Acid phosphatase locus 1 (ACP1): Possible relationship of allelic variation to body size and human population adaptation to thermal stress-A theoretical perspective

A revised Fisher model on analysis of quantitative trait loci with multiple alleles

Zeng et al. (2005) proposed a general two-allele (G2A) model to model bi-allelic quantitative trait loci (QTL). Comparing with the classical Fisher model, the G2A model can avoid using redundant parameters and be fitted directly using standard least square (LS) approach. In this study, we further extend the G2A model to general multi-allele (GMA) model. First, we propose a one-locus GMA model for phase known genotypes based on modeling the inheritance of paternal and maternal alleles. Next, we develop a one-locus GMA model for phase unknown genotypes by treating it as a special case of the phase known one-locus GMA model. Thirdly, we extend the one-locus GMA models to multiple loci. We discuss how the genetic variance components can be analyzed using these GMA models in equilibrium as well as disequilibrium populations. Finally, we apply the GMA model to a published experimental data set.

Multiallelic models of genetic effects and variance decomposition in non-equilibrium populations

Quantitative genetics stems from the theoretical models of genetic effects, which are re-parameterizations of the genotypic values into parameters of biological (genetic) relevance. Different formulations of genetic effects are adequate to address different subjects. We thus need to generalize and unify them under a common framework for enabling researchers to easily transform genetic effects between different biological meanings. The Natural and Orthogonal Interactions (NOIA) model of genetic effects has been developed to achieve this aim. Here, we further implement the statistical formulation of NOIA with multiple alleles under Hardy-Weinberg departures (HWD). We show that our developments are straightforwardly connected to the decomposition of the genetic variance and we point out several emergent properties of multiallelic quantitative genetic models, as compared to the biallelic ones. Further, NOIA entails a natural extension of one-locus developments to multiple epistatic loci under linkage equilibrium. Therefore, we present an extension of the orthogonal decomposition of the genetic variance to multiple epistatic, multiallelic loci under HWD. We illustrate this theory with a graphical interpretation and an analysis of published data on the human acid phosphatase (ACP1) polymorphism.

Schizophrenia and vitamin D related genes could have been subject to latitude-driven adaptation

Background

Many natural phenomena are directly or indirectly related to latitude. Living at different latitudes, indeed, has its consequences with being exposed to different climates, diets, light/dark cycles, etc. In humans, one of the best known examples of genetic traits following a latitudinal gradient is skin pigmentation. Nevertheless, also several diseases show latitudinal clinals such as hypertension, cancer, dismetabolic conditions, schizophrenia, Parkinson's disease and many more.

Results

We investigated, for the first time on a wide genomic scale, the latitude-driven adaptation phenomena. In particular, we selected a set of genes showing signs of latitude-dependent population differentiation. The biological characterization of these genes showed enrichment for neural-related processes. In light of this, we investigated whether genes associated to neuropsychiatric diseases were enriched by Latitude-Related Genes (LRGs). We found a strong enrichment of LRGs in the set of genes associated to schizophrenia. In an attempt to try to explain this possible link between latitude and schizophrenia, we investigated their associations with vitamin D. We found in a set of vitamin D related genes a significant enrichment of both LRGs and of genes involved in schizophrenia.

Conclusions

Our results suggest a latitude-driven adaptation for both schizophrenia and vitamin D related genes. In addition we confirm, at a molecular level, the link between schizophrenia and vitamin D. Finally, we discuss a model in which schizophrenia is, at least partly, a maladaptive by-product of latitude dependent adaptive changes in vitamin D metabolism.

Interaction between obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-q21

One of the chief complexities of genetic influences on human obesity appears to be gene-gene interactions. Here, we employed model-free approaches to look for gene-gene interaction effects in human obesity using genome scan data from 260 European American families. We found consistent evidence for statistical interaction between 2p25-p24 (18-38 cM) and 13q13-q21 (26-47 cM). For discrete traits, the positive correlations were significant at P<0.0001 (P</=0.0023 after correction for multiple tests) in both IBD-based and NPL-based analyses for BMI>/=40 kg/m(2). Other analytic approaches gave consistent, supportive results. For quantitative traits, interaction effects were significant for BMI (P=0.0012), percent fat (P=0.0265) and waist circumference (P=0.0023) in a Haseman-Elston regression model, and for BMI (P=0.0043) in variance component analysis. Our findings suggest that obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-21 may interact to influence extreme human obesity. The identification of gene-gene interactions may prove crucial to understanding the contributions of genes, which, by themselves, have relatively small effects on obesity susceptibility and resistance.

Intrauterine programming of fetal islet gene expression in rats--effects of maternal protein restriction during gestation revealed by proteome analysis

AIMS/HYPOTHESIS

Fetal undernutrition can result in intrauterine growth restriction and increased incidence of Type 2 diabetes mellitus. Intrauterine malnutrition in form of an isocaloric low-protein diet given to female rats throughout gestation decreases islet-cell proliferation, islet size and pancreatic insulin content, while increasing the apoptotic rate and sensitivity to nitrogen oxide and interleukin-1beta. Hence, the influence of a low-protein diet on the development of beta-cells and islets could also be of interest for the pathogenesis of Type 1 and Type 2 diabetes mellitus. We hypothesise that the effects of a low-protein diet in utero are caused by intrauterine programming of beta-cell gene expression.

METHODS

Pregnant Wistar rats were fed a low-protein diet (8% protein) or a control diet (20% protein) throughout gestation. At day 21.5 of gestation fetal pancreata were removed, digested and cultured for 7 days. Neoformed islets were collected and analysed by proteome analysis comprising 2-dimensional gel electrophoresis and mass spectrometry.

RESULTS

A total of 2810 different protein spots were identified, 70 of which were changed due to the low-protein diet. From 45 of the changed protein spots, identification was obtained by mass spectrometry (64% success rate). Proteins induced by the low-protein diet were grouped according to their biological functions, e.g. cell cycle and differentiation, protein synthesis and chaperoning.

CONCLUSIONS/INTERPRETATION

Our study offers a possible explanation of the alterations induced by a low-protein diet in islets. It shows that in Wistar rats the intrauterine milieu could program islet gene expression in ways unfavourable for the future of the progeny. This could be important for our understanding of the development of Type 1 and Type 2 diabetes mellitus.

Neandertal cold adaptation: physiological and energetic factors

European Neandertals employed a complex set of physiological cold defenses, homologous to those seen in contemporary humans and nonhuman primates. While Neandertal morphological patterns, such as foreshortened extremities and low relative surface-area, may have explained some of the variance in cold resistance, it is suggested the adaptive package was strongly dependent on a rich array of physiological defenses. A summary of the environmental cold conditions in which the Neandertals lived is presented, and a comparative ethnographic model from Tierra del Fuego is used. Muscle and subcutaneous fat are excellent "passive" insulators. Neandertals were quite muscular, but it is unlikely that they could maintain enough superficial body fat to offer much cold protection. A major, high-energy metabolic adaptation facilitated by modest amounts of highly thermogenic brown adipose tissue (BAT) is proposed. In addition, Neandertals would have been protected by general mammalian cold defenses based on systemic vasoconstriction and intensified by acclimatization, aerobic fitness, and localized cold--induced vasodilation. However, these defenses are energetically expensive. Based on contemporary data from circumpolar peoples, it is estimated that Neandertals required 3,360 to 4,480 kcal per day to support strenuous winter foraging and cold resistance costs. Several specific genetic cold adaptations are also proposed--heat shock protein (actually, stress shock protein), an ACP*1 locus somatic growth factor, and a specialized calcium metabolism not as yet understood.