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Tami Lieberman @contaminatedsci.bsky.social · 11h

We did not explicitly do that, but our assumption of varying local selective pressures is quite similar to some types of frequency dependent selection.

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Tami Lieberman @contaminatedsci.bsky.social · 14h

I believe that similar signatures have been found in mammals. academic.oup.com/mbe/article/...

Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

Abstract. Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged

academic.oup.com

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Tami Lieberman @contaminatedsci.bsky.social · 14h

Indeed it may be the same claim. We were cautious to restrict ourselves to species for which we have the most evidence, but perhaps this is generalizable.

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Tami Lieberman @contaminatedsci.bsky.social · 14h

Yes, thats our hypothesis. Its comes from observations of frequent in-person adaptive evolution involving stop codons in key genes (potentially phage receptors).

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Tami Lieberman @contaminatedsci.bsky.social · 14h

We've made a related but different claim in bacteria:
elifesciences.org/articles/93146

Reversions mask the contribution of adaptive evolution in microbiomes

The timescale dependence of dN/dS in bacteria is better explained by adaptive than purifying dynamics, suggesting comparative genomics can underestimate past adaptation.

elifesciences.org

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Reposted by Tami Lieberman

C. Brandon Ogbunu @cbo.bsky.social · 16h

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

In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS

Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...

www.pnas.org

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Reposted by Tami Lieberman

Claus Wilke @clauswilke.com · 19h

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Reposted by Tami Lieberman

Ryan Flynn @raflynn5.bsky.social · 21h

We found that csDNA is not restricted to cultured cells, but in health donors, B cells and monocytes had clear csDNA accumulation while T cells and NK cells did not.

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Reposted by Tami Lieberman

Ryan Flynn @raflynn5.bsky.social · 21h

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells

The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...

www.biorxiv.org

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Tami Lieberman @contaminatedsci.bsky.social · 19h

The response from the senator was quite bad-- talking only about policy and paperwork, when there was the opportunity to refute her claims about caring for the state and talk about freedoms.

Reposted by Tami Lieberman

Erik Bakkeren @erikbakkeren.bsky.social · 20h

Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️

MEEhubs @meehubs.bsky.social · 20h

We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org

Home

meehubs.org

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Reposted by Tami Lieberman

Maddy Seale @maddyseale.bsky.social · 1d

Wonderful to see this beautiful image on the cover of Science this week highlighting a paper that uses high resolution imaging to show the spatial patterns of bacterial attraction to glutamine from roots.
Paper here: www.science.org/doi/10.1126/...
Perspective here: www.science.org/doi/10.1126/...

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Reposted by Tami Lieberman

Dave Baltrus 🦦 @surtlab.bsky.social · 1d

Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination

academic.oup.com/g3journal/ad...

Genomic correlates of tailocin sensitivity in Pseudomonas syringae

Abstract. Phage-derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular enviro

academic.oup.com

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Reposted by Tami Lieberman

Richard Sever @richardsever.bsky.social · 1d

New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...

Preprint mandates gather momentum - openRxiv

By Richard Sever, PhD. Chief Science & Strategy Officer, openRxiv Preprints speed up science by enabling researchers to disseminate reports of new findings immediately. They also represent a simple wa...

openrxiv.org

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Reposted by Tami Lieberman

Michael Brockhurst @brockhurstlab.bsky.social · 2d

Rosanna designed a high-throughput evolutionary screen with ~20k populations comparing CRISPR+ vs CRISPR- Pseudomonas against 351 phage treatments

Benefit of CRISPR varied among phages and increased 📈 as surface receptor resistance mutations supply decreased 📉

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Reposted by Tami Lieberman

Michael Brockhurst @brockhurstlab.bsky.social · 2d

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...

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...

www.biorxiv.org

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Reposted by Tami Lieberman

Oliver Schwengers @oschwengers.bsky.social · 2d

Unbelievable, Bakta reached its 1,000th citation!

A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...

...just the entire incredibly supporting binfie community!

Without you, Bakta wouldn't be the same.

Thank you!

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Reposted by Tami Lieberman

Edward Nirenberg @enirenberg.bsky.social · 1d

This year's Nobel Prize in Physiology or Medicine was just announced:
www.nobelprize.org/prizes/medic...

This seems like a good opportunity for me to explain a bit about peripheral immune tolerance and where the prizewinners' work comes in 🧵

6 October 2025

The Nobel Assembly at Karolinska Institutet has decided to award the 2025 Nobel Prize in Physiology or Medicine to:

Mary E. Brunkow
Institute for Systems Biology,
Seattle, USA

Fred Ramsdell
Sonoma Biotherapeutics,
San Francisco, USA

Shimon Sakaguchi
Osaka University,
Osaka, Japan

“for their discoveries concerning peripheral immune tolerance”

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Reposted by Tami Lieberman

Kai Kupferschmidt @kakape.bsky.social · 1d

“Anyone who does not have an autoimmune disease, that’s because of these regulatory T cells,” says Markus Feuerer, an immunologist at the Leibniz Institute for Immunotherapy.

www.science.org/content/arti...

Medicine Nobel for researchers who identified immune system’s security guards

Mary Brunkow, Fred Ramsdell, and Shimon Sakaguchi discovered regulatory T cells that prevent autoimmune disease

www.science.org

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Reposted by Tami Lieberman

Paul Rainey @paulbrainey.bsky.social · 1d

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...

Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology

The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

www.evolbio.mpg.de

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Reposted by Tami Lieberman

Erin Green @erinrgreen.bsky.social · 3d

Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404

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Reposted by Tami Lieberman

Julia Van Etten @couchmicroscopy.bsky.social · 4d

Rutgers Newark is hiring multiple new profs who work in microbial pathogenesis, structural bio, human/microbial genetics, genomics, biochemistry, or computational biophysics. I loved doing my PhD at Rutgers and I LOVE New Jersey. Reach out if you’re applying and have questions about the school/area.

Open Rank Faculty Position on the Tenure Track - Newark, New Jersey (US) job with Rutgers | 12844885

MULTIPLE TENURE-TRACK FACULTY POSITIONS AVAILABLE The Dept. of Microbiology, Biochemistry, and Molecular Genetics at Rutgers New Jersey Medical School

www.nature.com

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Reposted by Tami Lieberman

Vaughn Cooper @vscooper.micropopbio.org · 5d

DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce?

We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE.

"Filamentous cheater phages drive bacterial and phage populations to lower fitness"

🔗 authors.elsevier.com/c/1lt5I3QW8S...

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Reposted by Tami Lieberman

Kate Cavanaugh @katecavanaugh.bsky.social · 6d

See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...

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Reposted by Tami Lieberman

Science Vs @sciencevs.bsky.social · 6d

This moment from our latest episode with science writer @edyong209.bsky.social is 🔥

We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪

Listen wherever, or watch on Spotify 👇

open.spotify.com/episode/7Evh...

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