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PLOS BiologyThe <a href="https://fediscience.org/tags/macrophage" class="mention hashtag" rel="nofollow noopener" target="_blank">#macrophage</a> CD163 receptor clears free <a href="https://fediscience.org/tags/hemoglobin" class="mention hashtag" rel="nofollow noopener" target="_blank">#hemoglobin</a> in the bloodstream by binding the HpHb complex. The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> structure of CD163-HpHb complex, by <a href="https://mstdn.science/@chingshinhuang" class="u-url mention" rel="nofollow noopener" target="_blank">@chingshinhuang</a> &co, reveals how CD163-mediated endocytosis clears different HpHb isoforms <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4nNBbGI" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/4nNBbGI</a>

eLife🧪 C. thermocellum is a biofuel workhorse, but its ethanol yield still falls short.A new <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a> structure of its key enzyme, AdhE, shows how the microbe safely handles harmful by-products and keeps its internal chemistry in balance. <a href="https://elifesciences.org/articles/96966?utm_source=mastodon&utm_medium=social&utm_campaign=organic" rel="nofollow noopener" translate="no" target="_blank">https://elifesciences.org/articles/96966?utm_source=mastodon&utm_medium=social&utm_campaign=organic</a>

François Ferron 🇪🇺 🔷️🔶️The major 🇨🇵 structural biology event of 2025 co-organized with the Association Française de Cristallographie (<a href="https://fediscience.org/tags/AFC" class="mention hashtag" rel="nofollow noopener" target="_blank">#AFC</a>) and the Société Française de Biophysique (<a href="https://fediscience.org/tags/SFB" class="mention hashtag" rel="nofollow noopener" target="_blank">#SFB</a>) is coming : <a href="https://fediscience.org/tags/BSI4" class="mention hashtag" rel="nofollow noopener" target="_blank">#BSI4</a> | 4th edition of the Integrative Structural Biology Meeting (BSI), 15-19 December 2025, <a href="https://fediscience.org/tags/Bordeaux" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bordeaux</a>, France more information ➡️ <a href="https://bsi4.org/" rel="nofollow noopener" translate="no" target="_blank">https://bsi4.org/</a> <a href="https://bsky.brid.gy/r/https://bsky.app/profile/afmblab.bsky.social" class="u-url mention" rel="nofollow noopener" target="_blank">@afmblab.bsky.social</a> <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener" target="_blank">@strucbio</a> <a href="https://mstdn.science/@ActaCrystF" class="u-url mention" rel="nofollow noopener" target="_blank">@ActaCrystF</a> <a href="https://sciencemastodon.com/@sciencemagazine" class="u-url mention" rel="nofollow noopener" target="_blank">@sciencemagazine</a> <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://fediscience.org/tags/biophysics" class="mention hashtag" rel="nofollow noopener" target="_blank">#biophysics</a> <a href="https://fediscience.org/tags/crystalography" class="mention hashtag" rel="nofollow noopener" target="_blank">#crystalography</a> <a href="https://fediscience.org/tags/SAXS" class="mention hashtag" rel="nofollow noopener" target="_blank">#SAXS</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>

PLOS Biology<a href="https://fediscience.org/tags/Glycoprotein" class="mention hashtag" rel="nofollow noopener" target="_blank">#Glycoprotein</a> 2 (GP2) filaments protect against infections by acting as decoys for the bacterial <a href="https://fediscience.org/tags/lectin" class="mention hashtag" rel="nofollow noopener" target="_blank">#lectin</a> FimH. The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> structure of GP2 filaments provides insights into filament assembly and <a href="https://fediscience.org/tags/antibacterial" class="mention hashtag" rel="nofollow noopener" target="_blank">#antibacterial</a> function in the digestive tract <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/3HP2obF" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/3HP2obF</a>

Guillaume GaullierAn interesting use case of LLMs is as a conversational interface to some body of text, as a complement to other forms of navigation: from a table of content or index, via full-text search, or reading specific sections or even the whole text cover-to-cover.Of course the LLM can still make up nonsense, but this is a similar limitation to a full-text search leading to a section irrelevant to your current question if the search terms match too broadly. With any navigation method, eventually you need to read the material once you find the section you need.The Phenix documentation, papers, newsletters and tutorial videos have been fed to an LLM, so now we can navigate it as a conversation: <a href="https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html" rel="nofollow noopener" translate="no" target="_blank">https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html</a> A quick test trying to answer a question I knew the answer to suggests that it is working pretty well for sufficiently specific questions. This will likely be useful.<a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#StructuralBiology</a> <a href="https://fediscience.org/tags/crystallography" class="mention hashtag" rel="nofollow noopener" target="_blank">#crystallography</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>

eLifeA new method called MagIC-Cryo-EM allows scientists to use powerful <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a> techniques to examine proteins that have been difficult to study so far. <a href="https://elifesciences.org/digests/103486/the-molecular-shape-of-you?utm_source=mastodon&utm_medium=social&utm_campaign=organic" rel="nofollow noopener" translate="no" target="_blank">https://elifesciences.org/digests/103486/the-molecular-shape-of-you?utm_source=mastodon&utm_medium=social&utm_campaign=organic</a>

Guillaume GaullierContinuing this thread of important <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> papers. ❄️ 🔬 📰 🧵I finally read: Henderson R (1995) The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Quarterly Reviews of Biophysics 28: 171–193 <a href="https://doi.org/10.1017/S003358350000305X" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1017/S003358350000305X</a>Some key points from this review:- Neutrons would be ideal if we had much brighter sources, lenses, and better detectors. 30 years after this review, sources have become brighter but still far from enough. Even if all of this was solved, it would be beneficial to use 15N labeled, per-deuterated biological macromolecules. NMR spectroscopists do this, but it is difficult and costly. All of this makes neutron microscopy very impractical. - The next best option is electrons, because they have the most favorable ratio of radiation damage per elastic scattering. - 30 years after the review, most of what was written about electron microscopy presenting the best opportunity for rapid improvement has indeed happened. See the growth of cryoEM as a structure determination method, and the 2017 Nobel Prize in chemistry. - The review has interesting calculations about the number of particles of a certain molecular weight necessary to achieve interpretable 3D reconstructions, assuming perfect images. Today's average cryoEM structure often achieves this with smaller or fewer particles (or even both smaller and fewer).

SBGridMeharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a PNAS publication from the laboratory of Paul Riegelhaupt of Weill Cornell Medicine that reveals how anesthetics shut down brain activity by closing the THIK1 potassium channel, offering new insight into how anesthesia works at the molecular level.Read more here: <a href="https://medium.com/sbgrid-community-news/unlocking-the-secrets-of-anesthesia-a-closer-look-at-the-thik1-k2p-channel-622d5cb89a27" rel="nofollow noopener" translate="no" target="_blank">https://medium.com/sbgrid-community-news/unlocking-the-secrets-of-anesthesia-a-closer-look-at-the-thik1-k2p-channel-622d5cb89a27</a><a href="https://mstdn.science/tags/SBGrid" class="mention hashtag" rel="nofollow noopener" target="_blank">#SBGrid</a> <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a> <a href="https://mstdn.science/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#StructuralBiology</a>

Guillaume GaullierI'm going to keep appending to this thread when I catch up with reading important <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> papers. ❄️ 🔬 📰 🧵I recently read: Marques MA, Purdy MD & Yeager M (2019) CryoEM maps are full of potential. Current Opinion in Structural Biology 58: 214–223 <a href="https://doi.org/10.1016/j.sbi.2019.04.006" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1016/j.sbi.2019.04.006</a>It's a good review, full of pointers to important papers. Some of these were already on my radar, others not. I have a few I need to read now.Important bits from this review:- Asp and Glu side chains are often not detectable in cryoEM maps, for two reasons: carboxylate groups are more sensitive to radiation damage than other groups, and negatively charged oxygen has negative scattering factors at low resolution ranges. - We can learn a lot more from cryoEM maps than only atom coordinates, for example charges. - Because all charges scatter electrons, peak centroids in cryoEM maps (= Coulomb potential maps) don't perfectly coincide with atom centers, making atomic model refinement a bit trickier. Coulomb potential maps can be converted to charge density maps, making the peak centroids coincide with atom centers. One of the references cited explains how to do this conversion. I need to try this on a good map.

Guillaume GaullierCouple of highlights from today Thursday (well, technically yesterday now, since it's getting late).LocScale version 2 from Arjen Jakobi's group seems very helpful and I will try it as soon as I am back at the lab.Doppio seems super nice, and has been made easier to install. I also need to try it. It would be nice to have an alternative to CryoSPARC, with a nicer workflow visualization than stand-alone RELION. Not sure what are the pros/cons between Doppio and Scipion, since they seem to do similar things. I need to read up about this.RECOVAR from Amit Singer's group seems like a good tool to analyze heterogeneity. Main take-away from the talk: enough noise in the particle images can make most such programs "hallucinate" heterogeneity, so one must be very careful when interpreting results!<a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CCPEM</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>

Guillaume GaullierA first highlight: Stephen Muench's talk yesterday about rapid vitrification.I had read some papers from his group before, and enjoyed them a lot. The talk was excellent, and there are some great things brewing. Set a PubMed alert if you are interested in rapid vitrification.My take-aways:- We cannot outrun particles colliding with the air-water interface (brownian motion in a thin film is simply too fast). - But vitrifying fast is still very helpful in many cases. - Revisiting conventional blotting and plunge-freezing still has potential. See <a href="https://cryopreparation.com" rel="nofollow noopener" translate="no" target="_blank">https://cryopreparation.com</a><a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>

Guillaume GaullierAt the <a href="https://fediscience.org/tags/CCPEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CCPEM</a> Spring Symposium since yesterday, and it's been so nice! ❄️ 🔬The schedule is packed and I try to pay attention to the talks, so no live posting. But I'll try to post some of my personal highlights under this post as I find time to reflect. 🧵Schedule: <a href="https://www.ccpem.ac.uk/symposium/spring-symposium-2025/" rel="nofollow noopener" translate="no" target="_blank">https://www.ccpem.ac.uk/symposium/spring-symposium-2025/</a><a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>

Rich WaldoDo you have a <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> dataset with significant orientation bias? I'd love to play with it!

PLOS BiologyA precursor procapsid is initially formed during <a href="https://fediscience.org/tags/bacteriophage" class="mention hashtag" rel="nofollow noopener" target="_blank">#bacteriophage</a> assembly, but how? The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> structure of the scaffolding protein complex & portal within <a href="https://fediscience.org/tags/phage" class="mention hashtag" rel="nofollow noopener" target="_blank">#phage</a> P22 procapsid reveals how this complex orchestrates the initiation of procapsid assembly <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/44B71iE" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/44B71iE</a>

Amelia Cervera 🧬Complex water networks visualized by cryogenic electron microscopy of RNA.<a href="https://genomic.social/tags/RNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#RNA</a> <a href="https://genomic.social/tags/Ribozymes" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ribozymes</a> <a href="https://genomic.social/tags/Tetrahymena" class="mention hashtag" rel="nofollow noopener" target="_blank">#Tetrahymena</a> <a href="https://genomic.social/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a><a href="https://www.nature.com/articles/s41586-025-08855-w" rel="nofollow noopener" translate="no" target="_blank">https://www.nature.com/articles/s41586-025-08855-w</a>

Guillaume GaullierLooking for a <a href="https://fediscience.org/tags/postdoc" class="mention hashtag" rel="nofollow noopener" target="_blank">#postdoc</a> position?Come work with us on CO2 fixation in <a href="https://fediscience.org/tags/cyanobacteria" class="mention hashtag" rel="nofollow noopener" target="_blank">#cyanobacteria</a> using <a href="https://fediscience.org/tags/biochemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#biochemistry</a> and <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a>! 🦠 🧪 🧫 ❄️🔬We are a friendly group. 🙂 <a href="https://www.blikstadlab.org/open-positions.html" rel="nofollow noopener" translate="no" target="_blank">https://www.blikstadlab.org/open-positions.html</a><a href="https://fediscience.org/tags/job" class="mention hashtag" rel="nofollow noopener" target="_blank">#job</a> <a href="https://fediscience.org/tags/postdoc" class="mention hashtag" rel="nofollow noopener" target="_blank">#postdoc</a>

PLOS BiologyReports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its <a href="https://fediscience.org/tags/cytokine" class="mention hashtag" rel="nofollow noopener" target="_blank">#cytokine</a> ligand ALKAL2. <a href="https://mstdn.science/@janfelix" class="u-url mention" rel="nofollow noopener" target="_blank">@janfelix</a> &co reanalyze <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> data to clarify the situation <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4lvRfvu" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/4lvRfvu</a>

Amelia Cervera 🧬Structural mechanism of LINE-1 target-primed reverse transcription. <a href="https://genomic.social/tags/Transposons" class="mention hashtag" rel="nofollow noopener" target="_blank">#Transposons</a> <a href="https://genomic.social/tags/Retrotransposons" class="mention hashtag" rel="nofollow noopener" target="_blank">#Retrotransposons</a> <a href="https://genomic.social/tags/LINE1" class="mention hashtag" rel="nofollow noopener" target="_blank">#LINE1</a> <a href="https://genomic.social/tags/ReverseTranscription" class="mention hashtag" rel="nofollow noopener" target="_blank">#ReverseTranscription</a> <a href="https://genomic.social/tags/CryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#CryoEM</a> <a href="https://www.science.org/doi/10.1126/science.ads8412" rel="nofollow noopener" translate="no" target="_blank">https://www.science.org/doi/10.1126/science.ads8412</a>

Ed EngHave you used one of the NIH sponsored <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> centers and thought that was a great resource but looking to meet & interact with your peers? Ready to share and learn about other people’s experiences with using cryoEM?Then join us at the <a href="https://fediscience.org/tags/MM2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#MM2025</a> Pre-Meeting Congress (PMCX61) on Transformative CryoEM in Salt Lake City, UT on Sunday, July 27, 2025.Early registration deadline is May 8, 2025:<a href="https://mmconference.microscopy.org/registration-information" rel="nofollow noopener" translate="no" target="_blank">https://mmconference.microscopy.org/registration-information</a>

PLOS BiologyBacterial ABC peptide transporters are involved in processes like nutrient uptake. This study solves <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#cryoEM</a> structures of the <a href="https://fediscience.org/tags/Ecoli" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ecoli</a> dipeptide <a href="https://fediscience.org/tags/transporter" class="mention hashtag" rel="nofollow noopener" target="_blank">#transporter</a> DppABCDF in both apo & ATP analog-bound forms, providing insights into assembly & import mechanism <a href="https://fediscience.org/tags/plosbiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#plosbiology</a> <a href="https://plos.io/3DxP8pU" rel="nofollow noopener" translate="no" target="_blank">https://plos.io/3DxP8pU</a>

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