Peter Hill

www.science.org/doi/10.1126/... 🦠 #AMR

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Epigenetics Update - Regulation of inflammatory responses by pH-dependent transcriptional condensates bit.ly/4kJ2Ju0

Ruslan Medzhitov and Xu Zhou reporting in Cell

#Epigenetics #Condensates #Chromatin
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Perfect for cancer, immunology, and aging research; epigenometech.com

🧫🦠🔬🧬🖥 A much needed review on #plasmids from @eprocha.bsky.social lab!

Salmonella Effector SteE Reprogrammes the Macrophage Regulatory Network to Drive Specific Hyperactivation of STAT3 Target Genes The ability of Salmonella Typhimurium to exploit macrophages as a niche for survival, replication and dissemination is central to its pathogenesis. The effector SteE, which polarises macrophages into ...

We have a new preprint on Salmonella effector SteE! Here we describe how kinase reprogramming drives transcriptional remodelling of the infected macrophage www.biorxiv.org/cgi/content/... - work led by @ines-ddo.bsky.social and fantastic collaboration with @peterwshill.bsky.social

🌟 paper tweetorial! 🌟 check out my first first-author paper from my Ph.D! We wrote a small (=easy-to-read) Perspective piece trying to bridge the gap between #evolutionarybiology and the expanding world of #genomic assays, specifically #chromatin conformation capture (3C and related approaches) 🧵1/7

A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics Nature Medicine - A large single-cell transcriptomic-based reference model for hematopoietic stem and progenitor cells from 148 age- and sex-diverse individuals identifies physiological and...

🧬🖥️ scAtlas of CD34+ cells from 148 people reveals how circulating hematopoietic stem/progenitor cells (cHSPCs) shift with age, sex & disease. Reference model enables myelodysplastic syndrome (MDS) diagnosis. From great Liran Shlush & Amos Tanay ‪@natmed.nature.com‬: doi.org/10.1038/s415... 🧪

#Medsky🧪 #IDsky #immunosky Macrophages are versatile innate immune cells that act as sentinels, warriors & healers in virtually every tissue. This review on current insights into their developmental origins and the organ-specific cues that imprint diverse tissue-resident & monocyte derived programs

In this episode of the Epigenetics Podcast, Petra Hajkova from the @mrc-lms.bsky.social‬ discusses her research on mammalian development, focusing on DNA methylation, histone modifications and TET enzymes. #podcast #epigenetics

🎧 Listen here: activemotif.com/podcasts-pet...

Neonatal antibiotics impair infant vaccine responses - Nature Reviews Immunology A prospective observational study of human immune responses to vaccination after early-life antibiotic exposure shows that neonatal exposure reduces the immune response to several vaccine antigens and...

NEW Highlight of @nature.com paper by @davidjlynn.bsky.social and colleagues @sahmri.bsky.social reporting a prospective observational study of human immune responses to #vaccination after early-life #antibiotic exposure.
#immunology #immunosky #medsky #IDsky #pedsky #publichealth

Brief antibiotic use drives human gut bacteria towards low-cost resistance - Nature Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...

Reporting in Nature, Eitan Yaffe and colleagues demonstrate that resistance to an antibiotic can rapidly emerge in commensal gut bacteria in vivo, and that such resistant lineages can persist for a long period following cessation of the antibiotic. 👇 🧪
www.nature.com/articles/s41...

🚨 Exciting news for #UKCellMicro2025!

The meeting is now supported by the EMBO Young Investigator Programme
We’re thrilled to have their backing for this year’s meeting. 🌟
🔗 Full details & programme: www.ukcellmicro.org
#CellMicro #ECR #EMBO

Adapting systems biology to address the complexity of human disease in the single-cell era - Nature Reviews Genetics Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review systems-focused approaches to identify and co...

Adapting systems biology to address the complexity of human disease in the single-cell era go.nature.com/3XBo6Vh #Review by @davidsebfischer.bsky.social, Martin A. Villanueva, Peter S. Winter & Alex K. Shalek @broadinstitute.org @mitofficial.bsky.social @ragoninstitute.bsky.social

🚨 New paper on ArXiv:

“Uncertainty quantification and posterior sampling for network reconstruction”

TL;DR; We present an efficient method to sample the entire ensemble of possible network reconstructions that are compatible with an indirect observation, e.g. a dynamics.

Short thread: 1/N

Arming the enemy: the evolution of resistance to self-proteins A remarkable range of novel antibiotics is attracting increasing interest as a major new weapon in the campaign against bacterial infection. They are based on the toxic peptides that provide the innat...

Given hyperbole about this paper www.nature.com/articles/s41... in the news today (eg www.bbc.co.uk/news/article...) it is a good day to post this classic from >20 years ago: www.microbiologyresearch.org/content/jour...

#Immunology out now @science.org

Machine learning, using the sequences of an individual's B and T cell receptors, has the potential to diagnose immune-related diseases.

https://buff.ly/3QvxSVf

By Maxim Zaslavsky, Erin Craig, @anshulkundaje.bsky.social , @scottboydlab.bsky.social et al.

Are you interested in bacterial pathogen physiology 🧫 and their interactions with our tissues during infections?

Alex and I wrote about how organoids + microbiology offer a powerful, tractable way to decode these interactions. Check it out! 👇

🔗 doi.org/10.1038/s443...

@embojournal.org  #MicroSky

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

Nature whispering
(from Crow & Casanova,
Human life within a narrow range: The lethal ups and downs of type I interferons)
#Immunology
www.science.org/doi/abs/10.1...

Identifying perturbation targets through causal differential networks #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2410.03380

#MicroSky

Fun to share our experience using tissue micro arrays to lower cost and increase throughput in spatial transcriptomic studies.

Highly multiplexed spatial transcriptomics in bacteria Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

Awesome data from the Moffit lab!
#spatialbiology

www.science.org/doi/abs/10.1...

How cool! Amit Singh lab shows M. tuberculosis exploits macrophage metabolism to dodge drugs. Flipping macrophages from OXPHOS to glycolysis with FDA-approved meclizine subverts redox heterogeneity & cuts drug tolerance 🚀 #TBResearch #DrugResistance #MicroSky

www.biorxiv.org/content/10.1...

Is it anything Hfq-like (RNA chaperone)? Or similar to CsrA (global translation modulator)? We don't know yet. But as it stands, Bacteroidota RRM proteins appear as excellent candidates to map post-transcriptional networks in a substantial fraction of the microbiota. www.nature.com/articles/s41...

pH-FISH: coupled microscale analysis of microbial identity and acid–base metabolism in complex biofilm samples - Microbiome Background Correlative structural and chemical imaging of biofilms allows for the combined analysis of microbial identity and metabolism at the microscale. Here, we developed pH-FISH, a method that co...

🌟 Exciting news! Our latest collaborative research with team @aarhusuni.bsky.social introduces pH-FISH, a novel technique combining pH ratiometry and FISH to simultaneously unravel microbial identity and local biofilm pH. 🔬 🧪 #MicroSky

link.springer.com/article/10.1...

#Microbiome #Biofilms

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1

Regulation of human interferon signaling by transposon exonization Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.

I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Check out this bombshell publication by Michael Fischbach @mfgrp.bsky.social and coworkers @stanford-chemh.bsky.social @stanfordmedicine.bsky.social, imagine a cancer immune therapy/vaccine where treatment begins and ends with a painless topical skin treatment! 🤯

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