Rahul K

Exercise induces microbiota to produce formate which in turn enhances CD8+ T cell anti-tumour functionality. 💪 #gains

Check out my research highlight below for more deets 🤓🐛🧫

The strain on scientific publishing Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...

If I could change one thing about #ScientificPublishing I'd ask funding bodies to stipulate all work they fund be published in non-profit journals.

The knock-on effects would alleviate most of the strain on #AcademicSky.

This isn't hard. It's big, but actually, it's pretty easy.

1/n

I wrote about AI foundation models for biology last year: www.nytimes.com/2024/03/10/s... Benchmarking tests since then aren't finding that they're better than simpler models of how genes and cells work.

three scientists discuss. Text: "MDC Global Fellow postdoctoral program"

Lead your independent research project as a #postdoc in our 3-year #fellowship.

The program includes full-time employment with competitive salary, budget, structured co-supervision, mentoring and advanced training

Apply from August 4 to August 28
👉 www.mdc-berlin.de/postdocs#t-g...

Please share!

Independent Fellowship in Plant-Associated Microbial Interactions | John Innes Centre An exciting opportunity for an Independent Fellowship in Plant-Associated Microbial Interactions has arisen at the John Innes Centre. To read the full job description for this role…

New Independent Fellowship position in Microbiology to launch your lab in our department @johninnescentre.bsky.social (UK). We are conducting a broad search in the area of plant-associated microbial interactions. Message me if you have any questions.

Apply here: www.jic.ac.uk/vacancies/in...

Macrophages say NO to nucleotide synthesis and salvage instead - Nature Metabolism Metabolic reprogramming is a well-established hallmark of macrophage activation, coordinating bioenergetic and biosynthetic pathways to support immune effector functions. A new study now reveals a pre...

It was a pleasure to write this News & Views piece with Eloïse marques on the latest work from the lab of Jing Fan @natmetabolism.nature.com ⬇️⬇️

News & Views:
Macrophages say NO to nucleotide synthesis and salvage instead
nature.com/articles/s42...

Article:
nature.com/articles/s42...

Conservation and divergence of metabolic phenotypes between patient tumours and matched xenografts - PubMed Patient-derived xenografts (PDXs) are frequently used as preclinical models, but their recapitulation of tumour metabolism in patients has not been closely examined. We developed a parallel workflow t...

how well do xenografts model metabolism of human tumors? this is a really helpful resource, congrats to @rjdlab.bsky.social et al!

pubmed.ncbi.nlm.nih.gov/40731149/

The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux Nature Cell Biology - Rudinskiy et al. examine organellophagy receptor features, finding modules of functionally conserved intrinsically disordered regions and defining shared features despite...

Selective autophagy of organelles: the “disorder” is key. Intrinsically disordered regions of organellophagy receptors are interchangeable, required, and sufficient for organelle fragmentation and lysosomal delivery … and all about ORGATACs 😉
rdcu.be/ey8iL

Critically evaluating the relative importance of phage in shaping microbial community composition The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial com...

Hello new phage phollowers!

I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"

www.cell.com/trends/micro...

Ultrahigh-Throughput Multiplexed Screening of Purified Protein from Cell-Free Expression Using Droplet Microfluidics Screening large libraries is essential for protein engineering, but traditional approaches are limited by low throughput and biological variability. Here, we present an ultrahigh-throughput droplet mi...

Ultrahigh-Throughput Multiplexed Screening of Purified Protein from Cell-Free Expression Using Droplet Microfluidics
pubs.acs.org/doi/10.1021/...

The Lancet Countdown on health and plastics Plastics are a grave, growing, and under-recognised danger to human and planetary health. Plastics cause disease and death from infancy to old age and are responsible for health-related economic losse...

The Lancet Countdown on health and plastics - The Lancet www.thelancet.com/journals/lan...

Preprint: PIEZO1 mechanosensing at the plasma membrane as a key regulatory event in nucleic acid-induced immunity, with different functional outcomes based on the cargo structure
www.biorxiv.org/content/10.1...

Oligomer-based functions of mitochondrial porin - Nature Communications Cryo-EM structure of yeast Por1 hexamer reveals functions beyond metabolite and ion transport, including regulation of protein import via Tom22, maintaining lipid composition through scramblase activi...

Oligomer-based functions of mitochondrial porin | Nature Communications
www.nature.com/articles/s41...

Low-dose metformin requires brain Rap1 for its antidiabetic action Metformin lowers blood glucose by inhibiting Rap1 in ventromedial hypothalamic neurons that regulate glucose balance.

Metformin, the first line drug for Type 2 diabetes, has been used for 60 years without a clearcut mechanism of action. It turns out it's not just reducing glucose output from the liver. Metformin also works via the brain www.science.org/doi/10.1126/...

Mitochondrial glutathione import enables breast cancer metastasis via integrated stress response signaling url: aacrjournals.org/cancerdiscov...

Cool work from the Birsoy lab!

A Novel Phosphatase Reverses the Leloir Pathway to Promote Tagatose Synthesis from Glucose D-Tagatose is a natural, low-calorie, rare monosaccharide that has gained substantial interest as an alternative sweetener. It offers numerous benefits, including a low glycemic index, prebiotic prope...

New pre-print from the lab! We show for the first time that tagatose can be synthesized from glucose! After assessing several pathways, we identified a phosphatase specific to gal-1-P. We also perform modeling to understand the molecular determinants of specificity.
www.biorxiv.org/content/10.1...

Escherichia coli with a 57-codon genetic code The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here we designed and generated Escherichia coli with a 4 Mb synthetic genome in which we re...

Escherichia coli with a 57-codon genetic code | Science. Syn57, uses 55 codons to encode the 20 canonical amino acids. #rnasky #microsky 🦠 www.science.org/doi/10.1126/...

The small adipocyte-specific transmembrane protein, Nrac, interacts with scavenger receptor CD36 to fine-tune fatty acid uptake and lipid clearance
Siegfried Ussar and collaborators @www.helmholtz-munich.de
www.embopress.org/doi/full/10....

Making sense of oxygen sensing - Thomas Keeley & Peter Ratcliffe describe challenges encountered in measuring and manipulating cell monolayer oxygenation in vitro, and innovative approaches to overcome them
www.embopress.org/doi/full/10....

Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago.

fuerstlab.shinyapps.io/SeqNovelty/

quick 🧵

LOVTRAP: an optogenetic system for photoinduced protein dissociation - Nature Methods LOVTRAP enables rapid optogenetic control of protein dissociation and is complementary to related optogenetic tools that mediate light-induced protein association. LOVTRAP is applied to the study of o...

Source:

LOVTRAP: an optogenetic system for photoinduced protein dissociation

www.nature.com/articles/nme...

Application deadline for up to 5 @mrc-lms.bsky.social postdoc positions in developmental epigenetics closes soon - don’t miss out! Positions across both experimental and computational projects. Come and join our fantastic team science community!

Silencing mitochondrial gene expression in living cells Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, the central mechanis...

Silencing mitochondrial gene expression in living cells | Science www.science.org/doi/10.1126/...

Unveiling cancer crosstalk across spatial and temporal scales This collection focuses on how recent technological advancements in omics approaches (genomics, proteomics, metabolomics etc.) have enhanced our understanding of the mechanisms governing tumor progres...

Our new Collection on #cancer is out now! We delve into how #omics technologies are helping researchers to better understand what goes on in the tumor microenvironment 🧪

See 🧵⬇️ for more info on the articles 1/9

plos.io/4mgHDEw

Check out this exciting meeting and register! Fantastic line-up of speakers on cell biology of the nucleus and a great venue 🔥

Federal agencies hiding out in a bunker

GeneAgent: self-verification language agent for gene-set analysis using domain databases - Nature Methods GeneAgent is a language agent using large language models and self-verification to improve gene-set function annotation.

GeneAgent: self-verification language agent for gene-set analysis using domain databases
Paper: www.nature.com/articles/s41...
Code: github.com/ncbi-nlp/Gen...
Demo: www.ncbi.nlm.nih.gov/CBBresearch/...

I‘m thrilled to see our group‘s inaugural paper published in @science.org! Huge thanks to everyone who contributed to this project!

The histone core domain evolves at single-residue resolution to directly orchestrate transcription Nucleosomes are thought to be structural barriers to transcription, establishing a restrictive ground state that must be destabilized for gene express…

Happy to share our new paper out today in @cp-cellreports.bsky.social in collaboration with @tobiaswarnecke.bsky.social @akihisaosakabe.bsky.social about how evolution can do big things with small changes. www.sciencedirect.com/science/arti...