Lightnews — Scholar-powered news

Reposted by Anke Sparmann

Edda Schulz @eddaschulz.bsky.social · 2d

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology

Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

www.nature.com

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Reposted by Anke Sparmann

James Briscoe @jamesbriscoe.bsky.social · 8d

Meet the 2025 cohort of @dev-journal.bsky.social Pathway to Independence fellows

Read about the scientific visions of eight dev bio post-docs entering the academic job market

journals.biologists.com/dev/article/...

Pathway to Independence: a forecast for the future of developmental biology

ABSTRACT. In 2022, Development launched its Pathway to Independence (PI) programme, aimed at supporting postdocs as they transition to their first independent position. In 2025, we welcome our third c...

journals.biologists.com

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Reposted by Anke Sparmann

Nature Biotechnology @natbiotech.nature.com · 16d

Inspired by bacteria’s defense strategies, scientists pioneer a novel method for genome editing #NBTintheNews via @helmholtzhzi.bsky.social www.helmholtz-hzi.de/en/media-cen...

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Anke Sparmann @ankesparmann.bsky.social · 26d

2/2 @jorg-vogel-lab.bsky.social, @gerovac.bsky.social & team @helmholtz-hiri.bsky.social developed a non-genetic antisense oligomer approach to silence phage genes and probe their function—a powerful tool for functional genomics & phage therapy. Now out @nature.com go.nature.com/46b1XAQ

Cartoon depiction of the antisense oligomer approach to silence transcripts from phages in infected bacteria. In the top left, a bacteriophage infects a bacterial cells and injects its DNA, which is transcribed into an mRNA and expressed into a protein. In the top right, antisense oligomers (shown in red) delivered into the bacterium bind to the target phage mRNA and prevent synthesis of the phage protein. If the encoded protein is essential, phage replication and bacterial cell lysis (shown on the bottom right) are halted and the bacterium is protected, depicted by a red shield (bottom left).

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Anke Sparmann @ankesparmann.bsky.social · 26d

1/2 Bacteriophages are among Earth’s most diverse biological entities, but many resist genetic manipulation. This leaves much of their diversity unexplored and constrains efforts to discover new proteins and exploit their potential for biotechnology and therapeutic applications.

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Reposted by Anke Sparmann

Nature Biotechnology @natbiotech.nature.com · 26d

A systemic screen using programmable antisense oligomers to silence genes of DNA and RNA phages identifies proteins essential for phage propagation. This tool offers potential for optimizing phage therapy. #NBThighlight www.nature.com/articles/s41...

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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Life Science Editors @lifescienceeditors.bsky.social · 28d

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Karolin Luger @nucleosomepolice.bsky.social · Jul 26

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial.
rdcu.be/exXBX

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Danny IncaRNAto @incarnatolab.bsky.social · Jul 27

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

nature.com

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Mitch Guttman @mitchguttman.bsky.social · Jul 26

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...

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Research & Innovation | University of Toronto Mississauga @utm-research.bsky.social · Jul 15

Could lab-grown mini-organs help scientists research a range of infections? A new study published in Nature Genetics shows how researchers have mapped how the Shigella bacterium infects the human gut.

Read our interview with study co-author — and UTM Biology prof — Lars Barquist at uoft.me/bI7.

Prof. Lars Barquist. Story title: One the Map: Experimental Research Uses Cultured Mini-Organs to Study Infections

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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · Jun 19

Big thanks to scientific writer Libera Lo Presti for this great little piece on our recent work exploring how proton pump inhibitors (PPIs) and pH affect human gut microbes.
Check it out here: go.nature.com/4lf6jNk

The pill that might be relieving your heartburn but killing your gut microbes

Why drugs commonly used against heartburn harm your gut microbiome

go.nature.com

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Reposted by Anke Sparmann

Randall Munroe @xkcd.com · Jul 1

Laser Danger

xkcd.com/3108/

3-panel comic. (1) PERSON WITH SHORT HAIR to Person 2: Shining laser pointers at planes is a federal crime. It’s incredibly dangerous. PERSON 2: Oh, because it can blind the pilot? SHORT HAIR: That’s one reason… (2) [Laser pointed at flying airplane] (3) [Cat close to the size of the plane pouncing on airplane and taking it down]

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Anke Sparmann @ankesparmann.bsky.social · Jun 30

Apparently hell keeps business hours :)

Reposted by Anke Sparmann

Nature Portfolio @natureportfolio.nature.com · Jun 17

A study in Nature Genetics establishes the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. go.nature.com/4e7fdKp 🧬 🧪

This is figure 2, which shows a genome-wide map of the Shigella geneset required to invade the human enteroid infection model.

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Westermann Lab @westermannlab.bsky.social · Jun 17

Our latest: www.cell.com/cell-reports/fulltext/S2211-1247(25)00615-1. Links Bacteroides cell size w/ gene expression. Protocol works even for single cells. 🦠
Shoutout to @elisebor.bsky.social, @emmanuel-saliba.bsky.social, @lbarquist.bsky.social, @jorg-vogel-lab.bsky.social, Till Strowig & KC Huang.

Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium

Bornet et al. investigate the morphological heterogeneity of Bacteroides thetaiotaomicron cells observed both in laboratory culture and inside the mammalian GI tract. The authors show that cell size i...

www.cell.com

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Francesca Mattiroli @fmattiroli.bsky.social · Jun 13

Big shoutout to this amazing work from our colleagues in the Knipscheer lab. Congratulations on discovering and dissecting yet another new molecular mechanism that keeps our genome safe! 👏🍾

puckknipscheer.bsky.social @puckknipscheer.bsky.social · Jun 13

Excited our paper is out! G-quadruplex (G4) unwinding via an intricate G-loop assembly and disassembly mechanism maintains genome integrity. Pioneered by Koichi Sato with great collaborators Jing Lyu and @simonelsasser.bsky.social Check it out: www.science.org/doi/10.1126/science.adr0493 🧵(1/4)

RNA transcripts regulate G-quadruplex landscapes through G-loop formation

G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics are controlled remains poorly understood. Here, we report that RNA tra...

www.science.org

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Shazeb Ahmad @shazebahmad.bsky.social · Jun 11

Excited to share my first-author publication from my #PhD work at @helmholtz-hiri.bsky.social 🎉

We established mudRapp-seq, a spatial transcriptomic technique that combines direct RNA padlock probing and in-situ sequencing.

academic.oup.com/nar/article/...

Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq)

Abstract. Influenza A viruses (IAVs) contain eight negative-sense single-stranded viral RNA (vRNA) molecules, which are transcribed into messenger RNA (mRN

academic.oup.com

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Helmholtz Institute Würzburg @helmholtz-hiri.bsky.social · Jun 12

Thanks to lab-grown miniature intestines, researchers at #HIRI & Uppsala University have mapped how Shigella bacteria infect the human gut. This @natgenet.nature.com study opens the door to using cultured mini-organs to investigate a wide range of infections. 📍🦠
www.nature.com/articles/s41...

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen - Nature Genetics

A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

www.nature.com

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Helmholtz-Zentrum für Infektionsforschung (HZI) @helmholtzhzi.bsky.social · Apr 29

#Fusobakterien gehören zur normalen Mundflora, stehen aber auch im Verdacht, das Wachstum von Krebs zu fördern. Forscher:innen @helmholtz-hiri.bsky.social zeigen nun, dass eine Peptidnukleinsäure-Verbindung das Wachstum versch. Fusobakterien-Stämme stoppen kann.
www.helmholtz-hzi.de/media-center...

Unerwarteter Bakterienstopper

HIRI-Forschende entdecken Peptidnukleinsäure-Verbindung, die das Wachstum von fünf Arten der Tumor-assoziierten Fusobakterien stoppt.

www.helmholtz-hzi.de

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König Lab @koenig-lab.bsky.social · Apr 29

Join us this Wednesday at 4 pm! Cheers!

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Michael Eisen @mbeisen.bsky.social · Apr 15

Wow. They really ARE trying to destroy science.

Elinne Becket, PhD @bielleogy.bsky.social · Apr 15

Whyyyyyyyyyyyy did NIH study sections switch to Teams????

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Mona Alzheimer @monaalzheimer.bsky.social · Apr 8

New preprint from @westermannlab.bsky.social about a pair of antagonistic #Salmonella sRNAs. Check it out 👇🏻

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Apr 8

Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1

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Anke Sparmann @ankesparmann.bsky.social · Apr 9

Microbial single-cell MATQ-seq developed by @emmanuel-saliba.bsky.social & @jorg-vogel-lab.bsky.social allows detection of a large number of genes per single bacterium & stands out for its high rate of cell retention.
For a detailed protocol, see rdcu.be/eg0Xc, now available @natprot.bsky.social.

Transcriptomic profiling of individual bacteria by MATQ-seq

Nature Protocols - Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it...

rdcu.be

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Thomas Lemberger @tlemberger.bsky.social · Mar 19

Science under attack: a growing list of statements from journals
@jama.com
jamanetwork.com/journals/jam...

@plos.org
theplosblog.plos.org/2025/02/plos...

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

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

@embopress.org
www.embopress.org/doi/full/10....

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