Rauf Salamzade

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

MKado: a toolkit for McDonald-Kreitman tests of natural selection https://www.biorxiv.org/content/10.64898/2026.03.02.709122v1

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives.
www.nature.com/articles/s41...

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

An Enzyme System to Help Catalyze Bioproduction of Plastic | Joint Genome Institute By characterizing the structure and function of a methylthio-alkane reductase system, researchers could open avenues for using bacteria to produce ethylene and more.

By characterizing the structure and function of a methylthio-alkane reductase system, researchers could open avenues for using bacteria to produce ethylene and more. 🖥️ 🧬

Full story: https://jgi.doe.gov/user-science/science-stories/enzyme-system-help-catalyze-bioproduction-plastic

🚨 Registration is OPEN!
Join us for the 2026 Perlman Symposium on Antibiotic Discovery & Development
🗓 May 15, 2026 | ⏰ 9–5
📍 In-person or virtual (FREE!)
🔗 perlman.mmi.wisc.edu

Gut bacteria rewire fat tissue to burn more energy Study reveals how the gut microbiome and diet work together to transform white fat cells into energy-burning beige fat in mice.

New research from @thexavierlab.bsky.social finds that the gut microbiome fine-tunes fat tissue in mice in response to diet, converting it from energy-storing fat to more energy-burning fat when dietary protein is low.

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Diversity and ecological roles of hidden viral players in groundwater microbiomes - Nature Communications Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect domina...

New paper from @adjiep.bsky.social on viral impacts in groundwater at Nature Comms. Congratulations Adjie and team!

Read: www.nature.com/articles/s41...

#viruses #viromics #groundwater

Flexible paths to multicellularity Close relatives of animals can become multicellular if distinct individuals join together or if dividing cells remain attached. A species has been found to use both mechanisms.

This species can become multicellular using two mechanisms previously thought to be mutually exclusive

go.nature.com/4aTKdfF

🧫 Just out in Bioinformatics Advances: "AssiST: Convolutional neural network for analysis of antibiotic susceptibility testing" 

Read the full paper here:  https://doi.org/10.1093/bioadv/vbag063

Authors include: @carmenli.bsky.social, @amitchell.bsky.social

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Structural insights into metallocluster trafficking in the nitrogenase assembly scaffold NifEN - Nature Catalysis Structural insights into the assembly of the complex nitrogenase cofactor are scarce. Now, cryo-EM and AlphaFold analyses of NifEN, which converts the precursor (L-cluster) to a mature cofactor (M-clu...

So excited to share our cryo-EM study of the nitrogenase cofactor assembly scaffold NifEN expressed in E. coli!
@ribbehulab.bsky.social @ucibiosci.bsky.social @natcatal.nature.com
www.nature.com/articles/s41...

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions.

We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essen...

A nice collaboration from post-docs in my lab 😊 onlinelibrary.wiley.com/doi/full/10.... @jingdi.bsky.social @luismsilva.bsky.social @paradyseb.bsky.social @molecularecolup.bsky.social

A symbiotic origin of the ribosome? Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

"we propose that the protoribosome was a parasite (...). If this view is correct, then like the spliceosome in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from an RNA world"

How a tiny bacterium turns itself into a “tunneling machine” Some symbiotic bacteria can invade micron-scale host passages by wrapping their flagella around themselves and moving like a tunneling machine. Our study reveals how this clever motion enables them to overcome extreme confinement and successfully colonize their hosts.

How a tiny bacterium turns itself into a “tunneling machine”

http://dlvr.it/TRGZ7c

http://dlvr.it/TRGZ7k

New in JB: Smith, Unnikrishnan et al. connect daptomycin sensitivity to the staphylococcal type VII secretion system protein EsxC via changes in the membrane, linking pathogenesis to Abx sensitivity.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

Researchers in the US might be having feelings about writing grants atm-I know I am!

We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal.

His advice is gold, and helpful regardless of funder. Pls RT!

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

Thank you so much for this perspective, Elise...it's exciting to see lipids getting a little time in the spotlight!! 🤩 #lipidtime @elisecutts.bsky.social

Evolution and Ecology of Streptomyces - PubMed <span><i>Streptomyces</i> are among the most well-studied and important groups of bacteria, largely owing to their prolific production of biomedically important compounds like antibiotics and antifungals. Research over more than a half-century has elucidated the molecular and mechanistic details of <i>Str</i></span> …

Review article on the evolution and ecology of Streptomyces, the genus of bacteria that gave us so many antibiotics, anti-infectives, cancer therapeutics and immunosuppressants.

pubmed.ncbi.nlm.nih.gov/40829782/

Given that clonal biofilms of single bacterial species rapidly diversify into niche specialists, how do biofilms of multiple species evolve? Below is the TLDR to a🧵 w/pub links, h/t to @mozammel.bsky.social 🇦🇺 & Henriette Lyng Roder lab 🇩🇰 for extending our single-species work in clever ways!👇🏻

Epistasis and co-adaptation in bacterial genome evolution Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...

I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!

rdcu.be/e6pHY

STANFORD STAND UP FOR SCIENCE NATIONAL DAY OF ACTION RALLY LOCATION WHITE MEMORIAL PLAZA, STANFORD UNIVERSITY CAMPUS

STANFORD!!! Visit this link:
fight2win.standupforscience.net/Stanford-Mar...
to learn more about your local SATURDAY MARCH 7TH RALLY
to TAKE BACK OUR SCIENCE!

See map for location! Rally starts at 11am!!

#March7Stanford
#standupforscience
#science
#savescience

Students say NC State cybersecurity course left them in debt and without prospects NC State offers an online cybersecurity bootcamp powered by a third-party company. Some students say it made false promises.

Etcetera etcetera we are all LowerEd

www.newsobserver.com/news/local/e...

EBAMP: An efficient de novo broad-spectrum antimicrobial peptide discovery framework Zhao et al. propose EBAMP, a generative-discriminative framework for de novo design of broad-spectrum antimicrobial peptides (AMPs) targeting both bacteria and fungi. EBAMP achieves a high positive rate (37.5%), exhibiting strong antimicrobial activity against multidrug-resistant pathogens with low toxicity, offering a promising strategy against antibiotic resistance.

EBAMP: An efficient de novo broad-spectrum antimicrobial peptide discovery framework

Fluorescent Antimicrobial Peptides Based on Nile Red: Effect of Conjugation Site and Chemistry on Wash-Free Staining of Bacteria Fluorescent probes for bacterial detection can be obtained by conjugating antimicrobial peptides with fluorescent dyes. However, little is known about the effect of the conjugation site and linker che...

I’m excited to share the first chapter of the UNR-1 story! UNR-1 is a red #fluorescent #antimicrobial peptide that stains both Gram- and Gram+ bacteria with high selectivity over eukaryotes. Stay tuned for part two with some fascinating applications!
#chembio pubs.acs.org/doi/abs/10.1...

Bringing in @simrouxvirus.bsky.social because it feels like we as a community are going to begin having vigorous discussion about ground truthing phage-bacteria interactions and what data prove and don’t prove