Biology subjects

Ashworth, J.

Publications and source records attributed to Ashworth, J..

6 recordsLinked to original sources

bioRxiv2026

Developmental and physiological profiles define drought response diversity and genomic associations in common bean

Common bean (Phaseolus vulgaris L.) yields are strongly impacted by water deficit, yet there is substantial within-species diversity in how development, biomass accumulation, gas exchange, and photosynthetic performance are coordinated under stress. Based on this variation within a diversity panel, we characterise response profiles, define drought-response strategies, assess how these strategies relate to population structure and gene flow, and identify associated loci. A panel of 142 common bean accessions representing diverse genetic backgrounds was grown outdoors under controlled water-deficit conditions. Over five weeks, plants were monitored for phenology, biomass, pod production, and leaf traits related to stomatal and photosynthetic performance, including a brief recovery period. Genome-wide association analyses were then performed for developmental, physiological and recovery-related traits. Declining soil water availability revealed marked variation among accessions in developmental progression, biomass partitioning, stomatal behaviour and photosynthetic performance. We combined developmental and physiological traits to define above-ground response profiles and classify drought-response strategies in common bean, which were distributed across the diversity panel. GWAS identified multiple QTL and candidate loci associated with developmental, physiological and recovery-related traits. Common bean exhibits extensive diversity in overall above-ground responses to water deficit, likely reflecting local adaptation rather than population structure. Developmental data were essential for differentiating response strategies and, when combined with porometer and fluorometer measurements indicating the level of water stress experienced by the plants, for connecting traits and strategies to genomic variation. These results provide trait relationships, candidate loci and testable hypotheses for validation across environments and for future breeding-oriented studies.

plant biology↗

bioRxiv2021

Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still adapting to its new human host. Attention has focussed on the viral spike protein, but substantial variation has been seen in the ORF8 gene. Here, we show that SARS-CoV-2 ORF8 protein undergoes signal peptide-mediated processing through the endoplasmic reticulum and is secreted as a glycosylated, disulphide-linked dimer. The secreted protein from the prototype SARS-CoV-2 virus had no major effect on viability of a variety of cell types, or on IFN or NF-{kappa}B signalling. However, it modulated cytokine expression from primary CSF1-derived human macrophages, most notably by decreasing IL-6 and IL-8 secretion. Furthermore, a sequence polymorphism L84S that appeared early in the pandemic associated with the Clade S lineage of virus, showed a markedly different effect, of increasing IL-6 production. We conclude that ORF8 sequence polymorphisms can potentially affect SARS-CoV-2 virulence and should therefore be monitored in sequencing-based surveillance.

microbiology↗

bioRxiv2020

A plastid antiporter as a bioindicator of Thalassiosira pseudonana resilience

Acidification of the ocean due to high atmospheric CO2 levels may increase the resilience of diatoms causing dramatic shifts in abiotic and biotic cycles with lasting implications on marine ecosystems. Here, we report a potential bioindicator of a shift in the resilience of a coastal and centric model diatom Thalassiosira pseudonana under elevated CO2. Specifically, we have discovered, through EGFP-tagging, a plastid membrane localized putative Na+(K+)/H+ antiporter that is significantly upregulated at > 800 ppm CO2, with a potentially important role in maintaining pH homeostasis. Notably, transcript abundance of this antiporter gene was relatively low and constant over the diel cycle under contemporary CO2 conditions. In future acidified oceanic conditions, dramatic oscillations of >10-fold change between nighttime (high) and daytime (low) in transcript abundances of the antiporter gene were associated with increased resilience of T. pseudonana. By analyzing metatranscriptomic data from the Tara Oceans project, we demonstrate that phylogenetically diverse diatoms express homologs of this antiporter across the globe. We propose that the differential between night- and daytime transcript levels of the antiporter could serve as a bioindicator of a shift in the resilience of diatoms in response to high CO2 conditions in marine environments.

systems biology↗

bioRxiv2020

Overexpression of key sterol pathway enzymes in two model marine diatoms alters sterol profiles in Phaeodactylum tricornutum

Sterols are a class of triterpenoid molecules with diverse functional roles in eukaryotic cells, including intracellular signaling and regulation of cell membrane fluidity. Diatoms are a dominant eukaryotic phytoplankton group that produce a wide diversity of sterol compounds. The enzymes 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) and squalene epoxidase (SQE) have been reported to be rate-limiting steps in sterol biosynthesis in other model eukaryotes; however, the extent to which these enzymes regulate triterpenoid production in diatoms is not known. To probe the role of these two metabolic nodes in the regulation of sterol metabolic flux in diatoms, we independently over-expressed two versions of the native HMGR and a conventional, heterologous SQE gene in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Overexpression of these key enzymes resulted in significant differential accumulation of downstream sterol pathway intermediates in P. tricornutum. HMGR-mVenus overexpression resulted in the accumulation of squalene, cycloartenol, and obtusifoliol, while cycloartenol and obtusifoliol accumulated in response to heterologous NoSQE-mVenus overexpression. In addition, accumulation of the end-point sterol 24-methylenecholesta-5,24(24)-dien-3{beta}-ol was observed in all P. tricornutum overexpression lines, and campesterol increased 3-fold in P. tricornutum lines expressing NoSQE-mVenus. Minor differences in end-point sterol composition were also found in T. pseudonana, but no accumulation of sterol pathway intermediates was observed. Despite the successful manipulation of pathway intermediates and individual sterols in P. tricornutum, total sterol levels did not change significantly in transformed lines, suggesting the existence of tight pathway regulation to maintain total sterol content.

molecular biology↗

bioRxiv2018

Transcriptomic biomarkers for prediction/classification of sample conditions in marine microeukaryotes (diatoms)

Marine microeukaryotes express large and complex transcriptomes that often respond dynamically to environmental and physiological conditions. In parallel to developments in human disease research, the opportunity exists to employ transcriptomic features as \"biomarkers\" to understand and predict cellular and environmental states. Here, the prediction and classification of basic physiological and environmental states including light, growth phase and inorganic carbon status was explored for the model diatom T. pseudonana using publicly available data including 56 microarray and 316 mRNA-seq samples. Simple \"machine learning\" methods combined with integrative bootstrapped clustering were able to detect, recapitulate and expand biologically and environmentally relevant signals evident across hundreds of samples collected and processed independently by multiple laboratories. Agnostic, integrative and empirical \"data-driven\" approaches are likely applicable to modern questions in new environmental and experimental contexts.

microbiology↗

bioRxiv2018

An explorable public transcriptomics compendium for eukaryotic microalgae

Eukaryotic microalgae dominate primary photosynthetic productivity in fluctuating nutrient-rich environments, including coastal, estuarine and polar regions, where competition and complexity are presumably adaptive and dynamic traits. Numerous genomes and transcriptomes of these species have been carefully sequenced, providing an unprecedented view into the vast genetic repertoires and the diverse transcriptional programs operating inside these organisms. Here we collected, re-mapped, quantified and clustered publicly available transcriptome data for ten different eukaryotic microalgae in order to develop new insights into their molecular systems biology, as well as to provide a large new resource of integrated information to facilitate the efforts of others to further compare and contextualize the results of individual and new experiments within and between species. This is summarized herein and provided for public use by the eukaryotic microalgae research community.

systems biology↗