Patterns of DNA Methylation Across the Leptin Core Promoter in Four Diverse Asian and North American Populations.

DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process. Here we examine methylation patterns along a region of the metabolic gene leptin (LEP). LEP's putative functions include regulation of energy homeostasis, with its signals affecting energy intake and expenditure, adipogenesis and energy storage, lipid and glucose metabolism, bone metabolism, and reproductive endocrine function. A pattern of differential methylation across CpG sites of the LEP core promoter has been previously identified; however, any consistency of pattern or its phenotypic significance is not fully elucidated among populations. Using DNA extracted from unfractionated white blood cells of peripheral blood samples, our pilot study, divided into two parts, examined the significance of variation in DNA methylation patterns along the leptin core promoter in four populations (phase 1) and used biomarkers reflecting leptin's functional process in two of those populations, western Buryat of Siberia and the Mennonite of central Kansas, to investigate the relevance of the ethnic variation identified in the DNA methylation (phase 2). LEP's core promoter region contains both the binding site for C/EBPα (CCAAT/enhancer binding protein alpha), which tempers the final step in adipocyte maturity and capacity to synthesize leptin, and the TATA motif controlling leptin synthesis. Previous studies report that increased methylation in this region is correlated to decreased gene expression, suggesting tissue-specific methylation variation at this region ( Melzner et al. 2002 ). We hypothesized that evidence of nutritional epigenetic programming would be identified through variation in patterns of DNA methylation and that functional relevance of that variation among populations would be identified through biomarkers that reflect leptin's metabolic signals: serum leptin levels, lipoproteins of the lipid transport system, and anthropometric measures. In phase 1, our combined analyses of 313 individuals documented a distinct and consistent overall pattern of differential DNA methylation across seven CpG sites of LEP core promoter in all ethnicities and both sexes. This pattern replicates those identified in previous studies, suggesting a conserved core promoter region across populations. Phase 2 analyses of two of the four populations (n = 239), correlating methylation at the C/EBPα transcription binding site (TBS) with metabolic and anthropometric biomarkers reflecting LEP roles, showed that stature, which reflects bone growth and remodeling, was significantly and inversely correlated with the percentage of DNA methylation at this site in both sexes. We suggest that variation in DNA methylation along the LEP core promoter plays a substantial role in energy signals affecting both adipogenesis and bone metabolism.

Quantitative and depth-resolved deep level defect distributions in InGaN/GaN light emitting diodes.

Deep level defects in the multi-quantum well (MQW) region of InGaN/GaN light emitting diodes (LEDs) were investigated. InGaN quantum well and GaN quantum barrier defect states were distinguished using bias-dependent steady-state photocapacitance and deep level optical spectroscopy, and their possible physical origin and potential impact on LED performance is considered. Lighted capacitance-voltage measurements provided quantitative and nanoscale depth profiling of the deep level concentration within the MQW region. The concentration of every observed deep level varied strongly with depth in the MQW region, which indicates evolving mechanisms for defect incorporation during MQW growth.

Quantitative and depth-resolved deep level defect distributions in InGaN/GaN light emitting diodes.

Deep level defects in the multi-quantum well (MQW) region of InGaN/GaN light emitting diodes (LEDs) were investigated. InGaN quantum well and GaN quantum barrier defect states were distinguished using bias-dependent steady-state photocapacitance and deep level optical spectroscopy, and their possible physical origin and potential impact on LED performance is considered. Lighted capacitance-voltage measurements provided quantitative and nanoscale depth profiling of the deep level concentration within the MQW region. The concentration of every observed deep level varied strongly with depth in the MQW region, which indicates evolving mechanisms for defect incorporation during MQW growth.

Mitochondrial DNA diversity in Mennonite communities from the midwestern United States.

We examined mitochondrial DNA (mtDNA) variation in six Mennonite communities from Kansas (Goessel, Lone Tree, Garden View, Meridian, and Garden City) and Nebraska (Henderson) to determine their genetic structure and its relationship to population history. Mitochondrial DNA haplogroup and haplotype information were obtained from blood samples from 118 individuals. Molecular genetic variation was analyzed using diversity measures, neutrality test statistics, spatial analysis of molecular variance (SAMOVA), and multidimensional scaling plots. The Mennonite samples exhibited eight western European mtDNA haplogroups: H, HV0, I, J, K, T, U, and X. Comparable to other populations of European descent, haplogroup H was the most frequent in all six communities and ranged from 35% in Lone Tree to 75% in Old Order Mennonites from Garden City. Fifty-eight different mtDNA haplotypes were found in these groups with only one shared among all six populations. Haplotype diversities varied from 0.81 in Goessel to 0.96 in Henderson and Garden View. Multivariate statistical analysis of these populations indicates that these Anabaptist communities formed new congregations by fissioning along familial lines. Population subdivision of these communities into congregations supports previously documented patterns of fission-fusion. These haploid molecular data provide a more accurate reflection of biological relationships between midwestern Mennonite communities than evidence based on classical genetic markers.

Anthropometric variation among Bering Sea natives.

Recent research indicates that anthropometrics can be used to study microevolutionary forces acting on humans. We examine the use of morphological traits in reconstructing the population history of Aleuts and Eskimos of the Bering Sea. From 1979 to 1981, W. S. Laughlin measured a sample of St. Lawrence Island Eskimos and Pribilof Island Aleuts. These samples included adult participants from St. George and St. Paul in the Pribilof Islands and from Gambell and Savoonga on St. Lawrence Island. The Relethford-Blangero method was used to examine the phylogenetic relationship between Aleuts and Eskimos. Anthropometric measurements for Native North Americans (measured by Boas and a team of trained anthropometrists in 1890-1904) and Native Mesoamericans (compiled from the literature for 1898-1952) were used for comparison. A principal components analysis of means for measurements and a neighbor-joining tree were constructed using Euclidean distances. All these tests revealed the same strong relationship among the focus populations. The R matrix from the Relethford-Blangero method clusters Aleuts and Eskimos separately and accounts for 97.3% of the variation in the data. Phenotypic variation within the population is minimal and therefore minimum F(ST) values are low. Genetic distances were compared to a Euclidean distance matrix of anthropometric measurements using a Mantel test and gave a high but not significant correlation. Our results provide evidence of a close phylogenetic relationship between Aleut and Eskimo populations in the Bering Sea. However, it is apparent that history has affected the relationship among the populations. Despite previous findings of higher European admixture in Gambell (based on blood group markers) than in Savoonga, Savoonga has greater within-group variation in anthropometric measurements. Anthropometrics reveal a close relationship between Gambell and St. Paul as a result of European admixture. The St. George population was the most divergent of the populations, indicating that it diverged from the Eskimos and St. Paul because of the compounding effects of genetic drift and limited European gene flow. These findings are in agreement with previous anthropometric and genetic studies of the Aleut and Eskimo populations and support the utility of anthropometrics in inferring population history and structure.

Unangan past and present: the contrasts between observed and inferred histories.

Academic research focusing on the population and culture history of the Aleut (Unangan) people began in the late 19th century and continues to the present. The papers in this special issue of Human Biology summarize the latest results from archaeological, linguistic, genetic, and morphometric research approaches that bear on our current understanding of Unangan history and prehistory. Although these new analyses have provided a level of description and resolution previously unattainable, explanatory models and mechanisms for the patterned variation observed over time in the biological and cultural record of the Aleutian region remains elusive. Bringing the diverse data sets into concordance to represent an integrated synthesis of Aleut population and culture history and of Unangan origins and their relationships with other groups in the region remains a goal for future investigators.

Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA.

We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.

A private allele ubiquitous in the Americas.

The three-wave migration hypothesis of Greenberg et al. has permeated the genetic literature on the peopling of the Americas. Greenberg et al. proposed that Na-Dene, Aleut-Eskimo and Amerind are language phyla which represent separate migrations from Asia to the Americas. We show that a unique allele at autosomal microsatellite locus D9S1120 is present in all sampled North and South American populations, including the Na-Dene and Aleut-Eskimo, and in related Western Beringian groups, at an average frequency of 31.7%. This allele was not observed in any sampled putative Asian source populations or in other worldwide populations. Neither selection nor admixture explains the distribution of this regionally specific marker. The simplest explanation for the ubiquity of this allele across the Americas is that the same founding population contributed a large fraction of ancestry to all modern Native American populations.

Biological aging and Cox hazard analysis of mortality trends in a Mennonite community from south-central Kansas.

This study investigated mortality in 568 individuals from the Goessel Mennonite community in rural central Kansas. There were three main objectives to this research: 1) characterize mortality trends within a biologically well-defined Mennonite community; 2) determine what biochemical, morphological, and physiological risk factors could be related to all-cause mortality, stratified by age and sex; and 3) compare these results to previously described variables that were associated with both biological age and mortality in this population. Mortality data were obtained from three sources: Kansas Vital Records, the Social Security death index, and church records. In total, 221 (39%) individuals were found to have died in this population between January 1980-June 2002. Analogous to the larger US population, the three leading causes of death in this community were heart disease, cancer, and stroke, accounting for 60% of all deaths. Besides advancing age, the greatest biological risk factor in this population was decreased amounts of albumin in men (relative risk, 2.47), potentially indicating underreported cases of either chronic kidney disease or frailty syndrome for males. Cox proportional hazard models demonstrated that increased amounts of total cholesterol may provide a protective effect for elderly individuals. We conclude, based on the previously described heritability of both albumin (h(2) = 0.40) and total cholesterol (h(2) = 0.50) in this population, that underlying genetic factors associated with both chronic degenerative diseases and biological aging may have important implications for understanding mortality patterns in this community.

Autosomal STR variation in a Basque population: Vizcaya Province.

We have characterized 68 unrelated Basque individuals from Vizcaya, Spain, for 13 tetrameric short tandem repeat (STR) loci: CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and VWA. Interpopulational analyses were also performed for 21 European and North African population data sets for nine of the STRs typed in the Basque sample. Heterozygosity values for the Vizcayan Basques were found to be high, ranging from 0.662 to 0.882, and none of the STR loci significantly deviated from Hardy-Weinberg equilibrium. Based on the comparative population data set, the average G(ST) score is 0.7%, indicating a low degree of genetic differentiation. However, neighbor-joining trees and multidimensional-scaling plots of D(A) genetic distances indicate that the Vizcayan Basques are an outlier relative to both neighboring Iberians and North African populations.

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

Mid-ultraviolet light-emitting diode detects dipicolinic acid.

Dipicolinic acid (DPA, 2,6-pyridinedicarboxylic acid) is a substance uniquely present in bacterial spores such as that from anthrax (B. anthracis). It is known that DPA can be detected by the long-lived fluorescence of its terbium chelate; the best limit of detection (LOD) reported thus far using a large benchtop gated fluorescence instrument using a pulsed Xe lamp is 2 nM. We use a novel AlGaN light-emitting diode (LED) fabricated on a sapphire substrate that has peak emission at 291 nm. Although the overlap of the emission band of this LED with the absorption band of Tb-DPA (lambda(max) doublet: 273, 279 nm) is not ideal, we demonstrate that a compact detector based on this LED and an off-the-shelf gated photodetection module can provide an LOD of 0.4 nM, thus providing a basis for convenient early warning detectors.

Genetic variation among the Golla pastoral caste subdivisions of Andhra Pradesh, India, according to the HLA system.

The HLA allele frequency distributions have been characterized for the HLA class I and class II loci of the Golla pastoral caste, from Southeast India, subdivided into the subcastes (Puja, Punugu, Kurava, Pokanati, Karnam, and Doddi). Genetic distances, neighbor-joining, correspondence, and haplotype analyses all indicate that the subcastes exhibit a high haplotype variability and that their genetic substratum may be the result of European-Middle East/Asian admixture with the autochthonous populations. The Karnam subcaste seems to be the one that has undergone a higher degree of admixture, when compared with the other subcastes. The Golla speak an old Indian Dravidian language and should theoretically represent the basic Indian substratum that existed before the postulated "Aryan" invasion.

Genomic diversity at thirteen short tandem repeat loci in a substructured caste population, Golla, of southern Andhra Pradesh, India.

Genomic diversity based on 13 short tandem repeat (STR) loci was studied in seven population groups of a substructured Golla caste from Chittoor district in southern Andhra Pradesh, India. These groups are traditionally pastoral, culturally homogeneous, and strictly endogamous. Blood samples were drawn from 317 individuals from 30 Golla villages. The 13 STR loci analyzed in five standard multiplex polymerase chain reactions were: (1) CSF1R, TH01, and PLA2A; (2) F13A1, CYP19, and LPL; (3) D21S1446 and D21S1435; (4) D20S481, D20S473, and D20S604; and (5) D5S1453 and D6S1006. The average heterozygosity was found to be low among the Golla subgroups (0.64-0.70) in comparison to that of groups at the upper levels of the hierarchy. The coefficient of gene differentiation was found to be moderate (average GST = 0.031; range between 0.018 and 0.049 among the loci) when compared to that observed for a similar class of markers among populations with relatively higher levels of hierarchy, for example, among castes. It is, however, much higher when compared to the average observed for Indian caste and tribal populations, based on classical markers. Genetic distance measures revealed clusters of populations that are consistent with the known ethnohistorical and geographical backgrounds of the groups. We claim that these hypervariable markers are quite useful in understanding the process of substructuring within the Indian castes, leading to the formation of smaller breeding isolates, the basic Mendelian units within which microevolutionary forces operate.

Population substructure and patterns of quantitative variation among the Gollas of southern Andhra Pradesh, India.

Population substructure and biological differentiation was studied among the Golla, a pastoral caste living in the southern areas of Andhra Pradesh (AP) in India, using 11 anthropometric measurements and 20 quantitative dermatoglyphic variables. The data were collected from a sample of 334 adult males drawn from 30 villages distributed in the Chittoor district of AP, who belonged to 8 endogamous subunits of the same caste. Multiple discriminant analysis of the anthropometrics suggests a highly significant degree of discrimination that is consistent with the microgeographic variations of the groups. In contrast, in different sets of dermatoglyphs discrimination is low and generally inconsistent with both the geographic and ethnohistorical affiliations of the groups. These findings are reflected in the F(ST) value for anthropometry, which is more than double the value of dermatoglyphs. The patterns of gene flow as inferred through the regression of phenotypic variance on the distance of groups from the centroid is not generally consistent with the known backgrounds in the case of either dermatoglyphs or anthropometry. It is concluded that at the level of caste substructure representing the lowest level of population hierarchy, the quantitative variables examined here may not portray a complete picture of the historical process of subdivision. The results of this study are not in congruence with those based on another study of 13 short tandem repeat loci on the same set of populations (Reddy et al. 2001), which may provide better insights into the population structure and history of subdivision that are consistent with the known ethnohistorical backgrounds of the populations.

Prevalence of heart disease in asymptomatic chronic cocaine users.

To determine the prevalence of heart disease in outpatient young asymptomatic chronic cocaine users, 35 cocaine users and 32 age-matched controls underwent resting and exercise electrocardiography (ECG) and Doppler echocardiography. Findings consistent with coronary artery disease were detected in 12 (34%) patients and 3 (9%) controls (p = 0.01). Decreased left ventricular systolic function was demonstrated in 5 (14%) patients, but in none of the controls (p = 0.055). Finally, resting and peak exercise abnormal left ventricular filling was detected in 38 and 35% of patients as compared to 19 and 9% of controls, respectively (p = 0.11 and 0.02, respectively). We conclude that coronary artery or myocardial disease is common (38%) in young asymptomatic chronic cocaine users. Therefore, screening ECG and echocardiography may be warranted in these patients.

Heart failure disease management in an indigent population.

BACKGROUND: Multidisciplinary disease management programs (MDMP) have demonstrated reduced hospitalizations in motivated pretransplant heart failure populations, but little is known about their effectiveness in largely indigent patients who are not transplant candidates. METHODS AND RESULTS: We studied 35 patients with heart failure with left ventricular ejection fraction (EF) /=2 per year (group A) and 21 patients referred by their primary care physicians because they were difficult to manage (group B). Group A patients were New York Heart Association (NYHA) class III or IV, aged 25 to 87 years (mean 57 +/- 17 SD) and had an EF of 15% to 45% (29% +/- 11%). Group B patients were NYHA class II or III, aged 35 to 86 (57 +/- 16) years and had an EF of 20% to 45% (28% +/- 10%). Data were compared for the year before enrollment in the MDMP and the year afterward. In group A hospital admissions decreased from 33 to 3, a 91% reduction, and NYHA class improved to class II-III (P <.001). In group B hospital admissions decreased from 9 to 0, and NYHA class improved to class I-II (P <.001). When hospital and clinic charges were assessed for both groups, the net savings were $162,000 per year or $4600 per patient. CONCLUSIONS: A multidisciplinary heart failure program can improve functional status and reduce hospitalization and net costs compared with conventional care in indigent non-transplant candidate patients.

Genetic structure of Mongolic-speaking Kalmyks.

Genetic polymorphisms of blood groups ABO and RH D, serum proteins HP, TF, and GC, and red cell enzymes ACP1, PGM1, ESD, GLO1, and SOD-A have been reported for three tribes (Torguts, Derbets, and Buzavs) of the Volga's Kalmyk-Oyrats. The Kalmyks exhibit genetic markers that are characteristic of Central Asian populations, namely, high allelic frequencies for ABO*B, TF*C2, GC*IF, ESD*2, and GLO1*2, and the rare incidence of individuals with the RH-negative phenotype. Genetic distance measures reveal that close genetic affinities exist between the Derbets and Buzavs, but both populations differ significantly from the Torguts. Collectively as an ethnic group, the Kalmyks genetically resemble the contemporary Buryats of the Baikal region of southeastern Siberia and the Mongols of Mongolia. The transplantation of the Kalmyk-Oyrats from their homeland near Lake Baikal to their current residence (4500 km) near the Caspian Sea and their subsequent isolation for more than 300 years have not appreciably altered the gene frequencies from the parental populations for frequencies of standard genetic markers.