De-Sheng Ker
@kerds.bsky.social
Structural Biologist @ Pellegrini lab, Biochem department, Uni of Cambridge Studying Protein-nucleic acid complexes
We 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...
I 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...
Cryo-electron microscopy structure of the bovine ephemeral fever virus RNA-nucleoprotein assembly
Bovine 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 ...
biorxiv.org
A little summary of some events. Version 1.
@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?
mScarlet-I3 at FPbase
mScarlet-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...
fpbase.org
Better 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.
Hard drives on backorder for two years as AI data centers trigger HDD shortage — delays forcing rapid transition to QLC SSDs
The AI boom might help QLC overtake TLC in the next two years.
tomshardware.com
This ‘landmark’ study describes the structural mechanism of strand exchange by the RAD51 filament using cryogenic structural, biochemical, and single-molecule analyses. buff.ly/Ieh84gj
Over 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...
Structural 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.
biorxiv.org
TIL, New Zealand allows direct prescription drug advertising to consumer.
Join the first Keystone conference dedicated to DNA replication gaps and cancer! Send an abstract to be selected for a talk. www.keystonesymposia.org/conferences/...
DNA Replication Gaps, Cancer and Disease | Keystone Symposia
Join us at the Keystone Symposia on DNA Replication Gaps, Cancer and Disease, April 2025, in Daejeon, with field leaders!
keystonesymposia.org
Just 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.
Mastering 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.
Source 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 😫
Graphormer/distributional_graphormer/protein at dig-v1.0 · microsoft/Graphormer
Graphormer is a general-purpose deep learning backbone for molecular modeling. - microsoft/Graphormer
github.com
cryoSPARC benchmark of some GPU workstation in the department
Spent 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. 🥲
So it is possible to finish the RELION 2D classification with EM after VDAM using additional argument "--grad_em_iters 25"
Most cryoEM lab workstation: AMD ThreadRipper + 4090 Me: Ryzen 9 + 4070 Ti Super
Interesting, (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.
