Nick Pokorzynski

The many facets of immunometabolism This Collection of articles aims to shine a light on the many facets of immunometabolism, highlighting how molecular and cellular mechanisms impact diverse tissue and organismal functions and the exci...

PLOS Biology is proud to present our new collection of comment and opinionated review articles on the many facets of #immunometabolism!

🧪 #immunosky #immunology #metabolism

plos.io/4c5z6Cn

See 🧵⬇️ for more details

I don’t need enhanced blast speed if, when I put in a specific organism, all the hits I get back are “clusters” corresponding to sequences in *other* organisms!!

Has NCBI blast basically become unusable or am I doing something wrong? Why can’t I select my organism of interest and blast specifically against that? Why do I get hits that say they correspond to my species/serovar but they are absent in my genome. What is the value of this “clusternr” approach?

Ok never mind, you can hard code breaks using html formatting. Of course, they count toward your total character count, so it doesn’t really make it any less ridiculous but at least it’s a solution.

This feels like a ridiculous question but is there a way to get the new NIH biosketch supplement form to recognize spaces between paragraphs? It keeps slamming all my text together into an indecipherable blob. Whose idea was this?

Small RNA promotes negative feedback of the master virulence regulator PhoP by repressing the PhoQ sensor enhancer UgtL in acidic pH | mSphere To cause disease, pathogens must express their virulence genes at the right time and in proper levels. Here, we establish that a small RNA (sRNA) restricts the activation of a regulator critical for t...

Check out our new article! Congrats to Michelle Prophete, Alex Mabel and Payton Bowman for their great work!

Small RNA promotes negative feedback of the master virulence regulator PhoP by repressing the PhoQ sensor enhancer UgtL in acidic pH | mSphere journals.asm.org/doi/10.1128/...

Just got word that we are a go for the Bacterial Cell Biology and Development GRS and GRC at Southern New Hampshire University!

GRS will be on June 5-6, 2027

GRC will be from June 6-11, 2027

Block off your calendars Prokaryotic Cell Biologists!

More details to come! Please repost!

I also want to highlight the contribution of two talented undergrads, Elisabeth and Chris. They put in a ton of work to validate our CRP reporter and test CRP activity under various conditions and in different strains. Super proud of what they accomplished!

There are a lot of highlights from the control of Mg2+:ATP homeostasis, the transcriptional activity of CRP-cAMP, to a new plasmid reporter for CRP activity, and much more. Please give it a read if you are interested in the regulation of metabolism and gene expression.

The master virulence regulator PhoP dictates carbon metabolism by controlling cyclic AMP synthesis in Salmonella Inside macrophages, Salmonella faces magnesium scarcity that disrupts cAMP synthesis and carbon metabolism. This study shows that the PhoP regulator restores metabolic control by promoting Mg2+ uptake...

Very happy to share the second paper from my postdoc, published today @plosbiology.org. Here, we report that the master regulator of Salmonella virulence usurps the reign of cAMP over metabolism under infection-relevant conditions. journals.plos.org/plosbiology/...

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