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Reposted by Alex Crits-Christoph

Alan McNally @alanmcn1.bsky.social · 1d

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest

microbiologysociety.org

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Alex Crits-Christoph @acritschristoph.bsky.social · 19h

Really interesting to hear your bindcraft challenges. "BindCraft appears to be much better at targeting certain binding pockets than others" common wisdom right now, but hope we can start to generalize it....

Dumb q: any evidence many of your 100+ binders *are* binding, just not inhibiting >LOD?

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Reposted by Alex Crits-Christoph

Eric Topol @erictopol.bsky.social · 21h

www.washingtonpost.com/opinions/202...

Opinion | Six surgeons general: It’s our duty to warn the nation about RFK Jr.

We took an oath to declare dangers when we found them. We’re doing that again today.

www.washingtonpost.com

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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 Alex Crits-Christoph

Matthew Hahn @3rdreviewer.bsky.social · 1d

The most important paper in evolutionary biology I'd never heard of:

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www.sciencedirect.com/science/arti...

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Jeremy Berg @jeremymberg.bsky.social · 1d

I have been trying to get this published as an op-ed, but I am going to post it here since I think it is timely in light of the "consent" extortion events.

Deafening Quiet from the Scientific Establishment

jeremymberg.github.io/jeremyberg.g...

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jeremymberg.github.io

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Reposted by Alex Crits-Christoph

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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Alex Crits-Christoph @acritschristoph.bsky.social · 1d

The full language is even worse, asking to ban gene drives and microbes as well. Would exclude work like this on modified mosquitoes: www.npr.org/2024/01/26/1...

I love the IUCN, but also, they have no political authority, this is just a suggestion. Not a good one though!

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Alex Crits-Christoph @acritschristoph.bsky.social · 1d

I don't think there's any great answer here but running all of the HMMs with HMMsearch and then doing the stats separately

maybe github.com/WrightonLabC..., although I haven't used it recently myself ...

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Reposted by Alex Crits-Christoph

Climate Cabinet Action @climatecabinet.org · 4d

Since Trump took office the U.S. has been backsliding on climate. New data shows we’re now falling far behind on cutting pollution to protect people’s health and our future.

But this isn’t inevitable. State and local leaders have real power to step up, act boldly, and keep climate progress alive.

Chart: Trump is slowing climate progress. Here’s how much.

After Trump’s budget law and regulatory rollbacks, the country’s carbon emissions are set to fall much slower than they would have under the Biden admin.

www.canarymedia.com

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Reposted by Alex Crits-Christoph

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 Alex Crits-Christoph

The Daum Lab @daumlab.bsky.social · 1d

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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Alex Crits-Christoph @acritschristoph.bsky.social · 1d

The Baltimore aquarium have termed this a "pistachio tide", a phrase that doesn't appear ever in the literature, and I cannot find if any characterization of these blooms have ever actually been published. This is by far the worst I've seen, but they do occur every few years.

Pistachio Tides: An Explainer

The science behind pistachio tides, a type of water quality event that's common in the Inner Harbor in Baltimore, Maryland.

aqua.org

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Alex Crits-Christoph @acritschristoph.bsky.social · 1d

For a week now the harbor has been bright green and half of Baltimore has smelled like rotten eggs.

Most likely, this is a Chlorobi bloom!

Chlorobi are anoxygenic photosynthetic green sulfur bacteria brought up from the bottom of the harbor by warm waters aqua.org/stories/2023...

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Paul Carini @uncultured.carinilab.com · 14d

What are folks using for calling genes these days in isolate genomes: PGAP, Bakta, or Prokka? This is for a 70% GC genome of a very novel lineage.

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Reposted by Alex Crits-Christoph

Thibaut Brunet @thibautbrunet.bsky.social · 3d

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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Alex Crits-Christoph @acritschristoph.bsky.social · 4d

So, their argument here is that biology is uniquely dangerous because of ultra unlikely tail risks ("It only creates one AI-generated self-replicating mirror von neumann machine prion to kill us all!") as opposed to actual realistic safety issues

But, the error there is in poor intuition for bio

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Reposted by Alex Crits-Christoph

Roland Faure @rfaure.bsky.social · 4d

🧵5/6
The sketching makes assembly extremely fast: a gut metagenome sample of 138Gbp of sequencing data was assembled in less that 2h and 10G RAM on 8 threads ⚡. And thanks to MSRs, *highly similar strains are not collapsed*

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Roland Faure @rfaure.bsky.social · 4d

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

www.biorxiv.org

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Reposted by Alex Crits-Christoph

Jay 🦋 @jay.bsky.team · 5d

Why does Bluesky exist?

So that "you can just do things"

underreacted.leaflet.pub/3m23gqakbqs2j

we can just do things - underreacted

underreacted.leaflet.pub

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Reposted by Alex Crits-Christoph

Pablo Ivan Nikel @pabnik.bsky.social · 4d

A blueprint for designing the next-generation of #synthetic C1 #microbes @natureportfolio.nature.com / We outline how to engineer non-canonical hosts, apply modeling & C1-inducible promoters & integrate sustainability metrics for carbon-efficient #biomanufacturing
www.nature.com/articles/s41...

A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications

Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.

www.nature.com

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Reposted by Alex Crits-Christoph

Theres Luethi @theresluethi.bsky.social · 5d

Stammt #Covid aus einem chinesischen Labor oder entstand das Coronavirus durch natürliche Übertragung vom Tier auf den Menschen? In den USA glauben zwei Drittel der Leute, dass Covid aus dem Labor kam. In Europa dürfte es ähnlich sein. Kein Wunder: Die Medien ...
www.bazonline.ch/covid-warum-...

Eine dunkle Vermutung über Corona grassiert – und ist so ansteckend wie das Virus

Zunehmend berichten auch seriöse Medien über die sogenannte Laborthese. Demnach wurde der Erreger künstlich hergestellt. Was ist an der These dran?

www.bazonline.ch

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David Ho @davidho.bsky.social · 5d

Like all other CO₂ removal (CDR) techniques, significantly more research is needed over the next few decades to determine whether enhanced rock weathering is a viable method for CDR.

Challenges and opportunities in scaling enhanced weathering for carbon dioxide removal - Nature Reviews Earth & Environment

Commercial investment in enhanced rock weathering for carbon dioxide removal on agricultural lands is growing rapidly. This Review explores the potential of large-scale deployment, outlining the challenges faced in science, policy and governance to scale the technology.

www.nature.com

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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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Taylor priest @taylorpriest.bsky.social · 6d

Interested in aligning your long sequences or small genomes against huge reference databases containing millions of prokaryotic genomes ? A new tool has been released that can do this efficiently - LexicMap - www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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