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

A highly efficient and environmentally friendly strategy to obtain transgene-free genome-edited progeny in flowering plants Obtaining foreign DNA-free crops after genome editing is essential for agricultural applications, because of the current regulatory policies on gene-edited plants in various countries. However, it is ...

📜 A highly efficient and environmentally friendly strategy to obtain transgene-free genome-edited progeny in flowering plants

🧑‍🔬 Tianhe Cheng, Meng-Xiang Sun

📔 @mplantpcom.bsky.social

🔗 www.cell.com/molecular-pl...

#️⃣ #PlantScience #PlantTransformation #PlantNGTs #PlantGMOs #PlantMethods

📜 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

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.

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...

📜 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

Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis - Nature Plants Weiss et al. engineered the tobacco rattle virus to express the RNA-guided TnpB enzyme ISYmu1 and guide RNA for transgene-free germline editing in Arabidopsis thaliana.

📜 Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis

🧑‍🔬 Trevor Weiss, @jacobsenucla.bsky.social, et al.

📔 @natplants.nature.com

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantNGTs #PlantGenEditing #PlantGenomics #PlantMethods #PlantTools

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...

📜 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

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...

📜 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 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.

📜 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

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...

📜 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

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.

📜 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

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...

📜 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

📜 A pRK290-derived binary vector suitable for assembling large T-DNAs for plant transformation using Golden Gate cloning

🧑‍🔬 Mark Youles, @jonathandgjones.bsky.social, et al.

📔 Zenodo

🔗 zenodo.org/records/1451...

#️⃣ #PlantScience #PlantTransformation #PlantMolecularBiology #PlantMethods #PlantTools

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 ...

📜 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

Justin Walley on stage at the Max Planck Institute for Plant Breeding Research. The Acknowledgement slide is showing.

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 👌

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms ...

📜 Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

🧑‍🔬 Vlastimil Novak, John P. Vogel, Trent R. Northen, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantPhysiology #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...

📜 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

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".

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 👌

Diurnal.plant.tools in 2024: Expanding to Marchantia polymorpha and Four Angiosperms Abstract. Diurnal gene expression is a pervasive phenomenon occurring across all kingdoms of life, orchestrating adaptive responses to daily environmental

📜 Diurnal.plant.tools in 2024: Expanding to Marchantia polymorpha and Four Angiosperms

🧑‍🔬 Qiao Wen Tan, Emmanuel Tan, Marek Mutwil

📔 Plant & Cell Physiology

🔗 academic.oup.com/pcp/advance-...

#️⃣ #PlantScience #PlantDevelopment #PlantEvoDevo #Marchantia #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...

📜 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

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.....

📜 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

Root screening method using a salinity gradient Protocol Authors Afrasyab Rahnama, Rana Munns, Michelle Watt Overview This root screening method can be used for measuring the growth responses of the primary axile roots and the branch roots of wh…

📜 Root screening method using a salinity gradient

🧑‍🔬 Afrasyab Rahnama, Rana Munns, Michelle Watt

📔 Prometheus

🔗 prometheusprotocols.net/experimental...

#️⃣ #PlantScience #RootBiology #PlantMethods #PlantProtocols #PlantDevelopment

Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots Imaging the spatiotemporal dynamics of host-microbiota interactions is of particular interest for augmenting our understanding of these complex systems. This is especially true of plant–microbe ...

📜 Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots

🧑‍🔬 Jonathan M. Conway, Jeffery L. Dangl, et al.

📔 Tissue Morphogenesis: Methods and Protocols,

🔗 link.springer.com/10.1007/978-...

#️⃣ #PlantScience #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

📜 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

Capturing the phosphorylation-linked protein-complex landscape in plants Protein phosphorylation and protein interactions are core regulatory systems involved in plant growth and environmental adaptation. Elucidating the intricate isoforms of a protein and its complex-spec...

📜 Capturing the phosphorylation-linked protein-complex landscape in plants

🧑‍🔬 Yanmei Chen, Dongtao Ren, et al.

📔 Trends in Plant Science

🔗 www.cell.com/trends/plant...

#️⃣ #PlantScience #PlantMethods #PlantProteomics #PlantPhosphoproteomics

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.

📜 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

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

📜 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

Stable, fluorescent markers for tracking synthetic communities and assembly dynamics - Microbiome Background After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechani...

📜 Stable, fluorescent markers for tracking synthetic communities and assembly dynamics

🧑‍🔬 Beatriz Jorrin, Philip S. Poole, et al.

📔 Microbiome

🔗 microbiomejournal.biomedcentral.com/articles/10....

#️⃣ #PlantScience #PlantImmunity #PlantMethods #PlantMicrobiome #SynCom #PlantSynCom

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

📜 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

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....

📜 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