Biology subjects

Reid, R. W.

Publications and source records attributed to Reid, R. W..

6 recordsLinked to original sources

bioRxiv2025

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

Plasmodium falciparum is an obligate human parasite of the phylum Apicomplexa and is the causative agent of the most lethal form of human malaria. Although N6-methyladenosine modification is thought to be one of the major post-transcriptional regulatory mechanisms for stage-specific gene expression in apicomplexan parasites, the precise base position of m6A in mRNAs or noncoding RNAs in these parasites remains unknown. Here, we report global nucleotide-resolution mapping of m6A residues in P. falciparum using DART-seq technology, which quantitatively displayed a stage-specific, dynamic distribution pattern with enrichment near mRNA 3 ends. In this process we identified 894, 788, and 1,762 m6A-modified genes in Ring, Trophozoite and Schizont stages respectively, with an average of 5-7 m6A sites per-transcript at the individual gene level. Notably, several genes involved in malaria pathophysiology, such as KAHRP, ETRAMPs, SERA and stress response genes, such as members of Heat Shock Protein (HSP) family are highly enriched in m6A and therefore could be regulated by this RNA modification. Since we observed preferential methylation at the 3 ends of P. falciparum transcripts and because malaria polyadenylation specificity factor PfCPSF30 harbors an m6A reader YTH domain, we reasoned that m6A might play an important role in 3-end processing of malaria mRNAs. To investigate this, we used two complementary high-throughput RNA 3-end mapping approaches, which provided an initial framework to explore potential roles of m6A in the regulation of alternative polyadenylation (APA) during malaria development in human hosts.

genomics↗

bioRxiv2024

Enhanced pollen tube performance at high temperature contributes to thermotolerant fruit production in tomato.

Rising temperature extremes during critical reproductive periods threaten the yield of major grain and fruit crops. Flowering plant reproduction depends on development of sufficient numbers of pollen grains and on their ability to generate a cellular extension, the pollen tube, which elongates through the pistil to deliver sperm cells to female gametes for double fertilization. These critical phases of the life cycle are sensitive to temperature and limit productivity under high temperature (HT). Previous studies have investigated the effects of HT on pollen development, but little is known about how HT applied during the pollen tube growth phase affects fertility. Here, we used tomato as a model fruit crop to determine how HT affects the pollen tube growth phase, taking advantage of cultivars noted for fruit production in exceptionally hot growing seasons. We found that exposure to HT solely during the pollen tube growth phase limits fruit biomass and seed set more significantly in thermosensitive cultivars than in thermotolerant cultivars. Importantly, we found that pollen tubes from the thermotolerant Tamaulipas cultivar have enhanced growth in vivo and in vitro under HT. Analysis of the pollen tube transcriptomes response to HT allowed us to develop hypotheses for the molecular basis of cellular thermotolerance in the pollen tube and we define two response modes (enhanced induction of stress responses, and higher basal levels of growth pathways repressed by heat stress) associated with reproductive thermotolerance. Importantly, we define key components of the pollen tube stress response identifying enhanced ROS homeostasis and pollen tube callose synthesis and deposition as important components of reproductive thermotolerance in Tamaulipas. Our work identifies the pollen tube growth phase as a viable target to enhance reproductive thermotolerance and delineates key pathways that are altered in crop varieties capable of fruiting under HT conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/606234v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@25e5acorg.highwire.dtl.DTLVardef@98fb1org.highwire.dtl.DTLVardef@1b8b9cborg.highwire.dtl.DTLVardef@adcca4_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis

Elevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. The Solanum lycopersicum anthocyanin reduced (are) mutant has a FLAVANONE 3 HYDROXYLASE (F3H) gene mutation resulting in impaired synthesis of flavonol antioxidants. The are mutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation of are with the wild-type F3H gene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversed ares reduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with an F3H overexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas of are had reduced flavonols and elevated ROS, the growth of are pollen tubes were similarly impaired in both are and VF36 pistils. RNA-Seq was performed at optimal and stress temperatures in are, VF36, and the VF36 F3H overexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number in are. These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure. One sentence summaryFlavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.

plant biology↗

bioRxiv2022

Genetic basis and selection of glyceollin induction in wild soybean

O_LIGlyceollins, a family of phytoalexin induced in legume species, play essential roles in responding to environmental stresses and in human health. However, little is known about the genetic basis and selection of glyceollin induction. C_LIO_LIWe employed a metabolite-based genome-wide association (mGWA) approach to identify candidate genes involved in glyceollin induction from genetically diverse and understudied wild soybeans subjected to soybean cyst nematode stress. C_LIO_LIEight SNPs on chromosomes 3, 9, 13, 15, and 20 showed significant association with glyceollin induction. Six genes close to one of the significant SNPs (ss715603454) on chromosome 9 fell into two clusters, and they encode enzymes in the glycosyltransferase class within the phenylpropanoid pathway. Transcription factors (TFs) genes, such as MYB and WRKY were also found within the linkage disequilibrium of the significant SNPs on chromosome 9. Epistasis and a strong selection signal were detected on the four significant SNPs on chromosome 9. C_LIO_LIGene clusters and transcription factors may play important roles in regulating glyceollin induction in wild soybeans. Additionally, as major evolutionary factors, epistatic interactions and selection may influence glyceollin variation in natural populations. C_LI

plant biology↗

bioRxiv2022

EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms.

Here we release a new version of EchinoDB (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. The new version of EchinoDB includes RNA-seq data of the brittle star Ophioderma brevispinum and high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow BLAST searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. EchinoDB enjoys a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate how EchinoDB is used in discovering pathways and gene regulatory networks involved in the tissue regeneration process.

bioinformatics↗

bioRxiv2019

Automated Gene Data Integration with Databio

SummaryDatabio is capable of providing fast and accurate annotation of gene-oriented data sets, coupled with an integrated identifier conversion service to empower downstream data mining and computational analysis. Databio is enabled by fast real-time data structures applied to over 137 million unique identifiers, and uses automated heuristics to permit accurate data provenance without highly specialized knowledge and bioinformatics training.\n\nAvailability and ImplementationFreely available on the web at https://datab.io/. Source code and binaries are freely available for download at https://github.com/joiningdata/databio/, implemented in Go and supported on Linux, Windows, and macOS.

bioinformatics↗