Anke Sparmann

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

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.

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)

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...

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

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.

The pill that might be relieving your heartburn but killing your gut microbes Why drugs commonly used against heartburn harm your gut microbiome

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

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]

Laser Danger

xkcd.com/3108/

Apparently hell keeps business hours :)

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

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

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...

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.

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! 👏🍾

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

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/...

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.

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...

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

#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...

Join us this Wednesday at 4 pm! Cheers!

Wow. They really ARE trying to destroy science.

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

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...

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.

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....

RNA

xkcd.com/3056
#RNAsky

exit strategy:
🌿🏡🌿

Really nice issue of RNA this month featuring many Perspective pieces on RNA in disease. rnajournal.cshlp.org/content/31/3...

On the cover: This image shows a multicolored wave pattern, resembling longitudinal wave patterns or Weibull and other distributions, evoking the presence of data and knowledge everywhere. Image credit: Andriy Onufriyenko/Moment via Getty Images.

Our February issue is now live!

www.cell.com/patterns/iss...

This issue includes new research on gene fusion detection, AI model interpretability trade-offs, renewable energy potential assessments, & more. Plus, in an editorial, we share some thoughts from the journal on the EU AI Act.

Viruses that infect animals can frequently penetrate human cells, but their replication is blocked after entry. Are there intracellular human antiviral restriction factors we are not aware of yet? 🧐

Love Methods Week - Aktuelles - BIH at Charité In dieser Woche werden mehrere Workshops und Seminare rund um das Thema Reproduzierbarkeit von Methoden angeboten. (In Englisch)

#LoveMethods25 (24.02.2025 - 28.02.2025) features online events relating to method reproducibility. Nature Protocols editors will be present at three of these events (Monday, Wednesday, Thursday). Register to join the discussion!

www.bihealth.org/de/aktuell/l...

🧪 Today we celebrate Charles Darwin (born on this day in 1809) and his groundbreaking work on #evolution by #naturalselection — one of the most important scientific discoveries of all time

#BioSky #EduSky #SciArt #DarwinDay

Happy Birthday dem Sechsjährigen!

This is figure 1, which shows the effects of antibiotics on human health and the microbiome and hypothetical mechanisms of probiotics in ameliorating these effects.

A Review in Nature Reviews Gastroenterology & Hepatology discusses the evidence for antibiotic-mediated perturbation of the gut microbiota and whether probiotics can help restore an antibiotic-disrupted microbiota. https://go.nature.com/4gslPCt 🔒

Proud to see our lab’s work contribute to this fantastic study, and specifically: "[...]We have recently developed a new strategy to genetically trace cell fate transitions within a heterogeneous tissue37,38 [...]" Check it out! 👇

🚀 New Paper Alert! 🚀

𝐑𝟐𝐃𝐓: a comprehensive platform for visualising RNA secondary structure

Check it out in @narjournal.bsky.social:
academic.oup.com/nar/article/...

Here’s why you should give it a try 🧵👇

‘We are a target’: scientific society under pressure after Trump DEI crackdown The American Society for Microbiology deleted terms such as equity from its website, sparking protests from members.

The American Society for Microbiology has altered its website to remove references to diversity and equity

https://go.nature.com/416ufLy