Biology subjects

Rosado, D.

Publications and source records attributed to Rosado, D..

5 recordsLinked to original sources

bioRxiv2024

Understanding Ecological Systems Using Knowledge Graphs: An Application to Highly Pathogenic Avian Influenza

Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully applied to organize heterogeneous data systematically and to predict new linkages representing unobserved relationships in complex systems. Though not previously applied broadly in ecology, knowledge graphs have much to offer in an era of global change when system dynamics are responding to rapid changes across multiple scales simultaneously. We developed a knowledge graph to demonstrate the methods utility for ecological problems focused on highly pathogenic avian influenza (HPAI), a highly transmissible virus with a broad animal host range, wide geographic distribution, and rapid evolution with pandemic potential. We describe the development of a graph to include a wide range of data related to HPAI including pathogen-host associations, animal species distributions, and human population demographics, using a semantic ontology that defines relationships within the data and between datasets. We use the graph to perform a set of proof-of-concept analyses validating the method and identifying new relationships and features of HPAI ecology, underscoring the generalizable value of knowledge graphs to ecology including their utility in revealing previously known relationships between entities and generating testable hypotheses in support of a deeper mechanistic understanding of ecological systems.

ecology↗

bioRxiv2023

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Cryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found that cry1cry2 was hypersensitive, while ubp12ubp13 was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation in cry1cry2 plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued in cry1cry2, but elevated in ubp12ubp13 compared to WT. Through transcriptional modeling of the timecourse transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in the cry1cry2 mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.

plant biology↗

bioRxiv2021

Shade-induced WRKY transcription factors restrict root growth during the shade avoidance response

Shade-intolerant plants rapidly elongate their stems, branches, and leaf stalks to compete with their neighboring vegetation to maximize sunlight capture for photosynthesis. This rapid growth adaptation, known as the shade avoidance response (SAR), comes at a cost; reduced biomass, crop yield, and root growth. Significant progress has been made on the mechanistic understanding of hypocotyl elongation during SAR; however, the molecular account of how root growth is repressed is not well understood. Here, we explore the mechanisms by which low red:far-red induced SAR restrict the primary and lateral root (LR) growth. By analyzing whole-genome transcriptome, we identified a core set of shade-induced genes in the roots of Arabidopsis and tomato seedlings grown in the shade. Abiotic and biotic stressors also induce many of these shade-induced genes and are predominantly regulated by the WRKY transcription factors. Correspondingly, a majority of the WRKYs were also among the shade-induced genes. Functional analysis using transgenics of these shade-induced WRKYs revealed their role is essentially to restrict primary root and LR growth in the shade, and captivatingly, they did not affect hypocotyl elongation. Similarly, we also show that ethylene hormone signaling is necessary to limit root growth in the shade. Our study proposes that during SAR, shade-induced WRKY26, 45, and 75, and ethylene reprogram gene expression in the root to restrict its growth and development. The reduced growth of root organs helps the plant divert its critical resources to the elongating organs in the shoot to ensure competitiveness under limiting photosynthetic radiation. One sentence summaryShade represses root growth by inducing WRKY transcription factors.

plant biology↗

bioRxiv2020

Rapid expression of COVID-19 proteins by transient expression in tobacco.

In 2020 we suffered from a major global pandemic caused by the SARS-CoV-2 coronavirus. Efforts to contain the virus include the development of rapid tests and vaccines, which require a ready supply of viral proteins. Here we report the production of two SARS-CoV-2 proteins by transient transformation of tobacco, leading to high expression within three days, and subsequent purification of the intact proteins. Such efforts may help to develop testing resources to alleviate the major impacts of this global pandemic.

plant biology↗

bioRxiv2020

PHYTOCHROMES B1/B2 ARE MAJOR REGULATORS OF RIPENING-ASSOCIATED EPIGENOME REPROGRAMMING IN TOMATO FRUITS

Phytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, through integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from phyA and phyB1B2 null mutants, we report that PHYB1 and PHYB2 control genome-wide DNA methylation during fruit development from green towards ripe stages. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators leading in the altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.

plant biology↗