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Remco Stam @rstam.bsky.social · 1d

Now with official press release. I'm very much looking forward to welcome @cbarragan.bsky.social in January

www.uni-kiel.de/en/details/n...

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Signal @signal.org · 6d

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

signal.org

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Remco Stam @rstam.bsky.social · 8d

Very happy to see this work finally online!
Resistance against necrotrophic pathogens is not generally conserved. When comparing five wild tomato spp, we saw that one spp co-opted a different mechanism against Sclerotinia infection!

KunzLab@LMU @kunzlab.bsky.social · 8d

This looks very interesting. Congrats @rstam.bsky.social et al. Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen url: academic.oup.com/plcell/artic...

Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen

Quantitative disease resistance in a wild tomato genotype evolved through species-specific regulatory network rewiring, with an ancient transcription facto

academic.oup.com

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Reposted by Remco Stam

Helen Brabham @helenbrabs.bsky.social · 10d

Super excited to see our work on the NLRseek program finally published 🥳 Here we identify new NLRs against major wheat pathogens and present a pipeline for NLR identification. Huge thank you to all of the co-authors for bringing this work together! @matthewmoscou.bsky.social rdcu.be/eIGvv

Discovery of functional NLRs using expression level, high-throughput transformation and large-scale phenotyping

Nature Plants - Rapid discovery of functional resistance genes is enabled by a high-expression signature and high-throughput transformation. This approach identified 31 new resistance genes for...

rdcu.be

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Remco Stam @rstam.bsky.social · 7d

I had a couple of great days at our first @plantscochallenge.bsky.social annual meeting. Inspiring to discuss diverse aspects of multiple stress responses with colleagues from other parts of the plant sciences
www.uni-kiel.de/en/details/n...
Big thanks to @estukenbrock.bsky.social for organising.

www.uni-kiel.de

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Remco Stam @rstam.bsky.social · 8d

That's the plan... And the rejections in between we keep to ourselves... 😅

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Remco Stam @rstam.bsky.social · 8d

Very happy to see this work finally online!
Resistance against necrotrophic pathogens is not generally conserved. When comparing five wild tomato spp, we saw that one spp co-opted a different mechanism against Sclerotinia infection!

KunzLab@LMU @kunzlab.bsky.social · 8d

This looks very interesting. Congrats @rstam.bsky.social et al. Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen url: academic.oup.com/plcell/artic...

Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen

Quantitative disease resistance in a wild tomato genotype evolved through species-specific regulatory network rewiring, with an ancient transcription facto

academic.oup.com

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Reposted by Remco Stam

KunzLab@LMU @kunzlab.bsky.social · 8d

This looks very interesting. Congrats @rstam.bsky.social et al. Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen url: academic.oup.com/plcell/artic...

Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen

Quantitative disease resistance in a wild tomato genotype evolved through species-specific regulatory network rewiring, with an ancient transcription facto

academic.oup.com

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Remco Stam @rstam.bsky.social · 8d

We hypothesise that clade 2 might be a specialised A alternata from wild hosts, and that clade 1 is the "cultivated", global substrain? How this happened and whether this was facilitated by the starship element is something for the next part of the project. :)

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Remco Stam @rstam.bsky.social · 8d

In terms of gene content, the clades don't differ much. Clade 2 is slightly more diverse and has a slightly higher TE content on average, but not exclusively.
Interestingly, Clade 1 has one unique Starship!

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Remco Stam @rstam.bsky.social · 8d

Clade 2 seems to show some geographic structure; clade 1 does not. Interestingly, ALL other Alternaria alternata isolates NCBI from any host group with Clade 1.

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Remco Stam @rstam.bsky.social · 8d

We hypothesised that Alternaria would possibly show a north/south gradient or some indication of climatic adaptation.
We find some hints, but our study does not have the resolution to capture this in detail.
But we consistently find two genetic clades! Both infect Tomato throughout the range.

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Remco Stam @rstam.bsky.social · 8d

New preprint!
We looked at the genomes of Alternaria isolates collected from wild tomato hosts and found something really interesting!

www.biorxiv.org/content/10.1...

Evolutionary divergence in sympatric populations of the fungal pathogen Alternaria alternata across wild tomato hosts

Alternaria alternata is a globally distributed fungal pathogen with a broad host range, increasingly affecting both tomato crops and wild tomato relatives. The genomic basis of this ecological breadth...

www.biorxiv.org

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Max von Thun @maxvonthun.bsky.social · 12d

“We studied more than 70 different elections that took place in 12 western European countries over several decades, and found that when mainstream parties take more anti-immigration positions, it leads to more support for the radical right, not less.”

Tarik Abou-Chadi @tabouchadi.bsky.social · 13d

For the Guardian, @turnbulldugarte.com and I discuss our research that clearly shows one thing: Labour's anti-immigration strategy will only strengthen Reform and weaken its own electoral prospects. It won't win voters back but ultimately normalizes the far right

www.theguardian.com/commentisfre...

Our research makes it clear: by capitulating to the right, Labour is driving voters to Reform UK | Tarik Abou-Chadi and Stuart Turnbull-Dugarte

Mimicking Farage on immigration is senseless. Labour voters feel betrayed; anti-immigration voters see through the ruse, say academics Tarik Abou-Chadi and Stuart Turnbull-Dugarte

www.theguardian.com

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Jason Stajich @hyphaltip.bsky.social · 12d

Assistant Professor Plant or Fungal
Genomics. Univ of Wyoming. eeik.fa.us2.oraclecloud.com/hcmUI/Candid...

Asst Professor - Plant or Fungal Genomics

The Department of Botany and the School of Computing at the University of Wyoming invites applications for a tenure-track position in Plant or Fungal Genomics at the rank of Assistant Professor. We in...

eeik.fa.us2.oraclecloud.com

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Björn Usadel @usadellab.bsky.social · 13d

Anika in my department is looking for a Phd student on buckwheat stress responses. Maybe this is something for you?
#plantjobs
www.fz-juelich.de/en/careers/j...

PhD position in the field of plant sciences/transcriptome analyses

Do you want to contribute to sustainable plant use with your work? Then you are exactly right at the institute`s department Bioinformatics (IBG-4) of the Institute for Bio and Geosciences at the Forsc...

www.fz-juelich.de

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Karl Schmid @kjschmid.bsky.social · 14d

This looks interesting: Reference genome choice compromises population genetic analyses

www.cell.com/cell/fulltex...

Reference genome choice compromises population genetic analyses

Using a species-specific reference genome significantly improves the accuracy of population genetic analyses, as exemplified by mapping gray fox sequence data to genomes of several canid species. Mapp...

www.cell.com

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Reposted by Remco Stam

Leibniz IPK @leibnizipk.bsky.social · 15d

A research team led by the @leibnizipk.bsky.social has revealed that modern barley has a “mosaic origin”, meaning it stems from several wild populations across the Fertile Crescent. The findings were published in @nature.com.

➡️Paper: tinyurl.com/ytzyn4re
➡️PR: tinyurl.com/5e2v7cp5

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Oliver Bossdorf @bossdorf.bsky.social · 15d

Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply!
Please repost!

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Tiffany Lowe-Power 🌱🦠 @tlowepower.bsky.social · 16d

Please repost -- The Univ. California Davis dept of Plant Pathology is hiring a Fungal biologist / Mycologist

Applications due Dec 1

Application portal: recruit.ucdavis.edu/JPF07339

Screenshot shows part of the job posting (with alt-text of the same text)

he Department of Plant Pathology at the University of California, Davis is seeking applications for a fulltime, tenure-track Assistant Professor position in Mycology, with a focus on plant pathogenic, symbiotic,
or mycotoxigenic fungi and fungal-like organisms (e.g., oomycetes). We are looking for a highly
motivated and creative scientist with a strong background in mycology and/or the biology of fungi and
fungal-like organisms that interact with plants. The successful candidate will be expected to develop a
world-class, externally funded research program that integrates both fundamental and applied aspects
of fungal biology within the context of plant pathology. We welcome applicants pursuing a wide range
of research topics related to plant-associated fungi, including but not limited to mechanisms of fungal
pathogenesis or symbiosis with plants, population genomics and evolution of fungal plant pathogens,
plant-associated fungal microbiomes and plant-microbe interactions, and/or one health approaches to
fungal diseases and antifungal resistance. Applicants working in other relevant research areas involving
pathogenic, symbiotic, or mycotoxigenic fungi or fungal-like organisms that affect plant health are also
encouraged to apply. The successful candidate will have significant opportunities for collaboration with
faculty in plant pathology, microbiology, genomics, and agricultural sciences, and to contribute to
addressing issues of importance to California’s agricultural and natural ecosystems.
The appointee primary teaching responsibilities will be teaching Introductory Mycology, an upperdivision lab class, and SAS 30, Mushroom, Molds & Society, a general education class for non-majors.
Additional graduate and undergraduate teaching responsibilities may be assigned based on
departmental needs and the candidate’s expertise. The department offers modern instructional
facilities, including a newly renovated teaching laboratory.

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Gitta Coaker @gittacoaker.bsky.social · 16d

My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339

Assistant Professor of Plant Pathology

University of California, Davis is hiring. Apply now!

recruit.ucdavis.edu

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Remco Stam @rstam.bsky.social · 17d

This seems worse than crashing...

Philipp Bayer @philippbayer.bsky.social · 17d

Just asked Claude to code me some simple Entrez stuff that pulls down taxonomy IDs for NCBI mitochondrial accessions - the code works and returns a table of taxonomy IDs from the API in a nice table, *but the taxonomy IDs are all wrong*. I hadn't that before: normally AI-written code just crashes

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The Tattooed Professor @schwessinger.bsky.social · 18d

Important read if you use LLMs for science knowledge discovery around plants "What Large Language Models Know About Plant Molecular Biology" www.biorxiv.org/content/10.1.... As per usual LLMs appear to propagate biases.

What Large Language Models Know About Plant Molecular Biology

Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MoBiPlant, the first compreh...

www.biorxiv.org

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Karla Ortiz @kortizart.bsky.social · 18d

And literally four days later from this story Open AI admits what we all know to he true.

That when a model generates bullshit, that’s no flaw, that’s just how it works.

www.computerworld.com/article/4059...

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Aaron Rupar @atrupar.com · 21d

of all the things I am not going to buy, this is the thing I am not going to buy the most

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