De-Sheng Ker @kerds.bsky.social · 30/06/2026We solved a high resolution structure of the nucleosome core particle directly from nuclear extract from a single T25 flask (3 mL culture). No affinity purification. No sucrose gradients. Just lysate on grids. Raw data available now for anyone who wants to reprocess. www.biorxiv.org/content/10.6... 13615
Reposted by De-Sheng KerPavol Bardy @pavol.bsky.social · 29/06/2026I am very proud to my student Stasia whose manuscript about the nucleocapsid assembly of an ephemerovirus is now available to read. Within three years she managed to defend her thesis, submit the manuscript and secure a postdoc job, while adapting to the UK weather! www.biorxiv.org/content/10.6...biorxiv.orgCryo-electron microscopy structure of the bovine ephemeral fever virus RNA-nucleoprotein assemblyBovine ephemeral fever virus (BEFV), a member of the Rhabdoviridae family, is an arthropod-borne pathogen that causes acute febrile disease in cattle. The structural basis of its genome encapsidation ... 0124
Reposted by De-Sheng KerIan M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀 @mackayim.bsky.social · 11/05/2026A little summary of some events. Version 1. 2020385
Reposted by De-Sheng KerAlex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 17/04/2026@joachimgoedhart.bsky.social & #microscopy friends, we're using ymScarlet-i3. It's the best general purpose red FP we've tried in budding yeast. But in our hands it photobleaches really fast when exposed relatively low-intensity *488 nm* laser light (~20 W/cm^2). Have you seen this? Thoughts?fpbase.orgmScarlet-I3 at FPbasemScarlet-I3 is a basic (constitutively fluorescent) red fluorescent protein published in 2023, derived from synthetic construct. It is reported to be a very rapidly-maturing monomer with low acid sens... 8135
De-Sheng Ker @kerds.bsky.social · 14/11/2025Better and faster microscope generates large amount of data which then lead to high resolution image. With AI server hunger for more data storage too, look like data storage will be next bottleneck in image processing. Still this is pale in comparison with data generated by LHC per day.tomshardware.comHard drives on backorder for two years as AI data centers trigger HDD shortage — delays forcing rapid transition to QLC SSDsThe AI boom might help QLC overtake TLC in the next two years. 000
Reposted by De-Sheng KereLife @elife.bsky.social · 26/08/2025This ‘landmark’ study describes the structural mechanism of strand exchange by the RAD51 filament using cryogenic structural, biochemical, and single-molecule analyses. buff.ly/Ieh84gj 02210
Reposted by De-Sheng KerRobert Appleby @robertappleby.bsky.social · 27/03/2025Over five years of work has gone into our new preprint! The #cryoEM structure of a human RAD51 filament caught at the point of strand exchange 🧬 www.biorxiv.org/content/10.1...biorxiv.orgStructural mechanism of strand exchange by the RAD51 filament.Homologous Recombination (HR) preserves genomic stability by repairing double-strand DNA breaks and ensuring efficient DNA replication. Central to HR is the strand-exchange reaction taking place within the three-stranded synapsis wherein a RAD51 nucleoprotein filament binds to a donor DNA. Here we present the cryoEM structure of a displacement loop of human RAD51 that captures the synaptic state when the filament has become tightly bound to the donor DNA. The structure elucidates the mechanism of strand exchange by RAD51, including the filament engagement with the donor DNA, the strand invasion and pairing with the complementary sequence of the donor DNA, the capture of the non-complementary strand and the polarity of the strand-exchange reaction. Our findings provide fundamental mechanistic insights into the biochemical reaction of eukaryotic HR. ### Competing Interest Statement The authors have declared no competing interest. 0176
De-Sheng Ker @kerds.bsky.social · 22/02/2025TIL, New Zealand allows direct prescription drug advertising to consumer. 210
Reposted by De-Sheng KerVincenzo Costanzo @labvincenzo.bsky.social · 17/01/2025Join the first Keystone conference dedicated to DNA replication gaps and cancer! Send an abstract to be selected for a talk. www.keystonesymposia.org/conferences/...keystonesymposia.orgDNA Replication Gaps, Cancer and Disease | Keystone SymposiaJoin us at the Keystone Symposia on DNA Replication Gaps, Cancer and Disease, April 2025, in Daejeon, with field leaders! 02412
De-Sheng Ker @kerds.bsky.social · 05/10/2024Just only discover the "--reuse_scratch" and "--keep_scratch" option in RELION, to minimize repetitively copying the same particle set into the cache directory for each job. I should have read more carefully at the long list of command options available. 000
De-Sheng Ker @kerds.bsky.social · 01/06/2024Mastering the act to remotely wake up a workplace Linux machine from sleep using a smartphone at home with a single click. By putting PC to sleep, is estimated to reduce the machine's power consumption by ten times when compared to its idle power consumption. 000
De-Sheng Ker @kerds.bsky.social · 27/05/2024Source code available; easy to install; run test dataset without error; and job finish in less than a minute. 🤯 But it using a non-standard input and output format which require installation of additional software 😫github.comGraphormer/distributional_graphormer/protein at dig-v1.0 · microsoft/GraphormerGraphormer is a general-purpose deep learning backbone for molecular modeling. - microsoft/Graphormer 000
De-Sheng Ker @kerds.bsky.social · 11/04/2024cryoSPARC benchmark of some GPU workstation in the department 010
De-Sheng Ker @kerds.bsky.social · 13/03/2024Spent 1 hours trying to install a software, spent another 3 hours trying to work out how to use the software (poor documentation), only for the job to quit with an error: CUDA out of memory. 🥲 110
De-Sheng Ker @kerds.bsky.social · 09/03/2024So it is possible to finish the RELION 2D classification with EM after VDAM using additional argument "--grad_em_iters 25" 001
De-Sheng Ker @kerds.bsky.social · 03/03/2024Most cryoEM lab workstation: AMD ThreadRipper + 4090 Me: Ryzen 9 + 4070 Ti Super 000
De-Sheng Ker @kerds.bsky.social · 21/02/2024Human Primosome (Initiation state) doi.org/10.1111/febs... #MolecularNode 010
De-Sheng Ker @kerds.bsky.social · 13/12/2023Interesting, (1xMPI, 64 Threads, --cpu) RELION's VDAM rans faster than (1xMPI, 32 Threads, 1 GPU, --gpu) RELION's VDAM in our HPC. Also execute RELION's VRAM command with either mpirun or mpiexec are significant slower than srun command. 020