Progress and promise in understanding the genetic basis of common diseases

Susceptibility to common human diseases is influenced by both genetic and environmental factors. The explosive growth of genetic data, and the knowledge that it is generating, are transforming our biological understanding of these diseases. In this review, we describe the technological and analytical advances that have enabled genome-wide association studies to be successful in identifying a large number of genetic variants robustly associated with common disease. We examine the biological insights that these genetic associations are beginning to produce, from functional mechanisms involving individual genes to biological pathways linking associated genes, and the identification of functional annotations, some of which are cell-type-specific, enriched in disease associations. Although most efforts have focused on identifying and interpreting genetic variants that are irrefutably associated with disease, it is increasingly clear that—even at large sample sizes—these represent only the tip of the iceberg of genetic signal, motivating polygenic analyses that consider the effects of genetic variants throughout the genome, including modest effects that are not individually statistically significant. As data from an increasingly large number of diseases and traits are analysed, pleiotropic effects (defined as genetic loci affecting multiple phenotypes) can help integrate our biological understanding. Looking forward, the next generation of population-scale data resources, linking genomic information with health outcomes, will lead to another step-change in our ability to understand, and treat, common diseases.     

Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding

Conventional methods for quantitative trait locus (QTL) mapping require the selection of particular traits to be measured based on assumptions as to their importance. We have tested an alternative approach for the location of QTLs—marker-evaluated selection—that makes no prior assumptions as to which traits are important. The results of phenotype selection were evaluated in the products of modified bulk-population breeding that was replicated across a range of rice ecosystems. Selection was carried out in close collaboration with farmers in bulk populations that were all derived from a cross between an Indian upland variety (Kalinga III) and a high-yielding semi-dwarf variety (IR64). Twenty-seven diverse bulks were produced that were screened with molecular markers in order to determine whether shifts could be detected in marker allele frequency as a result of selection and if such changes varied by genomic region across ecosystems. Marker loci linked to important traits for adaptation to specific environments were identified without making any prior assumptions about which traits might be important. Genomic regions from Kalinga III were strongly selected in the upland environments and regions from IR64 in the lowland ones. However, exceptions occurred where the upland parent contributed positively to lowland adaptation and vice versa. The results can be used as a basis for the development of second-cycle varieties, using marker-assisted selection to produce genotypic ideotypes for specific target environments. The very strong selection for genomic regions from the adapted parents of the wide (upland × lowland) cross indicates that, in non-marker-assisted breeding, where genetically distant parents have been used, modified backcross breeding should be efficient. A single backcross to the adapted parent for a specific ecosystem will result in a higher frequency of segregants with the desired high genetic contribution from the adapted parent.     

Adaptations to floodplains in Populus and Salix: the role of collet hairs

There has been growing recent interest in the adaptations of tree species to seedling establishment in active northern temperate floodplains. In the case of Populus and Salix, most or all of the recent papers overlook a scattered, earlier literature showing that, in many Populus and Salix species, just after germination, the collet produces prominent hairs which, in young seedlings, may play an important role in anchorage and water absorption, the collet being the transition zone between the hypocotyl and the radicle. This earlier literature is briefly reviewed. The significance of collet hairs is then related to the very high seedling mortalities in riparian systems caused by high river flows (scour) or by drought stress arising from water level declines and coarse sediment textures. The need for work to establish just which species have collet hairs and to quantify the effect of collet hairs on anchorage and water absorption is emphasized.     

On the Prospects of Whole-Genome Association Mapping in Saccharomyces cerevisiae

Advances in sequencing technology have enabled whole-genome sequences to be obtained from multiple individuals within species, particularly in model organisms with compact genomes. For example, 36 genome sequences of Saccharomyces cerevisiae are now publicly available, and SNP data are available for even larger collections of strains. One potential use of these resources is mapping the genetic basis of phenotypic variation through genome-wide association (GWA) studies, with the benefit that associated variants can be studied experimentally with greater ease than in outbred populations such as humans. Here, we evaluate the prospects of GWA studies in S. cerevisiae strains through extensive simulations and a GWA study of mitochondrial copy number. We demonstrate that the complex and heterogeneous patterns of population structure present in yeast populations can lead to a high type I error rate in GWA studies of quantitative traits, and that methods typically used to control for population stratification do not provide adequate control of the type I error rate. Moreover, we show that while GWA studies of quantitative traits in S. cerevisiae may be difficult depending on the particular set of strains studied, association studies to map cis-acting quantitative trait loci (QTL) and Mendelian phenotypes are more feasible. We also discuss sampling strategies that could enable GWA studies in yeast and illustrate the utility of this approach in Saccharomyces paradoxus. Thus, our results provide important practical insights into the design and interpretation of GWA studies in yeast, and other model organisms that possess complex patterns of population structure.     

Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle

Background

Belgian Blue cattle are famous for their exceptional muscular development or “double-muscling”. This defining feature emerged following the fixation of a loss-of-function variant in the myostatin gene in the eighties. Since then, sustained selection has further increased muscle mass of Belgian Blue animals to a comparable extent. In the present paper, we study the genetic determinants of this second wave of muscle growth.

Results

A scan for selective sweeps did not reveal the recent fixation of another allele with major effect on muscularity. However, a genome-wide association study identified two genome-wide significant and three suggestive quantitative trait loci (QTL) affecting specific muscle groups and jointly explaining 8-21% of the heritability. The top two QTL are caused by presumably recent mutations on unique haplotypes that have rapidly risen in frequency in the population. While one appears on its way to fixation, the ascent of the other is compromised as the likely underlying MRC2 mutation causes crooked tail syndrome in homozygotes. Genomic prediction models indicate that the residual additive variance is largely polygenic.

Conclusions

Contrary to complex traits in humans which have a near-exclusive polygenic architecture, muscle mass in beef cattle (as other production traits under directional selection), appears to be controlled by (i) a handful of recent mutations with large effect that rapidly sweep through the population, and (ii) a large number of presumably older variants with very small effects that rise slowly in the population (polygenic adaptation).

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-796) contains supplementary material, which is available to authorized users.     

Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V(Q), the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.     

Expression of glucose transporter GLUT3 by endotoxin in cultured rat astrocytes: the role of nitric oxide

The induction of nitric oxide (NO) synthase in astrocytes by endotoxin and/or cytokine treatment is associated with increased glucose consumption and glycolysis, but the mechanism whereby this phenomenon occurs remains obscure. In this work, we have addressed this issue and found that incubation of cultured rat astrocytes with lipopolysaccharide (LPS; 1 microg/mL) for 24 h increased the level of constitutively expressed GLUT1 glucose transporter mRNA, and triggered GLUT3 mRNA expression, which was absent in normal astrocytes. The occurrence of GLUT3 protein after LPS treatment was corroborated by western blotting and immunocytochemistry. A 4-h incubation of astrocytes in the absence of glucose, or under an oxygen-poor (3%) atmosphere also resulted in GLUT3 mRNA overexpression. Experiments performed with 2-deoxy-D-[U-14C]glucose (at 0.1 mM of D-glucose) confirmed that LPS (0.1-10 microg/mL) dose-dependently increased the rate of glucose uptake (by a factor of 1.6 at 1 microg/mL of LPS), which was paralleled with the increase in NO synthesis. Furthermore, blockade of NO synthase with 2-amino-5,6-dihydro-6-methyl-(4H)-1,3-thiazine (AMT; 50 microM) partially (by 45%) prevented the LPS-mediated increase in glucose uptake. Finally, incubation of astrocytes with the NO donor 1-[2-(2-aminoethyl)-N-(2-ammonioethyl)amino]diazen-1-ium-1,2-diolate (DETA; 100 microM) increased by a factor of 1.4 the rate of glucose uptake. We conclude that the increase in GLUT3-driven glucose uptake in astrocytes would have a neuroprotective role under conditions in which NO formation is combined with hypoglycaemia, such as in brain ischemia.     

Tolerance of isolated rat hearts to low-flow ischemia and hypoxia of increasing duration: Protective role of down-regulation and ATP during ischemia

We tested the hypothesis that down-regulated hearts, as observed during low-flow ischemia, adapt better to low O₂ supply than non-down-regulated, or hypoxic, hearts. To address the link between down-regulation and endogenous ischemic protection, we compared myocardial tolerance to ischemia and hypoxia of increasing duration. To that end, we exposed buffer-perfused rat hearts to either low-flow ischemia or hypoxia (same O₂ shortage) for 20, 40 or 60 min (n = 8/group), followed by reperfusion or reoxygenation (20 min, full O₂ supply). At the end of the O₂ shortage, the rate·pressure product was less in ischemic than hypoxic hearts (p < 0.0001). The recovery of the rate·pressure product after reperfusion or reoxygenation was not different for t = 20 min, but was better in ischemic than hypoxic hearts for t = 40 and 60 min (p < 0.02 and p < 0.0002, respectively). The end-diastolic pressure remained unchanged during low-flow ischemia (0.024 ± 0.013 mmHg·min^–1), but increased significantly during hypoxia (0.334 ± 0.079 mmHg·min^–1). We conclude that, while the duration of hypoxia progressively impaired the rate·pressure product and the end-diastolic pressure, hearts were insensitive of the duration of low-flow ischemia, thereby providing evidence that myocardial down-regulation protects hearts from injury. Excessive ATP catabolism during ischemia in non-down-regulated hearts impaired myocardial recovery regardless of vascular, blood-related and neuro-hormonal factors. These observations support the view that protection is mediated by the maintenance of the ATP pool.     

Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms

Ultraconserved elements in the human genome likely harbor important biological functions as they are dosage sensitive and are able to direct tissue-specific expression. Because they are under purifying selection, variants in these elements may have a lower frequency in the population but a higher likelihood of association with complex traits. We tested a set of highly constrained SNPs (hcSNPs) distributed genome-wide among ultraconserved and nearly ultraconserved elements for association with seven traits related to reproductive (age at natural menopause, number of children, age at first child, and age at last child) and overall [longevity, body mass index (BMI), and height] fitness. Using up to 24,047 European-American samples from the National Heart, Lung, and Blood Institute Candidate Gene Association Resource (CARe), we observed an excess of associations with BMI and height. In an independent replication panel the most strongly associated SNPs showed an 8.4-fold enrichment of associations at the nominal level, including three variants in previously identified loci and one in a locus (DENND1A) previously shown to be associated with polycystic ovary syndrome. Finally, using 1430 family trios, we showed that the transmissions from heterozygous parents to offspring of the derived alleles of rare (frequency ≤0.5%) hcSNPs are not biased, particularly after adjusting for the rates of genotype missingness and error in the data. The lack of transmission bias ruled out an immediately and strongly deleterious effect due to the rare derived alleles, consistent with the observation that mice homozygous for the deletion of ultraconserved elements showed no overt phenotype. Our study also illustrated the importance of carefully modeling potential technical confounders when analyzing genotype data of rare variants.     

Daytime restricted feeding modifies the daily variations of liver gluconeogenesis: Adaptations in biochemical and endocrine regulators

Daytime restricted feeding (DRF) promotes circadian adaptations in the metabolic processing of nutrients. We explored the hepatic gluconeogenic response in DRF rats by the temporal profiles of the following: (1) the activity of glucose 6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PEPCK), as well as the periportal and pericentral distribution of PEPCK; (2) conversion of alanine to glucose; (3) glycemia and liver glycogen content; (4) presence of glycogen synthase (GYS) and its phosphorylated form (at Ser641, pGYS); (5) circulating levels of corticosterone, glucagon and insulin; (6) glucose-tolerance test; and (7) sirtuin 1 (SIRT1) and peroxisome proliferator-activated receptor-coactivator 1α (PGC-1α). The results showed that DRF promoted: (1) a phase shift in G6Pase activity and an increase in PEPCK activity as well as a change of PEPCK from periportal to pericentral hepatocytes, (2) a net conversion of alanine to circulating glucose, (3) a decrease in glycemic values and a phase shift in the liver glycogen content, (4) a phase shift in GYS and an increase of pGYS, (5) an increase in the daily levels of corticosterone and glucagon, but a reduction in the levels of insulin, (6) normal glucose homeostasis in all groups and (7) an enhanced presence of SIRT1 and PGC-1α. It is proposed that the increased gluconeogenic in DRF group promotes synthesis of hepatic glycogen and the production of glucose. These results could be a modulation of the gluconeogenic process due to rheostatic adaptations in the endocrine, metabolic and timing regulation of liver and could be associated with the physiology of the food entrained oscillator.     

Physiological flexibility: the key to success and survival for Antarctic fairy shrimps in highly fluctuating extreme environments

1. The anostracan fairy shrimp Branchinecta gaini inhabits one of the most hostile environments on earth, living in pools and lakes in Antarctica. Between January 2002 and January 2003 temperatures in two pools where B. gaini are extremely abundant on Adelaide Island ranged from ?18.6 to ?15.7 °C in winter, to 19.4 to 17.1 °C in summer, whilst air temperatures ranged from ?34 to 6.3 °C. 2. Branchinecta gaini survives winter as cysts, but endures large summer temperature fluctuations as adults. Cysts froze between ?24.4 and ?25.7 °C. In experiments adults survived 0–10 °C with no mortality for 1 week, 25 °C for nearly 48 h with 50% mortality, and at 32 °C complete mortality occurred in <1 h. 3. Oxygen consumption (M?O₂) in B. gaini approximately doubled for every 10 °C temperature rise (Q₁₀ = 2.04) up to 20 °C where it reached a peak. Females had, on average 19% higher M?O₂ than males. Females also had greater metabolic scopes, (maximum–minimum M?O₂ across temperatures was ×3.6 for females, ×3.1 for males). 4. Ventilation frequency increased linearly with temperature, and did not decline at 25 °C, indicating animals were ‘trying’ progressively harder to supply oxygen to tissues, and oxygen deficiency was the probable cause of death. Females had a higher ventilation frequency than males (8.6–17.1% higher) and they also exhibited greater scope to raise ventilation frequency (×2.4 for females versus ×1.5 for males). 5. Great metabolic flexibility allows B. gaini to exploit extreme, highly fluctuating environments, and larger ventilatory and respiratory scopes allow females to survive higher temperatures than males. Because of this flexibility their prospects for coping with physical environmental change are high.     

Escaping the heat: range shifts of reef coral taxa in coastal Western Australia

One of the most critical challenges facing ecologists today is to understand the changing geographic distribution of species in response to current and predicted global warming. Coastal Western Australia is a natural laboratory in which to assess the effect of climate change on reef coral communities over a temporal scale unavailable to studies conducted solely on modern communities. Reef corals composing Late Pleistocene reef assemblages exposed at five distinct localities along the west Australian coast were censused and the results compared with coral occurrence data published for the modern reefs offshore of each locality. The resulting comparative data set comprises modern and Late Pleistocene reef coral communities occurring over approximately 12° of latitude. For the modern reefs this gradient includes the zone of overlap between the Dampierian and Flindersian Provinces. Modern reef coral communities show a pronounced gradient in coral composition over the latitudinal range encompassed by the study, while the gradient in community composition is not as strong for Pleistocene communities. Tropical‐adapted taxa contracted their ranges north since Late Pleistocene time, emplacing two biogeographic provinces in a region in which a single province had existed previously. Beta diversity values for adjacent communities also reflect this change. Modern reefs show a distinct peak in beta diversity in the middle of the region; the peak is not matched by Pleistocene reefs. Beta diversity is correlated with distance only for comparisons between modern reefs in the north and the fossil assemblages, further supporting change in distribution of the biogeographic provinces in the study area. Coral taxa present in modern communities clearly expanded and contracted their geographic ranges in response to climate change. Those taxa that distinguish Pleistocene from modern reefs are predicted to migrate south in response to future climate change, and potentially persist in ‘temperature refugia’ as tropical reef communities farther north decline.     

Comparative properties of bovine heart and liver rhodaneses and the regulatory role of the rhodaneses in energy metabolism

In previous studies on the rhodanese activity of bovine liver mitochondria, we have shown that in addition to activity observed in the soluble protein fraction, there is rhodanese activity that is bound to the mitochondrial membrane. The latter activity accounts for as much as 40% of the total and, in situ, is associated in a multiprotein complex that forms iron-sulfur centers. In the present studies, we have investigated the rhodanese activity of bovine heart muscle. We have found that the major part of this enzyme activity is localized in the mitochondria and, further, that at least 25% of the total rhodanese activity of heart mitochondria is membrane-bound. As in liver tissue, the heart activity at least in part is associated in a multiprotein complex that forms iron-sulfur centers. Upon purification of the heart rhodanese in the soluble protein fraction, there is a 10- to 30-fold decrease inK_m values for the standard assay substrates thiosulfate and cyanide ions. These observations are consistent with the interpretation that there are activated and deactivated (low activity) forms of the heart enzyme in crude extracts, but only the activated form survives purification. The present results, together with our recent finding that liver mitochondrial rhodanese is subject to phosphorylation, lend support to our proposal that the rhodaneses serve as converter enzymes which regulate the rate of electron transport through sulfuration of respiratory chain components. The rhodaneses, in turn, are controlled by protein kinases and the local ATP concentration.     

Modifications of the EEG frequency pattern in humans related to a single neurofeedback session

We studied changes in the frequency pattern of EEG related to a single session of biological feedback by the EEG characteristics (neurofeedback, NFB) directed toward an increase in the ratio of α/θ spectral powers (SPs) (an experimental group; 30 subjects) and to a session of the supposedly indifferent acoustic influence (listening to a musical background; 30 persons). A standard technique of EEG recording was used; the loudness of white noise overlapping the musical background served as an NFB signal. EEG was recorded from the C3 and C4 leads. Within the examined experimental group, an NFB session elicited a trend toward statistically insignificant decreases in the SPs of δ, α, and β rhythms and increases in the SPs of θ and γ EEG components. Listening to a supposedly neutral musical background by the control group, with no attempts at self-control of the SPs of EEG rhythms, was followed by rather clear unidirectional (partially significant) decreases in the SPs of θ, α, β, and γ components; the δ activity in the left hemisphere decreased, while in the right hemisphere it increased. In general, results of the single NFB session were characterized by a high interindividual variability, which can be related mostly to the specificities of psychophysiological characteristics of the personality of the tested subject. Neirofiziologiya/Neurophysiology, Vol. 37, Nos. 5/6, pp. 443–451, September–December, 2005.     

The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations

Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1) to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2) to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.     

A new discriminant NMF algorithm and its application to the extraction of subtle emotional differences in speech

In this study we propose a new feature extraction algorithm, dNMF (discriminant non-negative matrix factorization), to learn subtle class-related differences while maintaining an accurate generative capability. In addition to the minimum representation error for the standard NMF (non-negative matrix factorization) algorithm, the dNMF algorithm also results in higher between-class variance for discriminant power. The multiplicative NMF learning algorithm has been modified to cope with this additional constraint. The cost function was carefully designed so that the extraction of feature coefficients from a single testing pattern with pre-trained feature vectors resulted in a quadratic convex optimization problem in non-negative space for uniqueness. It also resolves issues related to the previous discriminant NMF algorithms. The developed dNMF algorithm has been applied to the emotion recognition task for speech, where it needs to emphasize the emotional differences while de-emphasizing the dominant phonetic components. The dNMF algorithm successfully extracted subtle emotional differences, demonstrated much better recognition performance and showed a smaller representation error from an emotional speech database.     

The role of Ca2+ and hemodynamics in the action of diltiazem on hepatic energy metabolism

Diltiazem causes vasoconstriction in the liver when present at high concentrations, an action that is strictly Ca²⁺-dependent. Diltiazem is also active on energy metabolism. This toxic action could be partly a consequence of hemodynamic effects. In the absence of Ca²⁺, the hemodynamic effects are no longer present and, consequently, Ca²⁺-free experiments are useful for distinguishing between hemodynamics-dependent and hemodynamics-independent effects. The experimental system used was the hemoglobin-free perfused rat liver from fed and fasted rats. Diltiazem was infused at various concentrations in the presence and absence of Ca²⁺. Several metabolic parameters were measured: lactate and pyruvate production (glycolysis), glycogenolysis, oxygen uptake, gluconeogenesis, and the cellular levels of lactate, pyruvate, glucose, AMP, ADP, and ATP. The effects of diltiazem can be divided into three groups: (1) Effects that are strictly dependent on the Ca²⁺-mediated hemodynamic action. This group comprises inhibition of oxygen uptake at all concentrations (50–500 mol/L) inhibition of lactate, pyruvate, and glucose release at high concentrations; the decrease in cellular ATP; the increase in cellular AMP; and the cellular accumulation of glucose and lactate. (2) Effects that are independent of the hemodynamic action. The most relevant effect of this type is inhibition of gluconeogenesis. (3) Effects that are influenced by Ca²⁺ but are independent of the hemodynamic effects. This is the typical case of lactate and glucose release from endogenous glycogen, whose stimulation by low diltiazem concentrations is more pronounced in the presence of Ca²⁺ than in its absence.     

Convenient and quantitative determination of the frequency of a mutant allele using solid-phase minisequencing: application to aspartylglucosaminuria in Finland.

Aspartylglucosaminuria (AGU) is a recessively inherited lysosomal disease caused by inadequate aspartylglucosaminidase (AGA) activity. The disease is prevalent in the genetically isolated Finnish population. We have used a new method, solid-phase minisequencing, to determine the frequency of two missense mutations in the AGA gene in this population. In samples from 70% of the Finnish AGU families, we found that the two nucleotide changes were always associated, and they were identified in 98% of the AGU alleles analyzed. Thus, the high prevalence of AGU in the Finnish population is the consequence of a founder effect of one ancient mutation. The identification of asymptomatic carriers by the minisequencing test proved to be unequivocal. The method also allowed quantification of a mutated nucleotide sequence present in less than 1% of a sample. The frequency of AGU carriers in this population was 1/36 when estimated by quantifying the mutated AGU allele in a pooled leukocyte sample from 1350 normal Finnish individuals.