The role of adiposity in cardiometabolic traits:a Mendelian randomization analysis

The association between adiposity and cardiometabolic traits is well known from epidemiological studies. Whilst the causal relationship is clear for some of these traits, for others it is not. We aimed to determine whether adiposity is causally related to various cardiometabolic traits using the Mendelian randomization approach.

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.

Identification of quantitative trait loci for rice grain element composition on an arsenic impacted soil:Influence of flowering time on genetic loci

Elements in grain crops such as iron, zinc and selenium are essential in the human diet, whereas elements such as arsenic are potentially toxic to humans. This study aims to identify quantitative trait loci (QTLs) for trace elements in rice grain. A field experiment was conducted in an arsenic enriched field site in Qiyang, China using the Bala x Azucena mapping population grown under standard field conditions. Grains were subjected to elemental analysis by inductively coupled plasma mass spectroscopy. QTLs were detected for the elemental composition within the rice grains, including for iron and selenium, which have previously been detected in this population grown at another location, indicating the stability of these QTLs. A correlation was observed between flowering time and a number of the element concentrations in grains, which was also revealed as co-localisation between flowering time QTLs and grain element QTLs. Unravelling the environmental conditions that influence the grain ionome appears to be complex, but from the results in this study one of the major factors which controls the accumulation of elements within the grain is flowering time.

Developing the clinical components of a complex intervention for a glaucoma screening trial:a mixed methods study

BACKGROUND: Glaucoma is a leading cause of avoidable blindness worldwide. Open angle glaucoma is the most common type of glaucoma. No randomised controlled trials have been conducted evaluating the effectiveness of glaucoma screening for reducing sight loss. It is unclear what the most appropriate intervention to be evaluated in any glaucoma screening trial would be. The purpose of this study was to develop the clinical components of an intervention for evaluation in a glaucoma (open angle) screening trial that would be feasible and acceptable in a UK eye-care service.

METHODS: A mixed-methods study, based on the Medical Research Council (MRC) framework for complex interventions, integrating qualitative (semi-structured interviews with 46 UK eye-care providers, policy makers and health service commissioners), and quantitative (economic modelling) methods. Interview data were synthesised and used to revise the screening interventions compared within an existing economic model.

RESULTS: The qualitative data indicated broad based support for a glaucoma screening trial to take place in primary care, using ophthalmic trained technical assistants supported by optometry input. The precise location should be tailored to local circumstances. There was variability in opinion around the choice of screening test and target population. Integrating the interview findings with cost-effectiveness criteria reduced 189 potential components to a two test intervention including either optic nerve photography or screening mode perimetry (a measure of visual field sensitivity) with or without tonometry (a measure of intraocular pressure). It would be more cost-effective, and thus acceptable in a policy context, to target screening for open angle glaucoma to those at highest risk but for both practicality and equity arguments the optimal strategy was screening a general population cohort beginning at age forty.

CONCLUSIONS: Interventions for screening for open angle glaucoma that would be feasible from a service delivery perspective were identified. Integration within an economic modelling framework explicitly highlighted the trade-off between cost-effectiveness, feasibility and equity. This study exemplifies the MRC recommendation to integrate qualitative and quantitative methods in developing complex interventions. The next step in the development pathway should encompass the views of service users.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5–20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.

Gene regulatory mechanisms underpinning prostate cancer susceptibility

Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.

Macroinvertebrate traits as biomonitoring tools in agricultural scenarios

Os ecossistemas de água doce – responsáveis por funções ambientais importantes e pelo fornecimento de bens e serviços insubstituíveis – têm vindo a ser severamente afectados por perturbações antropogénicas. A conversão de floresta em terreno agrícola afecta os sistemas aquáticos através de uma série de mecanismos: sedimentação; excesso de nutrientes; contaminação; alterações hidrológicas; e remoção de vegetação ripícola. As comunidades de macroinvertebrados de água doce – devido à sua diversidade, ubiquidade e sensibilidade às perturbações ambientais – revelam-se como particularmente adequadas para estudos de avaliação da integridade ecológica destes sistemas expostos simultaneamente a múltiplos factores de impacto. O uso sistemático de respostas biológicas para avaliação de mudanças ambientais – ou biomonitorização – pode ser levado a cabo através de diversas metodologias, que, de uma forma geral, não consideram aspectos funcionais das comunidades biológicas e têm aplicabilidade geograficamente restrita. A biomonitorização através de atributos biológicos (características que reflectem a adaptação das espécies ao seu meio ambiente) revela-se como uma ferramenta promissora na resolução dos problemas referidos, apresentando vantagens adicionais: relações causa-efeito directas; melhoria na diferenciação de impactos; e integração da variabilidade natural. O presente estudo apresenta uma revisão critica do estado-da-arte actual na área do uso de atributos biológicos em biomonitorização. Até à data de publicação, não estava disponível nenhum outro trabalho com a base conceptual do uso de atributos de macroinvertebrados enquanto descritores de comunidades e para efeitos de biomonitorização e gestão de sistemas de água doce. Descrevem-se as teorias ecológicas de suporte destas metodologias (conceitos de habitat-molde e de filtros paisagísticos) e os estudos que aplicaram estas teorias em cenários reais, tendo-se chamado a atenção para questões técnicas e possíveis soluções. As necessidades futuras nesta área englobam: o desenvolvimento de uma só ferramenta de biomonitorização de aplicação alargada; uma maior compreensão da variabilidade natural nas comunidades biológicas; diminuição dos efeitos de soluções de compromisso biológico e sindromas; realização de estudos autoecológicos adicionais; e detecção de impactos específicos em cenários de impacto complexos. Um dos objectivos deste estudo foi contribuir para a melhoria das técnicas de biomonitorização através de atributos, focalizando em comunidades de macroinvertebrados ribeirinhas em diferentes regiões biogeográficas (as bacias hidrográficas dos rios: Little e Salmon em New Brunswick, Canadá; Anllóns na Galiza, Espanha; Reventazón em Cartago, Costa Rica). Em cada região, foram estudados gradientes de uso agrícola de solo, incluindo desde bacias hidrográficas quase exclusivamente cobertas por floresta até bacias sob a influência maioritária de actividades agrícolas intensivas. Em cada gradiente de uso de solo, a caracterização da comunidade biológica (por amostragem de macroinvertebrados em troços de rápidos) foi acompanhada pela caracterização do habitat circundante (incluindo propriedades da bacia hidrográfica, análise química das águas e outras propriedades à escala local). A comunidade de macroinvertebrados foi caracterizada através de informação taxonómica, métricas estruturais, índices de diversidade, métricas de tolerância, índices bióticos e através da compilação de atributos biológicos e fisiológicos gerais, de história de vida e de resistência a perturbações. Análises estatísticas univariadas e multivariadas foram usadas para evidenciar os gradientes biológicos e físico-químicos, confirmar a sua co-variação, testar a significância da discriminação de níveis de impacto e estabelecer comparações inter-regionais. A estrutura de comunidades revelou os complexos gradientes de impacto, que por sua vez co-variaram significativamente com os gradientes de uso de solo. Os gradientes de impacto relacionaram-se sobretudo com entrada de nutrientes e sedimentação. Os gradientes biológicos definidos pelas medidas estruturais seleccionadas co-variaram com os gradientes de impacto estudados, muito embora apenas algumas variáveis estruturais tenham individualmente discriminado as categorias de uso de solo definidas a priori. Não foi detectada consistência nas respostas das medidas estruturais entre regiões biogeográficas, tendo-se confirmadado que as interpretações puramente taxonómicas de impactos são difíceis de extrapolar entre regiões. Os gradientes biológicos definidos através dos atributos seleccionados também co-variaram com os gradientes de perturbação, tendo sido possível obter uma melhor discriminação de categorias de uso de solo. Nas diferentes regiões, a discriminação de locais mais impactados foi feita com base num conjunto similar de atributos, que inclui tamanho, voltinismo, técnicas reproductivas, microhabitat, preferências de corrente e substrato, hábitos alimentares e formas de resistência. Este conjunto poderá vir a ser usado para avaliar de forma predictiva os efeitos das modificações severas de uso de solo impostas pela actividade agrícola. Quando analisadas simultaneamente através dos atributos, as comunidades das três regiões permitiram uma moderada mas significativa discriminação de níveis de impacto. Estas análises corroboram as evidências de que as mudanças nas comunidades de macroinvertebrados aquáticos em locais sob a influência de agricultura intensiva podem seguir uma trajectória convergente no espaço multidimensional, independentemente de factores geográficos. Foram fornecidas pistas para a identificação de parâmetros específicos que deverão ser tidos em conta no planeamento de novos programas de biomonitorização com comunidades de macroinvertebrados bentónicos, para aplicação numa gestão fluvial verdadeiramente ecológica, nestas e noutras regiões. Foram ainda sugeridas possíveis linhas futuras de investigação.

Seawater acidification by CO2 in a coastal lagoon environment: Effects on life history traits of juvenile mussels Mytilus galloprovincialis

The carbonate chemistry of seawater fromthe Ria Formosa lagoon was experimentallymanipulated, by diffusing pure CO2, to attain two reduced pH levels, by−0.3 and−0.6 pH units, relative to unmanipulated seawater. After 84 days of exposure, no differences were detected in terms of growth (somatic or shell) or mortality of juvenile mussels Mytilus galloprovincialis. The naturally elevated total alkalinity of the seawater (≈3550 μmol kg−1) prevented under-saturation of CaCO3, evenunder pCO2 values exceeding 4000 μatm, attenuating the detrimental effects on the carbonate supply-side. Even so, variations in shell weight showed that net calcification was reduced under elevated CO2 and reduced pH, although the magnitude and significance of this effect varied among size-classes. Most of the loss of shell material probably occurred as post-deposition dissolution in the internal aragonitic nacre layer. Our results show that, even when reared under extreme levels of CO2- induced acidification, juvenileM. galloprovincialis can continue to calcify and grow in this coastal lagoon environment. The complex responses of bivalves to ocean acidification suggest a large degree of interspecific and intraspecific variability in their sensitivity to this type of perturbation. Further research is needed to assess the generality of these patterns and to disentangle the relative contributions of acclimation to local variations in seawater chemistry and genetic adaptation.

Machine learning methods for quantitative structure-property relationship modeling

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Detection of quasi-periodic processes in complex systems: how do we quantitatively describe their properties?

It has been shown that in reality at least two general scenarios of data structuring are possible: (a) a self-similar (SS) scenario when the measured data form an SS structure and (b) a quasi-periodic (QP) scenario when the repeated (strongly correlated) data form random sequences that are almost periodic with respect to each other. In the second case it becomes possible to describe their behavior and express a part of their randomness quantitatively in terms of the deterministic amplitude–frequency response belonging to the generalized Prony spectrum. This possibility allows us to re-examine the conventional concept of measurements and opens a new way for the description of a wide set of different data. In particular, it concerns different complex systems when the ‘best-fit’ model pretending to be the description of the data measured is absent but the barest necessity of description of these data in terms of the reduced number of quantitative parameters exists. The possibilities of the proposed approach and detection algorithm of the QP processes were demonstrated on actual data: spectroscopic data recorded for pure water and acoustic data for a test hole. The suggested methodology allows revising the accepted classification of different incommensurable and self-affine spatial structures and finding accurate interpretation of the generalized Prony spectroscopy that includes the Fourier spectroscopy as a partial case.

Experiments on new polymer based mortars filled with FRP waste recyclates - a quantitative analysis

Glass fibre-reinforced plastics (GFRP) have been considered inherently difficult to recycle due to both: cross-linked nature of thermoset resins, which cannot be remolded, and complex composition of the composite itself. Presently, most of the GFRP waste is landfilled leading to negative environmental impacts and supplementary added costs. With an increasing awareness of environmental matters and the subsequent desire to save resources, recycling would convert an expensive waste disposal into a profitable reusable material. In this study, efforts were made in order to recycle grinded GFRP waste, proceeding from pultrusion production scrap, into new and sustainable composite materials. For this purpose, GFRP waste recyclates, were incorporated into polyester based mortars as fine aggregate and filler replacements at different load contents and particle size distributions. Potential recycling solution was assessed by mechanical behaviour of resultant GFRP waste modified polymer mortars. Results revealed that GFRP waste filled polymer mortars present improved flexural and compressive behaviour over unmodified polyester based mortars, thus indicating the feasibility of the waste reuse in polymer mortars and concrete. © 2011, Advanced Engineering Solutions.

A simple genetic basis for complex social behaviour mediates widespread gene expression differences.

A remarkable social polymorphism is controlled by a single Mendelian factor in the fire ant Solenopsis invicta. A genomic element marked by the gene Gp-9 determines whether workers tolerate one or many fertile queens in their colony. Gp-9 was recently shown to be part of a supergene with two nonrecombining variants, SB and Sb. SB/SB and SB/Sb queens differ in how they initiate new colonies, and in many physiological traits, for example odour and maturation rate. To understand how a single genetic element can affect all these traits, we used a microarray to compare gene expression patterns between SB/SB and SB/Sb queens of three different age classes: 1-day-old unmated queens, 11-day-old unmated queens and mated, fully reproductive queens collected from mature field colonies. The number of genes that were differentially expressed between SB/SB and SB/Sb queens of the same age class was smallest in 1-day-old queens, maximal in 11-day-old queens and intermediate in reproductive queens. Gene ontology analysis showed that SB/SB queens upregulate reproductive genes faster than SB/Sb queens. For all age classes, genes inside the supergene were overrepresented among the differentially expressed genes. Consistent with the hypothesized greater number of transposons in the Sb supergene, 13 transposon genes were upregulated in SB/Sb queens. Viral genes were also upregulated in SB/Sb mature queens, consistent with the known greater parasite load in colonies headed by SB/Sb queens compared with colonies headed by SB/SB queens. Eighteen differentially expressed genes between reproductive queens were involved in chemical signalling. Our results suggest that many genes in the supergene are involved in regulating social organization and queen phenotypes in fire ants.

Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.

The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the 'missing heritability'. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10(-4) (95% confidence interval [9.6×10(-5)-3.1×10(-4)]); accounts overall for 0.5% [0.19%-0.82%] of severe childhood obesity cases (P = 3.8×10(-10); odds ratio = 25.0 [9.9-60.6]); and results in a mean body mass index (BMI) increase of 5.8 kg.m(-2) [1.8-10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.

The Influence of Male Diet on Life History Traits of Female Mosquitoes

In the field, mosquitoes characteristically feed on sugars soon after emergence and intermittently during their adult lives. Sugar meals are commonly derived from plant nectar and homopteran honeydew, and without them, adults can only survive for a few days on larval reserves. In addition to sugar, females of most species rely on blood for the initiation and maintenance of egg development; thus their reproductive success depends to some extent on the availability of blood hosts. Males, on the other hand, feed exclusively on sugars. Consequently, their sexual maturation and reproductive success is largely dependent upon access to sugar sources. Plant nectar and homopteran honeydew are the two main sugar sources utilized by mosquitoes in the wild. Previous laboratory studies had shown that differences between nectar sources can affect the survivorship and biting frequency of disease vectoring mosquitoes. However, little is known on how sugar composition influence the reproductive processes in male mosquitoes. Male mosquitoes transfer accessory gland proteins and other hormones to their mates along with sperm during mating. In the female, these seminal fluid constituents exert their influence on reproductive genes that control ovulation and vitellogenesis. The present study tests the hypothesis that the mates of males consuming different sugar meals will exhibit varying levels of induction of vitellogenin (a gene which regulates the expression of egg yolk precursor proteins). Real-time quantitative RT-PCR was used to investigate how each sugar meal indirectly influences vitellogenin mRNA abundance in female Anopheles stephensi following mating. Results indicate that mates of nectar-fed males exhibit 2-fold greater change in vitellogenin expression than the mates of honeydew-fed males. However, this response did not occur in non-blood fed controls. These findings suggest that the stimulatory effect of mating on vitellogenesis in blood meal-reliant (i.e. anautogenous) mosquitoes may only be synergistic in nature. The present study also sought to compare the potential fitness costs of mating incurred by females that do not necessarily require a blood meal to initiate a reproductive cycle (i.e., exhibit autogeny). Females of the facultatively autogenous mosquito, Culex molestus were allowed to mate with males sustained on either nectar or honedyew. Mean lifetime fecundity and survivorship of females under the two different mating regimes were then recorded. Additionally, one-dimensional gel electrophoresis was used to verify the transfer of male accessory gland proteins to the sperm storage organs of females during mating.While there was no significant difference in survival between the test treatments, the mates of nectar-fed males produced 11% more eggs on average than mates of honeydew-fed males. However, additional data are needed to justify the extrapolation of these findings to natural settings. These findings prompt further investigation as the differences caused by diet variation in males may be reflected across other life history traits such as mating frequency and insemination capacity.