Exome-based linkage disequilibrium maps of individual genes: functional clustering and relationship to disease

Exome sequencing identifies thousands of DNA variants and a proportion of these are involved in disease. Genotypes derived from exome sequences provide particularly high-resolution coverage enabling study of the linkage disequilibrium structure of individual genes. The extent and strength of linkage disequilibrium reflects the combined influences of mutation, recombination, selection and population history. By constructing linkage disequilibrium maps of individual genes, we show that genes containing OMIM-listed disease variants are significantly under-represented amongst genes with complete or very strong linkage disequilibrium (P = 0.0004). In contrast, genes with disease variants are significantly over-represented amongst genes with levels of linkage disequilibrium close to the average for genes not known to contain disease variants (P = 0.0038). Functional clustering reveals, amongst genes with particularly strong linkage disequilibrium, significant enrichment of essential biological functions (e.g. phosphorylation, cell division, cellular transport and metabolic processes). Strong linkage disequilibrium, corresponding to reduced haplotype diversity, may reflect selection in utero against deleterious mutations which have profound impact on the function of essential genes. Genes with very weak linkage disequilibrium show enrichment of functions requiring greater allelic diversity (e.g. sensory perception and immune response). This category is not enriched for genes containing disease variation. In contrast, there is significant enrichment of genes containing disease variants amongst genes with more average levels of linkage disequilibrium. Mutations in these genes may less likely lead to in utero lethality and be subject to less intense selection.     

No relationship between individual genetic diversity and prevalence of avian malaria in a migratory kestrel

Insight into the genetic basis of malaria resistance is crucial for understanding the consequences of this parasite group on animal populations. Here, we analyse the relationship between genotypic variation at 11 highly variable microsatellite loci and prevalence of three different lineages of avian malaria, two Plasmodium (RTSR1, LK6) and one Haemoproteus (LK2), in a wild population of the endangered lesser kestrel (Falco naumanni). Although we used a large sample size (584 typed individuals), we did not find any significant association between the prevalence of the studied parasite lineages and individual genetic diversity. Although our data set is large, the 11 neutral markers typed may have had low power to detect such association, in part because of the low parasite prevalence observed (less than 5% of infected birds). However, the fact that we have detected previous correlations between genetic diversity and other traits (ectoparasitism risk, fecundity) in the study population using the same panel of neutral markers and lower sample sizes suggests that other factors could underlie the absence of such a similar correlation with avian malaria. Differences in the genetics of the studied traits and in their particular basis of inbreeding depression (dominance vs. overdominance) may have led to malaria prevalence, but not other traits, being uncoupled with individual genetic diversity. Also, we cannot discard the possibility that the absence of association was a consequence of a low pathogenic effect of these particular malaria lineages on our lesser kestrel population, and thus we should not expect the evolution of genetic resistance against these parasites.     

Estimation of lipoperoxidative damage and antioxidant status in diabetic children: relationship with individual antioxidants

Increased oxidative stress has emerged as a potential mechanism implicated in the pathogenesis, progression and cell dysfunction associated with many diseases including diabetes. In routine clinical practice, the estimation of the degree of oxidative damage and antioxidant status, even in paediatric patients, by appropriate techniques appears to be of interest. The aim of this study was to reliably identify patients with increased oxidant stress and/or reduced antioxidant defence mechanisms with a small blood sample and verify the applicability to the study of diabetic children (DC) at clinical onset of the disease. In 1-ml blood samples from 30 DC and 34 controls, techniques for accurately measuring malondialdehyde (MDA) concentrations in plasma and erythrocytes (using HPLC analysis with fluorometric detection), total radical antioxidant potential (TRAP) and blood plasma oxidizability were adapted and validated. Plasma alpha-tocopherol (HPLC), uric acid and sulfhydryl (SH) groups were also determined. At clinical onset of diabetes a significant reduction in plasma TRAP values (P<0.01) was observed in DC compared with controls. Similarly, a significant fall in individual antioxidant levels (alpha-tocopherol/total lipids, uric acid and protein SH) was noted in plasma of DC. Highly significant increases were found in both plasma and erythrocyte MDA levels in DC (p-MDA:1.7+/-0.2 microM; er-MDA: 7.2+/-0.7 nmol/g Hb) compared with controls (p-MDA:0.86+/-0.09 microM; P<0.0003; er-MDA:3.8+/-0.2 nmol/g Hb, P<0.0001). Plasma MDA and triglyceride levels correlated directly only in DC (P<0.001). Whole plasma oxidizability was significantly higher in DC than in controls (P<0.0001) and this parameter correlated significantly with plasma cholesterol and triglyceride concentrations (P<0.0001). The micromethods adapted and applied to the simultaneous detection of lipid peroxidation products and antioxidant status permit accurate and reliable assessment of the oxidative stress process in small plasma samples. Our results clearly show systemic peroxidative damage associated with insufficient defence mechanisms against ROS to be already present at clinical onset of type 1 diabetes mellitus in children and adolescents.     

In vivo determination of the direction of rotation and moment-angle relationship of individual elbow muscles.

The direction of rotation (DOR) of individual elbow muscles, defined as the direction in which a muscle rotates the forearm relative to the upper arm in three-dimensional space, was studied in vivo as a function of elbow flexion and forearm rotation. Electrical stimulation was used to activate an individual muscle selectively, and the resultant flexion-extension, supination-pronation, and varus-valgus moments were used to determine the DOR. Furthermore, multi-axis moment-angle relationships of individual muscles were determined by stimulating the muscle at a constant submaximal level across different joint positions, which was assumed to result in a constant level of muscle activation. The muscles generate significant moments about axes other than flexion-extension, which is potentially important for actively controlling joint movement and maintaining stability about all axes. Both the muscle DOR and the multi axis moments vary with the joint position systematically. Variations of the DOR and moment-angle relationship across muscle twitches of different amplitudes in a subject were small, while there were considerable variations between subjects.     

A dialectic of cooperation and competition: solidarity and universal health care provision

The concept of solidarity has achieved relatively little attention from philosophers, in spite of its signal importance in a variety of social movements over the past 150 years. This means that there is a certain amount of preliminary philosophical work concerning the concept itself that must be undertaken before one can ask about its potential use in arguments concerning the provision of health care. In this paper, I begin with this work through a survey of some of the most prominent bioethical, political philosophical and intellectual historical literature concerned with the project of determining a philosophically specific and historically perspicacious meaning of the term 'solidarity'. This provides a conceptual foundation for a sketch of a four-tiered picture of social competition and cooperation within the nation-state. Corresponding to this picture is a four-tiered account of health care provision. These two models, taken together, provide a framework for articulating the conclusion that, while there are myriad examples of solidarity in claiming health care for some, or even many, the concept does not provide a basis for claiming health care for all.     

Microplates: a new tool for manipulation and mechanical perturbation of individual cells.

We present a new type of microinstrument allowing manipulation and mechanical perturbation of individual cells under an optical microscope. These instruments, which we call microplates, are pulled from rectangular glass bars. They have flat tips, typically 2 microm thick x 20 microm wide, whose specific shape and stiffness can be adjusted through the pulling protocol. After appropriate chemical treatment, microplates can support cell adhesion and/or spreading. Rigid microplates are used to hold cells, whereas more flexible ones serve as stress sensors, i.e. their deflexion is used to probe forces in the range of 1-1000 nN. The main advantages of microplates are their simple geometry and surface properties, and their ability to provide mechanical measurements. In this methodological paper, we give details about microplate preparation and adhesiveness, manipulation set-up, force calibration, and image analysis. Several manipulations have already been carried out on fibroblasts, including uniaxial deformation, micropipet aspiration of adherent cells, and cell-substrate separation. Our results to date provide new insights into the morphology, mechanical properties, and adhesive resistance of cells. Many future applications can be envisaged.     

Calcium and inositol 1,4,5-trisphosphate receptors: a complex relationship.

Increases in intracellular free Ca2+ concentration ([Ca2+]i), whether initiated by changes in plasma membrane potential or receptor-stimulated polyphosphoinositide hydrolysis, can be astonishingly complex, often occurring as repetitive Ca2+ spikes and regenerative Ca2+ waves that propagate through the cell and sometimes into neighbouring cells. The key to understanding these complex Ca2+ signals lies in understanding the interactions between the different pools from which Ca2+ can rapidly enter the cytosol and the activities of the various Ca(2+)-transporting systems that reverse the process.     

The relationship between beta-mannosidase and endo-beta-mannanase activities in tomato seeds during and following germination: a comparison of seed populations and individual seeds

beta-Mannosidase and endo-beta-mannanase are involved in the mobilization of the mannan-containing cell walls of the tomato seed endosperm. The activities of both enzymes increase in a similar temporal manner in the micropylar and lateral endosperm during and following germination. This increase in enzyme activities in the micropylar endosperm is not markedly reduced in seeds imbibed in abscisic acid although, in the lateral endosperm, endo-beta-mannanase activity is more suppressed by this inhibitor than is the activity of beta-mannosidase. Gibberellin-deficient (gib-1) mutants of tomato do not germinate unless imbibed in gibberellin; low beta-mannosidase activity, and no endo-beta-mannanase activity is present in seeds imbibed in water, but both enzymes increase strongly in activity in the seeds imbibed in the growth regulator. For production of full activity of both beta-mannosidase and endo-beta-mannanase in the endosperm, this tissue must be in contact with the embryo for at least the first 6 h of imbibition, which is indicative of a stimulus diffusing from the embryo to the endosperm during this time. These results suggest some correlation between the activities of beta-mannosidase and endo-beta-mannanase, particularly in the micropylar endosperm, in populations of tomato seeds imbibed in water, abscisic acid and gibberellin. However, when individual micropylar endosperm parts are used to examine the effect of the growth regulators and of imbibition in water on the production of the two enzymes, it is apparent that within these individual seed parts there may be large differences in the amount of enzyme activity present. Micropylar endosperms with high endo-beta-mannanase activity do not necessarily have high beta-mannosidase activity, and vice versa, which is indicative of a lack of co-ordination of the activities of these two enzymes within individuals of a population.     

The relationship of DNA base composition and individual protein composition in micro-organisms

Summary To investigate the dependence of protein composition on DNA base composition, a set of data on individual proteins with known amino acid compositions from a spectrum of bacterial species has been compiled. It is found that similar relationships of amino acid frequency to G + C content exist for these proteins as for the bulk proteins studied by Sueoka (1961). The data are analysed by linear and cubic regression, and a measure of the proportions of A + T-rich and G + C-rich codons in the underlying messenger RNAs is put forward. The theoretical limits on the G + C content of coding DNA are discussed, and inference are made about the various selective forces acting on DNAs of different G + C contents.     

The relationship of individual algal species to the surface microlayer of a small freshwater pond

Surface microlayer and subsurface algal communities were comparedon 14 sample dates over a 5 month period in a small Wisconsinpond. Similarities in species composition indicate that themicrolayer community had many species in common with the subsurfacecommunity. Relative species abundances, however, were differentfrom surface to subsurface. Analysis of the depth distributionof individual species indicates that the response to the uniquephysical/chemical conditions in the microlayer is species specific,with flagellates often in low numbers in the surface microlayeras a result of negative phototaxis; and diatoms often in highnumbers in the surface microlayer, as a result of a specificphysical/chemical affinity. These species specific differencesmay help to explain phytoneuston enrichment found in other studies. ¹Present address: University of Rhode Island, Department ofOceanography, Kingston, R1 02881, USA.²Author to whom reprint requests should be directed.