Ksenia Krasileva

Large-scale culturing of the tree microbiome enables targeted disease suppression The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...

🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social

Large-scale culturing of the tree microbiome enables targeted disease suppression

Here's what we found... 👇

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

CIFAR signs San Francisco Declaration on Research Assessment - CIFAR In an effort to promote responsible research assessment, CIFAR has signed the San Francisco Declaration on Research Assessment (DORA).

CIFAR signs San Francisco Declaration on Research Assessment cifar.ca/cifarnews/20...

The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis ### Competing Interest Statement The authors have declared no competing interest. Agriculture and Agri-Food Canada, https://ror.org/051dzs374 Alberta Grain Saskatchewan Wheat Development Commissio...

Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...

Symbiotic diversification relies on an ancestral gene network in plants | bioRxiv Symbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification of alternative intracellular symbioses, such as the ericoid mycorrhizae (ErM). We aimed at understanding how these diversifications occurred. We sequenced the genomes of ErM-forming liverworts, and reconstituted symbiosis under laboratory conditions. We demonstrated the existence of a nutrient-regulated symbiotic state that enables ErM and underlies intracellular colonization of plant tissues. Comparative transcriptomic analyses identified an ancestral gene module associated with intracellular symbiosis beyond ErM. Genetic manipulations in the liverwort Marchantia paleacea, phylogenetics and transactivation assays demonstrated its essential function for intracellular symbiosis. We conclude that plant have maintained, and convergently recruited, an ancestral gene module for intracellular symbioses.

Outstanding preprint from @leocastanedo.bsky.social, @katharinamel1.bsky.social, @pierremarcdelaux.bsky.social and coll. on an evolutionary conserved module for intracellular symbiosis. - > Symbiotic diversification relies on an ancestral gene network in plants | bioRxiv

Thanks! K-PROB GitHub link now in the preprint!
Try our k-mer–based tool for causal element discovery for pan-genomes 🌱🧬

The work is led by @weiweibio.bsky.social, a talented postdoc looking for faculty positions now and conceptualized both computational prediction and in lab validation. Computational implementation is a collaboration with Xing Wu, postdoc with @mexpositoalonso.bsky.social
Qs - contact us 💻🌱🧬

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of ge...

🚀 New preprint!
We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱
🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1
#Genomics #GeneRegulation #Maize #Soybean

The Department of Biology at UNC-Chapel Hill is searching for an organismal biologist whose research is focused on resilience.

unc.peopleadmin.com/postings/307...

For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6.
Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT!
docs.google.com/forms/d/e/1F...

Screening of expanded GRACE mutant collection at six temperatures reveals distinct functional enrichment in genes clustered by fitness profile. Top left: Schematic of GRACE mutant construction. Bottom left: Summary of GRACE mutant collection expansion based on manual curation of biological process gene ontology annotation on Candida Genome Database (CGD). Pie chart with four concentric rings visualizes the relative proportion of genes from various versions of the GRACE collection with biological process descriptions completely unannotated or annotated based on: experimentally characterization, S. cerevisiae ortholog, S. pombe ortholog, orthologs in other fungal species, conserved protein domains, or unannotated; see Materials and methods for full details. Right: Heatmap of genes ordered by hierarchical clustering of essentiality scores across screening temperatures. A score of 4 (red) represents no growth and 0 (yellow) represents growth comparable to wild type.

#Candida albicans is a leading opportunistic fungal #pathogen of humans. Ci Fu, Leah Cowen &co expand the GRACE #Calbicans #FunctionalGenomics resource, identifying genes important for temperature-dependent fitness & highlighting its power to reveal vulnerabilities @plosbiology.org 🧪 plos.io/3Wft0Xg

YouTube video by Plants in Jars The Laboratory That Creates Your Houseplants

I just spent 40 min watching a YouTube video about AgriStarts (www.agristarts.com), a tissue culture company that produce 30 million plants/year for horticultural crops (e.g., houseplants, berries). Really impressed. Highly recommend the video.

www.youtube.com/watch?v=l-TB...

When women researchers publish, media attention doesn’t always follow Men-led papers receive more media coverage than women’s, new study finds

When women researchers publish, media attention doesn’t always follow | Science | AAAS www.science.org/content/arti...

David Attenborough sitting in front of a row of greenery and smiling slightly. A headline reads: "David Attenborough Becomes Oldest Daytime Emmy Winner at 99." Photo by Jane Barlow/Press Association, via Associated Press.

Sir David Attenborough, the British documentarian and naturalist, became the oldest person to win a Daytime Emmy on Friday at age 99. He beat the record set last year by Dick Van Dyke. www.nytimes.com/2025/10/18/a...

NYPD announces that zero arrests were made at the massive No Kings protests today after Republicans spent days claiming the protestors are violent terrorists.

"Assistant Professor - Plant Resilience to Climate Change at University of California Berkeley, Berkeley, CA, USA
*Application Deadline: 11/1/2025"

Read more here: https://arabidopsis.org/news/jobs/view?file=job_10-16-25.pdf

#PlantSciJobs

Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social

#MicroSky

www.cell.com/molecular-ce...

Homepage - 33rd Fungal Genetics Conference Visit our website to learn more.

Registration open for #Fungal26 genetics-gsa.org/fungal-2026/ at Asilomar.

Careers | Arcadia Science Evolve with Arcadia.

We have a bunch of new job ads out @arcadiascience.com. If you haven’t checked them out, take a look!

www.arcadiascience.com/careers

Rewriting the code of plant immunity go.nature.com/475WgV7

3 unexpected things we owe to the plant pathogenic bacterium Xanthomonas I have a special relationship with the bacterium Xanthomonas. As a grad student at UC Davis, I did my thesis research on Xanthomonas…

3 unexpected things we owe to the plant pathogenic bacterium Xanthomonas kamounlab.medium.com/3-unexpected...

I am sorry to hear this.. my thoughts are with you and Saskia

Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.

Thinking about a postdoc in microbiome science?
Our lab at the MPI for Biology (Tübingen) builds on the culture I established at Cornell: collaborative, creative, and internationally diverse. Postdocs lead their own projects with secure funding. Join us!
#PostdocJobs #HostMicrobe #AcademicJobs

Start independent research at the JIC with us 👇.

Really interested in finding those with an interest in structural biology and biochemistry of plants and microbes.

Please do get in touch by email if you'd like to know more 👍

Only a few days left to apply!

My group is looking for a postdoc to engineer and deploy new tools to precisely manipulate and decode how auxin coordinates plant morphogenesis.

@starmorph-syg.bsky.social

Research Associate - Reprogramming Development (closes 7 October 2025)

Engineered geminivirus replicons enable rapid in planta directed evolution Directed evolution can rapidly generate genetic variants with new and enhanced properties, yet efficient platforms for performing such evolution directly in plant cells have been lacking. We developed...

Engineered geminivirus replicons enable rapid in planta directed evolution

www.science.org/doi/10.1126/...

The biosynthesis and immunity function of lettuce sesquiterpene lactones at Gatsby Charitable Foundation on FindAPhD.com PhD Project - The biosynthesis and immunity function of lettuce sesquiterpene lactones at Gatsby Charitable Foundation, listed on FindAPhD.com

Fantastic PhD opportunity to join myself, Nicola Patron and @lichmanlab.bsky.social in uncovering the biosynthesis and function of lettuce sesquiterpene lactones. 4-year fully-funded combining molecular & engineering biology, & plant pathology.

Deadline Nov 25th

www.findaphd.com/phds/project...

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...

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

Researchers Just Developed a Tasty New Tomato Called the Scarlet Sunrise The snackable grape variety is the brainchild of scientists at Rutgers University, who have spent more than a decade trying to produce a firm, crack-resistant fruit with a vibrant reddish-yellow color

www.smithsonianmag.com/smart-news/r...

Proteolytically activated antibacterial toxins inhibit the growth of diverse Gram-positive bacteria Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacterial proteins that share this broad-spectrum activity ...

A recent cool preprint by John Whitney's lab on a new family of antibacterial proteins secreted by Gram-positive bacteria that enter and kill a broad spectrum of bacteria. Cell entry is receptor-independent and relies on cleavage by a co-secreted protease and the PMF.
www.biorxiv.org/content/10.1...