Sign in

Nick Pokorzynski

@npokorzynski.bsky.social
273 followers 400 following 122 posts

Asst Professor @ Oregon State University Dept of Microbiology | Formerly Postdoc @ Yale | Investigating the metabolic basis of bacterial virulence | he/him | Views = mine pokorzynski-lab.squarespace.com

PostsRepliesMedia
Nick Pokorzynski @npokorzynski.bsky.social · 15/04/2026
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!)
030
Nick Pokorzynski @npokorzynski.bsky.social · 20/03/2026
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.
000
Reposted by Nick Pokorzynski
PLOS Biology @plosbiology.org · 03/02/2026
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
plos.io
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...
11612
Nick Pokorzynski @npokorzynski.bsky.social · 03/02/2026
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!!
000
Nick Pokorzynski @npokorzynski.bsky.social · 03/02/2026
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?
100
Nick Pokorzynski @npokorzynski.bsky.social · 27/01/2026
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.
000
Nick Pokorzynski @npokorzynski.bsky.social · 27/01/2026
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?
100
Reposted by Nick Pokorzynski
Hubert Salvail @hubertsalvail.bsky.social · 09/12/2025
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/...
journals.asm.org
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...
082
Reposted by Nick Pokorzynski
Anthony Vecchiarelli @cellforganized.bsky.social · 12/12/2025
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!
36337
Nick Pokorzynski @npokorzynski.bsky.social · 18/12/2025
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!
000
Nick Pokorzynski @npokorzynski.bsky.social · 18/12/2025
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.
110
Nick Pokorzynski @npokorzynski.bsky.social · 18/12/2025
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/...
journals.plos.org
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...
172
Reposted by Nick Pokorzynski
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 31/10/2025
Long-term control of Salmonella after transient T3SS-2 inhibition www.biorxiv.org/content/10.1101/202…
011
Nick Pokorzynski @npokorzynski.bsky.social · 08/11/2025
If you want to understand Jim Watson’s legacy, I think this passage from Lewontin’s “The Triple Helix” helps:
010
Nick Pokorzynski @npokorzynski.bsky.social · 17/10/2025
Office sign means it’s official, and it’s got my go-to Salmonella-infected macrophage cartoon on it.
060
Nick Pokorzynski @npokorzynski.bsky.social · 09/10/2025
Grant submitted/tossed into the abyss. Pray for me.
020
Nick Pokorzynski @npokorzynski.bsky.social · 04/10/2025
Georges Canguilhem, “A Vital Rationalist”
000
Nick Pokorzynski @npokorzynski.bsky.social · 02/10/2025
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...
hr.oregonstate.edu
Microbiology Postdoctoral Scholar | Office of University Human Resources
042
Nick Pokorzynski @npokorzynski.bsky.social · 30/09/2025
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 👇
001
Nick Pokorzynski @npokorzynski.bsky.social · 29/09/2025
My only criticism of One Battle After Another is that they got the molecular biology wrong
010
Nick Pokorzynski @npokorzynski.bsky.social · 16/09/2025
Our lab website is live, check it out: pokorzynski-lab.squarespace.com
pokorzynski-lab.squarespace.com
Pokorzynski Lab @ Oregon State University
042
Reposted by Nick Pokorzynski
Heather Feaga @heatherfeaga.bsky.social · 19/08/2025
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/...
journals.asm.org
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 ...
35122
Reposted by Nick Pokorzynski
John Helmann @johnhelmann.bsky.social · 14/08/2025
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/...
A metabolic diagram illustrating various ways the HPr protein interacts with other proteins to affect metabolism.
3157
Nick Pokorzynski @npokorzynski.bsky.social · 10/08/2025
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...
biorxiv.org
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...
021
Reposted by Nick Pokorzynski
Ran Blekhman @blekhman.bsky.social · 09/08/2025
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
316074
Reposted by Nick Pokorzynski
Amelia Randich @ameliarandich.bsky.social · 05/08/2025
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...
cell.com
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.
0238
Reposted by Nick Pokorzynski
Lauren Palmer @laurenpalmer.bsky.social · 04/08/2025
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
1310442
Reposted by Nick Pokorzynski
John Helmann @johnhelmann.bsky.social · 28/07/2025
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
rdcu.be
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,...
410042
Reposted by Nick Pokorzynski
Jeremy Berg @jeremymberg.bsky.social · 23/07/2025
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
211542
Reposted by Nick Pokorzynski
Jeremy Berg @jeremymberg.bsky.social · 22/07/2025
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.
105738
Nick Pokorzynski @npokorzynski.bsky.social · 22/07/2025
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!
000
Nick Pokorzynski @npokorzynski.bsky.social · 22/07/2025
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
100
Nick Pokorzynski @npokorzynski.bsky.social · 22/07/2025
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.
100
Nick Pokorzynski @npokorzynski.bsky.social · 22/07/2025
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.
110
Reposted by Nick Pokorzynski
Drug Monkey @drugmonkey.bsky.social · 18/07/2025
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.
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
13216
Reposted by Nick Pokorzynski
Laura Mike @lauraamike.bsky.social · 01/07/2025
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 🧵
Overview of paper revealing role of arginine in regulating K. pneumoniae mucoidy.
35224
Reposted by Nick Pokorzynski
UK Health Security Agency @ukhsa.bsky.social · 26/06/2025
#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...
Cases of Salmonella and Campylobacter reach 10-year high
116
Nick Pokorzynski @npokorzynski.bsky.social · 21/06/2025
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!
010
Nick Pokorzynski @npokorzynski.bsky.social · 21/06/2025
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.
100
Nick Pokorzynski @npokorzynski.bsky.social · 21/06/2025
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.
120
Reposted by Nick Pokorzynski
Daniel Plaza Sáez @dplazasaez.bsky.social · 15/06/2025
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
1101
Nick Pokorzynski @npokorzynski.bsky.social · 15/06/2025
That’s a wrap on the 2025 Mechanisms of Microbial Transcription GRS!
130
Nick Pokorzynski @npokorzynski.bsky.social · 14/06/2025
Kicking off the 2025 Mechanisms of Microbial Transcription GRS w/ keynote speaker Maria Hadjifrangiskou!
160
Nick Pokorzynski @npokorzynski.bsky.social · 06/06/2025
Did a control experiment that I did not expect to work, which would have sank an entire arm of this project, but it worked beautifully. Thank you biology gods for watching over me in these trying times.
030
Reposted by Nick Pokorzynski
Leigh Knodler @leighknodler.bsky.social · 03/06/2025
Just a few spots remaining for the GRC Salmonella Biology and Pathogenesis meeting to be held in August. The final program is now online. www.grc.org/salmonella-b... Apply now to hear about the latest scientific discoveries about Salmonella, meet up with old friends, make new friends......
11913
Reposted by Nick Pokorzynski
Sean Gibbons 🦠💩 @gibbological.bsky.social · 13/05/2025
One of my favorite history of science books: "Brave Genius" It's about Jacques Monod, discoverer of the lac operon, who risked everything to fight fascism/Nazis as a part of the French Resistance, along with his buddy Albert Camus. Be like Jacques. www.penguinrandomhouse.com/books/213596...
penguinrandomhouse.com
Brave Genius by Sean B. Carroll: 9780307952349 | PenguinRandomHouse.com: Books
The never-before-told account of the intersection of some of the most insightful minds of the 20th century, and a fascinating look at how war, resistance, and friendship can catalyze genius.  ...
34113
Reposted by Nick Pokorzynski
Jie Xiao @jiexiaolab.bsky.social · 27/05/2025
Our new paper on FtsN is out! Now there are three tracks for organized cell wall constriction-- the old, boring E. coli always manages to surprise us. A special shout-out to all the people who made this work possible, especially Dr. Jason Lyu, and Dr. David Weiss. www.nature.com/articles/s41...
nature.com
Third track model for coordination of septal peptidoglycan synthesis and degradation by FtsN in Escherichia coli - Nature Microbiology
Partitioning of FtsN and the septal peptidoglycan synthesis complex between an active synthesis track and an inactive denuded glycan track coordinates opposing peptidoglycan synthesis and degradation ...
13317
Nick Pokorzynski @npokorzynski.bsky.social · 24/05/2025
My view of cells is influenced heavily by Canguilhem’s recounting of the history of cell theory in the 18th and 19th century, where cells were viewed (ontologically) as inextricable from the whole organism. (Of course there is the exception of single-celled organisms!)
010
Nick Pokorzynski @npokorzynski.bsky.social · 24/05/2025
If by displaced you mean transferred from the organismal level to the cell/gene level, I completely agree.
100
Nick Pokorzynski @npokorzynski.bsky.social · 24/05/2025
Another common example that gets under my skin: you commonly hear that X “evolved to” do Y. Of course, evolution does not have a plan or direction, so this is just poor semantics, and I think most biologists would agree. Nevertheless, the tendency towards agency/purpose persists.
110