Choukri Ahmed

YouTube video by Fungal-Worm Lab IMB Academia Sinica The predation process of the nematode trapping fungus Arthrobotrys oligospora.

Did you know that some fungi are CARNIVOROUS? There are lots of species that do this, but I think Arthrobotrys oligospora is especially bonkers. These fungi sense when their prey (nematodes) are nearby by eavesdropping on the chemical signals that the nematodes use to communicate with each other 🧪🪲🍄

A shorter green-leafed plant on the left, marked "Ctrl" is about half the size of a similar looking plant on the right.

Scientists have identified a protein in poplar that, when turned off, results in increased growth, stronger cell walls and trees that are more disease-resistant.

More: jgi.doe.gov/user-science...

@jbei.lbl.gov @axelvisel.bsky.social @biosci.lbl.gov @berkeleylab.lbl.gov

Assemblies of long-read metagenomes suffer from diverse errors Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,

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

and tell you just a little bit about it in the following 🧵

I tried it, it's very interesting, maybe it's an oversight but i was unable to find a way to export UMAP graph (SVG, PNG etc)

Gibberellin transport affects lateral root growth through HY5 in response to far-red light (Kasper van Gelderen , Kyra van der Velde , Chia-kai Kang , Jessy Hollander , Alicia Koppenol , Orfeas Petropoulos , Putri Prasetyaningrum , Tuğba Akyüz , Ronald Pierik) doi.org/10.1093/plce... #PlantScience

CRISPR meets AlphaFold: guiding SWEET10-enhanced oil production Enhancing seed oil content significantly benefits both human welfare and environmental sustainability. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) and artificial intelligence (AI) are transformative tools for crop trait improvement. A recent study by Wang and colleagues reported that AlphaFold-guided CRISPR genome editing of SWEET10 boosts oil contents, highlighting a breakthrough in precision crop engineering.

CRISPR meets AlphaFold: guiding SWEET10-enhanced oil production #plantscience

Cracking the seed code: How nitrate directly breaks ABA signaling for germination (Nitin Uttam Kamble) doi.org/10.1093/plce... #PlantScience

Incredible opportunity #PlantSciJobs #plantscience #AcademicJobs

AP1 floral induction system and experimental strategy used. (A) The AP1 floral induction system (pAP1::AP1-GR ap1 cal) was used in Arabidopsis. On the left, an SEM image of overproliferation inflorescence meristems of the ap1 cal mutant and on the right, an SEM image of many synchronized floral buds 5 d after dexamethasone (DEX) treatment are shown. (B) Overview of the workflow and sampling scheme. The extraction buffer Trizol was used, so from the same tissue sample, RNA and protein could be extracted. Subsequently, RNA-seq and LC-MS/MS were performed, followed by data analyses. SEM images provided by José Luis Riechmann.

🌸🧬🔬 INSIGHT 🌸🧬🔬

Almost lost in translation: integrated transcriptome and proteome analyses for early Arabidopsis flower development - Stefan de Folter

📝 Insight: doi.org/10.1093/jxb/...
🔬 Research: doi.org/10.1093/jxb/...

#PlantScience 🧪

Image Text: Call for 2026 Plantae Fellows. Application Deadline: August 31, 2025. plantae.org/2025fellowsapp. Featuring the Plantae and Plantae Fellows logo on a Plantae-branded background.

📣 Are you a creative and articulate plant scientist looking to connect with other like-minded folks? Application is now open for the 2025-2026 Plantae Fellows program!🌱

👉 Learn more and apply by August 31! buff.ly/JqoDSHq

#plantscience

Cell Free Protein Synthesis (E. coli) Ginkgo’s cell free protein synthesis (CFPS) kit is an E. coli transcription/translation system optimized to produce proteins from a T7 RNA Polymerase promoter.  Reactions consist of a bacterial cell l...

Ginkgo has launched an E.coli-based Cell Free Protein Synthesis reagent!

reagents.ginkgo.bio/products/cel...

The project focuses on utilizing meta-omics approaches to explore the connection between the exudome of Arabidopsis thaliana, branched broomrape, and rhizosphere microbiota.

We're offering a Master's Level 2 research opportunity in the picturesque city of Nantes, western France, for a duration of six months starting in January. Feel free to apply or share this opportunity!. us2b.univ-nantes.fr
Link to the offer : uncloud.univ-nantes.fr/index.php/s/...

The role of cytokinin receptors in Arabidopsis thaliana seed development and how they affect the metabolomic profile - Planta Main conclusion Based on expression, functional, and metabolomic analyses in the seeds of the single-receptor mutants, each receptor has a specific function during seed development. Their redundant ro...

The role of cytokinin receptors in Arabidopsis thaliana seed development and how they affect the metabolomic profile
link.springer.com/article/10.1...

🤯🤯 and I ❤️ it! #2025ISMPMI @soreklab.bsky.social 👏🏻👏🏻

New Article: "A receptor–kinase cascade confers cold-induced root growth inhibition in Arabidopsis" rdcu.be/etNmI

A module involving KOIN and CRPK1 integrates membrane trafficking and kinase signalling to mediate cold-induced root growth inhibition.

Cover of the June issue of Nature Plants. The description is the following: "Accelerando for the DNA shuffle - Whereas flowers of wild-type tobacco plants have five petals, defects in DNA repair, caused by the endosymbiotic integration of a plastid DNA fragment into the plant’s nuclear genome, produce flowers with variable petal numbers (three, four or five). Such gene transfer from plastids to the nucleus occurs more frequently when double-strand break repair pathways are inactive.".

The June issue is now fully online:
www.nature.com/nplants/volu...

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

Congrats

Pseudomonas virulence factor SaxA detoxifies plant glucosinolate hydrolysis products, rescuing a commensal that suppresses virulence gene expression Plants produce a plethora of specialised metabolites that often play important roles in their defence against pathogenic microbes or herbivorous insects. Exposure of leaf colonising microbes to these ...

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

An inspiring long-term goal that is still worth pursuing -> Towards establishing functional nitrogenase activities within plants

Figure 2. Distribution of detectable glucosinolate accumulation across the Brassicaceae a. Histogram showing the distribution of the number of species found to accumulate detectable levels of each glucosinolates across 339 species [11]. Specific metabolites found in a large number of species and highlighted in panel C. are labeled. b. Upset plot showing how the metabolites distribute among the major supertribes of the Brassicaceae family [11,12]. c. Distribution of widely distributed glucosinolates in species with both phylogenetic and glucosinolate information [11,12]. Colors highlight different supertribes and the outer rings represent accumulation of specific metabolites in the species. From inner ring to outer ring the metabolites are But = but-3-enyl, 20HB= 2-hydroxy-but-3-enyl, 4MSO-4-methylsulfinylbutyl, 4MT 4-methylthiobutyl, 3MSO-3-methylsulfinylpropyl, 3MT= 3-methylthiopropyl, Allyl-2-Propenyl/sinigrin.

One cool consequence: This model of more rapid gene duplication & loss creates wild phylogenetic patterns, where metabolites are found throughout major lineages of a family but exhibit huge presence/absence within a lineage. Reconstructing evo history of this pathway by parsimony would be misleading

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks Abstract. Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between the

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks

#ISMECommun from @binfutrecht.bsky.social
@jwubs.bsky.social

academic.oup.com/ismecommun/a...

RESEARCH: "Flowers meet Newton: testing the role of gravitational pull in resupination of orchid flowers" - João C F Cardoso et al, doi.org/10.1093/jxb/...

#plantscience 🧪

Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice Root exudates regulate methane emissions in rice paddies, with fumarate and ethanol discovered as two main compounds regulating methane emissions. Employing this finding for breeding resulted in novel...

70% reduction of methane emissions from paddy rice by blocking root exudation of fumarate. Field-tested over 3 seasons with yield-stable results. Maintains 8.96t/ha yields.
www.cell.com/molecular-pl...

Nice work, quick question, that heatmap of m/z features (probably made using metaboanalyst) is it normalized by rows or columns ? Thanks so much 😊

Evolution of interorganismal strigolactone biosynthesis in seed plants Strigolactones (SLs) are methylbutenolide molecules derived from β-carotene through an intermediate carlactonoic acid (CLA). Canonical SLs act as signals to microbes and plants, whereas noncanonical S...

One more player in strigolactone biosynthesis just out @science.org 🔽

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

Last chance to apply for an Associate Professor position in our Plant Biology Department at SLU. Deadline Jan 20th. Come join us in Uppsala, Sweden!

Soil microbiomes show consistent and predictable responses to extreme events - Nature Soils from 30 grasslands across Europe were subjected to 4 contrasting extreme climatic events under drought, flood, freezing and heat conditions, with the results suggesting that soil microbiomes fro...

New Nature study: Soil microbiomes show consistent and predictable responses to extreme events @frantecol.bsky.social

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

PCP Special Issue on Parasitic Plants - International Parasitic Plant Society Plant & Cell Physiology (@PCP_EIC), the official journal of the Japanese Society of Plant Physiologists, will publish a special issue on parasitic plants in 2025. Research paper submissions are due by...

There's a special issue of Plant & Cell Physiology (@plantcellphysiol.bsky.social) on #ParasiticPlants coming up 👇

www.parasiticplants.org/2024/12/pcp-...

#PlantScience