Julien Limenitakis

Diet-derived LPS determines intestinal IgA induction and repertoire characteristics independently of the microbiota The microbiota’s impact on immune development is well appreciated. Mooser et al. show now that dietary LPS promotes intestinal germinal center reactions and IgA production independently of the microbi...

Interested in the effects of diets on B cell repertoires ? Have a look at our new publication: "Diet-derived LPS determines intestinal IgA induction and repertoire characteristics independently of the microbiota" www.cell.com/immunity/ful... This work was done at @unibe.ch. Share if you like it.

It's an exciting moment for immune repertoire research! At the end of December in Cell Systems, we shared our perspective on recent advances in ML for immune repertoire interpretation: www.sciencedirect.com/science/arti...

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Jobs — Imprint FRO Join our team—current openings at Imprint

Looking for a job in immunology or biotech research?
✨IMPRINT is #hiring! ✨

Join us to help revolutionize how we decode the body’s immune memory, uncover the causes of chronic diseases, and drive breakthroughs in autoimmunity and neuropsychiatric research.

#BiotechJobs #Immunology #sciencejobs

The AIRR Community Meeting VII #AIRRC7 is starting this Monday, June 3rd, at the University of Porto! A huge thank you to our sponsors. Your support is invaluable! Check out the full agenda and more details on the meeting page: tinyurl.com/airrcmeeting7
#Immunology

Bizarre bacteria defy textbooks by writing new genes Bacterial defensive systems scramble the standard workflow of life. Bacterial defensive systems scramble the standard workflow of life.

A new variety of reverse transcriptase discovered in bacteria “reads RNA as a template to make completely new genes written in DNA. These genes are then transcribed back into RNA, which is translated into protective proteins when a bacterium is infected by a virus.”

🐋🌱🧪🦋🦫 #EvoBio

AIRR Community Meeting VII - Learnings and Perspectives - The Antibody Society 15 years after the first AIRR-seq sequencing, what have we learned in the basic and biomedical research fields? What is next? Join us at the AIRR-C Meeting in Porto this June, the premiere event for g...

Register for the AIRR-C 7 meeting! Once registered, remember to sign up for the workshops and tutorials through the meeting app!. Also, if you haven’t already be sure to sign up for the fabulous Cálem Port Wine Cellars Tour & Group Dinner. www.antibodysociety.org/the-airr-com...
#AIRRC7 #Immunology

Our bit for PLOS Bio’s special on symbiosis thinking about the (under-appreciated) role of fitness trade-offs in the origins of endosymbiosis journals.plos.org/plosbiology/...

In new study led by Andrea Loes, we develop sequencing-based neutralization assay that measures replicate curves for hundreds of virus-serum pairs per 96-well plate (see image below)
www.biorxiv.org/content/10.1...
 
We apply assay to characterize response to repeat influenza vaccination

Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation biorxiv.org/cgi/content/... #biorxiv_genomic

Single-cell genomics meets human genetics - Nature Reviews Genetics In this Review, the authors describe the emerging field of single-cell genetics, which lies at the intersection of single-cell genomics and human genetics. They review the first single-cell expression...

Review: Single-cell genomics meets human genetics www.nature.com/articles/s41... 🧬🖥️

Bioframe: operations on genomic intervals in Pandas dataframes AbstractMotivation. Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from

Bioframe: operations on genomic intervals in Pandas dataframes academic.oup.com/bioinformati... 🧬🖥️ github.com/open2c/biofr...

Frontiers | An optimized culturomics strategy for isolation of human milk microbiota <p>Viable microorganisms and a diverse microbial ecosystem found in human milk play a crucial role in promoting healthy immune system and shaping the microbi...

An optimized culturomics strategy for isolation of human milk microbiota www.frontiersin.org/journals/mic... #jcampubs

A diagram titled 'Hallmarks of Cancer Research', designed in a clean, academic style, including funding, trend chasing, glam papers, and big data.

The Hallmarks of Cancer Research 🧪

Thrilled to share our latest paper on commensal colonization during early life! This study explores how human milk oligosaccharides trigger the colonization program in Bacteroides fragilis. 🦠🧫🧪 www.sciencedirect.com/science/arti...

A nice summary by Jon Cohen
'COVID'S COLD COUSINS'
www.science.org/content/arti...

Stochastic Models and Experiments in Ecology and Biology (SMEEB) 2024 L'Aquila, Italy from May 28th to 31st, 2024 poster

Stochastic Models and Experiments in Ecology and Biology (SMEEB) 2024 L'Aquila, Italy from May 28th to 31st, 2024

Theory, experiment and data in microbial ecology, evolution and systems biology!

Featuring @saramitri.bsky.social and @seppekuehnlab.bsky.social
#evosky #livingmatter

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

In new study led by Frances Welsh, we map how mutations to influenza affect neutralization by antibodies from humans of various ages
 
We find differences in mutation effects among age groups
 
Virus seems to evolve especially to escape antibodies of teenagers
 
www.biorxiv.org/content/10.1...

Closing out the year with a fresh preprint! 🤓🧪

A very nice method for detection of sweeps in gut microbial populations:

New paper on statistical predictions of bacterial traits from genomes. This is a deep technical dive into the intricacies of how to perform these predictions, when and how they work, and when they can reveal underlying mechanisms. journals.plos.org/ploscompbiol...

Extremely excited to share that our effort to identify and characterize novel gene families exclusive of uncultivated taxa is now published in Nature!

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

Multistability driven by cooperative growth in microbial communities bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Multistability driven by cooperative growth in microbial communities www.biorxiv.org/content/10.1... #jcampubs

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies www.biorxiv.org/content/10.1... #jcampubs

A big step forward in the science of aging: organ-specific tracking via plasma proteins
www.nature.com/articles/s41...
20% of people assessed had accelerated aging in 1 organ, 1.7% multi-organ

Gaining life expectancy up to a decade longer with a healthy diet nature.com/articles/s43...

The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chron... This study shows that chronic brain infection with African trypanosomes induces broad meningeal responses resulting in the development of ectopic lymphoid aggregates containing autoreactive B cells; m...

I’m so proud of @juanquintana.bsky.social for his latest paper & to have played a (very) small part in it! Interested in the brain, autoimmunity, B cells & parasitic infection? Then this is the pajar for you! 🧪🧬🔭 #LGBTQSTEM #Immunosky

On the 10 years anniversary of bioRxiv, John and I discuss the birth of bioRxiv, embedding sci comm within CSHL, the the pandemic, and career options for young scientists in a new podcast ebrcintranslation.buzzsprout.com/1581817/1390...

Conference Poster

EMBO|EMBL Symposium

AI and Biology

12-15 March 2024 in Heidelberg
with an exciting line-up of invited speakers and interactive sessions.
Submit your contributed talk before 5 Dec.

www.embl.org/about/info/c...

Defining the minimal components of the influenza A virus replication machinery via an in vitro recon... The influenza A virus genome is composed of eight single-stranded RNA segments. This study reconstitutes the replication of RNA genome segments in a test tube, using purified viral and host proteins, ...

Influenza virus RNA genome segments undergo a full cycle of replication in a test tube in the presence of viral RNA polymerase, viral nucleoprotein and human ANP32B, an essential host factor for influenza virus genome replication.
journals.plos.org/plosbiology/...