ICs have *paylines* around 10%ish.

Overview of paper revealing role of arginine in regulating K. pneumoniae mucoidy.

Our paper reporting a highly conserved mechanism by which arginine positively regulates hypervirulent K. pneumoniae mucoid phenotype is now fully online.
rdcu.be/euiWG

Summary picture is below, but details in the 🧵

Cases of Salmonella and Campylobacter reach 10-year high

#Salmonella and #Campylobacter are common causes of food poisoning, and can lead to serious illness in the young, elderly and those with weakened immune systems. Cases of both infection increased by 17% between 2023 and 2024.

Find out more on our news story: www.gov.uk/government/n...

If you are interested in the basic mechanisms of gene expression and regulation in microbes, make sure to put this conference on your calendar for 2027. I expect the conference will only keep getting better!

This year we got to honor the lifelong contributions of field-defining scientists Carol Gross and Steve Busby. It was truly humbling and such an honor to witness the enormous scope and impact of their science, mentorship, and advocacy over 40+ years.

The Mechanisms of Microbial Transcription GRC was excellent this year. This is a community of the highest caliber: rigorous science at the frontier of microbial gene expression, covering a wide range of organisms and processes, presented by first-time PhD students and legends alike.

The GRS on Microbial Transcription 2025 is now over!

Amazon science and people!
🦠🧬
Great experience to have served as a chair of this meeting along with @npokorzynski.bsky.social

Passing the power now to Celeste and Caroline for #MoMT2027 !!

#microbiology #microsky

That’s a wrap on the 2025 Mechanisms of Microbial Transcription GRS!