Biology subjects

Cabrera, J.

Publications and source records attributed to Cabrera, J..

5 recordsLinked to original sources

bioRxiv2025

Root growth promotion by Penicillium melinii: mechanistic insights and agricultural applications

O_LIThis study characterizes Penicillium melinii, an endophytic fungus isolated from Arabidopsis thaliana roots, as a plant growth-promoting fungus with potential use as a model to study root development and as a biostimulant for sustainable agriculture. Although endophytes are known to promote plant growth, the underlying molecular mechanisms often remain poorly understood. Here, we aimed to elucidate how P. melinii enhances root system development and to assess its applicability across different crops. C_LIO_LIPhenotypic assays were conducted in Arabidopsis, quinoa and tomato under in vitro, greenhouse and field conditions. Root architecture and biomass were quantified using image-based phenotyping. Transcriptomic and phytohormone profiling assessed plant responses, and fungal genome sequencing coupled with secretome analysis was used to identify candidate effectors and metabolic traits. C_LIO_LIP. melinii consistently promoted root growth and increased plant biomass across species and environments, both in vitro and in the greenhouse. In tomato field trials, this translated into a significant increase in yield. The fungus colonized root surfaces without vascular penetration and triggered a mild transcriptomic response: early activation of stress-response genes followed by their attenuation and sustained upregulation of auxin-related pathways. Notably, the interaction modulates the SLR-ARF-LBD pathway and the number of pre-branch sites probably through increased auxin signalling in the oscillation zone. Additional hormonal changes were limited and mainly associated with the attenuation of the plant response to microorganisms. C_LIO_LIP. melinii enhances lateral root formation through a subtle molecular and metabolic dialogue with the host plant, underscoring its relevance as a model for studying root developmental plasticity. Its strong and reproducible growth-promoting effect, demonstrated with different fungal strains and under controlled and field conditions, supports its potential as a biostimulant for sustainable crop production. C_LI

plant biology↗

bioRxiv2024

Open-source cell culture automation system with integrated cell counting for passaging microplate cultures

Tissue culture in 96-well microplates is conventionally a tedious, highly manual process sensitive to individual technique and experimenter error. Here, we describe the Automated Cell Culture Splitter (ACCS), a system for passaging plates of adherent or suspension cells, for routine culture maintenance or specialized applications such as seeding plates for microscopy. The system is built around the Opentrons OT-2 liquid handling robot and incorporates a novel on-deck imaging-based cell counter which allows it to compensate for density disparities across a source plate and control the number of cells seeded on a per-well basis. We find this solution can cut hands-on time by 61% and the results compare favorably to our existing manual cell culture processes in terms of both seeding density precision and bio-logical outcomes, achieving a control of seeding density with a well-to-well coefficient of variation (CV) under 11%. The system is designed to be adaptable and an accessible entry point into automation for high-throughput cell culture; to that end, all of the source code and hardware designs are released under open source licenses.

bioengineering↗

bioRxiv2024

UNVEILING STEM CELL INDUCTION MECHANISMS FROM SPATIOTEMPORAL CELL-TYPE-SPECIFIC GENE REGULATORY NETWORKS IN POSTEMBRYONIC ROOT ORGANOGENSIS

Plants grow continuously by developing new organs, a complex process that requires the formation of specific and functional tissue patterns. Tap root systems, as observed in Arabidopsis thaliana, undergo lateral root formation, a developmental mechanism that necessitates the establishment of stem cell lineages. However, the underlying mechanisms remain poorly understood. We have reconstructed a spatiotemporal cell-type-specific transcriptional map of early lateral root organogenesis in Arabidopsis, profiling single and double fluorescent markers across 8 different cell types in the root stem cell lineage. Employing dynamic Bayesian network inference, based on time-course experiments and developmental time, alongside tree-based methods, we investigated lineage developmental progression and precursor stem-cell specification. Our results reveal a morphogenic cascade of hierarchical interdependent transcription factors driving stem cell initiation, and identify the QC/Endodermis transitioning cells as root stem cell progenitors. The associated formative program involves a profound transcriptomic re-arrangement, which, remarkably, precedes the activation of known stem-cell transcriptional signatures. Our data support a model in which root-stem-cell networks do not initiate stem formation, although various stem cell regulators are involved. Collectively, our study identifies core transcriptional signatures associated with stem cell induction and elucidates the dynamic regulatory mechanism driving early stem cell lineage establishment.

developmental biology↗

bioRxiv2019

Stem Cell Activity And Regeneration In Roots Require Non-Cell Autonomous Regulation From The Ground Tissue

Stem cells are central to plant development. During root postembryonic development stem cells generating tissues are patterned in layers around a stem cell organizer or quiescent center (QC). How stem cell lineages are initially patterned is unclear. Here, we describe a role for BLUEJAY (BLJ), JACKDAW (JKD) and SCARECROW (SCR) transcription factors in patterning of cell lineages during growth and in patterning reestablishment during regeneration through regulation of number of QC cells and their regenerative capacities. In blj jkd scr mutants, QC cells are progressively lost which results in loss of tissue layers. Upon laser ablation blj jkd scr is impaired in QC division and specification resulting in severe impairment in pattern regeneration. Beyond direct regulation of QC activity by these transcription factors, reduced levels of SHORT-ROOT (SHR) and of PIN auxin transporters were observed in the vasculature of blj jkd scr, leading to strong reduction in the auxin response in the QC. We narrowed down non-cell-autonomous regulation of vascularly expressed genes in blj jkd scr to C-REPEAT BINDING FACTOR 3 (CBF3). cbf3 mutant shows reduced levels of SHR in the vasculature, and in addition QC disorganization and downregulation of the QC regulator WUSCHEL-RELATED HOMEODOMAIN 5 (WOX5). CBF3 gene is primarily expressed in the ground tissue downstream of BLJ, JKD and SCR, while CBF3 protein may move. Targeted-expression of CBF3 to the ground tissue of blj jkd scr recovers radial patterning and regeneration. We propose that BLJ, JKD and SCR regulate QC-mediated patterning, and that part of this regulation involves CBF3.

developmental biology↗

bioRxiv2017

Arabidopsis HIPP27 is a host susceptibility gene for the beet cyst nematode Heterodera schachtii

SummarySedentary plant-parasitic cyst nematodes are obligate biotrophs that infect the roots of their host plant. Their parasitism is based on modification of root cells to form a hypermetabolic syncytium from which the nematodes draw their nutrients. The aim of this study was to identify nematode susceptibility genes in Arabidopsis thaliana and to characterize their roles in supporting the parasitism of Heterodera schachtii. By selecting genes that were most strongly upregulated in response to cyst nematode infection, we identified HIPP27 (HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27) as a host susceptibility factor required for beet cyst nematode infection and development. Detailed expression analysis revealed that HIPP27 is a cytoplasmic protein and that HIPP27 is strongly expressed in leaves, young roots and nematode-induced syncytia. Loss-of-function Arabidopsis hipp27 mutants exhibited severely reduced susceptibility to H. schachtii and abnormal starch accumulation in syncytial and peridermal plastids. Our results suggest that HIPP27 is a susceptibility gene in Arabidopsis whose loss-of-function reduces plant susceptibility to cyst nematode infection without increasing susceptibility to other pathogens or negatively affecting plant phenotype.

plant biology↗