Biology subjects

Acosta-Gamboa, L.

Publications and source records attributed to Acosta-Gamboa, L..

5 recordsLinked to original sources

bioRxiv2025

PlantCV v4: Image analysis software for high-throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection. CORE IDEASO_LIPlantCV is an open-source, open-development, Python-based software package that has a new release for improved functionality and usability to make image analysis flexible and easier for researchers without a coding background. C_LIO_LIPlantCV is now capable of handling new data types that are relevant to researchers, such as thermal and hyperspectral, and has built in functionality for extracting information from these image types. C_LIO_LIThe software project aims to lower the barrier to entry into image analysis for researchers by providing numerous, versioned, interactive tutorials that cover most common use cases, particularly in plant science. C_LI

plant biology↗

bioRxiv2025

Remote sensing of endogenous pigmentation by inducible synthetic circuits in grasses

Plant synthetic biology holds great promise for engineering plants to meet future demands. Genetic circuits are being designed, built, and tested in plants to demonstrate proof of concept. However, developing these components in monocots, which the world relies on for grain, lags behind dicot models, such as Arabidopsis thaliana and Nicotiana benthamiana. Here, we show the successful adaptation of a ligand-inducible sensor to activate an endogenous anthocyanin pathway in the C4 monocot model Setaria viridis. We identify two transcription factors sufficient to induce endogenous anthocyanin production in S. viridis protoplasts and whole plants in a constitutive or ligand-inducible manner. We also test multiple ligands to overcome physical barriers to ligand uptake, identifying triamcinolone acetonide (TA) as a highly potent inducer of this system. Using hyperspectral imaging and a discriminative target characterization method in a near-remote configuration, we can non-destructively detect anthocyanin production in leaves in response to ligands. This work demonstrates the use of inducible expression systems in monocots to manipulate endogenous pathways, stimulating plants to overproduce secondary metabolites with value to human health. Applying inducible pigmentation coupled with sensitive detection algorithms could enable crop plants to report on the status of field contamination or detect undesirable chemicals impacting agriculture, ushering in an era of agriculture-based sensor systems. SummaryO_ST_ABSSynbio tools for C4 grass modelC_ST_ABS[bullet] Advantage of synthetic switches as tools for biopharming and functional genomics [bullet]Our workflow to optimize the gene circuits from a transient system to a stable transgenic [bullet]Testing and taming golden gate elements in monocot system, S. viridis

plant biology↗

bioRxiv2025

Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants

Light is essential for photosynthesis; however, excess light can increase the accumulation of photoinhibitory reactive oxygen species that reduce photosynthetic efficiency. Plants have evolved photoprotective non-photochemical quenching (NPQ) pathways to dissipate excess light energy. In tobacco and soybean (C3 plants), overexpression of three NPQ genes, violaxanthin de-epoxidase (VDE), Photosystem II Subunit S (PsbS), and zeaxanthin epoxidase (ZEP), hereafter VPZ, resulted in faster NPQ induction and relaxation kinetics, and increased crop yields in field conditions. NPQ is well-studied in C3 plants; however, NPQ and the translatability of the VPZ approach in C4 plants is poorly understood. The green foxtail Setaria viridis is an excellent model to study photosynthesis and photoprotection in C4 plants. To understand the regulation of NPQ and photosynthesis in C4 plants, we performed transient overexpression in Setaria protoplasts and generated (and employed) stable transgenic Setaria plants overexpressing one of the three Arabidopsis NPQ genes or all three NPQ genes (AtVPZ lines). Overexpressing (OE) AtVDE and AtZEP in Setaria produced similar results as in C3 plants, with increased or reduced zeaxanthin (thus NPQ), respectively. However, overexpressing AtPsbS appeared to be challenging in Setaria, with largely reduced NPQ in protoplasts and under-represented homozygous AtPsbS-OE lines, potentially due to competitive and tight heterodimerization of AtPsbS and SvPsbS proteins. Furthermore, Setaria AtVPZ lines had increased zeaxanthin, faster NPQ induction, higher NPQ level, but slower NPQ relaxation. Despite this, AtVPZ lines had improved growth as compared to wildtype under several conditions, especially high temperatures, which is not related to the faster relaxation of NPQ but may be attributable to increased zeaxanthin and NPQ in C4 plants. Our results identified shared and unique characteristics of the NPQ pathway in C4 model Setaria as compared to C3 plants and provide insights to improve C4 crop yields under fluctuating environmental conditions.

plant biology↗

bioRxiv2024

Overexpression of Xanthophyll Cycle Genes Leads to Faster NPQ Acclimation in the C4 Monocot Setaria viridis

Slow relaxation and induction of Non-Photochemical Quenching (NPQ) limits plant productivity under fluctuating light in C3 plants but it is unknown if this trait extends to C4 plants. Three genes have been implicated in determining NPQ induction and relaxation rates under intermittent leaf shading; VDE and ZEP interconvert the xanthophyll pigments violaxanthin and zeaxanthin, and PsbS regulates the overall level of NPQ. Here we report the overexpression of the Arabidopsis thaliana VDE, ZEP, and PsbS in the NADP-Malic Enzyme C4 monocot Setaria viridis. We demonstrate these transgenic plants have faster NPQ induction and relaxation under fluctuating light but observe no impact on Photosystem II photochemistry yield. Under illumination, faster NPQ induction resulted in higher transient NPQ levels and a lower overall chlorophyll fluorescence yield. Together this introduces the potential for lower productivity due to over-quenching of chlorophyll during light fluctuation. Although we observed faster NPQ acclimation rates in our transgenic lines, hyperspectral imaging and pigment analysis suggest that there is little photosynthetic advantage to increasing NPQ acclimation over wildtype due to naturally fast C4 acclimation rates. These results indicate that further work is necessary in evaluating the role of NPQ acclimation in C4 growth dynamics towards the goal of improving crop productivity.

plant biology↗

bioRxiv2020

An improved Nicotiana benthamiana strain for aphid and whitefly research

Nicotiana benthamiana is used extensively as a platform for transient gene expression and as a model system for studying plant-virus interactions. However, many tobacco-feeding generalist herbivores, including Myzus persicae (green peach aphid), Bemisia tabaci (whitefly), Macrosiphum euphorbiae (potato aphid), Heliothis virescens (tobacco budworm), Trichoplusia ni (cabbage looper), and Helicoverpa zea (corn earworm), grow poorly on N. benthamiana, limiting its utility for research on plant-insect interactions. Using CRISPR/Cas9, we generated knockout mutations in two N. benthamiana acylsugar acyltransferases, ASAT1 and ASAT2, which contribute to the biosynthesis of insect-deterrent acylsucroses. Whereas asat1 mutations reduced the abundance of two predominant acylsucroses, asat2 mutations caused almost complete depletion of foliar acylsucroses. The tested hemipteran and lepidopteran species survived, gained weight, and/or reproduced significantly better on asat2 mutant plants than on wildtype N. benthamiana. Furthermore, both asat1 and asat2 mutations reduced the water content and increased the temperature of leaves, indicating that foliar acylsucroses can protect against desiccation. Two experiments demonstrated the utility of the N. benthamiana asat2 mutant line for insect bioassays. Transmission of turnip mosaic virus by M. persicae was significantly improved by an asat2 mutation. Tobacco rattle virus constructs were used for virus-induced gene silencing of acetylcholinesterase, squalene synthase, toll-like receptor 7, and tubulin-specific chaperon D genes in B. tabaci, an experiment that would have been difficult with wild-type N. benthamiana due to high insect mortality. Additionally, the absence of acylsugars in asat2 mutant lines will simplify transient expression assays for the functional analysis of acylsugar biosynthesis genes from other Solanaceae.

plant biology↗