Reposted by Uday TakbioRxivpreprint @biorxivpreprint.bsky.social · 4hGalaxyMemMD: 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… 011
Reposted by Uday TakSeth 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! 1156
Reposted by Uday TakSternberg Lab @sternberglab.bsky.social · 05/10/20261/2 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.orgArc represses gene expression in IS605-family transposonsBacterial 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... 13612
Uday Tak @nokaryote.bsky.social · 05/10/2026JOB 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/191946apply.interfolio.com Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio 044
Reposted by Uday TakChrystal Starbird @drstarbird.bsky.social · 01/10/2026And… 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... 710222
Reposted by Uday TakBrian D. Wade @astrobrian.bsky.social · 02/10/2026How bacterial immune systems sense phage infection #bacteriophage #phage #microSky #scienceSky www.nature.com/articles/s41...nature.comHow bacterial immune systems sense phage infection - Nature Reviews MicrobiologyBacteria 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... 0214
Reposted by Uday TakKranzusch Lab @kranzuschlab.bsky.social · 01/10/2026Our 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.orgPhage proteases activate CBASS antiphage immunityCyclic 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. ... 08638
Reposted by Uday TakJoe Zackular @joeyzacks.bsky.social · 01/10/2026Congratulations 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.orgEmerging Voices in MicrobiologyAnnual initiative highlighting standout early-career Infection and Immunity researchers through invited, peer-reviewed minireviews in Emerging Voices. 1238
Reposted by Uday TakMark 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 153
Reposted by Uday TakEirik Lågeide @eiriklag.bsky.social · 01/10/2026Very 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.orgNO VEIN is an ancestral immunity protein involved in plant-virus interactionThe 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... 28851
Reposted by Uday TakJolyon 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 12261129
Reposted by Uday TakSternberg Lab @sternberglab.bsky.social · 28/09/20261/13 — 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... 15122
Reposted by Uday TakGeorge O'Toole (he/him/his) @geiselbiofilm.bsky.social · 26/09/2026Pls 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.eduAssistant/Associate Professor - Blacksburg, Virginia, United StatesJob 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 ... 01434
Reposted by Uday TakJörg Stülke @joergstuelke.bsky.social · 26/09/2026Identification of a novel RNA-modifying enzyme! RlmS! #SubtiWiki www.pnas.org/doi/10.1073/...pnas.orgActivity-based profiling of bacterial RNA-modifying enzymes reveals species-specific 5-methyluridine modification in Bacillus subtilis 23S rRNA | PNASRNA modifications play an important role in biological processes. Mapping the diversity of RNA chemistry and studying the biological function of in... 01910
Reposted by Uday TakAlexander Harms @aharms485.bsky.social · 25/09/2026The 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 515473
Reposted by Uday TakRasmus 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 1023696
Reposted by Uday TakVaughn Cooper @vscooper.micropopbio.org · 25/09/2026FYI 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! 78592
Reposted by Uday TakChimeraX @chimerax.ucsf.edu · 25/09/2026Make 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... 05217
Reposted by Uday TakÁkos T Kovács @evolvedbiofilm.bsky.social · 25/09/2026Here 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.comSystematic mapping of bacteriophage gene essentiality with HIDEN-SEQ - Nature MicrobiologyHIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing) is a transposon-insertion sequencing method for phages that systematically links their genes to selectable phenotypes. 0144
Reposted by Uday TakErin Hotchkiss @fluvialbenthos.bsky.social · 24/09/2026We (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... 🧪👩🔬🦠 #academicjobsjobs.apply.vt.eduAssistant/Associate Professor - Blacksburg, Virginia, United StatesJob 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 ... 03348
Reposted by Uday TakVasilii Mikirtumov @vasiliimikirtumov.bsky.social · 24/09/2026thrilled 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⬇️⬇️⬇️ 45820
Reposted by Uday TakMaya Voichek @mayavoichek.bsky.social · 24/09/2026Super 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) 20257148
Reposted by Uday TakJohn Helmann @johnhelmann.bsky.social · 23/09/2026Bacillus 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.comMeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation - npj Biofilms and Microbiomesnpj Biofilms and Microbiomes - MeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation 1279
Reposted by Uday TakKevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 23/09/2026A 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... 1177
Reposted by Uday TakDaniel Fisch @danielhfisch.bsky.social · 23/09/2026Out 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: 43214
Reposted by Uday TakDaria Van Tyne @dariavantyne.bsky.social · 22/09/2026My 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.netLaboratory TechnicianClick the link provided to see the complete job description. 0824
Reposted by Uday TakDavid Bikard @dbikard.bsky.social · 21/09/2026New 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 311256
Reposted by Uday TakMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026Fold 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/ 215759
Reposted by Uday TakVivek Mutalik @vivekmutalik.bsky.social · 19/09/2026Some 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 🧵👇 513557
Reposted by Uday TakPetra Levin @redrockcity.bsky.social · 19/09/20264 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.comBacterial growth rate in populations and single cells - Nature MicrobiologyIn 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... 17430
Reposted by Uday TakDoudna Lab @doudna-lab.bsky.social · 19/09/2026Out 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 & teamscience.orgA noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-CasCRISPR-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... 217570
Reposted by Uday TakKranzusch Lab @kranzuschlab.bsky.social · 17/09/2026New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac... 14319
Reposted by Uday TakÁkos T Kovács @evolvedbiofilm.bsky.social · 17/09/2026A 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.orgA lipid cue drives the subcellular localization of a self-inserting bacterial transmembrane protein | PNASThe correct subcellular localization of proteins is a critical step underlying myriad biological processes, but the cues that drive the specific lo... 1173
Reposted by Uday TakMalcolm White @mfwhite2.bsky.social · 16/09/2026Our 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... 14628
Reposted by Uday TakSergey Ovchinnikov @sokrypton.org · 14/09/2026Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr) 727698
Reposted by Uday TakMichael Hothorn @structplantbio.bsky.social · 11/09/2026Nice work by @cellsensing.bsky.social Glycan recognition by a plant damage-sensing immune receptor www.science.org/doi/10.1126/...science.orgGlycan recognition by a plant damage-sensing immune receptorPathogens 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... 06734
Reposted by Uday Takartemisaev.bsky.social @artemisaev.bsky.social · 11/09/2026Chromatin 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.orgH-NS silences antiviral immunity through 3D chromatin compactionBacterial 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... 02518
Reposted by Uday TakEllinor Alseth @ellinoralseth.bsky.social · 11/09/2026What 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... 32815
Reposted by Uday TakGranucciLab @granuccilab.bsky.social · 10/09/2026What 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.comMicrobial adhesion promotes Piezo1 activation to initiate innate immunity - Nature ImmunologyGranucci and colleagues identify microbial adhesion to myeloid cells as a critical initiating event that precedes engagement of pattern recognition receptors. 082
Reposted by Uday TakCell Host & Microbe @cp-cellhostmicrobe.bsky.social · 09/09/2026Gabija 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.comGabija restricts phage circularization and DNA replicationGabija 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... 0237
Reposted by Uday TakDrummond Lab @drummondlab.bsky.social · 08/09/2026We 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 190108
Reposted by Uday TakJim Sun, PhD @sunlab.bsky.social · 09/09/2026We 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.comPostdoctoral Research Fellow - Host-Pathogen Interactions & Host-Directed TherapeuticsAcademic Job Category Faculty Non Bargaining Job Title Postdoctoral Research Fellow - Host-Pathogen Interactions & Host-Directed Therapeutics Department Research I Sun I Department of Microbiology... 0919
Reposted by Uday TakFrançois 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.orgA widespread NADase domain links bacterial immunity with human TEP1Recent 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 ... 49354
Reposted by Uday TakPaul Rainey @paulbrainey.bsky.social · 07/09/2026A 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.orgInterspecies Exchange of Mobile Genetic Elements During a Plant Disease OutbreakAbstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out 16627
Reposted by Uday TakJim Hurley @jimhurley.bsky.social · 06/09/2026The 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/.... 14418
Reposted by Uday TakFred 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 1129
Reposted by Uday TakCarina 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.comSTING agonist profiling by nucleotide library defines structural determinants of cyclic dinucleotide recognitionBiochemistry; Genetics; Molecular structure 0155
Reposted by Uday TakMax Jordan @maxljordan.bsky.social · 04/09/2026Really 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.orgA conserved NLR activation switch governs global transcriptional control of antibiotic biosynthesis in StreptomycesNucleotide-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... 23022
Reposted by Uday TakTatta Bio @tattabio.bsky.social · 04/09/2026UniProt 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. 13811
Reposted by Uday TakPaul Thomas @pgtimmune.bsky.social · 04/09/2026TCR 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.orgUneven TCR chain pairing constraints govern epitope recognitionCombinatorial 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... 22210