#Biology, from the molecular to #cellular - beyond the biomedical. Maintained by David Kirschtel. #microbiology #microbialecology #molecularbiology #evolution

College Park, MD
Joined April 2017
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New online! Ciliate hydrogen organelles fuel rumen methanogenesis dlvr.it/TScgKf
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Cell Bio News retweeted
==Monthly Reminder === This feed is deprecated. Postings will remain indefinitely - or until closed down for lack of activity. Please join us on: +Bluesky: bsky.app/profile/cellbionews… or +Mastodon: scientificnetwork.de/@cellbi… (from any server - it's the fediverse!)
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Cell Bio News retweeted
ESMfold2, includes support for protein-protein interactions, DNA/RNA, small molecules. Including colab notebook! colab.research.google.com/gi…
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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Nifty work on plasmid chromatinization from @stergachislab ! "plasmids are indeed capable of recapitulating nuclear genome-encoded chromatin architectures, ... However, plasmids consistently adopt a heterogeneous and incomplete chromatin architecture relative to nuclear-encoded chromatin fibers, and surrounding sequence context plays an integral role in modulating whether a plasmid-encoded regulatory element will recapitulate nuclear genome-encoded chromatin architectures."
Online Now: Chromatin architectures underlying plasmid-based assays for regulatory variant effects dlvr.it/TSkLhj
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My entire team wrote an opinion paper about Common misconceptions of speciation research. Each section is written by 1-2 team members. The bulk of the writing happened during two writing retreats. It was a lot of fun and I am very happy with the result. academic.oup.com/evolinnean/…
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📌 6 years Postdoc Position in Microbial Biotechnology 🦠🧬; Metabolic Modelling and Bioprocess Engineering of Microorganisms at BOKU University in Vienna 🇦🇹... Please share and spread the word! For details visit: wp.me/pbv48T-9MK
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The microbial phosphorus cycle in aquatic ecosystems nature.com/articles/s41579-0…
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(1/🧵) How much of Earth's phytoplankton do space satellites not "see"? Can chlorophyll from satellites reliably describe phytoplankton biomass? 🛰️🦠 In our new paper in @PNAS, we answer these questions with a fleet of undersea Argo robots 🤖🌊: doi.org/10.1073/pnas.2405354…
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