PLEASE SHARE! New job openings in my lab @zmbp-tuebingen.bsky.social. We have a broad interest into the mechanistic basis of how molecular complexes are rewired during cellular development in plants and during invasion by pathogens. 🌱🍄🔬 See details below 👇 #PlantSciJobs

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

Ire1 membrane stress responses support cell growth upon disruptions in inter-organelle contacts

Disruptions in inter-organelle contacts result in membrane lipid homeostasis defects that ultimately impair cellular function and viability. Yet, essential responses to membrane lipid imbalances remai...

biorxiv.org

🚨🪲🧬🦠 We have a new preprint out! Link: doi.org/10.64898/202... Insects and microbes are more connected than we realize. Some insects owe part of their ability to feed on plants to genes acquired from bacteria millions of years ago 🤯 See what we found about glycoside hydrolases in leafhoppers.

One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵

GitHub - pachterlab/paperpush

Contribute to pachterlab/paperpush development by creating an account on GitHub.

github.com

It was very nice to present some of our work on antimicrobial proteins in lichens at the IAL10! Stop by at my poster number 4 today or tomorrow afternoon for further discussion #IAL10

The preprint of our work on ppGpp–immunity crossroads is out! We delved deeper into the regulation of plant immunity by alarmone ((p)ppGpp) in Arabidopsis and found surprising stuff 😱. www.biorxiv.org/content/10.6...

Alarmone ((p)ppGpp) signalling tunes Arabidopsis thaliana nuclear gene expression to shape the balance of plant immune outcomes

RSH enzymes (RelA/SpoT homologs) synthesize ppGpp (guanosine tetra-/pentaphosphate) in plastids, regulating organelle function. More importantly, whether ppGpp acts as a simple rheostat on immune outp...

biorxiv.org

Excited to see @puginiercamille.bsky.social presenting on secreted proteins in Xanthoria. I'm blown away by the work on algal cultures and protein-protein interaction modeling! #IAL10

📣 New preprint! 🧵 Fantastic work led by @antonkraege.bsky.social Fact: Cerato-platanins are everywhere in fungi. Found across the fungal kingdom, implicated in everything from development to virulence to immune activation. But what do they *actually* do? We finally found the answer 👇

A teaser from @spribille.bsky.social on lichen fungi G protein-coupled receptors in the context of the symbiosis evolution. A lot of independent data points to them being a key to the symbiosis #IAL10

Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00

biorxiv.org

See our review of bacteria-fungi interaction by Yixu Wang together with @jiyuxie.bsky.social from Zhihui Xu group (NAU) and Yicen Lin (Kunming) in Curr Opin Microbiol www.sciencedirect.com/science/arti... Microbiome Ecology at Institute of Biology Leiden / @leidenscience.bsky.social

Thousands of possible receptor-peptide combinations. One AI-powered solution. Led by @lariferg.bsky.social, a study from @schaferlab.bsky.social & Isabel Beets has developed DeorphaNN, a neural network to identify peptide pairings for GPCRs. Read more: mrclmb.ac.uk/news-events/... #LMBResearch

We proudly present @mibinet.bsky.social, @hhu.de

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

Complex multicellularity is linked with expanded specialized metabolite production in microorganisms - Nature Microbiology

The evolutionary emergence of complex multicellularity in bacteria and fungi, such as the ability for mycelial growth, is strongly associated with increased genomic carriage of biosynthetic machinery ...

nature.com

do this: proposia.ai/materials/er...

ERC Eligibility Calculator 2026/2027 | Proposia

Calculate your ERC eligibility window for Starting, Consolidator, Advanced, and Synergy Grants with automatic career break tracking.

proposia.ai

European Research Council (ERC)@erc.europa.eu · 2w ago

The ERC Work Programme 2027 has been adopted. Planning to apply for an ERC grant? The first call, Starting Grants, opens on 22 July. Find out more 👉 erc.europa.eu/news-events/...

We're recruiting a fungal biologist to our friendly department at the Hebrew University of Jerusalem, Rehovot, Israel. For details contact our chair. Talented non-Israli applicants are welcome to apply. See below.

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

www.pnas.org/doi/10.1073/...

A phase oscillator model of cell cycles reveals nuclear density control in a branched fungal network | PNAS

Maintaining an appropriate nuclear-to-cytoplasmic ratio is essential across cell types for physiological function, and mechanisms of size control h...

pnas.org

Available in MBoC A yeast study shows that depletion of the ribosomal protein Rpl32 disrupts ribosome biogenesis & triggers G1 arrest. Surprisingly, translation remains efficient, revealing links between ribosome assembly & cell cycle control. https://www.molbiolcell.org/doi/10.1091/mbc.E25-10-0479

How do bacteria recognize fungal competitors? @cp-trendsmicrobiol.bsky.social by Lingfang Zhu (朱玲芳), Changfu Li (李长富), Xihui Shen (沈锡辉) www.cell.com/trends/micro...

How do bacteria recognize fungal competitors?

Bacterial–fungal interactions (BFIs) are central to microbial community dynamics in diverse ecosystems, with profound implications for medicine, agriculture, and environmental microbiology. A critical...

cell.com

We are currently recruiting an Independent Junior Research Group Leader in the field of biotic and/or abiotic stress biology in plants at the University of Göttingen (starting in January 2027). www.uni-goettingen.de/de/644546.ht... Best, Salma Balazadeh & Volker Lipka

Preprint! How do "friendly" rhizobia build a legume nodule? @albinteulet.bsky.social found that some may carry hidden transcription factors - proteins that mimic DNA-binding folds to enter the plant nucleus and rewrite its developmental program. www.biorxiv.org/content/10.6... (1/6)

I'm excited to announce a new preprint from the lab just posted to bioRxiv: “Retrograde trafficking inhibitors allosterically trap Get3 to block tail-anchored protein biogenesis.” www.biorxiv.org/content/10.6...

Big surprise just out from our lab. Transcriptome from A. fumigatus conidiophore made at 50C is upregulated for MAT1-1. Why is this sexual master regulator up in asexual development? Maybe priming future progeny for survival? www.biorxiv.org/content/10.6...

Temperature during Aspergillus fumigatus conidiophore development primes spore transcriptome for asexual, parasexual or sexual development

Aspergillus fumigatus is a thermotolerant saprobe found in soils and plant debris worldwide and an important pathogen of humans causing two million deaths annually. A. fumigatus makes abundant asexual...

biorxiv.org

Excited to preprint this collaborative study led by @adamrbentham.bsky.social in which computationally-designed protein binders were generated that recognise pathogen effectors leading to a plant immune response when deployed within NLR immune receptors. www.biorxiv.org/content/10.6...

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.

The rapid evolution of plant pathogens poses a persistent threat to global agricultural sustainability, often outpacing the discovery and deployment of natural disease resistance genes. While bioengin...

biorxiv.org

International MibiNet Symposium 2026 Microbial Networking Event Website: www.sfb1535.hhu.de/en/internati... Registration Deadline: July 15, 2026 Abstract Submission Deadline: July 30, 2026 #MibiNet2026

Excited to share my paper! 🥳 Today in #Nature we reveal an 8 MDa Hdr electron bifurcating super-assembly in class I methanogens that couples the first and last steps of hydrogenotrophic methanogenesis. A lineage-specific adaptation to anaerobic niches. www.nature.com/articles/s41...

We often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...

The mycobiont of the lichen Xanthoria parietina produces the siderophore ferrichrome which enables iron acquisition and nutrient exchange with its algal photobiont. Great collaboration with my group & @metalichen.bsky.social led by Hubertus Haas 👇 www.nature.com/articles/s41...

“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unr...

biorxiv.org