Notes on the Morphology and Genesis of Mud Polygons on Mount Kenya, East Africa

Mud polygons forming in a valley train deposit in Teleki Valley on Mount Kenya were studied with respect to their physical, mineralogical, chemical and biological characteristics. Developing in fine-grained alluvium of postglacial age, those polygonal systems are composed of numerous, and nearly isomorphous units, that appear close to existing drainages in areas stripped of vegetation cover. Stream erosion and animal activity (particularly rodents and Mount Kenya hyrax, e.g. cony) appear to be primarily responsible for the loss of plant cover. Field tests show that periodic wetting and drying results in closure and reopening of polygonal cracks; freeze thaw activity was not observed to assist in developing polygonal ground shape. Subsequent laboratory tests on several samples confirm that the lack of expandable clay minerals might inhibit wetting-drying activity in individual polygon samples.Les polygones de boue, qui se forment dans les dépôts fluvio-glaciaires dans la vallée de Teleki sur le mont Kenya, ont été étudiés en fonction de leurs caractéristiques physiques, minéralogiques, chimiques et biologiques. Ces réseaux polygonaux, qui se développent dans des alluvions postglaciaires fins, sont composés de plusieurs unités presque isomorphes qui apparaissent près des chenaux d'écoulement là où il n'y a plus de couvert végétal. L'érosion fluviatile et l'activité animale (en particulier celle des rongeurs et le daman du mont Kenya) semblent être les principales causes de la perte du couvert végétal. Les expériences de terrain démontrent que les cycles mouillage-assèchement provoquent la fermeture et la réouverture des fissures polygonales; le phénomène gel-dégel ne semble pas contribuer au développement des sols polygonaux. Les tests de laboratoire subséquents faits sur plusieurs échantillons confirment le fait que l'absence de minéraux argileux dilatables peut empêcher l'opération mouillage-séchage de se produire dans les échantillons de polygones pris isolément

Evaluation of Amino Acid Composition as a Geochronometer in Buried Soils on Mount Kenya, East Africa

A sequence of surface and buried paleosols from the slopes of Mount Kenya, East Africa, has been identified and dated by radiocarbon and amino acid dating techniques in order to elucidate the Quaternary history of the area. Buried paleosols vary in radiocarbon age from 900 to > 40,000 yrs BP. They have developed in glacial and periglacial deposits of variable texture, consisting of a high percentage of clasts of phonolite, basalt and syenite. All but two paleosols are located in the Afroalpine zone (above 3200 m). D/L ratios of amino acids in Ab horizons were determined in order to establish their reliability for relative age dating. Alanine, aspartic acid, glutamic acid, leucine, valine, and phenylalanine were routinely analyzed. Aspartic acid, as in other cases, proved reliable yielding remarkably consistent results, with higher ratios corresponding to increasing age. Other acids analyzed showed distinct trends, although not as convincing as aspartic acid. In most cases, the aspartic acid ratio/ age relationships were supported by radiocarbon dates. D/L ratios of aspartic acid varied from approximately 0.07 for modern samples, to approximately 0.45 in samples > 40,000 years old.On a identifié et daté, au radiocarbone et à l'aide de techniques de datations à l'acide aminé, des paléosols enfouis et de surface afin de comprendre l'évolution quaternaire de la région. Les datations au radiocarbone des paléosols enfouis varient de 900 à plus de 40 000 BP. Les sols se sont développés dans des dépôts glaciaires et périglaciaires de différentes textures, constitués de fragments de roches détritiques, de phonolite, de basalte et de syénite. Tous les paléosols, sauf deux, sont situés dans la zone afroalpine (au-dessus de 3200 m). On a déterminé par racémisation les rapports D/L des acides aminés dans les horizons Ab en vue d'évaluer leur fiabilité pour la datation des âges relatifs. On a fait l'analyse de l'alaline, de l'acide aspartique, de l'acide glutamique, de la leucine, de la valine et du phénylalaline. L'acide aspartique, comme dans d'autres cas, a donné des résultats particulièrement satisfaisants, les quotients plus élevés correspondant aux âges les plus anciens. D'autres acides montraient des tendances bien distinctes, mais moins convaincantes que dans le cas de l'acide aspartique. Ainsi, dans la plupart des cas, les relations quotients/âges de l'acide aspartique étaient corroborées par les datations au radiocarbone. Les rapports D/L de l'acide aspartique variaient d'environ 0,07 pour les échantillons modernes à environ 0,45 pour les échantillons de plus de 40 000 ans.Eine Série von an der Oberflâche Negenden und begrabenen Palàobôden von den Hàngen des Mount Kenya, Ost-Afrika, wurde mittels Radiokarbon- und Aminosâuredatierungs-techniken identifiziert und datiert, um die Geschichte dieses Gebiets im Quaternàr zu erhellen. Das durch Radiokarbon bestimmte Alter der begrabenen Palàobôden variiert von 900 bis > 40,000 Jahren v.u.Z. Dièse Bôden haben sich in glazialen und periglazialen Ablagerungen verschiedener Beschaffenheit entwickelt, welche zu einem hohen Prozentsatz aus Trùmmern von Phonolith, Basait und Syenit bestehen. AuBer zweien befinden sich aile Palàobôden in der afroalpinen Zone (oberhalb 3200 m). Die D/L Anteile der Aminosâuren in den Ab-Horizonten wurden bestimmt, um ihre Verlâpiichkeit bei der relativen Altersbestimmung festzustellen. Alamin, aspartische Sàure, Glutamin-Sàure, Leuzin, Valin und Phenylalanin wurden laufend analysiert. Wie in anderen Fallen erwies sich die aspartische Sàure als verlàpiich, indem sie bemerkenswert bestàndige Ergebnisse ergab, bei denen die hôheren Quotienten dem hôheren Alter entsprachen. Andere analysierte Sàuren zeigten ausgepràgte Trends, wenn auch nicht so ùberzeugend wie die aspartische Sàure. In den meisten Fallen wurden die Beziehungen Quotient/Alter der aspartischen Sàure durch Radiokarbondatierungen gestùtzt. Die D/L Anteile der aspartischen Sàure variierten von ungefâhr 0.07 fur moderne Proben bis ungefâhr 0.45 in Proben, die > 40,000 Jahre ait sind

The quantitative trait linkage disequilibrium test: a more powerful alternative to the quantitative transmission disequilibrium test for use in the absence of population stratification

Linkage analysis based on identity-by-descent allele-sharing can be used to identify a chromosomal region harboring a quantitative trait locus (QTL), but lacks the resolution required for gene identification. Consequently, linkage disequilibrium (association) analysis is often employed for fine-mapping. Variance-components based combined linkage and association analysis for quantitative traits in sib pairs, in which association is modeled as a mean effect and linkage is modeled in the covariance structure has been extended to general pedigrees (quantitative transmission disequilibrium test, QTDT). The QTDT approach accommodates data not only from parents and siblings, but also from all available relatives. QTDT is also robust to population stratification. However, when population stratification is absent, it is possible to utilize even more information, namely the additional information contained in the founder genotypes. In this paper, we introduce a simple modification of the allelic transmission scoring method used in the QTDT that results in a more powerful test of linkage disequilibrium, but is only applicable in the absence of population stratification. This test, the quantitative trait linkage disequilibrium (QTLD) test, has been incorporated into a new procedure in the statistical genetics computer package SOLAR. We apply this procedure in a linkage/association analysis of an electrophysiological measurement previously shown to be related to alcoholism. We also demonstrate by simulation the increase in power obtained with the QTLD test, relative to the QTDT, when a true association exists between a marker and a QTL

Gene-by-Environment Expression and Calculation of the Frailty Index

Background: Frailty can be described as a phenotype (e.g., sarcopenia, reduced grip strength, decreased VO2 max) or as a ratio of deficits, i.e., a Frailty Index (FI). FI predicts survival, death, cognitive impairment, falls, and hospitalizations. Frailty is influenced by both genes and environment. We calculated the FI as the sum of measured deficits divided by the total number of items assessed in a pedigree-based sample of 1,029 Mexican Americans participants in the San Antonio Family Heart Study. We performed a novel search for genotype-by-environment interactions (GXE) influencing FI. Such interactions lead to heritable differences between individuals in their responses to the environment. Methods: We investigated a panel of 34 measured environmental factors to look for GXE influencing frailty. We employed a powerful polygenic approach to genotype-by-environment modeling, allowing for both dichotomous and continuous environmental measures. We performed likelihood-based estimation of parameters and tests for the presence of GXE. Results: GXE interactions influencing frailty were observed for the following environments: obesity (P=7.9E-10), hypertriglyceridemia (P=2.74E-09), low HDL (P=2.15E-06), impaired glucose status (P=.002), hypertension (P=0.01), and diabetes (P=0.02), Additionally, GXE interactions were detected for a number of quantitative dietary components: carbohydrates (P=5.73E-07), fats (P=2.01E-06), fiber (P=2.76E-05), dietary cholesterol (P=0.01), and protein ( P=0.006). These results document substantial statistical evidence for the interactive effects of genes and environmental factors on frailty. Conclusion: Our results support the presence of substantive gene-by-environmental interactions influencing frailty. This finding documents the presence of heritable differences between individuals that lead to differential response to environmental challenges

A comparison of univariate, bivariate, and trivariate whole-genome linkage screens of genetically correlated electrophysiological endophenotypes

We used a maximum-likelihood based multipoint linkage approach implemented in SOLAR to examine simultaneously linkage for three electrophysiological endophenotypes from the Collaborative Study of the Genetics of Alcoholism: TTTH1, TTTH2, and TTTH3. These endophenotypes have been identified as markers of alcohol dependence susceptibility. Data were from 905 individuals in 143 families. Measured covariates considered included sex, age at electrophysiology data collection, habitual smoking status, and the maximum number of drinks consumed in a 24-hour period. Comparisons were made among genome-wide univariate, bivariate, and trivariate linkage analyses using genotypes based on microsatellite markers supplied by the Center for Inherited Disease Research, and genotypes based on single-nucleotide polymorphism markers provided by Illumina. All LODs were corrected to a standard equivalent to 1 degree of freedom. Using the trivariate approach and the microsatellite-based genotypes, we estimated a maximum multipoint linkage signal of LOD = 2.66 on chromosome 7q at 157 cM. Analyses using the Illumina SNP genotypes produced similar results, yielding a maximum multipoint LOD of 2.95 on 7q at 174 cM. These regions of interest correspond to those identified in the univariate and bivariate linkage screens. Our results suggest that trivariate multipoint linkage analyses have utility in the further characterization of chromosomal regions potentially containing genes influencing the phenotypes being examined. Based on a comparison of the number of LOD scores achieving statistical significance, our results suggest that the microsatellite- and Illumina SNP-based genotypes have similar utility for detecting genomic regions of interest

X chromosome effects and their interactions with mitochondrial effects

We report a simple and rapid method for detecting additive genetic variance due to X-linked loci in the absence of marker data for this chromosome. We examined the interaction of this method with an established method for detecting mitochondrial linkage (another source of sex-asymmetric genetic covariance). When applied to data from the Collaborative Study on the Genetics of Alcoholism, this method found evidence of X-chromosomal linkage for one continuous trait (ntth1) and one discrete trait (SPENT). Evidence of mitochondrial contribution was found for one discrete trait (CRAVING) and three continuous traits (ln(CIGPKYR), ecb21, and tth1). Results for ntth1 suggest that methods that do not also allow for male-female heterogeneity in environmental variance may be overly conservative in detection of X-chromosomal effects

Mitochondrial genetic effects on latent class variables associated with susceptibility to alcoholism

We report the results of statistical genetic analyses of data from the Collaborative Study on the Genetics of Alcoholism prepared for the Genetic Analysis Workshop 14 to detect and characterize maternally inherited mitochondrial genetic effects on variation in latent class psychiatric/behavioral variables employed in the diagnosis of alcoholism. Using published extensions to variance decomposition methods for statistical genetic analysis of continuous and discrete traits we: 1) estimated the proportion of the variance in each trait due to the effects of mitochondrial DNA (mtDNA), 2) tested for pleiotropy, both mitochondrial genetic and residual additive genetic, between trait pairs, and 3) evaluated whether the simultaneous estimation of mitochondrial genetic effects on these traits improves our ability to detect and localize quantitative trait loci (QTL) in the nuclear genome. After correction for multiple testing, we find significant (p < 0.009) mitochondrial genetic contributions to the variance for two latent class variables. Although we do detect significant residual additive genetic correlations between the two traits, there is no evidence of a residual mitochondrial genetic correlation between them. Evidence for autosomal QTL for these traits is improved when linkage screens are conditioned on significant mitochondrial genetic effects. We conclude that mitochondrial genes may contribute to variation in some latent class psychiatric/behavioral variables associated with alcoholism

Diet-induced leukocyte telomere shortening in a baboon model for early stage atherosclerosis

Reported associations between leukocyte telomere length (LTL) attrition, diet and cardiovascular disease (CVD) are inconsistent. This study explores effects of prolonged exposure to a high cholesterol high fat (HCHF) diet on LTL in a baboon model of atherosclerosis. We measured LTL by qPCR in pedigreed baboons fed a chow (n = 105) or HCHF (n = 106) diet for 2 years, tested for effects of diet on LTL, and association between CVD risk factors and atherosclerotic lesions with LTL. Though not different at baseline, after 2 years median LTL is shorter in HCHF fed baboons (P \u3c 0.0001). Diet predicts sex- and age-adjusted LTL and LTL attrition (P = 0.0009 and 0.0156, respectively). Serum concentrations of CVD biomarkers are associated with LTL at the 2-year endpoint and LTL accounts approximately 6% of the variance in aortic lesions (P = 0.04). Although heritable at baseline (h2 = 0.27, P = 0.027) and after 2 years (h2 = 0.46, P = 0.0038), baseline LTL does not predict lesion extent after 2 years. Atherogenic diet influences LTL, and LTL is a potential biomarker for early atherosclerosis. Prolonged exposure to an atherogenic diet decreases LTL and increases LTL attrition, and shortened LTL is associated with early-stage atherosclerosis in pedigreed baboons

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%