Biology subjects

Perales, M.

Publications and source records attributed to Perales, M..

7 recordsLinked to original sources

bioRxiv2026

Probabilistic mouse-human brain correspondence by multimodal optimal transport

The mouse is the principal model for brain mechanism and disease, allowing experiments that cannot be performed in humans. However, findings often translate poorly because homologous regions differ in relative size and some human territories have no clear mouse counterpart. Here we present OTTER, which learns mouse-human brain correspondence as a probabilistic, parcel-resolution coupling using multimodal fused Gromov-Wasserstein optimal transport, integrating functional and structural connectivity with spatial position and curated homologies. OTTER recovers established homologues on a transcriptomic benchmark and preserves broad cross-species organisation along the cortical areal hierarchy. Applying the coupling to human functional connectivity reveals a graded decline in mouse-based reconstruction across evolutionarily expanded association cortex, with the lowest values in lateral prefrontal territory. Finally, the bidirectional map generates testable human predictions from mouse experiments and ranks mouse circuits corresponding to human clinical targets.

neuroscience↗

bioRxiv2025

MdBRC1 and MdFT2 Interaction Fine-Tunes Bud Break Regulation in Apple

Winter bud dormancy is a critical adaptive process in temperate fruit trees, safeguarding meristems from freezing temperatures and aligning growth with seasonal cues. Dormancy encompasses two primary phases: endodormancy, where internal signals, particularly elevated abscisic acid (ABA), block growth and necessitate chilling for release; and ecodormancy, where buds regain growth competence but remain quiescent until external conditions are favourable. In apple (Malus domestica), we demonstrated that BRANCHED1 (MdBRC1) serves as a central inhibitor of bud growth specifically during ecodormancy. In many plant species, BRC1-like transcription factors integrate environmental and hormonal signals, activating gene networks linked to growth repression, notably those involved in ABA biosynthesis and signalling. Gain-of-function studies in poplar confirmed that MdBRC1 robustly suppresses shoot growth in trees. Our comparative transcriptomic analyses revealed that MdBRC1 directly regulates a suite of dormancy-associated genes, reinforcing its role as a molecular brake on bud break. Importantly, we show that the apple gene FLOWERING LOCUS T2 (MdFT2) is transcriptionally upregulated after dormancy and might act as a key inducer of bud break. Our data reveal that MdFT2 physically interacts with MdBRC1, reducing MdBRC1 activity during ecodormancy. This antagonistic interaction acts as a molecular switch, facilitating the transition from ecodormancy to active bud growth as spring approaches. Together, these findings uncover a regulatory module that finely tunes bud break timing in apple trees and provide a foundation for breeding strategies to enhance fruit tree resilience and adaptability in the context of climate change.

plant biology↗

bioRxiv2025

OVEREXPRESSION OF TEMPRANILLO-LIKE PROTEINS PROMOTES ENDORMANCY RELEASE IN POPLAR

Trees in temperate and boreal latitudes synchronize their growth-dormancy cycles with seasonal environmental variations to ensure their survival over the years. Dormancy control is crucial during winter when plants cease growth and establish buds to protect their apical meristems from cold temperatures. To overcome endormancy, initiate bud break, and restore growth, plants must be exposed to a specific duration of chilling, referred to as the chilling requirement, which is species- and ecotype-dependent. In this work, we study the novel roles of two TEMPRANILLO-like genes (TEML1 and TEML2) in the annual cycle of poplar. We demonstrated that Populus TEML genes are regulated by photoperiod, cold temperatures and the circadian clock, and they play a role in the control of endodormancy. Notably, their function diverges from the role of its Arabidopsis ortholog AtTEM, which regulates FLOWERING LOCUS T (FT) transcription and the photoperiodic flowering transcription. Transcriptomic analysis of endodormant buds during winter revealed that the activation of TEML1 and TEML2 promotes endodormancy release by modulating the expression of endodormancy regulators and growth-promoting genes.

plant biology↗

bioRxiv2025

Single-nuclei transcriptomics revealed auxin-driven mechanisms of wood plasticity and severe drought tolerance in poplar

Drought significantly affects forests and woody crops by limiting their growth, increasing their susceptibility to diseases, and reducing productivity. Wood anatomical plasticity is a crucial adaptive mechanism that enables trees to cope with fluctuations in water availability. During severe drought, trees develop more and narrower vessels, enhancing hydraulic safety and reducing the risk of embolism. However, the molecular regulation of vessel formation is still not well understood. Using single-nucleus transcriptomics, we generated a cell type-specific gene expression map of the mature poplar stem under well-watered and drought conditions. Our findings revealed extensive gene expression reprogramming in xylem-forming cells, with changes in auxin homeostasis identified as a key mechanism for anatomical adaptation. Specifically, we showed that poplar WAT1-like genes control vessel spatial patterning. Additionally, the downregulation of WAT1-like gene expression in the dividing cells of the vascular cambium and the upregulation of MP-like gene in cells undergoing early vessel differentiation facilitate the formation of secondary xylem with narrower and more numerous vessels. Furthermore, the wat2 mutant exhibited greater drought tolerance than wild-type trees, underscoring its potential for developing drought-resilient tree varieties. These insights enhance our understanding of xylem plasticity and provide valuable targets for improving drought tolerance in woody plants.

plant biology↗

bioRxiv2022

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

plant biology↗

bioRxiv2017

Cross-talk between active DNA demethylation, resetting of cellular metabolism and shoot apical growth in poplar bud break

Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programs integrated with the environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy to growth promoting genetic program are still unknown. Here, we show that dynamics in genomic DNA methylation (gDNA) levels regulate dormancy-growth cycle in poplar. We proved that the reactivation of cell division in the apical shoot that lead bud break process in spring, is preceded by a progressive reduction of gDNA methylation in apex tissue. We also identified that the induction in apex tissue of a chilling-dependent poplar DEMETER-LIKE 10 (PtaDML10) DNA demethylase precedes shoot growth reactivation. Transgenic poplars showing down-regulation of PtaDML8/10 caused delayed bud break. Genome wide transcriptome and methylome analysis and data mining revealed the gene targets of active DML-dependent DNA demethylation genetically associated to bud break. These data point to a chilling dependent-DEMETER-like DNA demethylase controlling the genetic shift from winter dormancy to a condition that promotes shoot apical vegetative growth in poplar.

plant biology↗

bioRxiv2017

A DNA demethylase overexpression promotes early apical bud maturation in poplar through the biosynthesis and accumulation of flavonoids

ASBTRACTThe transition from active growth to dormancy is critical for the survival of perennial plants. We identified a DEMETER-like (CsDML) cDNA from a winter-enriched cDNA subtractive library in chestnut (Castanea sativa Mill.), an economically and ecologically important species. Next, we characterized this DNA demethylase and its putative orthologue in the more experimentally tractable hybrid poplar (Populus tremula x alba), under the signals that trigger bud dormancy in trees. We performed phylogenetic and protein sequence analysis, gene expression profiling and 5mC immunodetection studies to evaluate the role of CsDML and its homologue in poplar, PtaDML6. Transgenic hybrid poplars overexpressing CsDML were produced and analyzed. Short days (SD) and cold temperatures induced CsDML and PtaDML6. Overexpression of CsDML accelerated SD-induced bud formation, specifically from stage 1 to 0. Bud acquired a red-brown coloration earlier than wild type (WT) plants, alongside with the upregulation of flavonoid biosynthesis enzymes and accumulation of flavonoids in the SAM and bud scales. Our data shows that the CsDML gene induces bud formation needed for the survival of the apical meristem under the harsh conditions of winter. This study provides in planta evidence implicating chromatin remodeling by DNA demethylation during SD induction of bud maturation through the induction of flavonoids biosynthesis.

plant biology↗