Cellular and Viral Determinants for Hepatitis C Virus Replication

The recent discovery of an HCV isolate which replicates in cell culture has opened up opportunities to study the full viral life cycle in vitro. This genotype 2a isolate (JFH-1) and its derivatives are the only ones known to replicate efficiently in cell culture, and recent work has indicated that viral determinants for efficient replication may lie in the non-structural protein coding region of the genome. In this thesis chimaeric JFH-1 virus containing full length NS3, NS3 helicase and NS3 protease sequences from genotype 1a and 1b were constructed. The replication efficiencies of chimaeric viruses were tested in cell culture, and were shown not to replicate, indicating that vital viral determinants for JFH-1 replication exist in NS3. The JFH-1 model also provides the opportunity to study the effect of the full viral life cycle on the host cell. Microarray analyses were performed to identify gene expression changes in Huh7 and Huh7.5 cells that had been infected with JFH-1 for 6, 12, 18, 24 and 48 hours. A large number of host genes were found to be regulated during JFH-1 infection, including those involved in lipid metabolism, oxidative stress, apoptosis and intracellular transport. The microarray data were validated by quantitative PCR analyses of separate infection experiments. A selection of the most highly regulated genes was assessed for their necessity to HCV replication by RNA interference studies. The knockdown by siRNA of genes ABLIM3, SPTLC3 and CYP1A1 resulted in significant impairment of HCV replication. The knockdown by siRNA of gene TXNIP (thioredoxin interacting protein) resulted in up to 90% reduction in HCV replication. This is a novel finding which may be of importance to the study of HCV as TXNIP plays roles in oxidative stress, lipid metabolism and glucose metabolism, all of which have potential to influence the HCV lifecycle. Magnetic resonance spectroscopy indicated a change in levels of choline metabolites in JFH-1 infected cells, which has implications for the aspects of the HCV lifecycle associated with lipid membranes and other lipid structures

Strengthening the Baillie-PSW primality test

The Baillie-PSW primality test combines Fermat and Lucas probable prime tests. It reports that a number is either composite or probably prime. No odd composite integer has been reported to pass this combination of primality tests if the parameters are chosen in an appropriate way. Here, we describe a significant strengthening of this test that comes at almost no additional computational cost. This is achieved by including in the test what we call Lucas-V pseudoprimes, of which there are only five less than $10^{15}$.Comment: 25 page

The latent structure of cognitive and emotional empathy in individuals with autism, first-degree relatives and typical individuals

BACKGROUND: Empathy is a vital component for social understanding involving the ability to recognise emotion (cognitive empathy) and provide an appropriate affective response (emotional empathy). Autism spectrum conditions have been described as disorders of empathy. First-degree relatives may show some mild traits of the autism spectrum, the broader autism phenotype (BAP). Whether both cognitive and emotional empathy, rather than cognitive empathy alone, are impaired in autism and the BAP is still under debate. Moreover the association between various aspects of empathy is unclear. This study aims to examine the relationship between different components of empathy across individuals with varying levels of genetic vulnerability to autism. METHODS: Factor analyses utilising questionnaire and performance-based task data were implemented among individuals with autism, parents of a child with autism and controls. The relationship between performance-based tasks and behavioural measures of empathy was also explored. RESULTS: A four-factor model including cognitive empathy, emotional empathy, social skills and a performance-based factor fitted the data best irrespective of genetic vulnerability. Individuals with autism displayed impairment on all four factors, with parents showing intermediate difficulties. Performance-based measures of empathy were related in almost equal magnitude to cognitive and emotional empathy latent factors and the social skills factor. CONCLUSIONS: This study suggests individuals with autism have difficulties with multiple facets of empathy, while parents show intermediate impairments, providing evidence for a quantitative BAP. Impaired scores on performance-based measures of empathy, often thought to be pure measures of cognitive empathy, were also related to much wider empathy difficulties than impairments in cognitive empathy alone

Towards a radiocarbon calibration for oxygen isotope stage 3 using New Zealand kauri (Agathis australis)

It is well known that radiocarbon years do not directly equate to calendar time. As a result, considerable effort has been devoted to generating a decadally resolved calibration curve for the Holocene and latter part of the last termination. A calibration curve that can be unambiguously attributed to changes in atmospheric ¹⁴C content has not, however, been generated beyond 26 kyr cal BP, despite the urgent need to rigorously test climatic, environmental, and archaeological models. Here, we discuss the potential of New Zealand kauri (Agathis australis) to define the structure of the ¹⁴C calibration curve using annually resolved tree rings and thereby provide an absolute measure of atmospheric ¹⁴C. We report bidecadally sampled ¹⁴C measurements obtained from a floating 1050-yr chronology, demonstrating repeatable ¹⁴C measurements near the present limits of the dating method. The results indicate that considerable scope exists for a high-resolution ¹⁴C calibration curve back through OIS-3 using subfossil wood from this source

Environmental DNA captures elasmobranch diversity in a temperate marine ecosystem

Abstract: Many sharks, skates, and rays (elasmobranchs) are highly threatened by the activities of commercial fisheries, and a clear understanding of their distributions, diversity, and abundance can guide protective measures. However, surveying and monitoring elasmobranch species can be highly invasive or resource‐intensive, and utilization of non‐invasive environmental DNA‐based methods may overcome these problems. Here, we studied spatial and seasonal variation in the elasmobranch community of the Western English Channel using environmental DNA (eDNA) collected from surface and bottom waters periodically over an annual cycle (2017–2018). In total we recovered 13 elasmobranch species within eDNA samples, and the number of transformed eDNA reads was positively associated with species (hourly) catch data resolved from 105‐year time series trawl data (1914–2018). These results demonstrate the ability of eDNA to detect and semi‐quantitatively reflect the prevalence of historically dominant and rare elasmobranch species in this region. Notably, eDNA recorded a greater number of species per sampling event than a conventional trawl survey in the same area over the same sampling years (2017–2018). Several threatened species were recovered within the eDNA, including undulate ray, porbeagle shark, and thresher shark. Using eDNA, we found differences in elasmobranch communities among sampling stations and between seasons, but not between sampling depths. Collectively, our results suggest that non‐invasive eDNA‐based methods can be used to study the spatial and seasonal changes in the diversity and abundance of whole elasmobranch communities within temperate shelf habitats. Given the threatened status of many elasmobranchs in human‐impacted marine environments, eDNA analysis is poised to provide key information on their diversity and distributions to inform conservation‐focused monitoring and management

In Vitro Assay Development and HTS of Small-Molecule Human ABAD/17β-HSD10 Inhibitors as Therapeutics in Alzheimer's Disease

This research was funded by the Scottish Universities Life Science Alliance (SULSA) assay development fund. This research was also kindly supported by The Rosetrees Trust and The Alzheimer’s Society, specifically The Barcopel Foundation, and partly funded by the MSD Scottish Life Sciences fund. As part of an ongoing contribution to Scottish life sciences, MSD Limited, a global health care leader, has given substantial monetary funding to the Scottish Funding Council for distribution via SULSA to develop and deliver a high-quality drug discovery research and training program.A major hallmark of Alzheimer’s disease (AD) is the formation of neurotoxic aggregates composed of the amyloid-β peptide (Aβ). Aβ has been recognized to interact with numerous proteins, resulting in pathological changes to the metabolism of patients with AD. One such mitochondrial metabolic enzyme is amyloid-binding alcohol dehydrogenase (ABAD), where altered enzyme function caused by the Aβ-ABAD interaction is known to cause mitochondrial distress and cytotoxic effects, providing a feasible therapeutic target for AD drug development. Here we have established a high-throughput screening platform for the identification of modulators to the ABAD enzyme. A pilot screen with a total of 6759 compounds from the NIH Clinical Collections (NCC) and SelleckChem libraries and a selection of compounds from the BioAscent diversity collection have allowed validation and robustness to be optimized. The pilot screen revealed 16 potential inhibitors in the low µM range against ABAD with favorable physicochemical properties for blood-brain barrier penetration.PostprintPeer reviewe