Biology subjects

Taylor, H.

Publications and source records attributed to Taylor, H..

22 records · Page 2Linked to original sources

bioRxiv2020

Unveiling Crucivirus Diversity by Mining Metagenomic Data

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding ssDNA (CRESS-DNA) viruses that encode capsid proteins (CPs) that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of CP genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and ten CP-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins, and that the exchange of Rep protein domains between cruciviruses is rarer than gene exchange. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCEViruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and are viruses that appear to have multiple origins from prokaryotic plasmids. CRESS-DNA viruses such as the cruciviruses, have homologues of capsid proteins (CPs) encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

evolutionary biology↗

bioRxiv2019

Plumage redness signals mitochondrial function in the House Finch

Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of molting wild house finches (Haemorhous mexicanus), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modeling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.

evolutionary biology↗

bioRxiv2018

Characterizing Genetic Circuit Components in E. coli towards a Campylobacter jejuni Biosensor.

Campylobacter jejuni is responsible for most cases of bacterial gastroenteritis (food poisoning) in the United Kingdom. The most common routes of transmission are by contact with raw poultry. Current detection systems for the pathogen are time-consuming, expensive or inaccessible for everyday users. In this article we propose a cheaper and faster system for detection of C. jejuni using a synthetic biology approach. We aimed to detect C. jejuni by the presence of xylulose, an uncommon bacterial capsular saccharide. We characterized two sugar-based regulatory systems that displayed potential to act as tools for detection of xylulose. Using a two-plasmid reporter system in Escherichia coli, we investigated the regulatory protein component (MtlR) of the mannitol operon from Pseudomonas fluorescens. Our findings suggest that the promoter of mtlE is activated by MtlR in the presence of a variety of sugar inducer molecules, and may exhibit cross-activity with a native regulator of E. coli. Additionally, we engineered the L-arabinose transcriptional activator (AraC) of E. coli for altered ligand specificity. We performed site-specific saturation mutagenesis to generate AraC variants with altered effector specificity, with an aim to generate a mutant activated by xylulose. We characterized several mutant AraC variants which have lost the ability to respond specifically to the native L-arabinose effector. We promote this technique as a powerful tool for future iGEM teams to create regulatory circuits activated by novel small molecule ligands.

synthetic biology↗

bioRxiv2018

A Multi-layer, Self-aligning Hydrogel Micro-molding Process Offering a Fabrication Route to Perfusable 3D In-Vitro Microvasculature

The in-vitro fabrication of hierarchical biological systems such as human vasculature, which are made up of two or more cell types with intricate co-culture architectures, is by far one of the most complicated challenges that tissue engineers have faced. Here, we introduce a versatile method to create multi-layered, cell-laden hydrogel microstructures with coaxial geometries and heterogeneous mechanical and biological properties. The technique can be used to build in-vitro vascular networks that are fully embedded in hydrogels of physiologically realistic mechanical stiffness. Our technique produces free-standing 3D structures, eliminating rigid polymeric surfaces from the vicinity of cells and allowing layers of multiple cell types to be defined with tailored extracellular matrix (ECM) composition and stiffness, and in direct contact with each other. We demonstrate co-axial geometries with diameters ranging from 200-2000 m and layer thicknesses as small as 50-200 {micro}m in agarose- collagen (AC) composite hydrogels. Coaxial geometries with such fine feature sizes are beyond the capabilities of most bioprinting techniques. A potential application of such a structure is to simulate vascular networks in the brain with endothelial cells surrounded by multiple layers of pericytes and other glial cells. For this purpose, the composition and mechanical properties of the composite AC hydrogels have been optimized for cell viability and biological performance of endothelial and glial cell types in both 2D and 3D culture modes. Multi-layered vascular constructs with an endothelial layer surrounded by layers of glial cells have been fabricated. This prototype in-vitro model resembles vascular geometries and opens the way for complex multi-luminal blood vessels to be fabricated.

bioengineering↗