Chris LB Graham

Twitching motility suppressors reveal a role for FimX in type IV pilus extension dynamics Author summary Type IV pili enable Pseudomonas aeruginosa to attach to surfaces, move (twitch), and form biofilms. Pilus extension is powered by the motor protein PilB, which is regulated by other fac...

New paper alert! We used our fav technique, genetic suppression, to understand how FimX controls function of the T4P PilB motor ATPase in Pseudomonas aeruginosa. Great collab with the Ellison lab at U Georgia who helped with some fancy microscopy to capture pilus dynamics! doi.org/10.1371/jour...

All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods CaCoFold-R3D is a probabilistic model that simultaneously predicts the RNA 3D motifs jointly with the secondary structure in a structural RNA using evolutionary information.

CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.

www.nature.com/articles/s41...

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

www.nature.com/articles/s41...

Bit under the weather today, so stayed at home to write a paper…..instead I’ve made an image of a Lego bacterial outer membrane.

Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.

#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.

Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.

📄 www.nature.com/articles/s41...

@crodrigueslab.bsky.social

We have updated ConservFold. Now it can plot conservation onto whole protein complexes and can set the cutoffs you’d like! Thought it might be useful for people. colab.research.google.com/drive/1Lv-ak... @crodrigueslab.bsky.social

Discovery and chemical optimisation of a potent, Bi-cyclic antimicrobial inhibitor of Escherichia coli PBP3 Communications Biology - Discovery of a bicyclic peptide inhibitor of cell wall biosynthesis in the Enterobacterales demonstrates applicability of a modified phage display platform to antibiotic...

Beta-lactams covalently bind to Penicillin Binding Proteins and have been the mainstay of antimicrobial chemotherapy for decades.
In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets: rdcu.be/eoaRI

Down to Earth - Chemical-free farming brings life back to rural France Faced with widespread chemical pollution and a dramatic collapse in biodiversity, farmers and scientists in western France have been testing a revolutionary farming model for over 30 years. No pestici...

"Revolutionary"? More like reclaiming wisdom!

👏 French farmers & scientists prove nature-based farming (no #pesticides, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction

f24.my/BCO5.BS

The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent ‘omics’ technologies. Their limited bios...

Another great collaboration where we studied the type IV SS of CPRs, which certainly opens new avenues for the study of these enigmatic (mostly epibiotic) organisms! @frvalera.bsky.social
www.microbiologyresearch.org/content/jour...

AlphaFold’s success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction? @stephanieaw.bsky.social and I share some thoughts here 👇 Feedback is welcome!

Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social

Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social

Have you got a website with quotes to share?

ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics. www.rbvi.ucsf.edu/chimerax/dat...

The distribution of subsurface microplastics in the ocean - Nature Global data collected between 2014 and 2024 provide insights into the distribution and potential transport mechanisms of subsurface microplastics throughout the oceanic water column.

Nature research paper: The distribution of subsurface microplastics in the ocean

https://go.nature.com/4iHBBKS

PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co

A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...

Examples of the pre-survey outputs.

Introducing SAVEMONEY, AKA ‘Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You’

A new tool offering a faster, cheaper computational approach to democratise whole-plasmid sequencing.
buff.ly/ov7YumB

Structural Basis of Lipopolysaccharide Assembly by the Outer Membrane Translocon Holo-Complex Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane beta-barrel protein, LptD, and a...

Here our new preprint on the LPS holo-translocon doi.org/10.1101/2025... , collaboration with Yves Quentin @JulieMarcoux @fronzeslab.bsky.social @pstansfeld.bsky.social - @cbitoulouse.bsky.social

Bit crazy but could you restrict the ends off it? Hope you find a solution

Try genscript they will print this. I go to them in times of need.

(Or wolves)

I agree with your statement.. it’s showing the fallacy

I find de extinction of mammoths to at least to have some basis in a human caused event being rectified and useful in tundra grasslands where we no longer have megafauna. But dire wolves, are they meant to be reintroduced as a predator? we have tigers in the areas mammoths might be considered

Probing the mechanism of peptidoglycan amidase activation by FtsEX-EnvC The FtsEX-EnvC-AmiA/B system is a key component of the E. coli cell division machinery that directs breakage of the peptidoglycan layer during separation of daughter cells. Structural and mechanistic ...

New preprint!

FtsEX-EnvC is a Type VII ABC transporter that activates the periplasmic enzymes needed to break the peptidoglycan layer during cell division.

We tested the importance of structural features underpinning activation and the auto-inhibition mechanism that keeps it all in check.

This is why I’m sequencing worm poo

Landfill. Stock photo.

Enzymes found in landfills around the world may be able to break down plastic waste. By using metagenomics and machine learning, a global collection of plastic biocatalytic enzymes has been identified. Plastics may not be forever, anymore. In PNAS Nexus: academic.oup.com/pnasnexus/ar...

Optimal dietary patterns for healthy aging - Nature Medicine In two longitudinal cohorts followed for 30 years, the associations of eight different dietary patterns with healthy aging—encompassing cognitive, physical and mental health—were studied, identifying ...

Two esteemed colleagues both declared to me to eat more fries and more wine if we need to live longer. It’s gonna be a great Tuesday! I also hope the cafeteria adds more fried foods to the menu www.nature.com/articles/s41...

London April 11th and 12th, I’m doing a tiny workshop (I’ll be there the Saturday) with my friend on how to do PCR on worms plastic poop. It could be interesting if anyone wants to teach anyone a bit of hands on science on a weekend.

PCR: barcode bacterial DNA www.eventbrite.co.uk/e/pcr-barcod...