Lightnews — Scholar-powered news

Reposted by Sri Kosuri

Addgene @addgene.bsky.social · 15d

Tags, reporters, luciferase — oh my!
To celebrate the expansion of the Promega Plasmid Collection, we’re spotlighting some of our most popular blogs on the technologies researchers rely on every day — tools you can access through Addgene.

Learn the Science Behind the Tools, with Addgene and Promega logos and the Blugene mascot holding a light bulb

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Sri Kosuri @srikosuri.bsky.social · Jul 6

I wrote down some of my thoughts down on the current race to build virtual cell models. Overall, excited and wary about the work ahead. Also, it's my first post to Substack; getting more excited about it as a replacement for X and Blue Sky.

srikosuri.substack.com/p/the-elusiv...

The elusive virtual cell

Rosetta Stone or Moby Dick?

srikosuri.substack.com

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Sri Kosuri @srikosuri.bsky.social · May 9

Lux Capital & @wolfejosh.bsky.social are launching the Lux Science Helpline - a $100M commitment to support American scientists whose research is threatened by funding cuts, bureaucratic hurdles, and career roadblocks - that expands our Lux Labs program.

www.luxcapital.com/news/our-hel...

Our Helpline for American Scientists

www.luxcapital.com

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Sri Kosuri @srikosuri.bsky.social · Mar 4

An update: After the diagnosis change to AML/myeloid sarcoma, we got a lot of great input. We’ve decided to go to St Jude’s to enroll in a clinical trial. We left for Memphis yesterday. We’ll be staying here for the next several months. Anxious but ready for the path ahead.

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Sri Kosuri @srikosuri.bsky.social · Feb 22

bsky.app/profile/srik...

Sri Kosuri @srikosuri.bsky.social · Feb 22

Quick update: Thanks so much for the outpouring of support and help. We learned a lot in the last week and the tumor is actually a myeloid sarcoma likely derived from early AML, with the hope of possible targeted therapies as well (KMT2Ar).

Sri Kosuri @srikosuri.bsky.social · Feb 8

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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Sri Kosuri @srikosuri.bsky.social · Feb 22

We have a long road ahead of us, but the last week has made it much more clear on the diagnosis and what to do next. Thanks again for all the help. I feel like we have turned over every rock, we are getting great care and in touch with all the relevant folks. 🙏

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Sri Kosuri @srikosuri.bsky.social · Feb 22

Quick update: Thanks so much for the outpouring of support and help. We learned a lot in the last week and the tumor is actually a myeloid sarcoma likely derived from early AML, with the hope of possible targeted therapies as well (KMT2Ar).

Sri Kosuri @srikosuri.bsky.social · Feb 8

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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Sri Kosuri @srikosuri.bsky.social · Feb 8

I hadn’t seen this. Thank you.

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Sri Kosuri @srikosuri.bsky.social · Feb 8

People can contact me directly at my first name (as written in my profile) at octant.bio.

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Sri Kosuri @srikosuri.bsky.social · Feb 8

I'm trying to understand non-surgical chemo and targeted therapy options, new pathology markers to better diagnose subtypes, and any data on progression in pediatric patients. Please feel free to share – I’m trying to cast a wide net due to the rarity of this condition and how little is known.

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Sri Kosuri @srikosuri.bsky.social · Feb 8

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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Sri Kosuri @srikosuri.bsky.social · Jan 28

Serenity now

a man in a kitchen with a sweater on that says oh no i am fine serenity now .

ALT: a man in a kitchen with a sweater on that says oh no i am fine serenity now .

media.tenor.com

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Reposted by Sri Kosuri

Claus Wilke @clauswilke.com · Jan 8

This is part of my effort of rewriting all materials for my UT Austin dataviz class in Quarto. It's going very well. Most importantly, I now have live exercises integrated into the site, thanks to Quarto live. Check it out here: wilkelab.org/SDS366/

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Reposted by Sri Kosuri

Willow Coyote-Maestas @willowcoyote.bsky.social · Jan 6

Check out our work, where we discover how receptor GPCR senses pH! We solved a longstanding question by developing foundational GPCR DMS tech dev + structural bio! Led by brilliant PhD student @matthewkhoward.bsky.social and Nick Hoppe w/ @amanglik.bsky.social!

www.cell.com/cell/fulltex...

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Sri Kosuri @srikosuri.bsky.social · Dec 28

Noticed this last time I was there. Many a night at the Pig drinking golden monkeys and eating the curry fries.

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Sri Kosuri @srikosuri.bsky.social · Dec 27

Definitely beer.

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Reposted by Sri Kosuri

Jordan Meier @doc-jlmeier.bsky.social · Dec 24

Today's holiday ☕ reading is this 2024 paper on PARIS, a bacterial defense system shaped like a literal propeller that responds to viral infection by hitting the cellular self-destruct button - cleaving an essential tRNA. www.nature.com/articles/s41...

A virally encoded tRNA neutralizes the PARIS antiviral defence system - Nature

Structural and functional studies reveal how viral proteins trigger the phage antirestriction induced system (PARIS) to degrade host tRNA and how viral tRNAs suppress the PARIS nuclease and thereby ov...

www.nature.com

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Reposted by Sri Kosuri

Micha Rapé Lab @micharapelab.bsky.social · Dec 22

Really beautiful paper by @kjarmache.bsky.social revealing read-write mechanisms of histone ubiquitylation by Polycomb complexes - through an intricate interplay of ubiquitin binding and ubiquitin transfer. Congratulations to all authors!

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

Read–write mechanisms of H2A ubiquitination by Polycomb repressive complex 1 - Nature

Cryo-electron microscopy and biochemical studies elucidate the read–write mechanisms of non-canonical PRC1-containing RYBP in histone H2A lysine 119 monoubiquitination and their roles in maintaining e...

www.nature.com

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Reposted by Sri Kosuri

Lisa Fazio @lkfazio.bsky.social · Dec 19

Out now - National Academies consensus report on Understanding and Addressing Misinformation About Science 🧪

It was a privilege to serve as one of the 15 committee members from a wide range of scientific disciplines who put this report together. Quick 🧵1/

www.nationalacademies.org/our-work/und...

Cover of the report - it's in a blue/purple color scheme and shows an abstract illustration of a molecule and the title of the report "Understanding and Addressing Misinformation About Science Consensus Study Report"

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Reposted by Sri Kosuri

Bloom lab @jbloomlab.bsky.social · Dec 18

In new study, we measure how all mutations to rabies G affect cell entry & antibody neutralization

Sheds light on constraints on type III fusion proteins, suggests ways to stabilize G vaccine antigens, and quantifies antibody robustness to rabies variation

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

Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations

Rabies virus causes nearly 60,000 human deaths annually. Antibodies that target the rabies glycoprotein (G) are being developed as post-exposure prophylactics, but mutations in G can render such antib...

www.biorxiv.org

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Reposted by Sri Kosuri

Jeff Spence @jeffspence.github.io · Dec 17

What do GWAS and rare variant burden tests discover, and why?

Do these studies find the most IMPORTANT genes? If not, how DO they rank genes?

Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬)

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

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies

Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

www.biorxiv.org

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Sri Kosuri @srikosuri.bsky.social · Dec 16

The responses to this are why change is not really going to happen within the universities themselves. I’m excited that AI has the possibility to break the cost curves to broad access to education. Lots of work to do, and thanks to those putting in that work to build a brighter future.

Joshua Gans @joshgans.bsky.social · Dec 13

So excited to tell you about my new venture with @afinetheorem.bsky.social called All Day TA (@alldayta.bsky.social) open.substack.com/pub/joshuaga...

Introducing All Day TA

My new venture designed to bring AI responsibly into college education

open.substack.com

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Reposted by Sri Kosuri

Pat Walters @wpwalters.bsky.social · Dec 5

I'm thrilled to announce a new preprint describing collaborative work with Ajay Jain and Ann Cleves Jain, "Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows".

arxiv.org/abs/2412.02889

Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows

The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi...

arxiv.org

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Sri Kosuri @srikosuri.bsky.social · Dec 6

Or that releasing strategy memos saying the best bet for political prospects is blaming China in march/april 2020 is not the best way to ask a country to hand over data. www.forbes.com/sites/andrew...

Republicans See Attacking China As A Winning Strategy

A new memo from the NRSC doubles down on the Trump campaign’s strategy of addressing coronavirus by attacking China and labeling Democrats soft on China.

www.forbes.com

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Reposted by Sri Kosuri

Kristian G. Andersen @kgandersen.bsky.social · Dec 6

"Wuhan lab samples hold no close relatives to virus behind COVID"

That should settle it, right? The problem, of course, it won't because we're dealing with conspiracy theories and not scientific inquiry - no amount of additional data will change un-evidenced beliefs.

www.nature.com/articles/d41...

Wuhan lab samples hold no close relatives to virus behind COVID

Shi Zhengli, the virologist at centre of COVID lab-leak theory, reveals coronavirus sequences from Wuhan institute.

www.nature.com

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