Omar Kamileen
@omarkamileen.bsky.social
📤 88
📥 276
📝 20
An impatient optimist. 🇩🇪🇱🇰
reposted by
Omar Kamileen
Ryo Yokoyama
about 1 month ago
Mass spectrometry imaging: principles and applications in plant research
nph.onlinelibrary.wiley.com/doi/10.1111/...
@newphyt.bsky.social
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Mass spectrometry imaging: principles and applications in plant research
Mass spectrometry imaging (MSI) is an advanced analytical technique that combines mass spectrometry with spatial mapping, enabling the direct, label-free detection and visualization of molecular dist...
https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.70834
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5
1
reposted by
Omar Kamileen
bioRxiv Plant Bio
about 2 months ago
Dopamine biosynthesis in plants
https://www.biorxiv.org/content/10.64898/2025.12.10.693491v1
0
5
1
www.nature.com/articles/s41...
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Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods
Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis
https://www.nature.com/articles/s41592-025-02981-z
about 2 months ago
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1
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reposted by
Omar Kamileen
bioRxivpreprint
about 2 months ago
Nicotine biosynthesis completed by cryptic activating glucosylation
https://www.biorxiv.org/content/10.64898/2025.12.04.692101v1
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reposted by
Omar Kamileen
Natural Product Reports
about 2 months ago
🔓Don't miss in our latest issue this
#OpenAccess
review by
@maximilianfrey.bsky.social
& co.
@ipbhalle.bsky.social
,
@unihalle.bsky.social
&
@mpi-ce.bsky.social
looking at the biosynthesis of biologically active terpenoids in the mint family
#naturalproducts
#secmet
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Biosynthesis of biologically active terpenoids in the mint family (Lamiaceae)
Covering: 2000 to 2025 The Lamiaceae family, the sixth largest among angiosperms, is renowned for its rich diversity of terpenoids, many of which exhibit remarkable bioactivities, including…
https://pubs.rsc.org/en/content/articlelanding/2025/np/d5np00026b
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6
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www.nature.com/articles/s41...
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Next-generation method for preparing plant cells for single-cell RNA sequencing - Nature Methods
The plant cell wall makes the preparation of high-quality cells for single-cell RNA sequencing challenging. To tackle this issue, we developed FX-Cell, a method that enables the enzymatic digestion of...
https://www.nature.com/articles/s41592-025-02940-8
about 2 months ago
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0
reposted by
Omar Kamileen
Manuel Lera-Ramirez
2 months ago
#OpenCloning
is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software ✅ Free 🔓 Open Source 🧬 More cloning methods than SnapGene 🤖 Can be automated with python 👨🔬 Built by a researcher — for researchers! 👉 Check it out at
opencloning.org
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reposted by
Omar Kamileen
ETH Zurich
2 months ago
Researchers have manufactured organic light-emitting diodes (OLED) on a nanoscale – that’s around a hundred times smaller than a human cell. This not only enables ultra-sharp screens and microscopes, but also opens up entirely novel possibilities for wave optics applications.
ethz.ch/en/news-and-...
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Manufacturing the world's tiniest light-emitting diodes
Researchers from ETH Zurich have manufactured organic light-emitting diodes (OLEDs) on a nanoscale – that’s around a hundred times smaller than a human cell. This not only enables ultra-sharp screens ...
https://ethz.ch/en/news-and-events/eth-news/news/2025/11/manufacturing-the-worlds-tiniest-light-emitting-diodes.html
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reposted by
Omar Kamileen
Plaschka lab
2 months ago
How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take:
www.annualreviews.org/content/jour...
(1/3)
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reposted by
Omar Kamileen
Maddy Seale
2 months ago
And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in
@science.org
#PlantScience
Paper here:
www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
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CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...
https://www.science.org/doi/10.1126/science.adz8505
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38
reposted by
Omar Kamileen
Nature Biotechnology
3 months ago
Multimodal learning enables chat-based exploration of single-cell data -
@bocklab.bsky.social
@cemm.oeaw.ac.at
@meduniwien.ac.at
go.nature.com/3WPGJnW
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Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
https://go.nature.com/3WPGJnW
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reposted by
Omar Kamileen
Femke de Jong
3 months ago
Tension, suspense, or narrative arc in a story is the stuff that keeps the reader going. But how do you introduce suspense in a scientific article? That is what my latest post is all about.
aboutacademicwritingandzo.substack.com/p/how-to-wri...
#AcademicWriting
#WritingTips
#NarrativeArc
#Suspense
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How to write your paper like a page turner
Working my way through scientific articles I often lose my focus.
https://aboutacademicwritingandzo.substack.com/p/how-to-write-your-paper-like-a-page
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www.nature.com/articles/s41...
Really fabulous work! Animal pigments engineered in bacteria.
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Growth-coupled microbial biosynthesis of the animal pigment xanthommatin - Nature Biotechnology
A growth-coupled biosynthetic pathway enables xathommatin synthesis in the soil bacterium Pseudomonas putida.
https://www.nature.com/articles/s41587-025-02867-7
3 months ago
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reposted by
Omar Kamileen
Nature Biotechnology
3 months ago
Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants
go.nature.com/3CdewQS
rdcu.be/eNaje
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Binary vector copy number engineering improves Agrobacterium-mediated transformation - Nature Biotechnology
Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants.
https://go.nature.com/3CdewQS
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reposted by
Omar Kamileen
Moonyoung Kang
3 months ago
Excited to see our paper online! We combined scMS and scRNA-seq from the same plant cells 🌱 — a step toward true single-cell multi-omics in plants. Overview 👇
add a skeleton here at some point
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15
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reposted by
Omar Kamileen
Ryo Yokoyama
3 months ago
Discovery and engineering of the biosynthesis of rotenoids
www.nature.com/articles/s44...
@natsynth.nature.com
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Discovery and engineering of the biosynthesis of rotenoids - Nature Synthesis
Rotenoids are natural insecticides from Fabaceae plants. Here the complete biosynthetic pathway to make rotenoids is elucidated in Amorpha fruticosa and Tephrosia vogelii, revealing a unique Fe(II)-de...
https://www.nature.com/articles/s44160-025-00907-3
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reposted by
Omar Kamileen
Maite Colinas
4 months ago
Very exciting to finally see our iridoid cyclase ICYC online
@natplants.nature.com
! A joined effort with Robin Buell’s lab with Josh Wood generating snRNA-seq, and my student Chloée Tymen performing the initial experiment.
#natprod
#PlantScience
@mpi-ce.bsky.social
www.nature.com/articles/s41...
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Discovery of iridoid cyclase completes the iridoid pathway in asterids - Nature Plants
Iridoids are terpenoid metabolites found in thousands of plants. Using single-cell transcriptomics, the authors discovered an unexpected enzyme that has been neofunctionalized to catalyse the cyclization required to form the iridoid scaffold.
https://www.nature.com/articles/s41477-025-02122-6
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reposted by
Omar Kamileen
Maeda Plant Metabolism Lab
5 months ago
Our new study in Nature Plants maps how "multi-tasking" enzymes in plants transfer nitrogen, a key step toward improving crop N use efficiency. 🌱 Big thanks to our collaborators from Max Planck, Hokkaido Univ, & MSU, and for support from @NSF and @DOE. Learn more:
rdcu.be/eFOFN
#PlantMetabolism
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Mapping multi-substrate specificity of Arabidopsis aminotransferases
Nature Plants - Systematic characterization of Arabidopsis aminotransferase family enzymes uncovered many previously unrecognized activities and revealed their multi-substrate specificity, aspects...
https://rdcu.be/eFOFN
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reposted by
Omar Kamileen
SattelyLab
5 months ago
Beautiful work by Yaereen and former lab member Kevin! Learn more about the anti-cancer compound homoharringtonine and its'biosynthesis in plants here 🌿https://www.biorxiv.org/content/10.1101/2025.08.26.672243v1
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Discovery of homoharringtonine pathway enzymes reveals a whole plant model for coordinated biosynthesis
Plants have evolved to produce diverse molecules that inhibit protein translation. A lead example is homoharringtonine (HHT), both a key tool for ribosomal profiling and an FDA-approved treatment for ...
https://www.biorxiv.org/content/10.1101/2025.08.26.672243v1
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8
3
reposted by
Omar Kamileen
Ryo Yokoyama
5 months ago
The multilayered regulation of aromatic amino acid biosynthesis in plants: Trends in Biochemical Sciences
www.cell.com/trends/bioch...
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The multilayered regulation of aromatic amino acid biosynthesis in plants
The shikimate and aromatic amino acid (AAA) biosynthetic pathways are crucial for the production of L-phenylalanine (Phe), L-tyrosine (Tyr), and L-tryptophan (Trp), as well as vitamins, hormones, and ...
https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004%2825%2900185-9
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reposted by
Omar Kamileen
Itai Yanai
5 months ago
Discovery happens less when you're trying to be the expert and more when you're trying to be the learner.
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reposted by
Omar Kamileen
Ryo Yokoyama
5 months ago
Protein Structural Phylogenetics
academic.oup.com/gbe/article/...
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Protein Structural Phylogenetics
Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his
https://academic.oup.com/gbe/article/17/8/evaf139/8239332
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5
1
reposted by
Omar Kamileen
Mitja M. Zdouc
5 months ago
Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at
mite.bioinformatics.nl
. Preprint:
doi.org/10.26434/che...
(1/8)
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reposted by
Omar Kamileen
Nature Biotechnology
6 months ago
Inspired by natural molecular glues, drug hunters are chasing protein–protein interactions with next-gen small molecules tuned for enhanced tissue specificity and reduced toxicity
www.nature.com/articles/s41...
rdcu.be/eAC91
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Natural molecular glues spur next-gen small molecules for ‘undruggable’ targets - Nature Biotechnology
Inspired by natural molecular glues, drug hunters are chasing protein–protein interactions with next-gen small molecules tuned for enhanced tissue specificity and reduced toxicity.
https://www.nature.com/articles/s41587-025-02779-6
0
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reposted by
Omar Kamileen
SattelyLab
6 months ago
Couldn't have said it better! Great job
@taralowensohn.bsky.social
, Will, and Chun! Special thanks to the Gao lab at
@stanford.edu
#singlecell
#plantbiology
add a skeleton here at some point
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7
4
reposted by
Omar Kamileen
Conor McClune
6 months ago
A truly enabling new approach by
@taralowensohn.bsky.social
Will Cody and
@sattelylab.bsky.social
to probe plant genetics at scale. Single-gene-per-cell delivery coupled to an effective transcriptional selection system
www.biorxiv.org/content/10.1...
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20
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reposted by
Omar Kamileen
Maite Colinas
7 months ago
Ingenane biosynthesis enzymes in
@newphyt.bsky.social
by
@matildeflorean.bsky.social
,
@carstenschotte.bsky.social
from
@oconnorlab.bsky.social
@mpi-ce.bsky.social
in collaboration with Ian Graham lab members.
#natprod
#PlantScience
doi.org/10.1111/nph....
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Identification of BAHD‐acyltransferase enzymes involved in ingenane diterpenoid biosynthesis
The plant family Euphorbiaceae is an abundant source of structurally complex diterpenoids, many of which have reported anticancer, anti-HIV, and anti-inflammatory activities. Among these, ingenol-3-...
https://doi.org/10.1111/nph.70388
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reposted by
Omar Kamileen
Nature Chemical Biology
7 months ago
Here, the authors
@oconnorlab.bsky.social
@mpi-ce.bsky.social
uncover the mechanism of epimerization behind uncommon 3R-containing alkaloids in Mitragyna speciosa (Kratom) and study their inclusion in downstream biosynthesis
#PlantScience
#natprod
www.nature.com/articles/s41...
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Enzymatic epimerization of monoterpene indole alkaloids in kratom - Nature Chemical Biology
Monoterpene indole alkaloids are formed via a 3S stereoselective condensation between secologanin and tryptamine. Here the authors uncover the mechanism of epimerization behind uncommon 3R-containing ...
https://www.nature.com/articles/s41589-025-01970-9?utm_source=bluesky&utm_medium=social&utm_campaign=nchembio
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reposted by
Omar Kamileen
Laura Gunn
7 months ago
SynBio: it’s what plants crave
doi.org/10.1093/jxb/...
J Exp Bot Insights article from *Dan Hong Loh* - she discusses the impacts of Rubisco SynBio tool expansions from Archer et al. 2025 (
doi.org/10.1093/jxb/...
).
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A SynBio explosion: a whole new world for Rubisco engineering
This article comments on:Archer J, Kathpalia M, Lee B, Li S, Wang T. 2025. Effects of chaperone selectivity on the assembly of plant Rubisco orthologs in E
https://doi.org/10.1093/jxb/eraf189
0
8
5
reposted by
Omar Kamileen
eLife
7 months ago
Heron is a new intuitive software tool that helps researchers design complex experiments even if they don’t have in-depth technical expertise. 🔗
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Streamlining experimental setups
A new software tool called Heron helps researchers to design and run complex experimental systems without needing in-depth technical expertise.
https://buff.ly/AdAhzaW
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11
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reposted by
Omar Kamileen
Trends in Plant Science
7 months ago
July Issue. Read FREE: Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life (see cover); Decoding the evolution of C4 photosynthesis; Transcellular regulation of ETI-induced cell death; & much more
www.cell.com/trends/plant...
#plantscience
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10
3
reposted by
Omar Kamileen
Dr. Todd Ewing PhD.
7 months ago
Researchers
@emoryuniversity.bsky.social
observe
#longevity
benefit of
#psilocybin
#psychedelic
mushroom
news.emory.edu/stories/2025...
— extended human skin & lung cell lifespan by 50% — increase aged mice survival by 30% — reduces oxidative stress — improves DNA repair 🧪
#health
#science
#aging
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Psilocybin delays aging, extends lifespan, new Emory study suggests | Emory University | Atlanta GA
Emory University researchers identified that psilocin, a byproduct of consuming psilocybin, the active ingredient in psychedelic mushrooms, actively delays aging in cells and organisms.
https://news.emory.edu/stories/2025/07/hs_psilocybin_aging_study_10-07-2025/story.html
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11
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reposted by
Omar Kamileen
Addgene
7 months ago
Want to become a cloning wizard? 🪄 Our latest blog post is packed with hands-on tips for mastering Modular Cloning — advice on how to prepare for the process, handle reagents, high-throughput methods, and more. Start your MoClo quest here:
https://twp.ai/4io9Rn
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blog.addgene.org
Tips and Tricks for Using Golden Gate Modular Cloning (MoClo)
https://twp.ai/4io9Rn
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reposted by
Omar Kamileen
Pam Marrone, PhD
7 months ago
Yes when I was on the board of
@cornelluniversity.bsky.social
the women profs told us exactly this..and even moreso for the minority profs: minority students flocked to them as role models to ask for mentoring and advice, taking time away from the Prof's own research
#womeninscience
#womeninstem
add a skeleton here at some point
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reposted by
Omar Kamileen
Nature Portfolio
7 months ago
SNAP-tag is a widespread tool for labelling protein for bioimaging. An article published in Nature Chemical Biology presents SNAP-tag2 with increased labelling kinetics and brightness, which translates into a better performance in live-cell super-resolution imaging.
go.nature.com/46fMIZd
🧪
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reposted by
Omar Kamileen
Itai Yanai
7 months ago
'Night science' is what you do when you're not sure what's the question.
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reposted by
Omar Kamileen
Nature Biotechnology
7 months ago
Defining and benchmarking open problems in single-cell analysis -
@krishnaswamylab.bsky.social
@fabiantheis.bsky.social
bit.ly/4l8dsiF
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Defining and benchmarking open problems in single-cell analysis - Nature Biotechnology
Nature Biotechnology - Defining and benchmarking open problems in single-cell analysis
https://bit.ly/4l8dsiF
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reposted by
Omar Kamileen
Molecular Plant & Plant Communications
7 months ago
Broad application of the ALFA tagging technology for in planta nanobody-based imaging and biochemical characterization of plant proteins
#resource
#PlantCommunications
cell.com/plant-commun...
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www.science.org/doi/10.1126/...
Robots for precision agroinfiltration. Really cool engineering effort with the biology in mind 👍🏾
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In situ foliar augmentation of multiple species for optical phenotyping and bioengineering using soft robotics
A soft robotic gripper enables nondestructive delivery of nanosensors and genes into leaves of diverse plant species.
https://www.science.org/doi/10.1126/scirobotics.adu2394
7 months ago
0
1
0
reposted by
Omar Kamileen
Javier Santoyo
7 months ago
A composite universal DNA signature for the tree of life.
#DNAbarcoes
#DNAsignatures
#GenomeSequencing
@natecoevo.nature.com
www.nature.com/articles/s41...
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5
3
reposted by
Omar Kamileen
German Society for Plant Sciences (DBG)
7 months ago
A catalytically inactive enzyme enables the formation of free indole for plant defense + communication, researchers from
@oconnorlab.bsky.social
from
@mpi-ce.bsky.social
report in
@natchembio.nature.com
DOI: 10.1038/s41589-025-01943-y
www.ice.mpg.de/496511/PR_Fl...
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Flowering plants use a pseudoenzyme to form indole
A catalytically inactive enzyme enables the formation of free indole for plant defense and communication. • Indole biosynthesis occurs via a pseudoenzyme: Although TSB-like is essential for indole for...
https://www.ice.mpg.de/496511/PR_Florean
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1
reposted by
Omar Kamileen
Yuli Ding
7 months ago
I'm very pleased to present the
@cp-devcell.bsky.social
Voices on plant model organism:
www.sciencedirect.com/science/arti...
. While we appreciate the diversity of plant models, one often questions which model is the "best"?
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Exploring the diversity of plant model organisms
Increasing plant genome research, together with advanced transformation technology, enables researchers to address their research questions more effec…
https://www.sciencedirect.com/science/article/abs/pii/S1534580725003302
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reposted by
Omar Kamileen
Michael Booth
7 months ago
We have developed an entirely new mechanism of action for gene knockdown -> trafficking of targeted mRNAs to the lysosomal, using lysosomal trafficking oligonucleotides (LyTONs)! Published in
@chemicalscience.rsc.org
Led by Disha Kashyap
#chemsky
🧪
pubs.rsc.org/en/content/a...
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Engineering antisense oligonucleotides for targeted mRNA degradation through lysosomal trafficking
Antisense oligonucleotides (ASOs) can modulate gene expression at the mRNA level, providing the ability to tackle conventionally undruggable targets and usher in an era of personalized medicine. A key...
https://pubs.rsc.org/en/content/articlelanding/2025/sc/d5sc03751d
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reposted by
Omar Kamileen
Maite Colinas
8 months ago
Next preprint out from my work
@oconnorlab.bsky.social
@mpi-ce.bsky.social
: the discovery or iridoid cyclase in asterids! Thread below.
#PlantScience
#natprod
www.biorxiv.org/content/10.1...
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https://www.biorxiv.org/content/10.1101/2025.06.12.659277v1
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reposted by
Omar Kamileen
Tobias Jores
8 months ago
Our latest paper is out in its final form in
@theplantcell.bsky.social
We show that in plants the same DNA sequence can act as an insulator or silencer depending on the surrounding regulatory context. Read the full paper at:
doi.org/10.1093/plce...
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reposted by
Omar Kamileen
PlantEvolution 🌱🌾
8 months ago
Must read for all who use Nicotiana benthamiana as a platform: “Causes and consequences of experimental variation in Nicotiana benthamiana transient expression”
#plantscience
www.biorxiv.org/content/10.1...
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reposted by
Omar Kamileen
Arif Ashraf
8 months ago
🔬📊 Comment: A checklist for designing and improving the visualization of scientific data
@natcellbio.nature.com
www.nature.com/articles/s41...
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reposted by
Omar Kamileen
Itai Yanai
8 months ago
90% of doing science is being open to new ideas.
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Omar Kamileen
Conor McClune
8 months ago
Today in Nature we report a systematic strategy to activate & identify gene sets in plants. We identify 8 new genes from the yew tree's Taxol biosynthetic pathway, enabling us to engineer tobacco with 17- & 20-gene pathways to Taxol precursors baccatin III & deBz-deoxy-Taxol
#SingleCell
#secmet
🧬🧪🌾
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Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III - Nature
An approach that combines single-nucleus RNA sequencing and multiplexed perturbation identifies genes that enable the biosynthesis of direct precursors of the anti-cancer drug Taxol, whose curren...
https://www.nature.com/articles/s41586-025-09090-z
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www.nature.com/articles/s41...
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Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking - Nature Communications
Synthesis of complex molecules requires reactions from multiple pathways operating in balanced subnetworks. Here, the authors report a computational algorithm that combines the strength of constraint-...
https://www.nature.com/articles/s41467-025-59827-7
8 months ago
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