It was a pleasure to host Mike Gray from UAB for @oregonstate.edu Department of Microbiology seminar series yesterday. Many fascinating and head-scratching interactions between polyP and (p)ppGpp in E. coli! (Please disregard the weird rainbow phenomenon on the pic!)

Very proud to announce that my first plasmid electroporation in the new lab with all new equipment was a success, despite getting time constants of 0.2 ms. That’s the mark of a truly great transformation protocol.

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

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.io

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?

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?

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/...

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...

journals.asm.org

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!

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/...

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...

journals.plos.org

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

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/...

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 ...

journals.asm.org

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/...

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...

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...

biorxiv.org

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

Ran Blekhman@blekhman.bsky.social · last yr.

This is not some small foundation -- HHMI has a $24 billion endowment. It is the world's 2nd richest biomedical research foundation. If any funder can double down on their support for science right now, it's HHMI. But they are doing the opposite.

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...

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.

cell.com

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

Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · last yr.

Amino acid competition shapes A. baumannii gut carriage Acinetobacter baumannii uses ornithine to compete w/ microbiota & persist in gut. Amino acid supplementation & differences in diet promote A. baumannii gut colonization in mice & humans @laurenpalmer.bsky.social‬ www.cell.com/cell-host-mi...

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

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,...

rdcu.be

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.

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.

Needhi Bhalla 💅🏽@needhibhalla.bsky.social · 2y ago

Finally, I don't know why we resist defining scientific research as a creative endeavor. Any scientist who has achieved some degree of professional success recognizes the creativity and the bursts of conceptual understanding that accompany major innovation.

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.

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 🧵

#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...