Using AI as a teaching partner: enhancing critical thinking and digital literacy in microbiology journals.asm.org/doi/10.1128/... #jcampubs
Peter Hill
@peterwshill.bsky.social
Group Leader at KCL working on relapsing invasive non-typhoidal Salmonella infections. Wellcome CDA Fellow. 🇨🇦🇬🇧
Our paper is finally out! 🥳 If you want to know how a single Salmonella effector rewires the whole macrophage transcriptional landscape by hijacking one host transcription factor, check our latest research! Thanks to the @thurstonlab.bsky.social and @peterwshill.bsky.social labs for an amazing work!
Salmonella effector SteE reprograms 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. T…
sciencedirect.com
Thrilled to share the first paper from the lab, out now in Molecular Cell! A wonderful collaboration with @thurstonlab.bsky.social bridging Salmonella host-pathogen interactions and regulatory genomics - two of my favourite things in one story. www.cell.com/molecular-ce... 🦠 🧵1/10
Salmonella effector SteE reprograms the macrophage regulatory network to drive specific hyperactivation of STAT3 target genes
Diaz-del-Olmo et al. reveal how a Salmonella virulence protein alters the transcriptional layout of infected macrophages through hyperactivation of a transcription factor and coordinated chromatin rem...
cell.com
www.science.org/doi/10.1126/... 🦠 #AMR
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
science.org
Zamin Iqbal@zaminiqbal.bsky.social · 10mo agoDelighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
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...
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...
biorxiv.org
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 --- Perfect for cancer, immunology, and aging research; epigenometech.com
🧫🦠🔬🧬🖥 A much needed review on #plasmids from @eprocha.bsky.social lab!
Eduardo Rocha@epcrocha.bsky.social · last yr.Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
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
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 ...
biorxiv.org
🌟 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
Genome Biology and Evolution@genomebiolevol.bsky.social · last yr.As 3D genome tools become more accessible, studying three-dimensional genome architecture in non-model organisms offers powerful ways to integrate evolution and gene regulation. Read more in this new Perspective by @a-mack-s.bsky.social & Wray. 🔗 doi.org/10.1093/gbe/evaf113 #genome #evolution
🧬🖥️ 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... 🧪
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...
doi.org
#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
Payal Yokota@payalyokota.bsky.social · last yr.Check out the latest review article from #TeamKhanna superstars Eduardo Bernier and recent alumni Dr. Eric Bartnicki. Macrophages: sentinels, warriors, and healers Free Link: academic.oup.com/hmg/advance-... @khannakm.bsky.social
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...
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
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...
nature.com
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...
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...
nature.com
🚨 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 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
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...
go.nature.com
🚨 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
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...
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...
microbiologyresearch.org
#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!
Fernando Rossine@fernpizza.bsky.social · last yr.I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...
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
Fun to share our experience using tissue micro arrays to lower cost and increase throughput in spatial transcriptomic studies.
10x Genomics@10xgenomics.bsky.social · 2y agoHow was Dr. Nick Banovich able to achieve an eight-fold reduction in per-sample costs for Xenium and increase throughput for #singlecellspatial studies? Find out in this new Q&A blog!
Awesome data from the Moffit lab! #spatialbiology www.science.org/doi/abs/10.1...
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...
science.org
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...
🌟 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
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...
link.springer.com
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
