Lightnews — Scholar-powered news

Reposted by Sid Venkatesh

Science in Seattle @scienceinseattle.com · 7d

Dr. Meghan Koch from @fredhutch.org has discovered a biological mechanism sprung in the first week of life that trains a mouse pup’s #ImmuneSystem to tolerate harmless gut bugs and new foods.

⚗️ Abstract: https://bit.ly/4nt6qGh
📰 Press release: https://bit.ly/46N7vBY

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Sean Gibbons 🦠💩 @gibbological.bsky.social · 1d

Rubbing shoulders with a @nobelprize.bsky.social laureate! 🤩What a week!

Couldn’t have happened to a nicer person: isbscience.org/news/press-r...

@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social

Left to right: Sean Gibbons, Naeha Subramanian, Mary Brunkow, Anna Kuchina, and Sid Venkatesh

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Reposted by Sid Venkatesh

ISB @isbscience.org · 2d

This morning, @isbscience.org's Dr. Mary Brunkow was awarded the 2025 Nobel Prize in Physiology or Medicine! Dr. Brunkow shares the award with Fred Ramsdell and Shimon Sakaguchi. Read the press release here: www.nobelprize.org/.../medicine....

What a tremendous honor! Congratulations!

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Reposted by Sid Venkatesh

Science News @scinews.bsky.social · 2d

The 2025 #NobelPrize in Physiology or Medicine has been awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi “for their discoveries concerning peripheral immune tolerance.”

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Sid Venkatesh @flash-point.bsky.social · 2d

Inspirational stuff from a scientific pioneer who also happens to be incredibly modest. ♥️

Reposted by Sid Venkatesh

Ram Savan @ramlabuw.bsky.social · 2d

www.nobelprize.org/prizes/medic...

Nobel Prize in Physiology or Medicine 2025

The Nobel Prize in Physiology or Medicine 2025 was awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi “for their discoveries concerning peripheral immune tolerance.”

www.nobelprize.org

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Sid Venkatesh @flash-point.bsky.social · 2d

Many congratulations, Mary Brunkow! Couldn’t be happier for you and @isbscience.org ! ♥️

www.nobelprize.org

The official website of the Nobel Prize - NobelPrize.org

The Nobel Prize rewards science, humanism and peace efforts. This is one of the central concepts in the will of Alfred Nobel, and it also permeates the outreach activities that have been developed for...

www.nobelprize.org

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Elaine Hsiao @pipethero.bsky.social · Jan 4

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

Sean Gibbons 🦠💩 @gibbological.bsky.social · Jan 3

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...

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Elaine Hsiao @pipethero.bsky.social · Jan 4

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

Nature Reviews Microbiology @natrevmicro.nature.com · Jan 3

Microbiota–neuroepithelial signalling across the gut–brain axis

Nature Reviews Microbiology, Published online: 02 January 2025; doi:10.1038/s41579-024-01136-9In this Review, Ohara and Hsiao explore the pathways linking the gut and the brain, particularly the communication between the gut microbiota and neurons at the…

go.nature.com

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Sean Gibbons 🦠💩 @gibbological.bsky.social · Jan 3

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...

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Neel Shah @nshahlab.bsky.social · Dec 26

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....

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...

onlinelibrary.wiley.com

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Reposted by Sid Venkatesh

Neel Shah @nshahlab.bsky.social · Dec 24

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...

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...

www.biorxiv.org

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Reposted by Sid Venkatesh

Joseph Luna @virologistjoe.bsky.social · Dec 20

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

Nandan Gokhale @nandangokhale.bsky.social · Dec 19

Our work on cellular RNA interactions with MAVS that promote antiviral signaling is finally live. So grateful to our indispensable collaborators as well as reviewers who helped to strengthen our work. #RNA #innateimmunity #virology

@ramlabuw.bsky.social

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

Cellular RNA interacts with MAVS to promote antiviral signaling

Antiviral signaling downstream of RIG-I–like receptors (RLRs) proceeds through a multi-protein complex organized around the adaptor protein mitochondrial antiviral signaling protein (MAVS). Protein co...

www.science.org

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Sid Venkatesh @flash-point.bsky.social · Dec 17

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...

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.

www.nature.com

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Sid Venkatesh @flash-point.bsky.social · Dec 12

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...

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.

isbscience.org

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David Weiss @dweisslab.bsky.social · Dec 2

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

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...

rdcu.be

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Reposted by Sid Venkatesh

ISB @isbscience.org · Dec 2

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...

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.

isbscience.org

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Reposted by Sid Venkatesh

Neel Shah @nshahlab.bsky.social · Nov 28

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!

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

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Sid Venkatesh @flash-point.bsky.social · Nov 27

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...

Mapping RNA–protein interactions with subcellular resolution using colocalization CLIP

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

rnajournal.cshlp.org

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Reposted by Sid Venkatesh

colinhillucc.bsky.social @colinhillucc.bsky.social · Nov 26

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...

www.biorxiv.org

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Elaine Hsiao @pipethero.bsky.social · Feb 16

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!)

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Feb 14

Complex carbohydrate utilization by gut bacteria modulates host food preference https://www.biorxiv.org/content/10.1101/2024.02.13.580152v1

The gut microbiota interacts directly with dietary nutrients and has the ability to modify host feed

www.biorxiv.org

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Reposted by Sid Venkatesh

Joseph Luna @virologistjoe.bsky.social · Nov 25

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!

Sid Venkatesh @flash-point.bsky.social · Nov 25

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/...

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...

www.science.org

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Sid Venkatesh @flash-point.bsky.social · Nov 26

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 [email protected] and colleagues.

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

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.

www.nature.com

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Sid Venkatesh @flash-point.bsky.social · Nov 25

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...

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 ...

www.biorxiv.org

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Reposted by Sid Venkatesh

ISB @isbscience.org · Nov 22

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...

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.

isbscience.org

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