Vita Sukonthamarn

Beyond Viral Suppression: How the Right HIV Drug Helps the Gut Heal Itself Can specific HIV drugs heal the gut? For late-stage patients, viral suppression isn't enough to stop chronic inflammation. Our 2-year trial reveals that dolutegravir, unlike darunavir, profoundly restores the gut microbiome, offering a new pathway to long-term health and reduced inflammation.

Beyond Viral Suppression: How the Right #HIV Drug Helps the Gut Heal Itself

@rutgerwalls.bsky.social @fcatalamoll.bsky.social @irsicaixa.es @hospitalclinic.bsky.social
#Microbiome

An examination of the association between oral antibiotic use over eight years and the gut #microbiome in Swedish individuals found evidence that antibiotics can have long-lasting impacts on the gut microbiome. go.nature.com/40sw4kU #medsky 🧪

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

Very happy to see this out. 👏 @yinanwan.bsky.social
Bogdan Bintu and team.
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

First, a couple of weeks ago:

www.biorxiv.org/content/10.6...

Single cell RNAseq on blood from 200 donors across 4 sites in Indonesia spanning regional axes of genetic and environmental diversity. This is one of very few scRNA data sets from the Global South, including urban and rural settings.

Power is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLs https://www.biorxiv.org/content/10.64898/2026.02.26.708346v1

We posted a preprint on Zenodo: “The important role of community engagement in genetic research: Lessons from the study of Bornean contemporary hunter–gatherers” (zenodo.org/records/1875...). We present a practical, field-tested approach to doing genomics with Indigenous communities. 1/

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections https://www.biorxiv.org/content/10.64898/2026.02.16.706136v1

Demographic and genetic factors shape the epitope specificity of the human antibody repertoire against viruses - Nature Immunology Patin and colleagues present a mineable Resource database for identifying demographic and genetic factors that impact antiviral antibody repertoires in humans.

Happy to share our last study on how age, biological sex and genetics affect not only the extent of antibody responses against viruses but also the specific viral epitopes recognised. Thanks to Axel Olin @EtiennePatin @LabExMI @institutpasteur @cdf1530 @CNRS

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

Major Histocompatibility Complex Immunogenetic Diversity Differs Substantially Across Sea Turtle Species and Genomic Regions Abstract. Major histocompatibility complex (MHC) immune loci illustrate how natural selection shapes functional genetic diversity in wild populations. Bala

Martin et al. sequenced class I/II MHC genes in >300 individuals of four sea turtle species, with results suggesting that balancing selection maintains considerable MHC diversity, but with variation between species and gene copies.

🔗 doi.org/10.1093/gbe/evag008

#genome #evolution

Just discovered the wonderful covers of 'Genes to Cells', the journal of the Molecular Biology Society of Japan @mbsj-official.bsky.social – absolutely beautiful!

here some examples inspired by mitosis, CRISPR, the DNA helix, and plant pigments

Incredibly excited to be taking part in the EMBO Workshop Pathogen Immunity & Signalling. Thanks to Annemarthe van der Veen, @kajastelab.bsky.social, @iannaconelab.bsky.social, @maurogaya.bsky.social, @manellab.bsky.social, @jnpruneda.bsky.social, Jan Rehwinkel & Mads Gyrd-Hansen for organising.

I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.

Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.

Congratulations to all our SVI PhD students who completed their seminars this year: Navya Shukla, David De George, Angela (Yi) Wang, Pongsakorn Sukonthamarn, Laura Sanz Villanueva, Yali Deng, Aaron Kwok, Lara Abbouche, Maddy Comerford, Jenny Lam, Stephanie Rowe, Dhruti Parikh and Luke Spencer.

The Major Histocompatibility Complex region evolves via gene birth-and-death, resulting in short-lived genes, rapidly expanding gene subfamilies, and many gene fragments.
buff.ly/9SuftxO

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

Immune memory isn’t unique to vertebrates. This Review Article connects trained immunity and immune priming across plants and invertebrates, exploring shared mechanisms and their potential applications.

The latest from our Trained Immunity Focus Issue: buff.ly/cKomXjW

When your entire PhD depends on dry ice, FedEx, and clearing customs

RNA replicon vaccination confers long-lasting protection against H5N1 avian influenza in 23 zoo bird species - Nature Communications Highly pathogenic avian influenza H5N1 viruses cause mass mortality in birds and have infected over 50 mammalian species, including humans. Here, the authors report the use of a propagation-defective vesicular stomatitis virus replicon vaccine in captive birds, which provides protection against lethal H5N1 challenge.

Bird flu vaccine protects chickens and zoo birds

Prime-boost vaccination with RNA replicon particles protects multiple avian species, including 23 zoo bird species, from #H5N1 avian #influenza virus

#vaccines #flu

PhD student Kezia Gitareja is studying a new way to stop multiple myeloma, a type of blood cancer that affects the cells in our bone marrow.

Find out how Kezia is working to shut down cancer's protein factories: www.svi.edu.au/news-events/...

Cellular and molecular mechanisms of seahorse male pregnancy - Nature Ecology & Evolution Seahorses have a unique sex role reversal with male pregnancy involving the brood pouch, an evolutionarily novel organ. This study uses single-cell genomics and in vivo experiments to reveal the cellu...

Seahorses have a unique sex role reversal with male pregnancy involving a brood pouch, an evolutionarily novel organ. This study uses single-cell genomics and in vivo experiments to reveal the cellular basis and molecular mechanism of pouch development and diversity 🧪 www.nature.com/articles/s41...

Clinical use of polygenic risk scores: current status, barriers and future directions - Nature Reviews Genetics This article reviews the current state of implementation of polygenic risk scores in the clinical setting, highlights key challenges and outlines future directions for the use of such scores to improve disease risk prediction and to enable personalized prevention.

A Review in Nature Reviews Genetics examines the current state of implementation of polygenic risk scores in the clinical setting, highlights key challenges and outlines future directions for the use of such scores to improve disease risk prediction and to enable personalized prevention. 🔒

Selection and transmission of the gut microbiome alone can shift mammalian behavior - Nature Communications Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and its metabolite that independently reduce mouse locomotion.

Selection and transmission of the gut #microbiome alone, without changes in the host genome, can shift mammalian behaviour

(in mice)

@microbiome.bsky.social

Happy to share Jialin's first publication. She did a great job exploring the transition to land in animals. Co-supervised by the great Jordi Paps and me and in collaboration with Davide Pisani and @phil-donoghue.bsky.social

Scientists studying the fat-tailed dunnart, a tiny Australian marsupial, have uncovered genetic clues that explain how different mammals develop their facial features.

Find out more: www.svi.edu.au/news-events/...

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhan...

this looks very interesting with numerous implications for nuclear biology and gene expression.

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions: Cell www.cell.com/cell/fulltex...

Innate immunity was long thought to be devoid of immunological memory until a landmark study a decade ago.

Our new Focus Issue curates reviews and research in the field of Trained Immunity.
buff.ly/OoqVRjM

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

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

Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...

🧵 Our latest preprint is available.

It describes an extraordinary case of a boy with two very rare genetic conditions: Fanconi anaemia (FANCB, with a deep intronic pathogenic variant) and embryonic triploid–diploid mosaicism.

Read more here 👉 www.medrxiv.org/content/10.1...

The remarkably long lifespan of bowhead whales could be due to an increased ability to repair DNA mutations, according to research in Nature. go.nature.com/4hzvDN7 🌏 🧪