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Loïc Carrique

@loiccarrique.bsky.social
757 followers 906 following 0 posts

Structural biologist at Oxford Strubi. cryoEM | cryoET | FIB-milling | Generally interested in better understanding viruses replication.

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Reposted by Loïc Carrique
Sjors Scheres @sjorsscheres.bsky.social · 14h
We have 2 new preprints on @biorxivpreprint.bsky.social that describe reconstitution of #Alzheimers paired helical filaments in experimental model systems: one in human brain organoids and one in murine primary cultures. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
Templated seeding induces the formation of Alzheimer paired helical tau filaments in human brain organoids
The prion concept postulates that seeded aggregation results in the recruitment of soluble protein monomers and their assembly into amyloid filaments with the same structures as those of the seeds. He...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/10/2026
Plunge freezing tweezers with ultrasonic excitation for reducing preferred particle orientation in cryo-EM www.biorxiv.org/content/10.64898/20…
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Svetlana Dodonova @dodonova-sveta.bsky.social · 30/09/2026
New preprint from Dodonova lab 🔔! Capturing multiple states by cryo-EM❄️, we show for the first time how archaeal RNA Polymerase engages a nucleosome and forms direct contacts with histones! 🧬 Great work by Gabriele & a fantastic collaboration with Dina Grohmann! 🧵 www.biorxiv.org/content/10.6...
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Sjors Scheres @sjorsscheres.bsky.social · 30/09/2026
Our adventures into #proteinfolding: GuideFlip designs flexible molecular interactions by discrete flow matching to design sequence & structure together! Grateful for funding by Love Tito's (@titosvodka.bsky.social) and the @ukri.org. 🥳
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Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
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Arnaud Vanden Broeck @avbroeck.bsky.social · 23/09/2026
Very happy to share the first paper from our lab, out now in Nature Communications!🎉🥳 Structural basis of step II Spliced Leader RNA trans-splicing in trypanosomatid parasites 🧬🔬 🔗 www.nature.com/articles/s41... @natcomms.nature.com @universitedeliege.bsky.social @rockefeller.edu #cryoEM #cryo-EM
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
Cryo-EM peeps are living the dream www.science.org/doi/10.1126/...
science.org
In-cell structures visualize human pre-ribosome assembly in the nucleolus
In eukaryotes, ribosome biogenesis initiates within the nucleolus, a hallmark multilayered compartment of the nucleus. Structures of pre-ribosomes have been characterized ex situ, but their assembly p...
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Nicholas Schnicker @nschnick.bsky.social · 24/09/2026
Time to share a sneak peek of the #cryoEM portal I've been building for our core with #ClaudeCode and input from Zhen Xu CryoQ is an app that is helping the PSAD Core run our cryoEM microscope more efficiently by...
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Casper Berger @casperberger.bsky.social · 23/09/2026
We developed Adaptive Polishing for the consistent preparation of ~150 nm thin FIB-lamellae. This was done by using imaging feedback to adjust parameters for each lamella, or Adaptive Milling, rather than applying a fixed recipe. Preprint: doi.org/10.64898/202...
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Yuan He @yuanhejhu.bsky.social · 22/09/2026
A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.
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Thelonevirologist @thelonevirologist.bsky.social · 21/09/2026
Live imaging and interactome analysis of Zika and chikungunya viral RNAs via dual-action aptamer tag www.nature.com/articles/s41...
nature.com
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Daniel Hurdiss @danielhurdiss.bsky.social · 21/09/2026
Excited to share that our norovirus NS3 study is now online in Nature Communications! 🎉 These enzymes, found across an entire order of RNA viruses, have long been molecular motors in search of a function. We think we’ve uncovered their role. (🧵) www.nature.com/articles/s41... #virology #cryoEM
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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cryoEM papers @cryoempapers.bsky.social · 19/09/2026
EM3DFold: accurate de novo protein and nucleic acid model building for cryo-EM maps using language model-powered deep learning www.biorxiv.org/content/10.64898/2026.09.16.752067v1 #cryoEM
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Hauke Hillen @haukehillen.bsky.social · 11/09/2026
Happy to share our new preprint on the structure of the human mitochondrial RNA degradosome, a central player in organellar RNA metabolism! Work led by graduate student @paulafprado.bsky.social in our group. www.biorxiv.org/content/10.6... 🧵 1/9
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Alan Brown @alanbrownhms.bsky.social · 10/09/2026
Millions of beating cilia keep airways clean. At the base of each is the transition zone (TZ), a gate that controls which proteins enter and leave. In our paper out today in Science, we used cryo-FIB-ET to image the TZ inside human airway cells www.science.org/doi/10.1126/...
science.org
In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia
The ciliary transition zone (TZ) regulates ciliary proteome composition, yet its molecular architecture, protein content, and contribution to motile ciliopathies remain poorly defined. We applied in situ cryo-electron tomography and subtomogram averaging ...
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 08/09/2026
PIC-Med SWI/SNF 🤯 #CryoEM
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 08/09/2026
A wild publishing ride to get here... but finally! (first bioRxiv: January 5th, 2024 🙃) Amazing work from @lorenzlamm.bsky.social and colleagues 🤗 Special thanks to the community who jumped early on the boat, sharing feedback and training data to make MemBrain v2 a reality 🙏🏽
nature.com
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Nature Methods
MemBrain v2 enables streamlined analysis of membranes in cryo-electron tomography by providing user-friendly tools for membrane segmentation, membrane protein localization and spatial analysis, suppor...
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cryoEM papers @cryoempapers.bsky.social · 20/08/2026
Influenza A virus initiates genome selection through promoter-dependent nuclear export www.biorxiv.org/content/10.64898/2026.08.14.744863v1 #cryoEM
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Francis O'Reilly @fjoreilly.bsky.social · 14/08/2026
PhIX-MS is out in Molecular Cell! Rapid in situ photo-crosslinking traps transient proteasome interactions before purification; crosslinking MS, cryo-EM and AlphaFold tell us where they bind. Paper: doi.org/10.1016/j.mo... Preview: doi.org/10.1016/j.mo...
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Max Renner @maxrenner.bsky.social · 15/08/2026
Great to see our paper on mosquito carb-binding proteins out now 🦟🦟🦟 We solved structures of lectins from the yellow fever mosquito, revealing a shared conserved dimer architecture, with AF predictions suggesting hundreds of potential heterodimers too. febs.onlinelibrary.wiley.com/doi/epdf/10....
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cryoEM papers @cryoempapers.bsky.social · 07/08/2026
Structural cell biology by mega-expansion microscopy www.biorxiv.org/content/10.64898/2026.08.05.743040v1 #cryoEM
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Mart So-Last @mgflast.bsky.social · 31/07/2026
Made a little plugin for cryoEM map subboxing in ChimeraX: github.com/mgflast/Chim...
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Prof Sheena Cruickshank @sheencr.bsky.social · 31/07/2026
this is a great feature from @nature.com albeit not a good news story as shows how mosquitoes are spreading throughout the world driven by climate change and trade routes. 🧵 #ClimateChange
nature.com
How mosquitoes are conquering the world — in four charts
Mosquito-borne diseases are breaking records as climate change and other human influences allow the insects to expand their range.
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Miguel Hernandez Gonzalez @miguel-virus-cells.bsky.social · 29/07/2026
Great to see this finally published! We describe channels at the poxvirus core wall involved in nucleic acid release. www.nature.com/articles/s41...
nature.com
In situ structure of the poxvirus portal complex - Nature
Cryo-electron tomography uncovers the structure of a conserved hexameric ‘portal complex’ that spans the core wall in vaccinia virus, and shows how it is associated with viral functions such as a...
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Kathiravan Ezhilan @kathiravan-ezhilan.bsky.social · 16/07/2026
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
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Thelonevirologist @thelonevirologist.bsky.social · 13/07/2026
Super-resolution atlas of SARS-CoV-2 infection reveals protease-dependent organelle maturation, dsRNA landscapes, and intracellular structural proteins www.nature.com/articles/s41...
nature.com
Super-resolution atlas of SARS-CoV-2 infection reveals protease-dependent organelle maturation, dsRNA landscapes, and intracellular structural proteins - Nature Communications
Multi-color super-resolution microscopy provides an atlas of SARS-CoV-2 viral RNA and proteins in infected human cells, uncovering nanoscale aspects of protease-dependent replication organelle maturat...
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Reposted by Loïc Carrique
ChimeraX @chimerax.ucsf.edu · 10/07/2026
A new ChimeraX tool MorphometricsX from Ben Barad's lab colors cell membranes in electron tomography according to thickness, curvature and other properties. Available from ChimeraX menu Tools / More Tools....
ChimeraX user interface for MorphometricsX
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 01/07/2026
Thankfully quarantine for MV Hondius cruise passengers just ended without any new cases, but it is always a good time for Molecule of Month to explore how a family of rodent-borne viruses can cause severe illness in humans...
pdb101.rcsb.org
PDB101: Molecule of the Month: Hantavirus
Family of rodent-borne viruses that can cause severe illness in humans
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Chi-Min Ho @cmholab.bsky.social · 30/06/2026
Incredibly proud of Messi Haile @mehsehret.bsky.social, a founding member of the Ho Lab, for her beautiful work uncovering the inner workings of a central piece of the malaria parasite invasion machinery: the malarial moving junction, out today in @cellpress.bsky.social! tinyurl.com/4p3md2eb 🦠❄️🔬
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Ben Barad @baradlab.com · 27/06/2026
Just in time for the weekend, the 2nd beta for our Surface Morphometrics 2.0 release: github.com/GrotjahnLab/.... Beyond the major API change from the first beta (which used for the michigan class!), this one includes a major overhaul of the dual gaussian fitting for thickness and refinement.
github.com
Release 2.0.0b2 · GrotjahnLab/surface_morphometrics
A quality and robustness release on top of 2.0.0b1, focused on the density-profile bilayer fitting (mesh refinement and thickness measurement), a forgiving centralized config system, and packaging ...
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Guenter Resch @nexperion.net · 18/06/2026
Two more recordings from the #SerialEM Community Meeting 2026 are available on our channel at vimeo.com/serialem : * D. Bollschweiler & T. Schaefer - [...] A Multi-User Service Facility Perspective on SerialEM * P. Kirchweger - Advances in cryo-STET: from 3D-cryo-STET to 3.5D- and 4D-cryo-STET
vimeo.com
SerialEM Talks and Tutorials
SerialEM is a widely-used program that supports several kinds of automated acquisition from transmission electron microscopes: tilt series, single particle data,…
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Ben Barad @baradlab.com · 18/06/2026
Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...
Geopickr enables particle picking on surfaces, spheres, tubes, and filaments interactively in ChimeraX!
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Jean-Paul Armache @valendraica.bsky.social · 14/06/2026
We are sharing a tool developed initially for internal use called VOSE (Volume Operations Simplified Edition) today. It is written specifically to work in ChimeraX (version 1.5+), with no additional libraries necessary to be installed. github.com/jparmachelab...
github.com
GitHub - jparmachelab/ChimeraX-VOSE: ChimeraX Volume Operations Simplified Edition
ChimeraX Volume Operations Simplified Edition . Contribute to jparmachelab/ChimeraX-VOSE development by creating an account on GitHub.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 14/06/2026
An optimized RNA polymerase II minigenome system for Nipah virus www.biorxiv.org/content/10.64898/20…
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Yousuf A. Khan @yousufakhan.bsky.social · 11/06/2026
Today my laboratory is thrilled to announce a major breakthrough in the fight against the common cold and other diseases like hand,foot, and mouth disease acute flaccid myelitis caused by picornaviruses. We present the first structure of picornaviral 2C, bound to ssRNA (1/n)
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 11/06/2026
Evaluation of antiviral treatments for highly pathogenic avian influenza virus infections in feline species www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 11/06/2026
Sennoside A and Ceftazidime Inhibit Nucleocapsid RNA BindingAcross SARS-CoV-2, SARS-CoV, and MERS-CoV www.biorxiv.org/content/10.64898/20…
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Allegretti Lab @matteoall.bsky.social · 27/05/2026
We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇
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Roberto Vázquez Núñez @robertovn.bsky.social · 29/05/2026
🚨 New preprint: GATO-seq did it again! ELOF1 is the missing promoter-proximal factor that confers RNA Pol II resistance to TFIIF. Including ELOF1, DSIF, and NELF in GATO-seq reactions recapitulates promoter-proximal pausing in vitro at physiological conditions for the 1st time. tinyurl.com/ELOF1
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cryoEM papers @cryoempapers.bsky.social · 29/05/2026
The molecular architecture of tunneling nanotubes www.biorxiv.org/content/10.64898/2026.05.27.728322v1 #cryoEM
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Max Renner @maxrenner.bsky.social · 28/05/2026
I wish more people would understand this...
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Molecular Cell @cp-molcell.bsky.social · 25/05/2026
Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity
dlvr.it
Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity
In Mueller et al. the authors capture and visualize the native enzyme-substrate (Michaelis) and product complexes of nucleotide addition by bacterial RNA polymerase. Substrate coordination in a transition-state-like conformation, together with highly coordinated water molecules, suggests a positional (entropic) catalytic mechanism involving specific acid-base chemistry.
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cryoEM papers @cryoempapers.bsky.social · 22/05/2026
Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material www.biorxiv.org/content/10.64898/2026.05.20.726462v1 #cryoEM
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Oli Clarke @olibclarke.bsky.social · 14/05/2026
Hadn't read this until just now - super cool! In situ views of stomatin capping gap junctions: www.science.org/doi/10.1126/...
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Thelonevirologist @thelonevirologist.bsky.social · 14/05/2026
Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access www.science.org/doi/10.1126/...
science.org
Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access
Henipavirus nucleoprotein assemblies exist in different conformations, indicating temporary release of genome for RNA synthesis.
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Ed Hutchinson @socialinfluenza.bsky.social · 17/04/2026
🚨New pre-print!🚨 Because influenza virions are highly variable in form no single method can show their molecular architecture in detail. Here, we integrate multiple structural and compositional approaches to identify new features of these beautiful virus particles www.biorxiv.org/content/10.6...
An illustration of an apical region of an animal cell in cross section, shown crowded with individual molecules. The plasma membrane is densely occupied by influenza virus glycoproteins, and from the surface bud influenza virions with different morphologies (L-R): spherical, bacilliform, filamentous with a genome, filamentous and empty, filamentous with a helical inner layer, and filamentous with a cofilactin cytoskeleton.
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 13/05/2026
While BioNtech & Moderna become household names because of their Covid vaccines, those emerged from different projects: finding ways to treat the most challenging cancers. They hypothesized that we could vaccinate patients against their own tumors, & evidence is mounting that they were right! 1/n 🧪
https://www.nature.com/articles/s41586-025-10004-2
Individualized mRNA vaccines evoke durable T cell immunity in adjuvant TNBC

    U. Sahin, M. Schmidt, E. Derhovanessian, A. Cortini, I. Vogler, T. Omokoko, E. Godehardt, S. Attig, S. Newrzela, J. Grützner, N. Bidmon, S. Bolte, S. Brachtendorf, T. Stuhlmann, D. Langer, D. Brüne, J. Blake, A. Feldner, H. Lindman, A. Schneeweiss, M. Eichbaum & Ö. Türeci 
Triple-negative breast cancer (TNBC) is frequently associated with metastatic relapse, even at an early stage1. Here we assessed an individualized neoantigen mRNA vaccine in 14 patients with TNBC following surgery and after neoadjuvant or adjuvant therapy. In peripheral blood of nearly all patients, high-magnitude, vaccine-induced, mostly de novo T cell responses to multiple neoantigens were detected that remained functional for several years. Characterization of individual patients revealed that a large proportion of these T cells developed into two subsets: a late-differentiated phenotype with markers indicative of ‘ready-to-act’ cytotoxic effector T cells, and T cells with a stem cell-like memory phenotype. Eleven patients remained relapse-free for up to six years post-vaccination. Recurrence occurred in three patients: the individual with the weakest vaccine-induced T cell response relapsed, but achieved complete remission on subsequent anti-PD-1 therapy; another patient had a tumour with low major histocompatibility complex (MHC) class I expression with MHC class I-deficient cells growing out under vaccination; and the third patient was BRCA-positive and had a recurrence from a genetically distinct primary tumour. These findings demonstrate the feasibility of individualized RNA vaccines in TNBC, document persistence of vaccine-induced, functional neoantigen-specific T cells and provide insights into possible immune escape mechanisms that will guide future approaches.
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David Bhella @dbhella.bsky.social · 13/05/2026
Wow - this is just amazing. Hui Guo and colleagues from John Briggs’ lab use cryoEM helical reconstruction to discover how filamentous influenza virion assembly is directed by multiple conformations of M1 - explaining how NA is concentrated at the proximal pole. www.biorxiv.org/content/10.6...
biorxiv.org
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 12/05/2026
😀 see also www.nature.com/articles/s41...
nature.com
RNA-triggered cell killing with CRISPR–Cas12a2 - Nature
Cas12a2 enables RNA-triggered, sequence-specific killing of eukaryotic cells via widespread DNA shredding, allowing selective elimination of cells on the basis of gene expression, including virus-infe...
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