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somssich.bsky.social
📜 Identification of plant transcriptional activation domains

🧑‍🔬 Nicholas Morffy, @luciastrader.bsky.social, et al.

📔 @natureportfolio.bsky.social

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantGenomics #PlantBioInformatics #PlantMethods #PlantTools #PlantGenetics
Identification of plant transcriptional activation domains - Nature
A high-throughput yeast-based assay is used to identify more than 1,500 activation domains (ADs) in Arabidopsis transcription factors, and a deep learning approach applied to this dataset can predict ...
www.nature.com
November 14, 2024 at 7:49 AM
somssich.bsky.social
📜 CarboTag: a modular approach for live and functional imaging of plant cell walls

🧑‍🔬 Maarten Besten, Joris Sprakel, et al.

📔 @naturemethods.bsky.social

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantCellWalls #PlantTools #PlantMicroscopy #PlantImaging #PlantMethods
CarboTag: a modular approach for live and functional imaging of plant cell walls - Nature Methods
A suite of nontoxic and permeable CarboTag probes in various colors enables live quantitative imaging of a range of plant cell wall characteristics and dynamic, high-resolution mapping of cell wall ch...
www.nature.com
May 2, 2025 at 11:46 AM
somssich.bsky.social
#PlantScienceClassics #21: MS Medium. In 1962 Toshio Murashige & Folke Skoog published their revised plant tissue culture medium @pplplantarum.bsky.social, arguably the most high-cited #PlantScience paper of all time.

onlinelibrary.wiley.com/doi/10.1111/...
🧪 #PlantDevelopment #PlantMethods
The header of the paper: PHYSIOLOGIA PLANTARUM, Vol. 15. 1962. The title “A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures” is shown, followed by the author’s names Toshio Murashige, Folke Skoog. Their affiliation is Department of Botany, University of Wisconsin, Madison, 6, Wisconsin. The paper was received for publication on April 1, 1962. To the left of the paper header is a black and white headshot of a smiling Toshia Murashige, and to the right a black and white headshot of a serious looking Folke Skoog.
April 8, 2026 at 7:20 AM
somssich.bsky.social
Another Wednesday, another fantastic speaker. The perks of working at the MPIPZ. Today, we had @justinwwalley.bsky.social, hosted by @grandpahiro.bsky.social, to speak about his lab's integrative multi-omics approach to identify new immunity genes & pathways in #maize 🌽.
Very cool #PlantMethods 👌
Justin Walley on stage at the Max Planck Institute for Plant Breeding Research. The Acknowledgement slide is showing.
November 6, 2024 at 1:25 PM
somssich.bsky.social
📜 A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants

🧑‍🔬 Yanhao Cheng, Yiping Qi, et al.

📔 @theplantcell.bsky.social

🔗 academic.oup.com/plcell/advan...

#️⃣ #PlantScience #PlantCRISPR #PlantMethods #PlantGenomics #PlantNGTs #PlantGE #PlantGenomeEditing
A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants
An all-in-one CRISPR toolbox is developed to aid guide RNA library-based loss-of-function and gain-of-function screens in plants.
academic.oup.com
April 15, 2025 at 7:54 AM
somssich.bsky.social
📜 A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha

🧑‍🔬 Eftychios Frangedakis, @jmhibberd.bsky.social, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantGenomics #PlantMethods #PlantEvoDevo #Marchantia #PlantCRISPR
A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha
The liverwort Marchantia polymorpha is a widely used model organism for studying land plant biology, which has also proven to be a promising testbed for bioengineering. CRISPR/Cas9 technology has emer...
www.biorxiv.org
April 25, 2025 at 7:16 AM
somssich.bsky.social
"Rapid depletion of target proteins in plants by an inducible protein degradation system"

Linzhou Huang and Marcela Rojas-Pierce

Breakthrough Report in The Plant Cell that sounds like a useful tool. 👍

#PlantScience #PlantMethods
March 18, 2024 at 2:13 PM
somssich.bsky.social
📜 Non‐Invasive, Bioluminescence‐Based Visualisation and Quantification of Bacterial Infections in Arabidopsis Over Time

🧑‍🔬 Nanne W. Taks, Harrold A. van den Burg, et al.

📔 Molecular Plant Pathology

🔗 bsppjournals.onlinelibrary.wiley.com/doi/10.1111/...

#️⃣ #PlantScience #PlantImmunity #PlantMethods
Non‐Invasive, Bioluminescence‐Based Visualisation and Quantification of Bacterial Infections in Arabidopsis Over Time
Development of a non-invasive high-throughput phenotyping pipeline to visualise and quantify progression of bioluminescent bacterial pathogens in Arabidopsis rosettes over time.
bsppjournals.onlinelibrary.wiley.com
February 5, 2025 at 7:51 AM
somssich.bsky.social
📜 Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

🧑‍🔬 Sophia N. Tang, Mitchell G. Thompson, Patrick M. Shih, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantMethods #PlantReproducibility #Benthamiana
www.biorxiv.org
June 18, 2025 at 7:20 AM
somssich.bsky.social
📜 Establishing a suberin tool kit for determining suberization within classical and ‘orphan’ tissues

🧑‍🔬 Justin B. Nichol, Lorena S. Yeung, Mark A. Bernards, Marcus A. Samuel

📔 @cp-trendsplantsci.bsky.social

🔗 www.cell.com/trends/plant...

#️⃣ #PlantScience #Suberin #PlantMethods #PlantCellWalls
Establishing a suberin tool kit for determining suberization within classical and ‘orphan’ tissues
Suberin is a complex biopolymer found in land plants that serves as a natural barrier, regulating water and nutrient uptake while also providing defense against invading pathogens. Structurally, suber...
www.cell.com
April 30, 2025 at 11:29 AM
somssich.bsky.social
We had a fantastic seminar from @bertderybel.bsky.social on vascular development today at the MPIPZ. #PlantCellBiology #PlantDevelopment & #PlantEvoDevo. A new regulator of asymmetric cell divisions in the root, & evolutionary conserved xylem/phloem regulators. Impressive #PlantMethods & data 👌
Bert de Rybel on stage at the MPIPZ. His cover slides shows a cross section of a plant root meristem, and the title "Understanding vascular development using chemical and single cell biology".
October 31, 2024 at 1:35 PM
somssich.bsky.social
📜 Identification of Bioactive Phytocytokines Using Transcriptomic Data and Plant Bioassays

🧑‍🔬 @jackrhodes.bsky.social, Cyril Zipfel

📔 Methods in Molecular Biology

🔗 link.springer.com/10.1007/978-...

#️⃣ (Feeds) #PlantMethods #PlantScience #PeptideHormones #PlantPeptides #Phytocytokines
Plant Peptide Hormones and Growth Factors
This book describes state-of-the-art approaches for identification and functional characterization of plant peptide hormones and growth factors.
link.springer.com
December 5, 2023 at 9:34 AM
somssich.bsky.social
📜 MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions

🧑‍🔬 @chesneau-g.bsky.social, @hacquardst.bsky.social, et al.

📔 @naturecomms.bsky.social

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantImmunity #PlantMethods
MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions - Nature Communications
Metabolic interactions shape ecosystems but remain hard to study. Here, authors present MetaFlowTrain, a modular, low-cost fluidic system controlling metabolic fluxes between microbes, and show its va...
www.nature.com
April 15, 2025 at 7:50 AM
somssich.bsky.social
📜 SPIRO – the automated Petri plate imaging platform designed by biologists, for biologists

🧑‍🔬 Jonas A. Ohlsson, Jia Xuan Leong, Elena A. Minina, et al.

📔 The Plant Journal

🔗 onlinelibrary.wiley.com/doi/10.1111/...

#️⃣ #PlantScience #PlantMethods #PlantImaging
SPIRO – the automated Petri plate imaging platform designed by biologists, for biologists
PIRO addresses the main bottleneck preventing widespread use of many fantastic custom-made phenotyping platforms: feasibility to replicate the system without access to engineering skills. SPIRO is de....
onlinelibrary.wiley.com
April 26, 2024 at 11:52 AM
somssich.bsky.social
📜 Improving transient protein expression in agroinfiltrated Nicotiana benthamiana

🧑‍🔬 Konstantina Beritza, Emma C. Watts, Renier A. L. van der Hoorn

📔 @newphyt.bsky.social

🔗 nph.onlinelibrary.wiley.com/doi/10.1111/...

#️⃣ #PlantScience #PlantMethods #Agroinfiltration #PlantTransformation
Improving transient protein expression in agroinfiltrated Nicotiana benthamiana
<em>New Phytologist</em> is an international journal owned by the New Phytologist Foundation publishing original research in plant science and its applications.
nph.onlinelibrary.wiley.com
June 11, 2024 at 1:25 PM
somssich.bsky.social
📜 Agrobacterium-mediated Cuscuta campestris transformation as a tool for understanding plant-plant interactions

🧑‍🔬 Supral Adhikari, Asha Mudalige, So-Yon Park, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ (Feeds) #PlantScience #PlantMethods #ParasiticPlants
Agrobacterium-mediated Cuscuta campestris transformation as a tool for understanding plant-plant interactions
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
February 28, 2024 at 6:43 AM
somssich.bsky.social
📜 The secreted redox sensor roGFP2-Orp1 reveals oxidative dynamics in the plant apoplast

🧑‍🔬 Julian Ingelfinger, Stefanie J. Müller-Schüssele, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantPhysiology #PlantImaging #PlantMicroscopy #PlantMethods
The secreted redox sensor roGFP2-Orp1 reveals oxidative dynamics in the plant apoplast
Specific generation of reactive oxygen species (ROS) is important for signalling and defence in many organisms. In plants, different types of ROS perform useful biological functions in the extracellul...
www.biorxiv.org
January 17, 2025 at 7:04 AM
gsena.bsky.social
What are the most cutting-edge methods to image complex root systems in mature trees in field conditions? Ground-penetrating radar? X-ray CT?
What resolution can we get?

Anyone working on wilder techniques?

#science #imaging #plantroots #plantscience #plantmethods #root #phenotyping #soil
July 11, 2025 at 2:33 PM
somssich.bsky.social
Since I also did a lot of protein-protein interaction work, & tested & used many techniques to do so, I also thought that it is time to summarize everything on this topic to produce an overview article:
shorturl.at/YgFFX

#PlantScience #PlantMethods

This is my first corresponding author article.
May 30, 2025 at 9:53 AM
somssich.bsky.social
📜 Diurnal.plant.tools in 2024: expanding to Marchantia polymorpha and four angiosperms

🧑‍🔬 Qiao Wen Tan, Emmanuel Tan, Marek Mutwil

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantTools #PlantEvolution #PlantMethods #CompPlantBio
Diurnal.plant.tools in 2024: expanding to Marchantia polymorpha and four angiosperms
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
May 3, 2024 at 4:44 AM
somssich.bsky.social
📜 Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation

🧑‍🔬 Davide Annese, @jimhaseloff.bsky.social, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantTransformation #Agrobacterium #PlantMethods
Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation
High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline for Agrobacterium tumefaciens transformation a...
www.biorxiv.org
October 14, 2024 at 7:57 AM
somssich.bsky.social
📜 ExPOSE: A comprehensive toolkit to perform expansion microscopy in plant protoplast systems

🧑‍🔬 Kevin L. Cox, Sarah A. Pardi, Kirk J. Czymmek, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantMicroscopy #ExpansionMicroscopy #PlantMethods
ExPOSE: A comprehensive toolkit to perform expansion microscopy in plant protoplast systems
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
July 26, 2024 at 7:37 AM
somssich.bsky.social
📜 A history-dependent integrase recorder of plant gene expression with single-cell resolution

🧑‍🔬 Cassandra J. Maranas, Sarah Guiziou, et al.

📔 Nature Communications

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantSynthBio #PlantSynBio #PlantCellBiology #PlantMethods
A history-dependent integrase recorder of plant gene expression with single-cell resolution - Nature Communications
Understanding gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, the authors engineer a four-state history-dependent integra...
www.nature.com
November 5, 2024 at 8:04 AM
somssich.bsky.social
📜 Divide and conquer: using RHIZOVISION EXPLORER to aggregate data from multiple root scans using image concatenation and statistical methods

🧑‍🔬 Anand Seethepalli, @larrymyork.bsky.social, et al.

📔 @newphyt.bsky.social

🔗 nph.onlinelibrary.wiley.com/doi/10.1111/...

#️⃣ #PlantScience #PlantMethods
Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods
Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned.....
nph.onlinelibrary.wiley.com
October 8, 2024 at 12:39 PM
somssich.bsky.social
📜 An Efficient Sulfadiazine Selection Scheme for Stable Transformation in the Model Liverwort Marchantia polymorpha

🧑‍🔬 Kayla Robinson, @philcarella.bsky.social, et al.

📔 @jxbotany.bsky.social

🔗 academic.oup.com/jxb/advance-...

#️⃣ #PlantScience #PlantTransformation #Marchantia #PlantMethods
An Efficient Sulfadiazine Selection Scheme for Stable Transformation in the Model Liverwort Marchantia polymorpha
Abstract. Plant macroevolutionary studies leverage the phylogenetic position of non-flowering model systems like the liverwort Marchantia polymorpha to inv
academic.oup.com
June 6, 2024 at 5:53 AM