RESUMEN
The application of deep learning methods, specifically the utilization of Large Language Models (LLMs), in the field of plant biology holds significant promise for generating novel knowledge on plant cell systems. The LLM framework exhibits exceptional potential, particularly with the development of Protein Language Models (PLMs), allowing for in-depth analyses of nucleic acid and protein sequences. This analytical capacity facilitates the discernment of intricate patterns and relationships within biological data, encompassing multi-scale information within DNA or protein sequences. The contribution of PLMs extends beyond mere sequence patterns and structure--function recognition; it also supports advancements in genetic improvements for agriculture. The integration of deep learning approaches into the domain of plant sciences offers opportunities for major breakthroughs in basic research across multi-scale plant traits. Consequently, the strategic application of deep learning methodologies, particularly leveraging the potential of LLMs, will undoubtedly play a pivotal role in advancing plant sciences, plant production, plant uses and propelling the trajectory toward sustainable agroecological and agro-food transitions.
Asunto(s)
Aprendizaje Profundo , Procesamiento de Lenguaje Natural , Plantas , Plantas/genética , Plantas/metabolismoRESUMEN
When plants are subjected to drought, it is impossible to obtain xylem sap for subsequent biochemical and molecular analysis using root pressure exudate, the conventional approach. Here, we present a protocol for collecting xylem sap from drought-treated tomato plants using a pressure chamber. We describe steps for how to prepare plants, apply drought, and use the pressure chamber to collect the xylem sap. Using this technique, one can obtain 500-700 µL of xylem sap in just 5-7 min. For complete details on the use and execution of this protocol, please refer to Alexou and Peuke.1.
RESUMEN
Molecular identification of pollen carried by insects informs about their history of visited plants. For migratory butterflies, it can be used to trace long-range movements enduring days of flight over thousands of kilometers. Here, we present a protocol to (1) isolate pollen grains from butterfly bodies and (2) prepare metabarcoding libraries for their identification using the internal transcribed spacer 2 fragment, a common barcode used to identify plants. This protocol would be applicable to other insect groups and metabarcoding markers. For complete details on the use and execution of this protocol, please refer to Suchan et al.1 and Gorki et al.2.
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Global warming will change the photosynthesis and transpiration of plants greatly and ultimately affect water use efficiency (WUE). Here, we present a protocol to investigate the response of maize WUE to the coupling effect of CO2 and temperature at ear stage using a specialized designed gradient. We describe steps for plant culture, parameter measurements, model fitting, and statistical analysis. This protocol holds potential for studying the response of WUE and CO2 adaptation across various plant species. For complete details on the use and execution of this protocol, please refer to Sun et al.1.
Asunto(s)
Dióxido de Carbono , Fotosíntesis , Temperatura , Zea mays , Zea mays/fisiología , Dióxido de Carbono/metabolismo , Fotosíntesis/fisiología , Agua/metabolismo , Transpiración de Plantas/fisiologíaRESUMEN
Cellular protein homeostasis is maintained by the disposal of aggregated misfolded proteins. Here, we present a protocol for investigating the involvement of the proteins of interest in misfolded protein degradation via Agrobacterium-mediated transient expression in Nicotiana benthamiana. We describe in detail the steps of misfolded protein design, transient protein expression in N. benthamiana, subsequent total protein extraction, and quantification of misfolded proteins through western blotting. This generalizable system can be used for misfolded proteins derived from various plants or microbes. For complete details on the use and execution of this protocol, please refer to Ai et al.1.
Asunto(s)
Agrobacterium , Nicotiana , Pliegue de Proteína , Proteolisis , Nicotiana/genética , Nicotiana/metabolismo , Agrobacterium/genética , Agrobacterium/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/metabolismo , Plantas Modificadas Genéticamente/genéticaRESUMEN
In addition to proteins, microRNAs, and lipids, plant-derived exosome-like nanovesicles (ENVs) are also enriched with host plant bioactives. Both curcumin and piperine are water insoluble, lack bioavailability, and are extracted by non-ecofriendly solvents. Herein, we present an eco-friendly protocol for co-isolating both curcumin and piperine in the form of hybrid ENVs. We describe steps for sample pre-processing, combined homogenization of plant materials, filtration, and differential centrifugation. We then detail procedures for polyethylene glycol-based fusion and precipitation of hybrid ENVs. For complete details on the use and execution of this protocol, please refer to Kumar et al.1.
Asunto(s)
Alcaloides , Curcuma , Curcumina , Piperidinas , Alcamidas Poliinsaturadas , Polietilenglicoles , BenzodioxolesRESUMEN
Understanding the generation, movement, uptake, and perception of mobile defense signals is key for unraveling the systemic resistance programs in flowering plants against pathogens. Here, we present a protocol for analyzing the movement and uptake of isotopically labeled signaling molecule azelaic acid (AZA) in Arabidopsis thaliana. We describe steps to assess 14C-AZA uptake into leaf discs and its movement from local to systemic tissues. We also detail the assay for uptake and movement of 2H-AZA from roots to the shoot. For complete details on the use and execution of this protocol, please refer to Cecchini et al.1,2.