Physical activity and subclinical MRI cerebral infarcts: The ARIC Study

We hypothesized that physical activity (PA), which is often associated with reduced risk of ischemic stroke, may also be associated with reduced risk of subclinical cerebral infarcts

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

BackgroundDense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. ResultsSNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. ConclusionsThis manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection

Beyond heritage science: A review

Heritage science is an established and thriving field of enquiry. Initially considered as inherently cross-disciplinary, encompassing both the needs of conservators and practitioners and the high-quality evidence produced by scientists, heritage science has, through its expansion in recent years, formed a discipline in its own right. Here, we examine how heritage science can, and to an extent has, moved beyond the straightforward scientific analysis of historical materials and artefacts through an exploration of heritage science’s interactions with four key themes: (i) historical and archival research, (ii) conservation practice, (iii) policy at governmental, organisational and institutional levels, and (iv) a view to how new technologies, such as machine learning and artificial intelligence, can shape the future of heritage science. Much of the review narrative is framed via the analysis of UK-based case studies; however, they deal with issues that are international in nature (universal) and therefore transcend the UK context. Taken together, we demonstrate that heritage science as a discipline is capable of directly instigating or (re-)framing new areas or avenues of research, as well as enhancing and feeding into existing research questions, and has adapted and evolved along with emerging technologies and funding opportunities

Genetically Determined Plasma Lipid Levels and Risk of Diabetic Retinopathy: A Mendelian Randomization Study.

Results from observational studies examining dyslipidemia as a risk factor for diabetic retinopathy (DR) have been inconsistent. We evaluated the causal relationship between plasma lipids and DR using a Mendelian randomization approach. We pooled genome-wide association studies summary statistics from 18 studies for two DR phenotypes: any DR (N = 2,969 case and 4,096 control subjects) and severe DR (N = 1,277 case and 3,980 control subjects). Previously identified lipid-associated single nucleotide polymorphisms served as instrumental variables. Meta-analysis to combine the Mendelian randomization estimates from different cohorts was conducted. There was no statistically significant change in odds ratios of having any DR or severe DR for any of the lipid fractions in the primary analysis that used single nucleotide polymorphisms that did not have a pleiotropic effect on another lipid fraction. Similarly, there was no significant association in the Caucasian and Chinese subgroup analyses. This study did not show evidence of a causal role of the four lipid fractions on DR. However, the study had limited power to detect odds ratios less than 1.23 per SD in genetically induced increase in plasma lipid levels, thus we cannot exclude that causal relationships with more modest effect sizes exist

Fat mass and obesity gene and cognitive decline: The Atherosclerosis Risk in Communities Study

ABSTRACT Objective: To determine whether 4 genetic variants in the fat mass and obesity associated gene (FTO) identified in genome-wide association studies of diabetes and obesity are associated with cognitive change in midlife in the Atherosclerosis Risk in Communities (ARIC) Study.Methods: ARIC is a prospective cohort study of the development of atherosclerosis in 15,792 individuals aged 45 to 64 years at baseline from 1986 to 1989. FTO is highly expressed in human fetal and adult brain, and a single nucleotide polymorphism in FTO has previously been associated with reduced brain volume in cognitively normal subjects. Since a relationship between brain atrophy and diminished cognitive function has been demonstrated in ARIC participants, general linear models were used to evaluate the association between 6-year change in scores on 3 neuropsychological tests and FTO genotype.Results: In a sample of 8,364 white and 2,083 African American men and women with no clinical history of stroke, significantly greater mean change in performance on the Delayed Word Recall Test was associated with 2 of 4 FTO single nucleotide polymorphisms examined (rs9939609, rs805136, rs17817449, and rs1421085) in whites but not in African Americans (p ≤ 0.002). The association of the FTO polymorphisms with cognitive change was independent of potential confounding clinical and demographic variables including age, gender, education, diabetes, hypertension, and body mass index.Conclusions: Further studies will be needed to clarify the biological mechanisms and genetic pathways through which variants in FTO can increase susceptibility to decline in verbal memory detectable in middle-aged, community-dwelling adults

Beyond Heritage Science: A Review

Heritage science is an established and thriving field of enquiry. Initially considered as inherently cross-disciplinary, encompassing both the needs of conservators and practitioners and the high-quality evidence produced by scientists, heritage science has, through its expansion in recent years, formed a discipline in its own right. Here, we examine how heritage science can, and to an extent has, moved beyond the straightforward scientific analysis of historical materials and artefacts through an exploration of heritage science’s interactions with four key themes: (i) historical and archival research, (ii) conservation practice, (iii) policy at governmental, organisational and institutional levels, and (iv) a view to how new technologies, such as machine learning and artificial intelligence, can shape the future of heritage science. Much of the review narrative is framed via the analysis of UK-based case studies; however, they deal with issues that are international in nature (universal) and therefore transcend the UK context. Taken together, we demonstrate that heritage science as a discipline is capable of directly instigating or (re-)framing new areas or avenues of research, as well as enhancing and feeding into existing research questions, and has adapted and evolved along with emerging technologies and funding opportunities