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Xinya Pan

@xinyapan.bsky.social

Fascinated by plant-endophyte interactions under biotic stress🌱

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@adamoss.bsky.social · 3mo ago

Sometimes it's not only important WHAT you sample, but HOW you do it 🌱 Our new preprint is out! We introduce a scalable, reproducible framework for agricultural rhizosphere sampling that tackles operational definitions, pooling strategies & preservation methods head-on. tinyurl.com/muxehfvz

biorxiv.org

Kevin Bretscher@kevinbretscher.bsky.social · 3mo ago

We updated our comparative genomics pipeline bacLIFE, it will now make use of BAKTA and BiG-SCAPE in addition to the newest PFAM and DBCAN database. LAGs and GCFs are now better annotated. Several other minor changes are included too. @vcarryon.bsky.social github.com/Carrion-lab/...

Release V1.2.0 Bigscape, DBCAN, PFAM update · Carrion-lab/bacLIFE

Because of several major changes when updating baclife I recommend reinstalling all conda environments. Major changes We do not longer rely on PROKKA which will no longer be updated. BacLIFE now ...

github.com

Ákos T Kovács@evolvedbiofilm.bsky.social · 4mo ago

Chemical dialogues at the crossroads of host–bacteria interactions @cp-trendsplantsci.bsky.social by Emtinan Diab, Nicola Thome, Somayah Elsayed, @raaijmakersjm.bsky.social and @gillesvanwezel.bsky.social www.cell.com/trends/micro...

Chemical dialogues at the crossroads of host–bacteria interactions

Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is...

cell.com

Team_Zuccaro@algazuccaro.bsky.social · 4mo ago

Very proud to share our new paper led by Mathias Brands from my team at @UniCologne! With Markus Pauly team @HHU. Host-adapted enzymatic deconstruction of acetylated xylan limits immune activation and facilitates mutualistic colonization of monocot roots: Molecular Plant www.cell.com/molecular-pl...

Host-adapted enzymatic deconstruction of acetylated xylan limits immune activation and facilitates mutualistic colonization of monocot roots

This study identifies a monocot-specific enzymatic module in the beneficial root endophyte Serendipita indica, showing how ancestral saprotrophic enzymes have been repurposed into an immune-compatible...

cell.com

Ezgi Mehmetoglu Boz@ezgiboz.bsky.social · 4mo ago

A quick thread summarizing our new bioRxiv preprint on using CASTs for DNA barcoding to tell "look-alike" bacteria apart (Sphingomonas edition)!! Enjoy the read! ✨

Derek Severi Lundberg@derekseveri.bsky.social · 4mo ago

When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).

Mitja M. Zdouc@mmzdouc.bsky.social · 8mo ago

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

doi.org

Mitja M. Zdouc@mmzdouc.bsky.social · 2y ago

Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag

academic.oup.com