WorldWideScience

Sample records for f13a01 fesfps vwa

  1. Genetic data on nine STRs (CSF1PO, TPOX, THO1, F13AO1, FESFPS, vWA, D16S539, D7S820 and D13S317) and two VNTRs (D1S80 and D17S5) in Rosario population, Santa Fe Argentine.

    Science.gov (United States)

    Tenaglia, Mariano; Scollo, Adriana; Tripaldi, Regina; Grappiolo, Irene; Perichón, Armando M

    2004-05-10

    Allele frequencies for nine short tandem repeats (STRs) loci (CSF1PO, TPOX, THO1, F13AO1, FES/FPS, vWA, D16S539, D7S820 and D13S317) and two variable number tandem repeats (VNTRs) were obtained from a sample of 270 unrelated individuals born in the Rosario city, Santa Fe province of Argentina.

  2. Adviesaanvraag VWA : opheffing toelatingsverbod van pluimvee en postduiven

    NARCIS (Netherlands)

    Koch, G.; Elbers, A.R.W.; Rooij, van E.M.A.

    2008-01-01

    Deze adviesaanvraag van het VWA beoordeelt of het sinds 2003 bestaande verbod op het toelaten van buitenlands pluimvee en postduiven op Nederlands grondgebied voor tentoonstellingen, shows, wedstrijden en dergelijke kan worden opgeheven. Het verbod is ingesteld i.v.m. mogelijke insleep van hoog-path

  3. Association of vWA and TPOX Polymorphisms with Venous Thrombosis in Mexican Mestizos

    Science.gov (United States)

    Meraz-Ríos, Marco Antonio; Majluf-Cruz, Abraham; Santana, Carla; Noris, Gino; Camacho-Mejorado, Rafael; Acosta-Saavedra, Leonor C.; Calderón-Aranda, Emma S.; Hernández-Juárez, Jesús; Magaña, Jonathan J.; Gómez, Rocío

    2014-01-01

    Objective. Venous thromboembolism (VTE) is a multifactorial disorder and, worldwide, the most important cause of morbidity and mortality. Genetic factors play a critical role in its aetiology. Microsatellites are the most important source of human genetic variation having more phenotypic effect than many single nucleotide polymorphisms. Hence, we evaluate a possible relationship between VTE and the genetic variants in von Willebrand factor, human alpha fibrinogen, and human thyroid peroxidase microsatellites to identify possible diagnostic markers. Methods. Genotypes were obtained from 177 patients with VTE and 531 nonrelated individuals using validated genotyping methods. The allelic frequencies were compared; Bayesian methods were used to correct population stratification to avoid spurious associations. Results. The vWA-18, TPOX-9, and TPOX-12 alleles were significantly associated with VTE. Moreover, subjects bearing the combination vWA-18/TPOX-12 loci exhibited doubled risk for VTE (95% CI = 1.02–3.64), whereas the combination vWA-18/TPOX-9 showed an OR = 10 (95% CI = 4.93–21.49). Conclusions. The vWA and TPOX microsatellites are good candidate biomarkers in venous thromboembolism diseases and could help to elucidate their origins. Additionally, these polymorphisms could become useful markers for genetic studies of VTE in the Mexican population; however, further studies should be done owing that this data only show preliminary evidence. PMID:25250329

  4. Nationale 'good practices' voor de VWA : studie naar drie soortgelijke autoriteiten in Nederland

    NARCIS (Netherlands)

    Wubben, E.F.M.; Hubeek, F.B.

    2005-01-01

    In 2005 is door onderzoekers van Wageningen UR en LNV DK een verkennende studie verricht: drie inspectiediensten - PD, IVW-DL en AFM - zijn verkend voor 'good practices' voor de VWA bij de herziening van het financieringsstelsel dat per 1 januari 2006, behoudens de financiële artikelen, in

  5. Genetic polymorphism and forensic parameters of nine short tandem repeat loci in Ngöbé and Emberá Amerindians of Panama.

    Science.gov (United States)

    Castro, Edgardo A; Trejos, Diomedes E; Berovides-Alvarez, Vicente; Arias, Tomás D; Ramos, Carlos W

    2007-10-01

    Nine STR loci (CSF1PO, TPOX, TH01, F13A01, FESFPS, VWA, D16S539, D7S820, and D13S317) were analyzed in unrelated Ngöbé and Emberá Amerindians of Panama. The chi-square test demonstrated statistically significant differences (P linguistic stock [Chibchan (Ngöbé) and Chocoan (Emberá)], both retain strong similarities in their allele-frequency distributions. Three loci (TPOX, VWA, and F13A01) in the Ngöbé and two loci (TH01 and TPOX) in the Emberá departed from Hardy-Weinberg equilibrium. The analysis of the STR markers demonstrates that, despite their low levels of genetic polymorphisms, most of them could be informative for forensic purposes, showing a combined power of discrimination of 0.9999 for both Amerindian populations. However, powers of exclusion in the Ngöbé were very low, particularly at the TH01 (0.04) and FESFPS (0.08) loci. The combined powers of exclusion were 0.9338 and 0.9890 for the Ngöbé and the Emberá, respectively. Furthermore, the combined typical paternity index in the Ngöbé was considerably low (2.58), and in the Emberá it was 40.44, which is also very low. The low genetic polymorphism levels suggest that theuse of additional loci supplementing the battery of the nine loci is recommended for paternity and forensic tests in both populations, particularly for the Ngöbé.

  6. [Research of potentially linked variation of polymorphism of chromosome DNA in aspect of forensic expertise using molecular-genetic individualizing systems CD4, vWA and vWFII].

    Science.gov (United States)

    Ivanov, P L; Zemskova, E Iu; Turakulov, R I; Efremov, I A

    2005-01-01

    Investigated within the case study are parameters of disbalance of lineage (HC) for 4 micro-satellite locuses of human genome: LPL, CD4, vWA and vWFII. The above locuses are widely used, both in Russia and abroad, in molecular-genetic applications for personality identification. Meanwhile, according to cytogenetics criteria, CD4, vWA and vWFII, are located close to each other in the telomeric region 12pter-12p12 in the short chromosome 12 arm, therefore their potential genetic interdependence is still a topical issue. We found a reliable HC between locuses vWA and vWFII. Locus CD4 did not display HC with locuses vWA and vWFII or with locus LPL. The latter, which is located in chromosome 8 and which must have been negative control for HC, was shown to have no HC with any of the studied markers. Such results correlate well with data on the relative physical localization of CD4, vWA, vWFII and LPL. Multiplication of frequency of alleles (genotypes) is not acceptable in typing locuses vWA and vWFII within one multi-locus panel due to the genetic linkage of these markers demonstrated within the present case study, which is an important practical conclusion.

  7. Paternity analysis in special fatherless cases without direct testing of alleged father.

    Science.gov (United States)

    Mixich, Francisc; Ioana, Mihai; Mixich, Vlad A

    2004-12-02

    The ability to establish the biological father, in which the father of a person is not available, named "reverse paternity determination", is based on the determination of STR alleles in mother and her child, other children and brothers of the alleged father, and deduction of genetic constitution of the father by the basis of genetic laws. Presented herein are two cases of reverse paternity determinations. Mother and parenthood DNA was isolated from 300 microl of fresh blood collected into tubes containing the EDTA, using Wizard Genomic DNA purification kit (Promega). DNA amplification was performed using GenePrint STR System (CTT, FFv, and Silver STR III multiplex) (Promega). Amplification results were read on 0.4 mm thick sequencing size polyacrilamide gel (4% for CTT and FFv, and 6% for Silver STR III). Gels were silver stained using Silver Sequence DNA Staining Reagents (Promega). Possible alleles of the alleged father for the loci CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, D16S539, D7S820, D13S317, LPL, F13B, and HPRTB were established by the selection from alleles determined in mother and parenthood, as to as obligate alleles with which the alleged father contributes to the genetic constitution of investigated child. Probability of paternity was calculated using population data on STR allele frequencies for Romanian population established by our laboratory. These are the first cases of litigious reverse paternity determinations in Romania.

  8. 微卫星 vWA和 D5 S818与精神分裂症的多态性分析%Relationship between polymorphism of microsatellite vWA and D5 S818 with schizophrenia

    Institute of Scientific and Technical Information of China (English)

    杨光; 魏巍; 刘辉

    2014-01-01

    Objective To explore a genetic relationship between the polymorphism of microsatellites vWA and D 5S818 with schizophrenia .Methods DNA samples collected from patients with schizophrenia ( n=57 ) and random population ( n=123 ) were amplified by PE Profiler plus system for multiplex PCR .Then ABI 3130-Avent genetic analyzer was used for automatic capillary electrophoresis and genotyping .Results The detection ratios of vWA -14 were 21.9%and 33.3%in schizophrenia group and control group , respectively .The difference was statistically significant between the two groups (P0.05).No de-viations from the Hardy-Weinberg equilibrium were observed .Conclusion There is a strong association of vWA -14 with schizophrenia , suggesting a possible linkage between vWA -14 and some schizophrenia resistant genes .There may be genes on chromosome 12 associated with susceptibility to schizophrenia .%目的:探讨微卫星vWA和D5 S818的多态性与精神分裂症有关的易感基因区域。方法对57例精神分裂症患者(精神分裂症组)和123名随机人群(对照组)采用PE Profiler plus系统进行PCR复合扩增,然后用ABI公司的310型基因分析仪自动进行电泳分离和基因检测。结果精神分裂症组的vWA-14的检出率为21.9%,对照组检出率为33.3%,两者之间差异有显著性意义(P<0.05);D5S818位点的各等位基因频率的检出率两组之间差异无显著性意义( P>0.05)。经吻合度检验,2个微卫星各等位基因频率的分布,均符合Hardy-Weinberg平衡。结论 vWA-14位点与精神分裂症有明显关联,提示vWA-14可能与精神分裂症某种抵抗基因连锁,表明在第12号染色体上存在与精神分裂症相关的基因。

  9. 中国牡丹江地区朝鲜族群体九个STR基因座的遗传多态性研究%Genetic polymorphism of 9 STR loci in Korean population of Mudanjiang

    Institute of Scientific and Technical Information of China (English)

    卜晓波; 宋洁; 韩彦龙; 张书捷; 傅松滨

    2008-01-01

    目的 调查中国牡丹江地区朝鲜族群体CSFIPO,TPOX,TH01,D16S539.D7S820,D13S317,F13A01,FESFPS,vWA 9个短串联重复序列(short tandem repeats,STR)基因座的基因多态性.方法 应用扩增片段长度多态性分型技术,获得等位基因频率分布.结果 X2检验表明9个基因座基因型分布均符合Hardy.Weinberg平衡.总偶合率为5.43595E-09,总个体识别率达0.999999995,三联体累计非父排除率为0.9982,二联体累计非父排除率为0.9711.结论 9个基因座在牡丹江地区朝鲜族群体有较高的非父排除率和个人识别机率,可应用于法医学亲子鉴定和个体识别.中国牡丹江地区和中国延吉地区朝鲜族人群6个基因频率相比较,CSFIPO、TPOX和TP01 3个基因座的基因频率分布差异有统计学意义,D7S820、D17S317和vWA 3个基因座的基因频率分布差异无统计学意义.%Objective To investigate the genetic polymorphism of 9 short tandem repeats(STR) gene loci,namely CSFLPO,TPOX,TH01,D16S539,D7S820,D13S317,F13A01,FESFPS and vwA in Chinese Korean pop.dabon in Mudanjiang area.Methods Amplified fragment length polymorphism(Amp-FLP)method wLq uscd to get the allele frequeney distribution.Results The genotype distributions of the 9 STR loci are conformed to Hardy-Weinberg equilibrium by x2 test analysis. The total accord frequency,the accumulated total discrimination power and the accumulative exeluding probability of paternity were calculated.Conclusion The results snggested that all the 9 gene loci have high power of excluding probability of patemity and individual identification.They can be used in paternity testing and individual identificmion for forensic medicine.The gene frequencies of CSnP0.TP0X and TP01 gene loci have signifieant differences between the Korean population in Mudanjiang area and those in Yanji area,but there is no difference in gene loci 0f D7S820.D17S317 and vWA.

  10. Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers.

    Science.gov (United States)

    Martínez, Helios; Rodríguez-Larralde, Alvaro; Izaguirre, Mary Helen; De Guerra, Dinorah Castro

    2007-04-01

    The present Venezuelan population is the product of admixture of Amerindians, Europeans, and Africans, a process that was not homogeneous throughout the country. Blood groups, short tandem repeats (STRs), mtDNA, and Y-chromosome markers have been used successfully in admixture studies, but few such studies have been conducted in Venezuela. In this study we aim to estimate the admixture components of samples from two different socioeconomic levels from Caracas, Venezuela's capital city, compare their differences, and infer sexual asymmetry in the European Amerindian union patterns. Gene frequencies for blood groups ABO and Rh (CDE) and for the STRs VWA, F13A01, and FES/FPS and mtDNA and Y-chromosome haplogroups were studied in a sample of 60 individuals living in Caracas, taken from a private clinic (high socioeconomic level), and 50 individuals, also living in Caracas, drawn from a public maternity clinic (low socioeconomic level). The admixture analysis for the five autosomal markers gives a high European component (0.78) and an almost negligible African sub-Saharan component (0.06) for the high socioeconomic level, whereas for the low socioeconomic level the sub-Saharan, European, and Amerindian components were 0.21, 0.42, and 0.36, respectively. Estimates of admixture based on mtDNA and Y-chromosome markers reveal that the Amerindian contribution to these Caracas samples is almost entirely through females, because the Y-chromosome Amerindian and African sub-Saharan chromosomes found in this study were scarce. Our study reveals that the identification of the grandparents' geographic origin is an important methodological aspect to take into account in genetic studies related to the reconstruction of historical events.

  11. 随机人群与精神分裂症患者微卫星DNA vWA多态性的关联性分析%Polymorphism of microsatellite DNA vWA in random population and schizophrenic patients

    Institute of Scientific and Technical Information of China (English)

    刘辉; 于卫建; 方芳; 王学滨; 杨光; 刘奔; 梁晓华; 周杰

    2005-01-01

    于随机人群(19.5%),差异有显著性(RR=1.866,P=0.043);其他各等位基因检出率差异无显著性(P>0.05).结论:精神分裂症患者vWA-14的检出率显著低于随机人群,提示vWA-14在精神分裂症时可能会因某种原因而被负选择,其附近可能存在抵抗精神分裂症发病的基因.精神分裂症患者vWA-17的检出率显著高于随机人群,表明vWA-17与精神分裂症相关联,其附近可能存在精神分裂症易感基因.%BACKGROUND: Schizophrenia is substantially heritable, but specific susceptibility genes remain difficult to be identified. Therefore, it is necessary to explore hereditary markers first.OBJECTIVE: To investigate the relationship between schizophrenia and related vWA allele genes based on the analysis of microsatellite DNA vWA polymorphism.DESIGN: A case-controlled study with schizophrenic patients and randomly selected population as subjects.SETTING: Ward of Dalian Seventh People's Hospital and Molecular Biological Laboratory of Dalian Medical University.between March and July 2002 at Dalian Seventh People's Hospital which specializes in schizophrenia. Schizophrenia was diagnosed according to the diagnostic standard of the third edition of "the American Diagnostic Statistical Manual for Schizophrenic Diseases", and their clinical manifestations were predominantly negative signs. Altogether 123 normal blood samples were collected from random population at the Blood Center of Dalian Red Cross. They all denied psychological ailments and severe systematic diseases, and they had no kinship with each other.METHODS: Heparin anti-coagulation blood samples were collected and PCR compound amplification was carried out with the aid of PE Profiler plus system. Then the products were subjected to electrophoresis and gene detection with ABI310 type gene analysis system so as to calculate the frequency of allele genes; Hardy-Weinberg equation law was used to make coincidence test and linkage analysis of the theoretical frequency

  12. Comparison of allele frequencies of eight STR loci from Argentinian Amerindian and European populations.

    Science.gov (United States)

    Sala, A; Penacino, G; Corach, D

    1998-10-01

    Eight STR systems (THO1, FABP, VWA, FES/FPS, HPRTB, F13A1, CSF1PO, and D6S366) were investigated in different ethnic groups of Argentina. Allele and genotype frequencies, power of exclusion, and discriminative power were investigated. Hardy-Weinberg expectations were calculated from heterozygosity levels. FST and G tests demonstrated that significant differences exist among the investigated populations for some of the eight STRs markers. The Wichi Indians are clearly separated from the Mapuche and Tehuelche, who in turn are closer to the European population, suggesting non-Amerindian admixture.

  13. Structural variations of the VWA locus in humans and comparison with non-human primates.

    Science.gov (United States)

    Minaguchi, K; Takenaka, O

    2000-09-11

    The HUMVWA locus was examined in 160 samples from the Japanese population. A total of 142 fragments were sequenced, and the counterpart sequences were also determined in non-human primates. In humans, 10 different alleles were found; they could be grouped into seven allelic classes based on the total number of repeats. No variation was observed in the alleles 17, 18 and 19, which showed consensus sequence structures and in the allele 14, which showed a different structure. New variation was found in alleles 15, 16, and 20, which had differences occurred in a basic (TCTA)(TCTG)(n) repeat in the 5' side. The counterpart fragments were successfully amplified in three species (chimpanzees, gorilla, and orangutan) out of four kinds of anthropoids, three species (rhesus macaques, Japanese macaques, and green monkey) out of four kinds of old world monkeys, but not in one species of either new world monkey or prosimian. The sizes of the fragments distributed from 92 to 180 bp in non-human primates and showed allelic size differences in four species. The sequence of the 5' flanking region followed by primer sequences in humans and anthropoids, which consisted of 19 bp, was identical in all, but differed from that in old world monkeys. The basic repeat motifs of humans and anthropoids consisted of TCTA, TCTG, and TCCA but that of old world monkeys consisted of TCTG, TCCG and TCCA The structures of humans and anthropoids were essentially similar, but with characteristic difference in each species. Differences in the allelic structures of old world monkeys were complex. Seven different alleles were observed in two rhesus and two Japanese macaques and one type of allele was observed in two green monkeys. Duplication of more than two repeat units of 4 bp was found in an allele of an old world monkey. These data illuminate interesting features of mutational changes in STRs during the long generations and also some insight into evolutional aspects of primates.

  14. Genetic analysis of two STR loci (VWA and TPOX in the Iranian province of Khuzestan

    Directory of Open Access Journals (Sweden)

    Ali Mohammad Foroughmand

    2014-08-01

    Conclusion: The examined STR loci in this study have proven a relatively high genetic variation in the Iranian population. The data could be used for construction of a forensic genetic database for the Iranian population.

  15. Reference database of hypervariable genetic markers of Argentina: application for molecular anthropology and forensic casework.

    Science.gov (United States)

    Sala, A; Penacino, G; Carnese, R; Corach, D

    1999-06-01

    The population of Argentina is mostly composed of people of European ancestry. Aboriginal communities are at present very reduced in number and restricted to small geographically isolated patches. Three aboriginal communities, the Mapuche, Tehuelche and Wichi, were selected for short tandem repeat (STR) investigation. The metropolitan population of the city of Buenos Aires was analyzed, with both micro- and minisatellites. The minisatellite loci D1S7, D2S44, D4S139, D5S110, D8S358, D10S28, and D17S26 were typed on HaeIII-digested DNA obtained from unrelated individuals. D1S80 was typed by polymerase chain reaction (PCR). The autosomal STRs THO1, FABP, D6S366, CSF1PO, TPOX, F13A1, FES/FPS, vWA, MBPA/B, D16S539, D7S820, D13S317, and RENA4 and the sex chromosome STRs HPRTB, DYS385, DYS3891, DYS38911, DYS19, DYS390, DYS391, DYS392, DYS393 and YCAII were also investigated. As a by-product of our investigations, a reference database was created that is routinely used in forensic casework and paternity testing. STR allele frequency distributions are characterized by significant differences within and also between different populations. In contrast, the minisatellite bin distribution of the metropolitan population is not significantly different from other Caucasian populations.

  16. Europese 'good practices' voor de VWA : de implementatie van EG-verordening 882/2004 in België, het Verenigd Koninkrijk, Duitsland en Denemarken

    NARCIS (Netherlands)

    Wubben, E.F.M.; Hubeek, F.B.

    2006-01-01

    In dit rapport worden de resultaten van vier landenstudies gepresenteerd. Informatie is verkregen over en interviews zijn gehouden in de landen België, het Verenigd Koninkrijk,Duitsland en Denemarken met betrekking tot het beleid en uitvoering van de controles op de dier- en voedselveiligheid.

  17. Vaccination Week in the Americas, 2011: an opportunity to assess the routine vaccination program in the Bolivarian Republic of Venezuela.

    Science.gov (United States)

    Sánchez, Daniel; Sodha, Samir V; Kurtis, Hannah J; Ghisays, Gladys; Wannemuehler, Kathleen A; Danovaro-Holliday, M Carolina; Ropero-Álvarez, Alba María

    2015-04-17

    Vaccination Week in the Americas (VWA) is an annual initiative in countries and territories of the Americas every April to highlight the work of national expanded programs on immunization (EPI) and increase access to vaccination services for high-risk population groups. In 2011, as part of VWA, Venezuela targeted children aged less than 6 years in 25 priority border municipalities using social mobilization to increase institution-based vaccination. Implementation of social communication activities was decentralized to the local level. We conducted a survey in one border municipality of Venezuela to evaluate the outcome of VWA 2011 and provide a snapshot of the overall performance of the routine EPI at that level. We conducted a coverage survey, using stratified cluster sampling, in the Venezuelan municipality of Bolivar (bordering Colombia) in August 2011. We collected information for children aged 85%, with a few exceptions. Low levels of VWA awareness among caregivers probably contributed to the limited vaccination of eligible children during the VWA activities in Bolivar in 2011. However, vaccine coverage for most EPI vaccines was high. Additionally, high vaccination card availability and high participation in VWA among those caregivers aware of it in 2011 suggest public trust in the EPI program in the municipality. Health authorities have used survey findings to inform changes to the routine EPI and better VWA implementation in subsequent years.

  18. The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins

    Directory of Open Access Journals (Sweden)

    Bateman Alex

    2003-10-01

    Full Text Available Abstract Background Ribonucleoproteins carry out a variety of important tasks in the cell. In this study we show that a number of these contain a novel module, that we speculate mediates RNA-binding. Results The TROVE module – Telomerase, Ro and Vault module – is found in TEP1 and Ro60 the protein components of three ribonucleoprotein particles. This novel module, consisting of one or more domains, may be involved in binding the RNA components of the three RNPs, which are telomerase RNA, Y RNA and vault RNA. A second conserved region in these proteins is shown to be a member of the vWA domain family. The vWA domain in TEP1 is closely related to the previously recognised vWA domain in VPARP a second component of the vault particle. This vWA domain may mediate interactions between these vault components or bind as yet unidentified components of the RNPs. Conclusions This work suggests that a number of ribonucleoprotein components use a common RNA-binding module. The TROVE module is also found in bacterial ribonucleoproteins suggesting an ancient origin for these ribonucleoproteins.

  19. Extent of digestion affects the success of amplifying human DNA from blood meals of Anopheles gambiae (Diptera: Culicidae)

    NARCIS (Netherlands)

    Mukabana, W.R.; Takken, W.; Seda, P.; Killeen, G.F.; Hawley, W.A.; Knols, B.G.J.

    2002-01-01

    The success of distinguishing blood meal sources of Anopheles gambiae Giles through deoxyribonucleic acid (DNA) profiling was investigated by polymerase chain reaction (PCR) amplification at the TC-11 and VWA human short tandem repeats (STR) loci. Blood meal size and locus had no significant effect

  20. The genus Yersinia

    Energy Technology Data Exchange (ETDEWEB)

    Prpic, J.K.; Davey, R.B.

    1987-01-01

    This book contains papers presented at the Fourth International symposium on Yersinia. The topics covered include: Cloning and use of Vwa plasmid DNA as gene probes for virulent Yersiniae; Studies on the role of virulence determinants of Yersinia enterocolitica in gnotobiotic piglets; and significance of specific IgA antibodies in infections due to Yersinia enterocolitica and their complications.

  1. Melamine in sojaschilfers, oorzaak van verschillen tussen laboratoria

    NARCIS (Netherlands)

    Mol, J.G.J.; Egmond, van H.J.; Jong, de J.

    2009-01-01

    In november 2008 is door het bedrijfsleven in een tweetal partijen diervoedergrondstoffen (sojaschilfers/-meel) melamine aangetroffen op niveaus tussen 40 en 800 mg/kg. Naar aanleiding hiervan heeft de VWA aan RIKILT verzocht om deze monsters (genomen door het bedrijfsleven) te analyseren op melamin

  2. Turkish population data with the CODIS multiplex short tandem repeat loci.

    Science.gov (United States)

    Akbasak, B S; Budowle, B; Reeder, D J; Redman, J; Kline, M C

    2001-12-01

    Allele frequencies for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, D18S51, D3S1358, D21S11, D5S818, FGA, D7S820, HUMTH01, D8S1179, TPOX, D13S317, VWA, and D16S539 were determined on 198 Turkish blood samples.

  3. Residuen op groenten en fruit ter discussie

    NARCIS (Netherlands)

    Woltering, E.J.

    2011-01-01

    De nVWA en het RIVM doen al jaren onderzoek naar residuen van giftige stoffen op groenten en fruit. Uit onderzoek blijkt dat met name peuters en baby’s meer groenten en fruit binnenkrijgen dan eerder werd gedacht. Met meer groenten en fruit zouden ze ook meer residuen binnenkrijgen. Ernst Woltering

  4. Analytic index of Wittgenstein´s Nachlass

    DEFF Research Database (Denmark)

    2010-01-01

    Together with Professor Mark Addis Birmingham and the Research Team at AKSIS, Bergen University, I have developed an interactive analytic index to the whole of the Nachlass of LudwigWittgenstein. The project is funded by Nordforsk/WAB-Bergen/VWA-Helsinki , and is associated with the EU discovery...

  5. Residuen op groenten en fruit ter discussie

    NARCIS (Netherlands)

    Woltering, E.J.

    2011-01-01

    De nVWA en het RIVM doen al jaren onderzoek naar residuen van giftige stoffen op groenten en fruit. Uit onderzoek blijkt dat met name peuters en baby’s meer groenten en fruit binnenkrijgen dan eerder werd gedacht. Met meer groenten en fruit zouden ze ook meer residuen binnenkrijgen. Ernst Woltering

  6. Factor B structure provides insights into activation of the central protease of the complement system

    NARCIS (Netherlands)

    Milder, F.J.; Gomes, L.; Schouten, A.; Janssen, B.J.C.; Huizinga, E.G.; Romijn, R.A.; Hemrika, W.; Roos, A; Daha, M.R.; Gros, P.

    2007-01-01

    Factor B is the central protease of the complement system of immune defense. Here, we present the crystal structure of human factor B at 2.3-A° resolution, which reveals how the five-domain proenzyme is kept securely inactive. The canonical activation helix of the Von Willebrand factor A (VWA) domai

  7. AcEST: DK952132 [AcEST

    Lifescience Database Archive (English)

    Full Text Available sp|Q8VC74|COX18_MOUSE Mitochondrial inner membrane protein COX18... 31 5.2 sp|P07570|VPRT_MPMV Protease OS=Mason-Pfizer...VWA P GW AL S Sbjct: 27 WSSARLPALPVWAAASVSAASPGGWYEALAAS 58 >sp|P07570|VPRT_MPMV Protease OS=Mason-Pfizer mo

  8. Efficacy of DNA typing as an accurate method in forensic medicine

    Directory of Open Access Journals (Sweden)

    Namazi H

    2000-08-01

    Full Text Available DNA typing is a new method with important applications in forensic medicine. In the present study, we evaluated application of DNA typing in Iran. Loci Hum LPL, Hum Tpox, Hum F13, Hum vw 31A, Hum TH01 and Hum FES/FPS of DNA short tandem repeats were studied. To determine sensitivity of the test, 85 mother-child couples (1020 chromosomes that were referred to DNA section of legal medicine organization of Iran were included and for determination of it's specificity 42 brother-sister couples (1200 chromosomes and 58 non-relative couples were examined. The results show lack of mutations in the studied loci and acceptable sensitivity of the test. Of 12 alleles of siblings, there were 2-6 differences, in contrast with 3-9 differences in non-relatives, so the test has 100% specificity in these loci. Considering polymorphism, power of exclusion of these 6 sites was 99%.

  9. STR polymorphisms in Philippine ethnolinguistic groups: evaluation of forensic utility.

    Science.gov (United States)

    Miranda, Jasmin Jiji; Halos, Saturnina C

    2004-01-01

    Population data was collected for the STR loci F13AO1, FES/FPS, HUMvWA, and HUMTHO1, in three major Philippine ethnolinguistic groups and used to estimate statistical parameters for identity testing in forensic work on Filipinos. The Cebuano, Ilocano, and Pampango populations in the Philippines were studied because they are among the biggest linguistic groups in the country, thus their genotypic profiles should substantially represent those of many Filipinos. The number of alleles varied from 4 to 9 at all loci, falling within the range observed for other local and world populations. Pairwise comparisons of the allele frequency distributions showed no statistical differences among the populations. The test for linkage equilibrium showed no evidence of non-random association of alleles across the physically unlinked loci in any of the three populations. The four loci combined gave an exclusion power of > or =0.9995 and a power of paternity exclusion of 0.8859-0.9389.

  10. A study on ten short tandem repeat systems: African immigrant and Spanish population data.

    Science.gov (United States)

    Gamero, J J; Romero, J L; Gonzalez, J L; Arufe, M I; Cuesta, M I; Corte-Real, F; Carvalho, M; Anjos, M J; Vieira, D N; Vide, M C

    2000-06-05

    This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.

  11. Meiosis study in a population sample from Nigeria: allele frequencies and mutation rates of 16 STR loci.

    Science.gov (United States)

    Hohoff, Carsten; Schürenkamp, Marianne; Brinkmann, Bernd

    2009-05-01

    Allele frequencies for the 16 short tandem repeat (STR) loci D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, ACTBP2, CSF1PO, FGA, TH01, TPOX and VWA were determined for 337 immigrants from Nigeria. All loci were in Hardy-Weinberg equilibrium. More than 6,000 meiotic transfers were investigated and ten mutations were observed. Single mutations were observed in the STR systems D2S1338, D3S1358, D7S820, D8S1179, D16S539 and FGA, whereas two mutations were observed in the systems D21S11 and VWA.

  12. Aggregate exposure to chemicals

    OpenAIRE

    Wolterink G; van de Ven BM; ter Burg W; Verkaik-Kloosterman J; SIR; CVG

    2010-01-01

    Het risico van een chemische stof is lastig te beoordelen als mensen via verschillende routes en producten aan deze stof staan blootgesteld (geaggregeerde blootstelling). Dat komt meestal doordat relevante blootstellingsgegevens ontbreken. Het kan bijvoorbeeld onbekend zijn in welke producten de stoffen voorkomen en in welke concentratie. Dit is de conclusie van het RIVM op basis van studies naar vier stoffen. Het onderzoek is uitgevoerd in opdracht van de Voedsel en Waren Autoriteit (VWA) en...

  13. Analytic index of Wittgenstein´s Nachlass

    DEFF Research Database (Denmark)

    2010-01-01

    Together with Professor Mark Addis Birmingham and the Research Team at AKSIS, Bergen University, I have developed an interactive analytic index to the whole of the Nachlass of LudwigWittgenstein. The project is funded by Nordforsk/WAB-Bergen/VWA-Helsinki , and is associated with the EU discovery...... program, and the European Cultural Heritage program. The application is available on the web at the Philospace Home Page....

  14. Population genetic data for 15 STR loci (Identifiler kit) in Bolivia.

    Science.gov (United States)

    Rocabado, Omar; Taboada, Patricia; Inda, Francisco Javier; Yurrebaso, Inaki; García, Oscar

    2009-11-01

    Allele frequencies for 15 STR autosomal loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were obtained from a sample of 200 unrelated individuals from Bolivia, South America.

  15. Robust EMG sensing system based on data fusion for myoelectric control of a robotic arm

    OpenAIRE

    2009-01-01

    Abstract Background Myoelectric control of a robotic manipulator may be disturbed by failures due to disconnected electrodes, interface impedance changes caused by movements, problems in the recording channel and other various noise sources. To correct these problems, this paper presents two fusing techniques, Variance Weighted Average (VWA) and Decentralized Kalman Filter (DKF), both based on the myoelectric signal variance as selecting criterion. Methods Tested in five volunteers, a redunda...

  16. Pif97, a von Willebrand and Peritrophin Biomineralization Protein, Organizes Mineral Nanoparticles and Creates Intracrystalline Nanochambers.

    Science.gov (United States)

    Chang, Eric P; Evans, John Spencer

    2015-09-01

    The formation of the mollusk nacre layer involves the assembly and organization of mineral nanoparticles into fracture-toughened mesoscale-sized aragonite tablets that possess intracrystalline nanoporosities. At least one nacre protein family, known as the framework proteome, is strategically located as part of a macromolecular coating around each nacre tablet and is believed to participate in tablet formation. Here, we report new studies of a recombinant form (rPif97) of a unique Japanese pearl oyster (Pinctada fucata) nacre framework biomineralization protein, Pif97. This unique protein possesses both a von Willlebrand factor type A domain (vWA, F23-Y161) and a Peritrophin A chitin-binding domain (PAC, E234-D298). rPif97 self-associates or aggregates to form amorphous protein phases that organize both amorphous and single-crystal calcium carbonate nanoparticles in vitro. Further, in the presence of nucleating calcite crystals, rPif97 protein phases deposit onto these crystals and become occluded over time, forming nanochambers within the crystal interior. The formation of these mineral-modifying amorphous protein phases is linked to the presence of intrinsic disorder and amyloid-like cross-β-strand aggregation-prone regions, and three-dimensional modeling indicates that both the vWA and PAC domains are accessible for intermolecular interactions. Thus, the vWA- and PAC-containing Pif97 protein exhibits key functionalities that would allow its participation in mollusk nacre layer tablet assembly and porosity formation.

  17. A small molecule glycosaminoglycan mimetic blocks Plasmodium invasion of the mosquito midgut.

    Directory of Open Access Journals (Sweden)

    Derrick K Mathias

    Full Text Available Malaria transmission-blocking (T-B interventions are essential for malaria elimination. Small molecules that inhibit the Plasmodium ookinete-to-oocyst transition in the midgut of Anopheles mosquitoes, thereby blocking sporogony, represent one approach to achieving this goal. Chondroitin sulfate glycosaminoglycans (CS-GAGs on the Anopheles gambiae midgut surface are putative ligands for Plasmodium falciparum ookinetes. We hypothesized that our synthetic polysulfonated polymer, VS1, acting as a decoy molecular mimetic of midgut CS-GAGs confers malaria T-B activity. In our study, VS1 repeatedly reduced midgut oocyst development by as much as 99% (P<0.0001 in mosquitoes fed with P. falciparum and Plasmodium berghei. Through direct-binding assays, we observed that VS1 bound to two critical ookinete micronemal proteins, each containing at least one von Willebrand factor A (vWA domain: (i circumsporozoite protein and thrombospondin-related anonymous protein-related protein (CTRP and (ii vWA domain-related protein (WARP. By immunofluorescence microscopy, we observed that VS1 stains permeabilized P. falciparum and P. berghei ookinetes but does not stain P. berghei CTRP knockouts or transgenic parasites lacking the vWA domains of CTRP while retaining the thrombospondin repeat region. We produced structural homology models of the first vWA domain of CTRP and identified, as expected, putative GAG-binding sites on CTRP that align closely with those predicted for the human vWA A1 domain and the Toxoplasma gondii MIC2 adhesin. Importantly, the models also identified patches of electropositive residues that may extend CTRP's GAG-binding motif and thus potentiate VS1 binding. Our molecule binds to a critical, conserved ookinete protein, CTRP, and exhibits potent malaria T-B activity. This study lays the framework for a high-throughput screen of existing libraries of safe compounds to identify those with potent T-B activity. We envision that such compounds when

  18. Collagen VI microfibril formation is abolished by an {alpha}2(VI) von Willebrand factor type A domain mutation in a patient with Ullrich congenital muscular dystrophy.

    Science.gov (United States)

    Tooley, Leona D; Zamurs, Laura K; Beecher, Nicola; Baker, Naomi L; Peat, Rachel A; Adams, Naomi E; Bateman, John F; North, Kathryn N; Baldock, Clair; Lamandé, Shireen R

    2010-10-22

    Collagen VI is an extracellular protein that most often contains the three genetically distinct polypeptide chains, α1(VI), α2(VI), and α3(VI), although three recently identified chains, α4(VI), α5(VI), and α6(VI), may replace α3(VI) in some situations. Each chain has a triple helix flanked by N- and C-terminal globular domains that share homology with the von Willebrand factor type A (VWA) domains. During biosynthesis, the three chains come together to form triple helical monomers, which then assemble into dimers and tetramers. Tetramers are secreted from the cell and align end-to-end to form microfibrils. The precise molecular mechanisms responsible for assembly are unclear. Mutations in the three collagen VI genes can disrupt collagen VI biosynthesis and matrix organization and are the cause of the inherited disorders Bethlem myopathy and Ullrich congenital muscular dystrophy. We have identified a Ullrich congenital muscular dystrophy patient with compound heterozygous mutations in α2(VI). The first mutation causes skipping of exon 24, and the mRNA is degraded by nonsense-mediated decay. The second mutation is a two-amino acid deletion in the C1 VWA domain. Recombinant C1 domains containing the deletion are insoluble and retained intracellularly, indicating that the mutation has detrimental effects on domain folding and structure. Despite this, mutant α2(VI) chains retain the ability to associate into monomers, dimers, and tetramers. However, we show that secreted mutant tetramers containing structurally abnormal C1 VWA domains are unable to associate further into microfibrils, directly demonstrating the critical importance of a correctly folded α2(VI) C1 domain in microfibril formation.

  19. VASCULAR REMODELING AND HEART RATE VARIABILITY IN DIFFERENT ANTIHYPERTENSIVE THERAPIES

    Directory of Open Access Journals (Sweden)

    E. D. Golovanova

    2008-01-01

    Full Text Available Aim. To study the effect of the long-term antihypertensive monotherapy with indapamide (Arifon Retard, 1,5 mg/d, metoprolol tartrate (Egilok Retard, 50 mg/d and combined therapy with indapamide and perindopril (Noliprel Forte, 1 tab/d: perindopril 4 mg and indapamide 1,25 mg on pulse wave velocity (PWV, cardio-ankle vascular index (CAVI and the sympathetic system activity.Material and methods. 88 patients, aged 30-59 y.o. (32 normotensive patients, 56 with arterial hypertension [HT] of 1-2 grades were examined. Biological age (BA was determined by the linear regression and the vascular wall age (VWA was estimated with the use of volume sphygmography (“VaSera-1000”, “Fucuda Denshi”, Japan. 39 patients with HT were randomized into 3 parallel groups with studied therapies lasted for 6 months. PWV, CAVI of the vessels of elastic, muscular and mixed types, blood pressure, measured in upper and lower extremities and heart rate variability (HRV were determined before and at the end of the therapies.Results. BA and VWA were elevated in all of patients with HT as compared with normotensive patients. The reduction in PWV and CAVI of the vessels of elastic and mixed types, HRV increase were found in patients with Arifon Retard monotherapy. Monotherapy with metoprolol significantly improved HVR without any influence on the vascular remodeling. Noliprel Forte significantly decreased in blood pressure in the upper and lower extremities, PWV and CAVI of the vessels of all types, decreased in VWA and increased in parasympathetic drive.Conclusion. Long-term therapy with Arifon Retard and Noliprel Forte resulted in decrease in vascular remodeling and increase in HRV simultaneously with significant antihypertensive effect in patients with HT. Metoprolol low doses therapy resulted in normalization of autonomic drive independently on antihypertensive action.

  20. Investigation of altered microstructure in patients with drug refractory epilepsy using diffusion tensor imaging

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yuwei; Yan, Xu; Fan, Mingxia [East China Normal University, Key Laboratory of Magnetic Resonance, Shanghai (China); Mao, Lingyan; Wang, Xin; Ding, Jing [Fudan University, Department of Neurology, Zhongshan Hospital, Shanghai (China); Xu, Dongrong [Columbia University and New York State Psychiatric Institute, MRI Unit/Epidemiology Division, Department of Psychiatry, New York, NY (United States)

    2017-06-15

    The risk of refractory epilepsy can be more dangerous than the adverse effect caused by medical treatment. In this study, we employed voxel-wise analysis (VWA) and tract-based spatial statistics (TBSS) methods to measure microstructural changes using diffusion tensor imaging (DTI) in patients of drug refractory epilepsy (DRE) who had been epileptic for more than 10 years. To examine the specific microstructural abnormalities in DRE patients and its difference from medically controlled epilepsy (MCE), we acquired DTI data of 7 DRE patients, 37 MCE patients, and 31 healthy controls (HCs) using a 3 T MRI scanner. Comparisons between epileptic patients and HCs between MCE and DRE patients were performed based on calculated diffusion anisotropic indices data using VWA and TBSS. Compared to HCs, epileptic patients (including MCE and DRE) showed significant DTI changes in the common affected regions based on VWA, whereas TBSS found that widespread DTI changes in parts of microstructures of bilateral hemispheres were more obvious in the DRE patients than that in the MCE patients when compared with HCs. In contrast, significant reduction of fractional anisotropy values of thalamo-cortical fibers, including left superior temporal gyrus, insular cortex, pre-/post-central gyri, and thalamus, were further found in DRE patients compared with MCE. The results of multiple diffusion anisotropic indices data provide complementary information to understand the dysfunction of thalamo-cortical pathway in DRE patients, which may be contributors to disorder of language and motor functions. Our current study may shed light on the pathophysiology of DRE. (orig.)

  1. Identifikasi bite marks dengan ekstraksi DNA metode Chelex (Bite marks identification with Chelex methods in DNA extraction

    Directory of Open Access Journals (Sweden)

    Imelda Kristina Sutrisno

    2013-06-01

    Full Text Available Background: In the case of crime often encountered evidence in bite marks form that was found on the victim’s body. Generally, bitemarks identification use standard techniques that compare the interpretation picture with the tooth model of suspected person. However, sometimes the techniques do not obtain accurate results. Therefore another technique is needed to support the identification process,such as DNA analysis that use the remaining epithelium attached in saliva to identify the DNA of the suspected person. In this processes a limited DNA material could be met, not only less in quantity but also less in quality. Chelex known as one of an effective DNA extraction method in DNA forensic case is needed to overcome this problem. Purpose: The study was aimed to examine the use of Chelex as DNA extraction method on a bitemarks sample models. Methods: The blood and bitemarks of 5 persons with were taken. The DNA of each subject was exctracted with Chelex and quantified the quantity with UV Spechtrophotometer. The DNA results was amplified by PCR at locus vWA and TH01 then vizualised by electrophoresis. Results: The electrophoresis’s results showed band at locus vWA and TH01 for blood sample and bite marks with no significant differences. Conclusion: The study showed that Chelex method could be use to extract DNA from bitemarks.Latar belakang: Dalam kasus kejahatan sering dijumpai bukti dalam bentuk bekas gigitan (bitemarks yang ditemukan pada tubuh korban. Umumnya, untuk mengidentifikasi bite marks menggunakan teknik standar yaitu membandingkan foto interpretasi dengan model gigi dari orang yang dicurigai. Namun demikian teknik ini terkadang tidak mendapatkan hasil yang akurat, sehingga diperlukan teknik lain untuk menunjang keberhasilan proses identifikasi pelaku, yakni melalui analisis DNA bitemarks, yang diperoleh dari saliva yang mengandung sisa epitel tersangka pelaku. Sampel DNA yang berasal dari bitemarks umumnya terbatas, tidak hanya

  2. Population Genetic data for 15 Autosomal STR markers in Eastern Turkey.

    Science.gov (United States)

    Tokdemir, Mehmet; Tunçez, Ferhat Turgut; Vicdanli, Nazif Harun

    2016-07-15

    The allelic frequency distribution and statistical genetic parameters of forensic relevance for 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) in a population sample of 802 unrelated individuals in Eastern Turkey. The expected performance of these loci for personal identification and paternity testing in this population was estimated. Eastern Turkey and other 12 country population data were compared using allele frequencies.

  3. A report of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics

    DEFF Research Database (Denmark)

    Bjerre, A; Syndercombe-Court, Denise; Lincoln, P

    1997-01-01

    We report the results of the 1995 and 1996 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Haemogenetics. In 1995, 18 laboratories participated and in 1996, 21 laboratories participated. Each year, blood samples from three persons (child...... for investigations in crime cases by the European DNA Profiling Group. In 1996, eight laboratories reported the results of PCR based typing of the short tandem repeat (STR) locus HumTH01, six laboratories reported results of HumVWA31A typing, and five laboratories reported the results of typing of the STR locus Hum...

  4. Ensaio de proficiência para análise de ditiocarbamatos em polpa de banana Proficiency assay of the dithiocarbamates in banana pulp analysis

    Directory of Open Access Journals (Sweden)

    Lucia Helena Pinto Bastos

    2007-02-01

    Full Text Available A proficiency assay of the determination of dithiocarbamate pesticide residues in banana was carried out. Fourteen laboratories participated in this study. Homogeneity and stability testing were performed by INCQS on the samples sent to the laboratories. Analytical results supplied by the pesticide residues laboratory of the VWA/KvW, Amsterdam, Holland, were used to define the designated value for the thiram concentration in the study samples. RESULTS: Fifty percent of the participating laboratories had satisfactory results. Efforts are needed to improve the precision of the analytical results and to decrease the number of false negative results observed.

  5. Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif

    Directory of Open Access Journals (Sweden)

    Bürglin Thomas R

    2008-03-01

    Full Text Available Abstract Background The Hedgehog (Hh signaling pathway plays important roles in human and animal development as well as in carcinogenesis. Hh molecules have been found in both protostomes and deuterostomes, but curiously the nematode Caenorhabditis elegans lacks a bona-fide Hh. Instead a series of Hh-related proteins are found, which share the Hint/Hog domain with Hh, but have distinct N-termini. Results We performed extensive genome searches of the cnidarian Nematostella vectensis and several nematodes to gain further insights into Hh evolution. We found six genes in N. vectensis with a relationship to Hh: two Hh genes, one gene with a Hh N-terminal domain fused to a Willebrand factor type A domain (VWA, and three genes containing Hint/Hog domains with distinct novel N-termini. In the nematode Brugia malayi we find the same types of hh-related genes as in C. elegans. In the more distantly related Enoplea nematodes Xiphinema and Trichinella spiralis we find a bona-fide Hh. In addition, T. spiralis also has a quahog gene like C. elegans, and there are several additional hh-related genes, some of which have secreted N-terminal domains of only 15 to 25 residues. Examination of other Hh pathway components revealed that T. spiralis - like C. elegans - lacks some of these components. Extending our search to all eukaryotes, we recovered genes containing a Hog domain similar to Hh from many different groups of protists. In addition, we identified a novel Hint gene family present in many eukaryote groups that encodes a VWA domain fused to a distinct Hint domain we call Vint. Further members of a poorly characterized Hint family were also retrieved from bacteria. Conclusion In Cnidaria and nematodes the evolution of hh genes occurred in parallel to the evolution of other genes that contain a Hog domain but have different N-termini. The fact that Hog genes comprising a secreted N-terminus and a Hog domain are also found in many protists suggests that this

  6. A new pentaplex PCR system for forensic casework analysis.

    Science.gov (United States)

    Lederer, T; Seidl, S; Graham, B; Betz, P

    2000-01-01

    In 1998 the Federal Criminal Police Office of Germany (BKA) established a central genetic database of offenders and suspects to facilitate comparisons with biological samples from future criminal offences. The five obligatory short tandem repeat (STR) loci in this database (TH01, SE33, vWA, FGA and D21S11) were co-amplified in a new PCR pentaplex analysing system together with the sex-specific locus amelogenin. Due to overlapping fragment sizes, amplification products were fluorescent dye-labelled with different colours, separated by electrophoresis and detected directly using the ABI PRISM 310 Genetic Analyzer. Reproducible and reliable results were obtained from as low as 125 pg template DNA, indicating high specificity and sensitivity of the assay. Environmental studies and enzymatic digest with DNase I revealed an excellent stability of the pentaplex system with typeable results even in cases of partially degraded DNA. Complete and reproducible DNA typing was possible in blood-stain mixtures with the minor component as low as 10%. Mean stutter peak intensities were analysed for all loci and ranged from 2.7 +/- 0.8% (TH01) to 10.6 +/- 1.6% (vWA) of the main signal intensity. Allele frequencies were determined in a North Bavarian population sample (n = 121). The combination of five systems resulted in a mean exclusion chance of 99.86% and a power of discrimination of 99.999996%. No deviation from Hardy-Weinberg equilibrium could be found.

  7. Development of receptor-based inhibitory RNA aptamers for anthrax toxin neutralization.

    Science.gov (United States)

    Lee, Sang-Choon; Gedi, Vinayakumar; Ha, Na-Reum; Cho, Jun-Haeng; Park, Hae-Chul; Yoon, Moon-Young

    2015-01-01

    Anthrax toxin excreted by Bacillus anthracis is the key causative agent of infectious anthrax disease. In the present study, we targeted the binding of PA to the ATR/TEM8 Von Willebrand factor type A (VWA) domain, which we cloned into Escherichia coli and purified to homogeneity under denaturing conditions. To develop an anthrax toxin inhibitor, we selected and identified short single strand RNA aptamers (approximately 30mer) consisting of different sequences of nucleic acids with a high binding affinity in the 100 nanomolar range against the recombinant ATR/TEM8 VWA domain using systematic evolution of ligands by exponential enrichment (SELEX). Five candidate aptamers were further characterized by several techniques including secondary structural analysis. The inhibitor efficiency (IC50) of one of the aptamers toward anthrax toxin was approximately 5μM in macrophage RAW 264.7 cells, as determined from cytotoxicity analysis by MTT assay. We believe that the candidate aptamers should be useful for blocking the binding of PA to its receptor in order to neutralize anthrax toxin. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Tumor endothelium marker-8 based decoys exhibit superiority over capillary morphogenesis protein-2 based decoys as anthrax toxin inhibitors.

    Directory of Open Access Journals (Sweden)

    Chenguang Cai

    Full Text Available Anthrax toxin is the major virulence factor produced by Bacillus anthracis. The toxin consists of three protein subunits: protective antigen (PA, lethal factor, and edema factor. Inhibition of PA binding to its receptors, tumor endothelium marker-8 (TEM8 and capillary morphogenesis protein-2 (CMG2 can effectively block anthrax intoxication, which is particularly valuable when the toxin has already been overproduced at the late stage of anthrax infection, thus rendering antibiotics ineffectual. Receptor-like agonists, such as the mammalian cell-expressed von Willebrand factor type A (vWA domain of CMG2 (sCMG2, have demonstrated potency against the anthrax toxin. However, the soluble vWA domain of TEM8 (sTEM8 was ruled out as an anthrax toxin inhibitor candidate due to its inferior affinity to PA. In the present study, we report that L56A, a PA-binding-affinity-elevated mutant of sTEM8, could inhibit anthrax intoxication as effectively as sCMG2 in Fisher 344 rats. Additionally, pharmacokinetics showed that L56A and sTEM8 exhibit advantages over sCMG2 with better lung-targeting and longer plasma retention time, which may contribute to their enhanced protective ability in vivo. Our results suggest that receptor decoys based on TEM8 are promising anthrax toxin inhibitors and, together with the pharmacokinetic studies in this report, may contribute to the development of novel anthrax drugs.

  9. Population genetic analysis among five Indian population groups using six microsatellite markers.

    Science.gov (United States)

    Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

    2003-04-01

    Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

  10. Chaperone Role for Proteins p618 and p892 in the Extracellular Tail Development of Acidianus Two-Tailed Virus

    DEFF Research Database (Denmark)

    Scheele, Urte; Erdmann, Susanne; Ungewickell, Ernst J

    2011-01-01

    , is involved in this process. We propose that an additional chaperone system is required, consisting of a MoxR-type AAA ATPase (p618) and a von Willebrand domain A (VWA)-containing cochaperone, p892. Both proteins are absent from the other known bicaudavirus, STSV1, which develops a single tail intracellularly....... p618 exhibits ATPase activity and forms a hexameric ring complex that closely resembles the oligomeric complex of the MoxR-like protein RavA (YieN). ATV proteins p387, p653, p800, and p892 interact with p618, and with the exception of p800, all bind to DNA. A model is proposed to rationalize...

  11. An Omnidirectional Mobile Millimeters Size Micro-Robot with Novel Duel-Wheels

    Directory of Open Access Journals (Sweden)

    Chen Zhang

    2008-11-01

    Full Text Available A millimeters size omni-directional mobile micro-robot is presented in this paper. A unique duel-wheel structure is designed for no-slip motion during the steering, by turning the slip friction between the wheel and ground into rolling friction. The robot was driven by four electromagnetic micromotors with 2.1mm?2.1mm?1.3mm size. Three of them are for translation and the other one is for rotation. Kinematics model is analyzed to prove the omni-directional mobility. Virtual-Winding Approach (VWA and PWM-Based VectorSynthesize Approach(PBVSA current control methods are presented to satisfy a requirement of higher positioning accuracy. Experimental results demonstrate the feasibility of this concept.

  12. Allele frequencies of 14 STR loci in the population of Malta.

    Science.gov (United States)

    Cassar, M; Farrugia, C; Vidal, C

    2008-05-01

    Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands.

  13. Population data of nine STRs of Mexican-Mestizos from Mexico City.

    Science.gov (United States)

    Luna-Vazquez, A; Vilchis-Dorantes, G; Paez-Riberos, L A; Muñoz-Valle, F; González-Martin, A; Rangel-Villalobos, H

    2003-09-09

    One hundred and thirteen individuals were PCR-typed for nine STR loci with the AmpFlSTR Profiler Plus PCR amplification kit, including the following autosomal STRs: D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. Allele frequencies for each STR were estimated, and they were compared to other populations. Genotype distribution by locus and by two-loci combination was in agreement with Hardy-Weinberg expectations for all nine STRs. For this region of Mexico, the combined probability of exclusion (PE) and power of discrimination (PD) were estimated: PE=99.964% and PD>99.999%.

  14. Allele frequencies of the 15 AmpF/Str Identifiler loci in the population of Metztitlán (Estado de Hidalgo), México.

    Science.gov (United States)

    Gorostiza, A; González-Martín, A; Ramírez, C López; Sánchez, C; Barrot, C; Ortega, M; Huguet, E; Corbella, J; Gené, M

    2007-03-02

    The 15 AmpF/STR Identifiler loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were analyzed in the sample of 180 unrelated autochthonous healthy adults born in Meztitlán City from the valley of Metztitlán (Estado de Hidalgo, México). The agreement with Hardy-Weinberg equilibrium was confirmed for all loci. From the forensic point of view, the heterozygosity value, power of discrimination and the a priori chance of exclusion were calculated.

  15. Population genetics of 15 AmpflSTR Identifiler loci in Macedonians and Macedonian Romani (Gypsy).

    Science.gov (United States)

    Havas, Dubravka; Jeran, Nina; Efremovska, Ljudmila; Dordević, Dobrivoje; Rudan, Pavao

    2007-12-20

    Allele frequencies of 15 AmpFlSTR Identifiler STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were analysed in a sample of 100 unrelated autochthonous Macedonian and 102 Macedonian Romani individuals, representing different ethnic groups residing within the same country of Former Yugoslav Republic of Macedonia. The interpopulation comparisons between Macedonians and Macedonian Romani with four south eastern European populations, Kosovo Albanians, Serbians from Vojvodina Province, western Romanians and northern Greeks were performed as well as comparison between Macedonian Romani and Assam population from Asia (India). Reported data point that Macedonian Romani, as an example of an endogamous population of Asian (Indian) origin, show significant allelic differences when compared to neighbouring south eastern European populations.

  16. Prenatal diagnosis of a fetus in a family with mandibulofacial dysostosis%颅面畸形家系的胎儿产前诊断与分析

    Institute of Scientific and Technical Information of China (English)

    刘彦慧; 石少权; 张艳亮; 戴勇; 商璇; 吴亚敏; 李超强; 黎丽芬

    2010-01-01

    Objective To measure the feasibility of application of comparative genomic hybridization technique in the prenatal diagnosis of fetus with mandibulofacial dysostosis. Methods A pregnant woman having a fetus with mandibulofacial dysostosis diagnosed by prenatal ultrasound test was selected. The amniotic fluid and blood of the pregnant and blood of her husband were collected and conventional cytogenetic analysis was performed. The whole genome was scanned by array comparative genomic hybridization assay (array-CGH). Reverse transcription fluorescence quantitative PCR(RT-qPCR) analysis was used to verify the result of array-CGH. Results No abnormality was found in conventional cytogenetic analysis while a duplicated region in 1p36.33 was detected by array-CGH assay. The region spans 722 kb and contains two genes, VWA1 and PYGO2, which play roles in the development of cartilage. The result of array-CGH was confirmed by the RT-qPCR assay. The diagnosis of mandibulofacial dysostosis was confirmed after birth. Conclusion Author diagnosed a fetus with mandibulofacial dysostosis by array-CGH assay and found two candidate genes related to the development of craniofacial bone: VWA1 and PYGO2.%目的 探讨先天性颅面畸形胎儿的产前诊断技术.方法 选择产前检查B超显示胎儿具有颅面畸形的孕妇1例,采集孕妇羊水、外周血和其丈夫外周血样本,进行常规G显带核型分析.再采用比较基因组杂交技术(aaray comparative genomic hybridization,array-CGH)进行全基因组高分辨扫描和分析,逆转录荧光定量PCR方法对array-CGH结果进行验证.并在患儿出生后再进行重复检测确认.结果 G显带核型分析未见异常,array-CGH显示胎儿1p36.33区域有重复,长度约为722 kb,该片段中VWA1和PYGO2基因与软骨发育有关,定量PCR实验证实了比较基因组杂交的结果,拟诊为颅面畸形,胎儿出生后得到进一步确认.结论 应用比较基因组杂交技术,成功对1例先天性

  17. CODIS STR loci data from 41 sample populations.

    Science.gov (United States)

    Budowle, B; Shea, B; Niezgoda, S; Chakraborty, R

    2001-05-01

    Allele distributions for 12 or 13 CODIS core tetrameric short tandem repeat (STR) loci CSFIPO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA were determined in 41 population data sets. The major population groups comprise African Americans, U.S. Caucasians, Hispanics, Far East Asians, and Native Americans. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. The FST estimates over all thirteen STR loci are 0.0006 for African Americans, -0.0005 for Caucasians, 0.0021 for Hispanics, 0.0039 for Asians, and 0.0282 for Native Americans.

  18. Comparison of STR polymorphism among a Kirgiz ethnic group from Sinkiang and other groups

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    STR(Short tandem repeats)loci consist ofsi mple repeated sequences with2-6bp in length.The range of STR polymorphis m fragments is ap-proxi mately from100bp to350bp.STR appears tobe abundant in human genome and occurs every20kb on average[1-2].In present study,the frequencydistributions for nine STRloci were analyzed usingAmpFLSTR(ProfilerTMPCR Amplification Kit(Perkin-El mer).These STRs are D3S1358,VWA,CSF1PO,FGA,THO1,TPOX,D5S818,D13S317and D7S820.All these loci were analyzedby genescan.Establishment of a ...

  19. Genetic Analysis of 15 STR Loci in Chinese Han Population from West China

    Institute of Scientific and Technical Information of China (English)

    Ya-Jun Deng; Jiang-Wei Yan; Xiao-Guang Yu; Yuan-Zhe Li; Hao-Fang Mu; Yan-Qing Huang; Xiao-Tie Shi; Wei-Min Sun

    2007-01-01

    Allele frequencies for 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001-0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.

  20. Robust EMG sensing system based on data fusion for myoelectric control of a robotic arm

    Directory of Open Access Journals (Sweden)

    Soria Carlos M

    2009-02-01

    Full Text Available Abstract Background Myoelectric control of a robotic manipulator may be disturbed by failures due to disconnected electrodes, interface impedance changes caused by movements, problems in the recording channel and other various noise sources. To correct these problems, this paper presents two fusing techniques, Variance Weighted Average (VWA and Decentralized Kalman Filter (DKF, both based on the myoelectric signal variance as selecting criterion. Methods Tested in five volunteers, a redundant arrangement was obtained with two pairs of electrodes for each recording channel. The myoelectric signals were electronically amplified, filtered and digitalized, while the processing, fusion algorithms and control were implemented in a personal computer under MATLAB® environment and in a Digital Signal Processor (DSP. The experiments used an industrial robotic manipulator BOSCH SR-800, type SCARA, with four degrees of freedom; however, only the first joint was used to move the end effector to a desired position, the latter obtained as proportional to the EMG amplitude. Results Several trials, including disconnecting and reconnecting one electrode and disturbing the signal with synthetic noise, were performed to test the fusion techniques. The results given by VWA and DKF were transformed into joint coordinates and used as command signals to the robotic arm. Even though the resultant signal was not exact, the failure was ignored and the joint reference signal never exceeded the workspace limits. Conclusion The fault robustness and safety characteristics of a myoelectric controlled manipulator system were substantially improved. The proposed scheme prevents potential risks for the operator, the equipment and the environment. Both algorithms showed efficient behavior. This outline could be applied to myoelectric control of prosthesis, or assistive manipulators to better assure the system functionality when electrode faults or noisy environment are present.

  1. The Receptors that Mediate the Direct Lethality of Anthrax Toxin

    Directory of Open Access Journals (Sweden)

    Stephen H. Leppla

    2012-12-01

    Full Text Available Tumor endothelium marker-8 (TEM8 and capillary morphogenesis protein-2 (CMG2 are the two well-characterized anthrax toxin receptors, each containing a von Willebrand factor A (vWA domain responsible for anthrax protective antigen (PA binding. Recently, a cell-based analysis was used to implicate another vWA domain-containing protein, integrin β1 as a third anthrax toxin receptor. To explore whether proteins other than TEM8 and CMG2 function as anthrax toxin receptors in vivo, we challenged mice lacking TEM8 and/or CMG2. Specifically, we used as an effector protein the fusion protein FP59, a fusion between the PA-binding domain of anthrax lethal factor (LF and the catalytic domain of Pseudomonas aeruginosa exotoxin A. FP59 is at least 50-fold more potent than LF in the presence of PA, with 2 μg PA + 2 μg FP59 being sufficient to kill a mouse. While TEM8−/− and wild type control mice succumbed to a 5 μg PA + 5 μg FP59 challenge, CMG2−/− mice were completely resistant to this dose, confirming that CMG2 is the major anthrax toxin receptor in vivo. To detect whether any toxic effects are mediated by TEM8 or other putative receptors such as integrin β1, CMG2−/−/TEM8−/− mice were challenged with as many as five doses of 50 μg PA + 50 μg FP59. Strikingly, the CMG2−/−/TEM8−/− mice were completely resistant to the 5-dose challenge. These results strongly suggest that TEM8 is the only minor anthrax toxin receptor mediating direct lethality in vivo and that other proteins implicated as receptors do not play this role.

  2. Forensic Profiling of Javanese and Madurese Families in Malang and Madura, East Java Indonesia.

    Directory of Open Access Journals (Sweden)

    Nikmatul Iza

    2014-02-01

    Full Text Available Purpose: The aims of this study are to identify the heritability of fingerprint patterns among three generations of Javanese and Madurese families and to determine the similarities, genetic variability and allele patterns for paternity testing. Material and Methods: The methods used in this study were the identification of the fingerprint patterns, DNA extraction from blood samples by salting out, PCR amplification use 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11, and visualized by 8% polyacrylamide gel. The allele of individual band profile was analyzed by using QuantityOne software. Results: The results of fingerprint patterns showed that the families of Javanese ethnic has specific in ulnar patterns on both the middle and little fingers, meanwhile the families of Madurese ethnic has a plain whorl patterns on the right thumb and left index fingers which were inherited from the first generation to the next generation. The similarities of profile DNA forensic in Javanese ethnic generally have the same band patterns were produced by using D7S820 and CSF1PO markers, whereas in Madurese ethnic by using VWA and D18S51 markers. The genetic variability in Javanese ethnic by using D3S1358 and D21S11 markers, meanwhile the Madurese ethnic by using TH01 and D21S11 markers. Conclusion: We can conclude that there are the different characteristic of the fingerprint pattern of Javanese and Madurese families and the similarities and genetic variability in families of Javanese were different with the families of Madurese on the some markers.

  3. Population genetic data for 15 autosomal STR markers in Turkish Cypriots from Cyprus.

    Science.gov (United States)

    Gurkan, Cemal; Demirdov, Damla Kanliada; Yamaci, Rezan Fahrioglu; Sevay, Huseyin

    2015-01-01

    Fifteen autosomal short tandem repeat (STR) markers [D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA] were analyzed in 501 unrelated, randomly selected Turkish Cypriot individuals from the island of Cyprus. While no locus duplications or null alleles were detected in these samples, eight allelic variants were observed in total, 75% of which were intermediate allelic variants that were absent in the system allelic ladder. Allelic frequencies and statistical parameters of forensic interest were calculated at each locus. For the 15 STR loci tested, combined matching probability (pM) was 2.15717 × 10(-18) and combined power of exclusion (PE) was 0.9999995213. No deviations from the Hardy-Weinberg equilibrium were observed, except for the vWA locus, which became insignificant after the Bonferroni correction for multiple testing. Locus-by-locus comparisons of the Turkish Cypriot allelic frequencies with those published for the neighboring and/or historically related populations with similar loci coverage (Turkish, Greek, Greek Cypriot, Italian and Lebanese) revealed some statistically significant differences at one to five loci. In general, an increase in the number of such significant differences between the Turkish Cypriot data and those for other populations correlated closely with an increase in the geographic distance and/or a decrease in the amount of historical contact. The Turkish Cypriot autosomal STR population study will find immediate use in the Committee on Missing Persons in Cyprus Project on the "Exhumation, Identification and Return of Remains of Missing Persons" and it will also be available for criminal, parentage and other missing person investigations.

  4. Robust EMG sensing system based on data fusion for myoelectric control of a robotic arm.

    Science.gov (United States)

    López, Natalia M; di Sciascio, Fernando; Soria, Carlos M; Valentinuzzi, Max E

    2009-02-25

    Myoelectric control of a robotic manipulator may be disturbed by failures due to disconnected electrodes, interface impedance changes caused by movements, problems in the recording channel and other various noise sources. To correct these problems, this paper presents two fusing techniques, Variance Weighted Average (VWA) and Decentralized Kalman Filter (DKF), both based on the myoelectric signal variance as selecting criterion. Tested in five volunteers, a redundant arrangement was obtained with two pairs of electrodes for each recording channel. The myoelectric signals were electronically amplified, filtered and digitalized, while the processing, fusion algorithms and control were implemented in a personal computer under MATLAB environment and in a Digital Signal Processor (DSP). The experiments used an industrial robotic manipulator BOSCH SR-800, type SCARA, with four degrees of freedom; however, only the first joint was used to move the end effector to a desired position, the latter obtained as proportional to the EMG amplitude. Several trials, including disconnecting and reconnecting one electrode and disturbing the signal with synthetic noise, were performed to test the fusion techniques. The results given by VWA and DKF were transformed into joint coordinates and used as command signals to the robotic arm. Even though the resultant signal was not exact, the failure was ignored and the joint reference signal never exceeded the workspace limits. The fault robustness and safety characteristics of a myoelectric controlled manipulator system were substantially improved. The proposed scheme prevents potential risks for the operator, the equipment and the environment. Both algorithms showed efficient behavior. This outline could be applied to myoelectric control of prosthesis, or assistive manipulators to better assure the system functionality when electrode faults or noisy environment are present.

  5. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers

    Indian Academy of Sciences (India)

    V. K. Kashyap; Richa Ashma; Sonali Gaikwad; B. N. Sarkar; R. Trivedi

    2004-04-01

    The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy–Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%–89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic

  6. Organic acids and aldehydes in rainwater in a northwest region of Spain

    Energy Technology Data Exchange (ETDEWEB)

    Pena, R.M.; Garcia, S.; Herrero, C. [Universidad de Santiago de Compostela, Lugo (Spain). Departamento de Quimica Analitica, Nutricion y Bromatologia

    2002-11-01

    During a 1 year period, measurements of carboxylic acids and aldehydes were carried out in rainwater samples collected at nine different sites in NW Spain surrounding a thermal power plant in order to determine concentration levels and sources. In addition, certain major ions (Cl{sup -}, NO{sub 3}{sup -}, SO{sub 4}{sup 2-}, Na{sup +}, NH{sub 4}{sup +}, K{sup +}, Mg{sup 2+}, Ca{sup 2+}) were also determined. Aldehyde and carboxylic acid concentration patterns and their effects on rainwater composition concerning temporal, seasonal and spatial variations were evaluated. Among carboxylic acids, formic and acetic were predominant (VWA 7.0 and 8.3 {mu}M), while formaldehyde and acroleine were the dominant aldehydes (VWA 0.42 and 1.25 {mu}M). Carboxylic acids were estimated to account for 27.5% of the total free acidity (TFA), whereas sulphuric and nitric acid accounted for 46.2% and 26.2%, respectively. Oxalic acid was demonstrated to be an important contributing compound to the acidification in rainwater representing 7.1% of the TFA. The concentration of aldehydes and carboxylic acids, which originated mainly from biogenic emissions in the area studied, was strongly dependent on the season of the year (growing and non-growing). The ratios of formic to acetic acids are considerably different in the two seasons suggesting that there exist distinct sources in both growing and non-growing seasons. Principal component analysis was applied in order to elucidate the sources of aldehydes and organic acids in rainwater. The prevalence of natural vegetative origins for both of these compounds versus anthropogenic emissions was demonstrated and the importance of the oxidation of aldehydes as a relevant source of organic acids was also established. (author)

  7. Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India.

    Science.gov (United States)

    Eaaswarkhanth, Muthukrishnan; Dubey, Bhawna; Ramakodi Meganathan, Poorlin; Noor, Sabahat; Haque, Ikramul

    2009-08-01

    In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.

  8. Allele frequency data of 21 autosomal short tandem repeat loci in Mesan and Basra provinces in South Iraq

    Directory of Open Access Journals (Sweden)

    Imad Hadi Hameed

    2015-12-01

    Full Text Available We focused on a sample of 100 unrelated persons from the provinces of southern Iraq. This is an analysis of the allele frequency and genotyping of those STR loci in an Iraqi population and this is the first study of its kind in Iraq. As such the data available could be utilized in the Iraqi database for the STR polymorphic markers. Chelex® kit was utilized to extract DNA then Power Plex21® kit (D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433 was used to amplify the isolated DNA. The mean PIC values and heterozygosity observed across 21 loci were 0.713 and 0.696, respectively. This shows high gene diversity. Those loci can be safely used to establish a DNA-based database for the Iraqi population because the power of discrimination values for all tested loci was from 71% to 97%.

  9. The contribution of genetic diversity to subdivide populations living in the silk road of China.

    Science.gov (United States)

    Zhang, Zhe; Wei, Shuguang; Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin

    2014-01-01

    There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.

  10. Optimization of the Phenol -Chloroform Silica DNA Extraction Method in Ancient Bones DNA Extraction

    Directory of Open Access Journals (Sweden)

    Morteza Sadeghi

    2014-04-01

    Full Text Available Introduction: DNA extraction from the ancient bones tissues is currently very difficult. Phenol chloroform silica method is one of the methods currently used for this aim. The purpose of this study was to optimize the assessment method. Methods: DNA of 62 bone tissues (average 3-11 years was first extracted with phenol chloroform silica methods and then with changing of some parameters of the methods the extracted DNA was amplified in eight polymorphisms area including FES, F13, D13S317, D16, D5S818, vWA and CD4. Results from samples gained by two methods were compared in acrylamide gel. Results: The average of PCR yield for new method and common method in eight polymorphism regions was 75%, 78%, 81%, 76%, 85%, 71%, 89%, 86% and 64%, 39%, 70%, 49%, 68%, 76%, 71% and 28% respectively. The average of DNA in optimized (in 35l silica density and common method were 267.5 µg/ml with 1.12 purity and 192.76 g/ml with 0.84 purity respectively. Conclusions: According to the findings of this study, it is estimated that longer EDTA attendance is an efficient agent in removing calcium and also adequate density of silica particles can be efficient in removal of PCR inhibitors.

  11. Reconstructing recent human phylogenies with forensic STR loci: A statistical approach

    Directory of Open Access Journals (Sweden)

    Khan Faisal

    2005-09-01

    Full Text Available Abstract Background Forensic Short Tandem Repeat (STR loci are effective for the purpose of individual identification, and other forensic applications. Most of these markers have high allelic variability and mutation rate because of which they have limited use in the phylogenetic reconstruction. In the present study, we have carried out a meta-analysis to explore the possibility of using only five STR loci (TPOX, FES, vWA, F13A and Tho1 to carry out phylogenetic assessment based on the allele frequency profile of 20 world population and north Indian Hindus analyzed in the present study. Results Phylogenetic analysis based on two different approaches – genetic distance and maximum likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out. The ensuing tree topologies and PC plots were further compared with those obtained in earlier phylogenetic investigations. The compiled database of 21 populations got segregated and finely resolved into three basal clusters with very high bootstrap values corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. Conclusion Based on this study we conclude that if appropriate and logistic statistical approaches are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the recent human phylogenies despite of their relatively high mutation rates.

  12. Reconstructing recent human phylogenies with forensic STR loci: a statistical approach.

    Science.gov (United States)

    Agrawal, Suraksha; Khan, Faisal

    2005-09-28

    Forensic Short Tandem Repeat (STR) loci are effective for the purpose of individual identification, and other forensic applications. Most of these markers have high allelic variability and mutation rate because of which they have limited use in the phylogenetic reconstruction. In the present study, we have carried out a meta-analysis to explore the possibility of using only five STR loci (TPOX, FES, vWA, F13A and Tho1) to carry out phylogenetic assessment based on the allele frequency profile of 20 world population and north Indian Hindus analyzed in the present study. Phylogenetic analysis based on two different approaches - genetic distance and maximum likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out. The ensuing tree topologies and PC plots were further compared with those obtained in earlier phylogenetic investigations. The compiled database of 21 populations got segregated and finely resolved into three basal clusters with very high bootstrap values corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. Based on this study we conclude that if appropriate and logistic statistical approaches are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the recent human phylogenies despite of their relatively high mutation rates.

  13. Genetic polymorphism study at 15 autosomal locus in central Indian population.

    Science.gov (United States)

    Shrivastava, Pankaj; Jain, Toshi; Trivedi, Veena Ben

    2015-01-01

    The analysis of 15 autosomal STR locus (TH01, D3S1358, vWA, D21S11, TPOX, D7S820, D19S433, D5S818, D2S1338, D16S539, CSF1PO, D13S317, FGA, D18S51, D8S1179) was done in 582 healthy unrelated individuals (Male-366, Female-216) originating from the various geographical regions of Madhya Pradesh, India. All locus fall under Hardy-Weinberg equilibrium except TPOX. These STR loci were highly informative and discriminating with combined power of discrimination (CPD) >0.99999. Locus wise allele frequencies of the studied population were compared with the other published populations. Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations. The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

  14. Nitric oxide affects ERK signaling through down-regulation of MAP kinase phosphatase levels during larval development of the ascidian Ciona intestinalis.

    Directory of Open Access Journals (Sweden)

    Immacolata Castellano

    Full Text Available In the ascidian Ciona intestinalis larval development and metamorphosis require a complex interplay of events, including nitric oxide (NO production, MAP kinases (ERK, JNK and caspase-3 activation. We have previously shown that NO levels affect the rate of metamorphosis, regulate caspase activity and promote an oxidative stress pathway, resulting in protein nitration. Here, we report that NO down-regulates MAP kinase phosphatases (mkps expression affecting positively ERK signaling. By pharmacological approach, we observed that the reduction of endogenous NO levels caused a decrease of ERK phosphorylation, whereas increasing levels of NO induced ERK activation. We have also identified the ERK gene network affected by NO, including mpk1, mpk3 and some key developmental genes by quantitative gene expression analysis. We demonstrate that NO induces an ERK-independent down-regulation of mkp1 and mkp3, responsible for maintaining the ERK phosphorylation levels necessary for transcription of key metamorphic genes, such as the hormone receptor rev-erb and the van willebrand protein vwa1c. These results add new insights into the role played by NO during larval development and metamorphosis in Ciona, highlighting the cross-talk between different signaling pathways.

  15. The structure of the TFIIH p34 subunit reveals a von Willebrand factor A like fold.

    Directory of Open Access Journals (Sweden)

    Dominik R Schmitt

    Full Text Available RNA polymerase II dependent transcription and nucleotide excision repair are mediated by a multifaceted interplay of subunits within the general transcription factor II H (TFIIH. A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these vital cellular processes. The importance of this complex becomes further evident in the context of severe diseases like xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy, that arise from single point mutations in TFIIH subunits. Here we describe the structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum. The structure revealed that p34 contains a von Willebrand Factor A (vWA like domain, a fold which is generally known to be involved in protein-protein interactions. Within TFIIH p34 strongly interacts with p44, a positive regulator of the helicase XPD. Putative protein-protein interfaces are analyzed and possible binding sites for the p34-p44 interaction suggested.

  16. Analysis of short tandem repeat (STR polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice.

    Directory of Open Access Journals (Sweden)

    Okamoto O

    2003-04-01

    Full Text Available Allele and genotype frequencies for 15 short tandem repeat (STR polymorphisms--D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA--in a Japanese population were estimated. No deviations of the observed allele frequency from Hardy-Weinberg equilibrium expectations were found for any of the systems studied. Between 2 new pentanucleotide STR loci, Penta E and Penta D, for which there is only limited data regarding the allelic distribution in Japanese, the Penta E locus was found to be highly polymorphic and exhibited a tri- or tetra-modal distribution pattern having allelic peaks with 5, 11, 15 and 20 repeats. The distribution was significantly different from that of the other ethnic groups. Statistical parameters of forensic importance, the power of discrimination (PD, observed and expected heterozygosity values (H, polymorphism information content (PIC, power of discrimination (PD, matching probability (pM, power of exclusion (PE, and typical paternity index (PI, were calculated for the loci. These parameters indicated the usefulness of the loci in forensic personal identification and paternity testing among Japanese. The systems Penta E, FGA, D18S51 and D8S1179 were the most informative. This method was successfully applied to forensic personal identification and paternity testing among Japanese, thereby confirming its efficacy for forensic practice.

  17. Mutations of microsatellite autosomal loci in paternity investigations of the Southern Poland population.

    Science.gov (United States)

    Wojtas, Marta; Piniewska, Danuta; Polańska, Nina; Stawowiak, Agnieszka; Sanak, Marek

    2013-05-01

    In this study, germline mutations were analyzed for 26,040 parent-child allelic transfers among subjects referred to paternity testing and originating from the Slavonic population of the Southern Poland. Mutation rates were estimated for 15 autosomal microsatellite loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA. There were 35 mutation events observed at 11 from 15 analyzed loci. No mutations were found at TH01, D2S1338, D19S433 and TPOX loci. The mutation rate estimate was 0.0019 [0.0012-0.0028 95% CI] for paternal and 0.0004 [0.0002-0.0009] for maternal meiosis, while 25% mutations remained unassigned. The locus-specific mutation rate ranged from 0.0000 [0.0000-0.0014] to 0.0046 [0.0022-0.0087]. Mutations observed in male germlines were more frequent than in female germlines.

  18. Differential dependence on N-glycosylation of anthrax toxin receptors CMG2 and TEM8.

    Directory of Open Access Journals (Sweden)

    Sarah Friebe

    Full Text Available ANTXR 1 and 2, also known as TEM8 and CMG2, are two type I membrane proteins, which have been extensively studied for their role as anthrax toxin receptors, but with a still elusive physiological function. Here we have analyzed the importance of N-glycosylation on folding, trafficking and ligand binding of these closely related proteins. We find that TEM8 has a stringent dependence on N-glycosylation. The presence of at least one glycan on each of its two extracellular domains, the vWA and Ig-like domains, is indeed necessary for efficient trafficking to the cell surface. In the absence of any N-linked glycans, TEM8 fails to fold correctly and is recognized by the ER quality control machinery. Expression of N-glycosylation mutants reveals that CMG2 is less vulnerable to sugar loss. The absence of N-linked glycans in one of the extracellular domains indeed has little impact on folding, trafficking or receptor function of the wild type protein expressed in tissue culture cells. N-glycans do, however, seem required in primary fibroblasts from human patients. Here, the presence of N-linked sugars increases the tolerance to mutations in cmg2 causing the rare genetic disease Hyaline Fibromatosis Syndrome. It thus appears that CMG2 glycosylation provides a buffer towards genetic variation by promoting folding of the protein in the ER lumen.

  19. Identification of Candidate Genes for Reactivity in Guzerat (Bos indicus) Cattle: A Genome-Wide Association Study

    Science.gov (United States)

    Fonseca, Pablo Augusto de Souza; Pires, Maria de Fátima Ávila; Ventura, Ricardo Vieira; Rosse, Izinara da Cruz.; Bruneli, Frank Angelo Tomita; Machado, Marco Antonio; Carvalho, Maria Raquel Santos

    2017-01-01

    Temperament is fundamental to animal production due to its direct influence on the animal-herdsman relationship. When compared to calm animals, the aggressive, anxious or fearful ones exhibit less weight gain, lower reproductive efficiency, decreased milk production and higher herd maintenance costs, all of which contribute to reduced profits. However, temperament is a trait that is complex and difficult to assess. Recently, a new quantitative system, REATEST®, for assessing reactivity, a phenotype of temperament, was developed. Herein, we describe the results of a Genome-wide association study for reactivity, assessed using REATEST® with a sample of 754 females from five dual-purpose (milk and meat production) Guzerat (Bos indicus) herds. Genotyping was performed using a 50k SNP chip and a two-step mixed model approach (Grammar-Gamma) with a one-by-one marker regression was used to identify QTLs. QTLs for reactivity were identified on chromosomes BTA1, BTA5, BTA14, and BTA25. Five intronic and two intergenic markers were significantly associated with reactivity. POU1F1, DRD3, VWA3A, ZBTB20, EPHA6, SNRPF and NTN4 were identified as candidate genes. Previous QTL reports for temperament traits, covering areas surrounding the SNPs/genes identified here, further corroborate these associations. The seven genes identified in the present study explain 20.5% of reactivity variance and give a better understanding of temperament biology. PMID:28125592

  20. Genetic analysis of allelic variants, single-step mutations, three allelic variants of the 15 STR loci in the population of Northeast Bosnia

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna

    2013-01-01

    Full Text Available Diversity of nuclear DNA microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping STR loci with PowerPlextm16. Genetic analysis of allelic variants of the 15 STR loci detected 17 samples determined as microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II.

  1. Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese

    Institute of Scientific and Technical Information of China (English)

    Shuangding Li; Chunxia Yan; Yajun Deng; Ruilin Wang; Jian Wang; Huanming Yang; Shengbin Li

    2003-01-01

    Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX,CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with afour-color fluorescence method in samples from 174 unrelated Han individuals inNorth China. The allele frequencies, genotype frequencies, heterozygosity, prob-ability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstratedthat the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was1.05 × 10-10 within nine STR loci analyzed and the probability of paternity exclusion(EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternitytesting and sex determination in forensic sciences.

  2. Using hydrophilic adhesive tape for collection of evidence for forensic DNA analysis.

    Science.gov (United States)

    Li, Richard C; Harris, Howard A

    2003-11-01

    Known exemplar samples of human DNA have traditionally been body fluids, such as blood, saliva, and semen. In each case, the presence of water is a risk for the bacterial growth, which may degrade the DNA evidence. In this study, the authors have developed a method that employed a hydrophilic adhesive tape (HAT) for collecting DNA evidence. The HAT method was used to remove surface cells from relatively hairless areas on the body. The area examined were ankle, arm, behind the ear, between fingers and back of the neck. The HAT was then dissolved in the extraction buffer. DNA typing was performed at vWA, THo1, F13A1, and FES loci using the short tandem repeat (STR) analysis. Our results show that the samples collected from ear give the best results with a success rate of 100%. All subjects tested by this method had known STR genotypes established from buccal swabs. The authors' results suggest that the HAT method can be used as a less invasive method for collecting biological evidence for forensic DNA analysis. In addition, this collection method should reduce the risk of DNA degradation due to the moisture, which is encountered using conventional collecting methods.

  3. THE STUDY OF POPULATION GENETIC RELATION AMONG TEN ETHNIC GROUPS IN NORTHWEST CHINA

    Institute of Scientific and Technical Information of China (English)

    康龙丽; 金天博; 陈腾; 李生斌

    2004-01-01

    Objective To investigate the genetic relation among ten ethnic groups in northwest China. Methods Allele frequencies of six STR(short tandem repeat ) loci in D13S1358, VWA, FGA, D5S818, D13S317, and D7S820 were collected from Lasa Tibetan, Changdu Tibetan, Xian Han, Gansu Dongxiang, Gansu Yugu, Xinjiang Uygur, Ozbak, Kirgiz, Sibe, Ningxia Hui by the results of State Key laboratory, Forensic Science Department, school of medical, Xian Jiaotong University and internet biological information data bank, and compared with that of the Mongolian, Zhuang in China, and White and Negro in USA. The polymorphism index (H, DP, PPE, PIC) and genetic distance, then the phylogenetic tree of all population were reported. Results The resulting tree topology exhibited strong geographic and racial partitioning consistent with that obtained with HLA and classical genetic polymorphisms. Conclusion The results suggest that forensic STR loci may be particularly powerful tools and provide the necessary fine resolution for the reconstruction of recent human evolutionary history.

  4. Regulation of archaella expression by the FHA and von Willebrand domain-containing proteins ArnA and ArnB in Sulfolobus acidocaldarius.

    Science.gov (United States)

    Reimann, Julia; Lassak, Kerstin; Khadouma, Sunia; Ettema, Thijs J G; Yang, Nuan; Driessen, Arnold J M; Klingl, Andreas; Albers, Sonja-Verena

    2012-10-01

    The ability of microorganisms to sense and respond to sudden changes in their environment is often based on regulatory systems comprising reversible protein phosphorylation. The archaellum (former: archaeal flagellum) is used for motility in Archaea and therefore functionally analogous to the bacterial flagellum. In contrast with archaellum-mediated movement in certain members of the Euryarchaeota, this process, including its regulation, remains poorly studied in crenarchaeal organisms like Sulfolobus species. Recently, it was shown in Sulfolobus acidocaldarius that tryptone limiting conditions led to the induction of archaella expression and assembly. Here we have identified two proteins, the FHA domain-containing protein ArnA and the vWA domain-containing protein ArnB that are involved in regulating archaella expression in S. acidocaldarius. Both proteins are phosphorylated by protein kinases in vitro and interact strongly in vivo. Phenotypic analyses revealed that these two proteins are repressors of archaella expression. These results represent the first step in understanding the networks that underlie regulation of cellular motility in Crenarchaeota and emphasize the importance of protein phosphorylation in the regulation of cellular processes in the Archaea.

  5. Developmental validation of the PowerPlex(®) Fusion System for analysis of casework and reference samples: A 24-locus multiplex for new database standards.

    Science.gov (United States)

    Oostdik, Kathryn; Lenz, Kristy; Nye, Jeffrey; Schelling, Kristin; Yet, Donald; Bruski, Scott; Strong, Joshua; Buchanan, Clint; Sutton, Joel; Linner, Jessica; Frazier, Nicole; Young, Hays; Matthies, Learden; Sage, Amber; Hahn, Jeff; Wells, Regina; Williams, Natasha; Price, Monica; Koehler, Jody; Staples, Melisa; Swango, Katie L; Hill, Carolyn; Oyerly, Karen; Duke, Wendy; Katzilierakis, Lesley; Ensenberger, Martin G; Bourdeau, Jeanne M; Sprecher, Cynthia J; Krenke, Benjamin; Storts, Douglas R

    2014-09-01

    The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. Yet there remain situations that argue for inclusion of more loci and increased discrimination. The PowerPlex(®) Fusion System allows simultaneous amplification of the following loci: Amelogenin, D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, DYS391, D8S1179, D12S391, D19S433, FGA, and D22S1045. The comprehensive list of loci amplified by the system generates a profile compatible with databases based on either the expanded CODIS or European Standard Set (ESS) requirements. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the PowerPlex(®) Fusion System across a number of variables. Consistent and high-quality results were compiled using data from 12 separate forensic and research laboratories. The results verify that the PowerPlex(®) Fusion System is a robust and reliable STR-typing multiplex suitable for human identification.

  6. Developmental validation of the GlobalFiler(®) Express PCR Amplification Kit: A 6-dye multiplex assay for the direct amplification of reference samples.

    Science.gov (United States)

    Wang, Dennis Y; Gopinath, Siddhita; Lagacé, Robert E; Norona, Wilma; Hennessy, Lori K; Short, Marc L; Mulero, Julio J

    2015-11-01

    In order to increase the power of discrimination, reduce the possibility of adventitious matches, and expand global data sharing, the CODIS Core Loci Working Group made a recommendation to expand the CODIS core loci from the "required" 13 loci to 20 plus three additional "highly recommended" loci. The GlobalFiler(®) Express Kit was designed to incorporate all 20 required and 3 highly recommended loci along with a novel male-specific Y insertion/deletion marker. The GlobalFiler(®) Express Kit allows simultaneous amplification of the following loci: D3S1358, vWA, D16S539, CSF1PO, TPOX, Yindel, AMEL, D8S1179, D21S11, D18S51, DYS391, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, and D2S1338. The kit enables direct amplification from blood and buccal samples stored on paper or swab and the chemistry features an optimized PCR protocol that yields time to results in less than an hour. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the GlobalFiler(®) Express Kit over a number of variables. The validation results demonstrate that the 24-locus multiplex kit is a robust and reliable identification assay as required for forensic DNA typing and databasing.

  7. Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit.

    Science.gov (United States)

    Collins, Patrick J; Hennessy, Lori K; Leibelt, Craig S; Roby, Rhonda K; Reeder, Dennis J; Foxall, Paul A

    2004-11-01

    Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.

  8. Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system.

    Science.gov (United States)

    Ricci, U; Sani, I; Guarducci, S; Biondi, C; Pelagatti, S; Lazzerini, V; Brusaferri, A; Lapini, M; Andreucci, E; Giunti, L; Giovannucci Uzielli, M L

    2000-11-01

    We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

  9. The Contribution of Genetic Diversity to Subdivide Populations Living in the Silk Road of China

    Science.gov (United States)

    Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin

    2014-01-01

    There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations. PMID:24828511

  10. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

    Science.gov (United States)

    Budowle, B; Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M

    1999-11-01

    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

  11. Genetic characteristics of Sasang typology: a systematic review.

    Science.gov (United States)

    Sohn, Kyungwoo; Jeong, Ansuk; Yoon, Miyoung; Lee, Sunkyung; Hwang, Sangmoon; Chae, Han

    2012-12-01

    A systematic review on studies related to the genetic characteristics of Sasang types was conducted with the goal of delineating genetic characteristics of Sasang typology. Six electronic databases of up to the March 2011 were examined with the key words of Sasang typology, constitution, and genetics in both Korean and English. Predefined review criteria were used, including demographic characteristics, type classification methods, genotyping methods, and genotypes. Fifty-nine potentially relevant studies were identified and 40 peer reviewed research articles that contained genetic data were included. Fourteen articles reported statistically significant differences among Sasang types, which are heritability, structural variation, genome-wide screening, and pathophysiological function. Although significant genotypes were reported with vWA, CSF1PO, Penta D, HLA-Cw*04, HLA-Cw*07, PPAR-γ, MDR1, IL-α, IL-β, and IL-6 receptor, results of the review indicate that there was no conclusive genotype related to the Sasang typology. Considering the features of Sasang typology, it is recommended that the macroscopic systems medical approach on genetics be employed, rather than the single genes association approach.

  12. Analysis of 15 autosomal STR loci from Mar del Plata and Bahia Blanca (Central Region of Argentina).

    Science.gov (United States)

    Parolin, María Laura; Carreras-Torres, Robert; Sambuco, Lorena Andrea; Jaureguiberry, Stella Maris; Iudica, Celia Estela

    2014-05-01

    Allele frequencies for the 15 short tandem repeats (STRs) loci included in the AmpFlSTR® Identifiler kit were estimated in a sample of unrelated individuals from Mar del Plata (MDQ; N = 180) and Bahia Blanca (BB; N = 85) (Buenos Aires, Argentina). Biological samples were obtained from voluntary donors and forensic cases. Both populations were in Hardy-Weinberg equilibrium after Bonferroni correction, except for locus vWA in MDQ and D2S1338 in BB. FGA was the most informative locus, and the least discriminating locus was TPOX in both samples. The combined power of discrimination (PDc) and the combined probability of exclusion (PEc) were similar in MDQ and BB samples (0.999999998 < PDc < 0.999999999 and 0.999999979 < PEc < 0.999999989). The multidimentional scaling plot from Rst genetic distance matrix and the interethnic admixture estimation supported a higher European contribution in populations of the central region compared with populations from other regions of Argentina with higher Amerindian composition. These results enlarge the Argentine databases of autosomal STR loci, revealed as an excellent tool for human identification tests and population genetic analysis.

  13. The contribution of genetic diversity to subdivide populations living in the silk road of China.

    Directory of Open Access Journals (Sweden)

    Zhe Zhang

    Full Text Available There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3% can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.

  14. Genetic variation among four Mexican populations (Huichol, Purepecha, Tarahumara, and Mestizo) revealed by two VNTRs and four STRs.

    Science.gov (United States)

    Rangel-Villalobos, H; Rivas, F; Sandoval, L; Ibarra, B; Garcìa-Carvajal, Z Y; Cantú, J M; Figuera, L E

    2000-12-01

    Allele distributions of two polymorphisms with variable number of tandem repeats (VNTR), D1S80 and APOB, and four polymorphisms with short tandem repeats (STR), VWA, TH01, CSF1PO, and HPRTB, were analyzed in three Mexican ethnic groups: Huichol, Purepecha, and Tarahumara. Genotype distribution was in agreement with Hardy-Weinberg expectations for each locus and ethnic group. Heterozygosity (H), power of discrimination, and probability of exclusion were estimated. The three groups presented some distinctive genetic features: (1) a diminished genetic diversity (H = 66.8% to 73.4%) and mean number of alleles by locus (5.8 to 6.3) in comparison with Mexican mestizos (H = 78.3%, 10.5 alleles/locus), and (2) uneven allele distributions as evidenced by "distinctive alleles" with high frequencies, especially in the Tarahumara and the Huichol. Genetic relatedness analysis included data from a previously typed mestizo population, the largest and most widely distributed population in Mexico. Allele distribution differentiation was observed among all four groups, except between mestizo and Purepecha (p > 0.05), which was interpreted as indicating a larger Spanish component in the Purepecha as a result of gene flow effects. Although intrapopulation inbreeding (FIS) was not significant, heterozygote deficiency in the total population (FIT) and divergence among populations (FST) were significant (p Purepechas, and Huichols in relation to Tarahumaras. Correlation between the observed genetic features and the geographic isolation level points to genetic drift as the main cause of differentiation among these Mexican populations.

  15. Mapping regions in Ste5 that support Msn5-dependent and -independent nuclear export.

    Science.gov (United States)

    Hu, Zhenhua; Wang, Yunmei; Yu, Lu; Mahanty, Sanjoy K; Mendoza, Natalia; Elion, Elaine A

    2016-04-01

    Careful control of the available pool of the MAPK scaffold Ste5 is important for mating-pathway activation and the prevention of inappropriate mating differentiation in haploid Saccharomyces cerevisiae. Ste5 shuttles constitutively through the nucleus, where it is degraded by a ubiquitin-dependent mechanism triggered by G1 CDK phosphorylation. Here we narrow-down regions of Ste5 that mediate nuclear export. Four regions in Ste5 relocalize SV40-TAgNLS-GFP-GFP from nucleus to cytoplasm. One region is N-terminal, dependent on exportin Msn5/Ste21/Kap142, and interacts with Msn5 in 2 hybrid assays independently of mating pheromone, Fus3, Kss1, Ptc1, the NLS/PM, and RING-H2. A second region overlaps the PH domain and Ste11 binding site and 2 others are on the vWA domain and include residues essential for MAPK activation. We find no evidence for dependence on Crm1/Xpo1, despite numerous potential nuclear export sequences (NESs) detected by LocNES and NetNES1.1 predictors. Thus, Msn5 (homolog of human Exportin-5) and one or more exportins or adaptor molecules besides Crm1/Xpo1 may regulate Ste5 through multiple recognition sites.

  16. Genetic polymorphism at 15 STR loci among three important subpopulation of Bihar, India.

    Science.gov (United States)

    Ashma, R; Kashyap, V K

    2002-11-05

    Genotype polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in three genetically important minor caste groups (Yadav, Kurmi and Baniya) of Bihar, a eastern state of India to evaluate their significance in human identification and population genetics study. The selected communities practice endogamy. Despite of same geographical area, the physical features of Yadavs and Baniyas resemble North Indian Indo-Caucasoids whereas Kurmis resemble more to Indo-Austroloids. Among the chosen 15 loci, two are penta-nucleotide repeat: Penta-D and Penta-E, and 13 are tetra-nucleotide repeat: vWA D8S1179, TPOX, FGA, D5S818, D13S317, D7S820, D16S539, D3S1358, THO1, CSF1PO, D21S11, D18S51 and are validated for other population of India and world for forensic testing and human population study. Thirteen of these STR loci are present in the combined DNA index system (CODIS) [J. Forensic Sci. 44 (1999) 1277] and world-wide data is available.

  17. Genetic diversity at two pentanucleotide STR and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of central India.

    Science.gov (United States)

    Sarkar, N; Kashyap, V K

    2002-08-28

    Genetic diversity study at STR loci in 208 individuals belonging to two backward groups, one caste and one tribal community of Central India called "Chhattisgarh" has been carried out to evaluate significance of Powerplex System loci in human identification and population diversity. Populations are Agharia (72), Satmani (50), Dheria Gond (36) and Teli (50). Fifteen loci (Powerplex 16 Kit) studied are Penta E, D18S51, D21S11, THO1, D3S1358, FGA, TPOX, D8S1179, vWA, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818. The studied penta nucleotide STR (two) and 13 tetranucleotide (CODIS ) STR are found to be highly polymorphic genetic markers in all studied populations. Most common allele for the four studied population has been found to be same at THO1 (allele 9), D8S1179 (allele 14), CSF1PO (allele 12), Penta E (allele 11) and D16S539 (allele 11). Penta E is found to be most polymorphic (PD=0.89373) among studied 15 STR loci in four populations of Central India.

  18. [First outbreak of bluetongue in goats in The Netherlands].

    Science.gov (United States)

    Dercksen, D; Groot Nibbelink, N; Paauwe, R; Backx, A; van Rijn, P; Vellema, P

    2007-10-15

    For the first time, bluetongue has been diagnosed in goats in the Netherlands and in Northwest-Europe. On the 17th of August 2006, bluetongue was for the first time diagnosed in sheep and a little later in cattle in The Netherlands. The clinical symptoms, diagnostics and differential diagnosis of bluetongue (BT) in goats in the Netherlands are described. The most obvious clinical signs were an acute drop in milk production and high fever (up to 42 degrees C). Clinical signs were less obvious than usually seen for clinically diseased sheep and cattle. A few goats showed oedema of the lips and the head, some nasal discharge and scabs on the nose and lips. Further erythema of the skin of the udder and small subcutaneous hemorrhages were seen. Just like one year ago, for the very first suspicion of bluetongue in Northwest-Europe, a good collaboration between practitioners, specialists of the Animal Health Service (GD Deventer), the Specialist Team of the Food and Consumer Product Safety Authority (VWA), and the Central Institute for animal Disease Control (CIDC-Lelystad) in The Netherlands, led to the first and rapid notification and confirmation of the suspicion of bluetongue.

  19. Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers.

    Science.gov (United States)

    Juárez-Cedillo, Teresa; Zuñiga, Joaquín; Acuña-Alonzo, Victor; Pérez-Hernández, Nonanzit; Rodríguez-Pérez, José Manuel; Barquera, Rodrigo; Gallardo, Guillermo J; Sánchez-Arenas, Rosalinda; García-Peña, Maria Del Carmen; Granados, Julio; Vargas-Alarcón, Gilberto

    2008-06-01

    The 15 AmpFlSTR Identifiler loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico. Significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected. The D18S51 locus had the highest power of discrimination (0.970). Genetic admixture estimations revealed a 69% of Amerindian, 26% of European and 5% of African contribution. Comparative analyses between Mexicans and other neighboring populations reveal significant differences in genetic diversity. Our results are important for future comparative genetic studies in different Latin American ethnic groups, particularly Mexican Mestizos and Amerindians. They should also be helpful in genetics, population evolution, forensic and paternity testing.

  20. Exploitation of latent allostery enables the evolution of new modes of MAP kinase regulation.

    Science.gov (United States)

    Coyle, Scott M; Flores, Jonathan; Lim, Wendell A

    2013-08-15

    Allosteric interactions provide precise spatiotemporal control over signaling proteins, but how allosteric activators and their targets coevolve is poorly understood. Here, we trace the evolution of two allosteric activator motifs within the yeast scaffold protein Ste5 that specifically target the mating MAP kinase Fus3. One activator (Ste5-VWA) provides pathway insulation and dates to the divergence of Fus3 from its paralog, Kss1; a second activator (Ste5-FBD) that tunes mating behavior is, in contrast, not conserved in most lineages. Surprisingly, both Ste5 activator motifs could regulate MAP kinases that diverged from Fus3 prior to the emergence of Ste5, suggesting that Ste5 activators arose by exploiting latent regulatory features already present in the MAPK ancestor. The magnitude of this latent allosteric potential drifts widely among pre-Ste5 MAP kinases, providing a pool of hidden phenotypic diversity that, when revealed by new activators, could lead to functional divergence and to the evolution of distinct signaling behaviors.

  1. STR allele sequence variation: Current knowledge and future issues.

    Science.gov (United States)

    Gettings, Katherine Butler; Aponte, Rachel A; Vallone, Peter M; Butler, John M

    2015-09-01

    This article reviews what is currently known about short tandem repeat (STR) allelic sequence variation in and around the twenty-four loci most commonly used throughout the world to perform forensic DNA investigations. These STR loci include D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, SE33, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045. All known reported variant alleles are compiled along with genomic information available from GenBank, dbSNP, and the 1000 Genomes Project. Supplementary files are included which provide annotated reference sequences for each STR locus, characterize genomic variation around the STR repeat region, and compare alleles present in currently available STR kit allelic ladders. Looking to the future, STR allele nomenclature options are discussed as they relate to next generation sequencing efforts underway.

  2. Microsatellite data support subpopulation structuring among Basques.

    Science.gov (United States)

    Pérez-Miranda, Ana M; Alfonso-Sánchez, Miguel A; Kalantar, Arif; García-Obregón, Susana; de Pancorbo, Marian M; Peña, José A; Herrera, Rene J

    2005-01-01

    Genomic diversity based on 13 short tandem repeat (STR) loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, and CSF1PO) is reported for the first time in Basques from the provinces of Guipúzcoa and Navarre (Spain). STR data from previous studies on Basques from Alava and Vizcaya provinces were also examined using hierarchal analysis of molecular variance (AMOVA) and genetic admixture estimations to ascertain whether the Basques are genetically heterogeneous. To assess the genetic position of Basques in a broader geographic context, we conducted phylogenetic analyses based on F(ST) genetic distances [neighbor-joining trees and multidimensional scaling (MDS)] using data compiled in previous publications. The genetic profile of the Basque groups revealed distinctive regional partitioning of short tandem repeat (STR) diversity. Consistent with the above, native Basques clearly segregated from other populations from Europe (including Spain), North Africa, and the Middle East. The main line of genetic discontinuity inferred from the spatial variability of the microsatellite diversity in Basques significantly overlapped the geographic distribution of the Basque language. The genetic heterogeneity among native Basque groups correlates with the peculiar geography of peopling and marital structure in rural Basque zones and with language boundaries resulting from the uneven impact of Romance languages in the different Basque territories.

  3. A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA.

    Science.gov (United States)

    Meissner, C; Bruse, P; Mueller, E; Oehmichen, M

    2007-03-02

    Analysis of short tandem repeat makers has become the most powerful tool for DNA typing in forensic casework analysis. Unfortunately, typing of DNA extracted from telogen shed hairs, bones buried in the soil or from paraffin-embedded, formalin-fixed tissue often reveals no results due to the degradation of DNA. The reduction in size of the target fragments by development of new primers and their combination in multiplex approaches open a new field of DNA analysis. Here we present a new sensitive short pentaplex PCR including the loci amelogenin, TH01, VWA, D3S1358 and D8S1179. Validation tests of our new method included sensitivity, mixtures, human specificity, artificial degradation of DNA by DNase I and case work analysis on a panel of different forensic samples. The detection limit was 12.5 pg of human DNA, and mixtures of 50 pg in a total of 1000 pg were clearly detectable and revealed complete profiles. Only DNA extracts of human primates displayed a few signals, whereas other animal, fungal or bacterial DNA showed no signals. Our method proved extremely valuable in the analysis of artificially degraded DNA and in forensic cases, where only poorly preserved DNA was available. This approach and other similar methods can aid in the analysis of samples where allelic drop out of larger fragments is observed. It is highly recommended to develop more of these multiplexes to improve poor quality DNA typing.

  4. Long-term trends in aerosol and precipitation composition over the western North Atlantic Ocean at Bermuda

    Science.gov (United States)

    Keene, W. C.; Moody, J. L.; Galloway, J. N.; Prospero, J. M.; Cooper, O. R.; Eckhardt, S.; Maben, J. R.

    2014-08-01

    Since the 1980s, emissions of SO2 and NOx (NO + NO2) from anthropogenic sources in the United States (US), Canada, and Europe have decreased significantly suggesting that the export of oxidized S and N compounds from surrounding continents to the atmosphere overlying the North Atlantic Ocean (NAO) has also decreased. The chemical compositions of aerosols and precipitation sampled daily on Bermuda (32.27° N, 64.87° W) from 1989 to 1997 and from 2006 to 2009 were evaluated to quantify the magnitudes, significance, and implications of associated tends in atmospheric composition. The chemical data were stratified based on FLEXPART (FLEXible PARTicle dispersion model) retroplumes into four discrete transport regimes: westerly flow from eastern North America (NEUS/SEUS); easterly trade-wind flow from northern Africa and the subtropical NAO (Africa); long, open-ocean, anticyclonic flow around the Bermuda High (Oceanic); and transitional flow from the relatively clean open ocean to the polluted eastern North America (North). Based on all data, annual average concentrations of non-sea-salt (nss) SO42- associated with aerosols and annual volume-weighted-average (VWA) concentrations in precipitation decreased significantly (by 22% and 49%, respectively) whereas annual VWA concentrations of NH4+ in precipitation increased significantly (by 70%). Corresponding trends in aerosol and precipitation NO3- and of aerosol NH4+ were insignificant. Nss SO42- in precipitation under NEUS/SEUS and Oceanic flow decreased significantly (61% each) whereas corresponding trends in particulate nss SO42- under both flow regimes were insignificant. Trends in precipitation composition were driven in part by decreasing emissions of SO2 over upwind continents and associated decreases in anthropogenic contributions to nss SO42- concentrations. Under NEUS/SEUS and Oceanic flow, the ratio of anthropogenic to biogenic contributions to nss SO42- in the column scavenged by precipitation were relatively

  5. Trace samples of human blood in mosquitoes as a forensic investigation tool.

    Science.gov (United States)

    Rabêlo, K C N; Albuquerque, C M R; Tavares, V B; Santos, S M; Souza, C A; Oliveira, T C; Oliveira, N C L; Crovella, S

    2015-11-23

    Investigations of any type of crime invariably starts at the crime scene by collecting evidence. Thus, the purpose of this research was to collect and analyze an entomological trace from an environment that is similar to those of indoor crime scenes. Hematophagous mosquitoes were collected from two residential units; saliva of volunteers that were residents in the units was also collected for genetic analysis as reference samples. We examined the allele frequencies of 15 short tandem repeat loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) and amelogenin. A total of 26 female hematophagous mosquitoes were identified as Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus; we were able to obtain 11 forensically valid genetic profiles, with a minimum of 0.028203 ng/μL of human DNA. Thus, the results of this study showed that it was possible to correlate human genetic information from mosquitoes with the volunteer reference samples, which validates the use of this information as forensic evidence. Furthermore, we observed mixed genetic profiles from one mosquito. Therefore, it is clearly important to collect these insects indoors where crimes were committed, because it may be possible to find intact genetic profiles of suspects in the blood found in the digestive tract of hematophagous mosquitoes for later comparison to identify an offender and/or exclude suspects.

  6. Mutation analysis of 24 short tandem repeats in Chinese Han population.

    Science.gov (United States)

    Lu, Dejian; Liu, Qiuling; Wu, Weiwei; Zhao, Hu

    2012-03-01

    Germline mutations of 24 short tandem repeat (STR) loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, Penta E, D16S539, D18S51, Penta D, D21S11, D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05) were studied for 6,441 parent-child meioses taken from the paternity testing cases in Chinese Han population. In total, 195 mutations were identified at 22 of the 24 loci. Among them, 189 (96.92%) mutations were one step, five mutations (2.56%) were two step, and one mutation (0.51%) was three step. No mutation was found at the TH01 and TPOX loci. The overall mutation rate estimated was 0.0013 (95% CI 0.0011-0.0015), and the locus-specific mutation rate estimated ranged from 0 to 0.0034. There was a bias in the STR mutations that repeat gains were more common than losses (∼1.7:1). Mutation events in the male germline were more frequent than in the female germline (∼4.3:1). Furthermore, loci with a larger heterozygosity tended to have a higher mutation rate. Mutation in short alleles was biased towards expansion, whereas mutation in long alleles favored contraction. The long alleles have a higher allelic mutational probability than short alleles.

  7. An incest case with three biological brothers as alleged fathers: Even 22 autosomal STR loci analysis would not suffice without the mother.

    Science.gov (United States)

    Canturk, Kemal Murat; Emre, Ramazan; Gurkan, Cemal; Komur, Ilhami; Muslumanoglu, Omer; Dogan, Muhammed

    2016-07-01

    Here, we report an incest paternity case involving three biological brothers as alleged fathers (AFs), their biological sister and her child that was investigated using the Investigator ESSplex Plus, AmpFLSTR Identifiler Plus/Investigator IDplex Plus and PowerPlex 16 kits. Initial duo paternity investigations using 15-loci autosomal short tandem repeat (STR) analyses failed to exclude any of the AFs. Despite the fact that one of the brothers, AF1, had a mismatch with the child at a single locus (D2S1338), the possibility of a single-step mutation could not be ruled out. When the number of autosomal STR loci analysed was increased to 22 without the inclusion of the mother, AF2 and AF3 still could not be excluded, since both of them again had no mismatches with the child. A breakthrough was possible only upon inclusion of the mother so that trio paternity investigations were carried out. This time AF1 and AF2 could be excluded at two loci (D2S1338 and D1S1656) and six loci (vWa, D1S1656, D12S391, FGA, PENTA E and PENTA D), respectively, and AF3 was then the only brother who could not be excluded from paternity. Subsequent statistical analyses suggested that AF3 could be the biological father of the child with a combined paternity index >100 billion and a probability of paternity >99.99999999%. These findings consolidate the fact that complex paternity cases such as those involving incest could benefit more from the inclusion of the mother than simply increasing the number of STR loci analysed.

  8. Germline mutations of STR-alleles include multi-step mutations as defined by sequencing of repeat and flanking regions.

    Science.gov (United States)

    Dauber, Eva-Maria; Kratzer, Adelgunde; Neuhuber, Franz; Parson, Walther; Klintschar, Michael; Bär, Walter; Mayr, Wolfgang R

    2012-05-01

    Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.

  9. Genetic polymorphism of 15 STR loci in Qingdao Hah population%青岛地区汉族群体15个STR基因座的遗传多态性研究

    Institute of Scientific and Technical Information of China (English)

    张红岩; 万加华; 高自华; 戚其玮; 赵晶; 徐俐; 王雪倩

    2011-01-01

    Objective; To know the population genetic data of 15 short tandem repeat (STR) loci in Chinese Han population in the Qingdao aren Methods; 200 cases of ACD-blood specimens were collected form the unrelated individuals in Qingdao, The DNA samples were extracted with Chelex methed and amplified by multiplex PCR technique, The PCR produces and afterward genetyped were analyzed by an automatic genetic analyzer of ABI, Statistical analysis was carried out Matrix Laboratory Results; This study of IS loci of parameter on genetic polymorphisms were obtained. Conclusion; All of the IS loci have higher combined discrimination power and the exclusion probability, it can meet the needs of the parentage testing and personal identification in forensic medicine.%目的 了解15个短串联重复STR基因座在青岛地区汉族群体的遗传学数据.方法 对来自青岛地区汉族的200个无关个体的血样,Chelex法提取DNA,PCR复合扩增,采用ABI的全自动遗传分析仪进行基因分型,用Matlab编程进行统计学处理.结果 获得了D21S11,D7S820,D13S317,D19S433,D3S1358,D8S1179,CSF1P0,THO1,D16SS39,D2S1338,VWA,TPOX,D18S51,D5S818,FGA十五个STR基因座的遗传多态性参数.结论 15个STR基因座的累计个人识别率和非父排除率较高,适用于法医学亲子鉴定和个体识别

  10. Developmental validation of the PowerPlex(®) 21 System.

    Science.gov (United States)

    Ensenberger, Martin G; Hill, Carolyn R; McLaren, Robert S; Sprecher, Cynthia J; Storts, Douglas R

    2014-03-01

    The PowerPlex(®) 21 System is a STR multiplex that has been optimized for casework samples while still being capable of database workflows including direct amplification. The loci included in the multiplex offer increasing overlap with core loci used in different countries and regions throughout the world. The PowerPlex(®) 21 System contains D1S1656, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, Amelogenin, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA. These loci represent all 13 core CODIS loci in addition to loci commonly used in Asia and Europe. A developmental validation study was completed to document performance capabilities and limitations of the PowerPlex(®) 21 System. Data from this validation work served as the basis for the following conclusions: genotyping of single-source samples was reliable across a range of template DNA concentrations with >95% alleles called at 50 pg. Direct amplification of samples from FTA(®) storage cards was successfully performed using the reagents provided with the system and modified cycling protocols provided in the technical manual. Mixture analysis showed that over 95% of minor alleles were detected at 1:9 ratios. Reaction conditions including volume and annealing temperature as well as the concentrations of primers, DNA polymerase, magnesium, and Master Mix were shown to be optimal and able to withstand moderate variations without affecting system performance. Reproducible results were generated by different users at different sites. Finally, concordance studies showed consistent results when comparing the PowerPlex(®) 21 System with other commercially available STR-genotyping systems.

  11. 基于视觉词模糊权重的视频语义标注%Video Semantic Annotation Based on Visual Word Fuzzy Weighting

    Institute of Scientific and Technical Information of China (English)

    霍华; 赵刚

    2012-01-01

    This paper proposes a formulation of visual word weighting scheme Fuzzy Weighting Scheme(FWS) aiming at the Bag of Visual Word(BoVW) model vector quantization loss and visual word ambiguity. Based on It-Nearest Neighbors(KNN) pre-clustering results, One-Class Support Vector Machine(OC-SVM) on each clustering samples subset is trained. Visual words corresponding to a single local visual feature vector are determined according to the spatial distribution information ef clustering-hyperspheres and fuzzy weights are evaluated according to the distance function between sample feature and center of clustering-hypersphere. FWS is designed to boost the visual word expressiveness and discriminativeness. Experimental results show that the scheme outperforms TF scheme and VWA scheme by 34% and 16% respectively on video semantic annotation precision.%针对视觉词袋模型的量化误差与视觉词含糊性,提出一种基于视觉词模糊权重的视频语义标注方案.该方案在训练样本集的预聚类基础上,逐个聚类训练单类支持向量机OC-SVM.根据样本特征与聚类超球球心的距离函数及聚类超球的空间分布确定视觉词映射及权重,以提高视觉词的表达力、区别力.实验结果表明,基于该方案的视频语义标注精度分别比TF方案和VWA方案提高34%和16%.

  12. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye

    2015-01-01

    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  13. [Attitude of primary care professionals to gender violence. A comparative study between Catalonia and Costa Rica].

    Science.gov (United States)

    Rojas Loría, Kattia; Gutiérrez Rosado, Teresa; Alvarado, Ricardo; Fernández Sánchez, Anna

    2015-10-01

    Describe the relationship between the attitude towards violence against women (VAW) of professionals of the health of primary care with variables such professional satisfaction, workload, orientation of professional practice, knowledge, training and use of network in Catalonia and Costa Rica. Cross-exploratory and comparative study. Primary care in Barcelona and nearby counties and the Greater Metropolitan Area (GAM) of Costa Rica. 235 primary health professionals of Medicine, Nursing, Psychology and Social Work. Questionnaire with eight sections about attitudes, professional satisfaction, and orientation of professional practice, workload, knowledge, training and use of network. Three types of analysis were carried out: a descriptive one by country; a bivariate analysis; and a multivariable linear regression model. Primary Health Professionals attitudes towards VAW health were similar in both contexts (Catalonia: 3.90 IC 95% 3.84-3.96; Costa Rica: 4.03 IC 95% 3.94-4.13). The variables associated with attitudes towards VAW were: Use of network resources (B=0.20, 95% CI -0.14-0.25, P=<.001), Training (B=0.10, 95% CI 0.04 to 0.17, P=<0.001), and country, Costa Rica (B=0.16, 95% CI 0.06 to 0.25, P=<0.001). There was no interaction between the country and the other variables, suggesting that the association between the variables and the attitude is similar in both countries. The results suggest that increased use of network resources and training are related to a positive attitude towards VWA in primary health professionals, both in Catalonia and Costa Rica. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

  14. 孕妇外周血浆胎儿DNA的STR检测

    Institute of Scientific and Technical Information of China (English)

    魏建波; 秦斐; 王伟; 俞禾涛

    2010-01-01

    目的探讨利用孕妇血浆中游离胎儿DNA进行遗传病产前基因诊断的可行性。方法用QIAamp DNA Kit抽提孕妇血浆DNA,应用AmpFl STR profiler试剂盒扩增9个(D3S1358,VWA,FGA,D5S818,D13S317,D7S820,D8S1179,D21S11,D18S51)具有高度多态性的短串联重复序列(short tandem repeat,STR)位点,以多重荧光PCR方法对不同孕期的36份孕妇血浆标本中DNA进行STR等位基因扩增,同时扩增孕妇丈夫外周血DNA。PCR产物经ABI Prism377序列分析仪电泳后,用基因扫描软件进行分析,以胎儿父源性STR等位基因在孕妇血浆中DNA的检出确认胎儿DNA存在。结果孕早期4份(4/6)、孕中期19份(19/20)、孕晚期9份(9/10)检出胎儿父源性等位基因,即胎儿DNA。4份样本未检到胎儿DNA。结论应用多重荧光PCR方法对孕妇血浆中DNA进行STR多态位点的复合扩增,可获得男性和女性胎儿DNA信息,可用于无创伤性产前诊断。

  15. Polymorphism analysis of 15 STR loci in a large sample of Guangdong (Southern China) Han population.

    Science.gov (United States)

    Chen, Ling; Lu, Huijie; Qiu, Pingming; Yang, Xingyi; Liu, Chao

    2015-11-01

    AmpFℓSTR Sinofiler PCR Amplification Kit is specially developed for Chinese forensic laboratories, but there are little population-genetic data about this kit for Southern China. This kit contains 15 STR loci: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, D6S1043, D12S391, D5S818 and FGA. We have conducted genotyping experiments on the 15 STR loci in 5234 unrelated individuals from Guangdong (Southern China). We observed a total of 243 alleles in the group with the allelic frequency values ranging from less than 0.0001 to 0.3686. Our statistic analysis indicates that the 15 STR loci conform to the Hardy-Weinberg's equilibrium (p>0.05). The highest polymorphism was found at D6S1043 locus and the lowest was found at D3S1358. The combined power of discrimination reached 0.99999999999999999977431 and the combined probability of paternity exclusion reached 0.999999721 for 15 STR loci. Guangdong Han population had significant differences compared with Shaanxi, Shandong and Henan province of Northern China. A Neighbor-joining tree indicates that the Guangdong Han has a close genetic relationship with the Yunnan population. Significant differences were found between Guangdong Han population and other reported populations (Japanese, Philippine, African American, Caucasian, Hispanic and Western Romanian) at 2-11 STR loci. The results may provide useful information for forensic sciences and population genetics studies. The present findings indicate that all the 15 STR loci are highly genetically polymorphic in the Han population of Guangdong.

  16. Tri-allelic pattern of short tandem repeats identifies the murderer among identical twins and suggests an embryonic mutational origin.

    Science.gov (United States)

    Wang, Li-Feng; Yang, Ying; Zhang, Xiao-Nan; Quan, Xiao-Liang; Wu, Yuan-Ming

    2015-05-01

    Monozygotic twins can be co-identified by genotyping of short tandem repeats (STRs); however, for distinguishing them, STR genotyping is ineffective, especially in the case of murder. Here, a rarely occurring tri-allelic pattern in the vWA locus (16, 18, 19) was identified only in the DNA of one identical twin, which could help to exonerate the innocent twin in a murder charge. This mutation was defined as primary through genotyping of the family and could be detected in blood, buccal and semen samples from the individual; however, two alternative allele-balanced di-allelic patterns (16, 18 or 16, 19) were detected in hair root sheath cells. Such a kind of segregation indicates a one-step mutation occurs in cell mitosis, which is after embryonic zygote formation and during the early development of the individual after the division of the blastocyte. Sequencing revealed the insertion between the allele 18 and 19 is a repeat unit of TAGA/TCTA (plus/minus strand), which belongs to "AGAT/ATCT"-based core repeats identified from all tri-allelic pattern reports recorded in the STR base and a detailed model was proposed for STR repeat length variation caused by false priming during DNA synthesis. Our model illustrates the possible origination of allele-balanced and unbalanced tri-allelic pattern, clarifies that the genotypes of parent-child mismatches, aberrant di-allelic patterns, and type 1 or 2 tri-allelic patterns should be considered as independent, but interconnected forms of STR mutation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. The next generation of DNA profiling--STR typing by multiplexed PCR--ion-pair RP LC-ESI time-of-flight MS.

    Science.gov (United States)

    Pitterl, Florian; Niederstätter, Harald; Huber, Gabriela; Zimmermann, Bettina; Oberacher, Herbert; Parson, Walther

    2008-12-01

    For the first time a multiplexed PCR approach suitable for mass spectrometric STR allele identification is presented. Thirteen forensically important STR markers (vWA, D21S11, D3S1358, D16S539, D8S1179, D7S820, D13S317, D5S818, TPOX, CSF1PO, D2S441, D10S1248, and D22S1045) and the gender typing locus amelogenin were simultaneously amplified. Ion-pair reversed-phase high-performance liquid chromatography electrospray-ionization time-of-flight mass spectrometry (ICEMS) was applied for genotyping, and allowed for highly efficient characterization of multiple PCR amplicons. Compared with electrophoretic sizing ICEMS enabled for the simultaneous detection of length and nucleotide variations. Thus, the obtained amount of biological information present within STR profiles was significantly increased even though the compatibility of typing results with electrophoretically generated data(bases) was maintained. Other advantages of the ICEMS platform included the abandonment of internal size standards, allelic ladders, and any kind of spectral calibration. The 14-plex PCR was tailor-made for ICEMS analysis by designing primer pairs that bind close to the repeat region, by using a proof reading polymerase for amplification, and by implementing molecular mass modifiers for prevention of molecular mass overlaps. In a series of experiments, the performance of the multiplexed PCR-ICEMS assay was evaluated. The ICEMS-based DNA profiling assay was found to be competitive regarding detection sensitivity and analyzability of degraded and casework samples with commercially available electrophoretic typing approaches, which suggests that multiplexed PCR-ICEMS assays could represent a valuable tool for (forensic) genetics.

  18. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.

    Science.gov (United States)

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng

    2014-09-01

    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

  19. Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform.

    Science.gov (United States)

    Guo, Fei; Zhou, Yishu; Liu, Feng; Yu, Jiao; Song, He; Shen, Hongying; Zhao, Bin; Jia, Fei; Hou, Guangwei; Jiang, Xianhua

    2016-07-01

    The Early Access STR Kit v1 is designed to detect 25-plex loci with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 16 of 20 expanded Combined DNA Index System (CODIS) core loci (CSF1PO, D1S1656, D2S1338, D2S441, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D13S317, D16S539, D19S433, D21S11, TH01, TPOX and vWA), 8 non-CODIS core loci (D1S1677, D2S1776, D4S2408, D5S2500.AC008791, D6S1043, D6S474, D9S2157 and D14S1434) and Amelogenin. In this study, we compared the Early Access STR Kit v1 with the Ion Torrent™ HID STR 10-plex to find out its improvements and explored an appropriate analytical threshold to enhance the performance. In addition, seven experiments were conducted to evaluate the Early Access STR Kit v1 such as studies of repeatability, concordance, sensitivity, mixtures, degraded samples, case-type samples and pedigrees. Other than a little discordance (0.95%) with CE-STR results observed at D21S11, NGS-STR results correctly reflected the sample being tested. Repeatable results were obtained from both initial PCRs and emPCRs aside from a few variations of allele coverage. Full profiles could be obtained from 100pg input DNA and >48.84% profiles from 10pg input DNA. Mixtures were easily detected at 9:1 and 1:9 ratios. This system could be adapted to case-type samples and degraded samples. As a whole, the Early Access STR Kit v1 is a robust, reliable and reproducible assay for NGS-STR typing and a potential tool for human identification.

  20. Characterization and expression analysis of a complement component gene in sea cucumber ( Apostichopus japonicus)

    Science.gov (United States)

    Chen, Zhong; Zhou, Zunchun; Yang, Aifu; Dong, Ying; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-12-01

    The complement system plays a crucial role in the innate immune system of animals. It can be activated by distinct yet overlapping classical, alternative and lectin pathways. In the alternative pathway, complement factor B (Bf) serves as the catalytic subunit of complement component 3 (C3) convertase, which plays the central role among three activation pathways. In this study, the Bf gene in sea cucumber ( Apostichopus japonicus), termed AjBf, was obtained by rapid amplification of cDNA ends (RACE). The full-length cDNA of AjBf was 3231 bp in length barring the poly (A) tail. It contained an open reading frame (ORF) of 2742 bp encoding 913 amino acids, a 105 bp 5'-UTR (5'-terminal untranslated region) and a 384 bp 3'-UTR. AjBf was a mosaic protein with six CCP (complement control protein) domains, a VWA (von Willebrand factor A) domain, and a serine protease domain. The deduced molecular weight of AjBf protein was 101 kDa. Quantitative real time PCR (qRT-PCR) analysis indicated that the expression level of AjBf in A. japonicus was obviously higher at larval stage than that at embryonic stage. Expression detection in different tissues showed that AjBf expressed higher in coelomocytes than in other four tissues. In addation, AjBf expression in different tissues was induced significantly after LPS or PolyI:C challenge. These results indicated that AjBf plays an important role in immune responses to pathogen infection.

  1. Diversity of nuclear short tandem repeat loci in representative sample of North-eastern Bosnian and Herzegovina population

    Directory of Open Access Journals (Sweden)

    Hadžiavdić Vesna

    2012-01-01

    Full Text Available Diversity of nuclear microsatellite markers were analyzed in a reference sample of the population of northeast Bosnia and Herzegovina. 437 samples taken from unrelated individuals were processed and three samples of paternity proof were shown. Detection effectiveness profile of the research, points to a valid choice of method of extraction, amplification and genotyping short tandem repeat (STR loci with PowerPlextm16 kit. Genetic analysis of allelic variants of the 15 STR loci PowerPlextm16 kit detected 17 samples determined as rare allelic variants or microvariants. Samples were divided into 15 different allelic variants at 7 different loci, and are: in locus D7S820, D16S539, D3S1358, D18S51, PENTA D, PENTA E and in locus vWA. Genetic analysis of mutations in cases of paternity determined three examples of single-step mutations in the loci FGA, Penta D and D3S1358. Genetic analysis of observed STR loci detected three allelic variant of genotype combination 7/10/11.3 in locus D7S820 Type II. Population genetic analysis of STR loci in a representative sample of the population of northeast Bosnia and Herzegovina included the application of the assessment tests of within-population genetic diversity and interpopulation diversity, as well as genetic differentiation between populations: North-eastern Bosnia and Herzegovina (BH and BH general reference, then the Croatian population, Macedonian, Serbian and Slovenian. Based on the result analysis of specific forensic parameters, it can be assumed that the most informative marker is PENTA E for population genetic analysis and forensic testing in the population of northeast Bosnia and Herzegovina. Research results fit regional STR database of this part of Europe.

  2. Casework testing of the multiplex kits AmpFlSTR SEfiler Plus PCR amplification kit (AB), PowerPlex S5 System (Promega) and AmpFlSTR MiniFiler PCR amplification kit (AB).

    Science.gov (United States)

    Müller, Kathrin; Sommerer, Thomas; Miltner, Erich; Schneider, Harald; Wiegand, Peter

    2010-04-01

    The short tandem repeat (STR) kits SEfiler Plus (D3S1358, FGA, D8S1179, D18S51, D21S11, TH01, VWA, SE33, D2S1338, D16S539, D19S433 and Amelogenin), PowerPlex S5 System (D18S51, D8S1179, TH01, FGA and Amelogenin) and MiniFiler (D13S317, D7S820, Amelogenin, D2S1338, D21S11, D16S539, D18S51, CSF1PO and FGA) were comparatively tested for their robustness and sensitivity. About 50 stains with highly degraded DNA and little DNA quantity served as examination material (e.g., hair with a telogen root, bones, degraded saliva stains on drinking vessels and skin cell mixtures). The PowerPlex S5 with five German DNA database (DAD) systems and the MiniFiler kit with four topical DAD systems and further STR markers show reduced amplicon lengths. The SEfiler Plus kit represents no MiniSTR multiplex, but contains the nine current DAD systems and further three systems D2S1338, D16S539 and D19S433, which are the potential expansion markers for the German DNA database. We have found on the basis of our comparative stain investigations, that the SEfiler Plus kit was less sensitive than the PowerPlex S5 and the MiniFiler kits. The MiniFiler and the PowerPlex S5 kit showed comparatively high sensitivity. Especially in analysing skin cell mixtures, the MiniFiler kit showed larger differences with regard to the performance of the fluorescent dyes/primer concentration co-ordination than the PowerPlex S5. The SEfiler Plus kit generated - just as both MiniSTR kits - relative robust typing results, but there appeared an increased sensitivity for 'allelic drop-outs' and 'imbalances'. Since the SEfiler Plus kit was not planned as MiniSTR concept, 'allelic drop-outs' were observed, as expected, more frequent in typing stains with degraded DNA and little DNA quantity, especially in the long polymerase chain reaction (PCR) products (e.g., D18S51).

  3. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea.

    Science.gov (United States)

    Chen, Jing; Xie, Bingbing; Yang, Yaran; Yang, Meng; Liu, Chao; Lv, Yuexin; Chen, Chuguang; Liu, Xu; Fang, Xiangdong; Wu, Huijuan; Yan, Jiangwei

    2017-08-01

    Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10(-38). The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

  4. Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry.

    Science.gov (United States)

    Planz, John V; Sannes-Lowery, Kristen A; Duncan, David D; Manalili, Sheri; Budowle, Bruce; Chakraborty, Ranajit; Hofstadler, Steven A; Hall, Thomas A

    2012-09-01

    and vWA produced θ estimates of 0.0477 and 0.0234, respectively, when the expanded allele complement (i.e., nominal allele and SNPs) was considered compared to 0.0145 and 0.01266, respectively when only nominal repeat number was considered. These differences may indicate underlying population specific allele distributions exist within these populations. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms.

  5. STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups.

    Science.gov (United States)

    Amir, Nadir; Sahnoune, Mohamed; Chikhi, Lounes; Atmani, Djebbar

    2015-12-10

    Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is

  6. The development of miniplex primer sets for the analysis of degraded DNA

    Science.gov (United States)

    McCord, Bruce; Opel, Kerry; Chung, Denise; Drabek, Jiri; Tatarek, Nancy; Meadows Jantz, Lee; Butler, John

    2005-05-01

    In this project, a new set of multiplexed PCR reactions has been developed for the analysis of degraded DNA. These DNA markers, known as Miniplexes, utilize primers that have shorter amplicons for use in short tandem repeat (STR) analysis of degraded DNA. In our work we have defined six of these new STR multiplexes, each of which consists of 3 to 4 reduced size STR loci, and each labeled with a different fluorescent dye. When compared to commercially available STR systems, reductions in size of up to 300 basepairs are possible. In addition, these newly designed amplicons consist of loci that are fully compatible with the the national computer DNA database known as CODIS. To demonstrate compatibility with commercial STR kits, a concordance study of 532 DNA samples of Caucasian, African American, and Hispanic origin was undertaken There was 99.77% concordance between allele calls with the two methods. Of these 532 samples, only 15 samples showed discrepancies at one of 12 loci. These occurred predominantly at 2 loci, vWA and D13S317. DNA sequencing revealed that these locations had deletions between the two primer binding sites. Uncommon deletions like these can be expected in certain samples and will not affect the utility of the Miniplexes as tools for degraded DNA analysis. The Miniplexes were also applied to enzymatically digested DNA to assess their potential in degraded DNA analysis. The results demonstrated a greatly improved efficiency in the analysis of degraded DNA when compared to commercial STR genotyping kits. A series of human skeletal remains that had been exposed to a variety of environmental conditions were also examined. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only sixteen percent of the samples tested generated full profiles with a commercial kit. In addition, complete profiles were obtained for eleven of the twelve Miniplex loci which had amplicon size ranges less than 200 base pairs

  7. Polymorphisms of 15 short tandem repeat loci in Mongolian nationality of Gansu province%甘肃蒙古族人群15个短串联重复序列基因座遗传多态性

    Institute of Scientific and Technical Information of China (English)

    范瑾; 任甫

    2012-01-01

    目的:调查甘肃蒙古族人群无关个体的15个短串联重复序列(STR)基因座(D8S1179,D21S11,D7S820,CSF1P0,D3S1358,D5S818,D13S317,D16S539,D2S1338,D19S433,vWA,D12S391,D18S51,D6S1043,FGA)的遗传多态性.方法:采用AmpFeSTR Sinofiler荧光标记复合扩增系统对198名甘肃肃北地区蒙古族个体血样DNA进行15个STR基因座的复合扩增,用3130 xl遗传分析仪对扩增产物进行检测.结果:15个STR基因座均符合Hardy-Weinberg平衡,杂合度在0.707 1~0.873 7之间,累积个人识别概率和累积非父排除率分别为0.999 999 3和0.999 999 997.结论:上述15个STR基因座在甘肃蒙古族人群中等位基因分布较好,个体识别率高,适合法医个体识别和亲子鉴定.%Objective: To investigate the polymorphism of 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, D5S818, D13S317, D16S539, D2S1338, D19S433, vWA, D12S391, D18S51, D6S1043, FGA) in Mongolian nationality of Gansu province. Methods: The genotypes of 15 STR loci in Mongolian population of Gansu province were generated by multiplexing PCR using the Sinofiler PCR system and genotyping using ABI 3130 xl Genetic Analyzer. Results: All loci met Hardy-Weinberg equilibrium expectations. The heterozygosity of the 15 STR loci was between 0. 707 1 and 0. 873 7, cumulate PE was 0. 999 999 3, and cumulate DP was 0. 999 999 997. Conclusion: The genetic polymorphisms of the 15 STR loci in Mongolian population of Gansu province are high. Present data suggest that the 15 loci of Sinofiler system can be applied as candidate markers of forensic individual identification and paternity testing.

  8. Evaluation of reliability on STR typing at leukemic patients used for forensic purposes.

    Science.gov (United States)

    Filoglu, G; Bulbul, O; Rayimoglu, G; Yediay, F E; Zorlu, T; Ongoren, S; Altuncul, H

    2014-06-01

    Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010-2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in

  9. Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™.

    Science.gov (United States)

    Fordyce, Sarah L; Mogensen, Helle Smidt; Børsting, Claus; Lagacé, Robert E; Chang, Chien-Wei; Rajagopalan, Narasimhan; Morling, Niels

    2015-01-01

    Second-generation sequencing (SGS) using Roche/454 and Illumina platforms has proved capable of sequencing the majority of the key forensic genetic STR systems. Given that Roche has announced that the 454 platforms will no longer be supported from 2015, focus should now be shifted to competing SGS platforms, such as the MiSeq (Illumina) and the Ion Personal Genome Machine (Ion PGM™; Thermo Fisher). There are currently several challenges faced with amplicon-based SGS STR typing in forensic genetics, including current lengths of amplicons for CE-typing and lack of uniform data analysis between laboratories. Thermo Fisher has designed a human identification (HID) short tandem repeat (STR) 10-plex panel including amelogenin, CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX and vWA, where the primers have been designed specifically for the purpose of SGS and the data analysis is supported by Ion Torrent™ software. Hence, the combination of the STR 10-plex and the Ion PGM™ represents the first fully integrated SGS STR typing solution from PCR to data analysis. In this study, four experiments were performed to evaluate the alpha-version of the STR 10-plex: (1) typing of control samples; (2) analysis of sensitivity; (3) typing of mixtures; and (4) typing of biological crime case samples. Full profiles and concordant results between replicate SGS runs and CE-typing were observed for all control samples. Full profiles were seen with DNA input down to 50 pg, with the exception of a single locus drop-out in one of the 100 pg dilutions. Mixtures were easily deconvoluted down to 20:1, although alleles from the minor contributor had to be identified manually as some signals were not called by the Ion Torrent™ software. Interestingly, full profiles were obtained for all biological samples from real crime and identification cases, in which only partial profiles were obtained with PCR-CE assays. In conclusion, the Ion Torrent™ HID STR 10-plex panel offers an

  10. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs.

    Science.gov (United States)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter; Børsting, Claus; Morling, Niels

    2016-03-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase (http://www.cstl.nist.gov/strbase/). The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a

  11. Towards simultaneous individual and tissue identification: A proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM.

    Science.gov (United States)

    Zubakov, D; Kokmeijer, I; Ralf, A; Rajagopalan, N; Calandro, L; Wootton, S; Langit, R; Chang, C; Lagace, R; Kayser, M

    2015-07-01

    DNA-based individual identification and RNA-based tissue identification represent two commonly-used tools in forensic investigation, aiming to identify crime scene sample donors and helping to provide links between DNA-identified sample donors and criminal acts. Currently however, both analyses are typically performed separately. In this proof-of-principle study, we developed an approach for the simultaneous analysis of forensic STRs, amelogenin, and forensic mRNAs based on parallel targeted DNA/RNA sequencing using the Ion Torrent Personal Genome Machine(®) (PGM™) System coupled with the AmpliSeq™ targeted amplification. We demonstrated that 9 autosomal STRs commonly used for individual identification (CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX, and vWA), the AMELX/AMELY system widely applied for sex identification, and 12 mRNA markers previously established for forensic tissue identification (ALAS2 and SPTB for peripheral blood, MMP10 and MMP11 for menstrual blood, HTN3 and STATH for saliva, PRM1 and TGM4 for semen, CYP2B7P1 and MUC4 for vaginal secretion, CCL27 and LCE1C for skin) together with two candidate reference mRNA markers (HPRT1 and SDHA) can all be successfully combined. Unambiguous mRNA-based tissue identification was achieved in all samples from all forensically relevant tissues tested, and STR sequencing analysis of the tissue sample donors was 100% concordant with conventional STR profiling using a commercial kit. Successful STR analysis was obtained from 1ng of genomic DNA and mRNA analysis from 10ng total RNA; however, sensitivity limits were not investigated in this proof-of-principle study and are expected to be much lower. Since dried materials with noticeable RNA degradation and small DNA/RNA amplicons with high-coverage sequencing were used, the achieved correct individual and tissue identification demonstrates the suitability of this approach for analyzing degraded materials in future forensic applications. Overall

  12. Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation.

    Science.gov (United States)

    Quinto-Cortés, Consuelo D; Arriola, Luis A; García-Hughes, Gianella; García-López, Rodrigo; Molina, Diana P; Flores, Margarita; Palacios, Rafael; Piñero, Daniel

    2010-08-01

    We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both

  13. 云南汉族15个短串联重复序列基因座遗传多态性特征及分析%Analysis on characteristics of fifteen short tandem repeat genetic polymorphisms in Yunnan Han population

    Institute of Scientific and Technical Information of China (English)

    靳婵婵; 贺静; 王蕾; 陈鹏; 杨继青; 李秀玲; 苏洁; 朱宝生

    2016-01-01

    目的::调查云南地区汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA 15个短串联重复序列( Short tandem repeat,STR)基因座的遗传多态性。方法:收集云南汉族313名无关个体血样,提取DNA,PCR复合扩增并利用ABI-3130型基因分析仪进行毛细管电泳检测每个样本各基因座的等位基因大小,分别统计每个STR基因座各基因型的频率,并进行Hardy-Weinberg遗传平衡检验。结果:云南汉族这15个STR基因座各基因型频率分布符合Hardy-Weinberg平衡(P>0.05),杂合度在0.636~0.901,匹配概率在0.034~0.220,单一STR位点的个体识别率在0.780~0.966、非父排除率在0.336~0.797、多态性信息总量在0.555~0.860,联合使用这15个位点所产生的累积个体识别率大于0.99999999,累积非父排除率等于0.999998408。与中国其他地区汉族群体这15个STR基因座等位基因频率分布相比有较高的相似性,但也有轻微的地区差异。结论:云南汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA这15个STR基因座具有高度的多态性,与中国其他地区汉族群体有较高的相似性,在法医学中的亲子鉴定和个人识别方面具有较高应用价值。%Objective:To research on the genetic polymorphism distributions of fifteen short tandem repeat ( STR ) loci (D8S1179,D21S11,D7S820,CSF1PO,D3S1358,TH01,D13S317,D16S539,D2S1338,D19S433,VWA,TPOX,D18S51,D5S818, FGA) in Han race of Yunnan. Methods:A total of 313 specimens were collected from the unrelated individuals in Yunnan Han popu-lation. Genome DNA was extracted and amplified by multiplex PCR technique,the PCR products were analyzed by ABI-3130 genetic analyzer capillary electrophoresis detection, collected statistics of each STR loci genotypic frequency, and carried out the Hardy-Weinberg Genetic balance

  14. 亲子鉴定中IdentifilerTM系统15个STR基因座突变分析%Gene mutation of 15 STR loci analysis of the IdentifilerTM system in parentage testing

    Institute of Scientific and Technical Information of China (English)

    张丹妍; 张丹媚; 万凌; 吕静; 陈晓星; 赵乐天; 李练兵

    2011-01-01

    目的:观察和分析IdentifilerTM系统15个短串联重复序列(short tandem repeat,STR)基因座在亲子鉴定中的突变现象.方法:应用IdentifilerTM荧光标记复合扩增试剂盒检测710例亲子鉴定案,对其中发现突变基因座的案件加用STRtyper荧光标记复合扩增试剂盒进行等位基因检测,或6个mini Y-STR基因座检测.结果:在认定亲子关系的615例中,IdentifilerTM荧光标记复合扩增试剂盒中的15个基因座确定7例突变,其中vWA基因座2例,D13S17、FGA、D18S51、D21S11、D19S433基因座各1例;一步突变的6例,二步突变的1例.其突变均来自父亲,且年龄均在35岁以上.结论:在亲子鉴定中用IdentifileTM荧光标记复合扩增试剂盒检测到1~2个基因座不符合遗传规律时,有必要增加突变率低、稳定性好的STR基因座进行复核并排除近亲关系.%OBJECTIVE: Observation and analysis of gene mutation of 15 short tandem repeat (STR) loci of the IdentifilerTM system in paternity testing. METHODS: Make use of the IdentifilerTM fluorescent multiplex PCR kit for indentification of 710 paternity cases. If the gene mutant was found we would be perform STRtyper fluorescent multiplex PCR kit or six mini Y-STR loci for detection of alleles. RESULTS: In the 615 cases identified in the parent-child relationship, seven cases of mutation were found in IdentifilerTM fluorescent multiplex PCR kit detection, of which 2 cases at vWA loci, and one each at D13S17, FGA, D18S51, D21S11 and D19S433 loci; step mutation in the six cases, two-step mutation in l case. Mutations were found in the father, aged over 35 years. CONCLUSION: 1-2 STR loci found are not in line with the expected by fluorescent multiplex PCR IdentifilerTM kit, it is necessary to increase STR loci with low mutation rate and good stability to confirm and to exclude consanguinity.

  15. 云南傣族与广西侗族18个STR基因座的遗传多态性%Genetic polymorphisms of 18 STR loci in Dai population of Yunnan and Dong population of Guangxi

    Institute of Scientific and Technical Information of China (English)

    王玮; 孙启凡; 张涛; 王英元; 程宝文; 赵兴春; 李彩霞; 叶健

    2015-01-01

    目的 调查云南傣族和广西侗族无关个体18个STR基因座(D18S51、D21S11、D3S1358、FGA、D8S1179、vWA、CSF1PO、D16S539、D7S820、D13S317、D5S818、D2S1338、D19S433、D12S391、TPOX、TH01、Penta E和D6S1043)的遗传多态性并研究其法医学应用价值. 方法 采用DNA TyperTM 19试剂盒对100名云南傣族和70名广西侗族的无关个体血样进行复合扩增,用遗传分析仪3130XL对扩增产物检测,用GeneMapper ID v3. 2软件进行基因分型,并计算群体遗传学参数. 结果 在100名云南傣族和70名广西侗族的无关个体中,云南傣族共发现185种等位基因,广西侗族共发现162种等位基因. 傣族单个等位基因频率分布在0. 005-0. 600、侗族在0. 007-0. 493;傣族与侗族累计个人识别能力均大于99. 999 999 999 999 999 999 99%.结论 这18个 STR基因座在云南傣族和广西侗族地区具有高度多态性,可满足对这两个群体的个体识别和亲权鉴定.%Objective To investigate the genetic polymorphisms of 18 STR loci(D18S51, D21S11, D3S1358, FGA, D8S1179, vWA, CSF1PO, D16S539, D7S820, D13S317, D5S818, D2S1338, D19S433, D12S391, TPOX, TH01, Penta E and D6S1043) in unre-lated Dai individuals in Yunnan and Dong individuals in Guangxi and to explore its application value in forensic practice. Methods Blood samples from unrelated 100 Dai and 70 Dong individuals were amplified using DNA TyperTM 19 kit. The amplified products were detected using 3130XL Genetic Analyzer, and the genotyping was done using GeneMapper ID v3. 2, and the population genetics param-eters were calculated. Results Of 100 Dai and 70 Dong unrelated individuals, 185 alleles were detected in Dai population and 162 alleles were detected in Dong population. The allele frequency was 0. 005-0. 600 for Dai population and 0. 007-0. 493 for Dong pop-ulation. The TDP of both Dai and Dong population was more than 99. 999 999 999 999 999 999 99%. Conclusion The 18 STR loci in Dai population of Yunnan and

  16. Genetic Polymorphism Study on 15 STR Loci of Han Population in Hunan%湖南省汉族人群15个STR基因座多态性分析

    Institute of Scientific and Technical Information of China (English)

    欧阳曙明; 殷照初; 江源; 申琴; 倪斌

    2009-01-01

    The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were investigated in a Hunan Han population using AmpFlSTR indentifiler kit, GeneAmp PCR system 9700 and ABI 310 genetic analyzer. Gene frequency, heterozygosity (H), polymorphism information content (PIC), power of discrimination (DP) and probability of paternity exclusion (PE) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The H is at 0.593~0.900, PIC is at 0.54~0.85, DP is at 0.780~ 0.963, PE is at 0.282~0.785. Cumulative DP of the 15 STR is (1~1.6×10~(-17)) > 0.999 999 99, and the cumulative PE is 0.999 999 5. Therefore, the 15 STR loci used in this study are highly polymorphic in Hunan Han population and can be applied to population study, individual identification and paternity testing in forensic science.%应用美国AmpFISTR Indentifiler荧光标记复合扩增试剂盒,结合PE9700型PCR仪和美国ABI公司310型遗传分析仪,对湖南汉族人群D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、vWA、11POX、D18S51、D5S818和FGA共15个STR基因座进行多态性调查分析.结果显示15个SIR基因座的基因型分布符合Hardy-Weinberg平衡,其杂合度(H)介于0.593~0.900,多态信息含量(PIC)介于0.54~0.85,个体识别力(DP)介于0.780~0.963,非父排除率(PE)介于0.282~0.785,累计个体识别力为(1~1.6×10~(-17))>0.999 999 99,累计非父排除率为0.999 999 5.证明15个STR基因座在湖南省汉族人群中具有较高的多态性,可应用于该地区群体学研究、法医学个体识别和亲权鉴定等.

  17. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province.

    Science.gov (United States)

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  18. Large networks of artificial radar reflectors to monitor land subsidence in natural lowlying coastal areas

    Science.gov (United States)

    Tosi, Luigi; Strozzi, Tazio; Teatini, Pietro

    2014-05-01

    intensity of the surrounding area; (ii) the network must be established resembling a sort of levelling benchmark network, i.e. with the TCRs placed keeping to a value of about 1.0-1.5 km the maximum distance between the TCRs or between an 'artificial' and the adjacent 'natural' reflectors to reliably resolve the radar phase ambiguities in the presence of atmospheric artifacts. Moreover, our experiment provided new information in order to improve the knowledge of the regional and local processes acting in the Venice Lagoon. We found that the northern basin of the lagoon is subsiding at a rate of about 3-4 mm/yr, while the central and the southern lagoon regions are more stable. At the local scale, i.e., the scale of the single salt marshes, significant differences have been detected depending, for example, on the nature and the architecture of Holocene deposits (Tosi et al., 2009). Acknowledgments. This work was supported by Magistrato alle Acque di Venezia-Venice Water Authority (VWA) and Consorzio Venezia Nuova (CVN) through the INLET Project and partially developed within the RITMARE Flagship Project (CNR-MIUR), Action 2 (SP3-WP1). TERRASAR-X data courtesy COA0612, © DLR. References. Teatini, P., Tosi, L., Strozzi, T., Carbognin, L., Cecconi, G., Rosselli, R., & Libardo, S. (2012). Resolving land subsidence within the venice lagoon by persistent scatterer SAR interferometry. Physics and Chemistry of the Earth, 40-41, 72-79, doi: 10.1016/j.pce.2010.01.002. Strozzi, T., Teatini, P., Tosi, L., Wegmüller, U., & Werner, C. (2013). Land subsidence of natural transitional environments by satellite radar interferometry on artificial reflectors. Journal of Geophysical Research F: Earth Surface, 118(2), 1177-1191, doi: 10.1002/jgrf.2008. Tosi, L., Rizzetto, F., Zecchin, M., Brancolini, G., & Baradello, L. (2009). Morphostratigraphic framework of the venice lagoon (italy) by very shallow water VHRS surveys: Evidence of radical changes triggered by human-induced river diversions

  19. 九个非DNA联合索引系统短串联重复序列基因座在河北汉族群体的遗传学调查及在亲子鉴定中的应用%Genetic polymorphisms of nine non-DNA combined index system short tandem repeat loci in Hebei Han population and application in paternity testing

    Institute of Scientific and Technical Information of China (English)

    关亚卿; 付丽红; 张晓静; 李淑瑾; 丛斌; 马春玲

    2011-01-01

    Objective To investigate the polymorphisms of 9 non-DNA combined index system(CODIS) short tandem repeats (STRs), i. e., D7S3048, D8S1132, D11S2368, D2S1772, D6S1043,D13S325, D12S391, GATA198B05, D18S1364 in Hebei Han population, and evaluate the usage of them in paternity testing. Methods One hundred and forty-seven unrelated healthy individuals from the Han population of Hebei province were genotyped using STRtyper10G kit including 9 STR loci on ABI 3130 Genetic Analyzer. Hardy-Weinberg equilibrium and population genetic parameters were calculated. Fourteen cases of motherless paternity testing and 2 cases of standard trios with mutation in 1 locus were detected using STRtyper 10G. Results (1) Ninety-nine alleles and 336 genotypes were observed in the 9 STR loci in the population. The cumulative discrimination power(DP) was higher than 0. 999 999 999. The cumulative probability of exclusion(PE) for trios and duos were 0. 999 974 and 0. 998 759 respectively. Departure from Hardy-Weinberg equilibrium was not observed in any of the 9 loci. (2) The combined paternity index (PI)of the 14 cases of motherless paternity testing ranged from 103-104 for 15 STR loci in ID, whereas it reached 105-109 for 22 independent STR loci included in ID and STRtyper 10G. Possible mutation in FGA and vWA was observed in 2 cases of trios, and the combined PI was 5945 and 1840 respectively for 15 STR loci in ID.Adding STRtyper 10G to detect these 2 cases, the combined PI reached 2. 76 × 107 and 4. 88 × 107respectively. Conclusion The genetic polymorphism of the 9 non-CODIS STR loci included in STRtyper 10G was quite high in Chinese Hebei Han population, indicating the 9 STR loci are valuable as complement markers for ID and PP16 kit in motherless paternity testing, paternity testing with mutation and other kinds of complicated paternity testing.%目的 调查9个非DNA联合索引系统(DNA combined index system,CODIS)的短串联重复序列(short tandem repeat,STR)基因座在河北

  20. 新疆喀什地区维吾尔族18个STR基因座的遗传多态性%Genetic Polymorphisms of 18 STR Loci in Uygur Population of Kashi Prefecture of Xinjiang

    Institute of Scientific and Technical Information of China (English)

    张晓红; 李平; 翁玮霞; 刘长晖; 刘宏; 唐建新; 刘超

    2012-01-01

    目的 调查新疆喀什地区维吾尔族无关个体18个STR基因座(D18S51、D21S11、D3S1358、FGA、D8S1179、vWA、CSF1PO、D16S539、D7S820、D13S317、D5S818、D2S1338、D19S433、D12S391、TPOx、TH01、Penta E和D6S1043)的遗传多态性并研究其法医学应用价值.方法 采用DNA TyperTM 15 Plus试剂盒对1381名维吾尔族无关个体血样进行复合扩增,3130XL遗传分析仪对扩增产物检测,GeneMapper ID v3.2软件进行基因分型.计算群体遗传学参数,并与其他人群进行比较,计算Reynold's遗传距离,绘制系统发生树.结果 在1381名维吾尔族无关个体中,共发现231种等位基因,单个等位基因频率分布在0.0004~0.5304,H在0.644~0.923,PIC在0.587~0.918,DP在0.817~0.988,CPE大于0.9999999.与广州汉族人群遗传距离最大(0.088 3),与希腊人群遗传距离最小(0.0503).结论 这18个STR基因座在新疆喀什地区具有高度多态性,可满足该群体个体识别和亲权鉴定,其遗传多态性更接近欧洲.%Objective To investigate the genetic polymorphisms of 18 STR loci {D18S51, D21S11, D3S1358, FGA, D8S1179, vWA, CSF1PO, D16S539, D7S820, D13S317, D5S818, D2S1338, D19S433, D12S391, TPOX, TH01, Penta E and D6S1043) in unrelated Uygur individuals in Kashi prefecture of Xinjiang and to explore the application value in forensic practice. Methods Blood samples from 1 381 unrelated Uygur individuals were amplified by using DNA Typer?15 Plus kit. The amplified products were detected by using 3130XL Genetic Analyzer and the genotyping was done by using GeneMapper ID v3.2. Population genetics parameters were calculated and compared with that of the other population. The genetic distance of Reynold's was calculated and phylogenetic tree was constructed at last. Results Of the 1 381 unrelated Uygur individuals, 231 alleles were detected, with an allele frequency of 0.000 4-0.530 4. The H values were 0.644-0.923, PIC values were 0.587-0.918, and DP values were 0