Petar Penev

🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.

Check it out: doi.org/10.1093/isme...

Congrats!!!

Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org

Circular 23S rRNA within archaeal ribosomes The ribosomal RNAs (rRNAs) that form the core of ribosomes are believed to occur as linear molecules. Here, we investigated rRNAs from diverse and mostly uncultivated archaea and found evidence that, ...

Happy to share our recent work on rRNA processing and conformation: www.biorxiv.org/content/10.1...

Huge thanks to @ppenev.bsky.social @Amos Nissley @Dipti Nayak @Rohan Sachdeva @jhdcate.bsky.social @Jill Banfield @banfieldlab.bsky.social !!

I’m very excited to finally share the results of a passion project that has been on my mind for nearly a decade. You can find the pre-print below, but what follows is the saga of how this project came to be:

Very interesting paper! Do you happen to have an open access version of the full paper?

Two decades of bacterial ecology and evolution in a freshwater lake Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...

After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social

rdcu.be/d5put

A thread…

#PhD #position #alert

2 bioinfo PhD positions @ProbstLab @RESIST_CRC
#1 on microbial & epigenetic stress response in rivers
tinyurl.com/bdf8eu5a
#2 on virus-host stress response in rivers
tinyurl.com/43cjd6es (supervision Moraru)

Please share!

Every scientist I know switched over. It happened so fast I was surprised. ScienceTwitter no longer exists which was one of the nicer places back there.

the tool of the elite bioinformatician

A red ribosome in front of a figure showing the phylogenetic relationships between organisms in GARNET with information on growth temperatures and ribosome sequences

📰 Hot off the press at @naturecomms.bsky.social:
RNA language models predict mutations that improve RNA function
www.nature.com/articles/s41...

Congrats to @kshulgina.bsky.social @jhdcate.bsky.social and coauthors on a great C-GEM + @innovativegenomics.bsky.social collaboration! #NSFfunded #RNAsky

Excited to have our review 'Archaea and the origin of eukaryotes' in the @NatureRevMicro special issue celebrating the 40th anniversary of Woese and Fox's paper! With @anjspa1 @cstairs J. Lombard and @Ettema_lab
https://www.nature.com/articles/nrmicro.2017.133

Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio

Great job opportunity in my hometown! Pgh is a fantastic city.

A single soil megacosm holding a rice plant, surrounded by racks in a greenhouse

A pile of cut apart, discarded soil megacosm containers, and one blue lab glove, inside a greenhouse.

Three researchers cutting apart a one meter tall megacosm of soil on a table.

Two researchers standing in front of megacosms holding rice plants, next to equipment for measuring photosynthesis, inside a greenhouse.

And then there was one…
Celebrating the final ‘cosm harvest from our 7th/last 13CO2 experiment of 2024. We’re studying how the psY gene affects CH4 fluxes and soil C cycles.
Much gratitude to Rina Estera, Flor Ercoli, Pam Ronald Lab, Dave Savage Lab & many others @innovativegenomics.bsky.social

Fully Funded PhD Opportunity in Evolutionary Biology at the U of Rhode Island. Join us to explore the origin and early evolution of eukaryotes using cutting-edge comparative (meta)genomics and molecular evolution approaches. Applications are due December 15th. Contact me ASAP at laura.eme@uri.edu

We are searching for a postdoc to join our team, focused on anaerobic ciliate-methanogen symbiosis. Please share widely!

BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase The β and β′ subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the domain organizations of RN....

New paper out! We found evidence of sporadic domain insertion events that affected protein-coding genes hundreds of million years ago. These insertions were retained by the DNA-dependent RNA polymerase in bacteria and by ribosomal protein uL10 in archaea.

onlinelibrary.wiley.com/doi/full/10....

A virally encoded tRNA neutralizes the PARIS antiviral defence system - Nature Structural and functional studies reveal how viral proteins trigger the phage antirestriction induced system (PARIS) to degrade host tRNA and how viral tRNAs suppress the PARIS nuclease and thereby ov...

Reposting this here: Two years ago we published the discovery of hotspots of novel anti-phage defense systems in the genome of P4 phage satellites, including a mysterious Phage Anti-Restriction Induced System (PARIS). We have now published the mechanism in @Nature www.nature.com/articles/s41...

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sul... Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse ...

Many years in the making, our new paper in collaboration with the Banfield lab.

- Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

microbiomejournal.biomedcentral.com/articles/10....

first post on ~here~ to highlight the work of former Banfield lab undergrad @jettliu.bsky.social out today in mBio, examining the genetic characteristics of phages of CPR bacteria: journals.asm.org/doi/10.1128/...

Hey, we have a new paper out! In collaboration with Brian Hammer's group, we examine how E. coli evolves to *resist* being killed by the Type 6 Secretion System (basically a microbial poison-tipped spear attack).

www.cell.com/iscience/ful...

It has been proposed that the superphylum of Asgard Archaea may represent a historical link between ... Ribosomal Protein Cluster Organization in Asgard Archaea

The father of Archaea examines Asgards!

www.hindawi.com/journals/arc...

Our latest work on bacterial methane clathrate proteins in collaboration with @raquellieberman.bsky.social is featured in this article ! research.gatech.edu/seafloor-spa...

I’m really excited to share our new pre-print “Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi”, with co-first author Muntathar Al-Shimary  from the Doudna and the newly-minted Cress labs!
www.biorxiv.org/content/10.1...

Clustering-predicted structures at the scale of the known protein universe - Nature The novel Foldseek clustering algorithm defines 2.30 million clusters of AlphaFold structures, identifying remote structural similarity of human immune-related proteins in prokaryotic species.

Our work on clustering the 214M AlphaFold protein structure was published in @Nature. We identified 2.3M clusters using our fast structure cluster algorithm and analysed its annotations, evolution and novel domains. Work with Pedro Beltrao. 1/n
📄 www.nature.com/articles/s41...
💾 cluster.foldseek.com

Excited for my first Blue Skye post! 🚀
Our latest paper from the Baker lab is out today in mBio!
Interested in ocean hydrocarbon degradation & SIP-metagenomics?
Check this out!
👇
journals.asm.org/doi/10.1128/...
@archaeal.bsky.social

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and... Discovery and exploitation of natural competence in Patescibacteria enables visualization of the bacterial epibiont lifecycle and dissection of its genetic underpinnings.

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

Made it over! 🥳