iiinova — where your digital self keeps evolving

Reposted by Andy DeLaitsch

Przemek Dutka @przemekdut.bsky.social · 08/10/2026

Our latest development is now on bioRxiv: cryoSHIELDs — amphipathic peptide additives that make cryo-EM grid prep far more reliable. Tested across 24 protein systems, they enabled the first ABCC6 structure and GPCR–G protein structures at just 0.1–0.5 mg/mL! www.biorxiv.org/content/10.6...

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Andy DeLaitsch @delaitsch.bsky.social · 20/08/2026

@alisterburt.bsky.social presented a demonstration made in Napari of real space vs Fourier space for a 3d object (I think using simulated ribosome data) at a cryo-ET workshop and that was when I finally started understanding the concept enough to be useful

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Andy DeLaitsch @delaitsch.bsky.social · 20/08/2026

Fourier transform is top of that list for me. I think my understanding and execution of structural biology projects improved dramatically late-PhD when I had a better grasp of thinking in terms of Fourier space.

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Andy DeLaitsch @delaitsch.bsky.social · 29/07/2026

The origin is a quantitative Western blot with one strain of virus. Not that there's anything wrong with this experiment, it just seems to hold unjust weight over the years. journals.asm.org/doi/10.1128/...

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Andy DeLaitsch @delaitsch.bsky.social · 29/07/2026

I've always felt this way about the 7-14 Envs per HIV virion statistic that is commonly cited.

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Reposted by Andy DeLaitsch

Alisia Fadini @alisiafadini.bsky.social · 01/04/2026

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

rdcu.be

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...

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Andy DeLaitsch @delaitsch.bsky.social · 03/02/2026

Thanks to all the Klein lab in Cologne and the many other collaborators who contributed to this work!

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Andy DeLaitsch @delaitsch.bsky.social · 03/02/2026

We then probed the mechanism(s): modeling intra-spike crosslinking on open Env conformations, and observing 007 IgG-crosslinked "trimer dimers" in solution, structures that could drive viral aggregation. Ultimately, however, we could only speculate what was happening in neutralization assays. (4/5)

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Andy DeLaitsch @delaitsch.bsky.social · 03/02/2026

This led us to revisit neutralization assays. Comparing bivalent 007 (IgG1, IgG3) with monovalent forms revealed a key insight: bivalency plays a central role in 007's neutralization mechanism - surprising, given the HIV bNAbs by and large do not rely on avidity. (3/5)

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Andy DeLaitsch @delaitsch.bsky.social · 03/02/2026

Cryo-EM gave us the first clue that this bNAb Fab exhibited weak affinity for the BG505 Env trimer, despite being remarkably potent against BG505 SPR confirmed this: ~5uM affinity for the Fab Confusing... given how potent 007 is 🤔 (2/5)

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Andy DeLaitsch @delaitsch.bsky.social · 21/01/2026

Was such a great class last year! I’d highly recommend to ppl getting into tomography

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Reposted by Andy DeLaitsch

cryoEM papers @cryoempapers.bsky.social · 05/11/2025

Workflow Using a Cryogenic Coincident Fluorescence, Electron, and Ion Beam Microscope for Targeted Milling of Cells pubmed.ncbi.nlm.nih.gov/41182991/ #cryoEM

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

Huge thanks to Florian Klein's lab for this excellent collaboration and to the various lab members who provided so much help seeing this through!

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

The third bNAb, 05_B08, does not have any insertions and does not contact the adjacent gp120. This antibody, exhibited just over 50% breadth, which is much lower than the others.

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

Another of the bNAbs, 01_D03, has two separate insertions and a 20-residue long CDRH3, which together allow it to contact conserved residues on the adjacent gp120. This antibody has a 4-residue long FWRH3 insertion in the same location as a 4-residue insertion in 3BNC60/3BNC117.

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

Interestingly, a crystal structure of this antibody alone revealed this protruding loop was pre-organized for binding, which is expected to lower the entropic cost for binding.

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

These bNAbs differ in the length and position of insertions. The best-in-class bNAb, 04_A06, has an 11-residue long FWRH1 insertion which manifests in a long CDRH1 that reaches over to contact highly conserved residues on the adjacent gp120.

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Andy DeLaitsch @delaitsch.bsky.social · 06/10/2025

There's a new best-in-class HIV-1 antibody out today! Happy to have contributed to the structural characterization of this, and two other distinct VRC01-class bNAbs isolated from a single individual. www.nature.com/articles/s41...

a, Schematics illustrating the position and length of FWRH1 and/or FWRH3 insertions of 04_A06 (left), 01_D03 (middle) and 05_B08 (right; top), EM maps showing side views of 04_A06, 01_D03 and 05_B08 bnAb Fabs in complex with BG505SOSIP.664 Env trimers (middle) and insets illustrating a close-up of bnAb interactions with the adjacent gp120 protomer (gp1202; bottom); HC, heavy chain; LC, light chain. b, Canonical interactions of CD4 and bnAbs to the CD4bs (04_A06, IOMA and VRC01) with Env gp120 D368, the F43 pocket and gp120 N280/R456. c, Interactions between the CDRH1s of 04_A06 (blue cartoon representation) and 1-18 (red cartoon representation) with the secondary (gp1202) Env protomer, shown as a surface colored by percent conservation. The inset (top right) shows the Env trimer–04_A06 complex as a surface representation for orientation. d, Crystal structure of unbound 04_A06 Fab (bottom) and inset highlighting the 04_A06 CDRH1, with electron density contoured at 1.5σ (top). e, Molecular surface representation showing the surface area buried by VRC01-class bnAbs (04_A06, 01_D03, 05_08, 3BNC117 and VRC01) on primary (gp1201) or secondary (gp1202) Env protomers (top). Listing of Protein Data Bank (PDB) accession codes, breadth (%), heavy chain insertion length and position, buried surface area (BSA) on gp1201 and gp1202 as well as total BSA for VRC01-class bnAbs (bottom).

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Andy DeLaitsch @delaitsch.bsky.social · 04/10/2025

I second this bet. And then Shankar Balasubramanian for chemistry.

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Andy DeLaitsch @delaitsch.bsky.social · 01/10/2025

From what I gather, CXCR4 (previously called fusin) was identified as a co-receptor for HIV nearly 30 years ago (pubmed.ncbi.nlm.nih.gov/8629022/). Nice to see a structure, and interesting to see it was done with HIV-2 gp120.

pubmed.ncbi.nlm.nih.gov

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Reposted by Andy DeLaitsch

Caitie McCafferty @computingcaitie.bsky.social · 23/09/2025

I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪

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Reposted by Andy DeLaitsch

Debnath Ghosal @debnathghosal.bsky.social · 02/08/2025

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/ Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic ⚔️🦠❄️🔬

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Andy DeLaitsch @delaitsch.bsky.social · 28/07/2025

“On Being The Right Size” is a true classic, highly recommend! www.phys.ufl.edu/courses/phy3...

phys.ufl.edu

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Reposted by Andy DeLaitsch

Alister Burt @alisterburt.bsky.social · 24/07/2025

If Management is the Only Way Up, We're All F'd - Rand Fishkin sparktoro.com/blog/if-mana...

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Reposted by Andy DeLaitsch

Daniel Hurdiss @danielhurdiss.bsky.social · 18/06/2025

Latest preprint from the lab, many years in the making! By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase. This could have big implications for our understanding of viral replication & assembly (🧵) www.biorxiv.org/content/10.1...

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Andy DeLaitsch @delaitsch.bsky.social · 15/04/2025

Cool demo! Also, it’s nice to see your IgG binds bivalently!

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Reposted by Andy DeLaitsch

Jacob Parres-Gold @jacobparresau.bsky.social · 26/02/2025

My first project in the @elowitzlab.bsky.social is finally out in @cellpress.bsky.social! We explore how competitive, "many-to-many" dimerization allows complex, multi-input, and cell-type-specific biochemical computations🧵↓ doi.org/10.1016/j.ce...

doi.org

Redirecting

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Reposted by Andy DeLaitsch

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 14/01/2025

MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony www.biorxiv.org/content/10.1101/202…

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Reposted by Andy DeLaitsch

Derek Lowe @dereklowe.bsky.social · 10/12/2024

RSV vaccination attempts in young children have a troubled history. Which seems to be continuing:

science.org

Infant RSV Vaccination Trouble

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Andy DeLaitsch @delaitsch.bsky.social · 10/12/2024

For those interested: iubemcenter.indiana.edu/doc/ruska/ru...

iubemcenter.indiana.edu

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Andy DeLaitsch @delaitsch.bsky.social · 10/12/2024

100 years ago, De Broglie published his thesis, "On the Theory of Quanta". The ideas in it catalyzed the development of electron microscopy, though Ernst Ruska was apparently unaware of De Broglie's "material waves" when he and Max Knoll first started toying with the electron microscope.

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Reposted by Andy DeLaitsch

Micha Rapé Lab @micharapelab.bsky.social · 03/12/2024

Very excited to present the structural and mechanistic basis for stress response silencing by the monster E3 ligase SIFI. www.biorxiv.org/content/10.1...

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Andy DeLaitsch @delaitsch.bsky.social · 30/11/2024

🙋‍♂️ Great list, thank you!

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