Chemical inhibition of a bacterial immune system Bacteriophages are promising alternatives to antibiotics for treating bacterial infections. However, bacteria possess immune systems that neutralize bacteriophages. Zang et al. discover small molecule...

Really phenomenal work from the Gerdt lab at Indiana University... I hope this becomes a major boon for phage therapy:
"Chemical inhibition of a bacterial immune system"
www.cell.com/cell-host-mi...

Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation Development of LOV-domain-controlled ligase for translation localization (LOCL-TL), an optogenetic approach for monitoring translation with codon resolution at any defined subcellular location under p...

Proximity-specific ribosome profiling #ribosome #rnabiology in mitochondria
www.cell.com/cell/fulltex...

Diverse bacterial pattern recognition receptors sense the conserved phage proteome Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...

NLR-like immunity in bacteria

A new study from the Alex Gao lab. The scope of this work is incredible!!!

www.biorxiv.org/content/10.6...

A planetary atlas of plankton 🪐

Closing the year with a bang: out @cellcellpress.bsky.social the @dudinlab.bsky.social & @gautamdey.bsky.social labs used ultrastructure Expansion Microscopy to reveal the stunning cytoskeletal diversity of over 200 plankton species!

A #sciart 🧵

@embl.org

High-throughput transposon mutagenesis defines the essential genome of diverse phages Phages are important drivers of bacterial evolution with therapeutic potential as antimicrobials. However, gaps in our understanding of phages and our inability to rapidly engineer them with new genet...

#microsky #phagesky

The 3rd (? Lost track!) manuscript on a CRISPR/anti-CRISPR -based transposon tool to study gene essentiality in #phages

www.biorxiv.org/content/10.6...

'Twas the solstice in Woods Hole, when all through the labs, not a creature was stirring. Not even the crabs!

The Cape Cod Times is ringing in the longest night of the year with a celebration of all the science that happens here in Woods Hole! Catch the highlights go.whoi.edu/cct-winter

🌊📆 🌊 Ring in the new year with our 2026 wall calendar! Each of these amazing images of ocean life and field work was captured by our scientists and photographers—and your purchase helps support their work!

📲Order yours at the WHOI Store: go.whoi.edu/2025-calendar

📸 © #WHOI

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates - Nature Communications Ghatbale et al. adapted a co-evolutionary technique to develop Klebsiella pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates, including drug resistant isolate...

Congratulations to my student Josh Hensley and our amazing collaborators at UCSD David Pride lab! In press today, we developed a technique to evolve phages to broaden bacterial host range to tackle bacteria that evade antibiotics. #phagesky #phage #microsky #virussky

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

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

Amazing piece of work from @rtoshiro.bsky.social
& Kim Seed at UC Berkeley. 🙌
Played a tiny role in this work.

Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses

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

High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli Author summary Escherichia coli demonstrates a remarkable ability to adapt to diverse environments. This adaptability is in part connected to its ability to recombine incoming DNA in its chromosome, a...

#microsky 😮

journals.plos.org/plosgenetics...

Nested Connections: Local Phage and Broad Plasmid Sharing in the Honey Bee Mobilome Honey bees rely on bacterial symbionts for their nutritional needs and for protection against invading pathogens. Genetic diversity among strains within the colony has the potential to impact symbiont...

#microsky #phagesky #phage plasmids & other #MGE in the bee #microbiome

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

🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky

www.cell.com/cell/fulltex...

Wilkinson Lab We discover and study reverse transcriptases

The Wilkinson Lab is open for science! @mskcancercenter.bsky.social

🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬

annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)

Please join us next week for the second iteration of the DinoSphere Seminars! This time our two speakers will talk about host-associated dinoflagellates and any challenges they might have encountered when working with them. All current and future friends of dinoflagellates welcome!
#ProtistsOnSky

Bacterial TIR-based immune systems sense phage capsids to initiate defense - Nature Microbiology After sensing capsids, the Thoeris antiphage defense system triggers a cascade that leads to NAD+ cleavage and cell arrest, which are dynamics that are mirrored in some mammalian immune pathways.

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

#phagesky #phage defence system Thoeris

Emergence of antiphage functions from random sequence libraries reveals mechanisms of gene birth | PNAS De novo gene birth—the emergence of genes from nongenic sequences—drives biological innovation, yet its adaptive potential remains poorly understoo...

www.pnas.org/doi/10.1073/...

#phagesky #phage defence #synbio #microsky

This might be one of the coolest findings I’ve read this year!

Half of microbial eukaryote literature focuses on only twelve human parasites Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc

Half of microbial eukaryote literature focuses on only twelve human parasites

-in #ISMEJournal by Joanna Lepper, @hbrappap.bsky.social and @oliverio.bsky.social

academic.oup.com/ismej/advanc...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

THANK YOU FOR WRITING THIS!!!!

"Although this is a useful and even satisfying approach, the reality for MGEs is that they are best represented as a spectrum of inter-related elements (Fig. 1)."

Angomonas deanei with flourescent-labeled nucleus and endosymbiont. ETP9 localizes at the endosymbiont division site.

Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...

Delighted to see our work on #diatom motility published in @pnas.org !🎉
doi.org/10.1073/pnas...

These abundant single-celled algae are responsible for a significant portion of the air we breathe yet often overlooked. Here we show how how diatom (raphe) shape impacts their gliding function... 1/3

Vampyrella crystallifera sp. nov., an Amoeba That Dissolves Entire Algal Cells at a Remarkable Speed The new vampyrellid amoeba Vampyrella crystallifera inhabits wet Sphagnum plants in temperate moorlands. Unlike its congeners, it engulfs entire algal cells and breaks them down at a fascinating spee....

onlinelibrary.wiley.com/doi/10.1002/... #protistsonsky

Just out - The first global ocean 3-Domain microbial survey where all organisms can be directly compared quantitatively. Unfractionated and amplified from just 2 primers (vetted with mock communities and metagenomics), so all with the same denominator. www.biorxiv.org/content/10.1...

Some folks have asked, given recent news, “how do I show my friends/family the impact of NSF?” We have some easy Fact Sheets for you! Here’s a brief thread about this website: new.nsf.gov/about/fact-s... which hosts a ton of useful one-pagers.

Not all RNAs are created equal for the antiviral RNase ISG20 ISG20 is a broad-spectrum antiviral protein capable of specifically degrading viral RNA. Here, we examine the different strategies developed by viruses to evade ISG20-mediated restriction, shedding light on how this exonuclease distinguishes between self…

Not all RNAs are created equal for the antiviral RNase ISG20

Filamentous phages (viruses) spontaneously align into liquid crystals that protect the bacteria within from antibiotics, desiccation, and the immune system 🦠🧫🧪🧬
www.cell.com/cell-host-mi...

Alert to the #darkproteome community 👇

Here's a great article to get you fast-tracked into the world of #microproteins.

Such a pleasure to work on this piece with @nature.com, @sebastiaanvheesch.bsky.social, Marie Brunet, Jonathan Weissman and Jon Mudge.

#genomics
#bioinformatics
🧬 💻
#proteomics