Quantitative trait analysis in a panel of recombinant inbred rat strains

Expression quantitative trait loci (eQTLs) are generated by the combined use of microarray technology to measure gene expression and genetic linkage analysis to map the expression traits to the genome. This thesis describes co-expression and quantitative trait transcript (QTT) analysis carried out on a dataset consisting of thousands of cis- and trans-eQTLs. These were mapped in 29 rat Recombinant Inbred strains derived from a cross between the Spontaneously Hypertensive Rat (SHR), a widely used model of the human metabolic syndrome, and the normotensive Brown Norway (BN). Gene expression data from four tissues relevant to the metabolic syndrome and cardiovascular disease were analysed: fat, kidney, adrenal gland and left ventricle. By systematically applying a rigorous statistical methodology to the eQTL dataset, a consistent, distinct correlation structure was observed. Co-expression of groups of transcripts linked to a common region of the genome, referred to as trans-eQTL clusters, was investigated. Some of these cluster-forming groups were found to remain significantly correlated after the effect of genotype was accounted for, and functionally enriched. An example of successful application of QTT analysis to the dataset is described. This contributed to the identification of Ogn as a regulator of left ventricular mass in rodents and subsequent implication of the homologue of Ogn in a related role in humans. Correlation of a further 103 physiological traits with cis-eQTLs in each of the four tissues was also carried out; analysis which potentially informs a wide range of hypotheses concerning relevant phenotypes. Together, the findings described here demonstrate the utility of a systematic computational approach using correlation-based methodologies in combination with appropriate statistical techniques to inform the genetic analysis of complex traits. These findings indicate the importance of understanding potential confounding factors in eQTL analysis, as well as the potential of the eQTL approach to stimulate gene discovery

Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data

BACKGROUND: Gene Ontology (GO) terms are often used to assess the results of microarray experiments. The most common way to do this is to perform Fisher's exact tests to find GO terms which are over-represented amongst the genes declared to be differentially expressed in the analysis of the microarray experiment. However, due to the high degree of dependence between GO terms, statistical testing is conservative, and interpretation is difficult. RESULTS: We propose testing groups of GO terms rather than individual terms, to increase statistical power, reduce dependence between tests and improve the interpretation of results. We use the publicly available package POSOC to group the terms. Our method finds groups of GO terms significantly over-represented amongst differentially expressed genes which are not found by Fisher's tests on individual GO terms. CONCLUSION: Grouping Gene Ontology terms improves the interpretation of gene set enrichment for microarray data

Biologically relevant characteristics of dissolved organic carbon (DOC) from soil

Of the organic matter in soils typically < 1% by weight is dissolved in the soil solution (dissolved organic matter; DOM). DOM is a continuum of molecules of various sizes and chemical structures which has largely been operationally defined as the fraction of total organic carbon in an aqueous solution that passes through a 0.45 µm filter. Although only representing a relatively small proportion, it represents the most mobile part of soil organic carbon and is probably enriched with highly labile compounds. DOM acts as a source of nutrients for both soil and aquatic micro-organisms, influences the fate and transport of organic and inorganic contaminants, presents a potential water treatment problem and may indicate the mobilisation rate of key terrestrial carbon stores. The objective of this research was to ascertain some of the biologically relevant characteristics of soil DOM and specifically to determine: (1) the influence of method and time of extraction of DOM from the soil on its biochemical composition and concentration; (2) the dynamics of DOM biodegradation; and, (3) the effects of repeated applications of trace amounts of DOM on the rate of soil carbon mineralization. To examine the influence of method and time of extraction on the composition and concentration of DOM, soil solution was collected from a raised peat bog in Central Scotland using water extraction, field suction lysimetry, and centrifugation techniques on a bimonthly basis over the period of a year (Aug 2003 – Jun 2004). Samples were analysed for dissolved organic carbon (DOC), dissolved organic nitrogen (DON), protein, carbohydrate and amino acid content. For all of the sampled months except June the biochemical composition of DOC varied with extraction method, suggesting the biological, chemical and/or physical influences on DOC production and loss are different within the differently sized soil pores. Water-extractable DOC generally contained the greatest proportion of carbohydrate, protein and/or amino acid of the three extraction methods. Time of extraction had a significant effect on the composition of water- and suction-extracted DOC: the total % carbohydrate + protein + amino acid C was significantly higher in Oct than Dec, Feb and Jun for water-extracted DOC and significantly greater in Dec than Aug, Apr and Jun for suction-extracted DOC. There was no significant change in the total % carbohydrate + protein + amino acid C of centrifuge-extracted DOC during the sampled year. Time of extraction also had a significant effect on the % protein + amino acid N in water- and centrifuge-extracted DON: Oct levels were significantly higher than Feb for water-extracted DON and significantly higher in Aug and Apr for centrifuge-extracted DON. Concentrations of total DOC and total DON were also found to be dependent on time of extraction. DOC concentrations showed a similar pattern of variation over the year for all methods of extraction, with concentrations relatively constant for most of the year, rising in April to reach a peak in Jun. DON concentrations in water- and centrifuge-extracted DON peaked later, in Aug. There were no significant seasonal changes in the concentration of suction-extracted DON. A lack of correlation between DOC and DON concentrations suggested that DOC and DON production and/or loss are under different controls. Laboratory-based incubation experiments were carried out to examine the dynamics of DOC biodegradation. Over a 70 day incubation period at 20oC, the DOM from two types of peat (raised and blanket) and four samples of a mineral soil (calcaric gleysol), each previously exposed to a different management strategy, were found to be comprised of a rapidly degradable pools (half-life: 3 – 8 days) and a more stable pool (half-life: 0.4 to 6 years). For all soil types/treatments, excepting raised peat, the total net loss of DOC from the culture medium was greater than could be accounted for by the process of mineralization alone. A comparison between net loss of DOC and loss of DOC to CO2 and microbial biomass determined by direct microscopy suggested that at least some of the differences between DOC mineralised and net DOC loss were due to microbial assimilation and release. Changes in the microbial biomass during the decomposition process showed proliferation followed by decline over 15 days. The protein and carbohydrate fractions showed a complex pattern of both degradation and production throughout the incubation. The effects of repeated applications of trace amounts of litter-derived DOC on the rate of carbon mineralization over a 35 day period were investigated in a laboratory based incubation experiment. The addition of trace amounts of litter-derived DOC every 7 and 10.5 days appeared to ‘trigger’ microbial activity causing an increase in CO2 mineralisation such that extra C mineralised exceeded DOC additions by more than 2 fold. Acceleration in the rate of extra C mineralised 7 days after the second addition suggested that either the microbial production of enzymes responsible for biodegradation and/or an increase in microbial biomass, are only initiated once a critical concentration of a specific substrate or substrates has been achieved. The addition of ‘DOC + nutrients’ every 3.5 days had no effect on the total rate of mineralization. To date DOC has tended to be operationally defined according to its chemical and physical properties. An understanding of the composition, production and loss of DOC from a biological perspective is essential if we are to be able to predict the effects of environmental change on the rate of mineralization of soil organic matter. This research has shown that the pools of DOC extracted, using three different methods commonly used in current research, are biochemically distinct and respond differently to the seasons. This suggests some degree of compartmentalisation of biological processes within the soil matrix. The observed similarities between the characteristics of the decomposition dynamics of both peatland and agricultural DOC suggests that either there is little difference in substrate quality between the two systems or that the microbial community have adapted in each case to maximise their utilisation of the available substrate. The dependency of the concentration and biochemical composition of DOC on the seasons requires further work to ascertain which biotic and/or abiotic factors are exerting control. Published research has focussed on factors such as temperature, wet/dry cycles, and freeze/thawing. The effect of the frequency of doses of trace amounts of DOC on increasing the rate of soil organic C mineralization, evident from this research, suggests that the interval between periods of rainfall may be relevant. It also emphasises how it can be useful to use knowledge of a biological process as the starting point in determining which factors may be exerting control on DOC production and loss.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Effects of air pollution and the introduction of the London Low Emission Zone on the prevalence of respiratory and allergic symptoms in schoolchildren in East London: a sequential cross-sectional study

The adverse effects of traffic-related air pollution on children’s respiratory health have been widely reported, but few studies have evaluated the impact of traffic-control policies designed to reduce urban air pollution. We assessed associations between traffic-related air pollutants and respiratory/allergic symptoms amongst 8–9 year-old schoolchildren living within the London Low Emission Zone (LEZ). Information on respiratory/allergic symptoms was obtained using a parent-completed questionnaire and linked to modelled annual air pollutant concentrations based on the residential address of each child, using a multivariable mixed effects logistic regression analysis. Exposure to traffic-related air pollutants was associated with current rhinitis: NOx (OR 1.01, 95% CI 1.00–1.02), NO2 (1.03, 1.00–1.06), PM10 (1.16, 1.04–1.28) and PM2.5 (1.38, 1.08–1.78), all per μg/m3 of pollutant, but not with other respiratory/allergic symptoms. The LEZ did not reduce ambient air pollution levels, or affect the prevalence of respiratory/allergic symptoms over the period studied. These data confirm the previous association between traffic-related air pollutant exposures and symptoms of current rhinitis. Importantly, the London LEZ has not significantly improved air quality within the city, or the respiratory health of the resident population in its first three years of operation. This highlights the need for more robust measures to reduce traffic emissions

Cardiovascular outcomes in adults with hypertension with evening versus morning dosing of usual antihypertensives in the UK (TIME study):a prospective, randomised, open-label, blinded-endpoint clinical trial

Background: Studies have suggested that evening dosing with antihypertensive therapy might have better outcomes than morning dosing. The Treatment in Morning versus Evening (TIME) study aimed to investigate whether evening dosing of usual antihypertensive medication improves major cardiovascular outcomes compared with morning dosing in patients with hypertension. Methods: The TIME study is a prospective, pragmatic, decentralised, parallel-group study in the UK, that recruited adults (aged ≥18 years) with hypertension and taking at least one antihypertensive medication. Eligible participants were randomly assigned (1:1), without restriction, stratification, or minimisation, to take all of their usual antihypertensive medications in either the morning (0600–1000 h) or in the evening (2000–0000 h). Participants were followed up for the composite primary endpoint of vascular death or hospitalisation for non-fatal myocardial infarction or non-fatal stroke. Endpoints were identified by participant report or record linkage to National Health Service datasets and were adjudicated by a committee masked to treatment allocation. The primary endpoint was assessed as the time to first occurrence of an event in the intention-to-treat population (ie, all participants randomly assigned to a treatment group). Safety was assessed in all participants who submitted at least one follow-up questionnaire. The study is registered with EudraCT (2011-001968-21) and ISRCTN (18157641), and is now complete. Findings: Between Dec 17, 2011, and June 5, 2018, 24 610 individuals were screened and 21 104 were randomly assigned to evening (n=10 503) or morning (n=10 601) dosing groups. Mean age at study entry was 65·1 years (SD 9·3); 12 136 (57·5%) participants were men; 8968 (42·5%) were women; 19 101 (90·5%) were White; 98 (0·5%) were Black, African, Caribbean, or Black British (ethnicity was not reported by 1637 [7·8%] participants); and 2725 (13·0%) had a previous cardiovascular disease. By the end of study follow-up (March 31, 2021), median follow-up was 5·2 years (IQR 4·9–5·7), and 529 (5·0%) of 10 503 participants assigned to evening treatment and 318 (3·0%) of 10 601 assigned to morning treatment had withdrawn from all follow-up. A primary endpoint event occurred in 362 (3·4%) participants assigned to evening treatment (0·69 events [95% CI 0·62–0·76] per 100 patient-years) and 390 (3·7%) assigned to morning treatment (0·72 events [95% CI 0·65–0·79] per 100 patient-years; unadjusted hazard ratio 0·95 [95% CI 0·83–1·10]; p=0·53). No safety concerns were identified. Interpretation: Evening dosing of usual antihypertensive medication was not different from morning dosing in terms of major cardiovascular outcomes. Patients can be advised that they can take their regular antihypertensive medications at a convenient time that minimises any undesirable effects. Funding: British Heart Foundation

Source Handler telephone interactions with covert human intelligence sources: An exploration of question types and intelligence yield

Law Enforcement Agencies gather intelligence in order to prevent criminal activity and pursue criminals. In the context of human intelligence collection, intelligence elicitation relies heavily upon the deployment of appropriate evidence‐based interviewing techniques (a topic rarely covered in the extant research literature). The present research gained unprecedented access to audio recorded telephone interactions (N = 105) between Source Handlers and Covert Human Intelligence Sources (CHIS) from England and Wales. The research explored the mean use of various question types per interaction and across all questions asked in the sample, as well as comparing the intelligence yield for appropriate and inappropriate questions. Source Handlers were found to utilise vastly more appropriate questions than inappropriate questions, though they rarely used open‐ended questions. Across the total interactions, appropriate questions (by far) were associated with the gathering of much of the total intelligence yield. Implications for practise are discussed

Aloe barbadensis: how a miraculous plant becomes reality

Aloe barbadensis Miller is a plant that is native to North and East Africa and has accompanied man for over 5,000 years. The aloe vera plant has been endowed with digestive, dermatological, culinary and cosmetic virtues. On this basis, aloe provides a range of possibilities for fascinating studies from several points of view, including the analysis of chemical composition, the biochemistry involved in various activities and its application in pharmacology, as well as from horticultural and economic standpoints. The use of aloe vera as a medicinal plant is mentioned in numerous ancient texts such as the Bible. This multitude of medicinal uses has been described and discussed for centuries, thus transforming this miracle plant into reality. A summary of the historical uses, chemical composition and biological activities of this species is presented in this review. The latest clinical studies involved in vivo and in vitro assays conducted with aloe vera gel or its metabolites and the results of these studies are reviewed

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist