Lightnews — Scholar-powered news

Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 14h

🚀 Released gbdraw v0.6.0!

- Added dinucleotide skew plotting to linear mode. Fixed the bug where only GC skew could be drawn.

- Added links to relevant sections of the documentation throughout the web app help menu.

Try out:👉 gbdraw.streamlit.app

A grid of 12 circular E. coli genome maps showing dinucleotide skew plots for GC, CG, AG, GA, CT, TC, TG, GT, CA, AC, AT, and TA. Each circle displays color-coded genome annotations (CDS, rRNA, tRNA, etc.) around the outer ring, with inner line plots showing positive and negative dinucleotide skew values.
Below the grid, a linear representation of two E. coli genomes shows annotated tracks, GC content, and GC skew plots, with two genomes linked with ribbons representing BLASTN hits. Note that the lower track (pathogenic strain O157:H7 Sakai) has multiple prophage insertions (shaded with orange) that are absent from the upper track (the laboratory strain K-12). Further below are five linear genome comparison diagrams of Hepatoplasmataceae mollicutes, each with colored gene annotations, GC content and GC skew plots, and gray ribbons indicating TBLASTX hits across genomes.

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Asher Leeks @asherleeks.bsky.social · 2d

I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.

#socialviruses #evosky #virosky 🧪

The social lives of viruses | Asher Leeks | TEDxNewEngland

YouTube video by TEDx Talks

www.youtube.com

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The Daum Lab @daumlab.bsky.social · 3d

Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail

This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.

www.science.org

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Thibaut Brunet @thibautbrunet.bsky.social · 4d

Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵

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Jozef Nissimov @jinoceanvir.bsky.social · 6d

(1/9) Latest preprint from our lab at
@uwaterloo.ca conceived predominantly by our very talented #PhD #student Isaac Meza-Padilla:

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

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Lucas Farnung @lucas.farnunglab.com · 10d

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

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Evgenii Protasov @evgenii-protasov.bsky.social · 11d

“Paraxenoviridae”, a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes
#viruses #bacteriophages #phages
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...

“Paraxenoviridae”, a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes

Abstract. Metatranscriptome sequencing dramatically expanded the known diversity of the global RNA virome and, in particular, suggested several new candida

academic.oup.com

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Stèf Blanc @steffffff.bsky.social · 16d

It is now on air.
Please look it up and join us!
Great science and wonderful venue👍🏻

www.isdv2026.com

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Martial Marbouty @mmarbout.bsky.social · 20d

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

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

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com

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Enninga Lab @enningalab.bsky.social · 21d

🦠 Mycobacteria aren't just tough, they're interior designers! 🦠 Check out our latest #preprint 🚨, led by our PhD student @camimille.bsky.social , where we show that #Mycobacterium tuberculosis builds secret cytoplasmic membranes to adapt its metabolism and sneak past immunity 🤫

Thread coming soon!

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 21d

Nitrate-responsive Mycobacterial Intracytoplasmic Membranes dampen Inflammation during Mycobacterium tuberculosis Infection https://www.biorxiv.org/content/10.1101/2025.09.17.676823v1

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Sonja-Verena Albers @archaellum.bsky.social · 22d

Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...

Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social

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Andrian Gajigan @adi-gajigan.bsky.social · 22d

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail - Nature Communications

Rodrigues and Queiroz et al. report the discovery of Naiavirus, the largest enveloped virus, isolated from a Brazil biome. With an oval capsid and flexible tail, its giant genome holds many novel gene...

nature.com

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Thelonevirologist @thelonevirologist.bsky.social · 22d

Discovery of a novel double-stranded DNA virus associated with ant labial gland disease reveals its long-term interaction with ants journals.asm.org/doi/10.1128/...

Discovery of a novel double-stranded DNA virus associated with ant labial gland disease reveals its long-term interaction with ants | Journal of Virology

Ants, as highly eusocial insects, play vital roles in ecosystems worldwide. While numerous RNA viruses have been documented in ants, no double-stranded DNA (dsDNA) virus has previously been confirmed to infect them. Labial gland disease, reported for decades, lacks a clearly defined cause until now. Here, we identify and characterize a large filamentous dsDNA virus, Camponotus japonicus labial gland disease virus (CjLGDV), from the swollen labial gland of C. japonicus, and a closely related Anoplolepis gracilipes labial gland disease virus in A. gracilipes. Phylogenetic and genomic analyses of the two viruses support the establishment of a new viral family within the order Lefavirales, class Naldaviricetes. The discovery of endogenous viral elements related to CjLGDV in multiple ant genomes suggests the historical infection of CjLGDV-like viruses in ants. These findings broaden the known host range of naldaviricetes and shed new light on the diversity, evolution, and host interaction of large dsDNA viruses in arthropods.

journals.asm.org

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Sofya Garushyants @garushyants.bsky.social · 23d

Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today

Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics | mBio

The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct an...

journals.asm.org

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Franklin Nobrega @fnobrega.bsky.social · 23d

Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu.

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

YprA family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...

www.biorxiv.org

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Milan Gerovac @gerovac.bsky.social · 28d

No Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence.
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social
@uni-wuerzburg.de @helmholtzhzi.bsky.social
published now in @nature.com

Programmable antisense oligomers for phage functional genomics - Nature

Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagatio...

www.nature.com

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

Today, I'm excited to announce the publication of the Duplodnaviria realm Profile and Chapter.
The realm includes viruses of archaea, bacteria and eukaryotes and is best known for its inclusion of herpesviruses and tailed phages.

www.microbiologyresearch.org/content/jour...

ICTV Virus Taxonomy Profile: Duplodnaviria 2025

The realm Duplodnaviria includes viruses of archaea, bacteria and eukaryotes, with linear dsDNA genomes. Duplodnavirians share a distinct morphogenetic module of four hallmark genes encoding the HK97-...

www.microbiologyresearch.org

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

The ICTV Report chapters, which are linked to the profiles and get updated when the taxonomy changes, can be found on the ICTV website:
ictv.global/report

ICTV Report Chapters | ICTV

ictv.global

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Evelien Adriaenssens @evelienadri.bsky.social · Sep 3

We have expanded our ICTV Virus Taxonomy profiles and chapters to include higher ranks, which have been recently introduced and may not be familiar to all virologists.

You can find our 2-page Profiles (citable record) in JGV @microbiologysociety.org
www.microbiologyresearch.org/content/ictv...

ICTV Virus Taxonomy Profiles | Microbiology Society

Journal of General Virology ICTV Virus Taxonomy Profiles are a freely available series of concise, review-type articles that provide overviews of the classification, structure and properties of indivi...

www.microbiologyresearch.org

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Sorek Lab @soreklab.bsky.social · Sep 2

Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection

Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

www.biorxiv.org

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Mart Krupovic @mkrupovic.bsky.social · Sep 1

Many interesting PhD projects, including ours. Consider applying!

Institut Pasteur | 130 years of biomedical research @pasteur.fr · Sep 1

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry.

Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, [email protected], PPU-EID @upcite.bsky.social & more 🧬

Register now ✍️ www.pasteur.fr/en/education...

Pasteur-Paris University International Doctoral Programme, The call for enrollment of students in October 2026 will be open from September 1st to October 20th, 2025

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Institut Pasteur | 130 years of biomedical research @pasteur.fr · Sep 1

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry.

Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, [email protected], PPU-EID @upcite.bsky.social & more 🧬

Register now ✍️ www.pasteur.fr/en/education...

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Joe Peters Lab @joepeterslab.bsky.social · Aug 28

De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems www.biorxiv.org/content/10.1...

De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems

Programmable DNA integration using CRISPR-associated transposons (CASTs) offers powerful capabilities for genome engineering. The single effector Cas12k CAST examples evolved from a fixed guide TnpB n...

www.biorxiv.org

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Karthik Anantharaman @karthik-a.bsky.social · Aug 27

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

www.nature.com

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Stèf Blanc @steffffff.bsky.social · Aug 26

To all friends and colleagues virologists

SAVE THE DATE for the next International Symposium on Single Stranded DNA viruses

Ilhéus, Bahia, Brazil
June 15-19 2026

Stay put for more info soon when website goes on air !

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Caroline Puente-Lelievre @cpuentelelievre.bsky.social · Aug 22

#structuralphylogenetics #strphy #3di

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Mart Krupovic @mkrupovic.bsky.social · Aug 18

Check out our paper in PLoS Genetics with @umbertorosani.bsky.social and Marco Gerdol on the highly dynamic pangenome of basal chordates. It is enriched in defence and immunity genes (like in prokaryotes) and follows Mendelian inheritanceis rules. @plos.org journals.plos.org/plosgenetics...

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Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 18

See how phi3T phage shifts Bacillus subtilis cell shape in the absence of SPbeta prophage and alters its fitness - our new publication in @commsbio.nature.com from group of @annadragos.bsky.social together with @bramkamplab.bsky.social
www.nature.com/articles/s42...

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Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 17

Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes

@natcomms.nature.com Mike Sleutel et al from Han Remaut
w/ Marina Aspholm @jerryknowsnothing.bsky.social @mkrupovic.bsky.social @dbaquero.bsky.social

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

Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes - Nature Communications

B. thuringiensis spores contain uncharacterized protein filaments that extend from the surface of the exosporium. Here, the authors show that these filaments feature conserved β-barrel neck domains an...

www.nature.com

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Adrià Sogues @adriasogues.bsky.social · Aug 17

Many spores from the Firmicutes group are decorated with hair-like structures. Since the 60s, they remained a mystery. @remaut-lab.bsky.social named these fibres ENdospore Appendages (ENAs). Using Cryo-ID, we report the identity, structure and function of F-ENA.
www.nature.com/articles/s41...

Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes - Nature Communications

B. thuringiensis spores contain uncharacterized protein filaments that extend from the surface of the exosporium. Here, the authors show that these filaments feature conserved β-barrel neck domains an...

www.nature.com

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