Sid Venkatesh

It was an honor to highlight this fantastic work by Cheng and Venkatesh et al of the Gordon lab. Many thanks to them, and to Francis Chandra for doing all the heavy lifting on this Spotlight! @cp-cellchembiol.bsky.social

Happy to kick off 2025 with this new review on gut microbiota-neuroepithelial signaling by the very talented Taka Ohara!

Great highlight by Chandra and @pipethero.bsky.social on recently published work by my colleague @flash-point.bsky.social (from his postdoc work) on endocannabanoids produced by specific members of the gut microbiota that likely impact host satiety/appetite. @isbscience.org

doi.org/10.1016/j.ch...

Allosteric regulation of the tyrosine phosphatase PTP1B by a protein–protein interaction The rapid identification of protein–protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and pr...

Happy to see this paper, led by former grad student Cassie Chartier, out in its final form at Protein Science! We characterized the interaction between PTP1B and the ubiquitous signaling adaptor Grb2 and identified new PTP1B interactors along the way!

onlinelibrary.wiley.com/doi/full/10....

Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression Short linear peptide motifs play important roles in cell signaling. They can act as modification sites for enzymes and as recognition sites for peptide binding domains. SH2 domains bind specifically t...

Excited to share a new preprint from our lab, joint with the Bussemaker group, where we combined peptide display and selection with biophysically interpretable machine learning to build affinity models for SH2-phosphopeptide recognition.

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

Fantastic work! Congrats @nandangokhale.bsky.social, @ramlabuw.bsky.social and team.

Diverse viral cas genes antagonize CRISPR immunity - Nature We demonstrate that phages have co-opted cas genes from CRISPR defence systems, which subsequently evolved anti-defence functions.

Finally caught up with some beautiful work from Alex Meeske in Nature! His lab has identified proteins in Listeria that either substitute for Cas in Cascade complexes (anti-type I-B CRISPR immunity) or degrade crRNA (anti-type VI-A CRISPR immunity). Inspiring stuff!

www.nature.com/articles/s41...

ISB Named Winner of 2024-2025 Amazon Web Services IMAGINE Grant for Nonprofits ISB was selected as a winner of the 2024 Amazon Web Services (AWS) IMAGINE Grant, which will support continued development of My Digital Gut.

Warm congratulations to my @isbscience.org colleagues @gibbological.bsky.social, Andrew Magis, and team for winning a 2024 Amazon Web Services IMAGINE grant for developing "My Digital Gut", an online platform for personalized, predictive, and preventive healthcare!

isbscience.org/news/2024/12...

Bactericidal antibiotic treatment induces damaging inflammation via TLR9 sensing of bacterial DNA Nature Communications - The immunologic differences induced by bactericidal versus bacteriostatic antibiotics remain unclear. Gross et al. show that, in contrast to static antibiotics, cidal...

Bactericidal antibiotics release bacterial DNA that activates TLR9, while static antibiotics do not. This can profoundly impact treatment outcome. Should clinicians consider this when choosing antibiotics to prescribe?

Amazing work by Julia Gross and collaboration with Iain Fraser!
rdcu.be/d1Phk

ISB-Developed MetaboCore Offers Precision Cancer Care Faster Than Ever ISB's MetaboCore is a diagnostic tool that can help physicians quickly select the most effective systemic therapy for each cancer patient.

ISB Associate Professor Dr. Wei Wei has developed a promising new companion diagnostic tool called MetaboCore to help physicians quickly select the most effective systemic therapy for each cancer patient. Learn more: isbscience.org/news/2024/11...

Shah lab photo outside of Havemeyer Hall. Left to right: Jason, Minhee, Zijing, Yethmie, Loren, Katherine, Devon, Neel, Cassie, Andrew, Allyson, Anne, Anya

This job has so many ups and downs, but one constant that I’m always thankful for is this creative, hard-working, supportive group (they support me, too!!). I’m also thankful for all the awesome ideas and cool data they generate, which keep us all motivated and stimulated and make this so much fun!

Innovative and inspiring biochemistry from Joe Luna @virologistjoe.bsky.social and colleagues that combines CLIP with proximity labeling to reveal RNA:RBP interactions at subcellular resolution! Congratulations for your first paper as a corresponding author ♥️
rnajournal.cshlp.org/content/30/7...

First post on a lovely story from the lab that shows that Faecalibacterium prausnitzii can package its own genome in bite-size segments in phage-like capsids
www.biorxiv.org/content/10.1...

Delighted to share work by Kristie Yu, Celine Son, & co showing that selective fructan metabolism by the gut microbiome can contribute to host associative learning of dietary preference, even when it comes to choosing between diets with the same perceptual salience (and macronutrient composition!)

Some really beautiful biochemistry here. Seeing one dalton shifts to pinpoint how an enzyme from a nutrition-therapy-linked microbe works must be gratifying. Basic biochemistry lighting the way on an important problem. Congrats to my buddy Sid (@flash-point.bsky.social‬) and team on this one!

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts - Nature Microbiology Coffee consumption is associated with the presence and abundance of a specific member of the human gut microbiome, Lawsonibacter asaccharolyticus, and changes to the plasma metabolome.

Co-varying coffee-derived metabolites are associated with L. asaccharolyticus! A cool paper by multiple luminaries in the field that set the stage for causal roles.

Accompanied by a commanding News & Views piece by Nate McNulty@npmcnulty.bsky.social and colleagues.

www.nature.com/articles/s41...

Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity Multi-domain signaling enzymes are often regulated through extensive inter-domain interactions, and disruption of inter-domain interfaces by mutations can lead to aberrant signaling and diseases. For ...

Mulling over a preprint from @nshahlab.bsky.social and colleagues on deep mutational scanning to yield insights into activity and regulation of the tyrosine phosphatase SHP2, as well as uncharacterized clinical variants. Beautiful work! ❤️
www.biorxiv.org/content/10.1...

Sid Venkatesh Publishes Co-First Authored Paper in Science Dr. Sid Venkatesh, who joined ISB's faculty in 2023, is the co-first author of a paper in the journal Science.

We are elated for @isbsci.bsky.social Assistant Professor Dr. Sid Venkatesh, co-first author of a paper in Science. isbscience.org/news/2024/11...

Interleukin-2-mediated NF-κB-dependent mRNA splicing modulates interferon gamma protein production | EMBO reports imageimageIL-2 stimulation post-transcriptionally enhances splicing of IFNG mRNA in NK cells. Further, NF-κB signaling downstream of the IL-2 receptor is required for IFNG mRNA processing. IL-12 and ...

I read this work from @ramlabuw.bsky.social and colleagues about splicing of IFN-gamma transcripts being regulated by IL-2! Interesting and neat idea...

www.embopress.org/doi/full/10....

Gut microbiota regulates stress responsivity via the circadian system Gut microbes are known to modulate stress responsivity and behavior. Tofani et al. demonstrate that such modulations occur via the circadian system. The oscillations in gut microbiota composition regu...

Intriguing paper linking bacterial strains (L. reuteri) and corticosterone release in a circadian rhythm-dependent manner from @jfcryan.bsky.social and colleagues. Kudos for the Zeitgeber time experiments! On to L. reuteri-encoded molecules that mediate these effects...
www.cell.com/cell-metabol...

A gut microbial enzyme that impacts host signaling in undernourished children — Microbial Interactions & Microbiome Center Dr. Siddarth Venkatesh, now at the Institute for Systems Biology in Seattle, previously studied the gut microbiome's impact on childhood undernutrition and the therapeutic potential of microbiota-dire...

Heart warming stuff from UW’s Microbial Interactions and Microbiome Center (mim_c) helmed by Drs. Joseph Mougous and Kyle Asfahl!

Article by Neuroscience PhD candidate Monica Tschang.

mimcuw.org/newsevents/a...

A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase Undernutrition in Bangladeshi children is associated with disruption of postnatal gut microbiota assembly; compared with standard therapy, a microbiota-directed complementary food (MDCF) substantially...

Last month, my co-first author, Dr. Jiye Cheng and I reported the identification of a gut microbial enzyme that impacts satiety-related signaling pathways in undernourished children treated with a microbiota-directed complementary food.

www.science.org/doi/10.1126/...

Happy to join this community! Excited to learn and discuss science with y'all.