Biology subjects

Taylor, Z.

Publications and source records attributed to Taylor, Z..

3 recordsLinked to original sources

bioRxiv2025

CaneCestry : A Web-based Toolbox for Efficient Pedigree Analysis and Visualization.

Genetic variability is the lifeblood of all breeding programs. This variability is acted on via selection to identify elite progeny that can be utilized agronomically or exploited as parents. Sugarcane breeders are tasked with creating optimal genetic variation through crossing. Prior knowledge of pedigree and parental performance allows breeders to discern which crosses to prioritize, since the time to make crossing decisions and the space to evaluate tens and thousands of progenies are both limited resources in sugarcane variety development programs. In this project, we have developed a user-friendly, web-based platform called CaneCestry that provides a wide range of tools utilizing pedigree information. CaneCestry can be utilized to generate family trees for parents involved in a potential cross, enabling the breeder to efficiently display and visualize the lineage of the genotypes contained within. Kinship matrices are a powerful numerical representation of relationships between individuals in a population. While the calculation of kinship can be computationally intensive, CaneCestry is built upon a framework allowing for efficient cloud-based computation. These numerical representations of kinship elucidate the relatedness of potential parents, allowing the breeder to make the most informed crosses while avoiding inbreeding depression. Kinship matrices can also be utilized to enhance prediction models by adding the relatedness of the involved genotypes as a covariate, accounting for additive genetic control of traits. CaneCestry provides a comprehensive, web-based set of tools available in the office and field, enabling sugarcane breeders to utilize pedigree information in all stages of their breeding program.

bioinformatics↗

bioRxiv2022

Faster responses of photosynthesis to light transitions increase biomass and grain yield in transgenic Sorghum bicolor overexpressing Rieske FeS

Sorghum is one of the most important crops providing food and feed in many of the worlds harsher environments. Sorghum utilises the C4 pathway of photosynthesis in which a biochemical carbon concentrating mechanism results in high CO2 assimilation rates. Overexpressing the Rieske subunit of the Cytochrome b6f complex was previously shown to increase the rate of photosynthetic electron transport and stimulate CO2 assimilation in the model C4 plant Setaria viridis. To test whether productivity of C4 crops could be improved by Rieske overexpression, we created transgenic Sorghum bicolor plants with increased Rieske content. The transgenic plants showed no marked changes in abundance of other photosynthetic proteins or chlorophyll content. Increases in yield of Photosystem II and CO2 assimilation rate as well as faster responses of non-photochemical quenching during transient photosynthetic responses were observed as a result of an elevated in vivo Cytochrome b6f activity in plants overexpressing Rieske. The steady-state rates of electron transport and CO2 assimilation did not differ between transgenic and control plants, suggesting that Cytochrome b6f is not the only factor limiting electron transport in sorghum at high light and high CO2. Nevertheless, more agile responses of photosynthesis to light transitions led to increases in biomass and grain yield in plants overexpressing Rieske. Our results indicate that increasing Rieske content could boost productivity of C4 crops by improving the efficiency of light utilisation and conversion to biomass.

plant biology↗

bioRxiv2020

A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells

K777 is a di-peptide analog that contains an electrophilic vinyl-sulfone moiety and is a potent, covalent inactivator of cathepsins. Vero E6, HeLa/ACE2, Caco-2, A549/ACE2, and Calu-3, cells were exposed to SARS-CoV-2, and then treated with K777. K777 reduced viral infectivity with EC50 values of inhibition of viral infection of: 74 nM for Vero E6, <80 nM for A549/ACE2, and 4 nM for HeLa/ACE2 cells. In contrast, Calu-3 and Caco-2 cells had EC50 values in the low micromolar range. No toxicity of K777 was observed for any of the host cells at 10-100 M inhibitor. K777 did not inhibit activity of the papain-like cysteine protease and 3CL cysteine protease, encoded by SARS-CoV-2 at concentrations of [≤] 100 M. These results suggested that K777 exerts its potent anti-viral activity by inactivation of mammalian cysteine proteases which are essential to viral infectivity. Using a propargyl derivative of K777 as an activity-based probe, K777 selectively targeted cathepsin B and cathepsin L in Vero E6 cells. However only cathepsin L cleaved the SARS-CoV-2 spike protein and K777 blocked this proteolysis. The site of spike protein cleavage by cathepsin L was in the S1 domain of SARS-CoV-2, differing from the cleavage site observed in the SARS CoV-1 spike protein. These data support the hypothesis that the antiviral activity of K777 is mediated through inhibition of the activity of host cathepsin L and subsequent loss of viral spike protein processing. SIGNIFICANCEThe virus causing COVID-19 is highly infectious and has resulted in a global pandemic. We confirm that a cysteine protease inhibitor, approved by the FDA as a clinical-stage compound, inhibits SARS-CoV-2 infection of several human and monkey cell lines with notable(nanomolar) efficacy. The mechanism of action of this inhibitor is identified as a specific inhibition of host cell cathepsin L. This in turn inhibits host cell processing of the coronaviral spike protein, a step required for cell entry. Neither of the coronaviral proteases are inhibited, and the cleavage site of spike protein processing is different from that reported in other coronaviruses. Hypotheses to explain the differential activity of the inhibitor with different cell types are discussed.

biochemistry↗