The newly established Department of Systems Biology (systems.bio.uci.edu) @UCIrvine is hiring a tenure-track Assistant Professor in Systems Biology. Great science, incredible faculty support, and beautiful, sunny SoCal weather! ☀️🌴 Details: recruit.ap.uci.edu/JPF10377. Please share.

Hello, NYU! engineering.nyu.edu/news/new-pro...

New Professor Sean Gibbons Explores the Hidden World of the Human Microbiome | NYU Tandon School of Engineering

engineering.nyu.edu

Reposting this ongoing search (any discipline of biology) for an Assistant to Associate level colleague in the Division of Basic Sciences at Fred Hutch. Great city, great colleagues, great core facilities, great trainees.

Harmit Singh Malik@harmitmalik.bsky.social · last mo.

Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.

One question that we are often asked: are warmer temperatures playing a role in the emergence of this toxic mold in cheese caves? We are working on this! But my inclination is that extreme temperature events could be providing favorable conditions for this mold to establish in cheese caves.

Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...

A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔 doi.org/10.1093/gbe/...

Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak

Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out

doi.org

In our work agents develop the ability to trust differentially other agents based on the outcome of their decisions. A complex society and hierarchy can emerge. It is not mandatory. There is a phase diagram based on the interactions between agents. These can be tuned to avoid collectivism!! 🧪⚛️

Transferable genetic toolsets for nonmodel gut Clostridia enable in vivo reversible control of metabolite production www.nature.com/articles/s41... A nice update to the Jin et al. 2022 paper from Chun-Jun Guo: now with many promoters for gut clostridiales, screened from native metatranscriptomes:

Demographically, acceleration of Pol II degradation looks exactly like aging: it produces a temporal rescaling of the entire survival curve. Rescaled hazard trajectories superimpose, suggesting that Pol II declines can set the rate of aging itself. 17/22

The effect is fairly dramatic in both nematodes and mice. For example: a young adult nematode (equivalent to a teen-ager) contains ~700 million mRNA molecules total. This drops eight-fold by old-age. 3/22

Just preprinted my work on rapid evolution in fluctuating environments! When many linked mutations with different environmental tradeoffs compete, I found that mutations with stronger tradeoffs systematically outcompete beneficial “generalist” mutations. Read more here: doi.org/10.64898/202...

Anker et al. analyzed >123,000 SARS-CoV-2 genomes from the UK's COVID-19 Infection Survey, demonstrating that failing to mask artifactual sites can lead to erroneous downstream conclusions. 🔗 academic.oup.com/mbe/article/... #societyjournal #covid #sarscov2

1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...

This is now published! For those interested in microbial mechanotransduction: www.cell.com/current-biol...

Microbial GAIN domains undergo autoproteolysis and enable release of diverse cell-surface-associated proteins

Brogan and Rudner report the identification of a microbial autoproteolytic domain that is structurally homologous to the GAIN domain of eukaryotic adhesion GPCRs. Rather than participating in transmem...

cell.com

anna brogan@apbrogan.bsky.social · 4mo ago

My latest work! We found that the autoproteolytic GAIN domain which mediates force responsive signaling in adhesion GPCRs is not unique to eukaryotes. The microbial counterparts anchor diverse adhesion, enzymatic, and toxin domains to the cell surface, enabling release by likely mechanical stimuli.

Still curious if anyone's had to fight to justify insurance coverage for inpatient admissions when switching early from IV to PO antibiotics... of all the barriers to the early oral switch, this was one I hadn't encountered before, until yesterday #IDSky

Roby Bhattacharyya@roby-b.bsky.social · 2w ago

With all the data supporting early IV-to-PO switch, has anyone had trouble w insurance companies denying coverage for inpatient admission? Spent >2 hrs today dealing with that (and I'm not even on service). For a septic joint requiring washout! Where we could use a 100% bioavailable drug! #IDSky

New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect

The most surprising consequence is that presence/absence remained highly predictive of community function even after 10days of population dynamics. Communities moved far from their initial abundances, yet knowing which species were present at the start predicts community biomass at equilibrium!

Ribosomes have a strange protein modification in a universally-conserved protein uS11. This modification, isoaspartate, is also conserved in nearly all forms of life. We originally found this modification using cryo-EM, but had no idea how it was formed. 1/ elifesciences.org/articles/60482

Structure of the bacterial ribosome at 2 Å resolution

High-resolution maps and models of the bacterial ribosome provide new chemical insights into protein synthesis, and should enable the development of robust tools for cryo-EM structure modeling and ref...

elifesciences.org

ah, the ocelloid 🧿 already in 2015, Elio was thrilled by it... sure we will study this 👇 with great interest(we also have eyes) #ProtistsOnSky

The Awe­somest Thing in Bi­ol­ogy

by Elio — So says a blogger by the name of Psi Wavefunction regarding an eye-like structure of some protists called the ocelloid. She wrote this in a now defunct blog eponymously called 'The Ocell…

smallthingsconsidered.blog

Corey Holt@coreyholt.bsky.social · 2w ago

What's that? You wish we had more data on those bizarre dinoflagellates WITH EYES? Have no fear! With @protistwtmostest.bsky.social, Gordon Lax, and @pjkeelinglab.bsky.social, who also have eyes.

NSF just announced its GRFP solicitation due in October - deadline varies by field: www.nsf.gov/funding/oppo... Now for the bad news... * NSF estimates they will issue 1,500 awards, down from 2,500+ last year. * NSF removed STEM Education and Learning Research as a Major Field.

NSF Graduate Research Fellowship Program (GRFP)

nsf.gov

Most basic science departments at UCSF are having faculty searches this year. Biochemistry & Biophysics, Microbiology & Immunology, Cellular and Molecular Pharmacology, Physiology and more. We're looking for new and exciting science and nice people. You'll find them all at aprecruit.ucsf.edu

Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n

Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology

High-dimensional data are visualized through representation on tree structures.

nature.com

Erik van Nimwegen@erikvannimwegen.bsky.social · last yr.

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

The singular job of all known ribosomes: synthesizing protein. Enter the malaria parasite. In our new work, we show that Plasmodium evolved an entire new kind that does just the opposite - inhibit mRNA translation. www.biorxiv.org/content/10.6...

🎥 Sakalli et al. present Phylo-Movies, a browser-based tool that decomposes topological differences between consecutive phylogenetic trees into interpretable rooted subtree prune-and-regraft moves and animates these transformations. 🔗 academic.oup.com/mbe/article/... #societyjournal #compbio

Thrilled to see this project officially published in ISMEJ! We showed that filamentous prophages frequently acquired repressor mutations causing hyperactivity which, in turn, drove the evolution of phage resistance with pleiotropic consequences. academic.oup.com/ismej/advanc...

Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa

Abstract. Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the cond

academic.oup.com

Noah Houpt@noahhoupt.bsky.social · 8mo ago

Interested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages?? Check out our latest preprint, now up on BioRxiv! biorxiv.org/content/10.6... For a quick summary, peep the thread below...🧵 (1/10)

The Economist coming out in favour of selecting embryos for IQ while dismissing the many extremely good arguments against this - from “it doesn’t work” to “promoting the idea that a flawed metric is a useful indicator of human worth is not going to go well” - is disappointing, to say the least

The Economist@economist.com · last mo.

Progress in embryo screening will raise difficult ethical questions. But there is a big difference between the murderous coercion of early-20th-century eugenics programmes and parents seeking as much knowledge as possible when picking an embryo

Cuttlefish 3 is on bioconda! 🦑 A parallel, external-memory algorithm for building colored compacted de Bruijn graphs at collection scale — a RECOMB 2026 paper, and as of today a production release: v3.0.0. A thread on the algorithm, the numbers, and why the released tool is a Rust rewrite. 🧵 1/10

New from the lab--C. diff uses phase variation to initiate infection in a virulent state but that phenotype presents a fitness cost as disease develops. A programmed reset mechanism primes Clostridioides difficile virulence at the onset of infection | Science Advances www.science.org/doi/10.1126/...

A programmed reset mechanism primes Clostridioides difficile virulence at the onset of infection

Clostridioides difficile is a major cause of antibiotic-associated diarrhea. This pathogen produces toxins essential for disease and flagella that promote intestinal colonization. Flagella and toxins ...

science.org

you are (I am) never too old to make a reverse complement error

New paper from my group at @mitkochinstitute.bsky.social, MIT IMES, and MIT Biology! I am thrilled to share that our paper describing scAmp, a new method for analyzing extrachromosomal DNA amplifications at single-cell resolution, has been published in @natcomms.nature.com. Thread below 👇