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Uday Tak

@nokaryote.bsky.social
342 followers 655 following 11 posts

Bacteria and phage at UVA taklaboratory.org

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Reposted by Uday Tak
bioRxivpreprint @biorxivpreprint.bsky.social · 4h
GalaxyMemMD: an end-to-end Galaxy toolset for reproducible membrane embedding, molecular dynamics simulation, and analysis of membrane proteins www.biorxiv.org/content/10.64898/20…
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Reposted by Uday Tak
Seth Shipman @seth-shipman.bsky.social · 05/10/2026
@jihoon-han.bsky.social's new detectron technology -- out now in Nature Biotechnology. Toehold RNA sensing controls a retron-derived DNA barcode generator. Check it out!
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Reposted by Uday Tak
Sternberg Lab @sternberglab.bsky.social · 05/10/2026
1/2 Here we report the activity of Arc, a 50-aa DNA-binding protein encoded within IS605-family transposons. www.biorxiv.org/content/10.6...
biorxiv.org
Arc represses gene expression in IS605-family transposons
Bacterial insertion sequences (IS) are compact transposable elements that encode proteins required for their mobility and maintenance, yet many also encode accessory proteins with poorly understood fu...
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Uday Tak @nokaryote.bsky.social · 05/10/2026
JOB ALERT: University of Virginia School of Medicine, Department of Microbiology, Immunology, and Cancer Biology is recruiting a virologist (open rank). Please share and forward to anyone who may be interested! More information and link to application: apply.interfolio.com/191946
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Reposted by Uday Tak
Chrystal Starbird @drstarbird.bsky.social · 01/10/2026
And… I am SO excited to share the first research preprint from my group! In this paper we determined several cryoEM structures to visualize the entire cell-to-cell bridging complex formed by TAM receptor and ligand, bringing into 3D a common graphical depiction. www.biorxiv.org/content/10.6...
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Brian D. Wade @astrobrian.bsky.social · 02/10/2026
How bacterial immune systems sense phage infection #bacteriophage #phage #microSky #scienceSky www.nature.com/articles/s41...
nature.com
How bacterial immune systems sense phage infection - Nature Reviews Microbiology
Bacteria deploy diverse immune systems to counter phage infection, yet how these systems sense invasion remains incompletely understood. This Review categorizes phage-derived triggers and outlines eme...
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Reposted by Uday Tak
Kranzusch Lab @kranzuschlab.bsky.social · 01/10/2026
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...
science.org
Phage proteases activate CBASS antiphage immunity
Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...
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Reposted by Uday Tak
Joe Zackular @joeyzacks.bsky.social · 01/10/2026
Congratulations to Zackular Lab postdoc @rcglover.bsky.social on being selected as an Emerging Voice in Microbiology by Infection and Immunity! Rochelle is super talented scientist and a rising star in our field. Check out her mini-review in the upcoming collection! journals.asm.org/journal/iai/...
journals.asm.org
Emerging Voices in Microbiology
Annual initiative highlighting standout early-career Infection and Immunity researchers through invited, peer-reviewed minireviews in Emerging Voices.
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Reposted by Uday Tak
Mark O. Martin @markowenmartin.bsky.social · 01/10/2026
@baym.lol @sianowen.bsky.social I hope you and your colleagues' ears were burning this morning. Lab meeting with @drhhnz.bsky.social discussed this awesomely titled paper from your group, and how the ideas might be used locally: journals.asm.org/doi/10.1128/...
journals.asm.org
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Reposted by Uday Tak
Eirik Lågeide @eiriklag.bsky.social · 01/10/2026
Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵
biorxiv.org
NO VEIN is an ancestral immunity protein involved in plant-virus interaction
The conservation of immune systems from prokaryotes to eukaryotes can guide discovery of immunity genes across the tree of life. Most studies to date have focused on metazoan systems, while the extent...
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Reposted by Uday Tak
Jolyon Troscianko @jtroscianko.bsky.social · 30/09/2026
🦋 Butterfly wing patterns create motion illusions that protect them from predators! Our new study (8 years in the making) is out in Nature today doi.org/10.1038/s415... @grahancock.bsky.social @esbriolat.bsky.social @scienceanna.bsky.social @lauraakelley.bsky.social @uniexecec.bsky.social
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Sternberg Lab @sternberglab.bsky.social · 28/09/2026
1/13 — New pre-print from the Sternberg Lab in collaboration with Leifu Chang's Lab! TnpB nucleases have repeatedly given rise to TldRs, nuclease-dead RNA-guided transcription factors. Here we define the biological role of one TldR clade in its native host. Story: www.biorxiv.org/content/10.6...
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 26/09/2026
Pls share: Two tenure-track positions in Molecular Microbiology at Virginia Tech. I had a great visit there a couple of years ago! jobs.apply.vt.edu/jobs/assista...
jobs.apply.vt.edu
Assistant/Associate Professor - Blacksburg, Virginia, United States
Job Description The Department of Biological Sciences in the College of Science at Virginia Tech seeks applicants for two (2) tenure-track research and teaching positions at the Assistant/Associate ...
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Reposted by Uday Tak
Jörg Stülke @joergstuelke.bsky.social · 26/09/2026
Identification of a novel RNA-modifying enzyme! RlmS! #SubtiWiki www.pnas.org/doi/10.1073/...
pnas.org
Activity-based profiling of bacterial RNA-modifying enzymes reveals species-specific 5-methyluridine modification in Bacillus subtilis 23S rRNA | PNAS
RNA modifications play an important role in biological processes. Mapping the diversity of RNA chemistry and studying the biological function of in...
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Reposted by Uday Tak
Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
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Vaughn Cooper @vscooper.micropopbio.org · 25/09/2026
FYI to everyone submitting this October NIH cycle You need to re-certify your ScienCV AFTER Sept 26 (tomorrow) for your application or it may not be accepted. Great timing!
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Reposted by Uday Tak
ChimeraX @chimerax.ucsf.edu · 25/09/2026
Make natural language requests to ChimeraX with the new Pellaeon plugin developed by Yam Amir that works with many free and paid large language models. Get Pellaeon using ChimeraX menu Tools / More Tools.... cxtoolshed.rbvi.ucsf.edu/apps/chimera...
PAR1 molecular structure shown in ChimeraX using Pellaeon chat bot.
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Reposted by Uday Tak
Ákos T Kovács @evolvedbiofilm.bsky.social · 25/09/2026
Here it is online, a week after the teaser talk at #EMBOBacNet... @natmicrobiol.nature.com by @humollidorentina.bsky.social et al from @aharms485.bsky.social with @veeninglab.com Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ www.nature.com/articles/s41...
nature.com
Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ - Nature Microbiology
HIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing) is a transposon-insertion sequencing method for phages that systematically links their genes to selectable phenotypes.
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Erin Hotchkiss @fluvialbenthos.bsky.social · 24/09/2026
We (Biological Sciences at Virginia Tech) are #hiring TWO tenure-track Molecular Microbiology professors! Review of applications starts 1 Nov. I'm happy to answer questions about the department, VT, life in Blacksburg, etc.! More info / to apply: jobs.apply.vt.edu/jobs/assista... 🧪👩‍🔬🦠 #academicjobs
jobs.apply.vt.edu
Assistant/Associate Professor - Blacksburg, Virginia, United States
Job Description The Department of Biological Sciences in the College of Science at Virginia Tech seeks applicants for two (2) tenure-track research and teaching positions at the Assistant/Associate ...
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Reposted by Uday Tak
Vasilii Mikirtumov @vasiliimikirtumov.bsky.social · 24/09/2026
thrilled to share that my main phd project is finally out in @natcomms.nature.com we present high-resolution structures of RyR1 in native membranes across multiple functional states by both cryo-ET/StA #TeamTomo and SPA! paper: www.nature.com/articles/s41... and a thread below⬇️⬇️⬇️
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Maya Voichek @mayavoichek.bsky.social · 24/09/2026
Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)
AI-generated illustration of the soma-to-germline transmission of retrotransposons described in our work
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John Helmann @johnhelmann.bsky.social · 23/09/2026
Bacillus subtilis biofilm formation is strongly stimulated by manganese. New results from Sachla et al. show that a Mn export protein (MeeY) and YybP are important for biofilm regulation, maturation, and proper matrix metalation 🎉🧪🦠 #Microsky www.nature.com/articles/s41...
nature.com
MeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - MeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 23/09/2026
A genome language model reveals the interactions hidden in non-coding DNA, pointing to new putative RNAs and repetitive elements in bacterial genomes. @garykbrixi.bsky.social @maxewilkinson.bsky.social @mfgrp.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.6...
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Daniel Fisch @danielhfisch.bsky.social · 23/09/2026
Out now @nature.com! We report a new means of cell communication: receptor-free signal transduction. TLRs engage MyD88 for minutes, yet myddosomes signal for hours. TRAM releases myddosomes from TLRs, letting them mature and sustain signaling in the cytosol. rdcu.be/jGdKxErXyAsa Details below:
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Daria Van Tyne @dariavantyne.bsky.social · 22/09/2026
My lab at Pitt is looking for a Laboratory Technician to help our research and phage therapy efforts. Please share and apply! cfopitt.taleo.net/careersectio...
cfopitt.taleo.net
Laboratory Technician
Click the link provided to see the complete job description.
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Reposted by Uday Tak
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇
Schematics of how single strand RNA and DNA phages infect bacteria with F-pilus
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Petra Levin @redrockcity.bsky.social · 19/09/2026
4 years (!) in the making, in this review Jade Wang and I detail the fundamental processes underlying growth, the cell autonomous nature of homeostatic control, and the contribution of stochasticity to both. TL;DR Bacteria are more like teenagers than you think. www.nature.com/articles/s41...
nature.com
Bacterial growth rate in populations and single cells - Nature Microbiology
In this Perspective, Levin and Wang give a brief history of bacterial growth rate and discuss how it is connected to nutrient availability and macromolecule synthesis, with a focus on (p)ppGpp as a ce...
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Doudna Lab @doudna-lab.bsky.social · 19/09/2026
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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Kranzusch Lab @kranzuschlab.bsky.social · 17/09/2026
New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 17/09/2026
A lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein PNAS from @ramamurthilab.bsky.social www.pnas.org/doi/10.1073/...
pnas.org
A lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein | PNAS
The correct subcellular localization of proteins is a critical step underlying myriad biological processes, but the cues that drive the specific lo...
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Malcolm White @mfwhite2.bsky.social · 16/09/2026
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Michael Hothorn @structplantbio.bsky.social · 11/09/2026
Nice work by @cellsensing.bsky.social Glycan recognition by a plant damage-sensing immune receptor www.science.org/doi/10.1126/...
science.org
Glycan recognition by a plant damage-sensing immune receptor
Pathogens target and degrade the extracellular matrix surrounding plant cells. A central question is how cell wall-derived damage-associated molecular patterns (DAMPs) are recognized and integrated to...
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artemisaev.bsky.social @artemisaev.bsky.social · 11/09/2026
Chromatin structure controls defense island expression! Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and overcomes anti-defense proteins but raises toxicity. Common lab strains still hide novel immunity modules! www.biorxiv.org/content/10.6...
biorxiv.org
H-NS silences antiviral immunity through 3D chromatin compaction
Bacterial antiviral immunity systems can be toxic to their hosts and must be tightly regulated. Immunity genes are often encoded by AT-rich mobile genetic elements subjected to silencing by nucleoid b...
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Ellinor Alseth @ellinoralseth.bsky.social · 11/09/2026
What a Friday, finally seeing this published in @cp-trendsmicrobiol.bsky.social! We hope this will be of interest to anyone working in the bacterial immune system field (or microbiology in general), and who wants an evolutionary take on it 🦠🧫 Open Access link: authors.elsevier.com/a/1nllx,L%7E...
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GranucciLab @granuccilab.bsky.social · 10/09/2026
What if PRRs are not the first to sense #infection? 🚨Our new paper out in #NatureImmunology! @natimmunol.nature.com Microbial adhesion acts an unrecognized danger signal, activating #Piezo1 → LTB4 and triggering #PRR independent early #neutrophil recruitment. 🔗 www.nature.com/articles/s41...
nature.com
Microbial adhesion promotes Piezo1 activation to initiate innate immunity - Nature Immunology
Granucci and colleagues identify microbial adhesion to myeloid cells as a critical initiating event that precedes engagement of pattern recognition receptors.
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 09/09/2026
Gabija restricts phage circularization & DNA replication Gabija prevents phage genome circularization & replication w/out impacting bacterial host. Exposed DNA ends & phage end-binding proteins license DNA targeting while RecBCD protects host from Gabija www.cell.com/cell-host-mi...
cell.com
Gabija restricts phage circularization and DNA replication
Gabija acts early during phage infection, preventing phage genome circularization and replication. Phage DNA end-binding proteins prevent RecBCD loading onto linear DNA, and the absence of RecBCD lice...
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Drummond Lab @drummondlab.bsky.social · 08/09/2026
We are hiring! 🌟 Dept of Biochemistry and Molecular Biology at the University of Chicago is searching for a tenure-track assistant professor. It's a broad search: we want great colleagues doing serious biological work at the molecular scale. Join us! apply.interfolio.com/191981 bcmb.uchicago.edu
A picture of the University of Chicago campus, with downtown Chicago in the distance and Lake Michigan on the horizon. The campus's central quad is pictured, a classical collegiate quad with paths and old trees and stone architecture. It's really pretty and I love it.
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Jim Sun, PhD @sunlab.bsky.social · 09/09/2026
We are looking for a postdoctoral fellow to join the team @ubcmicroimmuno.bsky.social @science.ubc.ca to study TB pathogenesis and host-directed therapy! Please help disseminate amongst your network. ubc.wd10.myworkdayjobs.com/ubcfacultyjo...
ubc.wd10.myworkdayjobs.com
Postdoctoral Research Fellow - Host-Pathogen Interactions & Host-Directed Therapeutics
Academic Job Category Faculty Non Bargaining Job Title Postdoctoral Research Fellow - Host-Pathogen Interactions & Host-Directed Therapeutics Department Research I Sun I Department of Microbiology...
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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Paul Rainey @paulbrainey.bsky.social · 07/09/2026
A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔 doi.org/10.1093/gbe/...
doi.org
Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak
Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out
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Jim Hurley @jimhurley.bsky.social · 06/09/2026
The ULK1 complex triggers autophagy on membranes, but with no typical membrane binding domains, how does it get there? See the answer in a brilliant collective effort out now in Science Advances: www.science.org/doi/10.1126/....
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Fred Hutch @fredhutch.org · 04/09/2026
🔬 Fred Hutch Cancer Center is hiring an Assistant or Associate Professor in the Basic Sciences Division @basicsci.fredhutch.org. Join a world-class research community in Seattle and help advance discoveries in fundamental biology. Apply: apply.interfolio.com/190640
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Carina de Oliveira Mann @oliveiramann.bsky.social · 21/08/2026
@indrabekere.bsky.social probed a nucleotide library from bacterial & invertebrate signaling molecules in human cells, looking for new signaling. A great tool for mapping STING's preferences across cyclic nucleotides, incl. pyrimidine-purine hybrids.
cell.com
STING agonist profiling by nucleotide library defines structural determinants of cyclic dinucleotide recognition
Biochemistry; Genetics; Molecular structure
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Max Jordan @maxljordan.bsky.social · 04/09/2026
Really excited to share our new manuscript on how the #NLR protein #AfsR regulates #Streptomyces antibiotic production - and how we can use its similarity to plant NLR immune receptors to enhance this production! 📄🧵 (1/17) @johninnescentre.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
A conserved NLR activation switch governs global transcriptional control of antibiotic biosynthesis in Streptomyces
Nucleotide-binding and oligomerization domain-like receptors (NLRs) are conserved molecular switches that regulate innate immunity across diverse domains of life. While best known for their roles in i...
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Tatta Bio @tattabio.bsky.social · 04/09/2026
UniProt is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.
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Paul Thomas @pgtimmune.bsky.social · 04/09/2026
TCR specificity prediction is advancing rapidly. The central question is not only which TCR sequence recognizes an antigen, but also which TCR pairings make recognition possible & where is the binding boundary? Our new paper tackles these questions. 🧵 www.science.org/doi/10.1126/...
science.org
Uneven TCR chain pairing constraints govern epitope recognition
Combinatorial pairing of independently recombined T cell receptor (TCR) α- and β-chains is central to diversifying the TCR repertoire. Although sequence motifs in one chain correlate with epitope reco...
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