Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populations

The dopamine D2 receptor (DRD2) gene, with its known human‐specific derived alleles that can facilitate haplotype reconstruction, presents an important locus for anthropological studies. The three sites (TaqIA, TaqIB, and TaqID) of the DRD2 gene are widely studied in various world populations. However, no work has been previously published on DRD2 gene polymorphisms among North Indian populations. Thus, the present study attempts to understand the genetic structure of North Indian upper caste populations using the allele and haplotype frequencies and distribution patterns of the three TaqI sites of the DRD2 gene. Two hundred forty‐six blood samples were collected from five upper caste populations of Himachal Pradesh (Brahmin, Rajput and Jat) and Delhi (Aggarwal and Sindhi), and analysis was performed using standard protocols. All three sites were found to be polymorphic in all five of the studied populations. Uniform allele frequency distribution patterns, low heterozygosity values, the sharing of five common haplotypes, and the absence of two of the eight possible haplotypes observed in this study suggest a genetic proximity among the selected populations. The results also indicate a major genetic contribution from Eurasia to North Indian upper castes, apart from the common genetic unity of Indian populations. The study also demonstrates a greater genetic inflow among North Indian caste populations than is observed among South Indian caste and tribal populations. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Effects of volcanic ash on the forest canopy insects of Montserrat, West Indies

The impact of ash deposition levels on canopy arthropods was studied on the West Indian island of Montserrat, the site of an ongoing volcanic eruption since 1995. Many of the island's natural habitats have been buried by volcanic debris, and remaining forests regularly receive volcanic ash deposition. To test the effect of ash on canopy arthropods, four study sites were sampled over a 15-mo period. Arthropod samples were obtained using canopy fogging, and ash samples were taken from leaf surfaces. Volcanic ash has had a significant negative impact on canopy arthropod populations, but the decline is not shared equally by all taxa present, and total population variation is within the variance attributed to other aboitic and biotic factors. The affected populations do not differ greatly from those of the neighboring island of St. Kitts, which has not been subject to recent volcanic activity. This indicates that observed effects on Montserrat's arthropod fauna have a short-term acute response to recent ash deposition rather than a chronic depression caused by repeated exposure to ash over the last decade.     

Genetic population structure of Indian oil sardine, <Emphasis Type="Italic">Sardinella longiceps</Emphasis> assessed using microsatellite markers

Indian oil sardines, commercially and ecologically important pelagic fishes in Indian waters have not been the focus of major genetic studies as compared to their counter parts in Atlantic and Pacific oceans in spite of several reports suggesting stock complexity and intraspecific diversity. Hence, we investigated the genetic stock structure of Indian oil sardine, Sardinella longiceps using microsatellite markers by collecting a total of 768 individuals from eight locations along the Indian coast and one from Gulf of Oman over a 2 year period (2013–2015). Six polymorphic microsatellite markers revealed significant genetic differentiation between populations with the highest F_ST value (0.055) between Oman and Indian coastline. Within the Indian coastline another major subdivision between Mumbai & Mangalore vs. other regions was detected (F_ST value 0.047) which was also confirmed in Barrier analysis with the presence of two strong barriers between these eco-regions. There exist pronounced differences in oceanographic and environmental features between Gulf of Oman, Western Indian Ocean and Eastern Indian Ocean (Bay of Bengal) which may act as barriers for effective dispersal and gene flow resulting in genetic differentiation. Even though, the samples collected from Calicut, Kollam, Trivandrum, Chennai and Vizag showed the presence of admixed genotypes, the possible presence of distinct populations in some regions was evident in Bayesian analysis which needs to be confirmed further using more widespread sampling design and powerful markers. The present study provided insights into the biocomplexity and intra-specific diversity of Indian oil sardine populations, which needs to be preserved for maintaining resilience of these important fishes to climate change and habitat alterations in the Indian Ocean.     

Alaskan marine mammal tissue archival project

A project to establish an archive of Alaskan marine mammal tissues was conceived in 1987 to be a part of the National Biomonitoring Specimen Bank (NBSB). Protocols and field collection of marine mammals, long-term storage, and analysis are summarized in this paper. Instrumental neutron activation analysis has been used for an initial evaluation of trace element content in samples of northern fur seal (Callorhinus ursinus) from the Pribilof Islands. The findings agree with previously observed trace element levels in northern fur seals. The archived specimens can be used in future studies when comparisons of past and present pollution levels are needed.

     

Population and genomic lessons from genetic analysis of two Indian populations

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.     

First report of Perkinsus beihaiensis in Crassostrea madrasensis from the Indian subcontinent

Protozoan parasites of the genus Perkinsus are considered important pathogens responsible for mass mortalities in many wild and farmed bivalve populations. The present study was initiated to screen populations of the Indian edible oyster Crassostrea madrasensis, a promising candidate for aquaculture along the Indian coasts, for the presence of Perkinsus spp. The study reports the presence of P. beihaiensis for the first time in C. madrasensis populations from the Indian subcontinent and south Asia. Samples collected from the east and west coasts of India were subjected to Ray's fluid thioglycollate medium (RFTM) culture and histology which indicated the presence of Perkinsus spp. PCR screening of the tissues using specific primers amplified the product specific to the genus Perkinsus. The taxonomic affinities of the parasites were determined by sequencing both internal transcribed spacer (ITS) and actin genes followed by basic local alignment search tool (BLAST) analysis. Analysis based on the ITS sequences showed 98 to 100% identity to Perkinsus spp. (P. beihaiensis and Brazilian Perkinsus sp.). The pairwise genetic distance values and phylogenetic analysis confirmed that 2 of the present samples belonged to the P. beihaiensis clade while the other 4 showed close affinities with the Brazilian Perkinsus sp. clade. The genetic divergence data, close affinity with the Brazilian Perkinsus sp., and co-existence with P. beihaiensis in the same host species in the same habitat show that the remaining 4 samples exhibit some degree of variation from P. beihaiensis. As expected, the sequencing of actin genes did not show any divergence among the samples studied. They probably could be intraspecific variants of P. beihaiensis having a separate lineage in the process of evolution.     

High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from central Asia and West Asia into India

Linguistic evidence suggests that West Asia and Central Asia have been the two major geographical sources of genes in the contemporary Indian gene pool. To test the nature and extent of similarities in the gene pools of these regions we have collected DNA samples from four ethnic populations of northern India, and have screened these samples for a set of 18 Y-chromosome polymorphic markers (12 unique event polymorphisms and six short tandem repeats). These data from Indian populations have been analysed in conjunction with published data from several West Asian and Central Asian populations. Our analyses have revealed traces of population movement from Central Asia and West Asia into India. Two haplogroups, HG-3 and HG-9, which are known to have arisen in the Central Asian region, are found in reasonably high frequencies (41.7% and 14.3% respectively) in the study populations. The ages estimated for these two haplogroups are less in the Indian populations than those estimated from data on Middle Eastern populations. A neighbour-joining tree based on Y-haplogroup frequencies shows that the North Indians are genetically placed between the West Asian and Central Asian populations. This is consistent with gene flow from West Asia and Central Asia into India.     

Influence of ethnic background on left atrial markers of inflammation,endothelial function and tissue remodelling

Background

It has been suggested that ethnicity can make a significant difference to the likelihood of thromboembolic stroke related to atrial fibrillation. Ethnic differences have been shown to alter inflammatory and haemostatic factors; however, this may all be confounded by differences in cardiovascular risk factors between different ethnicity. The impact of different ethnicities on the thrombogenic profile is not known. The aim of this study was to investigate differences in markers of inflammation, endothelial function and tissue remodelling between Caucasian and Indian populations with supraventricular tachycardia (SVT).

A comparison of trace-elemental composition of natural color and gray hair

In order to get some information on the possible causes of graying of hair, we have used the technique of X-ray fluorescence (XRF) analysis for comparing the trace element contents of natural color and gray hair from a number of subjects. The technique of XRF was preferred to other analytical methods for this kind of comparative studies since it appeared to be simple, convenient, quick, and contamination free. Natural color and gray hair from each subject were obtained from the same scalp region. The hair samples were washed in the recommended fashion. The natural color and gray hair from different subjects were mounted separately on hollow plastic cylindrical sample holders, assuring that the hair were parallel to, and not on top of one another. The samples were analyzed in a commercial wave length dispersive XRF system, with different X-ray tubes being used for obtaining maximum sensitivity for different elements. The scattered X-ray peak from each sample was also monitored and gave a measure of the sample volume being investigated. So far, hair samples from 10 subjects have been analyzed. Their results are presented in the paper, and advantages of XRF, for trace element analysis on hair are discussed.     

Trace and non-trace elements in blood cells of bottlenose dolphins (Tursiops truncatus): variations with values from liver function indicators

Alterations in trace and non-trace element homeostasis have been associated with both normal physiologic and pathologic processes of many species. Changes in copper and zinc, for instance, have been associated with liver disease in humans and dogs. While liver disease has been documented in marine mammals, associations of liver disease with trace and non-trace elements have not been determined. The goal of this study was to assess potential elemental associations with clinically relevant changes in liver enzymes of bottlenose dolphins (Tursiops truncatus) and to compare observed associations to what has been reported in other species. Blood cell samples were collected from 37 healthy bottlenose dolphins, maintained by the Navy Marine Mammal Program (MMP), between 1991 and 1992. Twenty-one trace and non-trace elements were assessed along with a standard liver enzyme function profile, and trace element associations to specific liver enzymes were determined. In this study, of the 21 blood cell elements assessed, 19 were measured within detectable limits in at least one of the blood samples, and 10 trace elements were found to be associated with at least one of the liver function indicators. Many of these same associations have been documented in various forms of liver disease in other species, including the associations of increases in copper and decreases in zinc with both elevated alanine aminotransferase (ALT) and gamma-glutamyl transferase (GGT). The observed analogous associations between changes in blood trace and non-trace elements and liver function indicators of bottlenose dolphins and other species may indicate similar pathologic processes and functions of some elements. Given the results of this study, additional research is warranted to further elucidate associations of trace and non-trace elements to liver disease in bottlenose dolphins.     

Osteoporosis, bone mineralization, and status of selected trace elements in two populations of moose calves in Norway

This study was conducted to clarify the etiology of a high frequency of bone fractures and osteoporosis in the moose (Alces alces) population in southern Norway. Liver samples, both metacarpi, and carcass data were collected from 21 and 22 moose calves shot in 1994 in Birkenes (southern Norway), and Naer?y (central Norway), respectively. The liver samples were analyzed for copper, manganese, zinc, cobalt, chromium, molybdenum, and selenium. Bone samples were subject to histologic, radiologic, and chemical examinations. Three of the calves from Birkenes and one calf from Naer?y showed histologic and radiologic evidence of generalized osteoporosis consistent with osteoporosis due to starvation. The calves with osteoporosis had the lowest carcass weights and radio-opacities recorded. There was a positive correlation between carcass weight and bone radio-opacity. Density, ash content, phosphorus, and calcium contents and phosphorous/calcium ratio in bone samples, as well as hepatic trace element status, were within the normal range for all calves in both populations. Two of the osteoporotic calves, were reported to have been orphaned. Our results indicate that the high frequency of bone fractures reported in moose in southern Norway is not associated with regional differences in trace element status or bone mineral balance. We propose that the occurrence of osteoporosis in moose calves in Birkenes may have resulted from inadequate nutrition following general overcrowding and high pressure on feed resources in the southernmost part of Norway.     

Microphthalmia (mi) mice display an aberrant bone trace element composition

It has been recognized that bone trace element composition analysis provides clues when analyzing bone-related physiological conditions. Increasing numbers of bone-related genetic diseases have been identified recently. In this study, we have analyzed bone trace element composition in a genetic mutant animal model. Mutations in the mouse microphthalmia (mi) gene affect the development of a number of cell types, including melanocytes, mast cells, and osteoclasts. Previous studies have shown that different alleles of the mi locus show osteopetrosis. In order to gain insights into the effects of a particular genetic defect on bone trace element composition and bone structure, we performed bone trace element composition analysis using inductively coupled plasma atomic emissions spectrometry (ICP-AES). Marked changes in bone trace element levels were found in vertebrate bones of mi mutant mice. The implications and possible applications of bone trace element analysis will be discussed in this article.     

The Correlation Between Smoking Status of Family Members and Concentrations of Toxic Trace Elements in the Hair of Children

Hair analysis is a promising tool for routine clinical screening and diagnosis of heavy metal exposure and essential trace element status in the human body. Systemic intoxications have been identified by anomalously high values of toxins in hair samples. The aim of the present study is to evaluate the relationship between smoking habit of the family members and the levels of toxic and nontoxic trace elements in hair samples of children. The randomized cross-sectional controlled study comprised of 95 children (41 girls and 54 boys) between the ages of 1 and 6 years. After written informed consent was obtained, a face-to-face interview was conducted with the families about educational background, total income of the family, and smoking habits of family members. The mineral elements considered in this study were Zn, Se, B, V, Co, Mo, Mn, iron (Fe), Be, aluminum (Al), As, cadmium (Cd), lead (Pb), Hg, chromium (Cr), Ag, Be, nickel (Ni), copper (Cu), Sn, and antimony (Sb). Hair mineral contents were measured by inductively coupled plasma-mass spectrometry. The results showed that the levels of Cd, Pb, Cr, Sb, Fe, and Al in hair samples of children whose parents smoked were significantly higher than those whose parents were nonsmokers. The number of smokers and the frequency of smoking at home were positively correlated with Pb, Cd, Cu, Ni, and Sb levels found. At the same time, it was found that there was no correlation between toxic element concentrations and family income or educational background excluding the levels of Cd. A correlation was observed between the smoking status of family members and levels of toxic trace elements in hair where this correlation was more significant with the levels of Pb and Cd. High socioeconomic status and the level of education of family members did not have any effect on toxic trace levels in hair samples of children.     

Leaching of Trace Elements from Biological Tissue by Formalin Fixation

In studies of trace elements in biological tissue, it is imperative that sample handling does not substantially change element concentrations. In many cases, fresh tissue is not available for study, but formalin-fixed tissue is. Formalin fixation has the potential to leach elements from the tissue, but few studies have been published in this area. The concentrations of 19 elements were determined by high-resolution inductively coupled plasma mass spectrometry in formalin in which human and rat brain samples had been stored for different time durations ranging from weeks up to several years. Additional analysis was carried out in fixed brain samples. There was substantial leaching of elements from the tissue into the formalin, and the leaching varied considerably between different elements. For example, formalin concentrations of As, Cd, Mg, Rb, and Sb increased more than 100-fold upon long-term (years) storage, while for Ni and Cr, the leaching was negligible. The degree of leaching was strongly time-dependent. In conclusion, formalin fixation and storage of biological tissue has the potential to leach substantial fractions of several trace elements from the tissue. The potential of leaching must be critically considered when using formalin-fixed biological tissue in trace metal analysis.     

Genetic diversity and admixture patterns in Indian populations

India is a diverse land whose population holds the history of waves of human dispersal. Recent studies suggest two major ancestral contributions to most of the Indian sub-populations. However, present day Indians are thought to contain huge genetic diversity derived consequent to multiple cultural, linguistic and geographical variations. Genome-wide survey of individuals from current North (N-In) and South (S-In) India along with populations from HapMap Phase III and Indian sub-populations from HUGO Pan-Asian SNP Consortium is performed. Multivariate analysis (MDS and PCA) was carried out after merging data from the current study and other consortia. Indian sub-populations clustered separately from populations of major global geographical regions in MDS and PCA in a loose agglomeration except for two Indian subpopulations clustering near far eastern populations. F_st values indicated diversity among Indian sub-populations which was substantiated by STRUCTURE analysis suggesting the possibility of additional admixture events.     

Aquaculture related invasion of the exotic <Emphasis Type="Italic">Artemia franciscana</Emphasis> and displacement of the autochthonous <Emphasis Type="Italic">Artemia</Emphasis> populations from the hypersaline habitats of India

Autochthonous parthenogentic Artemia populations have been reported from Indian hypersaline habitats since 1950s. Exotic Artemia franciscana was imported and introduced into India as live food for aquaculture since the early eighties. To assess the present status of the Artemia populations and the possibility of invasion by the introduced A. franciscana in Indian Salinas, an extensive study was conducted using conventional and molecular approaches. Morphological and biometric observations, crossbreeding experiments and molecular and phylogenetic analysis using Internally Transcribed Spacer-1 sequence revealed the extensive presence of alien, sexual A. franciscana populations in various hypersaline areas. Individual culture experiments and crossbreeding studies further confirmed the absence of autochthonous parthenogentic Artemia populations. Lack of regional endemism in populations of distant origins was evident, indicating that the invaded populations have naturalized and are in the process of evolution. This forms the first report of invasion by A. franciscana in hypersaline habitats of Indian subcontinent and further studies are required to assess the biological implications of this invasion.     

Identification of 2-phenylethanol with a rose-like odor from anal sac secretions of the small Indian mongoose (Herpestes auropunctatus)

The small Indian mongoose (Herpestes auropunctatus) is an invasive species in Okinawa and Amami-Oshima, Japan. Major strategies for their eradication have been the use of baited traps, which suffer from decreasing efficiency with declining populations and the bycatch of native animals. To address these concerns, mongoose-specific lures are required. In this study, we aimed to identify species- and/or sex-specific compounds from anal sac secretions of small Indian mongooses. Volatile compounds emitted from male and female mongoose anal sac secretions were analyzed by thermal desorption-gas chromatography-mass spectrometry. In addition to several fatty acids, 2-phenylethanol was identified as a minor compound, which is uncommon in mammalian secretions but a dominant odorant in roses. Female samples emitted higher levels of 2-phenylethanol than male samples did. These findings indicate that 2-phenylethanol is a female-specific volatile compound of anal sac secretions in small Indian mongooses, and it may be useful as an ingredient of mongoose-specific scent lures.     

Use of human teardrop fluid for the determination of trace elements in healthy individuals and diabetic patients

BackgroundThe use of unconventional biological materials in human trace element studies has increased in terms of published research studies. The aim of present study was to develop and validate the use of teardrop fluid for determining trace element levels in the human body. No study has been published in this area yet. This is a new non-invasive approach in the possible early diagnosis of the pathogenesis of type 2 diabetes.Materials and methodsHuman teardrop fluid samples were obtained from Karbala (Iraq) (n = 111) healthy individuals and with type 2 diabetes (n = 44); and London (UK) healthy individuals (n = 18). The levels of V, Cr, Mn, Fe, Cu, Zn, As, Sr and Cd were determined using an inductively coupled plasma mass equipped with collision cell technology for polyatomic ion correction (ICP-MS).Statistical analysisDiscriminate function analysis (DFA) was carried out to determine the set of variables that discriminated between the trace elements in teardrop fluid samples from healthy individuals and diabetic patients.ResultsThe trace element levels of human teardrop fluid are similar for many elements to that reported for human blood serum in the literature. This is interesting since they have different physiological functions, although overall they are mainly water containing electrolytes (∼ 90 %) and solids (antibodies, hormones, etc). In general, for the study groups in Karbala, Iraq, significantly higher teardrop fluid levels of Mn and Sr were found in type 2 diabetic patients when compared with healthy individuals (evaluated using an F-test and a two-tailed t-test). The levels of V, Cu and As were found to be significantly higher (P < 0.05) in healthy individuals than type 2 diabetic patients. Although the levels of Fe and Zn were slightly higher in type 2 diabetic patients than healthy cases, the differences were not statistically significant (P > 0.05). Cr and Cd were found to have similar levels for both study groups. Significantly higher teardrop fluid levels of V, Cr, Mn, Fe, Zn, As and Sr were found in healthy individuals from Karbala (Iraq) when compared with those from London (UK). In contrast, the levels of Cd observed to be significantly higher in London (UK) than Karbala. No statistical difference was found for Cu between the two healthy groups.Statistical analysisDiscriminate analysis showed that human teardrop fluid V, Mn, Zn, As, Sr and Cd levels could be used to discriminate between healthy and type 2 diabetes study groups in Karbala, Iraq (83 % of cases correctly classified).ConclusionThe use of human teardrop fluid for determining the trace element levels of human health conditions has been evaluated. Trace elemental levels are like that for blood serum which is widely used as an invasive method for assessing human health conditions. Sample collection for teardrop fluid is non-invasive and the application has potential for determining the trace element levels in healthy individuals and disorder conditions (like type 2 diabetes) in countries where cultural and gender sensitivity are issues with respect to the collection methods used for other body fluid samples.     

Trace-element analysis by charged-particle-induced reactions as a tool for physicians and chemists

The object of this article is to apprise physicians and chemists of nuclear analytical techniques and, in particular, of ion beam analysis (PIXE and PIGE) for the purpose of application to the clinical diagnostic method. The feasibility of the technique, sampling, and sample preparation for trace element analysis in biological and biomedical samples has been described previously (1–3). Analysis data from normal human blood samples and biomedical samples by ion beam reactions have been compared at the end. Emphasis will be placed on the use of the analytical technique on determination of the range of trace and toxic elements in human blood samples.     

Mitochondrial sequence-based evolutionary analysis of riverine–swamp hybrid buffaloes of India indicates novel maternal differentiation and domestication patterns

In this study, mitochondrial D-loop sequence data on riverine, swamp and hybrid buffaloes from India have been generated and compared with other reported Indian riverine, Chinese and Bangladeshi swamp buffalo populations. Sequence analysis revealed the presence of 132 haplotypes, with a haplotype diversity of 0.9611 ± 0.0045 and a nucleotide diversity of 0.04801 ± 0.00126. For the first time, the existence of riverine–swamp hybrids among the Indian Chilika buffalo population has been recorded, having 49 chromosomes, which was also confirmed by mitochondrial haplotype sharing between Chilika and Indian swamp as well as Chinese swamp buffalo populations in the network analysis. Phylogenetic analysis documents the sharing of reported pre-domestication haplogroups ‘SA1’, ‘SA2’, ‘SA3’ and ‘SB1’ between the Chilika and swamp buffalo populations of India, China and Bangladesh, an indication of the migration of swamp buffaloes towards Bangladesh and adjoining lower parts of India and north towards Chinese domestication sites. The results have also been supplemented by multidimension scaling, grouping Indian and Chinese swamp buffaloes more closely together with Bangladeshi buffaloes, but into a separate quadrant, whereas Chilika grouped away from other riverine as well as swamp buffaloes. These findings thus confirm the previous reports that the northeast region of India, close to the Indo-China border, is the point of evolution of swamp buffaloes with multiple sites of domestication.