Mitochondrial DNA control region sequence polymorphism in four indigenous tribes of Chotanagpur plateau, India

The analysis of genetic variation, in the nucleotide sequences of mitochondrial DNA, provides unique information in tracing of maternal lineage, determination of population diversity, pharmacogenomics and human identification. This study characterizes the HVR-I and II sequence polymorphism in 80 tribal individuals, belonging to the Austro-Asiatic linguistic family of Chotanagpur plateau, India. A total of 115 polymorphic sites were observed in the sequenced regions and 77 unique haplotypes could be identified.     

Evaluation of 15 biparental STR loci in human identification and genetic study of the Kannada-speaking groups of India

Thirteen tetranucleotide and 2 pentanucleotide repeat units were analyzed in 167 unrelated Kannada-speaking individuals belonging to 3 important communities, namely, Kuruva, Bhovi, and Christians, residing in different districts of Karnataka, India. Allele frequency data obtained from the analysis of 15 short tandem report (STR) markers of the subpopulation groups included in the study were observed to be similar, indicating a common ancestry or gene flow among these communities. Departures from Hardy-Weinberg equilibrium were observed in Kuruva population at locus D5S818 and D18S51 and at locus CSF1PO in the Christian community. The data of these communities were analyzed with allele frequency data of 4 other populations from Karnataka, India-Iyengar Brahmin, Gowda, Lingayat, and Muslim-to compute the combined power of discrimination, ranged from 0.962 to 0.974, with negligible difference between populations. The combined power of exclusion, however, remained constant at 0.999 for all populations evaluated in the study. Thus, the 15 markers selected for this study were found to be highly suitable in human identification and for providing information on genetic polymorphism.     

A call for mtDNA data quality control in forensic science

There is increasing evidence that many of the mitochondrial DNA (mtDNA) databases published in the fields of forensic science and molecular anthropology are flawed. An a posteriori phylogenetic analysis of the sequences could help to eliminate most of the errors and thus greatly improve data quality. However, previously published caveats and recommendations along these lines were not yet picked up by all researchers. Here we call for stringent quality control of mtDNA data by haplogroup-directed database comparisons. We take some problematic databases of East Asian mtDNAs, published in the Journal of Forensic Sciences and Forensic Science International, as examples to demonstrate the process of pinpointing obvious errors. Our results show that data sets are not only notoriously plagued by base shifts and artificial recombination but also by lab-specific phantom mutations, especially in the second hypervariable region (HVR-II).     

Distribution of alleles of 15 STR loci of the Powerplex 16 Multiplex system in four predominant population groups of South India

Allele distribution of the 15 STR loci of Powerplex 16 Multiplex System were studied in four predominant population groups of South India for evaluating their significance in human identification and population study: Iyengar Brahmin (65), Gowda (59), Lingayat (98) and Muslim (45) from the state of Karnataka. The loci analyzed are--D3S1358, THOI, D2ISI I, D18S51, D5S818, Penta E, D13S317, D7S820, D16S539, CSFIPO, Penta D, vWA, D8S179, TPOX and FGA. Out of 15 STR loci Penta D and D18S51 were found highly polymorphic in the studied populations.     

Y-chromosomal STR haplotypes in two endogamous tribal populations of Karnataka, India

POPULATION: Approximately 5.0 mL of blood sample was collected from a total of 150 men belonging to two tribal populations of coastal Uttar Kannada district of Karnataka, with their informed written consent. Both the populations are endogamous and they belong to the Dravidian linguistic family. Halakki is a tribal group having a population size of c. 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, c. 35,214 in number. They were hunters and gatherers but presently they practice agriculture.     

Combating Violence against Women in India: Nari Adalats and Gender-Based Justice

Using qualitative methodology—field observations and in-depth interviews—the study examines the role of Mahila Samakhya (a group advocating women's equality) and Nari Adalats (informal women's courts) in India in combating violence against women. Interviews were conducted with members of a Mahila Samakhya in the southwest state of Karnataka and complainants who appeared before Nari Adalats. Nari Adalats in Karnataka are an innovation of Mahila Samakhya, a Government of India development program. The results indicate that Nari Adalats exercise broad authority to investigate and dispose of a wide range of domestic violence cases in India. The Mahila Samakhya serves as an advocacy group and provides shelter, legal assistance, and social help as well as education for victims of domestic violence.     

中国广东汉族群体mtDNA控制区的多态性

目的 探讨线粒体DNA控制区(包括HVⅠ区、HVⅡ区和HVⅢ区)的多态性。方法 采用PCR扩增和末端标记荧光循环测序的方法，对100名广东汉族无关个体进行了序列分析。结果 共观察到147个变异位点，序列变异包括了碱基转换、颠换、插入、缺失等各种类型。其中在HV Ⅰ区(nt16，024～nt16，365)内观察到88个变异位点，91种单倍型，基因多样度为0.9964；在HVⅡ区(nt73～nt340)观察到42个变异位点，67种单倍型，基因多样度为0.9861；在HVⅢ区(nt438～nt574)观察到9个变异位点，15种单倍型，基因多样度为0.8760。联合3个高变区域的序列，可观察到98种单倍型，基因多样度为0.9996。结论 本研究为线粒体DNA在法庭科学中的应用提供了较系统的实验依据。结果还表明，对于mtDNA等单倍型遗传标记，增加其检测范围，可提高该系统的个体识别能力，使其在法庭科学领域充分发挥作用。     

Genetic profile of nine autosomal STR loci among Halakki and Kunabhi populations of Karnataka, India

POPULATION: Blood samples were collected from a total of 84 healthy and unrelated Halakki (44) and Kunabhi (40) populations, with their informed written consent. The geographic location of the sampled area is shown in Fig. 1. Both the populations are endogamous, and they belong to Dravidian linguistic family. Halakki is a tribal group having a population size of approximately 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, who are approximately 35,214 in number. The male Kunabhi can be identified by their tattoo marks. A necklace is the symbol of married women. They were hunters and gatherers, but at present they practice agriculture.     

Mitochondrial DNA regions HVI and HVII population data.

Data from 1393 unrelated individuals have been compiled from eight population groups: African Americans, Africans (Sierra Leone), U.S. Caucasians, Austrians, French, Hispanics, Japanese, and Asian Americans. The majority of the mtDNA sequences were observed only once within each population group (i.e., ranging from a low of 60.3% (35/58) of the Asian American sequences to a high of 85.3% (93/109) of the French sequences). Genetic diversity ranged from 0.990 in the African sample to 0.998 in African Americans. Random match probability ranged from 2.50% in the Asian American sample to 0.52% in U.S. Caucasians. The average number of nucleotide differences between individuals in a database is greatest for the African American and African samples (14.1 and 13.1, respectively), and the least variable are the Caucasians (ranging from 7.2 to 8.4). Substitutions are the predominate polymorphism, and at least 92% of the substitutions are transitions. The most prevalent transversions are As substituted for Cs and Cs substituted for As. For most population groups these transversions occurred predominately in the HVI region; however, the African, African American, and Hispanic samples also demonstrated a large portion of their C to A and A to C transversions in the HVII region (at sites 186 and/or 189). Most insertions occur in the HVII region at sites 309.1 and 315.1, within a stretch of C's. Insertions of an additional C are common in all population groups. The sequence data were converted to SSO mtDNA types and compared with population data on Caucasians, Africans, Asians, Japanese, and Mexicans described by Stoneking et al. [M. Stoneking, D. Hedgecock, R.G. Higuchi, L. Vigilant, H.A. Erlich, Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes, Am. J. Hum. Genet. 48 (1991) 370-382] using an R x C contingency table test. Differences between major population groups (i.e., between African, Caucasian, and Asian) are quite evident, and similar ethnic population groups carried similar SSO polymorphism frequencies. There were only a few SSO types that showed significant differences between subpopulation groups. The SSO data alone can not be used to describe the population genetics with complete sequence data. However, the results of the SSO comparisons are similar to other analyses, and differences in sequence data in regions HVI and HVII are greater between major population groups than between subgroups.     

Personal identification from human remains by mitochondrial DNA sequencing

The authors report four cases in which severely damaged human remains were identified by mitochondrial DNA (mtDNA) sequencing. Degraded DNA was extracted from highly adipoceratous tissues using the phenol-chloroform method and polymerase chain reaction amplified for sequencing of two hypervariable regions, hypervariable region 1 and hypervariable region 2, of mitochondrial DNA. They also sequenced these regions of blood samples that were obtained from the presumptive mother or sister of the human remains. The sequencing results were compared with each other and with the Anderson's sequence. It was concluded from the sequence data that a lower part of a body in case 1 and some organs in case 2 were from the same woman, and a human head in case 3 and a female body in case 4 were from the relative of a presumptive mother and a sister, respectively.     

Different informativeness of the three hypervariable mitochondrial DNA regions in the population of Bologna (Italy)

Mitochondrial DNA (mtDNA) sequence variations at hypervariable regions HVI, HVII and HVIII were analysed in 100 unrelated Italians from Bologna. The values of the statistical parameters are in agreement with the range of European populations. We suggest that the less informative HVIII region may be useful to distinguish HVI-HVII identical sequences in forensic analysis especially when nuclear DNA cannot be investigated.     

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.     

Sequence analysis of STR polymorphisms at locus ACTBP2 in the Taiwanese population

A highly polymorphic sequence structure is reported in the human beta-actin related pseudogene 2 (ACTBP2) (SE33) locus in members of the Taiwanese Han population. A total of 100 unrelated members of the Taiwanese Han population were used in the study. Alleles that shared the same size but differ in their sequence are described to allow for inter laboratory sharing of data. PCR products amplified from this locus were separated by single-strand conformation polymorphism electrophoresis, the single-stranded DNA bands were excised from the gels, a second amplification performed, and then the PCR products were sequenced. All the alleles differed by either 2 or 4 bp. Sequence variations were observed as deletions or insertions in the repeat units AG (or AA) and AAAG. Additionally, transitions in the flanking regions were recorded. A total of 27 alleles with 71 associated genotypes were recorded if the alleles were defined by size, but 68 alleles with 88 associated genotypes were noted with the alleles were scored on the basis of sequence variation. The power of discrimination (Pd) of this single locus was 0.9874 making the human ACTBP2 a good alternative marker for individual identification and paternity testing.     

吗啡依赖鼠成瘾相关脑区腺苷酸环化酶的变化

目的观察吗啡依赖鼠成瘾相关脑区腺苷酸环化酶的变化,探讨成瘾相关脑区腺苷酸环化酶的变化与吗啡依赖机制的关系。方法建立吗啡依赖大鼠模型,应用酶组织化学的方法对吗啡依赖鼠七个相关脑区腺苷酸环化酶的变化进行观察,用图像分析系统测定其灰度值,并进行统计学处理。结果吗啡依赖组脑区腺苷酸环化酶含量升高。结论吗啡成瘾相关七个脑区腺苷酸环化酶含量随吗啡依赖时限的延长有增加的趋势,结果提示吗啡依赖机制与特定脑区腺苷酸环化酶的含量变化有密切关系。进一步揭示AC/cAMP-PKA系统上调与吗啡成瘾机制的关系。     

Morphological pattern of palatal rugae in children of Davangere

The aim of this study was to identify and compare the rugae pattern between males and females of two different communities in the city of Davangere, Karnataka, India, which may be an additional method of identification in cases of crimes or communal riots. Elastomeric impressions of the maxillary arch of 100 selected children were made; casts were poured in Type IV stone. The method of identification of rugae pattern followed was that of Lysell and Thomas and Kotze, which includes the number, shape, direction, and unification of rugae. The study revealed no significant difference in the total number or length of rugae between the two communities and sexes. However, with regard to shape and unification, females showed a significantly higher diverging rugae type while males had a significant number of circular and converging type of rugae. Also, discrimination function analysis allowed a moderate differentiation of the population. Hence, the rugae pattern can be an additional method of differentiation in conjunction with the other methods such as visual, fingerprints, and dental characteristics in forensic sciences.     

Genetic relationships between blowflies (Calliphoridae) of forensic importance.

Phylogenetic relationships among blowfly (Calliphoridae) species of forensic importance are explored using DNA sequence data from the large sub-unit (lsu, 28S) ribosomal RNA (rRNA) gene, the study includes representatives of a range of calliphorid species commonly encountered in forensic analysis in Britain and Europe. The data presented provide a basis to define molecular markers, including the identification of highly informative intra-sequence regions, which may be of use in the identification of larvae for forensic entomology. Phylogenetic analysis of the sequences also provides new insights into the different evolutionary patterns apparent within the family Calliphoridae which, additionally, can provide a measure of the degree of genetic variation likely to be encountered within taxonomic groups of differing forensic utility.     

Income and Expenditure Switching Among the Impoverished During Structural Adjustment in India1

The impoverishment during 1991–1993 was largely a result of policy reforms. In the absence of income switching, the impoverishment would have been greater. The patterns of income switching differed among the three Indian states, viz. Andhra Pradesh, Maharashtra and Karnataka. Confining the analysis to household expenditure on food, medical care and education, however, little, if any, expenditure switching occurred. To some extent, the effects of household expenditure cuts were compounded by cuts in public expenditure. But, given the aggregate expenditure categories, there is a risk of overstating the effects on the poor. A more fundamental concern nonetheless remains. Given the acute deprivation of a large segment of the rural population, it is imperative that public provision of basic goods and services is strengthened. A case in point is the public distribution system for food (PDS). Despite the revamping, the benefits to the poor have not increased while the subsidy has. Short of drastic reforms, it is unlikely that the cost-effectiveness of the PDS will improve.     

Polymorphic sites in human mitochondrial DNA control region sequences: population data and maternal inheritance

Sequence analysis of the mitochondrial DNA (mtDNA) control region is of central importance for forensic identity testing as well as for studies of human evolution. Here we report the sequencing data of the hypervariable regions I and II from 50 unrelated individuals from a western German population (Rhine area). In regions I and II, 52 and 26 sites of sequence polymorphism, respectively, were noted. Nucleotide substitution rather than insertion/deletion was the majority of variation. The distribution showed a large bias towards transitional changes than transversional changes. Furthermore we investigated uniparental inheritance in seven CEPH families each family with 7–9 maternal descendants. Most maternal relatives shared identical mtDNA sequences. Additionally sequences were compared for father:child pairs and as expected no evidence for paternal transmission of mtDNA was observed. The high variability of mtDNA control region sequences permits utility in forensic identity investigations. The data also indicate that the neomutation rate seems to be very low from one generation to the other.     

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System

Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.

Key Points

• Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population.
• STRinNGS v.1.0 was used to analyse the flanking regions of STRs.
• The concordance between PCR-CE and PCR-MPS results was 99.86%.
• Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.