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Sample records for repeat str profiling

  1. lobSTR: A short tandem repeat profiler for personal genomes

    OpenAIRE

    Gymrek, Melissa; Golan, David; Rosset, Saharon; Erlich, Yaniv

    2012-01-01

    Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times and a biased sampling of STR alleles. Here, we present lobSTR, a novel method for profiling STRs in p...

  2. lobSTR: A short tandem repeat profiler for personal genomes.

    Science.gov (United States)

    Gymrek, Melissa; Golan, David; Rosset, Saharon; Erlich, Yaniv

    2012-06-01

    Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times and a biased sampling of STR alleles. Here, we present lobSTR, a novel method for profiling STRs in personal genomes. lobSTR harnesses concepts from signal processing and statistical learning to avoid gapped alignment and to address the specific noise patterns in STR calling. The speed and reliability of lobSTR exceed the performance of current mainstream algorithms for STR profiling. We validated lobSTR's accuracy by measuring its consistency in calling STRs from whole-genome sequencing of two biological replicates from the same individual, by tracing Mendelian inheritance patterns in STR alleles in whole-genome sequencing of a HapMap trio, and by comparing lobSTR results to traditional molecular techniques. Encouraged by the speed and accuracy of lobSTR, we used the algorithm to conduct a comprehensive survey of STR variations in a deeply sequenced personal genome. We traced the mutation dynamics of close to 100,000 STR loci and observed more than 50,000 STR variations in a single genome. lobSTR's implementation is an end-to-end solution. The package accepts raw sequencing reads and provides the user with the genotyping results. It is written in C/C++, includes multi-threading capabilities, and is compatible with the BAM format.

  3. Authentication of newly established human esophageal squamous cell carcinoma cell line (YM-1) using short tandem repeat (STR) profiling method.

    Science.gov (United States)

    Ayyoob, Khosravi; Masoud, Khoshnia; Vahideh, Kazeminejad; Jahanbakhsh, Asadi

    2016-03-01

    Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently.

  4. Differential pre-amplification of STR loci for fragmented forensic DNA profiling.

    Science.gov (United States)

    Ham, Seon-Kyu; Kim, Se-Yong; Seo, Bo Young; Woo, Kwang-Man; Lee, Seung-Hwan; Choi, Cheol Yong

    2016-11-01

    DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre-amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre-amplification strategy. In addition, pre-amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre-amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. An unusual occurrence of repeated single allele variation on Y-STR locus DYS458

    Directory of Open Access Journals (Sweden)

    Pankaj Shrivastava

    2016-09-01

    Full Text Available Six brothers were accused of gagging and raping a woman. A single male Y-STR profile was obtained from vaginal smear swab and clothes of the victim, which did not match with the DNA profile of the accused brothers. As a reference point, the blood sample of their father (aged 87 years was also analyzed with the same kit. The Y-STR haplotype of all six brothers was found to be the same as that of their father except at locus DYS458. At this locus, while the eldest, second and fourth siblings share allele 18 with their father, a loss of one repeat (allele 17 instead of 18 is observed in the third son while fifth and sixth siblings have allele 19 representing a gain of one repeat. Thus, two changes viz. a gain (twice and loss of one repeat at this locus in one generation is both interesting and unusual.

  6. Optimization of STR locus enrichment for STR profiling of fragmented DNA.

    Science.gov (United States)

    Ham, Seon-Kyu; Kim, Se-Yong; Ahn, Jang-Won; Seo, Bo Young; Woo, Kwang-Man; Choi, Cheol Yong; Lee, Seung-Hwan

    2014-11-01

    DNA degradation is a major obstacle in gaining an accurate profile with standard DNA typing technology. Although alternative genotyping strategies such as mini-STRs and SNPs have proven to be more successful in profiling degraded DNA, these approaches also have limitations. Here, we show that locus enrichment by hybridization of degraded genomic DNA with an STR locus-specific biotinylated oligonucleotide is a powerful approach to overcome problems in STR typing of highly degraded DNA. An experimental investigation of factors affecting the efficiency of this method indicates that the choice of primer and molar ratio of primers to genomic DNA are critical factors in improving enrichment of the STR locus before genotyping with multiplex kits. In addition, we find that indirect capture rather than direct capture with magnetic beads yields better enrichment efficiency for STR locus enrichments. Using these strategies, we demonstrate an improvement in STR typing of DNA from cultured cells damaged by exposure to sunlight or UV. We suggest that this approach could be applied to highly degraded forensic samples alone or in combination with mini-STRs.

  7. Using probabilistic theory to develop interpretation guidelines for Y-STR profiles.

    Science.gov (United States)

    Taylor, Duncan; Bright, Jo-Anne; Buckleton, John

    2016-03-01

    Y-STR profiling makes up a small but important proportion of forensic DNA casework. Often Y-STR profiles are used when autosomal profiling has failed to yield an informative result. Consequently Y-STR profiles are often from the most challenging samples. In addition to these points, Y-STR loci are linked, meaning that evaluation of haplotype probabilities are either based on overly simplified counting methods or computationally costly genetic models, neither of which extend well to the evaluation of mixed Y-STR data. For all of these reasons Y-STR data analysis has not seen the same advances as autosomal STR data. We present here a probabilistic model for the interpretation of Y-STR data. Due to the fact that probabilistic systems for Y-STR data are still some way from reaching active casework, we also describe how data can be analysed in a continuous way to generate interpretational thresholds and guidelines.

  8. A simplified method for screening siblings for HLA identity using short tandem repeat (STR) polymorphisms.

    Science.gov (United States)

    Schiller, Jennifer J; Hopp, Kathleen A; Pietz, Bradley C; Bick, David P; Lau, Eduardo C; Ellis, Thomas M

    2013-05-01

    Identifying an HLA-matched sibling donor for hematopoietic stem cell transplantation (HSCT) is time-consuming and expensive, and often limited by reimbursement caps imposed by insurance providers. To improve the effectiveness and efficiency of screening for HLA-matched siblings, we developed an assay for determining HLA identity using a panel of nine informative short tandem repeat (STR) loci located throughout the HLA complex. The STR panel was assessed for accuracy in identifying HLA-matched siblings in 88 family workups comprising a total of 132 related donor and recipient typing comparisons. All sibling pairs with identical STR alleles were also HLA identical. Of the 48 pairs mismatched at one or more STR alleles, all were genotypically HLA non-identical at one or more loci. The sensitivity and specificity of STR analysis for identifying HLA-matched siblings were 91% and 100%, respectively. Three false negatives occurred due to an STR mutation or possible HLA-DPB1/DQB1 recombination. Additionally, STR genotyping provided additional information allowing determination of the extent of HLA identity in families where HLA haplotype inheritance was ambiguous, due to extensive homozygosity or shared parental haplotypes. The HLA STR assay is a reliable and rapid test that can be used to inexpensively screen potential sibling donors for HLA identity.

  9. Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification.

    Science.gov (United States)

    Robertson, James M; Dineen, Shauna M; Scott, Kristina A; Lucyshyn, Jonathan; Saeed, Maria; Murphy, Devonie L; Schweighardt, Andrew J; Meiklejohn, Kelly A

    2014-09-01

    Forensic scientists have used several approaches to obtain short tandem repeat (STR) profiles from compromised DNA samples, including supplementing the polymerase chain reaction (PCR) with enhancers and using procedures yielding reduced-length amplicons. For degraded DNA, the peak intensities of the alleles separated by electrophoresis generally decrease as the length of the allele increases. When the intensities of the alleles decrease below an established threshold, they are described as drop-outs, thus contributing to a partial STR profile. This work assesses the use of repair enzymes to improve the STR profiles from artificially degraded DNA. The commercial PreCR™ repair kit of DNA repair enzymes was tested on both purified DNA and native DNA in body fluids exposed to oxidizing agents, hydrolytic conditions, ultraviolet (UV) and ionizing radiation, and desiccation. The strategy was to restrict the level of DNA damage to that which yields partial STR profiles in order to test for allele restoration as opposed to simple allele enhancement. Two protocols were investigated for allele restoration: a sequential protocol using the manufacturer's repair procedure and a modified protocol reportedly designed for optimal STR analysis of forensic samples. Allele restoration was obtained with both protocols, but the peak height appeared to be higher for the modified protocol (determined by Mann-Kendall Trend Test). The success of the approach using the PreCR™ repair enzymes was sporadic; it led to allele restoration as well as allele drop-out. Additionally, allele restoration with the PreCR™ enzymes was compared with restoration by alternative, but commonly implemented approaches using Restorase™, PCRBoost™, bovine serum albumin (BSA) and the Minifiler™ STR system. The alternative methods were also successful in improving the STR profile, but their success also depended on the quality of the template encountered. Our results indicate the PreCR™ repair kit may

  10. Object-oriented Bayesian networks for evaluating DIP-STR profiling results from unbalanced DNA mixtures.

    Science.gov (United States)

    Cereda, G; Biedermann, A; Hall, D; Taroni, F

    2014-01-01

    The genetic characterization of unbalanced mixed stains remains an important area where improvement is imperative. In fact, with current methods for DNA analysis (Polymerase Chain Reaction with the SGM Plus multiplex kit), it is generally not possible to obtain a conventional autosomal DNA profile of the minor contributor if the ratio between the two contributors in a mixture is smaller than 1:10. This is a consequence of the fact that the major contributor's profile 'masks' that of the minor contributor. Besides known remedies to this problem, such as Y-STR analysis, a new compound genetic marker that consists of a Deletion/Insertion Polymorphism (DIP), linked to a Short Tandem Repeat (STR) polymorphism, has recently been developed and proposed elsewhere in literature. The present paper reports on the derivation of an approach for the probabilistic evaluation of DIP-STR profiling results obtained from unbalanced DNA mixtures. The procedure is based on object-oriented Bayesian networks (OOBNs) and uses the likelihood ratio as an expression of the probative value. OOBNs are retained in this paper because they allow one to provide a clear description of the genotypic configuration observed for the mixed stain as well as for the various potential contributors (e.g., victim and suspect). These models also allow one to depict the assumed relevance relationships and perform the necessary probabilistic computations.

  11. Development of STR profiles from firearms and fired cartridge cases.

    Science.gov (United States)

    Horsman-Hall, Katie M; Orihuela, Yvette; Karczynski, Stephanie L; Davis, Ann L; Ban, Jeffrey D; Greenspoon, Susan A

    2009-09-01

    Fired cartridge cases are a common type of evidence found at crime scenes. However, due to the high chamber temperatures and touch nature of this evidence, DNA testing is not commonly sought because it is believed DNA is only present in low levels, whether it is due to initial low levels of DNA and/or DNA degradation from the heat or inhibition of the PCR reaction. Moreover, very few laboratories report STR typing success with fired cases. This study focused on obtaining STR profiles from fired cartridge cases using the AmpFlSTR MiniFiler kit, which is designed to amplify DNA from low level, inhibited, and degraded samples. Comparisons to other STR amplification kits were also conducted. In attempt to simulate casework, random individuals loaded cartridges into a firearm. DNA was recovered from the fired cartridge cases using the double swab technique and extracted using an automated large volume DNA IQ method. Initially, testing focused on known shedders handling cartridges for 30s prior to firing. A significantly greater number of alleles was obtained following amplification with the MiniFiler kit versus the PowerPlex 16 BIO kit. No alleles were observed using the Identifiler kit. In an attempt to better simulate casework, a random selection of laboratory personnel handled shotshells for as long as needed to load and fire the weapon. In this mock sample study, the MiniFiler kit successfully amplified an average of 22% of expected alleles from DNA recovered from shotshell cases versus the PowerPlex 16 BIO kit where an average of 7% of alleles were observed. However, the total number of alleles obtained from the two kits was not significantly different. The quality of the DNA obtained from fired cases was studied with evidence of inhibition in at least 11% of shotshell case samples. After swabbing the head and the hull of three shotshell cases separately, a significantly greater number of alleles was obtained from the hull as opposed to the head of the fired

  12. Systematic Profiling of Short Tandem Repeats in the Cattle Genome.

    Science.gov (United States)

    Xu, Lingyang; Haasl, Ryan J; Sun, Jiajie; Zhou, Yang; Bickhart, Derek M; Li, Junya; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Lewin, Harris A; Liu, George E

    2017-01-01

    Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

  13. 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.

  14. Human Short Tandem Repeat (STR Markers for Paternity Testing in Pig-Tailed Macaques

    Directory of Open Access Journals (Sweden)

    DYAH PERWITASARI-FARAJALLAH

    2007-06-01

    Full Text Available This study investigated the use of human short tandem repeat (STR or microsatellite loci markers for assessing paternity and genetic structure of pig-tailed macaques (Macaca nemestrina breeding colony. Four human microsatellite primer pairs located at human map position D1S548, D3S1768, D5S820, and D2S1777, were amplified by polymerase chain reaction (PCR for pig-tailed macaques. Four loci were found to be clearly and reliably amplified, and three loci exhibited high levels of genetic heterogeneity. These loci were sufficiently informative to differentiate discretely between related and unrelated pairs.

  15. Analysis of Y-chromosomal short tandem repeat (STR) polymorphism in an Iranian Sadat population.

    Science.gov (United States)

    Rafiee, M R; Sokhansanj, A; Naghizadeh, M A; Farazmand, A

    2009-08-01

    The molecular genotyping of individuals and reconstruction of kinship through short and highly polymorphic DNA markers, so called short tandem repeats (STR), has become one of the important and efficient methods in anthropology studies and forensic science. Although many populations have been analyzed, no study has yet been carried out on Sadat populations who are putative descendents of Prophet Mohammad (peace be upon him). Polymorphisms of 6 Y-STR loci (DYS19, DYS385a/b, DYS389II, DYS390, DYS392, and DYS393) have been studied in an unrelated population of Sadat males. The aim of this study was to find possible similarities within Sadat males, resided in Iran. Among Sadat, DYS385b was proved to be the most polymorphic (GD = 0.8588), and DYS392 showed the lowest polymorphism (GD = 0.3527). In 50 samples, 45 different haplotypes were found, of which 39 haplotypes were unique. In the study, three samples had multi-allelic patterns. Haplotype diversity, in regard to these 7 markers was 0.9942.

  16. Genetic profile characterization and population study of 21 autosomal STR in Chinese Kazak ethnic minority group.

    Science.gov (United States)

    Yuan, Jing-Yi; Wang, Xiao-Ye; Shen, Chun-Mei; Liu, Wen-Juan; Yan, Jiang-Wei; Wang, Hong-Dan; Pu, Hong-Wei; Wang, Yan-Li; Yang, Guang; Zhang, Yu-Dang; Meng, Hao-Tian; Jing, Hang; Zhu, Bo-Feng

    2014-02-01

    Short tandem repeat loci have been recognized as useful tools in the routine forensic application and in recent decades, more and more new short tandem repeat (STR) loci have been constantly discovered, studied, and applied in forensic caseworks. In this study, we investigated the genetic polymorphisms of 21 STR loci in the Kazak ethnic minority as well as the genetic relationships between the Kazak ethnic minority and other populations. Allelic frequencies of 21 STR loci were obtained from 114 unrelated healthy Kazak individuals in the Ili Kazak Autonomous Prefecture, Xinjiang Uigur Autonomous Region of China. We observed a total of 159 alleles in the group with the allelic diversity values ranging from 0.0044 to 0.5088. The highest polymorphism was found at D19S433 locus and the lowest was found at D1S1627. Statistical analysis of the generated data indicated no deviation from Hardy-Weinberg equilibriums at all 21 STR loci. In order to estimate the population differentiation, allelic frequencies of all STR loci of the Kazak were compared with those of other neighboring populations using analysis of molecular variance method. Statistically significant differences were found between the studied population and other populations at 2-7 STR loci. A neighbor-joining tree was constructed based on allelic frequencies of the 21 STR loci and phylogenetic analysis indicates that the Kazak has a close genetic relationship with the Uigur ethnic group. The present results may provide useful information for forensic sciences and population genetics studies, and can also increase our understanding of the genetic background of this group. The present findings showed that all the 21 STR loci are highly genetically polymorphic in the Kazak group, which provided valuable population genetic data for the genetic information study, forensic human individual identification, and paternity tests.

  17. STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus

    Science.gov (United States)

    Rębała, Krzysztof; Rabtsava, Alina A.; Kotova, Svetlana A.; Kipen, Viachaslau N.; Zhurina, Natalja V.; Gandzha, Alla I.; Tsybovsky, Iosif S.

    2016-01-01

    A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products. PMID:27851802

  18. PCR typing of DNA fragments of the short tandem repeat (STR) system HUMTH01 in Danes and Greenland Eskimos

    DEFF Research Database (Denmark)

    Nellemann, L J; Møller, A; Morling, N

    1994-01-01

    DNA from the short tandem repeat (STR) system HUMTH01 was amplified by the polymerase chain reaction (PCR) and analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 100 unrelated Danes, 147 unrelated Greenland Eskimos, and 89 Danish mother/child...

  19. 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

  20. STR data for the AmpFlSTR Profiler loci from the three main ethnic population groups (Malay, Chinese and Indian) in Malaysia.

    Science.gov (United States)

    Lim, K B; Jeevan, N H; Jaya, P; Othman, M I; Lee, Y H

    2001-06-01

    Allele frequencies for the nine STRs genetic loci included in the AmpFlSTR Profiler kit were obtained from samples of unrelated individuals comprising 139-156 Malays, 149-153 Chinese and 132-135 Indians, residing in Malaysia.

  1. High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

    DEFF Research Database (Denmark)

    Fordyce, Sarah L; Avila-Arcos, Maria C; Rockenbauer, Eszter;

    2011-01-01

    The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR...... repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...

  2. A convenient guideline to determine if two Y-STR profiles are from the same lineage.

    Science.gov (United States)

    Liu, Hai; Li, Xiaoyang; Mulero, Julio; Carbonaro, Andrea; Short, Marc; Ge, Jianye

    2016-07-01

    Y chromosome STR loci are used in forensics primarily for identification purposes by determining the male lineages. The Henan province in China has established a large Y-STR (>200 000 profiles) database for criminal investigations. A large proportion of the Y-STR profiles in the database were generated using either the Applied Biosystems Yfiler(ۛ) or Yfiler(ۛ) Plus PCR Amplification kits. The additional loci in the Yfiler Plus kit as compared to the Yfiler kit results in a concomitant cumulative mutation rate increase across the loci. Therefore, in those cases when two profiles have one to a few mismatched loci, it is difficult to determine if they are from the same lineage. In this study, 7405 unrelated male profiles were manually selected from the database. Analysis showed higher power of discrimination than the corresponding Yfiler haplotypes. Further, the distributions of the number of mismatched loci and the mismatched steps were generated for father-son, grandfather-grandson, uncle-nephew, and cousins (i.e. one, two, three, and four meioses, respectively) by exhaustive pairwise comparison of the unrelated profiles using a dynamic programming approach. The same distributions were generated for unrelated pairs with mutation rates of the loci. With the distributions, the false negative and false positive rates were determined. Two Yfiler profiles with ≤2 mismatched loci or ≤2 steps are more likely from the same lineage than unrelated lineages, and two Yfiler Plus profiles with ≤4 mismatched loci or ≤5 mismatched steps are more likely from the same lineage.

  3. Report of the European DNA Profiling Group (EDNAP)--an investigation of the hypervariable STR loci ACTBP2, APOAI1 and D11S554 and the compound loci D12S391 and D1S1656

    DEFF Research Database (Denmark)

    Gill, P; d'Aloja, E; Dupuy, B;

    1998-01-01

    This paper describes the results of three collaborative exercises which continues the EDNAP theme to explore whether uniformity of DNA profiling results could be achieved between European laboratories using STRs. In an earlier exercise, complex hypervariable AAAG-repeat STR loci were investigated...

  4. 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.

  5. 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.

  6. Identification and Analysis of Novel Amino-Acid Sequence Repeats in Bacillus anthracis str. Ames Proteome Using Computational Tools

    Directory of Open Access Journals (Sweden)

    D. Satyanarayana Rao

    2007-02-01

    Full Text Available We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1 57-amino-acid-residue PxV domain, (2 122-amino-acid-residue FxF domain, (3 111-amino-acid-residue YEFF domain, (4 109-amino-acid-residue IMxxH domain, (5 103-amino-acid-residue VxxT domain, (6 84-amino-acid-residue ExW domain, (7 104-amino-acid-residue NTGFIG domain, (8 36-amino-acid-residue NxGK repeat, (9 95-amino-acid-residue VYV domain, (10 75-amino-acid-residue KEWE domain, (11 59-amino-acid-residue AFL domain, (12 53-amino-acid-residue RIDVK repeat, (13 (a 41-amino-acid-residue AGQF repeat and (b 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

  7. Selection pressure on human STR loci and its relevance in repeat expansion disease

    KAUST Repository

    Shimada, Makoto K.

    2016-06-11

    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases. © 2016, Springer-Verlag Berlin Heidelberg.

  8. Hierarchical modeling of genome-wide Short Tandem Repeat (STR) markers infers native American prehistory.

    Science.gov (United States)

    Lewis, Cecil M

    2010-02-01

    This study examines a genome-wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan-Paezan and Equatorial-Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan-Paezan populations in Central America emerge together at the tips of the Chibchan-Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan-Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial-Tucanoan and Ge-Pano-Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. 2009 Wiley-Liss, Inc.

  9. 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.

  10. Response to Grisedale and Van Daal: comparison of STR profiling from low template DNA extracts with and without the consensus profiling method

    Directory of Open Access Journals (Sweden)

    Kokshoorn Bas

    2013-01-01

    Full Text Available Abstract In a recent contribution to this journal Grisedale and Van Daal concluded that a single STR analysis of all available template DNA is to be preferred over replicate analyses and a consensus approach when analyzing low template DNA samples. A single STR analysis approach does not allow for an assessment of the validity of the resulting DNA profile. We argue that the use of replicate amplifications is the best way to objectively quantify the extent of the stochastic variation in the data. By applying consensus methodology and/or a probabilistic model, the interpretation of the data will therefore be more objective and reliable.

  11. Capillary electrophoresis of miniSTR markers to genotype highly degraded DNA samples.

    Science.gov (United States)

    Coble, Michael D

    2012-01-01

    The amplification of short tandem repeat (STR) markers throughout the human nuclear DNA genome are used to associate crime scene evidence to the perpetrator's profile in criminal investigations. For highly challenged or compromised materials such as stains exposed to the elements, skeletal remains from missing persons cases, or fragmented and degraded samples from mass disasters, obtaining a full STR profile may be difficult if not impossible. With the introduction of short amplicon STR or "miniSTR" typing, it is possible to obtain STR genetic information from highly challenged samples without the need to sequence the hypervariable regions of the mitochondrial DNA (mtDNA) genome. Non-Combined DNA Index System (CODIS) STR markers have been developed to obtain information beyond the core CODIS loci. This chapter will focus on the steps necessary to prepare and use one of the non-CODIS (NC) multiplexes, NC01 (Coble and Butler 2005), for analysis on capillary electrophoresis instrumentation.

  12. Mutation Rates of STR Systems in Danes

    DEFF Research Database (Denmark)

    Andersen, Kim Emil; Bøttcher, Susanne Gammelgaard; Christensen, Susanne

    Danish paternity cases in the period 1999 to 2005 were investigated regarding mutation rates in STR loci. STR-typing was performed by the Applied Biosystems AmplfStr Profiler Plus kit in the period 1999 to early 2005, hereafter named the PP9, and by Applied Biosystems AmplfStr Identifier kit...

  13. STR MARKERS. GENOTYPING APPLICATIONS

    Directory of Open Access Journals (Sweden)

    I. O. Sirbu

    2001-01-01

    Full Text Available STR (short tandem repeats loci consist of short, repetitive sequence elements of 2-8 bp in length. These abundant repeats are well distributed throughout the human genome and are rich source of highly polymorphic markers. There are literally hundreds of STR systems which have been mapped throughout the human genome. Several dozen have been investigated for application to human identity testing. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use. In this paper we intend (far from being exhaustive to present a synthesis of the characteristics of these genetic markers and their applications in genotyping, giving as an example the use of the STRs in a paternity testing case.

  14. Statistical modelling of Ion PGM HID STR 10-plex MPS Data

    DEFF Research Database (Denmark)

    Vilsen, Søren B; Tvedebrink, Torben; Mogensen, Helle Smidt

    2017-01-01

    We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions...... of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling...... of stutter ratio than the parental allele repeat length, when markers with compound and complex repeat patterns or markers which contained micro-variants were considered, such as marker TH01 showed R(2) of 0.02 and 0.78 for parent allele repeat length and LUS, respectively. The one-inflated negative binomial...

  15. Concordance study between the ParaDNA® Intelligence Test, a rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR® SGM Plus®).

    Science.gov (United States)

    Ball, G; Dawnay, N; Stafford-Allen, B; Panasiuk, M; Rendell, P; Blackman, S; Duxbury, N; Wells, S

    2015-05-01

    The ParaDNA® Intelligence Test enables STR profiling directly from human biological samples and evidence items collected from crime scene in 75min. Designed for non-expert use this system allows DNA information to be available to investigators before it would typically be available from a laboratory. The ParaDNA Intelligence Test system amplifies D3S1358, D8S119, D16S539, D18S1358 and TH01 STR loci and the gender typing locus amelogenin and detects the alleles present with HyBeacon® probes. Individual DNA samples from 381 UK Caucasian individuals were analysed using AmpFlSTR® SGM Plus® and the ParaDNA Intelligence Test with the derived STR profiles compared. Here we describe the high level of concordance demonstrated between the two systems and discuss this with reference to allele frequencies and the discriminatory power offered by the ParaDNA Intelligence Test.

  16. Determination of mini-short tandem repeat (miniSTR) loci by using the combination of polymerase chain reaction (PCR) and microchip electrophoresis.

    Science.gov (United States)

    Lin, Xuexia; Wu, Jing; Li, Haifang; Wang, Zhihua; Lin, Jin-Ming

    2013-09-30

    In this work, a simple and convenient method for the detection of mini-short tandem repeat (miniSTR) loci has been developed by the combination of polymerase chain reaction (PCR) and microchip electrophoresis (MCE). Degraded or inhibitor DNA greatly limited STR loci analysis. Therefore, The proper primers was designed as close as possible to the STRs region to produce smaller size STRs, and made the assay suitable for the destroyed samples. Two annealing temperatures were applied in one PCR procedure and the corresponding cycle numbers were studied to improve the sensitivity of PCR reaction. Under optimal conditions, 0.001 ng DNA templates were enough to generate miniSTRs. The relative standard deviations (n=3) of the size fifteen miniSTRs from DNA9947A ranged from 0.49% to 4.41%. The RSDs of concentrations were between 0.94% and 4.95%. Fifteen miniSTRs were also well produced from human hair, indicating that the method has great potential application in criminal identification and paternity testing.

  17. Repeated-sprint performance, locomotor profile and muscle oxygen uptake recovery: effect of training background.

    Science.gov (United States)

    Ufland, P; Ahmaidi, S; Buchheit, M

    2013-10-01

    The aim of the present study was to examine the respective importance of locomotor profile and muscle oxygen uptake (mV(˙)O₂) recovery on repeated-sprint ability (RSA) and overall repeated-sprint performance. 11 sprint- (STR) and 10 middle-distance-trained (MDTR) athletes (20.8±4.0 yr) performed an incremental test and a 40-to-50-m sprint to estimate their maximal aerobic (MAS) and sprinting (MSS) speeds. They also performed 6×30-m sprints, departing every 30 s, where mean (RS(mean)) sprint time was calculated. Muscle oxygenation (Near-infrared spectroscopy, NIRS, [Hb(diff)]) was measured for ~ 4 min post test. The mean response time of [Hb(diff)]-mV(˙)O₂ recovery (monoexponential curve fitting, MRT[Hb(diff)]-mV(˙)O₂) was calculated. Compared with MDTR, STR presented faster MSS (+11.4±6.7%, with 99% chances to observe a substantially greater value) and RS(mean) (-3.7±5.4%, 78%), but slower MAS (-15.8±8.0%, 100%) and MRT[Hb(diff)]-mV(˙)O₂ (+46.2±31.7%, 96%). RS(mean) was largely correlated with MSS [r=-0.83 (90%CL, -0.92;-0.67)], but neither with MAS [r=-0.12 (-0.47;0.25)] nor MRT[Hb(diff)]-mV(˙)O₂ [r=-0.27(-0.58;0.11)]. RS(mean) adjusted for MSS (which indirectly reflects RSA) was largely correlated with both MAS [r=0.51(0.18;0.74)] and MRT[Hb(diff)]-mV(˙)O₂ [r=0.53(0.20;0.75)]. While a fast mV(˙)O₂ recovery is associated with an improved RSA, MSS remains of primary importance for overall repeated-sprint performance (i.e., RS(mean)).

  18. Analysis of matches and partial-matches in a Danish STR data set.

    Science.gov (United States)

    Tvedebrink, Torben; Eriksen, Poul Svante; Curran, James Michael; Mogensen, Helle Smidt; Morling, Niels

    2012-05-01

    Over the recent years, the national databases of STR profiles have grown in size due to the success of forensic DNA analysis in solving crimes. The accumulation of DNA profiles implies that the probability of a random match or near match of two randomly selected DNA profiles in the database increases. We analysed 53,295 STR profiles from individuals investigated in relation to crime case investigations at the Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark. Incomplete STR profiles (437 circa 0.8% of the total), 48 redundant STR profiles from monozygotic twins (0.09%), 6 redundant STR profiles of unknown cause and 1283 STR profiles from repeated testing of individuals were removed leaving 51,517 complete 10 locus STR profiles for analysis. The number corresponds to approximately 1% of the Danish population. We compared all STR profiles to each other, i.e. 1.3×10(9) comparisons. With these large number of comparisons, it is likely to observe DNA profiles that coincide on many loci, which has concerned some commentators and raised questions about "overstating" the power of DNA evidence. We used the method of Weir [11,12] and Curran et al. [3] to compare the observed and expected number of matches and near matches in the data set. We extended the methods by computing the covariance matrix of the summary statistic and used it for the estimation of the identical-by-descent parameter, θ. The analysis demonstrated a number of close relatives in the Danish data set and substructure. The main contribution to the substructure comes from close relatives. An overall θ-value of 1% compensated for the observed substructure, when close familial relationships were accounted for.

  19. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    Science.gov (United States)

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  20. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    Science.gov (United States)

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  1. Characterization of genetic sequence variation of 58 STR loci in four major population groups.

    Science.gov (United States)

    Novroski, Nicole M M; King, Jonathan L; Churchill, Jennifer D; Seah, Lay Hong; Budowle, Bruce

    2016-11-01

    Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. A new strategy for sperm isolation and STR typing from multi-donor sperm mixtures.

    Science.gov (United States)

    Han, Jun-Ping; Yang, Fan; Xu, Cheng; Wei, Yi-Liang; Zhao, Xing-Chun; Hu, Lan; Ye, Jian; Li, Cai-Xia

    2014-11-01

    Mixed semen stains from multiple contributors are challenging samples in sexual assault casework, and it is crucial to obtain the DNA profiles of different donors to allow the evidence to play an important role in investigations and judicial proceedings. Current standard procedures, including preferential lysis, are incapable of separating single-source sperm from multiple male donors. Mixed profiles are often obtained and may not directly exclude or identify suspects. In this case, computational methods for mixture interpretation are often used, which rely on different types of calculation models. Here, we explored a new strategy for sperm cell isolation and detection from mixtures. It is a direct way to obtain genotypes of different sperm donors compared to computation-based mixture interpretation. Laser capture microdissection (LCM) and low volume-PCR (LV-PCR) were used for single sperm isolation and detection. The platform was sensitive; profiling of a single sperm cell generated a minimum of 13-16 loci in 73.1% of Y short tandem repeat (Y-STR) assays. A new Y-STR and autosomal STR multiplex system (YA-STR) were optimized by the combination of the Y-STR locus and 10 autosomal STR (auto STR) loci. The Y-STR locus acted as a tag to discriminate profile groups from different donors. Subsequently, consensus auto STR profiles of various persons could be received. The accuracy and availability of this method were evaluated on a three-donor semen mixture and found to be effective for the resolution of a multi-donor sperm mixture.

  3. Fully integrated, fully automated generation of short tandem repeat profiles

    Science.gov (United States)

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings. Results An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation. Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory. Conclusions The integrated system represents the

  4. Validation and development of interpretation guidelines for low copy number (LCN) DNA profiling in New Zealand using the AmpFlSTR SGM Plus multiplex.

    Science.gov (United States)

    Petricevic, Sue; Whitaker, Jonathan; Buckleton, John; Vintiner, Sue; Patel, Jayshree; Simon, Pauline; Ferraby, Helen; Hermiz, Waseem; Russell, Amanda

    2010-10-01

    The characteristics of STR profiles produced from approximately 1 ng starting template using the AMPFlSTR SGM Plus multiplex and 28 PCR cycles, are well documented. However, the analysis of samples perceived as low in starting template (less than 100 pg), and referred to as low template DNA (LTDNA), can require a test of higher sensitivity in order to achieve successful results. One way of increasing this sensitivity is to increase the number of PCR amplification cycles from 28 to 34. This type of analysis has become known as low copy number, or LCN, DNA profiling. Amplification of LTDNA under LCN conditions can result in increased incidents of profile characteristics such as allelic 'drop-in' and allelic 'drop-out'. Adopting a testing regime which includes duplicate analysis, and maintaining a laboratory environment of stringent and monitored cleanliness, enables the scientist to identify and control these phenomena for a reliable interpretation of the DNA profiling results. A recent court ruling has questioned the reliability of LCN analysis and commented on the paucity of publications surrounding the validation of the technique. We present data for the LCN validation undertaken in our laboratory, and describe the guidelines and working practices we have developed for the analysis and interpretation of profiles generated after LCN profiling. This study augments the published record relating to LCN validation and should act as a useful guide for other laboratories who are considering implementing LCN profiling.

  5. Multiplex PCR for 17 Y-Chromosome Specific Short Tandem Repeats (STR to Enhance the Reliability of Fetal Sex Determination in Maternal Plasma

    Directory of Open Access Journals (Sweden)

    Fang Zheng

    2012-05-01

    Full Text Available The aim of the study was to demonstrate the influence of target gene and amplification product length on the performance of fetal gender determination systems using maternal plasma. A total of 40 pairs of plasma DNA samples from pregnant women and genomic DNA samples from maternal blood, amniotic fluid and paternal blood were isolated for gender determination by amplification of the amelogenin gene and 17 Y-chromosome STR loci, using three different commercial kits. The gender of the fetuses was confirmed by cytogenetic analysis or phenotype at birth. Both the AmpFℓSTR-Identifiler amplification kit and the Mini-STR Amplification kit for amelogenin gene detection were reliable in determining fetal gender (92.0% and 96.0%, respectively, but false negatives were present in both systems. AmpFℓSTR-Yfiler was found to be fully reliable as it amplified Y-STR in all cases of pregnancies with male fetuses and thus was 100% correct in determining fetal gender. The results demonstrated that multiple fluorescent PCR for 17 Y-STR loci was more reliable than AMELY gene testing in fetal sex determination with maternal plasma. We also found that the shorter amplification products could improve the performance of fetal gender determination systems.

  6. Multiplex PCR for 17 Y-chromosome Specific Short Tandem Repeats (STR) to enhance the reliability of fetal sex determination in maternal plasma.

    Science.gov (United States)

    Rong, Yuan; Gao, Jiajia; Jiang, Xinqiang; Zheng, Fang

    2012-01-01

    The aim of the study was to demonstrate the influence of target gene and amplification product length on the performance of fetal gender determination systems using maternal plasma. A total of 40 pairs of plasma DNA samples from pregnant women and genomic DNA samples from maternal blood, amniotic fluid and paternal blood were isolated for gender determination by amplification of the amelogenin gene and 17 Y-chromosome STR loci, using three different commercial kits. The gender of the fetuses was confirmed by cytogenetic analysis or phenotype at birth. Both the AmpFℓSTR-Identifiler amplification kit and the Mini-STR Amplification kit for amelogenin gene detection were reliable in determining fetal gender (92.0% and 96.0%, respectively), but false negatives were present in both systems. AmpFℓSTR-Yfiler was found to be fully reliable as it amplified Y-STR in all cases of pregnancies with male fetuses and thus was 100% correct in determining fetal gender. The results demonstrated that multiple fluorescent PCR for 17 Y-STR loci was more reliable than AMELY gene testing in fetal sex determination with maternal plasma. We also found that the shorter amplification products could improve the performance of fetal gender determination systems.

  7. Genetic data for the 13 CODIS STR loci in Singapore Indians.

    Science.gov (United States)

    Lim, S E S; Tan-Siew, W F; Syn, C K C; Ang, H C; Chow, S T; Budowle, Bruce

    2005-02-10

    Allele frequencies for the 13 CODIS short tandem repeat (STR) loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 174 unrelated Indians in Singapore.

  8. Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males

    NARCIS (Netherlands)

    A.A. Westen (Antoinette); T. Kraaijenbrink (Thirsa); L. Clarisse (Lindy); L.J.W. Grol (Laurens J.W.); P. Willemse (Patricia); S.B. Zuniga (Sofia); E.A. Robles De Medina (Elizaveta); R. Schouten (Ron); K. van der Gaag (Kristiaan); J.M. Weiler; A.J. Kal (Arnoud J.); M.H. Kayser (Manfred); T. Sijen (Titia); P. de Knijff (Peter)

    2015-01-01

    textabstractThe genotypes of 36 Y-chromosomal short tandem repeat (Y-STR) marker units were analysed in a Dutch population sample of 2085 males. Profiling results were compared for several partially overlapping kits, i.e. PowerPlex Y, Yfiler, PowerPlex Y23, and two in-house designed multiplexes with

  9. 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.

  10. 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.

  11. Performance characteristics of commercial Y-STR multiplex systems.

    Science.gov (United States)

    Mayntz-Press, Kathleen A; Ballantyne, Jack

    2007-09-01

    In this work, a number of performance checks were carried out to evaluate the efficacy of commercial Y-short tandem repeats (Y-STR) kits for casework applications. The study evaluated the sensitivity, specificity and stability of the Y-STR markers used and the ability to obtain a male profile from postcoital samples taken at various time points after intercourse. All systems performed well with 1-3 ng of male DNA as recommended by the manufacturers. All systems gave full profiles at 100 pg of input DNA, which is within the realm of low copy number DNA analysis. Moreover all, except Y-Plex12, gave full profiles with 30-50 pg of male DNA. No increased performance was obtained with any of the systems by increasing the cycle number beyond that recommended by the various manufacturers. When up to 1 microg of female DNA was used (in the absence of male DNA) no female DNA cross reactivity was observed with the Y-Plex 12 and Y-Filer systems. PowerPlex Y produced female DNA derived products near the DYS438 and within the DYS392 loci at a rare allele position with high input DNA levels (300 ng and 1 microg, respectively). Male/female DNA admixture experiments indicated the particularly high specificity of the Y-Filer and PowerPlex Y systems under conditions of several thousand fold female DNA excess. All systems were able to detect the minor alleles in male/male DNA admixtures at a 1:5 dilution with the PowerPlex Y and Y-Filer being able to detect some minor alleles at 1:20. Species testing indicated some limited, minor cross reactivity of the commercial systems with some domestic male mammals although it is easily recognizable and would not pose any problems in casework analysis. As expected a significant number of cross-reacting products were obtained with nonhuman primate species. All Y-STR multiplex systems tested were able to produce complete Y-STR profiles from bloodstains and semen stains exposed up to 6 weeks when the samples were protected against precipitation and

  12. 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 ...

  13. Improving DNA data exchange: validation studies on a single 6 dye STR kit with 24 loci.

    Science.gov (United States)

    Martín, Pablo; de Simón, Lourdes Fernández; Luque, Gracia; Farfán, María José; Alonso, Antonio

    2014-11-01

    The idea of developing a new multiplex STR amplification system was conceived in 2011 as an effective way to implement the new European standard set (ESS) of 12 STR markers adopted by The Council of the European Union in 2009 while maintaining an effective compatibility and information exchange with the historical DNA profiles contained in the Spanish national DNA database (around 200,000 DNA profiles) mainly based on the 13 CODIS core STR loci plus D19S433 and D2S1338 markers. With this goal in mind we proposed to test and validate a single STR amplification system for simultaneous analysis of 21 STR markers covering both CODIS and ESS core STR loci plus three additional markers (D19S433, D2S1338, and SE33) also contained in commonly used STR kits and national DNA databases. In 2012, we started the first beta-testing with a 6-dye STR kit prototype containing 24 loci (now known as the GlobalFiler™ PCR Amplification Kit) developed by Life Technologies in response to the CODIS Core Loci Working Group's recommendation to expand the CODIS Core Loci. This prototype included our proposal of 21 autosomal STR markers and two Y-chromosome markers (DYS391 and Y-indel) and maximizes concordance with established databases and previously analyzed samples by maintaining primer sequences of previous Identifiler(®)/NGM SElect™ kits for the 21 STR markers except for TPOX. This paper describes the validation studies conducted with the first commercial available 6-dye STR kit for casework using a 3500 genetic analyzer for fragment detection that included the analysis of the following parameters and aspects: analytical threshold, sensitivity & stochastic threshold, heterozygous balance, stutter threshold, precision and accuracy, repeatability and reproducibility, genotype concordance, DNA mixtures, species specificity, and stability studies with case type samples. The studies demonstrated that the GlobalFiler™ system provided equivalent overall performance to previous forensic

  14. Enhanced DNA Profiling of the Semen Donor in Late Reported Sexual Assaults: Use of Y-Chromosome-Targeted Pre-amplification and Next Generation Y-STR Amplification Systems.

    Science.gov (United States)

    Hanson, Erin K; Ballantyne, Jack

    2016-01-01

    In some cases of sexual assault the victim may not report the assault for several days after the incident due to various factors. The ability to obtain an autosomal STR profile of the semen donor from a living victim rapidly diminishes as the post-coital interval is extended due to the presence of only a small amount of male DNA amidst an overwhelming amount of female DNA. Previously, we have utilized various technological tools to overcome the limitations of male DNA profiling in extended interval post-coital samples including the use of Y-chromosome STR profiling, cervical sample, and post-PCR purification permitting the recovery of Y-STR profiles of the male DNA from samples collected 5-6 days after intercourse. Despite this success, the reproductive biology literature reports the presence of spermatozoa in the human cervix up to 7-10 days post-coitus. Therefore, novel and improved methods for recovery of male profiles in extended interval post-coital samples were required. Here, we describe enhanced strategies, including Y-chromosome-targeted pre-amplification and next generation Y-STR amplification kits, that have resulted in the ability to obtain probative male profiles from samples collected 6-9 days after intercourse.

  15. Vertical profile of peroxyacetyl nitrate (PAN from MIPAS-STR measurements over Brazil in February 2005 and its contribution to tropical UT NOy partitioning

    Directory of Open Access Journals (Sweden)

    A. Roiger

    2008-08-01

    Full Text Available We report on the retrieval of PAN (CH3C(OOONO2 in the upper tropical troposphere from limb measurements by the remote-sensor MIPAS-STR on board the Russian high altitude research aircraft M55-Geophysica. The measurements were performed close to Araçatuba, Brazil, on 17 February 2005. The retrieval was made in the spectral range 775–820 cm−1 where PAN exhibits its strongest feature but also more than 10 species interfere. Especially trace gases such as CH3CCl3, CFC-113, CFC-11, and CFC-22, emitting also in spectrally broad not-resolved branches, make the processing of PAN prone to errors. Therefore, the selection of appropriate spectral windows, the separate retrieval of several interfering species and the careful handling of the water vapour profile are part of the study presented. The retrieved profile of PAN has a maximum of about 0.14 ppbv at 10 km altitude, slightly larger than the lowest reported values (<0.1 ppbv and much lower than the highest reported in the literature (0.65 ppbv. Besides the NOy constituents measured by MIPAS-STR (HNO3, ClONO2, HO2NO2, PAN, the in situ instruments aboard the Geophysica provide simultaneous measurements of NO, NO2, and the sum NOy. Comparing the sum of in-situ and remotely derived NO+NO2+HNO3+ClONO2+HO2NO2+PAN with total NOy a deficit of 30–40% (0.2–0.3 ppbv in the troposphere remains unexplained whereas the values fit well in the stratosphere.

  16. Vertical profile of peroxyacetyl nitrate (PAN from MIPAS-STR measurements over Brazil in February 2005 and the role of PAN in the UT tropical NOy partitioning

    Directory of Open Access Journals (Sweden)

    A. Roiger

    2008-04-01

    Full Text Available We report on the retrieval of PAN (CH3C(OOONO2 in the upper tropical troposphere from limb measurements by the remote-sensor MIPAS-STR on board the Russian high altitude research aircraft M55-Geophysica. The measurements were performed close to Araçatuba, Brazil, on 17 February 2005. The retrieval was made in the spectral range 775–820 cm−1 where PAN exhibits its strongest feature but also more than 10 species interfere. Especially trace gases such as CH3CCl3, CFC-113, CFC-11, and CFC-22, emitting also in spectrally broad not-resolved branches, make the processing of PAN prone to errors. Therefore, the selection of appropriate spectral windows, the separate retrieval of several interfering species and the careful handling of the water vapour profile are part of the study presented. The retrieved profile of PAN has a maximum of about 0.14 ppbv at 10 km altitude, slightly larger than the lowest reported values (<0.1 ppbv and much lower than the highest (0.65 ppbv. Besides the NOy constituents measured by MIPAS-STR (HNO3, ClONO2, PAN, the situ instruments aboard the Geophysica provide simultaneous measurements of NO, NO2, and the sum NOy. Comparing the sum of in-situ and remotely derived NO+NO2+HNO3+ClONO2+PAN with total NOy a deficit of 30–40% (0.2–0.3 ppbv in the troposphere remains unexplained whereas the values fit well in the stratosphere.

  17. Vertical profile of peroxyacetyl nitrate (PAN) from MIPAS-STR measurements over Brazil in February 2005 and its contribution to tropical UT NOy partitioning

    Science.gov (United States)

    Keim, C.; Liu, G. Y.; Blom, C. E.; Fischer, H.; Gulde, T.; Höpfner, M.; Piesch, C.; Ravegnani, F.; Roiger, A.; Schlager, H.; Sitnikov, N.

    2008-08-01

    We report on the retrieval of PAN (CH3C(O)OONO2) in the upper tropical troposphere from limb measurements by the remote-sensor MIPAS-STR on board the Russian high altitude research aircraft M55-Geophysica. The measurements were performed close to Araçatuba, Brazil, on 17 February 2005. The retrieval was made in the spectral range 775 820 cm-1 where PAN exhibits its strongest feature but also more than 10 species interfere. Especially trace gases such as CH3CCl3, CFC-113, CFC-11, and CFC-22, emitting also in spectrally broad not-resolved branches, make the processing of PAN prone to errors. Therefore, the selection of appropriate spectral windows, the separate retrieval of several interfering species and the careful handling of the water vapour profile are part of the study presented. The retrieved profile of PAN has a maximum of about 0.14 ppbv at 10 km altitude, slightly larger than the lowest reported values (<0.1 ppbv) and much lower than the highest reported in the literature (0.65 ppbv). Besides the NOy constituents measured by MIPAS-STR (HNO3, ClONO2, HO2NO2, PAN), the in situ instruments aboard the Geophysica provide simultaneous measurements of NO, NO2, and the sum NOy. Comparing the sum of in-situ and remotely derived NO+NO2+HNO3+ClONO2+HO2NO2+PAN with total NOy a deficit of 30 40% (0.2 0.3 ppbv) in the troposphere remains unexplained whereas the values fit well in the stratosphere.

  18. Vertical profile of peroxyacetyl nitrate (PAN) from MIPAS-STR measurements over Brazil in February 2005 and the role of PAN in the UT tropical NOy partitioning

    Science.gov (United States)

    Keim, C.; Liu, G. Y.; Blom, C. E.; Fischer, H.; Gulde, T.; Höpfner, M.; Piesch, C.; Ravegnani, F.; Roiger, A.; Schlager, H.; Sitnikov, N.

    2008-04-01

    We report on the retrieval of PAN (CH3C(O)OONO2) in the upper tropical troposphere from limb measurements by the remote-sensor MIPAS-STR on board the Russian high altitude research aircraft M55-Geophysica. The measurements were performed close to Araçatuba, Brazil, on 17 February 2005. The retrieval was made in the spectral range 775-820 cm-1 where PAN exhibits its strongest feature but also more than 10 species interfere. Especially trace gases such as CH3CCl3, CFC-113, CFC-11, and CFC-22, emitting also in spectrally broad not-resolved branches, make the processing of PAN prone to errors. Therefore, the selection of appropriate spectral windows, the separate retrieval of several interfering species and the careful handling of the water vapour profile are part of the study presented. The retrieved profile of PAN has a maximum of about 0.14 ppbv at 10 km altitude, slightly larger than the lowest reported values (<0.1 ppbv) and much lower than the highest (0.65 ppbv). Besides the NOy constituents measured by MIPAS-STR (HNO3, ClONO2, PAN), the situ instruments aboard the Geophysica provide simultaneous measurements of NO, NO2, and the sum NOy. Comparing the sum of in-situ and remotely derived NO+NO2+HNO3+ClONO2+PAN with total NOy a deficit of 30-40% (0.2-0.3 ppbv) in the troposphere remains unexplained whereas the values fit well in the stratosphere.

  19. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization.

    Science.gov (United States)

    Repnikova, Elena A; Rosenfeld, Jill A; Bailes, Andrea; Weber, Cecilia; Erdman, Linda; McKinney, Aimee; Ramsey, Sarah; Hashimoto, Sayaka; Lamb Thrush, Devon; Astbury, Caroline; Reshmi, Shalini C; Shaffer, Lisa G; Gastier-Foster, Julie M; Pyatt, Robert E

    2013-09-01

    Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.

  20. Evaluation of a 13-loci STR multiplex system for Cannabis sativa genetic identification.

    Science.gov (United States)

    Houston, Rachel; Birck, Matthew; Hughes-Stamm, Sheree; Gangitano, David

    2016-05-01

    Marijuana (Cannabis sativa) is the most commonly used illicit substance in the USA. The development of a validated method using Cannabis short tandem repeats (STRs) could aid in the individualization of samples as well as serve as an intelligence tool to link multiple cases. For this purpose, a modified 13-loci STR multiplex method was optimized and evaluated according to ISFG and SWGDAM guidelines. A real-time PCR quantification method for C. sativa was developed and validated, and a sequenced allelic ladder was also designed to accurately genotype 199 C. sativa samples from 11 U.S. Customs and Border Protection seizures. Distinguishable DNA profiles were generated from 127 samples that yielded full STR profiles. Four duplicate genotypes within seizures were found. The combined power of discrimination of this multilocus system is 1 in 70 million. The sensitivity of the multiplex STR system is 0.25 ng of template DNA. None of the 13 STR markers cross-reacted with any of the studied species, except for Humulus lupulus (hops) which generated unspecific peaks. Phylogenetic analysis and case-to-case pairwise comparison of 11 cases using F st as genetic distance revealed the genetic association of four groups of cases. Moreover, due to their genetic similarity, a subset of samples (N = 97) was found to form a homogeneous population in Hardy-Weinberg and linkage equilibrium. The results of this research demonstrate the applicability of this 13-loci STR system in associating Cannabis cases for intelligence purposes.

  1. Mutation Rate at Commonly Used Forensic STR Loci: Paternity Testing Experience

    Directory of Open Access Journals (Sweden)

    Faruk Aşıcıoğlua

    2004-01-01

    Full Text Available Paternity tests are carried out by the analysis of hypervariable short tandem repeat DNA loci. These microsatellite sequences mutate at a higher rate than that of bulk DNA. The occurrence of germline mutations at STR loci posses problems in interpretation of resulting genetic profiles. We recently analyzed 59–159 parent/child allele transfers at 13 microsatellite loci. We identified 12 mutations in 7 microsatellite loci. No mutations were occurred in other 6 loci. The highest mutation rate was observed with 5 mutations at D8S1179 locus at different alleles. The event was always single repeat related. The mutation rate was between 0 and 1.5 x 10-2 per locus per gamete per generation. The mutation event is very crucial for forensic DNA testing and accumulation of STR mutation data is extremely important for genetic profile interpretation.

  2. PCR typing of DNA fragments of the two short tandem repeat (STR) systems upstream of the human myelin basic protein (MBP) gene in Danes and Greenland Eskimos

    DEFF Research Database (Denmark)

    Nellemann, L J; Frederiksen, J; Morling, N

    1996-01-01

    -A and MBP-B were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 112 unrelated Danes, 140 unrelated Greenland Eskimos, and 88 Danish mother/child pairs were analyzed. The distributions of MBP phenotypes were in Hardy-Weinberg equilibrium in both...... in Eskimos (0.225) than in Danes (0.06). Strong gametic associations were found between fragments from MBP-A and MBP-B series in both Danes and Eskimos. Some of the associations were different in Danes and Eskimos. In the 88 Danish mother/child pairs, the segregation of the MBP genotypes were in accordance...... with a genetic model of co-dominant inheritance and no mutation was found. Two MBP STR regions with irregular structures were sequenced. One fragment had a single base G to A transition at position 124 in the primer binding region between the MBP-A and MBP-B regions. In the other fragment, a deletion starting...

  3. Statistical modelling of Ion PGM HID STR 10-plex MPS data.

    Science.gov (United States)

    Vilsen, Søren B; Tvedebrink, Torben; Mogensen, Helle Smidt; Morling, Niels

    2017-02-03

    We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences. We found that, due to MID sampling, the average coverage on a marker could not be used as an apt predictor of the amount of template DNA. The parental LUS was shown to be better predictor of stutter ratio than the parental allele repeat length, when markers with compound and complex repeat patterns or markers which contained micro-variants were considered, such as marker TH01 showed R(2) of 0.02 and 0.78 for parent allele repeat length and LUS, respectively. The one-inflated negative binomial method (OINB) and geometric model that can be used to remove non-systematic noise left on average 1.8 and 1.2 systematic errors per STR system, respectively.

  4. Development of internal amplification controls for DNA profiling with the AmpFℓSTR(®) SGM Plus(®) kit.

    Science.gov (United States)

    Zahra, Nathalie; Hadi, Sibte; Smith, Judith A; Iyengar, Arati; Goodwin, William

    2011-06-01

    DNA extracted from forensic samples can be degraded and also contain co-extracted contaminants that inhibit PCR. The effects of DNA degradation and PCR inhibition are often indistinguishable when examining a DNA profile. Two internal amplification controls (IACs) were developed to improve quality control of PCR using the AmpFℓSTR® SGM Plus® kit. The co-amplification of these controls with DNA samples was used to monitor amplification efficiency and detect PCR inhibitors. IAC fragments of 90 and 410 bp (IAC₉₀ and IAC₄₁₀) were generated from the plasmid pBR322 using tailed primers and then amplified with ROX-labelled primers. Co-amplification of IAC₉₀ and IAC₄₁₀ was performed with varying amounts of template DNA, degraded DNA and DNA contaminated with humic acid, heme and indigo dye. Both IAC₉₀ and IAC₄₁₀ were successfully amplified with human DNA without significantly affecting the quality of the DNA profile, even with DNA amounts lower than 0.5 ng. In the presence of inhibitors, the IAC₉₀ signal was still present after all human DNA loci fail to amplify; in contrast, the IAC₄₁₀ signal was reduced or absent at low levels of inhibition. Amplification of the two IACs provided an internal PCR control and allowed partial profiles caused by inhibition to be distinguished from degraded DNA profiles.

  5. EuroForMix: An open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts.

    Science.gov (United States)

    Bleka, Øyvind; Storvik, Geir; Gill, Peter

    2016-03-01

    We have released a software named EuroForMix to analyze STR DNA profiles in a user-friendly graphical user interface. The software implements a model to explain the allelic peak height on a continuous scale in order to carry out weight-of-evidence calculations for profiles which could be from a mixture of contributors. Through a properly parameterized model we are able to do inference on mixture proportions, the peak height properties, stutter proportion and degradation. In addition, EuroForMix includes models for allele drop-out, allele drop-in and sub-population structure. EuroForMix supports two inference approaches for likelihood ratio calculations. The first approach uses maximum likelihood estimation of the unknown parameters. The second approach is Bayesian based which requires prior distributions to be specified for the parameters involved. The user may specify any number of known and unknown contributors in the model, however we find that there is a practical computing time limit which restricts the model to a maximum of four unknown contributors. EuroForMix is the first freely open source, continuous model (accommodating peak height, stutter, drop-in, drop-out, population substructure and degradation), to be reported in the literature. It therefore serves an important purpose to act as an unrestricted platform to compare different solutions that are available. The implementation of the continuous model used in the software showed close to identical results to the R-package DNAmixtures, which requires a HUGIN Expert license to be used. An additional feature in EuroForMix is the ability for the user to adapt the Bayesian inference framework by incorporating their own prior information.

  6. The landscape of human STR variation.

    Science.gov (United States)

    Willems, Thomas; Gymrek, Melissa; Highnam, Gareth; Mittelman, David; Erlich, Yaniv

    2014-11-01

    Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome's representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.

  7. Direct Y-STR amplification of body fluids deposited on commonly found crime scene substrates.

    Science.gov (United States)

    Dargay, Amanda; Roy, Reena

    2016-04-01

    Body fluids detected on commonly found crime scene substrates require extraction, purification and quantitation of DNA prior to amplification and generation of short tandem repeat (STR) DNA profiles. In this research Y-STR profiles were generated via direct amplification of blood and saliva deposited on 12 different substrates. These included cigarette butts, straws, grass, leaves, woodchips and seven different types of fabric. After depositing either 0.1 μL of blood or 0.5 μL of saliva, each substrate containing the dry body fluid stain was punched using a Harris 1.2 mm micro-punch. Each of these punched substrates, a total of 720 samples, containing minute amount of blood or saliva was either amplified directly without any pre-treatment, or was treated with one of the four washing reagents or buffer. In each of these five experimental groups the substrates containing the body fluid remained in the amplification reagent during the thermal cycling process. Each sample was amplified with the three direct Y-STR amplification kits; AmpFℓSTR(®) Yfiler(®) Direct, Yfiler(®) Plus Amplification Kits and the PowerPlex(®) Y23 System. Complete and concordant Y-STR profiles were successfully obtained from most of these 12 challenging crime scene objects when the stains were analyzed by at least one of the five experimental groups. The reagents and buffer were interchangeable among the three amplification kits, however, pre-treatment with these solutions did not appear to enhance the quality or the number of the full profiles generated with direct amplification. This study demonstrates that blood and saliva deposited on these simulated crime scene objects can be amplified directly.

  8. Microchip-based forensic short tandem repeat genotyping.

    Science.gov (United States)

    Kim, Yong Tae; Heo, Hyun Young; Oh, Shin Hye; Lee, Seung Hwan; Kim, Do Hyun; Seo, Tae Seok

    2015-08-01

    Micro total analysis system (μTAS) or lab-on-a-chip (LOC) technology has advanced over decades, and the high performance for chemical and biological analysis has been well demonstrated with advantages of low sample consumption, rapid analysis time, high-throughput screening, and portability. In particular, μTAS or LOC based genetic applications have been extensively explored, and the short tandem repeat (STR) typing on a chip has garnered attention in the forensic community due to its special use for human identification in the field of mass disaster and missing person investigation, paternity testing, and perpetrator identification. The STR typing process consists of sample collection, DNA extraction, DNA quantitation, STR loci amplification, capillary electrophoretic separation, and STR profiling. Recent progress of microtechnology shows its ability to substitute the conventional analytical tools, and furthermore demonstrates total integration of the whole STR processes on a single wafer for on-site STR typing. In this review article, we highlighted some representative results for fluorescence labeling techniques, microchip-based DNA purification, on-chip polymerase chain reaction (PCR), a capillary electrophoretic microdevice, and a fully integrated microdevice for STR typing.

  9. Prediction of autosomal STR typing success in ancient and Second World War bone samples.

    Science.gov (United States)

    Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

    2017-03-01

    Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is

  10. Comparison of DNA yield and STR success rates from different tissues in embalmed bodies.

    Science.gov (United States)

    Wheeler, Amanda; Czado, Natalia; Gangitano, David; Turnbough, Meredith; Hughes-Stamm, Sheree

    2017-01-01

    Formalin fixation is commonly used to preserve tissue sections for pathological testing and embalming cadavers for medical dissection or burial. DNA extracted from formalin-fixed tissues may also provide an alternative source of genetic material for medical diagnosis and forensic casework, such as identifying unknown embalmed human remains. Formaldehyde causes DNA damage, chemical modifications, and degradation, thereby reducing the quantity and quality of DNA available for downstream genetic analyses. By comparing the DNA yield, level of DNA degradation, and short tandem repeat (STR) success of various tissue types, this study is the first of its kind to provide some guidance on which samples from embalmed bodies are likely to generate more complete STR profiles. Tissue samples were dissected from three male embalmed cadavers and included bone, cartilage, hair, muscle, internal organs, skin, teeth, and nail clippings. DNA was purified from all samples using the QIAamp® FFPE Tissue Kit (Qiagen), quantified using the QuantiFiler® Trio DNA Quantification kit (Life Technologies), and genotyped using the GlobalFiler® PCR Amplification Kit (Life Technologies). Results of this study showed variation in DNA quantity and STR success between different types of tissues and some variation between cadavers. Overall, bone marrow samples resulted in the highest DNA yields, the least DNA degradation, and greatest STR success. However, several muscle, hair, and nail samples generated higher STR success rates than traditionally harvested bone and tooth samples. A key advantage to preferentially using these tissue samples over bone (and marrow) and teeth is their comparative ease and speed of collection from the cadaver and processing during DNA extraction. Results also indicate that soft tissues affected by lividity (blood pooling) may experience greater exposure to formalin, resulting in more DNA damage and reduced downstream STR success than tissues under compression. Overall

  11. An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples.

    Science.gov (United States)

    Menotti-Raymond, Marilyn A; David, Victor A; Wachter, Leslie L; Butler, John M; O'Brien, Stephen J

    2005-09-01

    A forensic genotyping panel of 11 tetranucleotide STR loci from the domestic cat was characterized and evaluated for genetic individualization of cat tissues. We first examined 49 candidate STR loci and their frequency assessment in domestic cat populations. The STR loci (3-4 base pair repeat motifs), mapped in the cat genome relative to 579 coding loci and 255 STR loci, are well distributed across the 18 feline autosomes. All loci exhibit Mendelian inheritance in a multi-generation pedigree. Eleven loci that were unlinked and were highly heterozygous in cat breeds were selected for a forensic panel. Heterozygosity values obtained for the independent loci, ranged from 0.60-0.82, while the average cat breed heterozygosity obtained for the 11 locus panel was 0.71 (range of 0.57-0.83). A small sample set of outbred domestic cats displayed a heterozygosity of 0.86 for the 11 locus panel. The power of discrimination of the panel is moderate to high in the cat breeds examined, with an average P(m) of 3.7E-06. The panel shows good potential for genetic individualization within outbred domestic cats with a P(m) of 5.31E-08. A multiplex protocol, designed for the co-amplification of the 11 loci and a gender-identifying locus, is species specific and robust, generating a product profile with as little as 0.125 nanograms of genomic DNA.

  12. Identification and characterization of variant alleles at CODIS STR loci.

    Science.gov (United States)

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  13. Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances.

    Science.gov (United States)

    Andersen, Mikkel Meyer; Mogensen, Helle Smidt; Eriksen, Poul Svante; Olofsson, Jill Katharina; Asplund, Maria; Morling, Niels

    2013-05-01

    Y chromosome short tandem repeats (Y-STRs) are valuable genetic markers in certain areas of forensic case-work. However, when the Y-STR DNA profile is weak, the observed Y-STR profile may not be complete--i.e. locus drop-out may have occurred. Another explanation could be that the stain DNA did not have a Y-STR allele that was detectable with the method used (the allele is a 'null allele'). If the Y-STR profile of a stain is strong, one would be reluctant to consider drop-out as a reasonable explanation of lack of a Y-STR allele and would maybe consider 'null allele' as an explanation. On the other hand, if the signal strengths are weak, one would most likely accept drop-out as a possible explanation. We created a logistic regression model to estimate the probability of allele drop-out with the Life Technologies/Applied Biosystems AmpFlSTR(®) Yfiler(®) kit such that the trade-off between drop-outs and null alleles could be quantified using a statistical model. The model to estimate the probability of drop-out uses information about locus imbalances, signal strength, the number of PCR cycles, and the fragment size of Yfiler. We made two temporarily separated experiments and found no evidence of temporal variation in the probability of drop-out. Using our model, we found that for 30 PCR cycles with a 150 bp allele, the probability of drop-out was 1:5000 corresponding to the average estimate of the probability of Y-STR null alleles at a signal strength of 1249 RFU. This means that the probability of a null allele is higher than that of an allele drop-out at e.g. 4000 RFU and the probability of drop-out is higher than that of a null allele at e.g. 75 RFU. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  14. Comment on Kokshoorn, B, and Blankers, BJ ‘Response to Grisedale, KS and van Daal, A: comparison of STR profiling from low template DNA extracts with and without the consensus profiling method’

    Directory of Open Access Journals (Sweden)

    Grisedale Kelly

    2013-01-01

    Full Text Available Abstract Kokshoorn and Blankers responded to our recent article by saying that replicate analysis and consensus profiling of low template samples was best in terms of reliability and objectivity. We agree that the consensus approach has benefits, particularly in eliminating non-repeating spurious alleles from the final profile. However, with the development of statistical models that can accommodate stochastic effects and allele drop in, it may be beneficial to perform a single amplification with three times the amount of template, since much information is lost from the profile using the consensus approach.

  15. Next-Generation STR Genotyping Kits for Forensic Applications.

    Science.gov (United States)

    Mulero, J J; Hennessy, L K

    2012-01-01

    Forensic DNA typing has been a constantly evolving field driven by innovations from academic laboratories as well as kit manufacturers. Central to these technological advances has been the transition from multilocus-probe restriction fragment length polymorphism (RFLP) methods to short tandem repeat (STR) PCR-based assays. STRs are now the markers of choice for forensic DNA typing and a wide variety of commercial STR kits have been designed to meet the various needs of a forensic lab. This review provides an overview of the commercial STR kits made available since the year 2000 and explains the rationale for creating these kits. Substantial progress has been made in key areas such as sample throughput, speed, and sensitivity. For example, a significant advancement for databasing labs was the capability of direct amplification from a blood or buccal sample without need for DNA extraction or purification, enabling increased throughput. Other key improvements are greater tolerance for inhibitors (e.g., humic acid, hematin, and tannic acid) present in evidence samples, PCR cycling times decreased by 1-1.5 h, and greater sensitivity with improved buffer components and thermal cycling conditions. These improvements that have been made over the last 11 years have enhanced the ability of forensic laboratories to obtain a DNA profile from more challenging samples. However, with the proliferation of kits from different vendors the primer binding sequences of the loci vary, which could result in discordant events that would need to be resolved either via a database-driven software solution or simply by evaluating discordant samples with multiple kits.

  16. 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

  17. A 27-locus STR assay to meet all United States and European law enforcement agency standards.

    Science.gov (United States)

    Schumm, James W; Gutierrez-Mateo, Cristina; Tan, Eugene; Selden, Richard

    2013-11-01

    Different national and international agencies have selected specific STR sets for forensic database use. To enhance database comparison across national and international borders, a 27-locus multiplex system was developed comprising all 15 STR loci of the European standard set, the current 13 STR loci of the CODIS core, the proposed 22 STR loci of the expanded CODIS core, 4 additional commonly used STR loci, and the amelogenin locus. Development required iterative primer design to resolve primer-related artifacts, amplicon sizing, and locus-to-locus balance issues. The 19.5-min assay incorporated newly developed six-dye chemistry analyzed using a novel microfluidic electrophoresis instrument capable of simultaneous detection and discrimination of 8 or more fluorescent dyes. The 27-locus multiplex offers the potential for a new international STR standard permitting laboratories in any jurisdiction to use a single reaction to determine profiles for loci they typically generate plus an expanded common STR profiling set of global interest.

  18. Short Tandem Repeat DNA Internet Database

    Science.gov (United States)

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  19. A substantially lower frequency of uninformative matches between 23 versus 17 Y-STR haplotypes in north Western Europe.

    Science.gov (United States)

    Larmuseau, Maarten H D; Vanderheyden, Nancy; Van Geystelen, Anneleen; Decorte, Ronny

    2014-07-01

    The analysis of human short tandem repeats of the Y-chromosome (Y-STRs) provides a powerful tool in forensic cases for male sex identification, male lineage identification and identification of the geographical origin of male lineages. As the commonly used 12 and 17 Y-STR multiplexes do not discriminate between some unrelated males, additional Y-STRs were implemented in the PowerPlex(®) Y23 System to supplement the existing commercial Y-STR kits. Until today, the forensic value of a (near) 23 versus 17 Y-STR haplotype match between an unknown DNA donor and a certain biological sample in a database is not yet well studied. This will be of huge interest for cases where an autosomal DNA profile yields no match to a DNA database and the database is used for familial searching (male relative(s) of the offender) or for the estimation of the geographical origin of the offender. In order to value (near) 23 Y-STR haplotype matches in a local sample from Western Europe, we selected the region of Flanders (Belgium) due to the already present knowledge on its Y-chromosomal variants. Many Y-chromosomes of this region were previously genotyped with Y-SNPs at a high resolution of the most recently updated Y-chromosomal tree and the deep-rooted genealogy of each DNA donor was already established. By comparing (near) matches of 23 versus 17 Y-STR haplotypes between patrilineal-unrelated males, a substantial lower number of uninformative (near) 23 Y-STR haplotype matches has been observed compared to 17 Y-STR haplotypes. Furthermore, the use of SNP data was informative to discriminate >60% of unrelated males with an (near) identical 17 Y-STR match while SNP data was only necessary to discriminate about 10% of unrelated males with a 23 Y-STR haplotype that differed at only two Y-STRs. This shows the higher value of the Y23 haplotype within familial DNA searching and the estimation of the geographical origin of a DNA donor. Therefore, the use of the PowerPlex(®) Y23 System instead

  20. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

    Science.gov (United States)

    Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

    2011-09-01

    Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

  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. 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

  3. Single-cell forensic short tandem repeat typing within microfluidic droplets.

    Science.gov (United States)

    Geng, Tao; Novak, Richard; Mathies, Richard A

    2014-01-07

    A short tandem repeat (STR) typing method is developed for forensic identification of individual cells. In our strategy, monodisperse 1.5 nL agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet polymerase chain reaction (PCR) is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the coencapsulated microbeads. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis (CE) STR fragment size analysis. The 9-plex STR profiles of single cells from both pure and mixed populations of GM09947 and GM09948 human lymphoid cells show that all alleles are correctly called and allelic drop-in/drop-out is not observed. The cell mixture study exhibits a good linear relationship between the observed and input cell ratios in the range of 1:1 to 10:1. Additionally, the STR profile of GM09947 cells could be deduced even in the presence of a high concentration of cell-free contaminating 9948 genomic DNA. Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low-concentration samples.

  4. The Effect of Repeated Heating on Fatty Acid Profile of Beef and Spices of Rendang

    Directory of Open Access Journals (Sweden)

    Rina Yenrina

    2015-03-01

    Full Text Available Rendang is a traditional Minangkabau cuisine with the main ingredient of beef or buffalo meat which is cooked using coconut milk and some spices. Rendang is cooked more than 2 hours, and after that do the repeated heating. This study aimed to determine the effect of repeated heating on fatty acid profiles of beef and spices of rendang. The analysis carried out at Chemistry Lab. and Biochemistry Lab. In  Fateta Unand and Integrated Lab in IPB Bogor. This  study   designed  used a completely  randomized  design  with 5 treatments and 3 replications.  The treatments that used in this study were A (raw beef, B (freshly cooked rendang, C (first heating, D (second heating, E (third heating where the heating was done every 2 days. Data were collected for  fatty acids profile of beef and spices of rendang. Analysis of the Type of  Fatty Acid by HPLC method (AOAC, 1984. The results shown that repeated heating of beef and spice of rendang had significantly different effect on the type of fatty acids and an increased trans fatty Acid of rendang.

  5. 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.

  6. 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.

  7. A genetic portrait of Oraon Indian tribe drawn with 15 autosomal and 17 Y chromosomal STR markers.

    Science.gov (United States)

    Shrivastava, Pankaj; Jain, Toshi; Trivedi, V B

    2016-09-01

    An analysis of 15 autosomal short tandem repeat (STR) loci and 17 Y-STR loci was performed in 123 unrelated members of the Oraon tribal community of Central India. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were greater than 0.99999 and 0.999989, respectively, for autosomal STRs. In addition, a total of 58 distinct Y-STR haplotypes were observed out of which 54 Y-STR haplotypes were observed only once. The haplotype diversity and discrimination capacity for 17 Y-STR loci was 0.997 and 0.906, respectively.

  8. DNA profiling of extended tracts of primitive DNA repeats: Direct identification of unstable simple repeat loci in complex genome

    Energy Technology Data Exchange (ETDEWEB)

    Rogaeva, E.A.; Korovaitseva, G.; St. George-Hyslop, P. [Univ. of Toronto (Canada)] [and others

    1994-09-01

    The most simple DNA repetitive elements, with repetitive monomer units of only 1-10 bp in tandem tracts, are an abundant component of the human genome. The expansion of at least one type of these repeats ((CCG)n and (CTG)n) have been detected for a several neurological diseases with anticipation in successive generations. We propose here a simple method for the identification of particularly expanded repeats and for the recovery of flanking sequences. We generated DNA probes using PCR to create long concatamers (n>100) by amplification of the di-, tri-, tetra-, penta- and hexa-nucleotide repeat oligonucleotide primer pairs. To reduce the complexity of the background band pattern, the genomic DNA was restricted with a mixture of at least five different endonucleases, thereby reducing the size of restriction fragments containing short simple repeat arrays while leaving intact the large fragments containing the longer simple repeats arrays. Direct blot hybridization has shown different {open_quotes}DNA fingerprint{close_quotes} patterns with all arbitrary selected di-hexa nucleotide repeat probes. Direct hybridization of the (CTG)n and (CCG)n probes revealed simple or multiple band patterns depending upon stringency conditions. We were able to detect the presence of expanded unstable tri-nucleotide alleles by (CCG)n probe for some FRAXA subjects and by (CTG)n probe for some myotonic dystrophy subjects which were not present in the parental DNA patterns. The cloning of the unstable alleles for simple repeats can be performed by direct recover from agarose gels of the aberrant unstable bands detected above. The recovered flanking regions can be cloned, sequenced and used for PCR detection of expanded alleles or can be used to screen cDNA. This method may be used for testing of small families with diseases thought to display clinical evidence of anticipation.

  9. Mutation rate estimates for 13 STR loci in a large population from Rio Grande do Sul, Southern Brazil.

    Science.gov (United States)

    Mardini, Ana Carolina; Rodenbusch, Rodrigo; Schumacher, Simone; Chula, Fernanda Goulart Lanes; Michelon, Candice Tosi; Gastaldo, André Zoratto; Maciel, Lila Partichelli; de Matos Almeida, Sabrina Esteves; da Silva, Cláudia Maria Dornelles

    2013-01-01

    Short tandem repeat (STR) polymorphisms have been extensively used in forensic genetics analysis. Knowledge about the locus-specific mutation rates of STRs improves forensic probability calculations and interpretations of diversity data. To incorporate single-locus diversity information into autosomal STR mutation rate estimations, 13 STR loci were studied during 2007-2009 in 10,959 paternity investigation cases from Rio Grande do Sul, the southernmost state of Brazil, covering an overall number of 284,934 allelic transfers. A total of 355 mutations were identified; 348 repeats were gains or losses of one step, three were gains or losses of two steps, and four were gains or losses of not stepwise mutation. The mutation rates ranged from 4.6 × 10(-5) to 2.3 × 10(-3), and the overall mutation rate estimate was 1.2 × 10(-3). The average of the paternal mutation rate (1.8 × 10(-3)) was five times higher than the maternal rate (0.36 × 10(-3)). The observed mutational features for STRs have important consequences for forensic applications, including the definition of criteria for exclusion in paternity testing and the interpretation of DNA profiles in identification analysis.

  10. Estimating stutter rates for Y-STR alleles

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Olofsson, Jill; Mogensen, Helle Smidt;

    2011-01-01

    Stutter peaks are artefacts that arise during PCR amplification of short tandem repeats. Stutter peaks are especially important in forensic case work with DNA mixtures. The aim of the study was primarily to estimate the stutter rates of the AmpF/STR Yfiler kit. We found that the stutter rates...

  11. Analysis of matches and partial-matches in a Danish STR data set

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Curan, James Michael;

    2012-01-01

    Over the recent years, the national databases of STR profiles have grown in size due to the success of forensic DNA analysis in solving crimes. The accumulation of DNA profiles implies that the probability of a random match or near match of two randomly selected DNA profiles in the database...... increases. We analysed 53,295 STR profiles from individuals investigated in relation to crime case investigations at the Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark. Incomplete STR profiles (437 circa 0.8% of the total), 48 redundant STR profiles from...... other, i.e. 1.3 × 109 comparisons. With these large number of comparisons, it is likely to observe DNA profiles that coincide on many loci, which has concerned some commentators and raised questions about “overstating” the power of DNA evidence. We used the method of Weir [11] and [12] and Curran et al...

  12. High-accuracy, high-resolution gravity profiles from 2 years of the Geosat Exact Repeat Mission

    Science.gov (United States)

    Sandwell, David T.; Mcadoo, David C.

    1990-01-01

    Satellite altimeter data from the first 44 repeat cycles (2 years) of the Geosat Exact Repeat Mission (EWRM) were averaged to improve accuracy, resolution and coverage of the marine gravity field. Individual 17-day repeat cycles were first edited and differentiated, resulting in the along-track vertical deflection (i.e., gravity disturbance). To increase the signal-to-noise ratio, 44 of these cycles were then averaged to form a single highly accurate vertical deflection profile. The largest contribution to the vertical deflection error is short-wavelength altimeter noise and longer-wavelength oceanographic variability; the combined noise level is typically 6 microrad. Both types of noise are reduced by averaging many repeat cycles. Over most ocean areas the uncertainty of the average profile is less than 1 microrad which corresponds to 1 mgal of along-track gravity disturbance. However, in areas of seasonal ice coverage, its uncertainty can exceed 5 microrad. To assess the resolution of individual and average Geosat gravity profiles, the cross-spectral analysis technique was applied to repeat profiles. Individual Geosat repeat cycles are coherent (greater than 0.5) for wavelengths greater than about 30 km and become increasingly incoherent at shorter wavelengths.

  13. Repeated surveys by acoustic Doppler current profiler for flow and sediment dynamics in a tidal river

    Science.gov (United States)

    Dinehart, R. L.; Burau, J. R.

    2005-11-01

    A strategy of repeated surveys by acoustic Doppler current profiler (ADCP) was applied in a tidal river to map velocity vectors and suspended-sediment indicators. The Sacramento River at the junction with the Delta Cross Channel at Walnut Grove, California, was surveyed over several tidal cycles in the Fall of 2000 and 2001 with a vessel-mounted ADCP. Velocity profiles were recorded along flow-defining survey paths, with surveys repeated every 27 min through a diurnal tidal cycle. Velocity vectors along each survey path were interpolated to a three-dimensional Cartesian grid that conformed to local bathymetry. A separate array of vectors was interpolated onto a grid from each survey. By displaying interpolated vector grids sequentially with computer animation, flow dynamics of the reach could be studied in three-dimensions as flow responded to the tidal cycle. Velocity streamtraces in the grid showed the upwelling of flow from the bottom of the Sacramento River channel into the Delta Cross Channel. The sequential display of vector grids showed that water in the canal briefly returned into the Sacramento River after peak flood tides, which had not been known previously. In addition to velocity vectors, ADCP data were processed to derive channel bathymetry and a spatial indicator for suspended-sediment concentration. Individual beam distances to bed, recorded by the ADCP, were transformed to yield bathymetry accurate enough to resolve small bedforms within the study reach. While recording velocity, ADCPs also record the intensity of acoustic backscatter from particles suspended in the flow. Sequential surveys of backscatter intensity were interpolated to grids and animated to indicate the spatial movement of suspended sediment through the study reach. Calculation of backscatter flux through cross-sectional grids provided a first step for computation of suspended-sediment discharge, the second step being a calibrated relation between backscatter intensity and sediment

  14. Identifying contributors of DNA mixtures by means of quantitative information of STR typing

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2012-01-01

    identified using polymorphic genetic markers. However, modern typing techniques supply additional quantitative data, which contain very important information about the observed evidence. This is particularly true for cases of DNA mixtures, where more than one individual has contributed to the observed...... biological stain. This article presents a method for including the quantitative information of short tandem repeat (STR) DNA mixtures in the LR. Also, an efficient algorithmic method for finding the best matching combination of DNA mixture profiles is derived and implemented in an on-line tool for two......- and three-person DNA mixtures. Finally, we demonstrate for two-person mixtures how this best matching pair of profiles can be used in estimating the likelihood ratio using importance sampling. The reason for using importance sampling for estimating the likelihood ratio is the often vast number...

  15. Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

    Science.gov (United States)

    Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

    2002-02-01

    Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

  16. STR data for the 13 CODIS loci in Singapore Malays.

    Science.gov (United States)

    Ang, H C; Sornarajah, R; Lim, S E S; Syn, C K C; Tan-Siew, W F; Chow, S T; Budowle, Bruce

    2005-03-10

    Allele frequencies for the 13 CODIS (Combined DNA Index System, USA) STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 197 unrelated Malays in Singapore.

  17. Development of behavioural profile in the Northern common boa (Boa imperator): Repeatable independent traits or personality?

    Science.gov (United States)

    Šimková, Olga; Frýdlová, Petra; Žampachová, Barbora; Frynta, Daniel; Landová, Eva

    2017-01-01

    Recent studies of animal personality have focused on its proximate causation and ecological and evolutionary significance in particular, but the question of its development was largely overlooked. The attributes of personality are defined as between-individual differences in behaviour, which are consistent over time (differential consistency) and contexts (contextual generality) and both can be affected by development. We assessed several candidates for personality variables measured in various tests with different contexts over several life-stages (juveniles, older juveniles, subadults and adults) in the Northern common boa. Variables describing foraging/feeding decision and some of the defensive behaviours expressed as individual average values are highly repeatable and consistent. We found two main personality axes-one associated with foraging/feeding and the speed of decision, the other reflecting agonistic behaviour. Intensity of behaviour in the feeding context changes during development, but the level of agonistic behaviour remains the same. The juveniles and adults have a similar personality structure, but there is a period of structural change of behaviour during the second year of life (subadults). These results require a new theoretical model to explain the selection pressures resulting in this developmental pattern of personality. We also studied the proximate factors and their relationship to behavioural characteristics. Physiological parameters (heart and breath rate stress response) measured in adults clustered with variables concerning the agonistic behavioural profile, while no relationship between the juvenile/adult body size and personality concerning feeding/foraging and the agonistic behavioural profile was found. Our study suggests that it is important for studies of personality development to focus on both the structural and differential consistency, because even though behaviour is differentially consistent, the structure can change.

  18. Low-Profile Repeater Antenna with Parasitic Elements for On-On-Off WBAN Applications

    Directory of Open Access Journals (Sweden)

    Do-Gu Kang

    2016-01-01

    Full Text Available A low-profile repeater antenna with parasitic elements for on-on-off WBAN applications is proposed. The proposed antenna consists of a planar inverted-F antenna (PIFA, two parasitic elements, and a ground plane with a slot. Due to the slot, the impedance matching of the resonance formed by the PIFA is improved, which makes the proposed antenna operate in the 5.8 GHz industrial, scientific, and medical (ISM band. To cover the 5.2 GHz wireless local area network (WLAN band, a dual resonance characteristic is realized by the slot and the two parasitic elements. The first coupling between the PIFA and the slot not only makes the slot operate as a resonator, but also forms secondary coupling between the slot and the two parasitic elements. The two parasitic elements operate as an additional resonator due to secondary coupling. The antenna has the enhanced near surface radiation in the 5.8 GHz ISM band due to addition of the slot and radiation toward off-body direction in the 5.2 GHz WLAN band. In order to evaluate antenna performance considering the human body effect, the antenna characteristics on a human equivalent phantom are analyzed.

  19. Analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, NBS-Str1 and BLEC-Str8, of rice.

    Science.gov (United States)

    Ray, Swatismita; Kapoor, Sanjay; Tyagi, Akhilesh K

    2012-04-01

    Two abiotic stress-inducible upstream regulatory sequences (URSs) from rice have been identified and functionally characterized in rice. NBS-Str1 and BLEC-Str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (Oryza sativa L. var. IR64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. NBS-Str1 and BLEC-Str8 genes code for putative NBS (nucleotide binding site)-LRR (leucine rich repeat) and β-lectin domain protein, respectively. NBS-Str1 URS is induced in root tissue, preferentially in vascular bundle, during 3 and 24 h of desiccation stress condition in transgenic 7-day-old rice seedling. In mature transgenic plants, this URS shows induction in root and shoot tissue under desiccation stress as well as under prolonged (1 and 2 day) salt stress. BLEC-Str8 URS shows basal activity under un-stressed condition, however, it is inducible under salt stress condition in both root and leaf tissues in young seedling and mature plants. Activity of BLEC-Str8 URS has been found to be vascular tissue preferential, however, under salt stress condition its activity is also found in the mesophyll tissue. NBS-Str1 and BLEC-Str8 URSs are inducible by heavy metal, copper and manganese. Interestingly, both the URSs have been found to be non responsive to ABA treatment, implying them to be part of ABA-independent abiotic stress response pathway. These URSs could prove useful for expressing a transgene in a stress responsive manner for development of stress tolerant transgenic systems.

  20. Turkish population data on the short tandem repeat locus TPOX

    DEFF Research Database (Denmark)

    Vural, B; Poda, M; Atlioglu, E;

    1998-01-01

    Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals.......Allele and genotype frequencies were determined for the STR (short tandem repeat) locus TPOX in a random Turkish population sample of 200 individuals....

  1. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles

    DEFF Research Database (Denmark)

    Gelardi, Chiara; Rockenbauer, Eszter; Dalsgaard, Sigrun

    2014-01-01

    Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We...... report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed...

  2. Extended PCR conditions to reduce drop-out frequencies in low template STR typing including unequal mixtures.

    Science.gov (United States)

    Weiler, Natalie E C; Matai, Anuska S; Sijen, Titia

    2012-01-01

    Forensic laboratories employ various approaches to obtain short tandem repeat (STR) profiles from minimal traces (drop-out frequency is reduced for both pristine DNA and single or multiple donor mock case work samples. In addition, increased peak heights and slightly more drop-ins are observed while the heterozygous peak balance remains similar as with the conventional Identifiler protocol. By this extended protocol, full DNA profiles were obtained from only 12 sperm heads (which corresponds to 36 pg of DNA) that were collected by laser micro dissection. Notwithstanding the improved detection, allele drop-outs do persist, albeit in lower frequencies. Thus a LT interpretation strategy such as deducing consensus profiles from multiple independent amplifications is appropriate. The use of extended PCR conditions represents a general approach to improve detection of unequal mixtures as shown using four commercially available kits (AmpFℓSTR(®) Identifiler, SEfiler Plus, NGM and Yfiler). The extended PCR protocol seems to amplify more of the molecules in LT samples during PCR, which results in a lower drop-out frequency. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  3. Effects of moxifloxacin exposure on the conjunctival flora and antibiotic resistance profile following repeated intravitreal injections

    Institute of Scientific and Technical Information of China (English)

    Mustafa; Atas; Burhan; Baskan; Ayse; zkse; Fatma; Mutlu; Sarιgüzel; Süleyman; Demircan; Emine; Pangal

    2014-01-01

    AIM:To evaluate the effects of moxifloxacin exposure on the conjunctival flora and antibiotic resistance profile following repeated intravitreal injections.METHODS:Seventy-two eyes of 36 patients [36 eyes in control group, 36 eyes in intravitreal injection(IVI) group]were enrolled in the study. All the eyes had at least one IVI and had diabetic macular edema(DME) or age-related macular degeneration(ARMD). Moxifloxacin was prescribed to all the patients four times a day for five days following injection. Conjunctival cultures were obtained from the lower fornix via standardized technique with every possible effort made to minimize contamination from the lids, lashes, or skin. Before the application of any ophthalmic medication, conjunctival cultures were obtained from both eyes using sterile cotton culture. An automated microbiology system was used to identify the growing bacteria and determine antibiotic sensitivity.RESULTS:The bacterial cultures were isolated from 72 eyes of 36 patients, sixteen of whom patients(44.4%)were male and twenty(55.6%) were female. Average age was 68.4 ±9.0(range 50-86). The average number of injections before taking cultures was 3.1+1.0. Forty-eight(66.7%) of 72 eyes had at least one significant organism.There was no bacterial growth in 8(20.5%) of IVI eyes and in 16(44.4%) of control eyes(P =0.03). Of the bacteria isolated from culture, 53.8% of coagulase negative staphylococci(CoNS) in IVI eyes and 47.2%CoNS in control eyes. This difference between IVI eyes and control eyes about bacteria isolated from culture was not statistically significant(P =0.2). Eleven of 25 bacteria(44.0%) isolated from IVI eyes and 11(57.9%) of 19 bacteria isolated from control eyes were resistant to oxacillin. The difference in frequency of moxifloxacine resistance between two groups was not statistically significant(12.0% in IVI eyes and 21.1% in control eyes)(P =0.44). There were no cases of resistance to vancomycin, teicoplanin and linezolid

  4. [Application of 17 Y-chromosome specific STR loci in paternity testing].

    Science.gov (United States)

    Deng, Zhi-Hui; Li, Qian; Wu, Shuang; Li, Da-Cheng; Yang, Bao-Cheng

    2008-06-01

    The purpose of this study was to explore the ability of discrimination of the AmpFlSTR Yfiler PCR amplification kit containing 17 Y-STR loci and the allelic mutation in the practice of paternity testing in Chinese population. 36 non-paternity father/son pairs and 84 confirmed father/son pairs, which had been previously genotyped by using Reliagene Y-PLEX 6 commercial kit and the "9 Y-STR multiplex with reduced-size amplicons" developed by our laboratory, were subjected to Y-STR genotyping at 17 loci using the AmpFlSTR Yfiler PCR amplification kit. 17 Y-STR loci were amplified in single multiplex and the PCR products were detected by using ABI Prism 3100 DNA Sequencer. The number of Y-STR exclusion for each non-paternity father/son pair and the mutation events for each confirmed father/son pair were calculated and the observed results were compared with our previous reported data determined by Reliagene Y-PLEX 6 kit and the "9 Y-STR multiplex with reduced-size amplicons". The results showed that out of 36 non-paternity father/son pairs subjected to Y-STR genotyping by using the AmpFlSTR Yfiler kit, one case with no Y-STR exclusion of paternity and 35 cases with more than 3 Y-STR exclusions for each father/son pair were observed. The percentage of cases with more than 3 Y-STR exclusions in all the tested non-paternity cases for Yfiler kit was 97.22% (35/36), which was more than that of Reliagene Y-PLEX 6 kit (92.11%, 35/38) and our "9 Y-STR multiplex with reduced-size amplicons" (91.67%, 33/36). Except for single father/son pair with no Y-STR exclusion, an average of 11.3 Y-STR exclusions was observed in other 35 non-paternity father/son pairs. In the 84 confirmed father/son pairs, 5 mutation events with a single unit repeat change at DYS437, DYS439, DYS635, DYS389II and DYS19, respectively, were identified using the Yfiler kit. The average mutation rate was estimated at 3.50 x 10(-3) per locus per generation. The cases with Y-STR mutation events in all tested

  5. The development of reduced size STR amplicons as tools for analysis of degraded DNA.

    Science.gov (United States)

    Butler, John M; Shen, Yin; McCord, Bruce R

    2003-09-01

    New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

  6. Identifying the most likely contributors to a Y-STR mixture using the discrete Laplace method

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2015-01-01

    In some crime cases, the male part of the DNA in a stain can only be analysed using Y chromosomal markers, e.g. Y-STRs. This may be the case in e.g. rape cases, where the male components can only be detected as Y-STR profiles, because the fraction of male DNA is much smaller than that of female DNA...... demonstrate how the discrete Laplace method can be used to separate a two person Y-STR mixture, where the Y-STR profiles of the true contributors are not present in the reference dataset, which is often the case for Y-STR profiles in real case work. We also briefly discuss how to calculate the weight...... of the evidence using the likelihood ratio principle when a suspect's Y-STR profile fits into a two person mixture. We used three datasets with between 7 and 21 Y-STR loci: Denmark (n=181), Somalia (n=201) and Germany (n=3443). The Danish dataset with 21 loci was truncated to 15 and 10 loci to examine the effect...

  7. Quality Control of Isothermal Amplified DNA Based on Short Tandem Repeat Analysis.

    Science.gov (United States)

    Kroneis, Thomas; El-Heliebi, Amin

    2015-01-01

    This protocol describes the use of a 16plex PCR for the purpose assessing DNA quality after isothermal whole genome amplification (WGA). In short, DNA products, generated by amplification multiple displacement amplification, are forwarded to PCR targeting 15 short tandem repeats (STR) as well as amelogenin generating up to 32 different PCR products. After amplification, the PCR products are separated via capillary electrophoresis and analyzed based on the obtained DNA profiles. Isothermal WGA products of good DNA quality will result in DNA profiles with efficiencies of >90 % of the full DNA profile.

  8. Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling.

    Science.gov (United States)

    Calacal, Gayvelline C; Delfin, Frederick C; Tan, Michelle Music M; Roewer, Lutz; Magtanong, Danilo L; Lara, Myra C; Fortun, Raquel dR; De Ungria, Maria Corazon A

    2005-09-01

    In a fire tragedy in Manila in December 1998, one of the worst tragic incidents which resulted in the reported death of 23 children, identity could not be established initially resulting in the burial of still unidentified bodies. Underscoring the importance of identifying each of the human remains, the bodies were exhumed 3 months after the tragedy. We describe here our work, which was the first national case handled by local laboratories wherein conventional and molecular-based techniques were successfully applied in forensic identification. The study reports analysis of DNA obtained from skeletal remains exposed to conditions of burning, burial, and exhumation. DNA typing methods using autosomal and Y-chromosomal short tandem repeat (Y-STR) markers reinforced postmortem examinations using conventional identification techniques. The strategy resulted in the identification of 18 out of the 21 human remains analyzed, overcoming challenges encountered due to the absence of established procedures for the recovery of mass disaster remains. There was incomplete antemortem information to match the postmortem data obtained from the remains of 3 female child victims. Two victims were readily identified due to the availability of antemortem tissues. In the absence of this biologic material, parentage testing was performed using reference blood samples collected from parents and relatives. Data on patrilineal lineage based on common Y-STR haplotypes augmented autosomal DNA typing, particularly in deficiency cases.

  9. Investigation of extended Y chromosome STR haplotypes in Sardinia.

    Science.gov (United States)

    Lacerenza, D; Aneli, S; Di Gaetano, C; Critelli, R; Piazza, A; Matullo, G; Culigioni, C; Robledo, R; Robino, C; Calò, C

    2017-03-01

    Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n=40; Central Sardinia, n=56; Southern Sardinia, n=91) and three isolates (Desulo, n=34; Benetutti, n=45, Carloforte, n=42). The tested Y-STRs consisted of Yfiler(®) Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler(®) Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626). As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h=0.99997). Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis. Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations. The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.

  10. Analysis of 24 Y-STR haplotype data in a Chinese Han population from Guangdong Province.

    Science.gov (United States)

    Wang, Ying; Liu, Chao; Zhang, Chu-chu; Li, Ran; Liu, Hong; Ou, Xue-ling; Li, Hai-xia; Sun, Hong-yu

    2016-05-01

    In this study, we investigated the genetic polymorphisms of 24 Y-chromosomal short tandem repeat (Y-STR) loci in 885 unrelated Chinese Han male individuals from Guangdong Province, using a domestic AGCU Y24 STR kit. A total of 878 different haplotypes were observed at the 24 Y-STR loci; among them, 871 haplotypes were unique and 7 haplotypes occurred twice. The overall haplotype diversity was 0.99998 and the discrimination capacity was 99.2%. The gene diversity values ranged from 0.4354 at DYS438 to 0.9606 at DYS385a/b. Population relationships between the Guangdong Han population and seven other published Chinese populations were evaluated by Rst values and visualized in a two multi-dimensional scaling plot. The results showed the 24 Y-STR loci are highly polymorphic in Guangdong Han population and of great value in forensic application.

  11. 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.

  12. Trace minerals profile of blood serum and estrual mucus in repeat breeder Kankrej cows

    Directory of Open Access Journals (Sweden)

    N F Chaudhari

    2013-06-01

    Full Text Available Aim: The study was carried out with an idea to ascertain involvement of trace minerals in failure of conception in Knakrej cow. Materials and Methods: The animals under study were comprised of 10 normal (Group-I and 20 repeat breeder (Group-II Kankrej cows. Blood samples of each repeat breeding and normally cycling cows was collected before Artificial insemination. The mucus samples were collected aseptically before breeding. The cervical mucus was diluted with triple glass distilled water at the rate of 1: 3 using vertex machine. The diluted mucus and serum was used for the trace minerals estimation. Results: The values observed for copper, iron, zinc and manganese in blood serum of normal and repeat breeding animals was 2.27 ± 0.05 vs 0.87 ± 0.02, 1.41 ± 0.02 vs 0.65 ± 0.01, 1.94 ± 0.01 vs 1.78 ± 0.02 and 0.43 ± 0.02 vs 0.18 ± 0.01 ppm, respectively and in estrual mucus it was 1.37 ± 0.10 vs 0.44 ± 0.06, 0.74 ± 0.07 vs 0.33 ± 0.05, 1.47 ± 0.10 vs 0.82 ± 0.06 and 0.29 ± 0.04 vs 0.23 ± 0.03 ppm, respectively. All the values in blood serum and estrual mucus were significantly (p<0.01 higher in normal than repeat breeder cows except manganese in estrual mucus, which was non significantly higher in normal as compared to repeat breeder Kankrej cows. Conclusion: All trace minerals was higher in blood serum of normal animals as compared to repeat breeder. In estrual mucus except manganese, all trace minerals was higher in normal cows than repeat breeder. [Vet World 2013; 6(3.000: 143-146

  13. STR analysis of human DNA from maggots fed on decomposing bodies: Assessment of the time period for successful analysis

    Directory of Open Access Journals (Sweden)

    Daniel Gachuiri Njau

    2016-09-01

    Full Text Available Frequently, forensic entomology is applied in the use of insect maggots for the identification of specimens or remains of humans. Maggot crop analysis could be valuable in criminal investigations when maggots are found at a crime scene and a corpse is absent. Human short tandem repeat (STR has previously been used to support the association of maggots to a specific corpse but not in the period at which the body has been decomposing. The aim of this research was to assess the time period for successful STR analyses of human DNA from third instar maggots (Protophormia terraenovae obtained from decomposing human corpses as well as to investigate the human DNA turnover and degradation in the maggot crop after they are removed from food and/or are fed on a beef (a new/different food source. Results showed that the amount of human DNA recovered from maggots decreased with time in all cases. For maggots fed on beef, the human DNA could only be recovered up to day two and up to day four for the starved maggots. STR analyses of human DNA from maggots’ crop content using 16 loci generated profiles that matched those of reference samples although some of the alleles were not amplifiable therefore generating partial profiles for the samples starved for 4 days and those fed on beef. This may be due to nuclease activity present in the gut of larvae that may have caused degradation of DNA and consequently reduction in DNA yield. It was possible to identify the decomposing body using STRs as markers.

  14. Fetal gender determination through Y-STR analysis of maternal plasma during the third trimester of pregnancy

    Directory of Open Access Journals (Sweden)

    Hanaa M.H. Aal-Hamdan

    2015-01-01

    Conclusion: It is recommended to use Y-STR profiling as an alternative technique for fetal gender determination during the third trimester of pregnancy, in addition to its significance in forensic casework.

  15. Genetic variation study of 12 X chromosomal STR in central Thailand population.

    Science.gov (United States)

    Vongpaisarnsin, Kornkiat; Boonlert, Achara; Rasmeepaisarn, Kawin; Dangkao, Piyawan

    2016-11-01

    Genetic data from 12 short tandem repeats (STR) on the X chromosome are currently used in forensics studies to resolve issues related to complex kinship or when data is missing or ambiguous. In this study, we genotyped these 12 X chromosome STR in DNA collected from individuals from central Thailand (n = 391, 282 men and 109 women) and used this information to calculate allele and haplotype frequencies as well as forensic parameters for kinship calculations. Polymorphism information contents of the loci were range from 0.5283-0.9247, and powers of discrimination in females and males were 0.7666-0.9905 and 0.6085-0.9291, respectively. A diallelic pattern was observed at the locus DXS7132. Moreover, a comparison of genetic distance revealed a close relationship within Asian countries. Our results indicate that the X chromosomal short tandem repeat (X-STR) multiplex system provides highly informative genetic data and could be advantageous in forensic studies.

  16. The Colletotrichum graminicola striatin orthologue Str1 is necessary for anastomosis and is a virulence factor.

    Science.gov (United States)

    Wang, Chih-Li; Shim, Won-Bo; Shaw, Brian D

    2016-08-01

    Striatin family proteins are key regulators in signalling pathways in fungi and animals. These scaffold proteins contain four conserved domains: a caveolin-binding domain, a coiled-coil motif and a calmodulin-binding domain at the N-terminus, and a WD-repeat domain at the C-terminus. Fungal striatin orthologues are associated with sexual development, hyphal growth and plant pathogenesis. In Fusarium verticillioides, the striatin orthologue Fsr1 promotes virulence in the maize stalk. The relationship between fungal striatins and pathogenicity remains largely unexplored. In this study, we demonstrate that the Colletotrichum graminicola striatin orthologue Str1 is required for full stalk rot and leaf blight virulence in maize. Pathogenicity assays show that the striatin mutant strain (Δstr1) produces functional appressoria, but infection and colonization are attenuated. Additional phenotypes of the Δstr1 mutant include reduced radial growth and compromised hyphal fusion. In comparison with the wild-type, Δstr1 also shows a defect in sexual development and produces fewer and shorter conidia. Together with the fact that F. verticillioides fsr1 can complement Δstr1, our results indicate that C. graminicola Str1 shares five phenotypes with striatin orthologues in other fungal species: hyphal growth, hyphal fusion, conidiation, sexual development and virulence. We propose that fungal striatins, like mammalian striatins, act as scaffolding molecules that cross-link multiple signal transduction pathways. © 2015 BSPP AND JOHN WILEY & SONS LTD.

  17. STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.

    Science.gov (United States)

    Warshauer, David H; Lin, David; Hari, Kumar; Jain, Ravi; Davis, Carey; Larue, Bobby; King, Jonathan L; Budowle, Bruce

    2013-07-01

    Recent studies have demonstrated the capability of second generation sequencing (SGS) to provide coverage of short tandem repeats (STRs) found within the human genome. However, there are relatively few bioinformatic software packages capable of detecting these markers in the raw sequence data. The extant STR-calling tools are sophisticated, but are not always applicable to the analysis of the STR loci commonly used in forensic analyses. STRait Razor is a newly developed Perl-based software tool that runs on the Linux/Unix operating system and is designed to detect forensically-relevant STR alleles in FASTQ sequence data, based on allelic length. It is capable of analyzing STR loci with repeat motifs ranging from simple to complex without the need for extensive allelic sequence data. STRait Razor is designed to interpret both single-end and paired-end data and relies on intelligent parallel processing to reduce analysis time. Users are presented with a number of customization options, including variable mismatch detection parameters, as well as the ability to easily allow for the detection of alleles at new loci. In its current state, the software detects alleles for 44 autosomal and Y-chromosome STR loci. The study described herein demonstrates that STRait Razor is capable of detecting STR alleles in data generated by multiple library preparation methods and two Illumina(®) sequencing instruments, with 100% concordance. The data also reveal noteworthy concepts related to the effect of different preparation chemistries and sequencing parameters on the bioinformatic detection of STR alleles.

  18. Metabolite profiles of rats in repeated dose toxicological studies after oral and inhalative exposure.

    Science.gov (United States)

    Fabian, E; Bordag, N; Herold, M; Kamp, H; Krennrich, G; Looser, R; Ma-Hock, L; Mellert, W; Montoya, G; Peter, E; Prokudin, A; Spitzer, M; Strauss, V; Walk, T; Zbranek, R; van Ravenzwaay, B

    2016-07-25

    The MetaMap(®)-Tox database contains plasma-metabolome and toxicity data of rats obtained from oral administration of 550 reference compounds following a standardized adapted OECD 407 protocol. Here, metabolic profiles for aniline (A), chloroform (CL), ethylbenzene (EB), 2-methoxyethanol (ME), N,N-dimethylformamide (DMF) and tetrahydrofurane (THF), dosed inhalatively for six hours/day, five days a week for 4 weeks were compared to oral dosing performed daily for 4 weeks. To investigate if the oral and inhalative metabolome would be comparable statistical analyses were performed. Best correlations for metabolome changes via both routes of exposure were observed for toxicants that induced profound metabolome changes. e.g. CL and ME. Liver and testes were correctly identified as target organs. In contrast, route of exposure dependent differences in metabolic profiles were noted for low profile strength e.g. female rats dosed inhalatively with A or THF. Taken together, the current investigations demonstrate that plasma metabolome changes are generally comparable for systemic effects after oral and inhalation exposure. Differences may result from kinetics and first pass effects. For compounds inducing only weak changes, the differences between both routes of exposure are visible in the metabolome.

  19. Evaluation of safety profile of black shilajit after 91 days repeated administration in rats

    Institute of Scientific and Technical Information of China (English)

    Velmurugan C; Vivek B; Wilson E; Bharathi T; Sundaram T

    2012-01-01

    Objective: To evaluate the safety of shilajit by 91 days repeated administration in different dose levels in rats. Methods: In this study the albino rats were divided into four groups. Group I received vehicle and group II, III and IV received 500, 2500 and 5000 mg/kg of shilajit, respectively. Finally animals were sacrificed and subjected to histopathology and iron was estimated by flame atomic absorption spectroscopy and graphite furnace. Results: The result showed that there were no significant changes in iron level of treated groups when compared with control except liver (5000 mg/kg) and histological slides of all organs revealed normal except negligible changes in liver and intestine with the highest dose of shilajit. The weight of all organs was normal when compared with control. Conclusions: The result suggests that black shilajit, an Ayurvedic formulation, is safe for long term use as a dietary supplement for a number of disorders like iron deficiency anaemia.

  20. Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population.

    Science.gov (United States)

    Sufian, Abu; Hosen, Md Ismail; Fatema, Kaniz; Hossain, Tania; Hasan, Md Mahamud; Mazumder, Ashish Kumar; Akhteruzzaman, Sharif

    2016-12-08

    The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423). Allelic frequencies of the 12 X-STR loci and haplotype frequencies of the four linkage groups were investigated. No significant difference was observed in the allele frequencies of males and females. Distributions of heterozygosity were observed from 64.5 to 92.5% among the studied 12 X STR loci. DXS10135 and DXS10101 loci were found to be most polymorphic. For all the four linkage groups, the haplotype diversity was found to be greater than 0.986. A total of 95, 73, 66, and 74 haplotypes were observed in linkage groups I, II, III, and IV, respectively. Hardy-Weinberg equilibrium tests showed no significant deviation from expected values for all 12 loci (p > 0.05). The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples did not show any significant linkage disequilibrium except the DXS10103 and DXS10101 loci after the p values were corrected by Bonferroni's correction for multiple testing (p > 0.05/66). A combined power of discrimination in male and female individuals were 0.999999998159791 and 0.999999999999993, respectively. The combined mean exclusion chance were 0.999997635 in deficiency cases, 0.999999996 in normal trio cases, and 0.999999178 in duo cases. The currently investigated Bangladeshi population showed significant differences when compared with previously reported X-STR data from other 12 populations. The results of the

  1. Genetic polymorphism of 15 STR loci in El Salvador.

    Science.gov (United States)

    Muñoz, Pablo; Pinto de Erazo, Eugenia Leticia; Baeza, Carlos; Arroyo-Pardo, Eduardo; López-Parra, Ana Maria

    2015-09-01

    The aim of this study was to estimate the allelic frequencies of the 15 short tandem repeat (STR) loci included in AmpFlSTRIdentifiler PCR Amplification Kit. Biological samples were obtained from 109 unrelated individuals from El Salvador. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy-Weinberg equilibrium after Bonferroni correction. The obtained frequencies were compared with other previously reported population data. The multidimensional scaling plot and the neighbor-joining phylogeny supported a high native Mesoamerican contribution.

  2. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    DEFF Research Database (Denmark)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DY...

  3. Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci

    DEFF Research Database (Denmark)

    Rodríguez, V; Tomas Mas, Carmen; Sánchez, J J

    2008-01-01

    Haplotype and allele frequencies of 12 Y-chromosome short tandem repeat (Y-STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 a/b, DYS437, DYS438 and DYS439) included in the Powerplex(R) Y System were determined in seven western Mediterranean populations from Valencia, Ma...

  4. Elevation Change of Drangajokull, Iceland, from Cloud-Cleared ICESat Repeat Profiles and GPS Ground-Survey Data

    Science.gov (United States)

    Shuman, Christopher A.; Sigurdsson, Oddur; Williams, Richard, Jr.; Hall, Dorothy K.

    2009-01-01

    Located on the Vestfirdir Northwest Fjords), DrangaJokull is the northernmost ice map in Iceland. Currently, the ice cap exceeds 900 m in elevation and covered an area of approx.l46 sq km in August 2004. It was about 204 sq km in area during 1913-1914 and so has lost mass during the 20th century. Drangajokull's size and accessibility for GPS surveys as well as the availability of repeat satellite altimetry profiles since late 2003 make it a good subject for change-detection analysis. The ice cap was surveyed by four GPS-equipped snowmobiles on 19-20 April 2005 and has been profiled in two places by Ice, Cloud. and land Elevation Satellite (ICESat) 'repeat tracks,' fifteen times from late to early 2009. In addition, traditional mass-balance measurements have been taken seasonally at a number of locations across the ice cap and they show positive net mass balances in 2004/2005 through 2006/2007. Mean elevation differences between the temporally-closest ICESat profiles and the GPS-derived digital-elevation model (DEM)(ICESat - DEM) are about 1.1 m but have standard deviations of 3 to 4 m. Differencing all ICESat repeats from the DEM shows that the overall elevation difference trend since 2003 is negative with losses of as much as 1.5 m/a from same season to same season (and similar elevation) data subsets. However, the mass balance assessments by traditional stake re-measurement methods suggest that the elevation changes where ICESat tracks 0046 and 0307 cross Drangajokull are not representative of the whole ice cap. Specifically, the area has experienced positive mass balance years during the time frame when ICESat data indicates substantial losses. This analysis suggests that ICESat-derived elevations may be used for multi-year change detection relative to other data but suggests that large uncertainties remain. These uncertainties may be due to geolocation uncertainty on steep slopes and continuing cloud cover that limits temporal and spatial coverage across the

  5. Fast nuclear staining of head hair roots as a screening method for successful STR analysis in forensics.

    Science.gov (United States)

    Lepez, Trees; Vandewoestyne, Mado; Van Hoofstat, David; Deforce, Dieter

    2014-11-01

    The success rate of STR profiling of hairs found at a crime scene is quite low and negative results of hair analysis are frequently reported. To increase the success rate of DNA analysis of hairs in forensics, nuclei in hair roots can be counted after staining the hair root with DAPI. Two staining methods were tested: a longer method with two 1h incubations in respectively a DAPI- and a wash-solution, and a fast, direct staining of the hair root on microscope slides. The two staining methods were not significantly different. The results of the STR analysis for both procedures showed that 20 nuclei are necessary to obtain at least partial STR profiles. When more than 50 nuclei were counted, full STR profiles were always obtained. In 96% of the cases where no nuclei were detected, no STR profile could be obtained. However, 4% of the DAPI-negative hair roots resulted in at least partial STR profiles. Therefore, each forensic case has to be evaluated separately in function of the importance of the evidential value of the found hair. The fast staining method was applied in 36 forensic cases on 279 hairs in total. A fast screening method using DAPI can be used to increase the success rate of hair analysis in forensics.

  6. Thrombospondin-1 type 1 repeats in a model of inflammatory bowel disease: transcript profile and therapeutic effects.

    Directory of Open Access Journals (Sweden)

    Zenaida P Lopez-Dee

    Full Text Available Thrombospondin-1 (TSP-1 is a matricellular protein with regulatory functions in inflammation and cancer. The type 1 repeats (TSR domains of TSP-1 have been shown to interact with a wide range of proteins that result in the anti-angiogenic and anti-tumor properties of TSP-1. To ascertain possible functions and evaluate potential therapeutic effects of TSRs in inflammatory bowel disease, we conducted clinical, histological and microarray analyses on a mouse model of induced colitis. We used dextran sulfate sodium (DSS to induce colitis in wild-type (WT mice for 7 days. Simultaneously, mice were injected with either saline or one form of TSP-1 derived recombinant proteins, containing either (1 the three type 1 repeats of the TSP-1 (3TSR, (2 the second type 1 repeat (TSR2, or (3 TSR2 with the RFK sequence (TSR2+RFK. Total RNA isolated from the mice colons were processed and hybridized to mouse arrays. Array data were validated by real-time qPCR and immunohistochemistry. Histological and disease indices reveal that the mice treated with the TSRs show different patterns of leukocytic infiltration and that 3TSR treatment was the most effective in decreasing inflammation in DSS-induced colitis. Transcriptional profiling revealed differentially expressed (DE genes, with the 3TSR-treated mice showing the least deviation from the WT-water controls. In conclusion, this study shows that 3TSR treatment is effective in attenuating the inflammatory response to DSS injury. In addition, the transcriptomics work unveils novel genetic data that suggest beneficial application of the TSR domains in inflammatory bowel disease.

  7. Genetic variations of 21 STR markers on chromosomes 13, 18, 21, X, and Y in the south Iranian population.

    Science.gov (United States)

    Saberzadeh, J; Miri, M R; Tabei, M B; Dianatpour, M; Fardaei, M

    2016-12-19

    Quantitative fluorescent polymerase chain reaction (QF-PCR), in recent years, has been accepted as a rapid, high throughput, and sensitive method for prenatal diagnosis of common chromosomal aneuploidies. Since short tandem repeats (STRs) are the cornerstone of QF-PCR technique, selection of the most polymorphic STR markers is an essential step for a successful QF-PCR assay. The genetic variation parameters of each STR marker differ among different populations. In this study, we investigated the size, frequency, heterozygosity, polymorphism information content, power of discrimination, and other genetic polymorphism data for 21 STR markers on chromosomes 13, 18, 21, X, and Y in 1000 amniotic fluid samples obtained from south Iranian women. Our results showed that all the 21 STR markers are highly polymorphic and informative in our population. The heterozygosity, polymorphism information content, and power of discrimination of the markers were 62-91.1%, 0.61-0.91, and 0.830-0.976, respectively. The locus D18S386 was the most polymorphic STR, while the locus DXYS218 was the least polymorphic STR among all the studied STRs. The present study has provided extensive data regarding the efficiency of the 21 STR markers for diagnosis of chromosomes 13, 18, 21, X, and Y aneuploidies in the south Iranian population.

  8. Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups

    Science.gov (United States)

    Yang, Xingyi; Zhang, Xiaofang; Zhu, Junyong; Chen, Linli; Liu, Changhui; Feng, Xingling; Chen, Ling; Wang, Huijun; Liu, Chao

    2017-01-01

    A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups. PMID:28211539

  9. Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups.

    Science.gov (United States)

    Yang, Xingyi; Zhang, Xiaofang; Zhu, Junyong; Chen, Linli; Liu, Changhui; Feng, Xingling; Chen, Ling; Wang, Huijun; Liu, Chao

    2017-02-17

    A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups.

  10. DRPLA transgenic mouse substrains carrying single copy of full-length mutant human DRPLA gene with variable sizes of expanded CAG repeats exhibit CAG repeat length- and age-dependent changes in behavioral abnormalities and gene expression profiles.

    Science.gov (United States)

    Suzuki, Kazushi; Zhou, Jiayi; Sato, Toshiya; Takao, Keizo; Miyagawa, Tsuyoshi; Oyake, Mutsuo; Yamada, Mitunori; Takahashi, Hitoshi; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

    2012-05-01

    Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant progressive neurodegenerative disorder with intellectual deterioration and various motor deficits including ataxia, choreoathetosis, and myoclonus, caused by an abnormal expansion of CAG repeats in the DRPLA gene. Longer expanded CAG repeats contribute to an earlier age of onset, faster progression, and more severe neurological symptoms in DRPLA patients. In this study, we have established DRPLA transgenic mouse lines (sublines) harboring a single copy of the full-length mutant human DRPLA gene carrying various lengths of expanded CAG repeats (Q76, Q96, Q113, and Q129), which have clearly shown motor deficits and memory disturbance whose severity increases with the length of expanded CAG repeats and age, and successfully replicated the CAG repeat length- and age-dependent features of DRPLA patients. Neuronal intranuclear accumulation of the mutant DRPLA protein has been suggested to cause transcriptional dysregulation, leading to alteration in gene expression and neuronal dysfunction. In this study, we have conducted a comprehensive analysis of gene expression profiles in the cerebrum and cerebellum of transgenic mouse lines at 4, 8, and 12 weeks using multiple microarray platforms, and demonstrated that both the number and expression levels of the altered genes are highly dependent on CAG repeat length and age in both brain regions. Specific groups of genes and their function categories were identified by further agglomerative cluster analysis and gene functional annotation analysis. Calcium signaling and neuropeptide signaling, among others, were implicated in the pathophysiology of DRPLA. Our study provides unprecedented CAG-repeat-length-dependent mouse models of DRPLA, which are highly valuable not only for elucidating the CAG-repeat-length-dependent pathophysiology of DRPLA but also for developing therapeutic strategies for DRPLA.

  11. Thyroid profiles in a patient with resistance to thyroid hormone and episodes of thyrotoxicosis, including repeated painless thyroiditis.

    Science.gov (United States)

    Taniyama, Matsuo; Otsuka, Fumiko; Tozaki, Teruaki; Ban, Yoshiyuki

    2013-07-01

    Thyrotoxic disease can be difficult to recognize in patients with resistance to thyroid hormone (RTH) because the clinical symptoms of thyrotoxicosis cannot be observed, and thyrotropin (TSH) may not be suppressed because of hormone resistance. Painless thyroiditis is a relatively common cause of thyrotoxicosis, but its occurrence in RTH has not been reported. We assessed the thyroid profile in a patient with RTH and episodes of thyrotoxicosis who experienced repeated painless thyroiditis. A 44-year-old Japanese woman with RTH, which was confirmed by the presence of a P453A mutation in the thyroid hormone receptor β (TRβ) gene, showed a slight elevation of the basal levels of thyroid hormones, which indicated that her pituitary RTH was mild. She experienced a slight exacerbation of hyperthyroxinemia concomitant with TSH suppression. A diagnosis of painless thyroiditis was made because of the absence of TSH receptor antibodies, low Tc-99m pertechnetate uptake by the thyroid gland, and transient suppression followed by a slight elevation of TSH following the elevation of thyroid hormones. The patient's complaints of general malaise and occasional palpitations did not change throughout the course of painless thyroiditis. Three years later, painless thyroiditis occurred again without any deterioration of the clinical manifestations. Mild pituitary RTH can be overcome by slight exacerbation of hyperthyroxinemia during mild thyrotoxicosis. When pituitary resistance is severe and TSH is not suppressed, thyrotoxicosis may be overlooked.

  12. 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

    Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher θ than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358

  13. Population genetic analysis of the GlobalFiler STR loci in 748 individuals from the Kazakh population of Xinjiang in northwest China.

    Science.gov (United States)

    Zhang, Honghua; Yang, Shuping; Guo, Wei; Ren, Bo; Pu, Liwen; Ma, Teng; Xia, Mingying; Jin, Li; Li, Liming; Li, Shilin

    2016-09-01

    The six-dye GlobalFiler™ Express PCR amplification kit incorporates 21 commonly used autosomal short tandem repeat (STR) loci and three gender determination loci. In this study, we analyzed the GlobalFiler STR loci on 748 unrelated individuals from a Chinese Kazakh population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were observed within and between 21 autosomal STR loci. SE33 showed the greatest power of discrimination in Kazakh population. The combined power of discrimination of Kazakh was 99.999999999999999999999996797 %. No significant differences of allele frequencies were observed between Kazakh and Uyghur at all 15 tested STR loci, as well as Mongolian. Significant differences were only observed between Kazakh and the other Chinese populations at TH01. Multiple STR loci showed significant differences between Kazakh and Arab, as well as South Portuguese. The multidimensional scaling plot (MDS) plot and neighbor-joining tree also showed Kazakh is genetically close to Uyghur.

  14. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles.

    Science.gov (United States)

    Gelardi, Chiara; Rockenbauer, Eszter; Dalsgaard, Sigrun; Børsting, Claus; Morling, Niels

    2014-09-01

    Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed sequence information of possible sub-repeats and SNPs within the amplified fragment.

  15. Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans.

    Science.gov (United States)

    Wendt, Frank R; King, Jonathan L; Novroski, Nicole M M; Churchill, Jennifer D; Ng, Jillian; Oldt, Robert F; McCulloh, Kelly L; Weise, Jessica A; Smith, David Glenn; Kanthaswamy, Sreetharan; Budowle, Bruce

    2017-02-27

    Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11×10(-26) and 2.79×10(-29), respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49×10(-63). Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

  16. A Brief Review of Short Tandem Repeat Mutation

    Institute of Scientific and Technical Information of China (English)

    Hao Fan; Jia-You Chu

    2007-01-01

    Short tandem repeats (STRs) are short tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp. Because of their polymorphisms and high mutation rates, STRs are widely used in biological research. Strand-slippage replication is the predominant mutation mechanism of STRs, and the stepwise mutation model is regarded as the main mutation model. STR mutation rates can be influenced by many factors. Moreover, some trinucleotide repeats are associated with human neurodegenerative diseases. In order to deepen our knowledge of these diseases and broaden STR application, it is essential to understand the STR mutation process in detail. In this review, we focus on the current known information about STR mutation.

  17. Tolerance in the anxiolytic profile following repeated administration of diazepam but not buspirone is associated with a decrease in the responsiveness of postsynaptic 5-HT-1A receptors.

    Science.gov (United States)

    Khan, Asma; Haleem, D J

    2007-12-01

    To understand the role of serotonin (5-hydroxytryptamine; 5-HT)-1A receptors in the treatment of anxiety and the development of tolerance to benzodiazepines the present study was designed to monitor the responsiveness of postsynaptic 5-HT-1A receptors following repeated administration of diazepam and buspirone. Results show that tolerance in the anxiolytic profile is produced following repeated administration (2 weeks) of diazepam (2 mg/kg) but not buspirone (0.5 mg/kg). The behavioral effects of 8-OH-DPAT at a dose of 0.25 mg/kg were monitored 3 days after repeated administration of saline or buspirone or diazepam. The results show that 8-OH-DPAT elicited forepaw treading was smaller in repeated diazepam but not repeated buspirone injected rats, while hyperlocomotive effects of 8-OH-DPAT were smaller in both repeated buspirone and repeated diazepam injected rats. The results suggest that postsynaptic 5-HT-1A receptor-dependent responses were attenuated following long-term administration of diazepam but not buspirone. Role of 5-HT-1A receptors in the development of tolerance to the anxiolytic effects of diazepam but not buspirone is discussed.

  18. 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.

  19. Population data on 6 short tandem repeat loci in a sample of Caucasian-Mestizos from Colombia.

    Science.gov (United States)

    Yunis, J J; García, O; Uriarte, I; Yunis, E J

    2000-01-01

    Blood samples from 409-452 unrelated Colombian Caucasian-Mestizo individuals were amplified and typed for six short tandem repeat (STR) markers (HUMF13A01, HUMFES/FPS, HUMVWA, HUMCSF1PO, HUMTPOX, HUMTH01). The allele frequencies, genotype frequencies, heterozygosity, mean paternity exclusion chance, polymorphism information content, discrimination power, assumption of independence within and between loci and Hardy Weinberg equilibrium were determined. The results demonstrate that all markers conform to Hardy-Weinberg equilibrium expectations. In addition, the results demonstrate the assumption of independence within and between the loci analysed. The mean exclusion chance (MEC) was 0.9851 for all six STR loci analysed and the discrimination power (DP) was 0.9999973. Therefore, this Colombian population database can be used in identity testing to estimate the frequency of a multiple PCR-based locus DNA profile in forensic cases as well as in paternity testing.

  20. A simple Duplex-PCR to evaluate the DNA quality of anthropological and forensic samples prior short tandem repeat typing.

    Science.gov (United States)

    von Wurmb-Schwark, Nicole; Schwark, Thorsten; Harbeck, Michaela; Oehmichen, Manfred

    2004-04-01

    Typing of DNA from ancient or otherwise highly degraded material, e.g. formalin fixed tissues, can be difficult, time consuming and costly. Very often, genetic typing is not possible at all. We present an inexpensive and easy to use Duplex-PCR that amplifies a 164 bp fragment specific for nuclear DNA together with a 260 bp mitochondrial DNA fragment and that can be employed as a pretest prior to short tandem repeat (STR) typing. All together, we analyzed DNA from 20 ancient bones, 20 formalin fixed tissues and 20 other forensic samples in different concentrations. Each sample that failed in the presented Duplex-amplification was also negative for STR typing, while samples that showed strong and clear signals in the Duplex-PCR led to reproducible genetic profiles using the multiplex kits AmpFLSTR Identifiler and Powerplex ES. The Duplex-PCR worked as a reliable indicator of DNA quality in the sample.

  1. A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

    Science.gov (United States)

    Yuasa, Isao; Jin, Feng; Harihara, Shinji; Matsusue, Aya; Fujihara, Junko; Takeshita, Haruo; Akane, Atsushi; Umetsu, Kazuo; Saitou, Naruya; Chattopadhyay, Prasanta K

    2013-09-01

    Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics.

  2. Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper.

    Science.gov (United States)

    Ambers, Angie; Gill-King, Harrell; Dirkmaat, Dennis; Benjamin, Robert; King, Jonathan; Budowle, Bruce

    2014-03-01

    The 120-year-old skeletal remains of Confederate Civil War soldier Captain Ezekiel "Zeke" Harper were exhumed by court order in January 2011 for DNA analysis. The goal of the DNA testing was to support or refute whether Captain Harper had fathered a son (Earl J. Maxwell) with his Native American maid prior to his murder in 1892. Bones with adequate structural integrity (left tibia, right tibia, right femur, mandible, four teeth) were retrieved from the burial site and sent to the Institute of Applied Genetics in Fort Worth, Texas for analysis. Given the age and condition of the remains, three different extraction methods were used to maximize the probability of DNA recovery. The majority of the DNA isolates from over fifty separate bone sections yielded partial autosomal STR genotypes and partial Y-STR haplotypes. After comparing the partial results for concordance, consensus profiles were generated for comparison to reference samples from alleged family members. Considering the genetic recombination that occurs in autosomal DNA over the generations within a family, Y-STR analysis was determined to be the most appropriate and informative approach for determining potential kinship. Two of Earl J. Maxwell's grandsons submitted buccal samples for comparison. The Y-STR haplotypes obtained from both of these reference samples were identical to each other and to the alleles in Ezekiel Harper's consensus profile at all 17 loci examined. This Y-STR haplotype was not found in either of two major Y-STR population databases (U.S. Y-STR database and YHRD). The fact that the Y-STR haplotype obtained from Ezekiel's skeletal remains and Earl's grandsons is not found in either population database demonstrates its rarity and further supports a paternal lineage relationship among them. Results of the genetic analyses are consistent with the hypothesis that Earl J. Maxwell is the son of Ezekiel Harper.

  3. Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

    Science.gov (United States)

    Moon, Seo Hyun; Jang, Yoon-Jeong

    2016-01-01

    Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10−5 for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes. PMID:26645337

  4. House for Niels Strøyberg

    DEFF Research Database (Denmark)

    Welling, Helen

    2007-01-01

    The house for Niels Strøyberg in Hasseris near Aalborg, Denmark, is a notable example of early modernism in an unconventional way. Although Poul Henningsen's approach to the dwelling was thoroughly functional, he added a number of visual effects to provide a sense of dynamism to the spatial...

  5. 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

  6. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.

    Science.gov (United States)

    Willems, Thomas; Gymrek, Melissa; Poznik, G David; Tyler-Smith, Chris; Erlich, Yaniv

    2016-05-05

    Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.

  7. Dealing with Possible STR Mutation in Paternity Testing%亲子鉴定STR突变的考虑

    Institute of Scientific and Technical Information of China (English)

    吕德坚; 陆惠玲

    2009-01-01

    亲子鉴定中常会发生STR(short tandem repeats,短串联重复)突变的情况.突变对亲子关系的判定会造成困扰.对STR突变规律和亲子鉴定中所遇到的STR突变问题、突变的判定、突变下非父排除率和父权指数的计算以及需与突变区分的情形等问题进行综述和讨论.%STR (short tandem repeats) mutations are encountered frequently in paternity casework because STR has relatively high mutation rate. Dealing with possible mutations in paternity cases is a difficult task. This paper reviews the characteristics of STR mutation and the problems related with STR mutation. Issues, such as determination of mutation, calculation of paternity index and probability of exclusion and distinction between mutation and its similarity, are discussed.

  8. 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.

  9. [Genetic polymorphisms of X-STR loci in Chinese Yugur ethnic group and its application].

    Science.gov (United States)

    Chen, Yan-Jiong; Chen, Feng; Xin, Na; Zhang, Hong Bo; Zheng, Hai Bo; Yu, Bing; Li, Sheng-Bin; Chen, Teng

    2008-09-01

    To study the genetic polymorphism of nine short tandem repeats (STRs) loci (DXS7130, DXS7132, DXS6804, DXS7423, DXS7424, DXS6789, DXS6799, DXS8378, and HPRTB) on X chromosome in Chinese Yugur ethnic group. The allele and genotype frequency of nine X-STR loci among 120 unrelated individuals (55 female, 65 male) from Yugur ethnic group were analyzed using PCR and followed by polyacrylamide gel electrophoresis and silver staining. The numbers of alleles in the nine X-STR loci were 8, 6, 6, 5, 6, 7, 6, 4, and 6, respectively; the numbers of genotypes in the nine loci were 16, 14, 13, 6, 13, 20, 11, 6, and 12, respectively. The genotype frequencies in females were in accordance with Hardy-Weinberg equilibrium (P>0.05). The nine X-STR loci were relatively abundant in polymorphic information for individual identification, paternity testing and population genetics. A total of 15 haplotypes were detected in DXS7130 and DXS8378 loci, and 55 haplotypes were detected in DXS6789, DXS6799, DXS7424, and DXS6804 loci. The haplotype diversity reached 0.8212 and 0.9947, respectively. Phylogeny tree and cluster analysis based on X-STR allele frequencies in genesis showed that Yugur ethnic group share a close relationship with Mongolian ethnic group and Chinese Han, Tibetan population and far from Hui and Uygur ethnic group, who dwell in the northwest of China.

  10. Neurofibrillary tangles in Gerstmann-Sträussler-Scheinker syndrome with the A117V prion gene mutation

    OpenAIRE

    Tranchant, C.; Sergeant, N; Wattez, A; Mohr, M.; Warter, J; Delacourte, A

    1997-01-01

    One patient of a French family with Gerstmann-Sträussler-Scheinker syndrome with the mutation in codon 117 of the prion protein (PrP) gene displayed unexpected neuritic degeneration around PrP plaques and numerous diffuse neurofibrillary tangles, whereas other members did not. The tau profile in this patient's brain was analysed and compared with one from another member of the Gerstmann-Sträussler-Scheinker family as well as with the Alzheimer's tau profile. A panel of we...

  11. Low copy number DNA profiling from isolated sperm using the aureka®-micromanipulation system.

    Science.gov (United States)

    Schneider, C; Müller, U; Kilper, R; Siebertz, B

    2012-07-01

    A new cell isolation technique linked to the aureka® micromanipulation system (aureka®) was used to pick sperm from mixed samples containing sperm and epithelial cells. Both cell types were stained using the HY-LITER™ high-resolution, fluorescent staining kit. To isolate a single sperm of interest under a fluorescent microscope, a specific microsphere picking technique was used. This sensitive and reliable cell identification and isolation technique enables low-copy-number (LCN) DNA profiling, as few as 20 sperm are sufficient for obtaining a full short tandem repeat (STR) profile without any allelic drop out. The presented protocol covers the whole workflow, from sample staining and cell pick up to STR analysis.

  12. 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.

  13. A case of false mother included with 46 autosomal STR markers

    OpenAIRE

    Li, Li; Lin, Yuan; Liu, Yan; Zhu, Ruxin; Zhao, Zhenmin; Que, Tingzhi

    2015-01-01

    Background For solving a maternity case, 19 autosomal short tandem repeats (STRs) were amplified using the AmpFℓSTR® SinofilerTM kit and PowerPlex® 16 System. Additional 27 autosomal STR loci were analyzed using two domestic kits AGCU 21+1 and STRtyper-10G. The combined maternity index (CMI) was calculated to be 3.3 × 1013, but the putative mother denied that she had given birth to the child. In order to reach an accurate conclusion, further testing of 20 X-chromosomal short tandem repeats (X...

  14. Anxiolytic profile of fluoxetine as monitored following repeated administration in animal rat model of chronic mild stress

    Directory of Open Access Journals (Sweden)

    Muhammad Farhan

    2016-09-01

    Full Text Available Background: Fluoxetine, a selective serotonin re-uptake inhibitor (SSRI, has been proposed to be more effective as an antidepressive drug as compared to other SSRIs. After chronic SSRI administration, the increase in synaptic levels of 5-HT leads to desensitization of somatodentritic 5-HT autoreceptors in the raphe nuclei. Chronic stress may alter behavioral, neurochemical and physiological responses to drug challenges and novel stressors. Methods: Twenty four male rats were used in this study. Animals of CMS group were exposed to CMS. Animals of stressed and unstressed group were administrated with fluoxetine at dose of 1.0 mg/kg s well as 5.0 mg/kg repeatedly for 07 days 1 h before exposed to CMS. The objective of the present study was to evaluate that repeated treatment with fluoxetine could attenuate CMS-induced behavioral deficits. Results: Treatment with fluoxetine attenuated CMS-induced behavioral deficits. Fluoxetine administration induced hypophagia in unstressed as well as CMS rats. Acute and repeated administration of fluoxetine increased motor activity in familiar environment but only repeated administration increased exploratory activity in open field. Anxiolytic effects of fluoxetine were greater in unstressed rats. These anxiolytic effects were produced as result of repeated administration not on acute administration of fluoxetine at 1.0 mg/kg as well as 5.0 mg/kg. Conclusion: The present study demonstrated that CMS exposure resulted into behavioral deficits and produced depressive-like symptoms. Fluoxetine, an SSRI, administration attenuated behavioral deficits induced by CMS. Anxiolytic effects of repeated fluoxetine administration were greater in unstressed than CMS animals.

  15. Capillary electrophoresis and 5-channel LIF detection of a 26plex autosomal STR assay for human identification.

    Science.gov (United States)

    Hill, Carolyn R

    2012-01-01

    Multiplex polymerase chain reaction (PCR) is a common method used for DNA typing in forensic and paternity cases. There are numerous commercial short tandem repeat (STR) multiplex assays currently available to the forensic community. These assays amplify the core Combined DNA Index System (CODIS) STR loci for entry into the US. DNA database. Additional non-CODIS loci, which are considered genetically unlinked to the CODIS loci, can be useful in resolving challenging cases such as missing persons and mass disaster victim identification, paternity testing, and immigration testing. An STR multiplex has been successfully developed with 25 non-CODIS autosomal loci plus the sex-typing locus amelogenin for a total of 26 loci in a single 26plex amplification reaction. This chapter will focus on the preparation and the use of the 26plex assay with DNA samples for the purpose of human identification.

  16. Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province, Southwest China.

    Science.gov (United States)

    Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Xiran, Zeng; Nie, Shengjie

    2017-05-01

    The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex(®) 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. DNA Profiling Success Rates from Degraded Skeletal Remains in Guatemala.

    Science.gov (United States)

    Johnston, Emma; Stephenson, Mishel

    2016-07-01

    No data are available regarding the success of DNA Short Tandem Repeat (STR) profiling from degraded skeletal remains in Guatemala. Therefore, DNA profiling success rates relating to 2595 skeletons from eleven cases at the Forensic Anthropology Foundation of Guatemala (FAFG) are presented. The typical postmortem interval was 30 years. DNA was extracted from bone powder and amplified using Identifiler and Minifler. DNA profiling success rates differed between cases, ranging from 50.8% to 7.0%, the overall success rate for samples was 36.3%. The best DNA profiling success rates were obtained from femur (36.2%) and tooth (33.7%) samples. DNA profiles were significantly better from lower body bones than upper body bones (p = forensic DNA sampling strategies in future victim recovery investigations.

  18. Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing.

    Science.gov (United States)

    Haines, Alicia M; Tobe, Shanan S; Kobus, Hilton J; Linacre, Adrian

    2015-10-01

    We report on the effects of six dyes used in the detection of DNA on the process of DNA extraction, amplification, and detection of STR loci. While dyes can be used to detect the presence of DNA, their use is restricted if they adversely affect subsequent DNA typing processes. Diamond™ Nucleic Acid Dye, GelGreen™, GelRed™, RedSafe™, SYBR(®) Green I, and EvaGreen™ were evaluated in this study. The percentage of dye removed during the extraction process was determined to be: 70.3% for SYBR(®) Green I; 99.6% for RedSafe™; 99.4% for EvaGreen™; 52.7% for Diamond™ Dye; 50.6% for GelRed™, and; could not be determined for GelGreen™. It was then assumed that the amount of dye in the fluorescent quantification assay had no effect on the DNA signal. The presence of all six dyes was then reviewed for their effect on DNA extraction. The t-test showed no significant difference between the dyes and the control. These extracts were then STR profiled and all dyes and control produced full DNA profiles. STR loci in the presence of GelGreen(TM) at 1X concentration showed increased amplification products in comparison to the control samples. Full STR profiles were detected in the presence of EvaGreen™ (1X), although with reduced amplification products. RedSafe™ (1X), Diamond™ Dye (1X), and SYBR(®) Green I (1X) all exhibited varying degrees of locus drop-out with GelRed™ generating no loci at all. We provide recommendations for the best dye to visualize the presence of DNA profile as a biological stain and its subsequent amplification and detection. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

    2014-01-01

    method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous...... studies. We also compared pairwise distances (between geographically separated samples) with those obtained using the AMOVA method and found good agreement. Further analyses that are impossible with AMOVA were made using the discrete Laplace method: analysis of the homogeneity in two different ways......The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models...

  20. Population genetics of 17 Y-STR markers in West Libya (Tripoli region).

    Science.gov (United States)

    Triki-Fendri, Soumaya; Sánchez-Diz, Paula; Rey-González, Danel; Ayadi, Imen; Alfadhli, Suad; Rebai, Ahmed; Carracedo, Ángel

    2013-05-01

    Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both R(ST) pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations.

  1. 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.

  2. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)

    Yomi

    2012-03-15

    Mar 15, 2012 ... Short tandem repeat (STR) is widely used today for gene mapping ... minatory power for some difficult cases, such as complex kinship analysis ... Arlequin version 3.5 software (Computational and Molecular. Population ...

  3. Lipid Profile and Oxidative Stress Markers in Wistar Rats following Oral and Repeated Exposure to Fijk Herbal Mixture

    Directory of Open Access Journals (Sweden)

    Oluyomi Stephen Adeyemi

    2014-01-01

    Full Text Available This study determined the effect of the oral and repeated administration of Fijk herbal mixture on rat biochemical and morphological parameters. Twenty-four Wistar rats were distributed into four groups of 6. Group A served as control and received oral administration of distilled water daily. The experimental groups B, C, and D were daily and orally exposed to Fijk herbal mixture at 15, 30, and 45 mg/kg, respectively. Treatments lasted for 21 days. The rats were sacrificed under mild diethyl ether anesthesia 24 hr after cessation of treatment. The blood and liver samples were collected and used for the biochemical and morphological analyses. Oral exposure to Fijk caused elevated levels of rat plasma ALT, AST, triglycerides, LDL, and MDA. In contrast, rat plasma HDL, GSH, and ALP levels were lowered by Fijk oral exposure. Also, the herbal remedy caused a dose-dependent elevation in the plasma atherogenic index. The histopathology examinations of rat liver sections revealed inimical cellular alterations caused by repeated exposure to Fijk. Study provides evidence that oral and repeated exposure to Fijk in rats raised the atherogenic index and potentiated oxidative stress as well as hepatic injury.

  4. Variable pulse profiles of Her X-1 repeating with the same irregular 35d clock as the turn-ons

    CERN Document Server

    Staubert, R; Vasco, D; Postnov, K; Shakura, N; Wilms, J; Rothschild, R E

    2012-01-01

    The accreting X-ray pulsar Her X-1 shows two types of long-term variations, both with periods of ~35 days: 1) Turn-on cycles, a modulation of the flux}, with a ten-day long Main-On and a five-day long Short-On, separated by two Off-states, and 2) a systematic variation in the shape of the 1.24 s pulse profile. While there is general consensus that the flux modulation is due to variable shading of the X-ray emitting regions on the surface of the neutron star by the precessing accretion disk, the physical reason for the variation in the pulse profiles has remained controversial. Following the suggestion that free precession of the neutron star may be responsible for the variation in the pulse profiles, we developed a physical model of strong feedback interaction between the neutron star and the accretion disk in order to explain the seemingly identical values for the periods of the two types of variations, which were found to be in basic synchronization. In a deep analysis of pulse profiles observed by several ...

  5. Influence of repeated rectal ultrasound examinations on hormone profiles and behaviour around oestrus and ovulation in dairy cattle

    NARCIS (Netherlands)

    Roelofs, J.B.; Bouwman, E.G.; Dieleman, S.J.; Eerdenburg, van F.J.C.M.; Lansbergen, L.M.T.E.; Soede, N.M.; Kemp, B.

    2004-01-01

    Frequent rectal ultrasound is often used to assess time of ovulation. This study investigated whether frequent rectal ultrasound examination, affects behavioural oestrus and peri-ovulatory hormone profiles (LH, oestradiol and progesterone). Additionally, the relation between peri-ovulatory hormone p

  6. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

    NARCIS (Netherlands)

    Schouten, Philip C.; Grigoriadis, Anita; Kuilman, Thomas; Mirza, Hasan; Watkins, Johnathan A.; Cooke, Saskia A.; van Dyk, Ewald; Severson, Tesa M.; Rueda, Oscar M.; Hoogstraat, Marlous; Verhagen, Caroline V. M.; Natrajan, Rachael; Chin, Suet-Feung; Lips, Esther H.; Kruizinga, Janneke; Velds, Arno; Nieuwland, Marja; Kerkhoven, Ron M.; Krijgsman, Oscar; Vens, Conchita; Peeper, Daniel; Nederlof, Petra M.; Caldas, Carlos; Tutt, Andrew N.; Wessels, Lodewyk F.; Linn, Sabine C.

    Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively.

  7. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

    NARCIS (Netherlands)

    Schouten, P.C.; Grigoriadis, A.; Kuilman, T.; Mirza, H.; Watkins, J.A.; Cooke, S.A.; Van Dyk, E.; Severson, T.M.; Rueda, O.M.; Hoogstraat, M.; Verhagen, C.; Natrajan, R.; Chin, S.F.; Lips, E.H.; Kruizinga, J.; Velds, A.; Nieuwland, M.; Kerkhoven, R.M.; Krijgsman, O.; Vens, C.; Peeper, D.; Nederlof, P.M.; Caldas, C.; Tutt, A.N.; Wessels, L.F.A.; Linn, S.C.

    2015-01-01

    Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be ‘BRCA1-like’ or ‘non-BRCA1-like’, which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively.

  8. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

    NARCIS (Netherlands)

    Schouten, P.C.; Grigoriadis, A.; Kuilman, T.; Mirza, H.; Watkins, J.A.; Cooke, S.A.; Dyk, E. van; Severson, T.M.; Rueda, O.M.; Hoogstraat, M.; Verhagen, C.V.M.; Natrajan, R.; Chin, S.F.; Lips, E.H.; Kruizinga, J.; Velds, A.; Nieuwland, M.; Kerkhoven, R.M.; Krijgsman, O.; Vens, C.; Peeper, D.; Nederlof, P.M.; Caldas, C.; Tutt, A.N.; Wessels, L.F.; Linn, S.C.

    2015-01-01

    Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively.

  9. Establishing a DNA identification system for pigs (Sus scrofa) using a multiplex STR amplification.

    Science.gov (United States)

    Lin, Yu-Chih; Hsieh, Hsing-Mei; Lee, James Chun-I; Hsiao, Chung-Ting; Lin, Der-Yuh; Linacre, Adrian; Tsai, Li-Chin

    2014-03-01

    In this study we establish a novel STR multiplex using 13 tetra-nucleotide STRs and the amelogenin marker for the forensic identification of pigs. The genotypes and allele frequency were generated based on 341 samples from 11 pig breeds in Taiwan. Genetic variation was tested including Na, Ne, Ho, He, F-statistics, PIC, Pm and PE for each STR locus and for each breed. Based upon the 341 samples in this study, the CPm and CPEtrio of the 13 STR loci were 1.31 E-11 and 0.9996 respectively. The CPItrio based on ten family sets ranged from 4.012 E+4 to 4.332 E+6 for paternity test. Validation of the multiplex included: determining the sensitivity of the test, where reproducible full DNA profiles were obtained using an initial template of between 0.25 and 1 ng; a comprehensive range of tissue types generated the same genotype; and the specificity was confirmed as no DNA full profile was generated for any species other than Sus scrofa. Based on the phylogenetic analysis, the European domestic breeds clustered separately from the Asian breeds, as expected, and their hybrids formed unique clades respectively between the clades of Asian and European breeds. Eleven test samples, acting as unknown samples, matched all expected breeds. We demonstrate that this novel 14-plex PCR system is valuable in pig individualization, parentage testing, breed assessment, phylogenetic study and forensic applications.

  10. Improved Dead Sea sinkhole site characterization at Ghor Al Haditha, Jordan, based on repeated shear wave reflection seismic profiling

    Science.gov (United States)

    Polom, Ulrich; Alrshdan, Hussam; Al-Halbouni, Djamil; Sawarieh, Ali; Dahm, Torsten; Krawczyk, CharLotte M.

    2016-04-01

    In October 2014 a high-resolution shallow shear wave reflection seismic survey was carried out at the Dead Sea sinkhole site Ghor Al Haditha, Jordan. It extended a survey undertaken in 2013, also in order to gather time-lapse profiles. In the framework of the DEad SEa Research Venue (DESERVE), a virtual institute of the Helmholtz Association and international partners, this investigation is part of a cross-disciplinary and cooperative international project of the Helmholtz Centers KIT, GFZ, and UFZ. At the investigation site, characterized by alluvial fan deposits, ongoing subsidence and sinkhole processes in the subsurface create massive reshaping of farming areas, including the destruction of housings, industrial sites, and infrastructure. The sinkhole hazard at the Dead Sea is significant, since similar processes are observed at several coastal segments of the Dead Sea. The new survey (in total 2.1 profile km) was targeted to improve the knowledge about the subsurface structures and to confine the results of the initial survey (1.8 km profile km), with respect to the presence or non-presence of a massive salt layer proposed at nearly 40 m depth. This salt layer is the central part of a widely established process hypothesis to generate shallow cavities by salt subrosion, which subsequently collapse to sinkholes at the surface. Results of the initial survey carried out in 2013 highlighted a new process hypothesis of subsurface mass transport by Dead Sea mud mobilization enclosed in the alluvial fan, so that an extended survey was undertaken in 2014. This, indeed, confirmed that there are no reflection seismic signal responses that would be expected to occur in the presence of a massive salt layer. Since evaluation of both hypothesis by new drilling could not be carried out due to safety reasons and permissions, it remained unclear which hypothesis is valid for the investigation site. However, we combined the 2013 and 2014 reflection seismic profiles and the

  11. Changes in repeated-sprint performance in relation to change in locomotor profile in highly-trained young soccer players.

    Science.gov (United States)

    Buchheit, Martin; Mendez-Villanueva, Alberto

    2014-01-01

    The aim of this study was to examine the effects of changes in maximal aerobic (MAS) and sprinting (MSS) speeds and the anaerobic reserve (ASR) on repeated-sprint performance. Two hundred and seventy highly-trained soccer players (14.5 ± 1.6 year) completed three times per season (over 5 years) a maximal incremental running test to approach MAS, a 40-m sprint with 10-m splits to assess MSS and a repeated-sprint test (10 × 30-m sprints), where best (RSb) and mean (RSm) sprint times, and percentage of speed decrement (%Dec) were calculated. ASR was calculated as MSS-MAS. While ∆RSb were related to ∆MSS and ∆body mass (r(2) = 0.42, 90%CL[0.34;0.49] for the overall multiple regression, n = 334), ∆RSm was also correlated with ∆MAS and ∆sum of 7 skinfolds (r(2) = 0.43 [0.35;0.50], n = 334). There was a small and positive association between ∆%Dec and ∆MAS (r(2) = 0.02 [-0.07;0.11], n = 334). Substantial ∆MSS and ∆MAS had a predictive value of 70 and 55% for ∆RSm, respectively. Finally, ∆ASR per se was not predictive of ∆RSm (Cohen's = +0.8 to -0.3 with increased ASR), but the greater magnitude of ∆RSm improvement was observed when MSS, MAS and ASR increased together (0.8 vs. +0.4 with ASR increased vs. not, additionally to MSS and MAS). Low-cost field tests aimed at assessing maximal sprinting and aerobic speeds can be used to monitor ∆RS performance.

  12. Optimizing direct amplification of forensic commercial kits for STR determination.

    Science.gov (United States)

    Caputo, M; Bobillo, M C; Sala, A; Corach, D

    2017-04-01

    Direct DNA amplification in forensic genotyping reduces analytical time when large sample sets are being analyzed. The amplification success depends mainly upon two factors: on one hand, the PCR chemistry and, on the other, the type of solid substrate where the samples are deposited. We developed a workflow strategy aiming to optimize times and cost when starting from blood samples spotted onto diverse absorbent substrates. A set of 770 blood samples spotted onto Blood cards, Whatman(®) 3 MM paper, FTA™ Classic cards, and Whatman(®) Grade 1 was analyzed by a unified working strategy including a low-cost pre-treatment, a PCR amplification volume scale-down, and the use of the 3500 Genetic Analyzer as the analytical platform. Samples were analyzed using three different commercial multiplex STR direct amplification kits. The efficiency of the strategy was evidenced by a higher percentage of high-quality profiles obtained (over 94%), a reduced number of re-injections (average 3.2%), and a reduced amplification failure rate (lower than 5%). Average peak height ratio among different commercial kits was 0.91, and the intra-locus balance showed values ranging from 0.92 to 0.94. A comparison with previously reported results was performed demonstrating the efficiency of the proposed modifications. The protocol described herein showed high performance, producing optimal quality profiles, and being both time and cost effective. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  13. D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age.

    Science.gov (United States)

    Phillips, C; Parson, W; Amigo, J; King, J L; Coble, M D; Steffen, C R; Vallone, P M; Gettings, K B; Butler, J M; Budowle, B

    2016-07-01

    In the process of establishing short tandem repeat (STR) sequence variant nomenclature guidelines in anticipation of expanded forensic multiplexes for massively parallel sequencing (MPS), it was discovered that the STR D5S2500 has multiple positions and genomic characteristics reported. This ambiguity is because the marker named D5S2500 consists of two different microsatellites forming separate components in the capillary electrophoresis multiplexes of Qiagen's HDplex (Hilden, Germany) and AGCU ScienTech's non-CODIS STR 21plex (Wuxi, Jiangsu, China). This study outlines the genomic details used to identify each microsatellite and reveals the D5S2500 marker in HDplex has the correctly assigned STR name, while the D5S2500 marker in the AGCU 21plex, closely positioned a further 1643 nucleotides in the human reference sequence, is an unnamed microsatellite. The fact that the D5S2500 marker has existed as two distinct STR loci undetected for almost ten years, even with reported discordant genotypes for the standard control DNA, underlines the need for careful scrutiny of the genomic properties of forensic STRs, as they become adapted for sequence analysis with MPS systems. We make the recommendation that precise chromosome location data must be reported for any forensic marker under development but not in common use, so that the genomic characteristics of the locus are validated to the same level of accuracy as its allelic variation and forensic performance. To clearly differentiate each microsatellite, we propose the name D5S2800 be used to identify the Chromosome-5 STR in the AGCU 21plex.

  14. Genetic diversity and haplotype structure of 24 Y-chromosomal STR in Chinese Hui ethnic group and its genetic relationships with other populations.

    Science.gov (United States)

    Zhu, Bo-Feng; Zhang, Yu-Dang; Liu, Wen-Juan; Meng, Hao-Tian; Yuan, Guo-Lian; Lv, Zhe; Dong, Nan; Li, Qiong; Yang, Chun-Hua; Zhang, Yu-Hong; Hou, Yin-Ling; Qian, Li; Fan, Shuan-Liang; Xu, Peng

    2014-07-01

    In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 115 unrelated Hui male individuals from Haiyuan county or Tongxin county, Ningxia Hui Autonomous Region, China, to evaluate the forensic application of the 24 STR loci and to analyze interpopulation differentiations by making comparisons between the Hui group data and previously published data of other 13 populations. A total of 115 different haplotypes were observed on these 24 Y-STR loci. The gene diversities ranged from 0.4049 (DYS437) to 0.9729 (DYS385a, b). The overall haplotype diversity was 1 at AGCU 24 Y-STR loci level, while the values were reduced to 0.999237, 0.996949, and 0.996644 at the Y-filer 17 loci, 11 Y-STR loci of extended haplotype and 9 Y-STR loci of minimal haplotype levels, respectively; whereas, haplotype diversity for additional 7 loci (not included in Y-filer 17 loci) was 0.995271. The pairwise FST , multidimensional scaling plot and neighbor-joining tree indicated the Hui group had the closest genetic relationship with Sala in the paternal lineage in the present study. In summary, the results in our study indicated the 24 Y-STRs had a high level of polymorphism in Hui group and hence could be a powerful tool for forensic application and population genetic study.

  15. Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system

    KAUST Repository

    D'Amato, María Eugenia

    2011-03-01

    The Y-chromosome STRs (short tandem repeat) markers are routinely utilized in the resolution of forensic casework related to sexual assault. For this, the forensic community has adopted a set of eleven (core) Y-STR that is incorporated in all commercial diagnostic systems. Our previous studies of Y-STR polymorphisms in the South African population identified low levels of diversity and discrimination capacity for many commercial marker sets, determining a limited applicability of these systems to the local population groups. To overcome this shortcoming, we designed a Y-STR 10-plex system that shows higher discriminatory capacity (DC) than available commercial systems. The markers were selected from a population group of 283 individuals with African, European and Asian ancestry genotyped at 45 Y-STRs, applying an optimization based selection procedure to achieve the highest possible DC with the minimal number of markers. The 10-plex was satisfactorily subjected to developmental validation tests following the SWGDAM guidelines and shows potential for its application to genealogical and evolutionary studies. © 2010 Elsevier Ireland Ltd.

  16. [Information behavior of 7 STR loci on chromosome 9p in gene scanning].

    Science.gov (United States)

    Zeng, Zhao-Yang; Xiong, Wei; Xiong, Fang; Shen, Shou-Rong; Li, Xiao-Ling; Li, Wei-Fang; Wang, Rong; Xiao, Bing-Yi; Fan, Song-Qing; Huang, He; Zhou, Ming; Li, Gui-Yuan

    2003-09-01

    To get genotype and allele frequency distributions of seven short tandem repeat (STR) loci of chromosome 9p,D9S288,D9S157,D9S1748,D9S171,D9S161,D9S1817 and D9S1805 in Chinese Han population in Hunan area,blood samples were collected from the random Han individual in Hunan and the whole genomic DNA was extracted.STR loci were amplified by multiplex-PCR technique and genotyped by ABI 377 sequencer.Seventy-five alleles were detected,with frequencies ranging from 0.002 to 0.800,and constituted 243 genotypes. All the seven loci met Hardy-Weinberg equilibrium. The statistical analysis of seven STR loci showed H(heterozygosity) ranging from 0.347 to 0.844,DP(discrimination power) ranging from 0.346 to 0.841,PPE(probabilities of paternity exclusion) ranging from 0.308 to 0.738 and PIC(polymorphic information content) ranging from 0.328 to 0.822. The result indicated that there was a significant difference between Han ethnic group and the white and the black.

  17. Ages and Metallicities of Cluster Galaxies in A779 using Modified Str\\"omgren Photometry

    CERN Document Server

    Sreedhar, Yuvraj Harsha; Rakos, Karl D; Hensler, Gerhard; Zeilinger, Werner W

    2012-01-01

    In the quest for the formation and evolution of galaxy clusters, Rakos and co-workers introduced a spectrophotometric method using the modified Str\\"omgren photometry. But with the considerable debate toward the project's abilities, we re-introduce the system after a thorough testing of repeatability of colors and reproducibility of the ages and metallicities for six common galaxies in the three A779 data sets. A fair agreement has been found between the modified Str\\"omgren and Str\\"omgren filter systems to produce similar colors (with the precision of 0.09 mag in (uz-vz), 0.02 mag in (bz-yz), and 0.03 mag in (vz-vz)), ages and metallicities (with the uncertainty of 0.36 Gyr and 0.04 dex from the PCA and 0.44 Gyr and 0.2 dex using the GALEV models). We infer that the technique is able to relieve the age-metallicity degeneracy by separating the age effects from the metallicity effects, but still unable to completely break. We further extend this paper to re-study the evolution of galaxies in the low mass, dyn...

  18. A population genetic database of cat breeds developed in coordination with a domestic cat STR multiplex.

    Science.gov (United States)

    Menotti-Raymond, Marilyn; David, Victor A; Weir, Bruce S; O'Brien, Stephen J

    2012-05-01

    A simple tandem repeat (STR) PCR-based typing system developed for the genetic individualization of domestic cat samples has been used to generate a population genetic database of domestic cat breeds. A panel of 10 tetranucleotide STR loci and a gender-identifying sequence tagged site (STS) were co-amplified in genomic DNA of 1043 individuals representing 38 cat breeds. The STR panel exhibits relatively high heterozygosity in cat breeds, with an average 10-locus heterozygosity of 0.71, which represents an average of 38 breed-specific heterozygosities for the 10-member panel. When the entire set of breed individuals was analyzed as a single population, a heterozygosity of 0.87 was observed. Heterozygosities obtained for the 10 loci range from 0.72 to 0.96. The power for genetic individualization of domestic cat samples of the multiplex is high, with a probability of match (p(m)) of 6.2E-14, using a conservative θ = 0.05.

  19. An integrated system of ABO typing and multiplex STR testing for forensic DNA analysis.

    Science.gov (United States)

    Jiang, Xianhua; He, Juan; Jia, Fei; Shen, Hongying; Zhao, Jinling; Chen, Chuguang; Bai, Liping; Liu, Feng; Hou, Guangwei; Guo, Faye

    2012-12-01

    A new amplification system for ABO and STR genotyping in a single reaction has been successfully developed. Two types of information can be obtained from a biological sample at one time. One is the classical information of ABO blood group typing for screening suspects and the other is STR information for individual identification. The system allows for the simultaneous detection of 15 autosomal STR loci (containing all CODIS STR loci as well as Penta D and Penta E), six ABO genotypes (O/O, B/B, A/A, A/O, A/B, and B/O) and the gender-determining locus Amelogenin. Primers are designed so that the amplicons are distributed ranging from 75bp to 500bp within a four-dye fluorescent design, leaving a fourth dye for the internal size standard. With 30 cycles, the results showed that the optimal amount of DNA template for this multiplex ranges from 250pg to 2ng and the lowest detection threshold is 125pg (as low as 63pg for ABO loci). For the DNA template outside the optimal detection range, we could adjust the number of cycles to obtain the robust profiles. Mixture studies showed that over 83% of minor alleles were detected at 1:9 ratios. The full profiles were still observed when 4ng of degraded DNA was digested by DNase I and 1ng undegraded DNA was added to 40μM haematin. Polymerase chain reaction (PCR)-based conditions including the concentrations of primers, magnesium and the Taq polymerase as well as volume, cycle numbers and annealing temperature were examined and optimised. In addition, the system was validated by 364 bloodstain samples and 32 common casework samples. According to the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, our system demonstrates good detection performance and is an ideal tool for forensic DNA typing with potential application.

  20. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers.

    Science.gov (United States)

    Santos, Sara; Oliveira, Manuela; Amorim, António; van Asch, Barbara

    2014-11-01

    The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Repeated post-exercise administration with a mixture of leucine and glucose alters the plasma amino acid profile in Standardbred trotters

    Directory of Open Access Journals (Sweden)

    Nostell Katarina EA

    2012-02-01

    Full Text Available Abstract Background The branched chain amino acid leucine is a potent stimulator of insulin secretion. Used in combination with glucose it can increase the insulin response and the post exercise re-synthesis of glycogen in man. Decreased plasma amino acid concentrations have been reported after intravenous or per oral administration of leucine in man as well as after a single per oral dose in horses. In man, a negative correlation between the insulin response and the concentrations of isoleucine, valine and methionine have been shown but results from horses are lacking. This study aims to determine the effect of repeated per oral administration with a mixture of glucose and leucine on the free amino acid profile and the insulin response in horses after glycogen-depleting exercise. Methods In a crossover design, after a glycogen depleting exercise, twelve Standardbred trotters received either repeated oral boluses of glucose, 1 g/kg body weight (BW at 0, 2 and 4 h with addition of leucine 0.1 g/kg BW at 0 and 4 h (GLU+LEU, or repeated boluses of water at 0, 2 and 4 h (CON. Blood samples for analysis of glucose, insulin and amino acid concentrations were collected prior to exercise and over a 6 h post-exercise period. A mixed model approach was used for the statistical analyses. Results Plasma leucine, isoleucine, valine, tyrosine and phenylalanine concentrations increased after exercise. Post-exercise serum glucose and plasma insulin response were significantly higher in the GLU+LEU treatment compared to the CON treatment. Plasma leucine concentrations increased after supplementation. During the post-exercise period isoleucine, valine and methionine concentrations decreased in both treatments but were significantly lower in the GLU+LEU treatment. There was no correlation between the insulin response and the response in plasma leucine, isoleucine, valine and methionine. Conclusions Repeated post-exercise administration with a mixture of leucine

  2. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

    Science.gov (United States)

    2010-01-01

    Background Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations. Results Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global FST was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global FST for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment. Conclusion Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels. PMID:20051144

  3. 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.

  4. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    OpenAIRE

    Purps, J.; Siegert, S.; Willuweit, S.; Nagy, M.; C. Alves; Salazar, R.; Angustia, S.M.T.; Santos,L.H.; Anslinger, K.; Bayer, B.; Ayub, Q.; Wei, W; Xue, Y.; Tyler-Smith, C; Bafalluy, M.B.

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different\\ud populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci\\ud (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439,\\ud DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643)\\ud and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic\\ud spectra of...

  5. Gene expression profiling of R6/2 transgenic mice with different CAG repeat lengths reveals genes associated with disease onset and progression in Huntington's disease.

    Science.gov (United States)

    Tang, Bin; Seredenina, Tamara; Coppola, Giovanni; Kuhn, Alexandre; Geschwind, Daniel H; Luthi-Carter, Ruth; Thomas, Elizabeth A

    2011-06-01

    R6/2 transgenic mice with expanded CAG repeats (>300) have a surprisingly prolonged disease progression and longer lifespan than prototypical parent R6/2 mice (carrying 150 CAGs); however, the mechanism of this phenotype amelioration is unknown. We compared gene expression profiles in the striatum of R6/2 transgenic mice carrying ~300 CAG repeats (R6/2(Q300) transgenic mice) to those carrying ~150 CAG repeats (R6/2(Q150) transgenic mice) and littermate wildtype controls in order to identify genes that may play determinant roles in the time course of phenotypic expression in these mice. Of the top genes showing concordant expression changes in the striatum of both R6/2 lines, 85% were decreased in expression, while discordant expression changes were observed mostly for genes upregulated in R6/2(Q300) transgenic mice. Upregulated genes in the R6/2(Q300) mice were associated with the ubiquitin ligase complex, cell adhesion, protein folding, and establishment of protein localization. We qPCR-validated increases in expression of genes related to the latter category, including Lrsam1, Erp29, Nasp, Tap1, Rab9b, and Pfdn5 in R6/2(Q300) mice, changes that were not observed in R6/2 mice with shorter CAG repeats, even in late stages (i.e., 12 weeks of age). We further tested Lrsam1 and Erp29, the two genes showing the greatest upregulation in R6/2(Q300) transgenic mice, for potential neuroprotective effects in primary striatal cultures overexpressing a mutated human huntingtin (htt) fragment. Overexpression of Lrsam1 prevented the loss of NeuN-positive cell bodies in htt171-82Q cultures, concomitant with a reduction of nuclear htt aggregates. Erp29 showed no significant effects in this model. This is consistent with the distinct pattern of htt inclusion localization observed in R6/2(Q300) transgenic mice, in which smaller cytoplasmic inclusions represent the major form of insoluble htt in the cell, as opposed to large nuclear inclusions observed in R6/2(Q150) transgenic mice

  6. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs)

    Science.gov (United States)

    Shumayla; Sharma, Shailesh; Kumar, Rohit; Mendu, Venugopal; Singh, Kashmir; Upadhyay, Santosh K.

    2016-01-01

    The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

  7. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs).

    Science.gov (United States)

    Shumayla; Sharma, Shailesh; Kumar, Rohit; Mendu, Venugopal; Singh, Kashmir; Upadhyay, Santosh K

    2016-01-01

    The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

  8. Genomic dissection and expression profiling revealed functional divergence in Triticum aestivum leucine rich repeat receptor like kinases (TaLRRKs

    Directory of Open Access Journals (Sweden)

    Shumayla .

    2016-09-01

    Full Text Available The leucine rich repeat receptor like kinases (LRRK constitute the largest subfamily of receptor like kinases (RLK, which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat, which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought and salt stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

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

    DEFF Research Database (Denmark)

    Fordyce, Sarah L; Mogensen, Helle Smidt; Børsting, Claus

    2015-01-01

    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......) 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 50pg, with the exception of a single locus...... 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 all-in-one solution from amplification of STRs and amelogenin, and sequencing to data analysis....

  10. Genetic polymorphisms of 24 Y-STR loci in Hani ethnic minority from Yunnan Province, Southwest China.

    Science.gov (United States)

    Hu, Liping; Gu, Tao; Fan, Xiaodong; Yuan, Xiaokun; Rao, Min; Pang, Jing Bo; Nie, Aiting; Du, Lei; Zhang, Xiufeng; Nie, Shengjie

    2017-01-27

    In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 250 unrelated Hani male individuals from Lvchun county, Honghe Hani and Yi Autonomous Prefecture, Yunnan Province, Southwest China. The gene diversity of the 24 Y-STR loci in the studied Hani group ranged from 0.2683 (DYS437) to 0.8837 (DYS447). According to haplotypic analysis of the 24 Y-STR loci, 204 different haplotypes were obtained, 174 of which were unique. The haplotype diversity and discrimination capacity in Hani group were 0.9977 and 0.8160 at 24 STR loci, respectively. Six single non-fraction off-ladder alleles were observed at DYS447 in 103 samples, in addition to the alleles 19 to 28 included in the allelic ladder, alleles 13, 14, 15, 16, 17, and 18 were also observed at DYS447. One intermediate allele 20.2 was observed in one individual at DYS527a/b. We analyzed interpopulation differentiations by making comparisons between Yunnan Hani group and other 17 groups. The results of pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that Yunnan Hani group had the closer genetic relationships with Yunnan Han group. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationships between Hani and other groups.

  11. Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma.

    Science.gov (United States)

    Barra, Gustavo Barcelos; Santa Rita, Ticiane Henriques; Chianca, Camilla Figueiredo; Velasco, Lara Francielle Ribeiro; de Sousa, Claudia Ferreira; Nery, Lídia Freire Abdalla; Costa, Sandra Santana Soares

    2015-03-01

    The aim of this study is to determine the fetus Y-STR haplotype in maternal plasma during pregnancy and estimate, non-invasively, if the alleged father and fetus belong to the same male lineage. The study enrolled couples with singleton pregnancies and known paternity. All participants signed informed consent and the local ethics committee approved the study. Peripheral blood was collected in EDTA tubes (mother) and in FTA paper (father). Maternal plasma DNA was extracted by using NucliSens EasyMAG. Fetal gender was determined by qPCR targeting DYS-14 in maternal plasma and it was also confirmed after the delivery. From all included volunteers, the first consecutive 20 mothers bearing male fetuses and 10 mothers bearing female fetuses were selected for the Y-STR analysis. The median gestational age was 12 weeks (range 12-36). All DNA samples were subjected to PCR amplification by PowerPlex Y23, ampFLSTR Yfiler, and two in-house multiplexes, which together accounts for 27 different Y-STR. The PCR products were detected with 3500 Genetic Analyzer and they were analyzed using GeneMapper-IDX. Fetuses' haplotypes (Yfiler format) were compared to other 5328 Brazilian haplotypes available on Y-chromosome haplotypes reference database (YHRD). As a result, between 22 and 27 loci were successfully amplified from maternal plasma in all 20 cases of male fetuses. None of the women bearing female fetuses had a falsely amplified Y-STR haplotype. The haplotype detected in maternal plasma completely matched the alleged father haplotype in 16 out of the 20 cases. Four cases showed single mismatches and they did not configure exclusions; 1 case showed a mutation in the DYS 458 locus due to the loss of one repeat unit and 3 cases showed one DYS 385I/II locus dropout. All mismatches were confirmed after the delivery. Seventeen fetuses' haplotypes were not found in YHRD and one of them had a mutation, which corresponded to the paternity probability of 99.9812% and 95.7028%, respectively

  12. Investigation of a Gamma model for mixture STR samples

    DEFF Research Database (Denmark)

    Christensen, Susanne; Bøttcher, Susanne Gammelgaard; Lauritzen, Steffen L.

    The behaviour of PCR Amplification Kit, when used for mixture STR samples, is investigated. A model based on the Gamma distribution is fitted to the amplifier output for constructed mixtures, and the assumptions of the model is evaluated via residual analysis.......The behaviour of PCR Amplification Kit, when used for mixture STR samples, is investigated. A model based on the Gamma distribution is fitted to the amplifier output for constructed mixtures, and the assumptions of the model is evaluated via residual analysis....

  13. Evaluation of the RapidHIT™ 200, an automated human identification system for STR analysis of single source samples.

    Science.gov (United States)

    Holland, Mitchell; Wendt, Frank

    2015-01-01

    The RapidHIT™ 200 Human Identification System was evaluated to determine its suitability for STR analysis of single source buccal swabs. Overall, the RapidHIT™ 200 performed as well as our traditional capillary electrophoresis based method in producing useable profile information on a first-pass basis. General observations included 100% concordance with known profile information, consistent instrument performance after two weeks of buccal swab storage, and an absence of contamination in negative controls. When data analysis was performed by the instrument software, 95.3% of the 85 samples in the reproducibility study gave full profiles. Including the 81 full profiles, a total of 2682 alleles were correctly called by the instrument software, or 98.6% of 2720 possible alleles tested. Profile information was generated from as little as 10,000 nucleated cells, with swab collection technique being a major contributing factor to profile quality. The average peak-height-ratio for heterozygote profiles (81%) was comparable to conventional STR analysis, and while a high analytical threshold was required when offline profile analysis was performed (800 RFU), it was proportionally consistent with traditional methods. Stochastic sampling effects were evaluated, and a manageable approach to address limits of detection for homozygote profiles is provided. These results support consideration of the RapidHIT™ 200 as an acceptable alternative to conventional, laboratory based STR analysis for the testing of single source buccal samples, with review of profile information as a requirement until an expert software system is incorporated, and when proper developmental and internal validation studies have been completed.

  14. [Polymorphism of 17 Y-STR loci in She ethnic population in Fujian and genetic relationship with 11 populations].

    Science.gov (United States)

    Bai, Ru-Feng; Yang, Li-Hai; Yuan, Li; Liang, Quan-Zeng; Lu, Di; Yang, Xue; Shi, Mei-Sen

    2012-08-01

    To investigate the genetic polymorphisms of 17 Y-chromosomal short tandem repeats(Y-STR) loci in She ethnic population from Fujian province, and to evaluate their forensic application values and genetic relationship with other 11 populations, 152 unrelated male individuals of She ethnic population in Fujian were used to determine the distribution of allele frequencies and haplotypes by using Y-filerTM System. Cluster analysis and phylogenic trees were applied to show the genetic distance among the populations. As a result, 50 haplotypes were found in DYS385a/b loci, and 3~11 alleles were found in the rest 15 Y-STR loci. The GD value was from 0.4037(DYS391) to 0. 9725(DYS385a/b). This study has also revealed "off-ladder" alleles at several Y-loci, namely DYS448, DYS393, DYS458 and DYS635, and several occurrences of duplications at the DYS385a/b, DYS19 and DYS390 loci. One hundred and forty-four haplotypes were found in 17 Y-STR loci, of which 138 were unique, 5 were found in 2 individuals, 1 was found in 4 individuals, and the observed haplotypes diversity value was 0.9990. Comparing with 11 populations, the genetic distance between She ethnic and Han population in Zhejiang was the smallest (0.0042), while it was the largest between She ethnic and Tibet ethnic population (0.2380). Cluster analysis and phylogenetic tree both demonstrated that genetic distance between She ethnic and several south Han populations is closer than between She ethnic and non-Han populations. Multiplex detection of the 17 Y-STR loci revealed a highly polymorphic genetic distribution, which would be very powerful for establishing a Y-STR database, for population genetics and forensic practice.

  15. Genetic data for the 13 CODIS STR loci in Singapore Chinese.

    Science.gov (United States)

    Syn, C K C; Chuah, S Y; Ang, H C; Lim, S E S; Tan-Siew, W F; Chow, S T; Budowle, Bruce

    2005-09-10

    Allele frequencies for the 13 CODIS STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 209 unrelated Chinese in Singapore. The combined random match probability for the 13 loci is about 6.6 x10(-15) and the overall probability of excluding paternity is 0.9999899. The results demonstrate that the loci are useful for forensic human identification and parentage testing for the Chinese population in Singapore.

  16. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*

    Science.gov (United States)

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice. PMID:23733431

  17. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

    Science.gov (United States)

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-06-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.

  18. Sample-to-Result STR Genotyping Systems: Potential and Status.

    Science.gov (United States)

    Lounsbury, J A; Bienvenue, J M; Landers, J P

    2012-07-01

    Forensic DNA analysis using short tandem repeats (STRs) has become the cornerstone for human identification, kinship analysis, paternity testing, and other applications. However, it is a lengthy, laborious process that requires specialized training and numerous instruments, and it is one of the factors that has contributed to the formation and expansion of a casework backlog in the United States of samples awaiting DNA processing. Although robotic platforms and advances in instrumentation have improved the throughput of samples, there still exists a significant potential to enhance sample-processing capabilities. The application of microfluidic technology to STR analysis for human identification offers numerous advantages, such as a completely closed system, reduced sample and reagent consumption, and portability, as well as the potential to reduce the processing time required for biological samples to less than 2 h. Development of microfluidic platforms not only for forensic use, but clinical and diagnostic use as well, has exponentially increased since the early 1990s. For a microfluidic system to be generally accepted in forensic laboratories, there are several factors that must be taken into consideration and the data generated with these systems must meet or exceed the same guidelines and standards that are applicable for the conventional methods. This review covers the current state of forensic microfluidic platforms starting with microchips for the individual DNA-processing steps of extraction, amplification, and electrophoresis. For fully integrated devices, challenges that come with microfluidic platforms are covered, including circumventing issues with surface chemistry, monitoring flow control, and proper allele calling. Finally, implementation and future implications of a microfluidic rapid DNA system are discussed.

  19. 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.

  20. Mitochondrial DNA STR analysis as a tool for studying the green sea turtle (Chelonia mydas) populations: the Mediterranean Sea case study.

    Science.gov (United States)

    Tikochinski, Y; Bendelac, R; Barash, A; Daya, A; Levy, Y; Friedmann, A

    2012-06-01

    The Mediterranean population of the green sea turtle Chelonia mydas is critically endangered. Genetic analysis of this population using the ordinary haplotyping system, based on sequence analysis of a segment of the mitochondrial DNA (mtDNA) D-loop (control region), revealed very little variation. The most common haplotype, CM-A13, was observed in all but three individuals in hundreds of samples in previous studies. In search for a more informative marker we sequenced the 3' of the mitochondrial control region which contains an AT-rich microsatellite. We found a unique pattern that consists of four AT short tandem repeats (STRs) with varying copy numbers. This allowed us to construct a new haplotyping system composed of four different STR sizes for each mtDNA sequence. Our new mitochondrial STR (mtSTR) haplotyping approach revealed 33 different haplotypes within the nesting and stranded sea turtles along the Mediterranean Israeli seashore. The Israeli coast nesting females had 10 different haplotypes that can be used for monitoring and conservation purposes. The mtSTR haplotyping system can clearly assist in fingerprinting of individual turtles. Moreover, it can be used for estimating phylogenetic distances within populations. This case study shows that the mtSTR haplotyping is applicable for the study of global green sea turtle populations and could also be considered as markers of genetic variability in other species.

  1. Population data on 10 non-CODIS STR loci in Japanese population using a newly developed multiplex PCR system.

    Science.gov (United States)

    Asamura, H; Ota, M; Fukushima, H

    2008-11-01

    This paper describes a newly devised autosomal short tandem repeat (STR) multiplex polymerase chain reaction (PCR) systems for 10 loci (D1S1656, D2S1353, D8S1132, D12S1090, D14S608, D18S535, D19S253, D20S480, D21S226, and D22S689) unlinked to the core STR loci (non-CODIS loci). Of 252 samples taken from the Japanese population, PCR products ranged in length from 107 bp to 319 bp. No significant deviations from Hardy-Weinberg equilibrium were observed at any of the 10 loci. The accumulated power of discrimination and power of exclusion for the 10 loci were 0.999999999998 and 0.99991, respectively. We conclude that the present multiplex system for the 10 non-CODIS loci represents a powerful tool for forensic applications.

  2. Autosomal-STR based genetic structure of Chinese Xibe ethnic group and its relationships to various groups.

    Science.gov (United States)

    Meng, Haotian; Guo, Yuxin; Dong, Qian; Yang, Guang; Yan, Jiangwei; Shi, Jianfeng; Zhu, Bofeng

    2016-11-01

    The short tandem repeat (STR) is one of the most widely used genetic makers in forensic DNA labs worldwide. In the present study, we investigated the genetic structure of 19 autosomal STRs and 1 sex-determining locus (amelogenin) in the Xibe ethnic group in China, as well as its relationships to other groups. One hundred and ninety-five alleles were detected in 222 unrelated healthy Xibe individuals. The values of combined power of discrimination and probability of exclusion of all 19 STR loci were 0.99999999999999999999996912 and 0.999999997538, respectively. Principal component analysis revealed relationships between the Xibe group and other groups, which showed a relatively close genetic relationship between the Xibe and Korean groups.

  3. 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.

  4. INFLUENCE OF MORINGA OLEIFERA (DRUM-STICK FRUIT EXTRACT ON HAEMATOLOGICAL PROFILE FOLLOWING REPEATED EXPOSURE TO LOW LEVELS OF ARSENIC THROUGH FEED ON RATS

    Directory of Open Access Journals (Sweden)

    Vaibhav R. Pachade

    2012-01-01

    Full Text Available Effect of Moringa oleifera fruits hot methanolic extract (MFE, if any, in minimizing the adverse reactions of repeated exposure to arsenic trioxide (AT in feed was investigated in Wistar rats with reference to haematological profile. Three groups of rats each containing 10 (5male+5female were used. The group I served as negative control. Rats of group II were fed arsenic trioxide (AT alone @ 100 ppm in feed while those of group III simultaneously received AT (@100 ppm and MFE (50 mg/kg/day for 28 days. Blood samples were collected from retroorbital plexus for estimation of hematological parameters (haemoglobin, PCV, TEC, MCH, MCHC, MCV of different groups on 0 day, 15th day and 29th day respectively. Exposure to AT through feed in group II resulted in significant (P<0.05 decrease in haemoglobin, TEC and MCHC, accompanied by increased MCV, with no significant alteration of PCV or MCH of the rats. While rats of group III treated with AT (@100 ppm and MFE (50 mg/kg/day also resulted in same consequences as it was in group II but it was slightly less than that of group II suggesting of mild non significant protective effect.

  5. Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

    Science.gov (United States)

    Davoren, Jon; Vanek, Daniel; Konjhodzić, Rijad; Crews, John; Huffine, Edwin; Parsons, Thomas J.

    2007-01-01

    Aim To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves. Methods DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit. Results DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles. Conclusions The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method. PMID:17696302

  6. Short Tandem Repeats in Human Exons: A Target for Disease Mutations

    Directory of Open Access Journals (Sweden)

    Villesen Palle

    2008-09-01

    Full Text Available Abstract Background In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions, are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats are known to be hypermutable (indel-rich, but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect tandem repeats (STRs which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%, 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp and the limited length of STR regions.

  7. A novel, integrated forensic microdevice on a rotation-driven platform: Buccal swab to STR product in less than 2 h.

    Science.gov (United States)

    Cox, Jordan O; DeCarmen, Teresa Sikes; Ouyang, Yiwen; Strachan, Briony; Sloane, Hillary; Connon, Cathey; Gibson, Kemper; Jackson, Kimberly; Landers, James P; Cruz, Tracey Dawson

    2016-12-01

    This work describes the development of a novel microdevice for forensic DNA processing of reference swabs. This microdevice incorporates an enzyme-based assay for DNA preparation, which allows for faster processing times and reduced sample handling. Infrared-mediated PCR (IR-PCR) is used for STR amplification using a custom reaction mixture, allowing for amplification of STR loci in 45 min while circumventing the limitations of traditional block thermocyclers. Uniquely positioned valves coupled with a simple rotational platform are used to exert fluidic control, eliminating the need for bulky external equipment. All microdevices were fabricated using laser ablation and thermal bonding of PMMA layers. Using this microdevice, the enzyme-mediated DNA liberation module produced DNA yields similar to or higher than those produced using the traditional (tube-based) protocol. Initial microdevice IR-PCR experiments to test the amplification module and reaction (using Phusion Flash/SpeedSTAR) generated near-full profiles that suffered from interlocus peak imbalance and poor adenylation (significant -A). However, subsequent attempts using KAPA 2G and Pfu Ultra polymerases generated full STR profiles with improved interlocus balance and the expected adenylated product. A fully integrated run designed to test microfluidic control successfully generated CE-ready STR amplicons in less than 2 h (high-quality STR profiles were developed that were consistent with those produced using conventional DNA purification and STR amplification methods. This method is a smaller, more elegant solution than current microdevice methods and offers a cheaper, hands-free, closed-system alternative to traditional forensic methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. Analysis of 12 X-STR loci in the population of south Croatia.

    Science.gov (United States)

    Mršić, Gordan; Ozretić, Petar; Crnjac, Josip; Merkaš, Siniša; Račić, Ivana; Rožić, Sara; Sukser, Viktorija; Popović, Maja; Korolija, Marina

    2017-02-01

    The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator(®) Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org. Hardy-Weinberg equilibrium was confirmed for all X-STR markers in female samples. Biallelic patterns at DXS10079 locus were detected in four male samples. Polymorphism information content for the most (DXS10135) and the least (DXS8378) informative markers was 0.9212 and 0.6347, respectively. In both male and female samples, combined power of discrimination exceeded 0.999999999. As confirmed by linkage disequilibrium test, significant association of marker pair DXS10074-DXS10079 (P = 0.0004) within LG2 and marker pair DXS10101-DXS10103 (P = 0.0003) within LG3 was found only in male samples. Number of observed haplotypes in our sample pool amounted 3.01, 7.53, 5 and 3.25% of the number of possible haplotypes for LG1, LG2, LG3 and LG4, respectively. According to haplotype diversity value of 0.9981, LG1 was the most informative. In comparison of south Croatia with 26 world populations, pair-wise [Formula: see text] values increase in parallel with geographical distance. Overall statistical assessment confirmed suitability of Investigator(®) Argus X-12 kit for forensic casework in both identification and familial testing in the population of south Croatia.

  10. Y-STR haplotype diversity and population data for Central Brazil: implications for environmental forensics and paternity testing.

    Science.gov (United States)

    Vieira, T C; Gigonzac, M A D; Silva, D M; Rodovalho, R G; Santos, G S; da Cruz, A D

    2014-04-30

    The central region of Brazil was colonized by internal migration of individuals of different origins, who contributed to the genetic diversity existing in this population. This study determined the allele frequencies and haplotype diversity of Y-STRs in Goiás State, Central Brazil, and compared the data obtained with a sample of the Brazilian population, consisting of individuals from the five geographical regions of Brazil. A total of 353 males were typed for 12 Y-chromosome short tandem repeat (Y-STR) markers. We selected males who had no degree of relatedness, from the five mesoregions of Goiás State. DNA was extracted from blood samples followed by the amplification of the 12 Y-chromosome loci. The products were analyzed to obtain the allele profiles on an ABI3500 automated sequencer using the Gene Mapper software. Allele frequencies and haplotype diversity were estimated by direct counting, and gene diversity for each locus was computed using the Arlequin software. The results are consistent with the history of miscegenation of the population of Central Brazil, in which we observed 321 different haplotypes. The average gene diversity at the 12 loci was 0.645. DYS385b and DYS389I showed the highest (0.704) and lowest (0.520) genetic diversity values, respectively. The FST value between the Brazilian and Goiás populations was 0.00951, showing no statistical significance. The results of this study allowed the establishment of haplotypes found in the forensic samples of Goiás State serving as a reference in the elucidation of criminal cases and paternity tests, as well as population and evolutionary inferences.

  11. Assess drug resistance pattern and genetic profile of Mycobacterium tuberculosis clinical isolates by molecular typing methods using direct repeats and IS6110 in pulmonary tuberculosis cases

    Science.gov (United States)

    Kalo, Deepika; Kant, Surya; Srivastava, Kanchan; Sharma, Ajay K

    2017-01-01

    Background: Tuberculosis (TB), a highly contagious disease that sees no gender, age, or race is mainly a disease of lungs. According to World Health Organization, a TB patient can be completely cured with 6–9 months of anti-TB treatment under directly observed treatment short course. Objectives: The aim of this study was to check the mono, multi- and triple-drug resistance to first line drugs (FLDs) among TB patients and to access their genetic profile using DR 3074, DR 0270, DR 0642, DR 2068, and DR 4110 using molecular techniques. Material and Methods: To gain a better understanding of drug resistant TB, we characterized 121 clinical isolates recovered from 159 drug resistant pulmonary tuberculosis patients by IS6110 genotyping. MTB isolates recovered from HIV- negative, and smear positive cases of both genders, age varied from 18 to 70 years with drug resistant-TB that was refractory to chemotherapy given for > 12 months. Of a total of 159 sputum smear positive patients sum number of male and female patients was 121 (76.10%) and 38 (23.89%), respectively. Among these patients, number of literate and illiterate patients were 123 (77.3%) and 36 (22.6%). 25 (15.7%) patients had farming as their occupation, 80 (50.3%) had nonagricultural occupation and 54 (33.9%) women were housewives. Results: Mono drug resistant, multi-drug resistant, and totally drug resistant (TDR) cases of TB were calculated as 113.83%, 125.1%, and 67.9%. Isoniazid showed the highest percentage of resistance among the patients. Conclusion: Any noncompliance to TB medications, lack of knowledge, and poor management in health centers, etc., results in the emergence of deadly direct repeat forms of TB, which are further complicated and complex to treat. PMID:28360464

  12. GENETIC POLYMORPHISM OF STR LOCI IN CHINESE DRUNGS

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Objective:To study the STR polymorphism in Chinese Drungs.Methods:The genetic distributions of 15 STR loci and Amelogenin locus were generated through coamplification,genescan and genotype from 65 Drungs Results:There were 144 STR and 2 Amelogenin alleles in Drung nationality,with their frequencies ranging from 0.0077 to 0.7846,H0.3723-0.8639,DP0.5567-0.9548,EPP0.2738-0.8358,and PIC 0.3461-0.8456,the accumulative DP 0.9999998and EPP 0.9999894,Conclusion:The study founded a basis for the genetic structure of Chinese ethnic groups ,which is useful for the application to anthropology and forensic science.

  13. GENETIC POLYMORPHISM OF STR LOCI IN CHINESE DRUNGS

    Institute of Scientific and Technical Information of China (English)

    赖江华; 郑海波; 朱波峰; 李生斌

    2002-01-01

    Objective To study the STR polymorphism in Chi nese Drungs. Methods The genetic distributions of 15 STR loci a nd Amelogenin locus were generated through coamplification, genescan and genotyp e from 65 Drungs. Results There were 144 STR and 2 Amelogenin alleles in Drung n ationality, with their frequencies ranging from 0.0077 to 0.7846, H 0.3723~0.8 639, DP 0.5567~0.9548, EPP 0.2738~0.8358, and PIC 0.3461~0.8456, the accumul ative DP 0.99999998 and EPP 0.99999894. Conclusion The study f ounded a basis for the genetic structure of Chinese ethnic group s,which is useful for the application to anthropology and forensic science.

  14. Inferring population structure and demographic history using Y-STR data from worldwide populations.

    Science.gov (United States)

    Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

    2015-02-01

    The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

  15. Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples.

    Science.gov (United States)

    Gibson-Daw, Georgiana; Albani, Patricia; Gassmann, Marcus; McCord, Bruce

    2017-02-01

    In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s. The entire procedure takes less than 25 min from sample collection to result. This paper describes the rapid amplification protocol as well as studies of the reproducibility and sensitivity of the procedure and its optimisation. The amplification process utilises a small high-speed thermocycler, microfluidic device and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The four loci used for the multiplex were selected due to their rapid mutation rates and should proved useful in preliminary screening of samples and suspects. Overall, this technique provides a method for rapid sample screening of suspect and crime scene samples in forensic casework. Graphical abstract ᅟ.

  16. A novel microsatellite (STR) marker for forensic identification of big cats in India.

    Science.gov (United States)

    Singh, Anju; Gaur, Ajay; Shailaja, K; Satyare Bala, B; Singh, Lalji

    2004-05-10

    India is the home to five of the eight majestic big cats of the world. The three major big cats namely, lion, tiger, and leopard are listed in the Schedule I of the Indian Wildlife Protection Act, 1972. Apart from the severe loss of the habitat, these are continuously facing the danger of extinction mainly due to poaching and hunting for their body parts, which are being greatly valued by apothecaries marketing traditional Chinese medicines. With the advent of polymerase chain reaction (PCR), DNA-based markers have emerged as major tools in the arena of wildlife forensics. Microsatellites (short tandem repeats, STRs) are markers of choice because of their polymorphic and co-dominant nature. These strictly follow the Mendelian inheritance and are highly reproducible. We have identified a new microsatellite (STR) locus Ple 46, which shows amplification in a species-specific manner (size of STR) in all the members of the family felidae studied here. This PCR-based, non-invasive method opens a new avenue to forensic identification of big cats.

  17. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

    Science.gov (United States)

    Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cíntia; Salazar, Renato; Angustia, Sheila M.T.; Santos, Lorna H.; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martínez-Jarreta, Begoña; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bäßler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstätter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F.; Domingues, Patricia M.; Chamoun, Wafaa Takash; Coble, Michael D.; Hill, Carolyn R.; Corach, Daniel; Caputo, Mariela; D’Amato, Maria E.; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H.D.; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E.; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rüdiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E.; García, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; Andari, Ansar El; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martín, Pablo; Luque, Gracia M.; Alonso, Antonio; Miranda, Luís Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Neto, Rodrigo S. Moura; Nogueira, Tatiana L.S.; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Núñez, Carolina; Pancorbo, Marian Martínez de; Olofsson, Jill K.; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cárdenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L.; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U.; Guevara, Evelyn; Salvador, Jazelyn; Ungria, Maria Corazon De; Rodriguez, Jae Joseph Russell; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M.; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; Calvit, Lina Solis de; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H.; Gwynne, Gareth M.; Jobling, Mark A.; Whittle, Martin R.; Sumita, Denilce R.; Wolańska-Nowak, Paulina; Yong, Rita Y.Y.; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz

    2014-01-01

    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. PMID:24854874

  18. Identification of an avirulent Entamoeba histolytica strain with unique tRNA-linked short tandem repeat markers.

    Science.gov (United States)

    Escueta-de Cadiz, Aleyla; Kobayashi, Seiki; Takeuchi, Tsutomu; Tachibana, Hiroshi; Nozaki, Tomoyoshi

    2010-03-01

    Highly polymorphic, non-coding short tandem repeats (STR) are scattered between the tRNA genes in Entamoeba histolytica in a unique tandemly arrayed organization. STR markers that correlate with the virulence of individual E. histolytica strains have recently been reported. Here we evaluated the usefulness of tRNA-linked STR loci as genetic markers in identifying virulent and avirulent strains of E. histolytica from 37 Japanese E. histolytica samples (12 diarrheic/dysenteric, 20 amebic liver abscess (ALA), and 5 asymptomatic cases). Twenty three genotypes, assigned by combining the STR sequence types from all 6 STR loci, were identified. One to 8 new STR sequence types per locus were also discovered. Genotypes found in asymptomatic isolates were highly polymorphic (4 out of 5 genotypes were unique to this group), while in symptomatic isolates, almost half of the genotypes were shared between diarrhea/dysentery and ALA. One asymptomatic isolate (KU27) showed unique STR patterns in 4 loci. This strain, though associated with the typical pathogenic zymodeme II, failed to induce amebic liver abscess by animal challenge, which suggests that inherently avirulent E. histolytica strains exist, that are associated with unique genotypes. Furthermore, STR genotyping and in vivo challenge of 2 other asymptomatic isolates (KU14 and KU26) verified the covert virulence of these strains.

  19. Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

    Science.gov (United States)

    Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

    2009-09-01

    Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

  20. Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China.

    Science.gov (United States)

    Yao, Jun; Wang, Bao-Jie

    2016-01-01

    In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

  1. Mutations of short tandem repeat loci in cases of paternity testing in Chinese.

    Science.gov (United States)

    Sun, Mao; Zhang, XiaoNan; Wu, Dan; Shen, Qi; Wu, YuanMing; Fu, ShanMin

    2016-09-01

    In order to find out the characteristics of genetic mutations in 15 short tandem repeat (STR) loci, 3734 parentage cases were analyzed using AmpFlSTR Sinofiler kit. The allele source, mutation rate, and mutation rule of the STR loci were determined. Seventy mutations were observed in all cases for paternity testing. Among 15 STR loci, the highest mutation rate was observed in D12S391 (0.21 %), but the D5S818 gene mutation rate was relatively low (0.02 %). One-step mutation cases accounted for 95.7 % of all of the cases monitored. And the mutations in this study mainly showed paternal mutation (64/70). The research results are of great significance for identification and paternity tests and for the improvement of genetic studies on Chinese population in the future.

  2. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  3. Evaluation and In-House Validation of Five DNA Extraction Methods for PCR-based STR Analysis of Bloodstained Denims

    Directory of Open Access Journals (Sweden)

    Henry Perdigon

    2004-06-01

    Full Text Available One type of crime scene evidence commonly submitted for analysis is bloodstain on denim. However, chemicals (e.g., indigo used to produce denim materials may co-purify with DNA and hence, affect subsequent DNA analysis. The present study compared five methods (e.g., standard organic, organic with hydrogen peroxide (H2O2, modified FTA™, organic/Chelex®-Centricon®, and QIAamp® DNA Mini Kit-based procedures for the isolation of blood DNA from denim. A Short Tandem Repeat (STR-based analysis across two to nine STR markers, namely, HUMvWA, HUMTH01, D8S306, HUMFES/FPS, HUMDHFRP2, HUMF13A01, HUMFGA, HUMTPOX, and HUMCSF1PO, was used to evaluate successful amplification of blood DNA extracted from light indigo, dark indigo, indigo-sulfur, pure indigo, sulfur-top, and sulfur-bottom denim materials. The results of the present study support the utility of organic/Chelex®-Centricon® and QIAamp® Kit procedures in extracting PCR-amplifiable DNA from five different types of denim materials for STR analysis. Furthermore, a solid-based method using FTA™ classic cards was modified to provide a simple, rapid, safe, and cost-effective procedure for extracting blood DNA from light, dark indigo and pure indigo denim materials. However, DNA eluted from bloodstained sulfur-dyed denims (e.g., sulfur-top and sulfur-bottom using FTA™ procedure was not readily amplifiable.

  4. Genetic analysis of 24 Y-STR loci in the Miao ethnic minority from Yunnan Province, southwestern China.

    Science.gov (United States)

    Zhang, Xiufeng; Gu, Tao; Yao, Jinyong; Yang, Canming; Du, Lei; Pang, Jing Bo; Rao, Min; Nie, Aiting; Hu, Liping; Nie, Shengjie

    2017-02-14

    In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 252 unrelated Miao male individuals from Pingbian county, Honghe Hani and Yi Autonomous Prefecture, Yunnan province, southwestern China. The gene diversity of the 24 Y-STR loci in the studied group ranged from 0.2683 (DYS391) to 0.9312 (DYS527a/b). According to haplotypic analysis of the 24 Y-STR loci, 214 different haplotypes were obtained, 186 of which were unique. The overall haplotype diversity and discrimination capacity were calculated to be 0.9983 and 0.8492, respectively. In addition, three different triplications were observed at the DYS527a/b marker, and 1 intermediate allele and six single off-ladder alleles were observed at four markers. We analyzed interpopulation differentiations by making comparisons between the Yunnan Miao ethnic minority and 18 other ethnic groups. The results obtained using pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that Yunnan Miao had a closer genetic relationship with Yunnan Han and Hunan Miao individuals. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationship between Miao individuals and other groups.

  5. Validation of MIPAS-ENVISAT by Correlative Measurements of MIPAS-STR

    Science.gov (United States)

    Keim, C.; Blom, C. E.; von der Gathen, P.; Gulde, T.; Höpfner, M.; Liu, G. Y.; Oulanovski, A.; Piesch, C.; Ravegnani, F.; Sartorius, C.; Schlager, H.; Volk, C. M.

    2004-08-01

    We report on the validation of profiles from the MIPAS-Envisat on-line processor of ESA version 4.61 with correlative measurements derived from MIPASSTR onboard the high-altitude aircraft M55-Geophysica. The validation is made for the July 22, 2002, orbit 2051 in the region of the campaign base in Forlí, Italy [1] and for several orbits in February / March 2003 around Kiruna, northern Sweden. This paper includes a careful comparison of the MIPASSTR data with O3 sondes and with in-situ measurements from the Geophysica obtained during ascent, descent and occasional dives. To obtain accurate N2O and CH4 profiles close to the MIPAS-Envisat tangent points we used the MIPAS-STR measurements of CFC-11 and CFC-12 and correlations [2] obtained by the HAGAR instrument.

  6. A Gamma Model for Mixture STR Samples

    DEFF Research Database (Denmark)

    Christensen, Susanne; Bøttcher, Susanne Gammelgaard; Morling, Niels

    This project investigates the behavior of the PCR Amplification Kit. A number of known DNA-profiles are mixed two by two in "known" proportions and analyzed. Gamma distribution models are fitted to the resulting data to learn to what extent actual mixing proportions can be rediscovered in the amp......This project investigates the behavior of the PCR Amplification Kit. A number of known DNA-profiles are mixed two by two in "known" proportions and analyzed. Gamma distribution models are fitted to the resulting data to learn to what extent actual mixing proportions can be rediscovered...... in the amplifier output and thereby the question of confidence in separate DNA -profiles suggested by an output is addressed....

  7. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

    DEFF Research Database (Denmark)

    Glover, Kevin A.; Hansen, Michael Møller; Lien, Sigbjørn

    2010-01-01

    between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment...

  8. Effects of Applying STR for Group Learning Activities on Learning Performance in a Synchronous Cyber Classroom

    Science.gov (United States)

    Kuo, Tony C. T.; Shadiev, Rustam; Hwang, Wu-Yuin; Chen, Nian-Shing

    2012-01-01

    This study aimed to apply Speech to Text Recognition (STR) for individual oral presentations and group discussions of students in a synchronous cyber classroom. An experiment was conducted to analyze the effectiveness of applying STR on learning performance. Students' perceptions and behavioral intentions toward using STR were also investigated.…

  9. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

    Science.gov (United States)

    Saw, Jimmy H W; Yuryev, Anton; Kanbe, Masaomi; Hou, Shaobin; Young, Aaron G; Aizawa, Shin-Ichi; Alam, Maqsudul

    2012-03-19

    Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

  10. Genetic polymorphism of 21 non-CODIS STR loci in the Chinese Mongolian ethnic minority.

    Science.gov (United States)

    Zha, Lagabaiyila; Liu, Ying; Guo, Yadong; Li, Jun; Wang, Ke; Geng, Kun; Liao, Qiao; Liu, Jinshan; Chen, Hanchun; Cai, Jifeng

    2014-03-01

    In this research, we investigated the allele frequencies and forensic parameters of 21 non-, CODIS short tandem repeat (STR) loci (D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435 and D5S2500) among 523 unrelated, Chinese Mongolians in the city of Tongliao, Horqin district, Inner Mongolia Autonomous Region.

  11. 24 Y-chromosomal STR haplotypic structure for Chinese Kazak ethnic group and its genetic relationships with other groups.

    Science.gov (United States)

    Mei, Ting; Zhang, Li-Ping; Liu, Yao-Shun; Chen, Jian-Gang; Meng, Hao-Tian; Yan, Jiang-Wei; Zhu, Bo-Feng

    2016-09-01

    The Kazak ethnic minority is a large ethnic group in the Xinjiang Uygur Autonomous Region of China and is valuable resource for the study of ethnogeny. In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 201 unrelated Kazak male individuals from Ili Kazak Autonomous Prefecture, Xinjiang, China. The gene diversity of the 24 Y-STR loci in the studied Kazak group ranged from 0.0050 to 0.9104. According to haplotypic analysis of the 24 Y-STR loci, 113 different haplotypes were obtained, 96 of which were unique. The haplotype diversity and discrimination capacity in Kazak group were 0.9578 and 0.5622 at 24 STR loci, respectively. The haplotype diversity and discrimination capacity at Y-filer 17 loci, extended 11 loci, and minimal 9 loci were reduced to 0.9274 and 0.4279, 0.8459 and 0.3284, and 0.8354 and 0.2985, respectively, which could indicate that the more loci were detected, the higher forensic efficacy was obtained. We evaluated the application value of the 24 loci in forensic sciences and analyzed interpopulation differentiations by making comparisons between the Kazak1 (represent our samples from Ili Kazak Autonomous Prefecture) group and other 14 groups. The results of pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that the Kazak1 group had the closer genetic relationships with Kazak2 (represent samples from the whole territory of Xinjiang Uygur Autonomous Region), Mongolian, and Uygur ethnic groups. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationships between Kazak1 and other groups.

  12. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*

    OpenAIRE

    Wang, Hong-Dan; Shen, Chun-Mei; Liu, Wen-Juan; Zhang, Yu-Dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-Xia; Zhu, Bo-Feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capi...

  13. An Undergraduate Laboratory Experiment for Upper-Level Forensic Science, Biochemistry, or Molecular Biology Courses: Human DNA Amplification Using STR Single Locus Primers by Real-Time PCR with SYBR Green Detection

    Science.gov (United States)

    Elkins, Kelly M.; Kadunc, Raelynn E.

    2012-01-01

    In this laboratory experiment, real-time polymerase chain reaction (real-time PCR) was conducted using published human TPOX single-locus DNA primers for validation and various student-designed short tandem repeat (STR) primers for Combined DNA Index System (CODIS) loci. SYBR Green was used to detect the amplification of the expected amplicons. The…

  14. An Undergraduate Laboratory Experiment for Upper-Level Forensic Science, Biochemistry, or Molecular Biology Courses: Human DNA Amplification Using STR Single Locus Primers by Real-Time PCR with SYBR Green Detection

    Science.gov (United States)

    Elkins, Kelly M.; Kadunc, Raelynn E.

    2012-01-01

    In this laboratory experiment, real-time polymerase chain reaction (real-time PCR) was conducted using published human TPOX single-locus DNA primers for validation and various student-designed short tandem repeat (STR) primers for Combined DNA Index System (CODIS) loci. SYBR Green was used to detect the amplification of the expected amplicons. The…

  15. Genetic variation of polymorphic NOS STR locus in ten Indian population groups.

    Science.gov (United States)

    Shazia, A; Nithya, P; Seshadri, M

    2009-02-01

    The genotyping of 313 random individuals belonging to ten different population groups from three different states of India was performed for polymorphic pentanucleotide repeat present in the 5'-flanking region of nitric oxide synthase gene (NOS2A) to study the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Likelihood ratio tests showed that all the ten populations for this locus were in Hardy Weinberg equilibrium. Eleven different alleles ranging from 7 repeat to 17 repeats and 46 different genotypes were observed. The observed and the expected heterozygosity ranged from 0.72-0.94 and 0.84-0.89, respectively. The discriminating power of this locus is > or = 0.86 and the polymorphism information content of this locus in ten population groups ranged from 0.80 to 0.85. High PIC, PD and PE value of this STR showed this marker to be informative and can be used for DNA typing and population studies. The eight populations from Kerala showed a lower GST value of 0.016 compared to the GST of ten populations (G(ST) = 0.019), thereby showing that the populations from the same state showed higher genetic proximity probably due to linguistic and geographical proximity between them.

  16. 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).

  17. MIPAS-STR measurements in the Arctic UTLS in winter/spring 2010: instrument characterization, retrieval and validation

    Directory of Open Access Journals (Sweden)

    W. Woiwode

    2012-06-01

    Full Text Available The mid-infrared FTIR-limb-sounder Michelson Interferometer for Passive Atmospheric Sounding–STRatospheric aircraft (MIPAS-STR was deployed onboard the research aircraft M55 Geophysica during the RECONCILE campaign (Reconciliation of Essential Process Parameters for an Enhanced Predictability of Arctic Stratospheric Ozone Loss and its Climate Interactions in the Arctic winter/spring 2010. From the MIPAS-STR measurements, vertical profiles and 2-dimensional vertical cross-sections of temperature and trace gases are retrieved. Detailed mesoscale structures of polar vortex air, extra vortex air and vortex filaments are identified in the results at typical vertical resolutions of 1 to 2 km and typical horizontal sampling densities of 45 or 25 km, depending on the sampling programme. Results are shown for the RECONCILE flight 11 on 2 March 2010 and are validated with collocated in-situ measurements of temperature, O3, CFC-11, CFC-12 and H2O. Exceptional agreement is found for the in-situ comparisons of temperature and O3, with mean differences (vertical profile/along flight track of 0.2/−0.2 K for temperature and −0.01/0.05 ppmv for O3 and corresponding sample standard deviations of the mean differences of 0.7/0.6 K and 0.1/0.3 ppmv. The comparison of the retrieved vertical cross-sections of HNO3 from MIPAS-STR and the infrared limb-sounder Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere–New Frontiers (CRISTA–NF indicates a high degree of agreement. We discuss MIPAS-STR in its current configuration, the spectral and radiometric calibration of the measurements and the retrieval of atmospheric parameters from the spectra. The MIPAS-STR measurements are significantly affected by continuum-like contributions, which are attributed to background aerosol and broad spectral signatures from interfering trace gases, and are important for mid-infrared limb-sounding in the Upper

  18. MIPAS-STR measurements in the arctic UTLS in winter/spring 2010: instrument characterization, retrieval and validation

    Directory of Open Access Journals (Sweden)

    W. Woiwode

    2011-11-01

    Full Text Available The mid-infrared FTIR-limb-sounder Michelson Interferometer for Passive Atmospheric Sounding – STRatospheric aircraft (MIPAS-STR was deployed onboard the stratospheric aircraft M55 Geophysica during the RECONCILE campaign in the arctic winter/spring 2010. From the MIPAS-STR measurements, vertical profiles and 2-dimensional vertical cross-sections of temperature and trace gases are retrieved. Detailed mesoscale structures of polar vortex air, extra vortex air and vortex filaments are identified in the results at a typical vertical resolution of 1 to 2 km and typical horizontal sampling density of 45 or 25 km, depending on the sampling programme. Results are shown for the RECONCILE flight 11 on 2 March 2010 and are validated with collocated in-situ measurements of temperature, O3, CFC-11, CFC-12 and H2O. Exceptional agreement is found for the in-situ comparisons of temperature and O3, with mean differences (vertical profile/along flight track of 0.2/−0.2 K for temperature and −0.01/0.05 ppmv for O3 and corresponding sample standard deviations of the mean differences of 0.7/0.6 K and 0.1/0.3 ppmv. The comparison of the retrieved vertical cross-sections of HNO3 from MIPAS-STR and the infrared limb-sounder Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere – New Frontiers (CRISTA-NF indicates comprehensive agreement. We discuss MIPAS-STR in its current configuration, the spectral and radiometric calibration of the measurements and the retrieval of atmospheric parameters from the spectra. The MIPAS-STR measurements are significantly affected by continuum-like contributions, which are attributed to background aerosol and broad spectral signatures from interfering trace gases and are important for mid-infrared limb-sounding measurements in the Upper Troposphere/Lower Stratosphere (UTLS region. Considering for continuum-like effects, we present a scheme suitable for accurate

  19. MIPAS-STR measurements in the Arctic UTLS in winter/spring 2010: instrument characterization, retrieval and validation

    Science.gov (United States)

    Woiwode, W.; Oelhaf, H.; Gulde, T.; Piesch, C.; Maucher, G.; Ebersoldt, A.; Keim, C.; Höpfner, M.; Khaykin, S.; Ravegnani, F.; Ulanovsky, A. E.; Volk, C. M.; Hösen, E.; Dörnbrack, A.; Ungermann, J.; Kalicinsky, C.; Orphal, J.

    2012-06-01

    The mid-infrared FTIR-limb-sounder Michelson Interferometer for Passive Atmospheric Sounding-STRatospheric aircraft (MIPAS-STR) was deployed onboard the research aircraft M55 Geophysica during the RECONCILE campaign (Reconciliation of Essential Process Parameters for an Enhanced Predictability of Arctic Stratospheric Ozone Loss and its Climate Interactions) in the Arctic winter/spring 2010. From the MIPAS-STR measurements, vertical profiles and 2-dimensional vertical cross-sections of temperature and trace gases are retrieved. Detailed mesoscale structures of polar vortex air, extra vortex air and vortex filaments are identified in the results at typical vertical resolutions of 1 to 2 km and typical horizontal sampling densities of 45 or 25 km, depending on the sampling programme. Results are shown for the RECONCILE flight 11 on 2 March 2010 and are validated with collocated in-situ measurements of temperature, O3, CFC-11, CFC-12 and H2O. Exceptional agreement is found for the in-situ comparisons of temperature and O3, with mean differences (vertical profile/along flight track) of 0.2/-0.2 K for temperature and -0.01/0.05 ppmv for O3 and corresponding sample standard deviations of the mean differences of 0.7/0.6 K and 0.1/0.3 ppmv. The comparison of the retrieved vertical cross-sections of HNO3 from MIPAS-STR and the infrared limb-sounder Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere-New Frontiers (CRISTA-NF) indicates a high degree of agreement. We discuss MIPAS-STR in its current configuration, the spectral and radiometric calibration of the measurements and the retrieval of atmospheric parameters from the spectra. The MIPAS-STR measurements are significantly affected by continuum-like contributions, which are attributed to background aerosol and broad spectral signatures from interfering trace gases, and are important for mid-infrared limb-sounding in the Upper Troposphere/Lower Stratosphere (UTLS) region. Taking into consideration continuum

  20. Forensic Application of Expressmarker 22 STR Loci Direct PCR Amplification Kit%Expressmarker 22 STR荧光检测试剂盒的法医学应用

    Institute of Scientific and Technical Information of China (English)

    邹凯南; 曹禹; 夏子芳; 郑卫国; 周怀谷

    2012-01-01

    Objective To explore the application value of Expressmarker 22 STR loci direct PCR amplification kit. Methods One thousand nine hundred and forty-eight samples (including samples spotted on FTA cards, filter papers and case samples) were tested using Expressmarker 22 STR loci direct PCR amplification kit. At the same time, all were tested using Sinofiler? kit, Identifiler(R) kit and PowerPlex(R) 16 kit respectively for comparison. The genotypes were compared at the same STR loci among these four kits to test the sensitivity and accuracy of Expressmarker 22 STR loci direct PCR amplification kit. Results 97.79% samples were successfully typed using Expressmarker 22 STR loci direct PCR amplification kit. The genotype profiles of the same samples using Expressmarker 22 STR loci direct PCR amplification kit were consistent with Sinofiler? kit, Identifiler(R) kit and PowerPlex(R) 16 kit at the same STR loci. Conclusion Expressmarker 22 STR loci direct PCR amplification kit can provide huge information and accurate results and be applied to forensic DNA genotyping.%目的 验证Expressmarker 22 STR荧光检测试剂盒的法医学应用价值.方法 取FTA卡、滤纸上保存的建库血样和各类涉案生物性检材1948份,用Expressmarker 22 STR荧光检测试剂盒进行STR分型检测,同时采用SinofilerTM、Identifiler(R)、PowerPlex(R) 16试剂盒进行平行试验.对4个试剂盒相同基因座的分型进行比对,以确认Expressmarker 22 STR荧光检测试剂盒的灵敏度和准确性.结果 Expressmarker 22 STR荧光检测试剂盒的检测成功率为97.79%,同一样本在相同基因座与SinofilerTM、Identifiler(R)、PowerPlex(R) 16试剂盒的STR分型结果相同.结论 利用Expressmarker 22 STR荧光检测试剂盒进行STR分型,信息量大、结果准确可靠.可应用于法庭科学.

  1. Informativeness of the CODIS STR loci for admixture analysis.

    Science.gov (United States)

    Barnholtz-Sloan, Jill S; Pfaff, Carrie L; Chakraborty, Ranajit; Long, Jeffrey C

    2005-11-01

    Population admixture (or ancestry) is used as an approach to gene discovery in complex diseases, particularly when the disease prevalence varies widely across geographic populations. Admixture analysis could be useful for forensics because an indication of a perpetrator's ancestry would narrow the pool of suspects for a particular crime. The purpose of this study was to use Fisher's information to identify informative sets of markers for admixture analysis. Using published founding population allele frequencies we test three marker sets for efficacy for estimating admixture: the FBI CODIS Core STR loci, the HGDP-CEPH Human Genome Diversity Cell Line Panel and the set of 39 ancestry informative SNPS from the Shriver lab at Pennsylvania State University. We conclude that the FBI CODIS Core STR set is valid for admixture analysis, but not the most precise. We recommend using a combination of the most informative markers from the HGDP-CEPH and Shriver loci sets.

  2. Multi-Locus Variable-Number Tandem Repeat Profiling of Salmonella enterica Serovar Typhi Isolates from Blood Cultures and Gallbladder Specimens from Makassar, South-Sulawesi, Indonesia

    NARCIS (Netherlands)

    Hatta, M.; Pastoor, R.; Scheelbeek, P.F.D.; Sultan, A.R.; Dwiyanti, R.; Labeda, I.; Smits, H.L.

    2011-01-01

    Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity

  3. Multi-Locus Variable-Number Tandem Repeat Profiling of Salmonella enterica Serovar Typhi Isolates from Blood Cultures and Gallbladder Specimens from Makassar, South-Sulawesi, Indonesia

    NARCIS (Netherlands)

    Hatta, M.; Pastoor, R.; Scheelbeek, P.F.D.; Sultan, A.R.; Dwiyanti, R.; Labeda, I.; Smits, H.L.

    2011-01-01

    Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity

  4. Vergleichende Wandschubspannungsuntersuchungen in transsonischen Strömungen

    OpenAIRE

    Bose, Shibani

    2002-01-01

    Die vorliegende Arbeit konzentriert sich auf vergleichende Anwendungen bzw. Erweiterungen verschiedener Wandschubspannungsmeßtechniken im Hinblick auf deren Verwendung in transsonischen Strömungen. Die durchgeführte experimentelle Analyse gibt dabei insbesondere Aufschluß über die erzielbare Meßgenauigkeit sowie den Gültigkeitsbereich der jeweiligen Kalibrationsalgorithmen. Hierzu werden verschiedene Wandschubspannungsmeßtechniken, wie der am ILR entwickelte Oberflächendraht, die CPM3-Technik...

  5. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  6. Sensitive DIP-STR markers for the analysis of unbalanced mixtures from "touch" DNA samples.

    Science.gov (United States)

    Oldoni, Fabio; Castella, Vincent; Grosjean, Frederic; Hall, Diana

    2017-05-01

    Casework samples collected for forensic DNA analysis can produce genomic mixtures in which the DNA of the alleged offender is masked by high quantities of DNA coming from the victim. DIP-STRs are novel genetic markers specifically developed to enable the target analysis of a DNA of interest in the presence of exceeding quantities of a second DNA (up to 1000-fold). The genotyping system, which is based on allele-specific amplifications of haplotypes formed by a deletion/insertion polymorphism (DIP) and a short tandem repeat (STR), combines the capacity of targeting the DNA of an individual with a strong identification power. Finally, DIP-STRs are autosomal markers therefore they can be applied to any combination of major and minor DNA. In this study we aimed to assess the ability of DIP-STRs to detect the minor contributor on challenging "touch" DNA samples simulated with representative crime-associated substrates and to compare their performance to commonly used male-specific markers (Y-STRs). As part of a comprehensive study on the relative DNA contribution of two persons handling the same object, we selected 71 unbalanced contact traces of which 14 comprised a male minor DNA contributor mixed to a female major DNA contributor. Using a set of six DIP-STRs, one to four markers were found to be informative for the minor DNA detection across traces. When compared to Y-STRs (14 traces), the DIP-STRs showed similar sensitivity in detecting the minor DNA across substrate materials with a similar occurrence of allele drop-out. Conversely, because of the sex combination of the two users of the object, 57 remaining traces could only be investigated by DIP-STRs. Of these, 30 minor DNA contributors could be detected by all informative markers while 12 traces showed events of allele drop-out. Finally, 15 traces showed no amplification of the minor DNA. These last 15 samples were mostly characterized by a combination of short handling time of the object, low DNA recovery and

  7. Alterations in the baroreceptor-heart rate reflex in conscious inbred polydipsic (STR/N) mice.

    Science.gov (United States)

    Chu, C P; Cui, B R; Kannan, H; Qiu, D L

    2015-01-01

    STR/N is an inbred strain of mice which is known to exhibit extreme polydipsia and polyuria. We previously found central administration of angiotensin II enhanced cardiovascular responses in STR/N mice than normal mice, suggesting that STR/N mice might exhibit different cardiovascular responses. Therefore, in this study, we investigated daily mean arterial blood pressure and heart rate, and changes in the baroreceptor-heart rate reflex in conscious STR/N mice and control (ICR) mice. We found that variability in daily mean arterial blood pressure and heart rate was significantly larger in STR/N mice than in ICR mice (pSTR/N mice than in ICR mice. For baroreceptor reflex sensitivity, in the rapid response period, the slopes of PE and sodium nitroprusside (SNP) were more negative in STR/N mice than in ICR mice. In the later period, the slopes of PE and SNP were negatively correlated between heart rate and blood pressure in ICR mice, but their slopes were positively correlated in STR/N mice. These results indicated that STR/N mice exhibited the different cardiovascular responses than ICR mice, suggesting that the dysfunction of baroreceptor reflex happened in conscious STR/N mice.

  8. Isolation of human minisatellite loci detected by synthetic tandem repeat probes: direct comparison with cloned DNA fingerprinting probes.

    Science.gov (United States)

    Armour, J A; Vergnaud, G; Crosier, M; Jeffreys, A J

    1992-08-01

    As a direct comparison with cloned 'DNA fingerprinting' probes, we present the results of screening an ordered array Charomid library for hypervariable human loci using synthetic tandem repeat (STR) probes. By recording the coordinates of positive hybridization signals, the subset of clones within the library detected by each STR probe can be defined, and directly compared with the set of clones detected by naturally occurring (cloned) DNA fingerprinting probes. The STR probes vary in the efficiency of detection of polymorphic minisatellite loci; among the more efficient probes, there is a strong overlap with the sets of clones detected by the DNA fingerprinting probes. Four new polymorphic loci were detected by one or more of the STR probes but not by any of the naturally occurring repeats. Sequence comparisons with the probe(s) used to detect the locus suggest that a relatively poor match, for example 10 out of 14 bases in a limited region of each repeat, is sufficient for the positive detection of tandem repeats in a clone in this type of library screening by hybridization. These results not only provide a detailed evaluation of the usefulness of STR probes in the isolation of highly variable loci, but also suggest strategies for the use of these multi-locus probes in screening libraries for clones from hypervariable loci.

  9. Characterisation of genetic structure of the Mayan population in Guatemala by autosomal STR analysis.

    Science.gov (United States)

    Martinez-Gonzalez, L J; Alvarez-Cubero, M J; Saiz, M; Alvarez, J C; Martinez-Labarga, C; Lorente, J A

    2016-09-01

    Currently, the Guatemalan population comprises genetically isolated groups due to geographic, linguistic and cultural factors. For example, Mayan groups within the Guatemala population have preserved their own language, culture and religion. These practices have limited genetic admixture and have maintained the genetic identity of Mayan populations. This study is designed to define the genetic structure of the Mayan-Guatemalan groups Kaqchiquel, K'iche', Mam and Q'eqchi' through autosomal short tandem repeat (STR) polymorphisms and to analyse the genetic relationships between them and with other Mayan groups. Fifteen STR polymorphisms were analysed in 200 unrelated donors belonging to the Kaqchiquel (n = 50), K'iche' (n = 50), Mam (n = 50) and Q'eqchi' (n = 50) groups living in Guatemala. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between population groups. Within the Mayan population, the STRs D18S51 and FGA were the most informative markers and TH01 was the least informative. AMOVA and genetic distance analyses showed that the Guatemalan-Native American populations are highly similar to Mayan populations living in Mexico. The Mayan populations from Guatemala and other Native American groups display high genetic homogeneity. Genetic relationships between these groups are more affected by cultural and linguistic factors than geographical and local flow. This study represents one of the first steps in understanding Mayan-Guatemalan populations, the associations between their sub-populations and differences in gene diversity with other populations. This article also demonstrates that the Mestizo population shares most of its ancestral genetic components with the Guatemala Mayan populations.

  10. Study on STR Genotyping of Cell Free DNA in Plasma%血浆游离DNA的STR分型检测研究

    Institute of Scientific and Technical Information of China (English)

    陈阳; 胡利平; 马波; 马立宇; 聂胜洁

    2014-01-01

    目的:探讨利用血浆中游离DNA进行短串联重复序列(short tandem repeat,STR)分型检测,解决法医学个体识别和亲权鉴定问题的可行性。方法采集36例无关健康个体EDTA-Na2抗凝血样,分离血浆,采用经典酚-氯仿法分别处理血浆和血细胞,对提取的DNA进行15个STR基因座常规PCR扩增和荧光标记复合扩增,采用聚丙烯酰胺凝胶电泳和毛细管电泳检测2种STR分型方法进行检测。结果常规PCR扩增银染检测和荧光标记复合扩增毛细管电泳检测两种STR分型方法的结果表明,同一个体的血浆游离DNA和血细胞DNA STR分型一致,且分型效果接近。结论血浆游离DNA可作为一种有效的生物学样本进行STR分型检测,应用于法医个体识别和亲权鉴定。%Objective The purpose of this study was to investigate the feasibility of short tandem repeat(STR) genotyping of cell free DNA in plasma for individual identification and paternity testing. Methods EDTA-Na2 DNA anti-coagulant blood samples were collected from 36 unrelated healthy volunteers,and both DNA in leukocytes and cell free DNA in plasma were extracted respectively using phenol-chloroform method. Target DNA in blood cells and plasma were amplified using regular STR typing and fluorescent multiplex STR assay separately,accordingly,the PCR products were analyzed by polyacrylamide gel electrophoresis and capillary electrophoresis. Results Using either normal PCR-STR or fluorescent multiplex STR assay,the consistent STR genotyping results were detected with similar efficiency for cell DNA and plasma DNA samples from the same individual. Conclusion Cell free DNA in plasma samples can be used as useful biological samples for STR genotyping,which can be applied to individual identification and paternity testing in forensic practice.

  11. 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.

  12. Multi-locus variable-number tandem repeat profiling of Salmonella enterica serovar Typhi isolates from blood cultures and gallbladder specimens from Makassar, South-Sulawesi, Indonesia.

    Directory of Open Access Journals (Sweden)

    Mochammad Hatta

    Full Text Available Multi-locus variable-number tandem repeat analysis differentiated 297 Salmonella enterica serovar Typhi blood culture isolates from Makassar in 76 genotypes and a single unique S. Typhi genotype was isolated from the cholecystectomy specimens of four patients with cholelithiasis. The high diversity in S. Typhi genotypes circulating in Makassar indicates that the number of carriers could be very large, which may complicate disease prevention and control.

  13. Virulence Gene Profile and Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) of Enteroinvasive Escherichia coli (EIEC) Isolates From Patients With Diarrhea in Kerman, Iran

    OpenAIRE

    Hosseini Nave, Hossein; Mansouri, Shahla; Taati Moghadam, Majid; Moradi, Mohammad

    2016-01-01

    Background Enteroinvasive Escherichia coli (EIEC) isolates cause dysentery in humans. Several virulence factors associated with EIEC pathogenesis have been characterized. Multilocus variable-number tandem-repeat analysis (MLVA) is a PCR-based method that has been used for genotyping bacterial pathogens. Objectives The aim of this study was to investigate the distribution of virulence factor genes in EIEC isolates from patients with diarrhea in Kerman, Iran, as well as the genetic relationship...

  14. Study of the genus Cephennium Müler & Kunze, 1822 (Coleoptera, Staphylinidae, Scydmaeninae) from the Balkan Peninsula. Part II. New species of the subgenus Cephennium s. str.

    Science.gov (United States)

    Stevanović, Miroslav

    2014-07-18

    Twelve new species of the genus Cephennium Müler & Kunze, 1822 are described: C. (s. str.) irenae sp. n. (from Serbia, Bosnia and Herzegovina, and Montenegro); C. (s. str.) sladjanae sp. n. and C. (s. str.) fallax sp. n. (both from Serbia and Bulgaria); C. (s. str.) viti sp. n. (from Serbia, Macedonia, Greece and Bulgaria); C. (s. str.) fairchildi sp. n., C. (s. str.) ivanjicense sp. n., C. (s. str.) serbicum sp. n. and C. (s. str.) remisianum sp. n. (all from Serbia); C. (s. str.) assingi sp. n. and C. (s. str.) angelinii sp. n. (both from Greece); C. (s. str.) mlejneki sp. n. (from Montenegro) and C. (s. str.) vitoshae sp. n. (from Bulgaria). Aedeagi and male protibiae of all species are illustrated. Cephennium (s. str.) bosnicum Ganglbauer, 1899 is redescribed and its lectotype is designated.

  15. Population genetic data of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS STR loci in four Canadian populations.

    Science.gov (United States)

    Laurin, Nancy; Milot, Emmanuel

    2014-03-01

    Allele frequencies and forensically relevant population statistics were estimated for the short tandem repeat (STR) loci of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS amplification kits, including D2S1338, D19S433, Penta D, and Penta E, for three First Nations Aboriginal populations and for Caucasians in Canada. The cumulative power of discrimination was ≥ 0.999999999999984 and the cumulative power of exclusion was ≥ 0.999929363 for both amplification systems in all populations. No significant departure from Hardy-Weinberg equilibrium was detected for D2S1338, D19S433, Penta D, and Penta E or the 13 Combined DNA Index System core STR loci after correction for multiple testing. Significant genetic diversity was observed between these four populations. Comparison with published frequency data for other populations is also presented.

  16. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    Science.gov (United States)

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  17. Genetic polymorphisms of 26 Y-STR loci in the Mongolian minority from Horqin district, China.

    Science.gov (United States)

    Fu, Xiaoliang; Fu, Yong; Liu, Ying; Guo, Juanjuan; Liu, Yanfang; Guo, Yadong; Yan, Jie; Cai, Jifeng; Liu, Jinshan; Zha, Lagabaiyila

    2016-07-01

    To study the population data of Y chromosome STR (Y-STRs) of the Mongolian minority population residing in the Horqin district, we analyzed haplotypes of 26 Y-STRs (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, DYS388, DYS449, DYS460, and YGATAH4) in 298 unrelated Chinese Mongolian individuals using the commercially available Goldeneye® DNA ID 26Y system. We also investigated blood stains, saliva spots, semen spots, hair follicles, fingernails, and sweat latent fingerprints from ten healthy males for testing the efficiency of direct amplification of this new Y-STRs system. The calculated average gene diversity values of the Mongolian population ranged from 0.3024 to 0.9510 for the DYS389I and DYS385a/b loci, respectively. The discriminatory capacity was 92.95 % with 277 observed haplotypes using 23 Y-STR loci (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4). By adding three more Y-STRs (DYS388, DYS449, and DYS460) to the 26Y system, the discriminatory capacity was increased to 94.63 % with a total of 282 observed haplotypes. Population relationships were calculated and compared with seven populations available from the Y chromosome haplotype reference database and data from ten Asian populations published previously. The Mongolian minority population residing in Horqin district is significantly different from other populations. Our results indicated that these 26 Y-STRs were highly genetically polymorphic in the Mongolian group and this contributes greatly to existing Chinese ethnic genetic information. As a result of direct amplification, we have obtained full profile from all blood stains, saliva spots, hair follicles, and fingernails; six semen spots; and one sweat latent fingerprint. It revealed

  18. 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

    DEFF Research Database (Denmark)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter

    2016-01-01

    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......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...

  19. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  20. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  1. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Oussama Ahrazem; Benjamin Viñegla; Juan C. Linares; Lourdes Gómez-Gómez; David Candel-Perez; Tiscar, Pedro A.; Lucas-Borja, Manuel E.; Angela Rubio-Moraga

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina...

  2. 17 to 23: A novel complementary mini Y-STR panel to extend the Y-STR databases from 17 to 23 markers for forensic purposes.

    Science.gov (United States)

    Núñez, Carolina; Baeta, Miriam; Ibarbia, Nerea; Ortueta, Urko; Jiménez-Moreno, Susana; Blazquez-Caeiro, José Luis; Builes, Juan José; Herrera, Rene J; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

    2017-04-01

    A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evidences of the suitability of this novel Y-STR system for forensic purposes. Thus, the use of this multiplex for samples previously genotyped with 17 Y-STRs will be an efficient and low-cost alternative to complete the set of 23 Y-STRs and improve allele databases for population and forensic purposes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Genetic diversity of Pinus nigra Arn. populations in Southern Spain and Northern Morocco revealed by inter-simple sequence repeat profiles.

    Science.gov (United States)

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E; Tiscar, Pedro A; Viñegla, Benjamin; Linares, Juan C; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei's genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei's genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups-Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco-while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  4. Self-cloning in Streptomyces griseus of an str gene cluster for streptomycin biosynthesis and streptomycin resistance.

    OpenAIRE

    Ohnuki, T; Imanaka, T; Aiba, S

    1985-01-01

    An str gene cluster containing at least four genes (strR, strA, strB, and strC) involved in streptomycin biosynthesis or streptomycin resistance or both was self-cloned in Streptomyces griseus by using plasmid pOA154. The strA gene was verified to encode streptomycin 6-phosphotransferase, a streptomycin resistance factor in S. griseus, by examining the gene product expressed in Escherichia coli. The other three genes were determined by complementation tests with streptomycin-nonproducing muta...

  5. One Percent Strömvil Photometry in M 67

    Science.gov (United States)

    Philip, A. G. D.; Boyle, R. P.; Janusz, R.

    2005-05-01

    The Vatican Advanced Technology Telescope on Mt. Graham is being used in a program of CCD photometry of open and globular clusters. We are using the Ströomvil System (Straižys et al. 1996), a combination of the Strömgren and Vilnius Systems. This system allows stars to be classified as to temperature, surface gravity, metallicity and reddening from the photometric measures alone. However, to make accurate estimates of the stellar parameters the photometry should be accurate to 1 or 1.5 percent. In our initial runs on the VATT we did not achieve this accuracy. The problem turned out to be scattered light in the telescope and this has now been reduced so we can do accurate photometry. Boyle has written a routine in IRAF which allows us to correct the flats for any differences. We take rotated frames and also frames which are offset in position by one third of a frame, east-west and north-south. Measures of the offset stars give us the corrections that need to be made to the flat. Robert Janusz has written a program, the CommandLog, which allows us to paste IRAF commands in the correct order to reduce measures made on a given observing run. There is an automatic version where one can test various parameters and get a set of solutions. Now we have a set of Strömvil frames in the open cluster, M 67 and we compare our color-magnitude diagram with those of BATC (Fan et al. 1996) and Vilnius (Boyle et al. 1998). A preliminary report of the M 67 photometry will be found in Laugalys et al. (2004). Here we report on a selected set of stars in the M 67 frames, those with errors 1 percent or less.

  6. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    Directory of Open Access Journals (Sweden)

    David H. Warshauer

    2015-08-01

    Full Text Available Massively parallel sequencing (MPS technology is capable of determining the sizes of short tandem repeat (STR alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics. The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

  7. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    Institute of Scientific and Technical Information of China (English)

    David H Warshauer; Jennifer D Churchill; Nicole Novroski; Jonathan L King; Bruce Budowle

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

  8. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    Directory of Open Access Journals (Sweden)

    Oussama Ahrazem

    2012-05-01

    Full Text Available Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  9. Diversity of five novel Y-STR loci and their application in studies of north Chinese populations

    Indian Academy of Sciences (India)

    Zhaoyang Xu; Haiming Sun; Yang Yu; Yan Jin; Xaingning Meng; Donglin Sun; Jing Bai; Feng Chen; Songbin Fu

    2010-04-01

    Y-chromosomal short tandem repeats (Y-STRs) show sufficient variability among individuals in a population and high degree of geographical differentiation, so their polymorphic character makes them especially suited for population genetic studies. In this study, five novel Y-STR loci were analysed in 174 samples from five minority populations residing in north China (Daur, Kazak, Xibe, Uighur and Kirgiz) to determine the diversity of these loci in north China and to evaluate their usefulness in population study. Ninety-seven haplotypes were constructed, with 30 in Daur, 24 in Kazak, 28 in Uighur, 27 in Xibe and 16 in Kirgiz. Sixty-six (68.04%) of them were unique. The $R_{\\text{ST}}$ showed that there was no significant difference in Daur and Xibe ($R_{\\text{ST}} = 0.02231$, $P \\gt 0.05$), while among the Kazak, Uighur and Kirgiz, who reside in northwest China, there were significant differences. These results showed that these five Y-STR loci were polymorphic in the five populations. The results of AMOVA showed that majority of the differences were found within populations. By $R_{\\text{ST}}$, the relationships of the five populations were accordance with the historical records: Xibe migrated to Xinjiang during the Qing Dynasty, and Kazak, Uighur and Kirgiz have different ancestors.

  10. MiniSTR multiplex systems based on non-CODIS loci for analysis of degraded DNA samples.

    Science.gov (United States)

    Asamura, H; Fujimori, S; Ota, M; Fukushima, H

    2007-11-15

    We describe two short amplicon autosomal short tandem repeat (miniSTR) quadruplex systems for eight loci D1S1171, D2S1242, D3S1545, D4S2366, D12S391, D16S3253, D20S161, and D21S1437, unlinked from the combined DNA index system (non-CODIS) loci, using newly designed primer sets. The results of an assay of 411 Japanese individuals showed that polymerase chain reaction (PCR) products within the eight loci were less than 150bp in size, without the seven additional bases for adenylation. The frequency distributions in the loci showed no deviations from Hardy-Weinberg equilibrium expectations. The accumulated power of discrimination and power of exclusion for the eight loci were 0.9999999991 and 0.998, respectively. For assay of highly degraded DNA, including artificially degraded samples and the degraded forensic casework samples assessed with the present miniSTR quadruplex systems, the systems proved quite effective in analyzing degraded DNA.

  11. Forensic DNA profiling and database.

    Science.gov (United States)

    Panneerchelvam, S; Norazmi, M N

    2003-07-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  12. Forensic DNA Profiling and Database

    OpenAIRE

    Panneerchelvam, S.; Norazmi, M. N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  13. Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise.

    Science.gov (United States)

    Robino, C; Ralf, A; Pasino, S; De Marchi, M R; Ballantyne, K N; Barbaro, A; Bini, C; Carnevali, E; Casarino, L; Di Gaetano, C; Fabbri, M; Ferri, G; Giardina, E; Gonzalez, A; Matullo, G; Nutini, A L; Onofri, V; Piccinini, A; Piglionica, M; Ponzano, E; Previderè, C; Resta, N; Scarnicci, F; Seidita, G; Sorçaburu-Cigliero, S; Turrina, S; Verzeletti, A; Kayser, M

    2015-03-01

    Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative exercise aimed at generating an Italian quality controlled forensic RM Y-STR haplotype database. Overall 1509 male individuals from 13 regional populations covering northern, central and southern areas of the Italian peninsula plus Sicily were collected, including both "rural" and "urban" samples classified according to population density in the sampling area. A subset of individuals was additionally genotyped for Y-STR loci included in the Yfiler and PowerPlex Y23 (PPY23) systems (75% and 62%, respectively), allowing the comparison of RM and conventional Y-STRs. Considering the whole set of 13 RM Y-STRs, 1501 unique haplotypes were observed among the 1509 sampled Italian men with a haplotype diversity of 0.999996, largely superior to Yfiler and PPY23 with 0.999914 and 0.999950, respectively. AMOVA indicated that 99.996% of the haplotype variation was within populations, confirming that genetic-geographic structure is almost undetected by RM Y-STRs. Haplotype sharing among regional Italian populations was not observed at all with the complete set of 13 RM Y-STRs. Haplotype sharing within Italian populations was very rare (0.27% non-unique haplotypes), and lower in urban (0.22%) than rural (0.29%) areas. Additionally, 422 father-son pairs were investigated, and 20.1% of them could

  14. 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

  15. Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

    Science.gov (United States)

    Watanabe, G; Umetsu, K; Yuasa, I; Suzuki, T

    2000-06-01

    We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

  16. Evaluation of 12 Y-chromosome STR loci in Western Mediterranean populations

    DEFF Research Database (Denmark)

    Rodriguez, V.; Tomas, Carmen; Sanchez, Juan J.;

    2008-01-01

    With the aim to establish a Y-STR haplotype database, a total of 554 males from seven Western Mediterranean populations were genotyped for the 12 Y-chromosome STR loci (minimal haplotype extended by loci DYS437, DYS438 and DYS439) included in the Powerplex Y System (Promega). Among the 554 males ...

  17. A framework for the development of STR genotyping in domestic animal species

    DEFF Research Database (Denmark)

    van Asch, Barbara; Pinheiro, Raquel; Pereira, Rui

    2010-01-01

    offspring. Its use may complement the information obtained by autosomal STR analysis and contribute to the resolution of complex cases of kinship in dogs. The presented methodology for the de novo construction of an STR multiplex may also provide a helpful framework for analogous work in other animal...

  18. Variation of autosomes and X chromosome STR in breast cancer and gynecological cancer tissues

    Directory of Open Access Journals (Sweden)

    Hou Youxiang

    2017-04-01

    Full Text Available This study analyses 1000 cases of patients with breast cancer and 2000 cases of patients with gynecological cancer (1000 cases of malignant tumor, 1000 cases of benign tumors, where breast cancer and malignant tumor patients comprise the observation group, while patients with benign tumors comprise the control group. Through DNA extraction, STR genotyping and variation verification, microdissection, individual STR mutation rate and loci STR mutation rate of the two groups of patients were calculated. Results show that there are no significant (P > 0.05 differences in the STR variation of autosomes and X chromosome between patients in the observation group and those in the reference group. However, significant (P < 0.05 intergroup differences were found for STR variation typing between patients with malignant and benign tumors. Using STR genotyping for autosomes and X chromosomes, gynecological cancer patients were found to be more likely to mutate, with a clear relationship between STR variation and tumor differentiation degrees. The study on the variation analysis of autosomes and X chromosome STR in breast and gynecological cancer tissues is expected to have a high application value when applied to medical research and identification processes.

  19. Bengt Strömgren: Growing up with astronomy, 1908-1932

    DEFF Research Database (Denmark)

    Rebsdorf, S.O.

    2003-01-01

    Bengt Strömgren's (1908-1987) early career is examined down to 1932, the year of his first landmark article on astrophysics, in which, continuing the numerical tradition at the Copenhagen Observatory, Strömgren applied the still novel quantum mechanics with great faith in its validity. In additio...

  20. Bengt Strömgren: Growing up with astronomy, 1908-1932

    DEFF Research Database (Denmark)

    Rebsdorf, S.O.

    2003-01-01

    Bengt Strömgren's (1908-1987) early career is examined down to 1932, the year of his first landmark article on astrophysics, in which, continuing the numerical tradition at the Copenhagen Observatory, Strömgren applied the still novel quantum mechanics with great faith in its validity. In additio...

  1. Modellering af strømningsforhold og kanaldannelse i fixed bed koksbed

    DEFF Research Database (Denmark)

    Jensen, Torben Kvist; Henriksen, Ulrik Birk; Gøbel, Benny;

    2003-01-01

    For at kunne undersøge stabiliteten af en koksbed er der blevet udviklet forskellige modeller til beskrivelse af strømningsforholdene i bedden under iltfri forgasning af biomassekoks. Strømningsforholdene er blevet undersøgt på simple modeller og CFD-modeller...

  2. Combining autosomal and Y-chromosomal short tandem repeat data in paternity testing with male child: methods and application.

    Science.gov (United States)

    Ayadi, Imen; Mahfoudh-Lahiani, Nadia; Makni, Hafedh; Ammar-Keskes, Leila; Rebaï, Ahmed

    2007-09-01

    Paternity testing is being increasingly requested with the aim of challenging presumptive fatherhood. The ability to establish the biological father is usually based on the genotyping of autosomal short tandem repeat (STR) in alleged father, mother and child, but the use of Y-chromosomal STR has gained interest in the last few years. In this work, we propose a new probabilistic approach that combines autosomal and Y-chromosomal STR data in paternity testing with father/son pairs taking into account mutation events. We also suggest a new two-stage approach where we first type Y-STRs and possibly autosomal STR for the putative father and son, conditional on Y-STR results. We applied this approach to 22 cases. Our results show that Y-STRs can identify nonpaternity cases with high accuracy but need to be validated with autosomal STR to establish paternity. Moreover, the two-stage approach is less costly than the standard approach and is very useful in motherless cases.

  3. [Genetic variability and phylogenetic analysis of 39 short tandem repeat loci in Beijing Han population].

    Science.gov (United States)

    Xiuyan, Ruan; Weini, Wang; Yaran, Yang; Bingbing, Xie; Jing, Chen; Yacheng, Liu; Jiangwei, Yan

    2015-07-01

    In this study, we studied the genetic polymorphisms of short tandem repeat (STR) loci from 13 CODIS and 26 non-CODIS system in Beijing Han population for the first time, and established a database of 39 STR loci whose forensic parameters were further evaluated. Our results demonstrated no significant deviation from the Hardy-Weinberg equilibrium of 39 STR loci and no pairwise linkage disequilibrium between them. The power of discriminations, expected heterozygosity, polymorphic information content, and power of exclusion of 39 STR loci ranged from 0.7740-0.9818, 0.6000-0.9350, 0.5317-0.9047 and 0.2909-0.8673. The cumulated discrimination power and cumulative probability of exclusion were 0.999999999999999999999999999999999999999964971 and 0.999999999973878, respectively. Moreover, the genetic distance was calculated based on allele frequency and phylogenetic tree was built using STR loci data from Beijing Han and other 11 Chinese ethnic groups.This study provides important basic data for Chinese forensic DNA database and population genetics database, and has important significance in carrying out forensic individual identification, paternity testing, and population genetic study.

  4. Assessment of application value of 19 autosomal short tandem repeat loci of GoldenEye 20A kit in forensic paternity testing.

    Science.gov (United States)

    Huang, Yan-Mei; Wang, Jie; Jiao, Zhangping; Yang, Liu; Zhang, Xinning; Tang, Hui; Liu, Yacheng

    2013-05-01

    This study was carried out to assess the application value of 19 autosomal short tandem repeat (STR) loci of GoldenEye 20A kit, in which 13 combined DNA index system core STR loci and PentaE, PentaD, D2S1338, D19S433, D12S391, and D6S1043 of six STR loci could be used in forensic paternity testing in Chinese population. We amplified the genomic DNA from blood samples on FTA paper of 289 paternity testing cases by using the GoldenEye 20A kit. The amplified products were detected by capillary electrophoresis, and then the genotypes of 20 genetic markers including 19 STR loci as well as Amelogenin for sex determination were analyzed by GeneMapper v3.2 and GeneMarker HID Software. The results of genotypes were compared to the three commonly used commercial kits including AmpFℓSTR Identifiler, PowerPlex16, and AmpFℓSTR Sinofiler kits. Compared to the three other common commercial kits, the GoldenEye 20A kit had higher value of combined paternity index in certainty of paternity or non-exclusion paternity cases, and more numbers of STR loci were excluded in exclusionary paternity cases. Our data in this study showed that the GoldenEye 20A kit has a higher application value in forensic paternity testing and will be of help for kinship analysis.

  5. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Hong-dan WANG; Chun-mei SHEN; Wen-juan LIU; Yu-dang ZHANG; Guang YANG; Jiang-wei YAN; Hai-xia QIN

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus,which are not included in the combined DNA index system (CODIS),in a Russian ethnic minority group from the Inner Mongolia Autonomous Region,China.A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system.Using capillary electrophoresis,the PCR products of the 21 STR loci were separated and genotyped.A total of 161 alleles were observed in the Russian ethnic minority group,and corresponding allelic frequencies ranged from 0.0044 to 0.5965.The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background,for individual identification,and for paternity testing in forensic practice.

  6. PE-Swab Direct STR Amplification of Forensic Touch DNA Samples.

    Science.gov (United States)

    Liu, Jason Y

    2015-05-01

    The PE-Swab direct STR amplification workflow was developed to process low-level "touch DNA" samples. In this workflow, a forensic sample is first collected on a 4-mm PE-Swab (a novel sample collection device); two 2-mm punches containing collected samples are then generated from the PE-Swab and directly amplified for STR typing. Compared to the conventional STR workflow, which involves DNA extraction, purification, and elution volume reduction, the PE-Swab direct STR amplification workflow does not require sample preparation and takes DNA loss due to sample preparation, the PE-Swab workflow is more sensitive than the conventional STR workflow. The average peak height per sample obtained by the PE-swab workflow is 3 times higher than that from the conventional workflow with both low-level single source and two-contributor mixture samples tested in this study. © 2015 American Academy of Forensic Sciences.

  7. Genetic Polymorphisms of Nine X-STR Loci in Four Population Groups from Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Qiao-Fang Hou; Bin Yu; Sheng-Bin Li

    2007-01-01

    Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

  8. A novel approach in personal identification from tissue samples undergone different processes through STR typing.

    Science.gov (United States)

    Staiti, N; Di Martino, D; Saravo, L

    2004-12-01

    Short tandem repeats (STRs) or microsatellites have been recognized worldwide as a powerful tool for human identification. They have become widely used in human identification especially in criminal cases and mass disasters. Police departments are often interested in cases where tissues are already decomposed and only do bones remain to let them perform laboratory analyses. Bone is the most resistant tissue in animal body to time depending degradation and putrefaction, but it is often hard to extract DNA from it because of its highly mineralized structure, which makes DNA extraction and/or amplification hard to carry out. We have performed human nuclear DNA extraction and STR typing in three different cases, on bones and bone fragments from long time dead persons found buried, in the sea, almost completely burnt and whose tissues were already decomposed. We report these caseworks as we would like to show how forensic scientists are improving their skill in identifying people whose corps have undergone several kinds of processes, even independently on the time passed and the level of putrefaction of their tissues.

  9. Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

    Directory of Open Access Journals (Sweden)

    Joseph Schlecht

    2008-06-01

    Full Text Available Genetic variation on the non-recombining portion of the Y chromosome contains information about the ancestry of male lineages. Because of their low rate of mutation, single nucleotide polymorphisms (SNPs are the markers of choice for unambiguously classifying Y chromosomes into related sets of lineages known as haplogroups, which tend to show geographic structure in many parts of the world. However, performing the large number of SNP genotyping tests needed to properly infer haplogroup status is expensive and time consuming. A novel alternative for assigning a sampled Y chromosome to a haplogroup is presented here. We show that by applying modern machine-learning algorithms we can infer with high accuracy the proper Y chromosome haplogroup of a sample by scoring a relatively small number of Y-linked short tandem repeats (STRs. Learning is based on a diverse ground-truth data set comprising pairs of SNP test results (haplogroup and corresponding STR scores. We apply several independent machine-learning methods in tandem to learn formal classification functions. The result is an integrated high-throughput analysis system that automatically classifies large numbers of samples into haplogroups in a cost-effective and accurate manner.

  10. Allelic structure and distribution of 103 STR loci in a Southern Tunisian population

    Indian Academy of Sciences (India)

    Abdellatif Maalej; Ahmed Rebai; Adnen Ayadi; Jomaa Jouida; Hafedh Makni; Hammadi Ayadi

    2004-04-01

    Genotypes of 103 short tandem repeat (STR) markers distributed at an average of 40 cM intervals throughout the genome were determined for 40 individuals from the village of BirEl Hfai (BEH). This village of approximately 31.000 individuals is localized in the south-west of Tunisia. The allele frequency distributions in BEH were compared with those obtained for individuals in the CEPH (Centre d’Etude du Polymorphisme Humain) data using a Kolmogorov–Smirnov two-sample test. Fourteen out of the 103 markers (13.2%) showed significant differences ($P\\lt 0.05$) in distribution between the two populations. Population heterogeneity in BEH was indicated by an excess of observed homozygosity deviations from Hardy–Weinberg equilibrium at 3 loci ($P\\lt 0.0005$). No evidence for genotypic disequilibrium was found for any of the marker pairs. This demonstrated that in spite of a high inbreeding level in the population, few markers showed evidence for a different pattern of allelic distribution compared to CEPH.

  11. Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China.

    Science.gov (United States)

    Hou, Qiao-Fang; Yu, Bin; Li, Sheng-Bin

    2007-02-01

    Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance between Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

  12. Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

    Science.gov (United States)

    Venables, Samantha J; Daniel, Runa; Sarre, Stephen D; Soedarsono, Nurtami; Sudoyo, Herawati; Suryadi, Helena; van Oorschot, Roland A H; Walsh, Simon J; Widodo, Putut T; McNevin, Dennis

    2016-01-01

    Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.

  13. Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms

    Science.gov (United States)

    Vermeulen, Mark; Wollstein, Andreas; van der Gaag, Kristiaan; Lao, Oscar; Xue, Yali; Wang, Qiuju; Roewer, Lutz; Knoblauch, Hans; Tyler-Smith, Chris; de Knijff, Peter; Kayser, Manfred

    2012-01-01

    We analysed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely-studied simple single-copy (ss)Y-STRs and 18 widely-used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3-16 markers in regional datasets (89.6-100% resolution). From the 49 rarely-studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3-15 markers in the regional datasets (85.4-100%). Considerably lower haplotype resolutions were obtained with the three commonly-used Y-STR sets (Minimal Haplotype, PowerPlex Y®, and AmpFlSTR® Yfiler®). Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or – together with additional ssY-STRs - as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from ~4.8×10−4 for 31 ssY-STRs with no mutations observed to 1.3×10−2 and 1.5×10−2 for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly-used Y-STR sets, and support their application to forensic, genealogical and anthropological studies. PMID:19647704

  14. Population genetics of 17 Y-STR markers in Turkish Cypriots from Cyprus.

    Science.gov (United States)

    Teralı, K; Zorlu, T; Bulbul, O; Gurkan, C

    2014-05-01

    We analyzed seventeen Y-chromosomal short tandem repeats (STRs) [DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448] in 253 unrelated, male individuals from the Turkish Cypriot population of the Eastern Mediterranean island of Cyprus. While 206 out of the 253 haplotypes present in the dataset were unique, there are also 22 haplotypes that were observed in two individuals each, and 1 haplotype that was observed in three individuals. While no locus duplications or null alleles were observed in our dataset, we have detected 43 allelic variants in total, the majority of which (25 out of 253 haplotypes or 9.88%) comprised of .2 intermediate variants at the DYS458 locus (alleles 16.2, 17.2, 18.2, 19.2, and 20.2). For the 229 different haplotypes observed in the Turkish Cypriot dataset, the calculated discrimination capacity (DC) was 0.9051 and the haplotype diversity (HD) was 0.9992. The calculated average gene diversity (GD) values ranged from 0.3828 to 0.9631 for the DYS392 and DYS385a/b loci, respectively. Pairwise genetic distance comparisons of the Turkish Cypriot Y-STR dataset with those from the neighbouring (Turkey, Greece, Israel/Palestinian Authority area, Egypt and Italy) and relatively distant (Lithuania, Taiwan and Australia) countries through the use of analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) analyses confirmed that our data do not deviate significantly from the typical core haplotypes of the Eastern Mediterranean region. The Turkish Cypriot Y-STR haplotype dataset will find an immediate use in the Committee on Missing Persons in Cyprus Project on the "Exhumation, Identification and Return of Remains of Missing Persons" and it is also expected to contribute to the establishment of forensic genetic services in North Cyprus.

  15. Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains.

    Science.gov (United States)

    Ambers, Angie; Turnbough, Meredith; Benjamin, Robert; Gill-King, Harrell; King, Jonathan; Sajantila, Antti; Budowle, Bruce

    2016-01-01

    Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors. Published by Elsevier Ireland Ltd.

  16. Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.

    Science.gov (United States)

    Iacovacci, Giuseppe; D'Atanasio, Eugenia; Marini, Ornella; Coppa, Alfredo; Sellitto, Daniele; Trombetta, Beniamino; Berti, Andrea; Cruciani, Fulvio

    2017-03-01

    By using the recently introduced 6-dye Yfiler(®) Plus multiplex, we analyzed 462 males belonging to 20 ethnic groups from four eastern African countries (Eritrea, Ethiopia, Djibouti and Kenya). Through a Y-STR sequence analysis, combined with 62 SNP-based haplogroup information, we were able to classify observed microvariant alleles at four Y-STR loci as either monophyletic (DYF387S1 and DYS458) or recurrent (DYS449 and DYS627). We found evidence of non-allelic gene conversion among paralogous STRs of the two-copy locus DYF387S1. Twenty-two diallelic and triallelic patterns observed at 13 different loci were found to be significantly over-represented (p<10(-6)) among profiles obtained from cell lines compared to those from blood and saliva. Most of the diallelic/triallelic patterns from cell lines involved recurrent mutations at rapidly mutating loci (RM Y-STRs) included in the multiplex (p<10(-2)). At haplotype level, intra-population diversity indices were found to be among the lowest so far reported for the Yfiler(®) Plus, while statistically significant differences among countries and ethnic groups were detected when considering haplotype frequencies alone (FST) or by using molecular distances among haplotypes (ΦST). The strong population subdivision observed is probably the consequence of the patrilineal social organization of most eastern African ethnic groups, and suggests caution in the use of country-based haplotype frequency distributions for forensic inferences in this region.

  17. Population variation at the CODIS core short tandem repeat loci in Europeans.

    Science.gov (United States)

    Budowle, B; Chakraborty, R

    2001-03-01

    Substantial STR population data exist to estimate F(ST) (or theta) values across Europeans. Eleven populations across Europe were analyzed, and the estimate over all 13 CODIS core STR loci is 0.0028. This value is much less than the conservative estimate of 0.01 advocated by the second National Research Council Report in 1996. Because of the low value for theta, whether independence is assumed or an adjustment for substructure is employed, there is little practical consequence for forensic purposes for estimating the frequency of a multiple locus DNA profile. If theta is used, a value of 0.01 is very conservative for Europeans. The same STR population data can be used for evolutionary studies on Europeans, and the calculated genetic distances are consistent with the ethnohistory of the populations.

  18. 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.

  19. 超高分辨率OCT角膜上皮厚度自动测量的重复性研究%Study of repeatability of corneal epithelium thickness profiles automatically measured by ultra -high resolution OCT system

    Institute of Scientific and Technical Information of China (English)

    徐肃仲; 叶欣杰; 许哲; 杨纯; 沈梅晓

    2013-01-01

    目的:研究基于自动分层算法的超高分辨率谱域 OCT ( UHR-OCT)用于角膜上皮厚度测量的重复性。  方法:使用自行搭建的UHR-OCT系统采集18例健康受试者(年龄23.2±0.9岁)左眼的图像,应用一种基于轴向梯度信息和最短路径的分层算法对得到的SD-OCT图像进行边界探测获取角膜上皮厚度。  结果:自动与手动的上皮分层的位置有很好的相关性(P>0.05,配对t检验)。自动算法获取的6 mm范围平均上皮厚度为52.1±2.1μm,范围从50.3±1.8μm 到53.2±2.4μm,与手动分层之间的角膜上皮厚度差异为0.4±0.3μm。UHR-OCT自动算法重复测量上皮厚度的组内相关系数ICC和可重复性系数CoR分别为0.90±0.05,1.44±0.01μm。  结论:对于超高分辨率OCT,自动分层方法在角膜上皮厚度测量中有着很好的准确性和可重复性。%AIM:To assess the repeatability of thickness profiles of corneal epithelium produced by aautomatic hierarchic algorithm that was applied to images obtained by a custom-built ultra-high resolution OCT ( UHR-OCT ) system. METHODS:Eighteen left eyes of 18 subjects (23.2±0.9) years;mean age±standard deviation) were imaged twice on non-consecutive days by a custom-built ultra-high resolution OCT ( UHR -OCT ) system. A hierarchic algorithm based on the axial gradient information and a shortest path search was developed to measure the corneal epithelial thickness profiles from the SD-OCT images. RESULTS: There was good correlation between theautomatic and manual hierarchy positions of the epithelium ( p >0.05, paired t -test ). The average epithelial thickness of the 6mm central corneal region determined by the automatic hierarchic algorithm was 52.1±2.1μm, ranging from 50.3 ±1.8μm to 53.2 ±2.4μm along the horizontal meridian. The epithelial thickness differences between automatic and manual hierarchy by the UHR-OCT systems were 0.4 ±0

  20. 降落PCR扩增人类常染色体STR D15S128%Touchdown PCR for Amplification of Human Autosomal STR D15S128

    Institute of Scientific and Technical Information of China (English)

    张艳萍; 郭大玮; 马莉莉

    2010-01-01

    目的 优化PCR程序,尝试用降落PCR扩增人类常染色体STR D15S128.方法 用普通PCR和降落PCR扩增人类常染色体STR D15S128.结果 普通PCR扩增产物有非特异带,降落PCR无非特异带.结论 降落PCR简化了普通PCB中摸索最适退火温度的过程,可以一步找到人类常染色体STR D15S128的退火温度,是一种高效率的PCR方法.

  1. Vanishing Str M2 in the presence of anomalous U A(1)

    Science.gov (United States)

    Lopez, Jorge L.; Nanopoulos, D. V.

    1996-02-01

    We show that the presence of an anomalous U A(1) factor in the gauge group of string-derived models may have the new and important phenomenological consequence of allowing the vanishing of Str M2 in the “shifted” vacuum that results in the process of cancelling the anomalous U A(1). The feasibility of this effect seems to be enhanced by a vanishing vacuum energy, and by a “small” value of Str M2 in the original vacuum. In the class of free-fermionic models with vanishing vacuum energy that we focus on, a necessary condition for this mechanism to be effective is that Str M2 > 0 in the original vacuum. A vanishing Str M2 ameliorates the cosmological constant problem and is a necessary element in the stability of the no-scale mechanism.

  2. STR data for PowerPlex 16 System from Neuquen population, SW Argentina.

    Science.gov (United States)

    Toscanini, Ulises; Berardi, Gabriela; Raimondi, Eduardo

    2003-07-01

    Allele frequencies for the 15 autosomic STR loci included in the PowerPlex 16 System kit (Promega) were estimated from a sample of 111 unrelated individuals living in Neuquen province, southwest of Argentina. Population showed to be in HWE.

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

    Institute of Scientific and Technical Information of China (English)

    Gao Shuhui; Li Shengbin

    2007-01-01

    Objective To study the genetic relationship between Kirgiz individuals living in Sinkiang China and analyze the difference among Kirgiz and the other population with STR polymorphisms. Methods PCR amplification was performed using PE9700, the PCR products were typed by automated sequencer and genescan. Results A database of nine STR loci of Kirgiz was established. It shows there are at least 73 STR alleles and 191 genotypes in Kirgiz. Genotype frequencies distribution showed no deviation from Hardy-Weinberg equilibrium by χ2-test. Kirgiz was compared with the other Chinese ethnic groups, then the American Black and the White. Conclusion These results suggested that the nine STR loci and Amelogenin locus were very useful in human identification, biological archaeology and gene resource studies.

  4. 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.

  5. [Mutations in a Large Pedigree with Y-STR Genetic Markers].

    Science.gov (United States)

    Peng, Shan; Liu, Chao; Wang, Ying; Li, Yue; Zhang, Chu-chu; Hong, Li; Ou, Xue-ling; Sun, Hong-yu

    2015-04-01

    To explore the mutation of Y-STR loci in meiotic allelic transmission in a large pedigree. The oral swabs of 163 male individuals were collected from a Lin pedigree. Twenty-two Y-STR genetic markers were typed with AGCU Y24 fluorescent detection kit (AGCU Y24 system), which also contained 16 Y-STR markers included in Yfiler multiple amplification kit (Yfiler system). The genotyping results of Y-STR loci were compared between each two males in the pedigree. There were 20 and 30 kinds of haplotypes obtained with Yfiler and AGCU Y24 systems in 163 male individuals from the Lin pedigree, respectively. The rates referred to haplotype differences (RRHD) of these two typing systems between male pairs were 0.910 5 and 0.922 7, respectively. The average number of marker differences were 6.582 1 and 9.824 8, respectively. The RRHD increased along with the incidents of meiosis. Y-STR mutation leads to different Y-STR haplotypes among the male members in a paternal pedigree and the rate of difference increases along with the incidents of meiosis.

  6. ALLELE DISTRIBUTION OF FIVE X-CHROMOSOME SHORT TANDEM REPEAT LOCI IN EWENKE POPULATION OF NORTH CHINA

    Institute of Scientific and Technical Information of China (English)

    Shan-zhi Gu; Teng Chen; Qing-bo Liu; Bing Yu; Sheng-bin Li

    2005-01-01

    Objective To study the allele genetic polymorphism of five short tandem repeat (STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification.Methods Genomic DNA was extracted from EDTA-whole blood of Ewenke population by Chelex-100. The DNA samples were amplified by PCR and were analyzed by polyacrylamide gel electrophoresis and silver staining. The sequence length variations of DXS6799, DXS8378, DXS101, HPRTB, and DXS6789 loci on X-chromosome in 98unrelated Ewenke individuals were investigated.Results All five loci analyzed showed high polymorphism and genetic stability. The data of the five X-chromosome STR loci in Ewenke ethnic group of China was in accordance with Hardy-Weinberg equilibrium by Chi-square test.Conclusion Allele polymorphism of five X-chromosome STR loci can be used as a genetic marker for forensic identification and population genetic research.

  7. Genetic Polymorphism of 19 STR Loci in Han Population in Jincheng%晋城汉族人群19个STR基因座遗传多态性

    Institute of Scientific and Technical Information of China (English)

    刘雁军; 贺小华; 巩智刚; 李琳; 王冰; 张天林

    2015-01-01

    The genetic polymorphism of 19 short tandem repeats (STR) loci in Han population in Jincheng Shanxi was studied using Goldeneye 20A STR Amplification Kit. 1233 unrelated individuals were investigated to obtain allele frequencies and forensic genetic data. No deviations of allelic frequency from Hardy-Weinberg equilibrium were observed (P>0.05). Heterozygosity (H) of 19 loci ranges from 0.639 to 0.919,matching probability (PM) 0.014 to 0.177; power of discrimination (DP) 0.806 to 0.987; polymorphism information content (PIC) 0.58~0.91; power exclusion (PE) 0.342~0.821.The cumulative discrimination power (CDP) and cumulative probability of exclusion (CPE) are 1−1.27×10-23 and 0.999999991, respectively. The result indicates that 19 STR loci are highly polymorphic and suitable for forensic personal identification and paternity testing in this area.%采用 Goldeneye20A STR 试剂盒,对山西晋城汉族人群的遗传多态性进行调查,19个基因座等位基因频率分布均符合 Hardy-Weinberg 平衡(P >0.05),累积个人识别率和累积非父排除率分别为1−1.27×10-23和0.999999991。这19个 STR 基因座在晋城汉族人群中具有较高的个体识别能力和遗传多态性,对于法医学个体识别和亲子鉴定具有重要的应用价值。

  8. Repeat-until-success quantum repeaters

    Science.gov (United States)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  9. Population data of 21 non-CODIS STR loci in Han population of northern China.

    Science.gov (United States)

    Yuan, Li; Ge, Jianye; Lu, Di; Yang, Xue

    2012-07-01

    Allele frequencies and forensic statistics of 21 autosomal short tandem repeat loci (i.e., D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435 and D5S2500) were estimated in Han population from northern China (n = 220). Significant deviation from Hardy-Weinberg equilibrium was detected only for D22S1045. The observed heterozygosity, the expected heterozygosity, the discrimination power, the probability of paternity exclusion in trios, the probability of paternity exclusion in duos and the polymorphic information content ranged from 0.591 to 0.836, 0.594 to 0.830, 0.762 to 0.948, 0.341 to 0.659, 0.189 to 0.487 and 0.535 to 0.807, respectively. Triallelic patterns were observed at D19S433 and D10S1435. Mutations occurred at D22ATA63, D10S1248, D19S433 and D14S1434 loci with all single-step mutations. The expected mutation rates of these four loci are 0.0042 with 95% confidence interval [0.0001, 0.0232] in a total of 238 meioses. Our results show that these 21 non-CODIS STR loci are highly polymorphic and can be useful for human identification and kinship analysis in Northern Han population in China.

  10. 牛四核苷酸STR基因座的筛选和多态性分析%The screening and polymorphic analysis of bovine tetranucleotide STR loci

    Institute of Scientific and Technical Information of China (English)

    陈爱萍; 马晓燕; 孙宏钰

    2009-01-01

    目的 筛选阴影带出现率低且多态性较高的牛四核苷酸STR基因座.方法 用Tandem repeats finder软件搜索牛基因组中的四核苷酸重复STR序列片段,用Primer Premier 5.0软件设计引物,然后扩增、电泳,筛选出符合要求的STR基因座,并对100份无关黄牛个体血样进行STR基因座分型.结果 共筛选出6个具有多态性的牛四核苷酸重复STR基因座(B006、11007、B008、11022、B025、11026),其100份无关黄牛个体血样的累积个体识别率和累积非父排除概率分别为0.99995和0.859591.结论 本研究筛选出的6个四核苷酸STR基因座阴影带出现率低且多态性较高,可用于牛的个体识别和亲子鉴定的研究.%Objective To screen the microsatellites with low occurrence rate of stutter band and establish the effective bovine STR typing system.Methods The tetranucleotide STR loci in bovine genome were searched with Tandem Repeat Finder software.Primers were designed and used to amplify these candidate loci and the PCR products were separated with electrophoresis.DNA samples from 100 head of unrelated cattle were typed.Results Among these candidate loci,6 bovine tetranucleotide STR loci showed high polymorphism,and their CDP and CPE value were 0.99995 and 0.859591 respectively.Conclusion The 6 bovine tetranucleotide STR loci can be used for bovine identification and parentage testing.

  11. Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system.

    Science.gov (United States)

    Hwa, Hsiao-Lin; Lee, James Chun-I; Chang, Yih-Yuan; Yin, Hsiang-Yi; Chen, Ya-Hui; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2011-01-01

    A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

  12. Genome-wide identification of human- and primate-specific core promoter short tandem repeats.

    Science.gov (United States)

    Bushehri, A; Barez, M R Mashhoudi; Mansouri, S K; Biglarian, A; Ohadi, M

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation.

  13. 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.

  14. 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.

  15. Optimization and validation of a fast amplification protocol for AmpFlSTR® Profiler Plus® for rapid forensic human identification.

    Science.gov (United States)

    Laurin, Nancy; Frégeau, Chantal

    2012-01-01

    The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR(®) Profiler Plus(®) to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4h to 26 min. No modification to the commercial AmpFlSTR(®) Profiler Plus(®) primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n-4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR(®) Profiler Plus(®) primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases.

  16. Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpF lSTR® Yfiler® PCR amplification kit

    NARCIS (Netherlands)

    M.A. Goedbloed (Miriam); M. Vermeulen (Mark); R.N. Fang (Rixun); M. Lembring (Maria); A. Wollstein (Andreas); K. Ballantyne (Kaye); O. Lao Grueso (Oscar); S. Brauer (Silke); C. Krüger (Carmen); L. Roewer (Lutz); R. Lessig (Rüdiger); R. Ploski (Rafal); T. Dobosz (Tadeusz); J. Henke (Jürgen); M.R. Furtado (Manohar); M.H. Kayser (Manfred)

    2009-01-01

    textabstractThe Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpF lSTR® Yfiler® polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data in

  17. Monitoring of residual disease and guided donor leucocyte infusion after allogeneic bone marrow transplantation by chimaerism analysis with short tandem repeats

    NARCIS (Netherlands)

    de Weger, RA; Tilanus, MGJ; Scheidel, KC; van den Tweel, JG; Verdonck, LF

    2000-01-01

    In this study, we analysed the chimaeric status of peripheral blood leucocytes (PBLs) in recipients of allogeneic bone marrow transplantation (BMT) with the use of short tandem repeat (STR) microsatellite markers for monitoring the efficacy of BMT and donor leucocyte infusions (DLIs). A set of four

  18. 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.

  19. Association of the DRD2 CAn-STR and DRD3 Ser9Gly polymorphisms with Parkinson's disease and response to dopamine agonists.

    Science.gov (United States)

    Xu, Shaoqing; Liu, Jiujiang; Yang, Xiaodong; Qian, Yiwei; Xiao, Qin

    2017-01-15

    Dopamine agonists (DAs) play important roles in the treatment of Parkinson's disease (PD). Currently, it is thought that genetic variations in the genes encoding dopamine receptors (DR) are important factors in determining inter-individual variability in drug responses. To investigate the association between Dopamine receptor D type 2 (DRD2) dinucleotide short tandem repeat (CAn-STR) and Dopamine receptor D type 3 (DRD3) Ser9Gly polymorphisms and the risk of PD, as well as the possible reasons for PD patients using different doses of DAs, we recruited 168 idiopathic PD patients and 182 controls. There were no significant differences in DRD2 CAn-STR and DRD3 Ser9Gly genotypes (p=0.184, p=0.196) or in allele frequencies (p=0.239, p=0.290) between PD patients and controls. There was no association between DRD2 CAn-STR polymorphism and doses of DAs. Among three different DRD3 Ser9Gly genotypes (Ser/Ser, Ser/Gly, Gly/Gly), patients carrying Gly/Gly genotype used higher doses of DAs than patients with Ser/Gly and Ser/Ser genotypes (p=0.001). In pramipexole subgroup, the Gly/Gly group took more pramipexole than the other genotype groups (p<0.001), whereas the doses of piribedil were not significantly different among three genotypes (p=0.735). Our results suggest that genotype in DRD3 Ser9Gly was the main factor determining different doses of DAs and PD patients carrying Gly/Gly genotype require higher doses of pramipexole for effective treatment. This study may provide insights into understanding possible reasons for different responses to DAs in Chinese PD patients.

  20. Exceptional expansion and conservation of a CT-repeat complex in the core promoter of PAXBP1 in primates.

    Science.gov (United States)

    Mohammadparast, Saeid; Bayat, Hadi; Biglarian, Akbar; Ohadi, Mina

    2014-08-01

    Adaptive evolution may be linked with the genomic distribution and function of short tandem repeats (STRs). Proximity of the core promoter STRs to the +1 transcription start site (TSS), and their mutable nature are characteristics that highlight those STRs as a novel source of interspecies variation. The PAXBP1 gene (alternatively known as GCFC1) core promoter contains the longest STR identified in a Homo sapiens gene core promoter. Indeed, this core promoter is a stretch of four consecutive CT-STRs. In the current study, we used the Ensembl, NCBI, and UCSC databases to analyze the evolutionary trend and functional implication of this CT-STR complex in six major lineages across vertebrates, including primates, non-primate mammals, birds, reptiles, amphibians, and fish. We observed exceptional expansion (≥4-repeats) and conservation of this CT-STR complex across primates, except prosimians, Microcebus murinus and Otolemur garnettii (Fisher exact Pprimate lineages. Different length alleles across the PAXBP1 core promoter CT-STRs significantly altered gene expression in vitro (Pprimates and non-primates. To our knowledge, this is the first instance of expansion and conservation of a STR complex co-occurring specifically with the primate lineage.

  1. Algorithm-Based Fetal Gender Determination Using X and Y Mini-Short Tandem Repeats at Early Gestational Ages

    Directory of Open Access Journals (Sweden)

    Aghanoori

    2016-02-01

    Full Text Available Background Detection of fetal DNA in maternal blood has been examined by many research groups for a few years; thereby, scientists have a shorter way to take to approach prenatal diagnosis of abnormal pregnancies. The Y chromosome sequences have recently become the most common applicable indices for fetal sex determination. Objectives We conducted an algorithmic X and Y mini-Short Tandem Repeats (STRs genotyping method that could solve the problem of false negative (no detection of Y sequences results of previous methods. Patients and Methods Blood samples were obtained from 106 pregnant women and their spouses. Conventional PCR amplified 19 mini-Short Tandem Repeats (STRs and three non-STR markers, which were subsequently genotyped by the means of Polyacrylamide gel electrophoresis (PAGE. Results Sensitivity and specificity of the mini-STR genotyping method for fetal DNA detection were calculated (95.9% and 98%, respectively with a confidence interval of 95%. In addition, sensitivity and informativeness were computed for each of the single mini-STR markers in our conventional PCR method. We also introduced the minimum number of mini-STRs needed to reach maximum validity for fetal gender determination in clinical settings. Conclusions Algorithm-based mini-STR genotyping method significantly increases the reliability (sensitivity and specificity of gender determination using free fetal DNA and could be applied in prenatal clinical testing.

  2. Population genetic data for 17 Y STR markers from Benghazi (East Libya).

    Science.gov (United States)

    Elmrghni, Samir; Coulson-Thomas, Yvette M; Kaddura, Mahmoud; Dixon, Ron A; Williams, D Ross

    2012-03-01

    The seventeen Y-STR loci included in the AmpFℓSTR(®) Yfiler™ PCR Amplification kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458, DYS456, DYS635, and Y-GATA-H4) were used to type a sample population of 238 males from eastern Libya (Benghazi region). Of 238 observed haplotypes, 214 were unique (90%) and 24 (10%) were found more than once. The 17 loci gave a discriminating power of 0.999. DYS458 showed the highest diversity as a single-locus marker (0.73). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity and discrimination capacity (0.996) demonstrate the utility of these loci for human identification in forensic applications. Comparative analysis with Y-STR datasets of relevant populations and submission of the haplotypes to the Y-STR Haplotype Reference Database (YHRD) was undertaken.

  3. Forensic parameters of 19 X-STR polymorphisms in two Chinese populations.

    Science.gov (United States)

    Deng, Chuncao; Song, Feng; Li, Jienan; Ye, Yi; Zhang, Lushun; Liang, Weibo; Luo, Haibo; Li, Yingbi

    2017-01-18

    Application of X-STRs as complements of autosomal STR application in the forensic genetics has become a tendency for kinship testing, especially in deficiency paternity cases. Recently, a novel kit of 19 X-STR loci was developed, which permitted the analysis of 19 STR in the same PCR reaction, and these markers can be clustered into seven groups for the physical linkage. The objective of this study was to evaluate the allele and haplotype diversity of 19 X-STR loci in the Uygur (n = 220) and Tibetan nationality (n = 270) and to estimate the usefulness for complex kinship analysis. In the Tibetan and Uygur populations, a total of alleles of all loci were 188 and 212, with the allele frequencies ranged from 0.0037 to 0.5593 and from 0.0045 to 0.5409, respectively. Compared with previous studies, DXS10135 was the most polymorphic locus in the two population groups, whereas the least variant locus was DXS10164 in the Uygur population and DXS7423 in the Tibetan nationality. Haplotype diversity obtained in this investigation was greater than 0.9 across all LGs. This study indicated the new kit could be used as a supplementary tool in kinship testing in China. In addition, the data sets can be used as supplementary national X-STR references to enlarge the database.

  4. High-throughput STR analysis for DNA database using direct PCR.

    Science.gov (United States)

    Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

    2013-07-01

    Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner.

  5. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR loci

    Directory of Open Access Journals (Sweden)

    Babiker Hiba MA

    2011-05-01

    Full Text Available Abstract Background There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. Result We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  6. PCR typing of two short tandem repeat (STR) structures upstreams of the human myelin basic protein (MBP) gene

    DEFF Research Database (Denmark)

    Nellemann, L J; Frederiksen, J; Morling, N

    1995-01-01

    of the DNA fragments were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. We compared the DNA fragment frequencies of the two MBP regions in 34 patients suffering from multiple sclerosis and in 78 suffering from monosymptomatic idiopathic optic neuritis to those...

  7. I-DNASE21 system: development and SWGDAM validation of a new STR 21-plex reaction.

    Science.gov (United States)

    Aznar, Jose María; Celorrio, David; Odriozola, Adrian; Köhnemann, Stephan; Bravo, María Luisa; Builes, Juan Jose; Pfeiffer, Heidi; Herrera, René J; de Pancorbo, Marian M

    2014-01-01

    I-DNASE21 is a new STR multiplex system that amplifies 21 STR autosomal loci, plus the amelogenin locus in one reaction. This system has been designed to analyze all the STR loci included in the Combined DNA Index System (CODIS), Interpol Standard Set of Loci (ISSL), Extended European Standard Set (ESS-Extended), UK National Criminal Intelligence DNA Database (NDNAD) and German Core loci (GCL). This manuscript presents the validation of the I-DNASE21 system according to the revised guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). The results of this validation, added to the extremely high discriminatory power showed, suggest that I-DNASE21 could be a potentially helpful tool for identification and kinship determination even in complex paternity cases.

  8. Návrh internetových stránek

    OpenAIRE

    Chomo, Martin

    2009-01-01

    Táto bakalárska práca sa zaoberá návrhom internetových stránok pre novovznikajúcu firmu za účelom jej propagácie a prieniku na inak ťažko dostupné trhy. Obsah práce popisuje postup pri vytváraní internetovej prezentácie firmy, grafický design, samotné programovanie stránok ako aj umiestnenie stránok na internet a návrh ich zviditežnenia prostredníctvom i-marketingu. Nakoniec sa táto bakalárska práca zaoberá finančným zhodnotením navrhovaného projektu- nákladov a predpokladaných prínosov. T...

  9. Forensic genetic value of a 27 Y-STR loci multiplex (Yfiler(®) Plus kit) in an Italian population sample.

    Science.gov (United States)

    Rapone, Cesare; D'Atanasio, Eugenia; Agostino, Alessandro; Mariano, Martina; Papaluca, Maria Teresa; Cruciani, Fulvio; Berti, Andrea

    2016-03-01

    The analysis of Y chromosome short tandem repeat (Y-STR) haplotypes provides important information that can be used for investigative purposes and in population studies. The Yfiler(®) Plus PCR Amplification kit (Yfiler(®) Plus, Thermo Fisher Scientific, Waltham, MA, USA) allows the multiplex amplification of 27 Y-STRs, including 7 rapidly mutating markers (RM Y-STRs). In this study, 203 unrelated males from Italy, which were subdivided into 4 different geographical groups (North, Center, South and Sardinia) were analyzed. Several intra-population diversity indexes were computed and compared to those obtained using only loci either from the minimal haplotype or the 17-plex (Yfiler(®), Thermo Fisher Scientific, Waltham, MA, USA). In addition, inter-population diversity analysis (RST) among the four Italian samples was performed. The same analysis was also used to compare the Italian sub-sets to other European populations where the Yfiler(®) Plus haplotype frequency data were available. The Sardinians were significantly differentiated from the other three Italian groups, thus requiring a specific sub-national Y-STR haplotype database. The Yfiler(®) Plus kit showed a high power of discrimination which is useful for criminal investigations, principally due to the inclusion of RM Y-STRs.

  10. Fourteen non-CODIS autosomal short tandem repeat loci multiplex data from Taiwanese.

    Science.gov (United States)

    Hwa, Hsiao-Lin; Chang, Yih-Yuan; Lee, James Chun-I; Yin, Hsiang-Yi; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2011-03-01

    Interest in the development of polymorphic short tandem repeat (STR) markers unlinked to the CODIS loci is growing among forensic practitioners. We developed a multiplex system in which14 autosomal STR (D3S1744, D4S2366, D8S1110, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 572 unrelated Taiwanese Han subjects were analyzed using this 14 STR multiplex system. Thirty parent-child pairs of parentage testing cases with a combined paternity index (CPI) below 1,000 and 32 parent-child pairs with single-step mutations found in AmpFℓSTR Identifiler loci were also recruited for validation of the newly developed system. DNA sequencing was performed for novel STRs and novel alleles found in these subjects. The distributions of allelic frequencies for these autosomal STRs and sequence data, allele nomenclature for the STRs, and forensic parameters are presented. The discrimination power in our multiplex loci ranged from 0.6858 (D18S536) to 0.9168 (Penta E), with a combined discrimination power of 0.999999999. It provides additional power to distinguish the possible single-step mutations in parent-child pairs and improves the ability to prove parentage by increasing the CPI. The combined power of exclusion of these 14 loci in Taiwanese Han in this study was 0.9999995913. In conclusion, this 14-autosomal STRs multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing.

  11. Novas espécies de Esthlogena s. str. Thomson (Coleoptera, Cerambycidae, Lamiinae

    Directory of Open Access Journals (Sweden)

    Maria Helena M. Galileo

    2011-06-01

    Full Text Available Novas espécies de Esthlogena s. str. Thomson (Coleoptera, Cerambycidae, Lamiinae. Novas espécies de Pteropliini descritas: Esthlogena (E. nigrosuturalis do México e Panamá; E. (E. chicacaoensis e E. (E. amaliae da Guatemala; E. (E. dissimilis do Peru. Todas as espécies são ilustradas.New species of Esthlogena s. str. Thomson (Coleoptera, Cerambycidae, Lamiinae. New species described of Pteropliini: Esthlogena (E. nigrosuturalis from Mexico and Panama; E. (E. chicacaoensis and E. (E. amaliae from Guatemala; E. (E. dissimilis from Peru. All species are illustrated.

  12. Estimating the probability of allelic drop-out of STR alleles in forensic genetics

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt;

    2009-01-01

    In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop......-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework....

  13. Wärme- und Strömungssimulation in der Produktentwicklung

    OpenAIRE

    Klett, Sven

    2010-01-01

    Vortrag über die Vorteile konstruktionsbegleitender Wärmesimulation direkt durch den Konstrukteur am nativen CAD-System. Die Elinter AG als Spezialist für Wärmesimulationen und Strömungssimulationen empfiehlt FloEFD zusammen mit Pro/ENGINEER Wildfire. Schnelle thermische Bewertung von Konstruktionsvorschlägen und Designvarianten direkt durch den Konstrukteur. Die frühzeitige Wärmesimulation bzw. Strömungssimulation direkt im Desginprozess ist mit minimalem Aufwand möglich. Simulatione...

  14. A new autosomal STR nineplex for canine identification and parentage testing

    DEFF Research Database (Denmark)

    van Asch, Barbara; Alves, Cíntia; Gusmão, Leonor

    2009-01-01

    A single multiplex PCR assay capable of simultaneously amplifying nine canine-specific autosomal STR markers (FH3210, FH3241, FH2004, FH2658, FH4012, REN214L11, FH2010, FH2361 and the newly described C38) was developed for individual identification and parentage testing in domestic dogs. In order......-breed origin. Co-dominant inheritance of STR alleles was investigated in 101 father, mother and son trios. Expected heterozygosity values vary between 0.5648 for REN214L11 and 0.9050 for C38. The high level of genetic diversity observed for most markers provides this multiplex with a very high discriminating...

  15. Y-STR analysis on DNA mixture samples--results of a collaborative project of the ENFSI DNA Working Group

    DEFF Research Database (Denmark)

    Parson, Walther; Niederstätter, Harald; Lindinger, Alexandra;

    2008-01-01

    The ENFSI (European Network of Forensic Science Institutes) DNA Working Group undertook a collaborative project on Y-STR typing of DNA mixture samples that were centrally prepared and thoroughly tested prior to the shipment. Four commercial Y-STR typing kits (Y-Filer, Applied Biosystems, Foster C...

  16. Two new European species of Dicranomyia Stephens, 1829, related to D. (s.str.) chorea (Meigen, 1818) (Diptera, Limnoniidae)

    NARCIS (Netherlands)

    Stary, Jaroslav

    1993-01-01

    Diagnostic features of the so-called Dicranomyia chorea group are discussed. Two new species are described, D. (s. str.) radegasti sp. n. from Czechoslovakia and D. (s. str.) kamakensis sp. n. from Bulgaria, and their male genitalia are illustrated. Attention is paid to the shape of the tarsal claws

  17. Genetic polymorphism study on 12 X STR loci of investigator Argus X STR kit in Bhil tribal population of Madhya Pradesh, India.

    Science.gov (United States)

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

    2015-05-01

    The analysis of 12 X STR loci (DXS10103, DXS8378, DXS7132, DXS10134, DXS10074, DXS10101, DXS10135, DXS7423, DXS10146, DXS10079, HPRTB and DXS10148) belonging to four linkage group was done in 183 (100 males and 83 females) unrelated members of Bhil population. Heterozygosity among the studied 12 X STR loci showed a distribution of from 59.7% to 92.8%. No significant difference was recorded in the allele frequencies of males and females. The loci DXS10135 and DXS10101 were found to be most polymorphic. Haplotype diversity was found to be higher than 0.990 for all the four linkage groups. A total of 86, 69, 71 and 71 haplotypes were observed for linkage group I, II, III and IV, respectively. The results showed departure from Hardy-Weinberg equilibrium with respect to three loci DXS10079, DXS10135 and DXS10101. This is first report on these 12 X STR markers from India. All the loci in the Argus X 12 kit were fairly informative in the Bhil population and the population showed significant genetic variation with all the compared populations from other parts of the world.

  18. Serum Levels of MicroRNA-206 and Novel Mini-STR Assays for Carrier Detection in Duchenne Muscular Dystrophy

    Science.gov (United States)

    Anaya-Segura, Mónica Alejandra; Rangel-Villalobos, Héctor; Martínez-Cortés, Gabriela; Gómez-Díaz, Benjamín; Coral-Vázquez, Ramón Mauricio; Zamora-González, Edgar Oswaldo; García, Silvia; López-Hernández, Luz Berenice

    2016-01-01

    Duchenne Muscular Dystrophy (DMD) is an X-linked neuromuscular disorder in which the detection of female carriers is of the utmost importance for genetic counseling. Haplotyping with polymorphic markers and quantitation of creatine kinase levels (CK) allow tracking of the at-risk haplotype and evidence muscle damage, respectively. Such approaches are useful for carrier detection in cases of unknown mutations. The lack of informative markers and the inaccuracy of CK affect carrier detection. Therefore, herein we designed novel mini-STR (Short Tandem Repeats) assays to amplify 10 loci within the DMD gene and estimated allele frequencies and the polymorphism information content among other parameters in 337 unrelated individuals from three Mexican populations. In addition, we tested the utility of the assays for carrier detection in three families. Moreover, given that serum levels of miR-206 discern between DMD patients and controls with a high area under the curve (AUC), the potential applicability for carrier detection was assessed. The serum levels of miR-206 of non-carriers (n = 24) and carriers (n = 23) were compared by relative quantitation using real-time PCR (p < 0.05), which resulted in an AUC = 0.80 in the Receiver Operating Characteristic curve analysis. In conclusion, miR-206 has potential as a “liquid biopsy” for carrier detection and genetic counseling in DMD. PMID:27529242

  19. Serum Levels of MicroRNA-206 and Novel Mini-STR Assays for Carrier Detection in Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Mónica Alejandra Anaya-Segura

    2016-08-01

    Full Text Available Duchenne Muscular Dystrophy (DMD is an X-linked neuromuscular disorder in which the detection of female carriers is of the utmost importance for genetic counseling. Haplotyping with polymorphic markers and quantitation of creatine kinase levels (CK allow tracking of the at-risk haplotype and evidence muscle damage, respectively. Such approaches are useful for carrier detection in cases of unknown mutations. The lack of informative markers and the inaccuracy of CK affect carrier detection. Therefore, herein we designed novel mini-STR (Short Tandem Repeats assays to amplify 10 loci within the DMD gene and estimated allele frequencies and the polymorphism information content among other parameters in 337 unrelated individuals from three Mexican populations. In addition, we tested the utility of the assays for carrier detection in three families. Moreover, given that serum levels of miR-206 discern between DMD patients and controls with a high area under the curve (AUC, the potential applicability for carrier detection was assessed. The serum levels of miR-206 of non-carriers (n = 24 and carriers (n = 23 were compared by relative quantitation using real-time PCR (p < 0.05, which resulted in an AUC = 0.80 in the Receiver Operating Characteristic curve analysis. In conclusion, miR-206 has potential as a “liquid biopsy” for carrier detection and genetic counseling in DMD.

  20. Allele frequency distribution based on 17 STR markers in three major Dravidian linguistic populations of Andhra Pradesh, India.

    Science.gov (United States)

    Bindu, G Hima; Trivedi, R; Kashyap, V K

    2007-07-20

    Allele frequencies for 15 tetranucleotides and 2 pentanucleotides repeat loci were determined in 317 unrelated, healthy individuals of Andhra Pradesh, India, belonging to three pre-dominant endogamous populations namely, Kappu Naidu, Kamma Chaudhary and Kapu Reddy. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all loci with few exceptions, which were not significant after applying Bonferroni's correction. Statistical parameters of forensic interest; observed heterozygosity, probability of homozygosity, probability of extact test, power of discrimination, match probability, polymorphism information content, power of exclusion and mean paternity index were determined for all loci. The present study reveals that Penta E and D2S1338 are the most informative loci in all the studied populations. The combined power of discrimination was greater than 0.976, whereas the cumulative power of exclusion gave an expected value of 0.9999 for all the tested microsatellite loci. No difference was observed in the discriminatory power of 15 loci in studied populations on comparison with other populations of India. Population differentiation tests revealed significant differences between the studied and neighboring populations at several loci. Analyzed parameters indicate the utility and efficacy of the studied 17 STR systems as a powerful tool in forensic human identification, paternity testing and human population genetic studies.

  1. 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.

  2. Quantum repeated games revisited

    CERN Document Server

    Frackiewicz, Piotr

    2011-01-01

    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games.

  3. Grå strækninger i det åbne land

    DEFF Research Database (Denmark)

    Sørensen, Michael

    Det grå strækningsarbejde er i de sidste 10 år blevet en større og større del af de danske vejbestyrelsers stedbundne trafiksikkerhedsarbejde. Imidlertid er der hverken blevet formuleret en præcis og brugbar definition af begrebet, formuleret en overordnet filosofi for arbejdet eller blevet udvik...

  4. Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile.

    Science.gov (United States)

    Vergara, Ismael A; Villouta, Pamela; Herrera, Sandra; Melo, Francisco

    2012-05-01

    The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.

  5. Forensic Spanish allele and haplotype database for a 17 X-STR panel.

    Science.gov (United States)

    Prieto-Fernández, Endika; Núñez, Carolina; Baeta, Miriam; Jiménez-Moreno, Susana; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

    2016-09-01

    The currently developed 17 X-STR panel (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) offers a highly discriminative tool for forensic identification and kinship testing. With the aim of providing a global Spanish population X-STR database, we present haplotype and allele frequencies and parameters of forensic interest for the 17 X-STR panel obtained from 593 unrelated individuals from Alicante, Aragon, the Basque Country, Andalusia, Galicia, Madrid, and Barcelona that represent the most populated regions of the Spanish Peninsular territory. The seven populations were compared to test possible population genetic substructures. The lack of significant differences among the studied Spanish populations supports the use of the allele and haplotype frequency database presented herein as a global Spanish population sample useful for statistical evaluation in forensic casework. After conducting the LD plots derived from HapMap and pairwise linkage disequilibrium tests, DXS7132, DXS10075, and DXS10079 markers were included in a cluster and haplotype frequencies were calculated. The improvement in the forensic parameters for the Spanish population using 17 X-STRs in comparison to the previous 10 X-STR allele frequencies database is also shown.

  6. GENETIC POLYMORPHISM OF SIX Y CHROMOSOMAL STR IN CHINESE HUI ETHNIC GROUP

    Institute of Scientific and Technical Information of China (English)

    Zhu Bofeng; Lü Guiping; Yao Guifa; Zhu Jun; Dong Hongwang; Sun Qingdong; Huang Lei; Liu Yao

    2005-01-01

    Objective To study genetic polymorphism of 6 Y chromosomal STR in Hui ethnic group living in Ningxia Hui ethnic autonomous region, in order to evaluate their usefulness in forensic science and enrich the Chinese genetic information resources. Methods We investigated 101 unrelated, healthy, male individuals of Hui ethnic group and studied their allelic frequency distribution and haplotype diversity of 6 Y chromosomal STR. Primer for each loci was labeled with the fluorescent by FAM (blue) or TAMRA(yellow). The data of Hui ethnic group were generated co-amplification, GeneScan, genotype, and genetic distribution analysis. Results 31 alleles and 43 phenotype(DYS385) were detected, with the frequencies ranging from 0.0099-0.7129. Out of a total of 101 individuals, 96 showed different haplotypes; 91 were unique; 5 were found 2 times. The haplotype diversity for 6 Y-STR loci was 0.9990. Conclusion The date obtained can be valuable for individual identification, paternity testing in forensic fields and for population genetics because of 6 Y-STR loci high polymorphism.

  7. The Acquisition of Newly Emerging Sociophonetic Variation: /str-/ in American English

    Science.gov (United States)

    Rutter, Ben

    2014-01-01

    Eight children aged 4;1-8;1 and their primary caregivers participated in a study designed to evaluate their use of the onset cluster /str-/ in both read and conversational speech. The cluster is currently undergoing a reported sound change in many varieties of English, with the initial /s/ being retracted to [?]. The study compared the initial…

  8. 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.

  9. Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China.

    Science.gov (United States)

    Shi, Yunfang; Li, Xiaozhou; Ju, Duan; Li, Yan; Zhang, Xiuling; Zhang, Ying

    2015-08-01

    Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24-48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome.

  10. Application of D3S1358 and other 8 STR loci amplification on identification if disputed paternity%复合扩增D3S1358等9个STR位点在亲子鉴定中的应用

    Institute of Scientific and Technical Information of China (English)

    谢小虎; 林锦锋; 王万旭; 张建兵; 许卫平; 周文华; 杨国栋

    2003-01-01

    @@人类基因组中约有50万个短串联重复序列位点(short tandem repeat, STR),其核心序列一般为2~6bp,片段长度为100~500bp,由于核心单位重复数目的变化,构成STR位点的高度多态性。

  11. Diversity and constraints in the floral morphological evolution of Leandra s.str. (Melastomataceae).

    Science.gov (United States)

    Reginato, Marcelo; Michelangeli, Fabián A

    2016-09-01

    Putative processes related to floral diversification and its relation to speciation are still largely unaccounted for in the Melastomataceae. Leandra s.str. is one of the most diverse lineages of the Neotropical Miconieae and ranks among the ten most diverse groups in the Atlantic Forest. Here, we describe the floral diversity of this lineage in a continuous framework and address several questions related to floral evolution and putative developmental and environmental constraints in its morphology. The morphological data set includes individual size measurements and shape scores (from elliptical Fourier analysis) for hypanthia, petals, stamens and styles. We evaluate whether there is evidence of correlation among these floral structures, shifts and convergent patterns, and association of these traits with elevation. Leandra s.str. flower structures present a strong phylogenetic signal and tend to be conserved among close relatives. The extremes in flower regimes seem to be quite distinct, but non-overlapping discrete flower types are not observed. Overall, the morphology of Leandra s.str. floral structures is correlated, and anther colour and inflorescence architecture correlate with flower structures. Additionally, the rates of species diversification and morphological evolution are correlated in most clades. Although some flower regimes tend to occur in different elevational ranges, no significant association is observed. The general idea that hypanthium-ovary fusion is associated with fruit types in the Melastomataceae does not hold for Leandra s.str., where, instead, hypanthium-ovary fusion seems to be associated with anther shape. The lowest rate of flower morphological change, when compared with species diversification rates, is observed in the clade that possesses the most specialized flowers in the group. While stuck on a single general pollination system, Leandra s.str. seems to be greatly wandering around it, given the flower diversity and convergent

  12. Stochastic sampling effects in STR typing: Implications for analysis and interpretation.

    Science.gov (United States)

    Timken, Mark D; Klein, Sonja B; Buoncristiani, Martin R

    2014-07-01

    The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies.

  13. The investigation on genetic polymorphisms of 19 STR loci in Han population in Gaoping of Shanxi%山西省高平地区汉族人群19个短串联重复系列基因座遗传多态性调查

    Institute of Scientific and Technical Information of China (English)

    刘雁军; 贺小华; 巩智刚; 李琳; 王冰; 张天林

    2016-01-01

    目的:调查19个短串联重复系列(STR)基因座在山西省高平市汉族人群中的遗传多态性,并对其法医学应用进行评价。方法:采用 Goldeneye20A STR 荧光标记复合扩增试剂盒,对山西省高平市汉族210份无关个体进行扩增,利用3130XL 遗传分析仪对扩增产物进行电泳分型,统计 D19S433等19个 STR 基因座的等位基因频率和法医遗传学数据。结果:获得19个 STR 基因座的等位基因频率分布,分别检出10,9,15,13,13,6,8,7,7,7,10,8,9,5,17,6,11,13,17个等位基因,并分别获得19个 STR 基因座的杂合度观察值(Ho)、杂合度期望值(He)、个人设别能力(DP)、偶合率(PM)、非父排除率(PE)及多态信息总量(PIC)等法医遗传学参数,累积个人识别率和累积非父排除率分别为1~1.49×10-22和0.999999993。结论:Goldeneye20A STR 荧光标记复合扩增体系的19个 STR 基因座在山西省高平市汉族人群中具有较高的个体识别能力和遗传多态性,对于法医学个体识别和亲子鉴定具有重要的应用价值。%Objective:To study the genetic polymorphisms of short tandem repeats(STR)loci in Han population in Gaop-ing of Shanxi province,and evaluate their forensic application. Methods:Nineteen STR loci including D19S433 were amplified by using a Goldeneye 20A STR Amplification Kit,and analyzed by 3130XL genetic analyzer. 210 unrelated individuals of Han population in Gaoping city of Shanxi province were investigated to obtain the allele frequencies and forensic genetics data. Re-sults:Allele distributions of the 19 STR loci have been obtained. 10,9,15,13,13,6,8,7,7,7,10,8,9,5,17,6,11,13 and 17 alleles were found in the preview 19 STR loci. We also obtained some parameter of forensic genetics respectively,such as het-erozygosit(Ho),expected heterozygosity(He),discrimination power(DP),matching probability(PM),probability of paternity

  14. A Novel Framework for Short Tandem Repeats (STRs Using Parallel String Matching

    Directory of Open Access Journals (Sweden)

    D. Bala MuraliKrishna,

    2015-09-01

    Full Text Available Short tandem repeats (STRs have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both Plants and bacteria. Most of the computer programs that find STRs failed to report its number of occurrences of the repeated pattern, exact position and it is difficult task to obtain accurate results from the larger datasets. So we need high performance computing models to extract certain repeats. One of the solution is STRs using parallel string matching, it gives number of occurrences with corresponding line number and exact location or position of each STR in the genome of any length. In this, we implemented parallel string matching using JAVA Multithreading with multi core processing, for this we implemented a basic algorithm and made a comparison with previous algorithms like Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms and from the results our new basic algorithm gives better results than the previous algorithms. We apply this algorithm in parallel string matching using multi-threading concept to reduce the time by running on multicore processors. From the test results it is shown that the multicore processing is a remarkably efficient and powerful compared to lower versions and finally this proposed STR using parallel string matching algorithm is better than the sequential approaches.

  15. A Case of Maternal Half-sisters Sharing Alleles at 18 X-chromosomal Short Tandem Repeat Loci

    Directory of Open Access Journals (Sweden)

    Qiu-Ling Liu

    2016-01-01

    Full Text Available Analysis of X-chromosome short tandem repeats (STRs is very helpful in deficiency paternity testing. Here, we reported a case of kinship analysis that showed a potentially erroneous inclusion of paternal sisters between two women. The two women shared alleles at 18 X-chromosomal STR loci spanned from 14.76cM (DXS6807 to 184.19cM (DXS7423. When their relatives were not available for testing, biostatistical analysis for the 18 X-chromosomal STR loci and 24 autosomal STR loci revealed the most possible relationship between the two women was paternal sisters. However, when the father of one woman was available, the other father-daughter possibility was excluded. In the end, the likelihood ratio of STR marker and mitochondrial DNA (mtDNA sequences confirmed the two women were maternal sisters. This case emphasizes a cautionary interpretation of X chromosomal marker in deficiency paternity cases with female offspring. Even though large parts of the X-chromosome haplotypes shared by two females, additional relatives and extended DNA typing (such as mtDNA may be needed further to ascertain whether they are paternal or maternal sisters.

  16. Allele frequency of 19 autosomal STR loci in the Bai population from the southwestern region of mainland China.

    Science.gov (United States)

    Li, Yi; Hong, Yine; Li, Xiujiang; Yang, Jinmeng; Li, Lanjiang; Huang, Ying; Wang, Chuanchao; Li, Hui; Xu, Bingying

    2015-10-01

    The aim of this study was to investigate a 19 STR loci database using the Bai population from China. This multiplex amplification kit included 13 CODIS STR markers and six plus STR markers (D19S433, Penta E, D2S1338, Penta D, D6S1043, and D12S391) that were successfully analyzed by using 1158 DNA samples from the Bai population from the southwestern part of mainland China. These results indicate that this multiplex amplification kit may provide significant polymorphic information for kinship testing and relationship investigations.

  17. Reconfigurable multiport EPON repeater

    Science.gov (United States)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  18. Revisiting the TALE repeat.

    Science.gov (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  19. Application of STR genetic marker system in the detection of hemophilia A carriers in Guangxi, China%STR遗传标记在广西地区血友病A携带者诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    周峻荔; 韦红英; 吴华; 胡艳玲; 梁伟玲

    2012-01-01

    Objective To establish a fast and simple genetic diagnosis technique based on a reliable, short tandem repeat (STR) genetic marker system for the detection of hemophilia A carriers in Guangxi, China. Methods Fluorescent PCR and + capillary electrophoresis were used for allele genotyping at three intragenic/extragenic STR loci (F81ntl3, DXS1073, and DXS9901) of FVIII gene in the members of 10 hemophilia A families in Guangxi, so as to evaluate the diagnostic efficiency of the STR genetic marker system for detection of hemophilia A carriers. Then the STR genetic marker system was used to detect hemophilia A carriers among examinees. Results In the 10 hemophilia A families, 11 confirmed female carriers had the same allele fragment lengths at the three STR loci (F8Intl3, DXS1O73, and DXS9901) as the probands. Of the 8 females examined, 5 had allele fragments at the three STR loci (F8Intl3, DXS1073, and DXS9901) which were identical to those of the probands, and thus they were diagnosed as hemophilia A carriers. Conclusions Genetic analysis at the three STR loci (F8Intl3, DXS1073, and DXS9901) can be used to detect hemophilia A carriers rapidly and provide reliable basis for prenatal diagnosis of hemophilia A.%目的 建立理想的STR 遗传标记体系,对广西地区血友病A携带者进行快速简便的基因诊断.方法 选取广西地区10个血友病A家系作为研究对象,运用荧光PCR联合毛细管电泳的方法,对家系成员中FⅧ基因内外具有高度遗传性的3个STR位点F8Int13、DXS1073、DXS9901进行等位基因分型,评估该体系用于家系中血友病A携带者的诊断效率,并对待检者进行携带者诊查.结果 10个血友病A家系中,11例肯定女性携带者均含有与相应先证者完全一致的3个STR等位基因(F8Int13、DXS1073、DXS9901)片段长度;在待检的8例女性中,5例检出3个STR等位基因片段与相应家系中先证者完全相同,被诊断为血友病A携带者.结论 联合应用3

  20. Recursive quantum repeater networks

    CERN Document Server

    Van Meter, Rodney; Horsman, Clare

    2011-01-01

    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  1. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    Directory of Open Access Journals (Sweden)

    Seman Ali

    2012-10-01

    Full Text Available Abstract Background Y-Short Tandem Repeats (Y-STR data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH, obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91, k-Modes-RVF (0.81, New Fuzzy k-Modes (0.80, k-Modes (0.76, k-Modes-Hybrid 1 (0.76, k-Modes-Hybrid 2 (0.75, Fuzzy k-Modes (0.74, and k-Modes-UAVM (0.70. Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k and considered to be linear.

  2. [Polymorphisms of 21 short tandem repeat loci of Salar minority ethnic group in Qinghai Province].

    Science.gov (United States)

    Ma, Jun; Wang, Yan-bin; Li, Kai; Wang, Jian-wen

    2013-10-01

    To investigate the polymorphisms of 21 short tandem repeat (STR)loci of Salar minority ethnic group in Qinghai Province. Blood samples were collected from 120 unrelated healthy Salar individuals from Gandu town in Hualong county. DNA templates were screened by home-made AGCU21+1 kit. The findings were further compared with those of Hans in Zhejiang Province, Hans in Ningxia Hui Autonomous Region, Tibetans in Tibet Autonomous Region, and Tujias in Hubei Province. The allele frequencies of 21 STR loci ranged 0.0042-0.4917, the genotype frequencies ranged 0.0083-0.3750, the power of discrimination ranged 0.796-0.948, the heterozygosity ranged 0.650-0.817, the polymorphism information contents ranged 0.590-0.810, and the power of exclusion ranged 0.355-0.630. The cumulative coupling probability was 1.75×10(-20), and the cumulative power of exclusion was 0.9999999. Significant differences were found at 14, 12, 12, 13 of the 21 STR loci between Salar and Hans of Zhejiang Province, Ningxia Hui Autonomous Region, Tibetans of Tibet Autonomous Region, and Tujias of Hubei Province (Pethnic group from Qinghai Province and therefore suitable for population genetics study, screening of disease-related genes, and forensic individual identification.

  3. A NORTHWEST DATABASE MODEL OF SHORT TANDEM REPEAT LOCI IN FORENSIC MEDICINE

    Institute of Scientific and Technical Information of China (English)

    王振原; 朱波峰; 刘雅诚; 严江伟; 霍振义; 金天博; 李涛; 樊拴良; 方杰

    2003-01-01

    Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5-FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036-0.8562. PM was less than 10-11. The observed and expected genotype frequencies were evaluated using χ2-test and all were in accordance with Hardy-Weinberg equilibrium (P>0.05). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.

  4. In naming the dead: Autosomal and Y-chromosomal STR typing on human skeletal remains from an 18th/19th century aristocratic crypt in Gallspach, Upper Austria.

    Science.gov (United States)

    Schwarz, Reinhard; Renhart, Silvia; Gruber, Heinz; Kli Mesch, Wolfgang; Neuhuber, Franz; Cemper-Kiesslich, Jan

    2015-01-01

    Ancient DNA analyses have shown to be a powerful tool in the joint transdisciplinary assessment of archaeological records involving human remains. In this study we set out to identify single inhumations by synoptically evaluating the historical, archaeological, anthropological and molecular records on human remains from the crypt of the aristocratic family of Hoheneck (or: Hohenegg) dating to the 18(th) and 19(th) century AD. A total of 11 individuals were under investigation, yielding complete autosomal and Y-chromosomal STR profiles for 5 persons clearly showing a family group. DNA results, anthropological data and archaeological records taken together resulted in (almost) unambiguous correlation to historical records on the persons entombed in the crypt.

  5. Šķidrumu brīvās strūklas trajektorijas izpēte

    OpenAIRE

    Jaudzems, G; Gjunsburgs, B

    2008-01-01

    Brīvu, turbulentu šķidruma strūklu izmantošana aktuāla vairākās specifiskās nozarēs- ugunsdzēsībā, kalnrūpniecībā (hidromonitori), agrotehnikā (laistīšanas sistēmas), strūklaku būvē u.c. Izstrādājot aprīkojumu brīvu šķidruma strūklu struktūras veidošanai, nepieciešams pārzināt šādas strūklas īpašības dažādos darbības režīmos.

  6. 和田地区哈萨克族人群23个STR基因座遗传多态性%Genetic Polymorphism of 23 STR Loci of Kazak Population in HotanArea

    Institute of Scientific and Technical Information of China (English)

    刘胜; 贾菲; 刘锋

    2015-01-01

    The genetic polymorphism of 23 short tandem repeat (STR) loci of 1130 unrelated Kazak individuals in Hotan area of Xinjiang, was investigated with GoldeneyeTM24A PCR amplification Kit and the population genetics parameters were calculated with PowerStats statistic software. 22 loci were found no deviation from Hardy-Weinberg equilibrium (P>0.05) except D13S317 locus. Matching probability (PM) ranged from 0.0113 to 0.2035 together with the power of discrimination (DP) 0.7965 to 0.9887, polymorphism information content (PIC) 0.5688 to 0.9208, power of exclusion (PE) 0.3355 to 0.8408, heterozygosity (He) 0.6354 to 0.9221. The total discrimination power (TDP) and the combined power of exclusion (CPE) of 23 loci were 1−4.53×1029 and 0.999 999 999 804, respectively. The 23 STR loci were highly polymorphic in Kazak population of Hotan area. The polymorphic information would serve as reference data for forensic personal identification and paternity testing.%调查新疆和田地区哈萨克族人群23个 STR 基因座的遗传多态性。除 D13S317基因座外,其他22个STR 基因座的基因分布均符合 Hardy-Weinberg 平衡(P>0.05)。23个基因座的 TDP 达1−4.53×1029,CPE 达0.999999999804。23个 STR 基因座在新疆和田地区的哈萨克族人群中有较高的多态性,所得的群体遗传学数据可为该地区的法医学个体识别、亲权鉴定提供基础数据。

  7. 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.

  8. 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.

  9. Evaluation of the genetic parameters and mutation analysis of 22 STR loci in the central Chinese Han population.

    Science.gov (United States)

    Hongdan, Wang; Bing, Kang; Ning, Su; Miao, He; Bo, Zhang; Yuxin, Guo; Bofeng, Zhu; Shixiu, Liao; Zhaoshu, Zeng

    2017-01-01

    At present, the Han nationality is China's main ethnic group and also the most populous nation in the world. This is a great resource to study microsatellite mutations and for the study of ethnogeny. The aim of this study is to investigate the genetic polymorphisms and mutations of 22 autosomal STR loci in 2475 individuals from Henan province, China. DNA is amplified and genotyped using PowerPlex™24 system. The gene frequencies, forensic parameters, and the mutation rate of the 22 STR loci are analyzed. A total of 295 alleles are observed in this Henan Han population, and the allelic frequencies ranged from 0.0003 to 0.5036. In order to investigate the genetic relationships between the Henan Han and the other 14 different populations, our present data were compared with previously published data for the same 15 STR loci. The results indicated that the Henan Han had closer genetic relationships the groups including Minnan Han, Maonan, Yi and Guangdong Han groups while the South morocco population, the Moroccan population, the Malay group, and the Uigur stand away from Henan Han. Except of D2S441, D13S317, PentaE, D2S1338, D5S818, TPOX and D19S433, the mutation events are found in the other 15 STR loci. A total of 40 mutation events are observed in the 15 STR loci. The mutation rates are ranged from 0 to 4.85 × 10(-3). In this study, 39 mutations are single-step mutations, and only one at FGA comprised two steps. STR mutation is commonly existed in paternity testing, while there are no STR mutation studies of the 22 STR loci in the Henan Han population. It is of great importance in forensic individual discrimination and paternal testing.

  10. Disentangling multiple stellar populations in globular clusters using the Str\\"omgren system

    DEFF Research Database (Denmark)

    Alonso-García, J.; Catelan, M.; Amigo, P.

    2012-01-01

    clusters, both in our Galaxy and in others. We have started a series of observations of Galactic globular clusters using the Str\\"omgren photometric system in order to find the signatures of these multiple populations and establish their presence in a more complete sample of globular clusters in the Milky...... Way, and to study their radial distributions and extensions. We present here the first results of our survey....

  11. 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.

  12. Comparative Studies of Population Synthesis Models in the Framework of Modified Strömgren Filters

    Indian Academy of Sciences (India)

    Yuvraj Harsha Sreedhar; Karl Rakos; Gerhard Hensler

    2014-03-01

    Evolutionary models form a vital part of stellar population research in understanding their evolution, but despite their long history of development, they are often misrepresented and the properties of stellar population observed through broadband and spectroscopic measurements are also misinterpreted. With growing numbers of these synthesis models, model comparison becomes an important analysis to choose a suitable model for understanding stellar populations and model up-gradation. Along with model comparison, we reinvestigate the technique ofmodified Strömgren photometry to measure reliable parameter-sensitive colours and estimate precise model ages and metallicities. The assessment of Rakos/Schulz models with GALEV and Worthey’s Lick/IDS model find smaller colour variation: ( - ) ≤ 0.056, ( - ) ≤ -0.05 and ( − ) ≤ 0.061. The study conveys a good agreement of GALEV models with modified Strömgren colours but with poor UV model predictions and observed globular cluster data, while the spectroscopic models perform badly because of outdated isochrone and stellar spectral libraries with inaccurate/insufficient knowledge of various stellar phases and their treatment. Overall, the assessment finds modified Strömgren photometry well suited to study different types stellar populations by mitigating the effects of age-metallicity degeneracy.

  13. Genetic polymorphism of 13 non-CODIS STR loci in three national populations from China.

    Science.gov (United States)

    Liu, Qiu-Ling; Huang, Kai-Kai; Wu, Ye-Da; Zhao, Hu; Li, Cheng-Tao; Lu, De-Jian

    2014-12-01

    The aim of this study was to investigate a 13 non-CODIS STR loci database using three national populations from China. A new multiplex PCR system that simultaneously amplified 13 loci in the same PCR reaction was developed. This multiplex system included the 13 STR markers (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2364, D4S2404, AC001348A, AC001348B, D17S975, and D17S1294), which were successfully analyzed by using 441 DNA samples from three national populations in China (154 Mongol, 177 Kazakh, and 110 Uigur). Allele frequencies and mutation rates of the 13 non-CODIS STR loci were investigated. A total of 4-10 alleles at each locus were observed and altogether 84, 88, and 87 alleles for the all selected loci were found in the Mongol, Kazakh, and Uigur, respectively. Eight mutations were detected from the 13 selected loci in 9880 meioses in kinship cases. These results indicate that this multiplex system may provide significant polymorphic information for kinship testing and relationship investigations.

  14. Detection of Y STR markers of male fetal dna in maternal circulation

    Directory of Open Access Journals (Sweden)

    Nair Seema

    2007-01-01

    Full Text Available Background: Circulating fetal cells and cell free DNA in the maternal blood has been shown to help in prenatal diagnosis of genetic disorders without relying on invasive procedures leading to significant risk of pregnancy loss. Aim: The current study was undertaken to detect the male fetal population using Y STR markers DYS 19, DYS 385 and DYS 392 and also to study the extent of persistence of fetal DNA in the mother following delivery. Materials and Methods: Blinded study was conducted on 50 mothers delivering male and female babies. Cellular and cell free DNA was extracted from maternal and fetal cord blood and amplified for Y STR markers by PCR. Results: The amplification sensitivity of Y specific STR, DYS19 was 100% (22/22 in the male fetal DNA samples. The incidence of other STRs, i.e., DYS385 and DYS392 were 91% (20/22 each. Analysis of results revealed that thirteen of the twenty six women had detectable male fetal DNA at the time of delivery. However fetal DNA was not detectable twenty four hours after delivery. Conclusion: Preliminary results show that the separation of fetal cell-free DNA in the maternal circulation is a good low-cost approach for the future development of novel strategies to provide non-invasive techniques for early prenatal diagnosis.

  15. ANALYSIS ON GENETIC POLYMORPHISM OF 6 STR LOCI ON CHROMOSOME 12 IN CHINESE HAN POPULATION

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To analyze the genetic polymorphism of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613) on chromosome 12 in Chinese Han population. Methods EDTA-blood specimens were collected from 153 unrelated individuals of Chinese Han population in Shaanxi province. Allele and genotype frequencies for the 6 STR loci were estimated and statistical parameters of polymorphism were calculated. Results 8 alleles and 18 genotypes, 10 alleles and 17 genotypes, 9 alleles and 15 genotypes, 12alleles and 29 genotypes, 12 alleles and 31 genotypes, 8 alleles and 11 genotypes were observed at D12S358, D12S1675, D12S1663, D12S1697, D12S1725 and D12S1613, respectively. No deviations of the observed allele frequency from Hardy-weinberg equilibrium expectations were found for any of these loci. The Heterozygotes of these 6 loci were 78.89%, 66.10%, 54.95%, 79.10%, 71.98% and 59.48%, respectively. It indicated the high genetic polymorphism of the loci in Chinese Han population. Conclusion The 6 STR loci belonged to the genetic marker system of high discriminutesation and high information in Chinese Han population and can be used in the study of gene-related diseases.

  16. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  17. Repeating the Past

    Science.gov (United States)

    Moore, John W.

    1998-05-01

    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  18. 马鞍山地区汉族人群15个STR基因座遗传多态性调查%Investigation on the genetic polymorphism of 15 STR loci in Han population in Ma′anshan area

    Institute of Scientific and Technical Information of China (English)

    陈蓉华; 侯杰; 晏斌; 周豫军

    2014-01-01

    目的:调查292名马鞍山地区汉族无关个体15个STR基因座的等位基因类型及其频率。方法:用硅珠法提取DNA,采用AmpFISTR Identifiler荧光标记复合扩增系统进行复合扩增;扩增产物用ABI3130 xl型遗传分析仪检测,得到STR分型结果后统计15个基因座的基因频率。结果:15个STR基因座,累计个人识别率达0.999999999999999985,累计非父排除率为0.99999896。结论:该系统在马鞍山地区汉族人群中具有高度多态性,适用于法医学亲权鉴定、个体识别以及DNA数据库的建立。%Objective:To investigate the alleles and their frequencies of 15 short tandem repeates(STR) loci from 292 unrelated individuals of Han nation-ality living in Ma′anshan area.Methods:DNA was extracted with silica particles,amplified by PCR with AmpF1STR Identifiler kit,and analyzed with ABI 3130XL Genetic Analyzer.The repeated sequences were statistically summed up for the 15 STRs after genotyping.Results:In the 15 STR loci of Ma′anshan Han population,the total discrimination power(TDP) was 0.999 999 999 999 999 985 and 0.999 998 96 for the combined probabilities of paternity exclu-sion.Conclusion:The 15 STR loci has higher genetic polymorphism in the Han population in Ma′anshan area,and may be applied to paternity testing,in-dividual identification and DNA database reference.

  19. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Science.gov (United States)

    Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

    2015-01-01

    In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

  20. 济宁地区汉族人群16个Y-STR基因座遗传多态性%Genetic Polymorphism of 16 Y-STR Loci in Han Population in Jining Area

    Institute of Scientific and Technical Information of China (English)

    孙庆东; 侯伟光

    2015-01-01

    应用 Y-filer 荧光标记复合扩增试剂盒对济宁地区5585名汉族男性个体血样 DNA 进行分型,统计分析16个 Y-STR 基因座的遗传学参数,DYS391、DYS389I、DYS439、DYS389II、DYS438、DYS456、DYS458、DYS437、DYS635、DYS448、Y_GATA_H4、DYS19、DYS393、DYS390、DYS392、DYS385a/b 基因座分别检出5~13种等位基因,DYS385a/b 基因座共检出99个单倍型。基因座频率分布在0.0002~0.7560之间,基因多样性(GD)分布在0.3972~0.9634之间。16个 Y-STR 基因座在济宁汉族群体具有丰富的遗传多态性,可用于群体遗传学及法医学研究。%Objective To investigate the genetic polymorphism of 16 Y-chromosomal short tandem repeats (Y-STR) loci in Han population in Jining area and to evaluate its forensic significance through comparison with the frequencies distribution of some loci in settlement-different people. Methods Blood samples were collected from 5585 male individuals of Han-population in Jining area. 16 Y-STR loci were amplified with Y-filer PCR Amplification Kit. Genotypes and frequencies of alleles were obtained by ID-X GeneMapper analysis software. The frequency distribution on some loci was statistically compared with same or different people in various settlements. Results Of 5585 male individuals, 5~13 kinds of alleles were found among the 16 Y-STR loci of DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS456, DYS458, DYS437, DYS635, DYS448, Y_GATA_H4, DYS19, DYS393, DYS390, DYS392, DYS385a/b and with the last one DYS385a/b having 99 haplotypes. Frequencies of the above 16 Y-STR loci ranged from 0.0002 to 0.640, and the gene diversity 0.3972 to 0.9634. Conclusions The 16 Y-STR loci are of highly genetic polymorphism in Han population in Jining area, suitable for genetics and forensic research.

  1. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling.

    Science.gov (United States)

    Haines, Alicia M; Linacre, Adrian

    2016-05-01

    We report a simple screening method to assess the viability of successful DNA profiling from single hair follicles. A total of 48 hair samples (shed and plucked) were collected from male and female donors and the root tips (0.5cm) were stained using one of three DNA binding dyes (EvaGreen™, Diamond™ Nucleic Acid Dye and RedSafe™) at 20× concentration. The hairs were subsequently viewed under a Nikon Optiphot fluorescent microscope to count the approximate number of nuclei in one plane of view. The hairs were then processed using either (1) a DNA extraction kit (QIAmp(®) Mini Kit) and then amplified using the AmpFLSTR(®) NGM™ kit, which amplifies 15 short tandem repeat (STR) loci plus the gender marker amelogenin, or (2) by direct PCR amplification using the same DNA profiling kit. Diamond™ dye had the lowest background signal and plucked hairs treated with this dye produced full DNA profiles when amplified directly and was chosen to screen a further 150 mixed hair samples. These hairs were separated into one of five categories (1, >100 nuclei; 1.5, 50-99 nuclei; 2, 1-49 nuclei; 2.5, no nuclei but high fluorescent signal; 3, no nuclei and very low fluorescent signal) from which 60 of the hairs were chosen to undergo direct amplification using the NGM™ kit. It was found that there was a direct correlation to the category designation and the ability to obtain a DNA profile up-loadable to the Australian DNA Database. Approximately 91% of category 1 hairs resulted in either a full or high partial (12-29 alleles) profile by direct PCR whereas about 78% of category 3 hairs exhibited no amplification. The results show that this method can be used to predict successful STR amplification from single hair follicles. It is a rapid, sensitive, cheap, non-destructive and easy to perform methodology applicable for screening multiple hairs in order to aid forensic investigators in predicting hairs that will yield DNA results.

  2. All-optical repeater.

    Science.gov (United States)

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  3. Bidirectional Manchester repeater

    Science.gov (United States)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  4. Evaluation of the MeltPro TB/STR assay for rapid detection of streptomycin resistance in Mycobacterium tuberculosis.

    Science.gov (United States)

    Zhang, Ting; Hu, Siyu; Li, Guoli; Li, Hui; Liu, Xiaoli; Niu, Jianjun; Wang, Feng; Wen, Huixin; Xu, Ye; Li, Qingge

    2015-03-01

    Rapid and comprehensive detection of drug-resistance is essential for the control of tuberculosis, which has facilitated the development of molecular assays for the detection of drug-resistant mutations in Mycobacterium tuberculosis. We hereby assessed the analytical and clinical performance of an assay for streptomycin-resistant mutations. MeltPro TB/STR is a closed-tube, dual-color, melting curve analysis-based, real-time PCR test designed to detect 15 streptomycin-resistant mutations in rpsL 43, rpsL 88, rrs 513, rrs 514, rrs 517, and rrs 905-908 of M. tuberculosis. Analytical studies showed that the accuracy was 100%, the limit of detection was 50-500 bacilli per reaction, the reproducibility in the form of Tm variation was within 1.0 °C, and we could detect 20% STR resistance in mixed bacterial samples. The cross-platform study demonstrated that the assay could be performed on six models of real-time PCR instruments. A multicenter clinical study was conducted using 1056 clinical isolates, which were collected from three geographically different healthcare units, including 709 STR-susceptible and 347 STR-resistant isolates characterized on Löwenstein-Jensen solid medium by traditional drug susceptibility testing. The results showed that the clinical sensitivity and specificity of the MeltPro TB/STR was 88.8% and 95.8%, respectively. Sequencing analysis confirmed the accuracy of the mutation types. Among all the 8 mutation types detected, rpsL K43R (AAG → AGG), rpsL K88R (AAG → AGG) and rrs 514 A → C accounted for more than 90%. We concluded that MeltPro TB/STR represents a rapid and reliable assay for the detection of STR resistance in clinical isolates.

  5. Estimating the probability of identity in a random dog population using 15 highly polymorphic canine STR markers.

    Science.gov (United States)

    Eichmann, Cordula; Berger, Burkhard; Steinlechner, Martin; Parson, Walther

    2005-06-30

    Dog DNA-profiling is becoming an important supplementary technology for the investigation of accident and crime, as dogs are intensely integrated in human social life. We investigated 15 highly polymorphic canine STR markers and two sex-related markers of 131 randomly selected dogs from the area around Innsbruck, Tyrol, Austria, which were co-amplified in three PCR multiplex reactions (ZUBECA6, FH2132, FH2087Ua, ZUBECA4, WILMSTF, PEZ15, PEZ6, FH2611, FH2087Ub, FH2054, PEZ12, PEZ2, FH2010, FH2079 and VWF.X). Linkage testing for our set of marker suggested no evidence for linkage between the loci. Heterozygosity (HET), polymorphism information content (PIC) and the probability of identity (P((ID)theoretical), P((ID)unbiased), P((ID)sib)) were calculated for each marker. The HET((exp))-values of the 15 markers lie between 0.6 (VWF.X) and 0.9 (ZUBECA6), P((ID)sib)-values were found to range between 0.49 (VWF.X) and 0.28 (ZUBECA6). Moreover, the P((ID)sib) was computed for sets of loci by sequentially adding single loci to estimate the information content and the usefulness of the selected marker sets for the identification of dogs. The estimated P((ID)sib) value of all 15 markers amounted to 8.5 x 10(-8). The presented estimations turned out to be a helpful approach for a reasonable choice of markers for the individualisation of dogs.

  6. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  7. Evaluation of incest cases of Turkey in terms of DNA profiling difficulties.

    Science.gov (United States)

    Emre, Ramazan; Canturk, Kemal Murat; Komur, Ilhami; Dogan, Muhammed; Demirel, Husrev; Baspınar, Bunyamin

    2015-11-01

    We scanned suspicious 1200 paternity cases and 650 sexual abuse victims in Council of Forensic Medicine of Turkey between 2011 and 2014 and detected 50 incest cases and evaluated the forensic and genetic data of incest cases for source of DNA evidence, gender, age, SES (Socioeconomic status) and geographic location of victim, abusive person, extent of incest, pregnancy from incest and date of gestation termination and also aimed to discuss some DNA profiling difficulties. We detected incest from DNA evidences of curettage material (34%; Chorionic Villi (12%) and fetal tissue (22%)), alive baby after pregnancy (28%), sperm in vaginal swab (10%), sperm in anal swab (2%), sperm on clothing (24%) and in one case both sperm on clothing and in vaginal swab (2%). It was found that the most common incestuous relationship was elder-brother-sister incest (34%) and the second most common relationship was father-daughter incest (28%). The rarest incest was mother-son incest with only one reported case (2%). Forty-three victims (86%) were younger than 18 years old and 7 victims (14%) were older than 18 years old. Thirty-eight cases described full sexual intercourse and 31 of them culminated in pregnancy and 14 of them gave birth at the end of pregnancy. We had paternity rejection problem 3 (10%) of 31 incest cases between tested genetically related alleged fathers. Totally 20 STR loci did not discriminate the alleged fathers in two cases and we treated this problem increasing the number of STR loci and finally got the discrimination. In one case we detected same triallelic variant pattern at the same D3S1358 STR locus in both tested parents but child had not got STR variant; had only two alleles at this loci. We then evaluated the peak height values of STR variant alleles of tested persons and concluded a tetra-allelic baby without any STR incompatibility of 15 STR loci. Finally, forensic experts should aware of some DNA profiling difficulties while analyzing paternity incest

  8. Validation of first chemistry mode retrieval results from new limb-imaging FTS GLORIA with correlative MIPAS-STR observations

    Science.gov (United States)

    Woiwode, W.; Suminska-Ebersoldt, O.; Oelhaf, H.; Höpfner, M.; Belyaev, G. V.; Ebersoldt, A.; Friedl-Vallon, F.; Grooß, J.-U.; Gulde, T.; Kaufmann, M.; Kleinert, A.; Krämer, M.; Kretschmer, E.; Kulessa, T.; Maucher, G.; Neubert, T.; Piesch, C.; Preusse, P.; Riese, M.; Rongen, H.; Sartorius, C.; Schardt, G.; Schönfeld, A.; Schuettemeyer, D.; Sha, M. K.; Stroh, F.; Ungermann, J.; Volk, C. M.; Orphal, J.

    2014-12-01

    We report first chemistry mode retrieval results from the new airborne limb-imaging infrared FTS (Fourier transform spectrometer) GLORIA and comparisons with observations by the conventional airborne limb-scanning infrared FTS MIPAS-STR. For GLORIA, the flights aboard the high-altitude research aircraft M55 Geophysica during the ESSenCe campaign (ESa Sounder Campaign 2011) were the very first in field deployment after several years of development. The simultaneous observations of GLORIA and MIPAS-STR during the flight on 16 December 2011 inside the polar vortex and under the conditions of optically partially transparent polar stratospheric clouds (PSCs) provided us the unique opportunity to compare the observations by two different infrared FTS generations directly. The retrieval results of temperature, HNO3, O3, H2O, CFC-11 and CFC-12 show reasonable agreement of GLORIA with MIPAS-STR and collocated in-situ observations. For the horizontally binned hyperspectral limb-images, the GLORIA sampling outnumbered the horizontal cross-track sampling of MIPAS-STR by up to one order of magnitude. Depending on the target parameter, typical vertical resolutions of 0.5 to 2.0 km were obtained for GLORIA and are typically by factors of 2 to 4 better compared to MIPAS-STR. While the improvement of the performance, characterisation and data processing of GLORIA are subject of ongoing work, the presented first results already demonstrate the considerable gain in sampling and vertical resolution achieved with GLORIA.

  9. Extraction of nuclear DNA from rhinoceros horn and characterization of DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros.

    Science.gov (United States)

    Harper, Cindy K; Vermeulen, Gerhard J; Clarke, Amy B; de Wet, Jacobus I; Guthrie, Alan J

    2013-07-01

    Rhinoceros horn is now worth more, per unit weight, than gold, diamonds, or cocaine. Rhinoceros horn has been used in traditional Asian medicine as a presumed cure for a wide range of ailments. Rhinoceros poaching in South Africa has, on average, more than doubled each year over the past 5 years with the rapid economic growth in east and southeast Asia being assumed to be the primary factor driving the increased demand for horn. Here we report on the characterization of methods for genomic DNA extraction from rhinoceros horn and on DNA profiling systems for white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. The DNA profiling system described includes 22 short tandem repeat (STR), or microsatellite, markers and a gender marker (ZF1), which have been used previously in various studies on rhinoceros. Using a θ value of 0.1, a conservative estimate of random match probability in 5 white rhinoceros ranged from 1:7.3x10(6) to 1:3.0x10(8). Given that the total population of white rhinoceros is approximately 20,000 such random match probabilities indicate that the genotyping system described provides data which can be used for evidentiary purposes. Furthermore, the methods are appropriate for use in investigations involving trace amounts of rhinoceros horn and the matching of profiles obtained from seized rhinoceros horn with material collected from live animals or poached carcasses.

  10. Monitoring of hematopoietic chimerism after transplantation for pediatric myelodysplastic syndrome: real-time or conventional short tandem repeat PCR in peripheral blood or bone marrow?

    Science.gov (United States)

    Willasch, Andre M; Kreyenberg, Hermann; Shayegi, Nona; Rettinger, Eva; Meyer, Vida; Zabel, Marion; Lang, Peter; Kremens, Bernhard; Meisel, Roland; Strahm, Brigitte; Rossig, Claudia; Gruhn, Bernd; Klingebiel, Thomas; Niemeyer, Charlotte M; Bader, Peter

    2014-12-01

    Quantitative real-time PCR (qPCR) has been proposed as a highly sensitive method for monitoring hematopoietic chimerism and may serve as a surrogate marker for the detection of minimal residual disease minimal residual disease in myelodysplastic syndrome (MDS), until specific methods of detection become available. Because a systematic comparison of the clinical utility of qPCR with the gold standard short tandem repeat (STR)-PCR has not been reported, we retrospectively measured chimerism by qPCR in 54 children transplanted for MDS in a previous study. Results obtained by STR-PCR in the initial study served as comparison. Because the detection limit of qPCR was sufficiently low to detect an autologous background, we defined the sample as mixed chimera if the proportion of recipient-derived cells exceeded .5%. The true positive rates were 100% versus 80% (qPCR versus STR-PCR, not significant), and mixed chimerism in most cases was detected earlier by qPCR than by STR-PCR (median, 31 days) when chimerism was quantified concurrently in peripheral blood and bone marrow. Both methods revealed a substantial rate of false positives (22.7% versus 13.6%, not significant), indicating the importance of serial testing of chimerism to monitor its progression. Finally, we propose criteria for monitoring chimerism in pediatric MDS with regard to the subtypes, specimens, PCR method, and timing of sampling.

  11. TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2007-01-01

    Full Text Available Abstract Background Solenoid repeat proteins of the Tetratrico Peptide Repeat (TPR family are involved as scaffolds in a broad range of protein-protein interactions. Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units. Results We have developed TPRpred, a profile-based method which uses a P-value-dependent score offset to include divergent repeat units and which exploits the tendency of repeats to occur in tandem. TPRpred detects not only TPR-like repeats, but also the related Pentatrico Peptide Repeats (PPRs and SEL1-like repeats. The corresponding profiles were generated through iterative searches, by varying the threshold parameters for inclusion of repeat units into the profiles, and the best profiles were selected based on their performance on proteins of known structure. We benchmarked the performance of TPRpred in detecting TPR-containing proteins and in delineating the individual repeats therein, against currently available resources. Conclusion TPRpred performs significantly better in detecting divergent repeats in TPR-containing proteins, and finds more individual repeats than the existing methods. The web server is available at http://tprpred.tuebingen.mpg.de, and the C++ and Perl sources of TPRpred along with the profiles can be downloaded from ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/.

  12. Development of 19-plex Y STR system and polymorphism studies in Pakistani population

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    For the development of 19-plex Y STR system and polymorphism studies in local ethnic populations sixteen markers of non-recombining regions (NRY) of Y chromosome, which show high power of discrimination among individuals, were selected in this study. Blood samples (600) were collected from the males of three most common castes of Pakistani population (Arain, Awan and Rajput) with different parent lineages. Three markers (DYS385a/b, DYS389I/II and YCAIIa/b) among 16 Y STRs are double-targeted regions of the ...

  13. Y-STR多态性与人类学%The Polymorphism of Y-STR and Anthropology

    Institute of Scientific and Technical Information of China (English)

    刘秀梅; 吴江平; 席焕久

    2007-01-01

    人类Y染色体短串联重复序列(Y-STR)具有父系遗传、缺乏重组、分型简单、信息量大、多态性高等特点,是研究人类的起源进化、民族差异、种族差异、群体及地区分布等的有力工具.本文就Y-STR多态性与其在人类学方面的应用作一综述.

  14. 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.

  15. Strømmålinger ved Sæby Udløbsledning

    DEFF Research Database (Denmark)

    Larsen, Torben

    Med henblik på at vurdere tidevandsstrømningens amplitude i det kystnære område ud for Sæby har man i ca. 14 dage fra 25.5.81 til 11.6.81 haft udlagt en Aanderraa RCM 4 strømmåler ca. 1 m under overfladen på ca. 4 m vanddybde. Måleren la ca. 900 m fra land i en linje, som var en forlængelse af ud...

  16. Native American population data based on the Globalfiler(®) autosomal STR loci.

    Science.gov (United States)

    Ng, Jillian; Oldt, Robert F; McCulloh, Kelly L; Weise, Jessica A; Viray, Joy; Budowle, Bruce; Smith, David Glenn; Kanthaswamy, Sreetharan

    2016-09-01

    Native American population data are limited and thus impact computing accurate statistical parameters for forensic investigations. Thus, additional information should be generated from geographically representative tribes in North America, particularly from those that are not included in existing population databases for forensic use. The Globafiler(®) PCR Amplification kit was used to produce STR genotypic data for 533 individuals who represent 31 Native American tribal populations derived from eight geographically diverse regions in North America. Population genetic estimates from 21 autosomal STRs are reported.

  17. 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.

  18. Multiple populations in Galactic globular clusters: a survey in the Strömgren system

    DEFF Research Database (Denmark)

    Alonso-García, J.; Catelan, M.; Amigo, P.

    2013-01-01

    We are coming to believe that stellar populations in globular clusters are not as simple as they were once thought to be. A growing amount of photometric and spectroscopic evidence shows that globular clusters host at least two different stellar populations. In our contribution to these proceedings...... we present the first results of a survey we are conducting to look for the presence of multiple populations in a significant number of Galactic globular clusters, using the Strömgren system. We intend to photometrically separate these populations and characterize their radial distributions...

  19. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium

    OpenAIRE

    Saw, Jimmy H. W.; Yuryev, Anton; Kanbe, Masaomi; Hou, Shaobin; Young, Aaron G; Aizawa, Shin-Ichi; Alam, Maqsudul

    2012-01-01

    Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as ‘ixotrophy’. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of ...

  20. Geotechnical variability of permafrozen glaciomarine clays in Sdr. Strømfjord in Greenland

    DEFF Research Database (Denmark)

    Foged, Niels Nielsen; Ingeman-Nielsen, Thomas; Belmonte, Louise Josefine

    2014-01-01

    This contribution presents the geotechnical properties of some permafrozen glaciomarine clays near to the Kangerlussuaq Airport at Sdr. Strømfjord in West Greenland.This fjord system was established by glacial erosion into the bedrock consisting of Nagssugtoqidian banded gneisses with amphibolitic...... y BC) 5 km east of the Airport. Subformations found are; glaciomarine clay deposited in a coastal environment as very fine flocculated suspended matter ("rock flour"), deltaic sediments of silt and finesand and meltwater gravel and sand carried by the meltwater rivers. This sedimentation is still on...

  1. Assessing the Statistical Significance of the Achieved Classification Error of Classifiers Constructed using Serum Peptide Profiles, and a Prescription for Random Sampling Repeated Studies for Massive High-Throughput Genomic and Proteomic Studies

    Directory of Open Access Journals (Sweden)

    William L Bigbee

    2005-01-01

    Full Text Available source of patient-specific information with high potential impact on the early detection and classification of cancer and other diseases. The new profiling technology comes, however, with numerous challenges and concerns. Particularly important are concerns of reproducibility of classification results and their significance. In this work we describe a computational validation framework, called PACE (Permutation-Achieved Classification Error, that lets us assess, for a given classification model, the significance of the Achieved Classification Error (ACE on the profile data. The framework compares the performance statistic of the classifier on true data samples and checks if these are consistent with the behavior of the classifier on the same data with randomly reassigned class labels. A statistically significant ACE increases our belief that a discriminative signal was found in the data. The advantage of PACE analysis is that it can be easily combined with any classification model and is relatively easy to interpret. PACE analysis does not protect researchers against confounding in the experimental design, or other sources of systematic or random error.We use PACE analysis to assess significance of classification results we have achieved on a number of published data sets. The results show that many of these datasets indeed possess a signal that leads to a statistically significant ACE.

  2. 云南汉族人群20个常染色体STR 基因座遗传多态性%Genetic Polymorphism of 20 Autosomal STR Loci in Yunnan Han Popolation

    Institute of Scientific and Technical Information of China (English)

    胡利平; 杜雷; 张秀峰; 钟树荣; 聂爱婷; 李佳珏; 聂胜洁

    2016-01-01

    目的:研究云南汉族群体20个常染色体基因座的遗传多态性.方法采用PowerPlexR21 System试剂盒,对1085例云南汉族无关个体20个常染色体基因座(D3S1358、D1S1656、D6S1043、D13S317、Penta E、D16S539、D18S51、D2S1338、CSF1PO、Penta D、TH01、vWA、D21S11、D7S820、D5S818、TPOX、D8S1179、D12S391、D19S433、FGA)进行复合扩增,用AB 3130自动遗传分析仪进行扩增产物的电泳分离,用Genemapper ID v3.2软件进行STR基因分型分析,用Modified-Powerstates软件进行法医学遗传学参数统计分析以及H ardy-W einberg 平衡检验.结果在1085例云南汉族人群中,除T H 01和T PO X 基因座,其余ST R 基因座的均具有高度遗传多态性,杂合度( H)分布在0.6130~0.8743之间,随机匹配率( PM)分布在0.0179~0.2030之间,个体识别力(DP)在0.7970~0.9821之间,非父排除率(PE)在0.3067~0.7432之间,父权指数(PI)在1.2919-3.9766之间,多态性息含量( PIC)在0.5598~0.8958之间.基因型分布均符合 H ardy-W einberg 平衡定律.结论这20个常染色体基因座在云南汉族人群中具有较高的多态性和较好的个体识别能力,能满足法医学个体识别和亲权鉴定的需要.%Objective To study the genetic polymorphism of 20 autosomal short tandem repeats(STR)loci in Yunnan Han population. Methods The 20 STR loci(D3S1358,D1S1656,D6S1043,D13S317,Penta E,D16S539,D18S51,D2S1338,CSF1PO,Penta D,TH01,vWA,D21S11,D7S820,D5S818,TPOX, D8S1179,D12S391,D19S433 and FGA)which were included in the PowerPlexR21 System kit were genotyped in 1085 unrelated Han individuals living in Yunnan province using multiplex amplication. PCR products were separated and analyzed by the AB 3130 automatic genetic analyzer and GeneMapper ID v3.2 software. Forensic parameters of each locus were calculated by Modified-Powerstates software. Results All the studied loci except for TH01 and TPOX were highly

  3. A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping☆

    Science.gov (United States)

    Wei, Wei; Ayub, Qasim; Xue, Yali; Tyler-Smith, Chris

    2013-01-01

    We have compared phylogenies and time estimates for Y-chromosomal lineages based on resequencing ∼9 Mb of DNA and applying the program GENETREE to similar analyses based on the more standard approach of genotyping 26 Y-SNPs plus 21 Y-STRs and applying the programs NETWORK and BATWING. We find that deep phylogenetic structure is not adequately reconstructed after Y-SNP plus Y-STR genotyping, and that times estimated using observed Y-STR mutation rates are several-fold too recent. In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data. In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data. PMID:23768990

  4. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  5. Y-STR variation in the Basque diaspora in the Western USA: evolutionary and forensic perspectives.

    Science.gov (United States)

    Valverde, Laura; Rosique, Melania; Köhnemann, Stephan; Cardoso, Sergio; García, Ainara; Odriozola, Adrián; Aznar, Jose María; Celorrio, David; Schuerenkamp, Marianne; Zubizarreta, Josu; Davis, Michael C; Hampikian, Greg; Pfeiffer, Heidi; de Pancorbo, Marian M

    2012-03-01

    Individuals of Basque origin migrated in large numbers to the Western USA in the second half of the nineteenth century, and the flow continued with less intensity during the last century. The European source population, that of the Basque Country, has long been a cultural and geographical isolate. Previous studies have demonstrated that Y-STR frequencies of Basques are different from those of other Spanish and European populations [1]. The Basque diaspora in the Western USA is a recent migration, but the founder effect and the incorporation of new American Y chromosomes into the paternal genetic pool of the Basque diaspora could have influenced its genetic structure and could thus have practical implications for forensic genetics. To check for genetic substructure among the European source and Basque diaspora populations and determine the most suitable population database for the Basque diaspora in the Western USA, we have analysed the haplotype distribution of 17 Y-STRs in both populations. We have found that the Basque diaspora in the Western USA largely conserve the Y chromosome lineage characteristic of the autochthonous European Basque population with no statistically significant differences. This implies that a common 17 Y-STR Basque population database could be used to calculate identification or kinship parameters regardless of whether the Basque individuals are from the European Basque Country or from the Basque diaspora in the Western USA.

  6. Gerstmann, Sträussler, and Scheinker: the persecution of the men behind the syndrome.

    Science.gov (United States)

    Zeidman, Lawrence A; Ziller, Matthias Georg; Shevell, Michael

    2014-07-15

    In 1936, Austrian neuroscientists Josef Gerstmann and Ernst Sträussler, along with expatriate Russian neuroscientist Ilya Mark Scheinker, described the familial prion disorder later named for them from a case they mutually treated at a Viennese neurologic hospital. In 1938, Austria was annexed to Nazi Germany in the Anschluss, effectively ending any collaboration between the 3 men. Gerstmann and Scheinker eventually immigrated to America, and Sträussler, although dismissed from his faculty position, remained protected from persecution in Vienna throughout the war likely because of his marriage to an "Aryan woman." Although he attained some degree of success in exile, Gerstmann was never again director of a hospital and primarily maintained a private practice after some brief consulting positions in New York in the 1940s. His medical degree was retroactively stripped by the Nazis without his knowledge, and was not reinstated until 1955. Gerstmann also became embroiled in a bitter struggle to regain his confiscated property in Vienna. Scheinker, aided by the refugee resettlement committee, settled in Cincinnati where he had several successful years and published 3 textbooks, but was denied university tenure and entered private practice until his untimely death. All 3 neurologists lost significant career momentum, and had to pick up the pieces of their fractured lives after the war or their forced exile. Their stories reflect many of the tragic realities of Nazi persecution of Jewish physicians.

  7. Ethnically distinct populations of historical Tibet exhibit distinct autosomal STR compositions.

    Science.gov (United States)

    Tsering, Thupten; Gayden, Tenzin; Chennakrishnaiah, Shilpa; Bukhari, Areej; Garcia-Bertrand, Ralph; Herrera, Rene J

    2016-03-01

    At an average altitude of 4000m above sea level, the Tibetan plateau is one of the highest plains on the planet. It is surrounded on three sides by massive mountain ranges: the Kunlun, the Karakoram and the Himalayas. These natural barriers have kept Tibet relatively isolated. In the present study, 15 autosomal STR loci were genotyped in 338 unrelated individuals from three traditional provinces of historical Tibet: Amdo (86), Kham (101) and U-Tsang (151). All the studied loci were in Hardy-Weinberg equilibrium except for the D19S433 locus in the Kham province. FGA, D21S11 and D2S1338 show the highest observed heterozygosity values in Amdo (0.8954), Kham (0.9208) and U-Tsang (0.8940), respectively, whereas TPOX is the least variable marker displaying the lowest value for the same parameter. U-Tsang exhibits the highest total numbers of alleles (139) followed by Kham (130) and Amdo (128) groups. The allele frequency data from this study were compared to relevant global reference populations. Our results indicate that although these three Tibetan populations group together in both the Correspondence Analysis (CA) plot and the Neighbor Joining (NJ) tree, they exhibit some degree of genetic differentiation among themselves congruent with their unique dialects, cultures and traditions. The 15 autosomal STR loci studied were found to be informative and discriminating, thereby providing a useful set of markers for population genetic studies.

  8. Y-STR diversity and sex-biased gene flow among Caribbean populations.

    Science.gov (United States)

    Simms, Tanya M; Wright, Marisil R; Martinez, Emanuel; Regueiro, Maria; McCartney, Quinn; Herrera, Rene J

    2013-03-01

    In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Y chromosome STR allelic and haplotype diversity in five ethnic Tamil populations from Tamil Nadu, India.

    Science.gov (United States)

    Balamurugan, Kuppareddi; Suhasini, G; Vijaya, M; Kanthimathi, S; Mullins, Nicole; Tracey, Martin; Duncan, George

    2010-09-01

    We have analyzed 17 Y chromosomal STR loci in a population sample of 154 unrelated male individuals of the Tamil ethnic group residing in the state of Tamil Nadu, Southern India using AmpFlSTR(R) Yfiler PCR amplification kit. The population samples consist of the following castes: Kongu Gounder (KOG), Nadar Hindu (NAH), Agamudayar (AGA), Parayar (PAR) and other Tamil individuals (MCT) of mixed castes. A total of 152 unique haplotypes were identified among the 154 individuals studied. The haplotype diversity was found to be 0.9935 or higher for all the five groups. The results of population pairwise Fst p values indicate no statistically significant differentiation between the five populations in this study, but the results were highly significant when compared with 12 other global populations (p<0.05). Comparison of populations in this study with other national and global populations using Principal co-ordinate analysis (PCA) using Rst distance matrix indicates a delineation of all the Indian populations from other unrelated populations.

  10. Population data for 12 Y-chromosome STR loci in a sample from Honduras.

    Science.gov (United States)

    Matamoros, Mireya; Yurrebaso, Iñaki; Gusmão, Leonor; García, Oscar

    2009-09-01

    Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 128 unrelated male individuals from Honduras, Central America. A total of 112 haplotypes were identified by the 12 Y-STR loci of which 98 were unique. The haplotype diversity (98.99%) and the proportion of different haplotypes (87.50%) were estimated. Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa. The analysis of a Multi Dimensional Scaling (MDS) plot, based on pairwise R(ST) genetic distances, allowed to conclude that Honduras is highly differentiated from the African samples (0.343Honduras showed a lower genetic distance to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Central American cluster (Mexico and El Salvador).

  11. Population data for 12 Y-chromosome STR loci in a sample from El Salvador.

    Science.gov (United States)

    Monterrosa, Juan Carlos; Morales, Josefina A; Yurrebaso, Iñaki; Gusmão, Leonor; García, Oscar

    2010-01-01

    Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 150 unrelated male individuals from El Salvador, Central America. A total of 131 haplotypes were identified by the 12 Y-STR loci of which 118 were unique. The haplotype diversity (99.08%) and the proportion of different haplotypes (87.33%) were estimated. R(ST) genetic distances were calculated between El Salvador and other populations from Southern and Central America, Europe and Africa. The highest R(ST) genetic distances were found when comparing El Salvador with African populations (0.334 El Salvador and Southern and Central Native groups presented a wide range of values (from 0.024 to 0.210) that can be explained by the differences in the proportion of European versus Amerindian contributions in these population groups. The Multi Dimensional Scaling (MDS) plot analysis, based on pairwise R(ST) values, showed that the general population of El Salvador is closer to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Southern/Central American cluster of Native and Mestizo populations.

  12. The young open cluster NGC 7067 using Strömgren photometry

    Science.gov (United States)

    Monguió, M.; Negueruela, I.; Marco, A.; González-Fernández, C.; Alonso-Santiago, J.; Costado, M. T.; Casamiquela, L.; López-Corredoira, M.; Molgó, J.; Vilardell, F.; Alfaro, E. J.; Antoja, T.; Figueras, F.; Garcia, M.; Jordi, C.; Romero-Gómez, M.

    2017-04-01

    NGC 7067 is a young open cluster located in the direction between the first and the second Galactic quadrants and close to the Perseus spiral arm. This makes it useful for studies of the nature of the Milky Way spiral arms. Strömgren photometry taken with the Wide Field Camera at the Isaac Newton Telescope allowed us to compute individual physical parameters for the observed stars and hence to derive the cluster's physical parameters. Spectra from the 1.93-m telescope at the Observatoire de Haute-Provence helped to check and improve the results. We obtained photometry for 1233 stars, individual physical parameters for 515 and spectra for 9 of them. The 139 selected cluster members lead to a cluster distance of 4.4 ± 0.4 kpc, with an age below log10(t(yr)) = 7.3 and a present mass of 1260 ± 160 M⊙. The morphology of the data reveals that the centre of the cluster is at (α, δ) = (21: 24: 13.69, +48: 00: 39.2) J2000, with a radius of 6.1 arcmin. Strömgren and spectroscopic data allowed us to improve the previous parameters available for the cluster in the literature.

  13. Genetic polymorphism of 14 non-CODIS STR loci for forensic use in southeast China population.

    Science.gov (United States)

    Shi, Meisen; Yu, Xiaojun; Bai, Rufeng; Shu, Xiji; Zhu, Guanghui; Lv, Junyao; Tu, Youhua

    2008-01-15

    We investigated 14 polymorphic STR loci (D1S2142, D2S1360, D3S1545, D7S1517, D10S2325, D12S391, D13S1492, D14S306, D15S659, D16S3253, D18S1270, D19S253, D20S470, D21S1437) which are not included in the standard sets of forensic loci (CODIS) in a sample of 216 unrelated healthy southeast Chinese individuals. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. The accumulated powers of discrimination and power of exclusion for the 14 loci were 99.9999999999 and 99.999998%, respectively. No linkage was observed between the 14 loci and the traditional set of STR markers included in commercially available kits (the AmpFLSTR IdentifilerTM 15 System loci). We thus considered the studied 14 STRs are informative and when necessary, can be used as the candidate genetic markers in the study and application in genetics and forensic practice.

  14. Historical sketch of Slovak Haban (Hutterite) population based on autosomal STR analysis.

    Science.gov (United States)

    Soták, M; Petrejčíková, E; Siváková, D; Rębała, K; Bôžiková, A; Bernasovský, I; Carnogurská, J; Boronová, I; Mačeková, S; Homol'ová, L; Sovičová, A; Gabriková, D; Rusínová, L; Bernasovská, J

    2011-10-01

    According to the Hutterite chronicles, the Habans arrived from Austrian Tyrol, Switzerland, and northernmost Italy and stayed in four regions of Slovakia (Sobotište, Vel'ké Leváre, Moravský Svätý Ján, Trenčín). There are some communities in western Slovakia that retained their Haban cultural identity and still identify themselves as descendents of the Hutterite population with their own specific customs. Slovak Habans are typical founder population with significant social isolation for which high degree of inbreeding is typical. Present study investigated STR polymorphisms as a powerful genetic tool for population genetic studies. The aim was to perform a comparative, population genetic study based on 15 STR loci widely used in forensic genetics, of the Haban population, the Slovak majority population and the population of Tyrol. We analyzed allele frequencies and other statistical parameters in three selected populations in order to identify groups of specific ethnic origin and establish their genetic relationship. The data set included 110 unrelated Habans and 201 unrelated individuals from the Slovak majority population, as well as allelic frequencies for the population of Austrian Tyrol available in the literature. Population pairwise FST values used as a short term genetic distance between populations showed significant differentiation between the Habans and both reference populations (FST=0.0025 and 0.0042 for comparison with the Slovaks and Austrians, respectively; ppopulation, which may be at least partially explained by gene flow between neighboring Haban and Slovak populations.

  15. [Significance of additional RFLP single locus probes analysis after STR based determination of sibship].

    Science.gov (United States)

    Mályusz, Victoria; Schmidt, Maren; Simeoni, Eva; Poetsch, Micaela; Schwark, Thorsten; Oehmichen, Manfred; von Wurmb-Schwark, Nicole

    2007-01-01

    Autosomal STR typing alone seems to be no sufficient tool for resolving deficiency cases (e.g. cases of questioned paternity or half-sibships). Therefore, we investigated whether the additional analysis of RFLP single locus probes can improve the solution of such complicated kinship cases. We analyzed 207 children and men from 101 families using the AmpFlSTRIdentifiler multiplex PCR kit and three RFLP single locus probes. A comparison between each child and all unrelated men resulted in 11,023 man / child pairs. Less than three excluding STRs were found in 125 child / unrelated man pairs (1.13%). Additional analysis of RFLP results reduced the number of ambiguous cases to 35. Half-sibling pairs were simulated using STR results from 20 cases with high paternity probabilities (group 1) and relatively low paternity probabilities (group 2). Using a commercially available computer program we calculated probabilities for 778 half-sibling pairs. In 35 pairs (4.49%) half-sibling probabilities over 90.0% could be calculated. Additional investigation of RFLP single locus probes did not lead to a more reliable evaluation of these results. The combined investigation of autosomal STRs and RFLP single locus probes can satisfactorily solve deficient paternities but does not contribute to the solution of questioned half-sibships.

  16. Strömgren survey for asteroseismology and galactic archaeology: Let the saga begin

    Energy Technology Data Exchange (ETDEWEB)

    Casagrande, L.; Dotter, A.; Milone, A. P.; Marino, A. F.; Asplund, M.; Schlesinger, K. J. [Research School of Astronomy and Astrophysics, Mount Stromlo Observatory, The Australian National University, Canberra, ACT 2611 (Australia); Aguirre, V. Silva; Lund, M. N.; Grundahl, F.; Nissen, P. E. [Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C (Denmark); Stello, D. [Sydney Institute for Astronomy (SIfA), School of Physics, University of Sydney, Sydney, NSW 2006 (Australia); Huber, D. [NASA Ames Research Center, Moffett Field, CA 94035 (United States); Serenelli, A. M. [Institute of Space Sciences (IEEC-CSIC), Campus UAB, Fac. Ciéncies, Torre C5 parell 2, E-08193 Bellaterra (Spain); Cassisi, S.; Pietrinferni, A. [INAF-Osservatorio Astronomico di Collurania, via Maggini, I-64100 Teramo (Italy); Hodgkin, S. [Institute of Astronomy, Madingley Road, Cambridge CB3 0HA (United Kingdom); Feltzing, S. [Lund Observatory, Department of Astronomy and Theoretical Physics, P.O. Box 43, SE-22100 Lund (Sweden); Flynn, C. [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, VIC 3122 (Australia); Schönrich, R. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210-1173 (United States); Wang, W., E-mail: luca.casagrande@anu.edu.au [National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2014-06-01

    Asteroseismology has the capability of precisely determining stellar properties that would otherwise be inaccessible, such as radii, masses, and thus ages of stars. When coupling this information with classical determinations of stellar parameters, such as metallicities, effective temperatures, and angular diameters, powerful new diagnostics for Galactic studies can be obtained. The ongoing Strömgren survey for Asteroseismology and Galactic Archaeology has the goal of transforming the Kepler field into a new benchmark for Galactic studies, similar to the solar neighborhood. Here we present the first results from a stripe centered at a Galactic longitude of 74° and covering latitude from about 8° to 20°, which includes almost 1000 K giants with seismic information and the benchmark open cluster NGC 6819. We describe the coupling of classical and seismic parameters, the accuracy as well as the caveats of the derived effective temperatures, metallicities, distances, surface gravities, masses, and radii. Confidence in the achieved precision is corroborated by the detection of the first and secondary clumps in a population of field stars with a ratio of 2 to 1 and by the negligible scatter in the seismic distances among NGC 6819 member stars. An assessment of the reliability of stellar parameters in the Kepler Input Catalog is also performed, and the impact of our results for population studies in the Milky Way is discussed, along with the importance of an all-sky Strömgren survey.

  17. Arcuate nucleus transcriptome profiling identifies ankyrin repeat and suppressor of cytokine signalling box-containing protein 4 as a gene regulated by fasting in central nervous system feeding circuits.

    Science.gov (United States)

    Li, J-Y; Kuick, R; Thompson, R C; Misek, D E; Lai, Y-M; Liu, Y-Q; Chai, B-X; Hanash, S M; Gantz, I

    2005-06-01

    The arcuate nucleus of the hypothalamus is a primary site for sensing blood borne nutrients and hormonal messengers that reflect caloric status. To identify novel energy homeostatic genes, we examined RNA extracts from the microdissected arcuate nucleus of fed and 48-h fasted rats using oligonucleotide microarrays. The relative abundance of 118 mRNA transcripts was increased and 203 mRNA transcripts was decreased during fasting. One of the down-regulated mRNAs was ankyrin-repeat and suppressor of cytokine signalling box-containing protein 4 (Asb-4). The predicted structure of Asb-4 protein suggested that it might encode an intracellular regulatory protein, and therefore its mRNA expression was investigated further. Reverse transcription quantitative polymerase chain reaction was used to validate down-regulation of Asb-4 mRNA in the arcuate nucleus of the fasted Sprague-Dawley rat (relative expression of Asb-4 mRNA: fed = 4.66 +/- 0.26; fasted = 3.96 +/- 0.23; n = 4, P regulation was also demonstrated in the obese fa/fa Zucker rat, another model of energy disequilibrium (relative expression of Asb-4 mRNA: lean Zucker = 3.91 +/- 0.32; fa/fa = 2.93 +/- 0.26; n = 5, P fasted state, the percentage of POMC neurones expressing Asb-4 mRNA drops to 73.2% (P fasted POMC neurone is markedly decreased. Conversely, expression of Asb-4 mRNA by NPY neurones in the fasted state is modestly increased to 52.7% (P < 0.05). Based on its differential expression, neuroanatomical distribution and colocalisation, we hypothesise that Asb-4 is a gene involved in energy homeostasis.

  18. Polimorfismos de 17 marcadores STR del cromosoma-Y en una muestra poblacional del altiplano cundiboyacense

    Directory of Open Access Journals (Sweden)

    Korina María Rojas

    2011-03-01

    Full Text Available Introducción: La tipificación molecular de ADN de cromosoma-Y es una herramienta de reconocida importancia en el proceso de identificación de individuos de género masculino en diversos casos forenses. Actualmente es una herramienta de apoyo para los laboratorios de genética estatales en la identificación de víctimas del conflicto armado en Colombia, dentro de los procesos enmarcados en la Ley de Justicia y Paz. En este estudiose determina el haplotipo del cromosoma-Y que será comparado con parientes por línea paaterna de género masculino, con el fin de realizar el análisis estadístico de estos marcadores, aportar a una base de datos colombiana y comparar con parientes de la línea masculina.Objetivo: Realizar una caracterización de haplotipos mediante análisis de marcadores moleculares, STR del cromosoma-Y en una muestra de población del altiplano cundiboyacense colombiano.Metodología: De las muestras del «Programa de Banco de muestras de sangre de funcionarios de la Fiscalía General de la Nación (FGN» fueron seleccionadas aleatoriamente 74 muestras de individuos que no reportaron relación por línea paterna entre sí y cuyo origen geográfico por línea paterna dos generaciones atrás correspondía a los departamentos de Cundinamarca o Boyacá. Se amplificaron y tipificaron 17 polimorfismos de repeticiones en tandem en el cromosoma-Y, el que se aplicó el kit comercial AmpFiSTR®YFiler™ (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438 y DYS448.Resultados: Distribución de frecuencias alélicas y haplotípicas para los 17 marcadores analizados: se determinaron 71 haplotipos con 17 marcadores STR-Y, de los que 68 eran únicos y 3 fueron observados en 2 individuos con un haplotipo compartido para los dos departamentos del altiplano cundiboyacense. La diversidad haplotípica para la muestra poblacional fue de 99.9% con un poder de discriminaci

  19. Polimorfismos de 17 marcadores STR del cromosoma-Y en una muestra poblacional del altiplano cundiboyacense*

    Directory of Open Access Journals (Sweden)

    Korina María Rojas

    2011-04-01

    Full Text Available Introducción: La tipificación molecular de ADN de cromosoma-Y es una herramienta de reconocida importancia en el proceso de identificación de individuos de género masculino en diversos casos forenses. Actualmente es una herramienta de apoyo para los laboratorios de genética estatales en la identificación de víctimas del conflicto armado en Colombia, dentro de los procesos enmarcados en la Ley de Justicia y Paz. En este estudiose determina el haplotipo del cromosoma-Y que será comparado con parientes por línea paaterna de género masculino, con el fin de realizar el análisis estadístico de estos marcadores, aportar a una base de datos colombiana y comparar con parientes de la línea masculina. Objetivo: Realizar una caracterización de haplotipos mediante análisis de marcadores moleculares, STR del cromosoma-Y en una muestra de población del altiplano cundiboyacense colombiano. Metodología: De las muestras del «Programa de Banco de muestras de sangre de funcionarios de la Fiscalía General de la Nación (FGN» fueron seleccionadas aleatoriamente 74 muestras de individuos que no reportaron relación por línea paterna entre sí y cuyo origen geográfico por línea paterna dos generaciones atrás correspondía a los departamentos de Cundinamarca o Boyacá. Se amplificaron y tipificaron 17 polimorfismos de repeticiones en tandem en el cromosoma-Y, el que se aplicó el kit comercial AmpFiSTR®YFiler™ (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438 y DYS448. Resultados: Distribución de frecuencias alélicas y haplotípicas para los 17 marcadores analizados: se determinaron 71 haplotipos con 17 marcadores STR-Y, de los que 68 eran únicos y 3 fueron observados en 2 individuos con un haplotipo compartido para los dos departamentos del altiplano cundiboyacense. La diversidad haplotípica para la muestra poblacional fue de 99.9% con un poder de discriminaci

  20. Fifteen non-CODIS autosomal short tandem repeat loci multiplex data from nine population groups living in Taiwan.

    Science.gov (United States)

    Hwa, Hsiao-Lin; Chang, Yih-Yuan; Lee, James Chun-I; Lin, Chun-Yen; Yin, Hsiang-Yi; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2012-07-01

    The analysis of autosomal short tandem repeat (STR) loci is a powerful tool in forensic genetics. We developed a multiplex system in which 15 non-Combined DNA Index System autosomal STRs (D3S1744, D4S2366, D8S1110, D10S2325, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 1,098 unrelated subjects of nine population groups living in Taiwan, including Taiwanese Han, indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, Thais, Vietnamese, Indonesians, and Caucasians, were collected and analyzed using this system. The distributions of the allelic frequencies and the forensic parameters of each population group were presented. The combined discrimination power and the combined power of exclusion were high in all population groups tested in this study. A multidimensional scaling plot of these nine population groups based on the Reynolds' genetic distances calculated from 15 autosomal STRs was constructed, and the genetic substructure in this area was presented. In conclusion, this 15 autosomal STR multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing in different populations.

  1. New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards.

    Directory of Open Access Journals (Sweden)

    Maud Gits-Muselli

    Full Text Available Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker and multiple (more than one allele per marker genotypes were observed in 34 (32% and 72 (68% samples, respectively. A genotype could be assigned to 55 samples (54 patients and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21 in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.

  2. 圈C4的(St(r),St(r+1)Gr,St(r+1)-冠的优美性%On the gracefulness of the(St(r), St(r+1)Gr, St(r+1)- corona of the cycle C4

    Institute of Scientific and Technical Information of China (English)

    康芳茂; 吴跃生

    2014-01-01

    给出了圈C4的(St(r), St(r+1)Gr, St(r+1)-冠的定义,讨论了圈C4的(St(r), St(r+1)Gr, St(r+1)-冠的优美性,用构造性的方法给出了圈C4的(St(r), St(r+1)Gr, St(r+1)-冠的优美标号。%Gave the definition of the (St (r ), St (r +1), Gr , St (r +1)) - corona of the cycle C4.Discussed the gracefulness of the (St (r ), St (r +1), Gr , St (r +1)) - corona of the cycleC4.The graceful labelings was given by the method of construction.

  3. Genetic analysis of 17 Y-chromosomal STR loci of Chinese Tujia ethnic group residing in Youyang Region of Southern China.

    Science.gov (United States)

    Yang, Ya-Ran; Jing, Yu-Ting; Zhang, Guo-Dong; Fang, Xiang-Dong; Yan, Jiang-Wei

    2014-05-01

    Y-STR haplotype data were obtained in a population sample of 197 unrelated healthy male individuals of Chinese Tujia ethnic minority group residing in an autonomous county of Southern China using 17 Y-chromosome STR markers. A total of 197 haplotypes were identified in the set of Y-STR loci. The overall haplotype diversity for the Tujia population at 17 Y-STR loci was 1.0000±0.0005. Genetic distance was estimated between this population and other 14 Chinese populations including Paiwan and Atayal populations of Taiwan, and Southern Han, Dong, Jing, Miao, Yao, Zhuang, Yi, Maonan, She, Hui, Sala, and Tibetan ethnic groups. The results demonstrated that the 17 Y-STR loci analyzed were highly polymorphic in Tujia ethnic group examined and hence useful for forensic cases, paternity testing, and population genetic studies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  4. Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample.

    Science.gov (United States)

    Penna, Larissa Siqueira; Silva, Fernanda Gamio; Salim, Patricia Hartstein; Ewald, Gisele; Jobim, Mariana; Magalhães, José Antônio de Azevedo; Jobim, Luiz Fernando

    2012-03-01

    We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni's correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PD(F)) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F (ST) between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.

  5. 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.

  6. 新疆巴州维吾尔族17个Y-STR位点遗传多态性%Genetic polymorphism of seventeen Y-chromosomeal STR loci in XinJiang Bazhou Uygur population

    Institute of Scientific and Technical Information of China (English)

    陈慧锦; 蒲红伟; 胡佳; 王伟; 张丽萍

    2011-01-01

    Objective:To investigate the allelic and haplotype frequency distribution of seventeen short tandem repeat loci of Y chromosome in Xinjiang Uygur population in Bazhou. Methods:The template DNAs were extracted from blood samples of 149 unrelated Uygur male individuals,and seventeen Y-STR loci were amplified by the AmpFlSTR YfilerTM.The PCR products were analyzed and genotyped with ABI3130XL Sequencer. Results:The values of genetic diversity of DYS456,DYS389 Ⅰ /Ⅱ ,DYS390,DYS458,DYS19, DYS385a/b,DYS393,DYS391,DYS439,DYS635,DYS392,Y-GATA-H4,DYS437,DYS438,and DYS448 were between 0.4 982 and 0.9 485.A total of 148 different haplotypes were observed,and the value of genetic diversity of haplotypes was 0.99 986. Conclusion: The 17 Y-STR loci in Xinjiang Uygur population in Bazhou are highly polymorphic and suitable for paternity testing and paternal genetic lineage evolution.%目的:调查17个Y染色体短串联重复序列(Y-Short tandem repeat,Y-STR)基因座及其单倍型在新疆巴州维吾尔族人群中的分布情况.方法:应用AmpFlSTR YfilerTM荧光标记复合扩增系统,对149名维吾尔族无关男性个体血样进行17个Y-STR位点的复合扩增,用ABI 3130XL遗传分析仪对扩增产物进行检测分析.结果:DYS456、DYS389 Ⅰ/Ⅱ、DYS390、DYS458、DYS19、DYS385a/b、DYS393、DYS391、DYS439、DYS635、DYS392、Y-GATA-H4、DYS437、DYS438、DYS448各位点遗传多样性(Genetic diversity,GD)值分布在0.498 2~0.948 5之间;17个Y-STR位点共观察到单倍型148种,其单倍型多样性(Haplotype diversity,HD)值为0.999 86.结论:新疆巴州维吾尔族17个Y-STR位点具有丰富的遗传多样性,可为父权鉴定和父系进化研究提供有价值的遗传学资料.

  7. Grå strækninger på det overordnede vejnet i det åbne land

    DEFF Research Database (Denmark)

    Sørensen, Michael

    2006-01-01

    Det grå strækningsarbejde er i de sidste 10 år blevet en større og større del af de danske vejbestyrelsers stedbundne trafiksikkerhedsarbejde. Imidlertid er der hverken blevet formuleret en præcis og brugbar definition af begrebet, formuleret en overordnet filosofi for arbejdet eller blevet udvik...

  8. 24 Y-chromosomal STR haplotypic polymorphisms for Chinese Uygur ethnic group and its phylogenic analysis with other Chinese groups.

    Science.gov (United States)

    Liu, Wen-Juan; Pu, Hong-Wei; Yang, Chun-Hua; Meng, Hao-Tian; Zhang, Yu-Dang; Zhang, Li-Ping; Yan, Jiang-Wei; Wang, Hong-Dan; Ren, Jian-Wen; Sun, Jun-Yi; Liu, Chao; Wang, Hui; Zhu, Bo-Feng

    2015-02-01

    The Uygur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and is a precious resource for the study of ethnogeny and forensic biology. Previous studies have focused on the genetic background of the Uygur group, however, the patrilineal descent of the group is still unclear. In this study, we investigated the genetic diversity of 24 Y-STR loci in the Uygur group and analyzed the population differentiations as well as the genetic relationships between the Uygur group and other previously reported populations using 17 Y-filer loci. According to haplotypic analysis of the 24 Y-STR loci in 109 Uygur individuals, 104 different haplotypes were obtained, 99 of which were unique. The haplotypic diversity and discrimination capacity of these 24 Y-STR loci in Uygur group were 0.9992 and 0.9541, respectively. An additional 7 loci (DYS388, DYS444, DYS447, DYS449, DYS522, and DYS527a,b) showed high genetic diversity and improved the overall discrimination capacity of the 24 Y-STR system. Pairwise Fst and neighbor-joining analysis showed that the Uygur group was genetically close to the Han populations from different regions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Genetic Polymorphism of Nine Non-CODIS STR Loci in Hu-nan Province-based Chinese Han Population

    Institute of Scientific and Technical Information of China (English)

    GUO Juan-juan; LIU Ying; GUO Ya-dong; YAN Jie; CHANG Yun-feng; CAI Ji-feng; LU Ting; ZHA Lagabaiyila

    2014-01-01

    Objective To determine the allelic frequency distribution and genetic parameters of nine non-CODIS DNA index systems of the short tandemrepeat (STR ) loci (D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05). Methods A total of 353 blood samples were collected, extracted, amplified, and analyzed fromunrelated healthy individuals of Han na-tionality in Hunan Province, China. Results O ne hundred and fourteen alleles were observed in the pop-ulation with corresponding allelic frequencies ranged from0.001 0 to 0.323 0. For all the nine non-CODIS STR loci, the observed genotypic data showed no significant deviations fromthe Hardy-W einberg equi-librium. The Ho, He, PIC, D P, and PE of the studied non-CODIS STR loci ranged from0.108 0 to 0.195 0, 0.805 0 to 0.892 0, 0.770 0 to 0.860 0, 0.925 0 to 0.966 0 and 0.607 0 to 0.780 0, respectively. Conclusion N ine non-CODIS STR loci have high degrees of polymorphisms, which may be useful in in-dividual forensic identification and parentage testing in forensic practice.

  10. STR3 and CYS3 Contribute to 2-Furfurylthiol Biosynthesis in Chinese Sesame-Flavored Baijiu Yeast.

    Science.gov (United States)

    Zha, Musu; Yin, Sheng; Sun, Baoguo; Wang, Xin; Wang, Chengtao

    2017-07-12

    2-Furfurylthiol is an important aroma compound with characteristic sesame flavor. It was recently identified as the representative aroma compound of Chinese sesame-flavored Baijiu. But its formation mechanism is unclear. In this study, the dominant yeast species Saccharomyces cerevisiae, Pichia kudriavzevii, and Wickerhamomyces anomalus were isolated from samples of Chinese sesame-flavored fermentation and were screened for the capacity of 2-furfurylthiol biosynthesis. Some isolates were found to be capable of generating 2-furfurylthiol using furfural and l-cysteine as precursors, among which S. cerevisiae G20 exhibited the strongest capacity with a yield of 3.03 mg/L. Furthermore, the genes STR3 and CYS3 from S. cerevisiae were cloned and overexpressed in the reference strain S. cerevisiae S288c and the isolate strain G20, respectively, which resulted in a significant increase in 2-furfurylthiol release in the two strains. Moreover, inactivation of STR3 gene in S288c and G20 led to obvious reduction in 2-furfurylthiol production, demonstrating that STR3 got involved in 2-furfurylthiol biosynthesis in S. cerevisiae. It is the first time that the yeast isolates with high capacity of 2-furfurylthiol biosynthesis were found during Chinese sesame-flavored Baijiu fermentation and confirmed that the genes STR3 and CYS3 were closely relevant to 2-furfurylthiol biosynthesis.

  11. Impact of a chromosome X STR Decaplex in deficiency paternity cases

    Science.gov (United States)

    Trindade-Filho, Aluisio; Ferreira, Samuel; Oliveira, Silviene F.

    2013-01-01

    Deficiency paternity cases, characterized by the absence of the alleged father, are a challenge for forensic genetics. Here we present four cases with a female child and a deceased alleged father in which the analysis of a set of 21 or 22 autosomal STRs (AS STRs) produced results within a range of doubt when genotyping relatives of the alleged father. Aiming to increase the Paternity Index (PI) and obtain more reliable results, a set of 10 X-linked STR markers, developed by the Spanish and Portuguese Group of the International Society for Forensic Genetics (ISFG), was then added. Statistical analysis substantially shifted the results towards the alleged fatherhood in all four cases, with more dramatic changes when the supposed half-sister and respective mother were the relatives tested. PMID:24385853

  12. Oligomerisation of C. elegans Olfactory Receptors, ODR-10 and STR-112, in Yeast

    KAUST Repository

    Tehseen, Muhammad

    2014-09-25

    It is widely accepted that vertebrate G-Protein Coupled Receptors (GPCRs) associate with each other as homo- or hetero-dimers or higher-order oligomers. The C. elegans genome encodes hundreds of olfactory GPCRs, which may be expressed in fewer than a dozen chemosensory neurons, suggesting an opportunity for oligomerisation. Here we show, using three independent lines of evidence: co-immunoprecipitation, bioluminescence resonance energy transfer and a yeast two-hybrid assay that nematode olfactory receptors (ORs) oligomerise when heterologously expressed in yeast. Specifically, the nematode receptor ODR-10 is able to homo-oligomerise and can also form heteromers with the related nematode receptor STR-112. ODR-10 also oligomerised with the rat I7 OR but did not oligomerise with the human somatostatin receptor 5, a neuropeptide receptor. In this study, the question of functional relevance was not addressed and remains to be investigated.

  13. Haplotype diversity of 17 Y-str loci in an admixed population from the Brazilian Amazon

    Science.gov (United States)

    Francez, Pablo Abdon da Costa; Ramos, Luiz Patrick Vidal; de Jesus Brabo Ferreira Palha, Teresinha; dos Santos, Sidney Emanuel Batista

    2012-01-01

    The allelic and haplotype frequencies of 17 Y-STR loci most commonly used in forensic testing were estimated in a sample of 138 unrelated healthy males from Macapá, in the northern Amazon region of Brazil. The average gene diversity was 0.6554 ± 0.3315. 134 haplotypes of the 17 loci were observed, 130 of them unique and four present in two individuals each. The haplotype diversity index was 0.9996 + 0.0009, with the most frequent haplogroups being R1b (52.2%), E1b1b (11.6%), J2 (10.1%) and Q (7.2%). Most haplogroups of this population belonged to European male lineages (89.2%), followed by Amerindian (7.2%) and African (3.6%) lineages. PMID:22481873

  14. Forensic and population genetic analyses of eighteen non-CODIS miniSTR loci in the Korean population.

    Science.gov (United States)

    Jin, Han Jun; Kim, Ki Cheol; Yoon, Cha Eun; Kim, Wook

    2013-11-01

    We analyzed the variation of eighteen miniSTR loci in 411 randomly chosen individuals from Korea to increase the probability that a degraded sample can be typed, as well as to provide an expanded and reliable population database. Six multiplex PCR systems were developed (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161; multiplex IV: D3S4529, D8S1115 and D18S853; multiplex V: D6S1017, D11S4463 and D17S1301; multiplex VI: D5S2500, D9S1122 and D21S1437). Allele frequencies and forensic parameters were calculated to evaluate the suitability and robustness of these non-CODIS miniSTR systems. No significant deviation from Hardy-Weinberg equilibrium expectations were observed, except for D4S2364, D5S2500 and D20S161 loci. A multidimensional scaling plot based on allele frequencies of the six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045) showed that Koreans appeared to have most genetic affinity with Chinese and Japanese than to other Eurasian populations compared here. The combined probability of match calculated from the 18 miniSTR loci was 2.902 × 10(-17), indicating a high degree of polymorphism. Thus, the 18 miniSTR loci can be suitable for recovering useful information for analyzing degraded forensic casework samples and for adding supplementary genetic information for a variety of analyses involving closely related individuals where there is a need for additional genetic information.

  15. Identification of population substructure among Jews using STR markers and dependence on reference populations included

    Directory of Open Access Journals (Sweden)

    Mutirangura Apiwat

    2010-06-01

    Full Text Available Abstract Background Detecting population substructure is a critical issue for association studies of health behaviors and other traits. Whether inherent in the population or an artifact of marker choice, determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Jewish populations, among which association studies are often conducted, have a known history of migrations. As a necessary step in understanding population structure to conduct valid association studies of health behaviors among Israeli Jews, we investigated genetic signatures of this history and quantified substructure to facilitate future investigations of these phenotypes in this population. Results Using 32 autosomal STR markers and the program STRUCTURE, we differentiated between Ashkenazi (AJ, N = 135 and non-Ashkenazi (NAJ, N = 226 Jewish populations in the form of Northern and Southern geographic genetic components (AJ north 73%, south 23%, NAJ north 33%, south 60%. The ability to detect substructure within these closely related populations using a small STR panel was contingent on including additional samples representing major continental populations in the analyses. Conclusions Although clustering programs such as STRUCTURE are designed to assign proportions of ancestry to individuals without reference population information, when Jewish samples were analyzed in the absence of proxy parental populations, substructure within Jews was not detected. Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from previous studies as well as historical records of migration and intermarriage.

  16. 21个非CODISSTR基因座的遗传多态性%21 non-CODIS STR loci on the genetic polymorphism

    Institute of Scientific and Technical Information of China (English)

    孙克盛; 张宏斌; 陈浩

    2012-01-01

    目的:探讨研究江浙汉族人群 21 个非 CODIS STR 基因座的遗传多态性.方法:使用 AGCU 21 + 1 STR 荧光标记复合扩增系统对江浙地区汉族的250 个无关个体的 21 个非 CODIS STR 基因座进行扩增,统计 STR 基因座的遗传学参数.结果:扩增后取得了 21 个 STR 基因座的等位基因频率分布,检测出 6、5、8、11、9、10、15、7、13、9、6、11、13、8、7、9、6、16、8、15、9 个等位基因,也获得了 21 个 STR 基因座的 H,He,DP,PM 及 PE 等的法医遗传学资料.结论:21 个非 CODIS STR 基因座具有良好的遗传多态性,适用于法医学亲权鉴定和个体识别.

  17. Association between a Tetranucleotide Repeat Polymorphism of SPAG16 Gene and Cataract in Male Children

    Directory of Open Access Journals (Sweden)

    Shipra Mehra

    2013-01-01

    Full Text Available Purpose. Studies involving genotyping of STR markers at 2q34 have repeatedly found the region to host the disease haplotype for pediatric cataract. Present study investigated the association of D2S2944 marker, in sperm associated antigen 16 (SPAG16 gene and rs2289917 polymorphism, in γ-crystallin B gene, with childhood cataract. Methods. 97 pediatric cataract cases and 110 children with no ocular defects were examined for tetranucleotide repeat marker/SNP using PCR-SSLP/RFLP techniques. Polymorphisms were assessed for association using contingency tables and linkage disequilibrium among alleles of the markers was estimated. Energy-optimization program predicted the secondary structure models of repeats of D2S2944. Results. Seven alleles of D2S2944, with 9–15 “GATA” repeats, were observed. Frequency of the longer allele of D2S2944, ≥(GATA13 repeats, was 0.73 in cases and 0.56 in controls (P=0.0123. Male children bearing ≥(GATA13 repeats showed >3-fold higher risk for cataract (CI95% = 1.43–7.00, P=0.0043, Pc=0.0086 as compared to female children (OR=1.19, CI95% = 0.49–2.92, P=0.70. Cases with haplotype—≥(GATA13 of D2S2944 and “C” allele rs2289917—have a higher risk for pediatric cataract (OR=2.952, CI95% = 1.595~5.463, P=0.000453. >(GATA13 repeats formed energetically more favorable stem-loop structure. Conclusion. Intragenic microsatellite repeat expansion in SPAG16 gene increases predisposition to pediatric cataract by probably interfering posttranscriptional events and affecting the expression of adjacent lens transparency gene/s in a gender bias manner.

  18. [Analysis of allelic drop-out at short tandem repeat loci].

    Science.gov (United States)

    Chen, Wen-jing; Li, Yue; Wu, Xiao-jie; Zhang, Yin-ming; Liu, Su-juan; Chen, Yong; Chen, Wei-hong; Sun, Hong-yu

    2012-06-01

    To explore the cause for allelic drop-out at short tandem repeat (STR) loci upon paternity testing with a PowerPlex® 16 kit. A total of 10 642 DNA confirmed paternity testing cases (18 314 parent/child allelic transfers) were analyzed with the PowerPlex® 16 kit. Samples suspected for having allelic drop-out were verified with an Identifiler™ kit and/or locus-specific singleplex amplification systems. PCR products of null alleles were separated and directly sequenced. Eight cases of allelic drop-out were found. The overall rate of null allele in the PowerPlex® 16 system was 0.437 × 10(-3). DNA sequencing has confirmed single base variations within the binding region of published primers, in which 4 cases involved the D18S51 locus (2 cases with G>A transitions at 79 bp upstream of the repeats, 1 case with G>T transversion at 162 bp downstream of the repeats and 1 case with G>C transversion at 74 bp upstream of the repeats), 2 cases involved the D21S11 locus (1 case with C>A transversion at 17 bp upstream of the repeats and 1 case with A>G transition at 12 bp upstream of the repeats). One case involved the FGA locus (1 case with G>A transition at 142 bp downstream of the repeats) and 1 case involved TPOX locus (1 case with G>A transition at 198 bp downstream of the repeats). Base variation in the primer binding region may cause failed PCR and result in null allele reports. Alternative primer sets should be used to verify the suspected allelic drop-out. Attention should be paid to this during paternity testing and data exchange for personal identification.

  19. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  20. Evaluation of different methods for DNA extraction from human burnt bones and the generation of genetic profiles for identification.

    Science.gov (United States)

    Uzair, Anum; Rasool, Nouman; Wasim, Muhammad

    2017-01-01

    Bone exposure to heat in the presence of moisture breaks the phosphodiester bonds of the backbone, leaving sheared DNA in bone cells. This also limits the possibility of generating a complete profile of the victim. With the increasing incidence of fire outbreaks over the past few years, a paradigm shift to establish identity has been observed, from morphological identification of victims to STR profiling. For this study, 10 bone samples were taken from burnt human bodies that were recovered from different fire outbreak scenes. The DNA from these burnt human tissues was isolated using four different extraction methods: the organic extraction method, the total demineralisation method, the Qiagen kit method, and the Chelex extraction method. STR profiles of victims were generated on a genetic analyser using an AmpFlSTR Identifiler® Plus Kit and analysed on Gene Mapper ID-X. DNA isolated from bones using the total demineralisation extraction method and organic extraction method was of the highest quality due to the efficient removal of inhibitors. DNA obtained using these two methods successfully generated the STR profiles of the victims. The quality of isolated DNA obtained through the Qiagen kit was comparatively low, but STR profiles of the victims were successfully generated. The Chelex kit failed to extract good quality DNA of high quantity from the burnt bones, encountering inhibition in all samples at varying degrees. This study concludes that total demineralisation and the Qiagen kit are sophisticated and reliable methods to obtain a good yield of DNA from burnt human bones, which can be used for the identification of victims.

  1. DWI Repeaters and Non-Repeaters: A Comparison.

    Science.gov (United States)

    Weeber, Stan

    1981-01-01

    Discussed how driving-while-intoxicated (DWI) repeaters differed signigicantly from nonrepeaters on 4 of 23 variables tested. Repeaters were more likely to have zero or two dependent children, attend church frequently, drink occasionally and have one or more arrests for public intoxication. (Author)

  2. To Repeat or Not to Repeat a Course

    Science.gov (United States)

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  3. Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system

    Directory of Open Access Journals (Sweden)

    Lillis Rebecca

    2008-07-01

    Full Text Available Abstract Background Several methods have been reported for strain typing of Mycoplasma genitalium. The value of these methods has never been comparatively assessed. The aims of this study were: 1 to identify new potential genetic markers based on an analysis of short tandem repeat (STR sequences in the published M. genitalium genome sequence; 2 to apply previously and newly identified markers to a panel of clinical strains in order to determine the optimal combination for an efficient multi-locus genotyping system; 3 to further confirm sexual transmission of M. genitalium using the newly developed system. Results We performed a comprehensive analysis of STRs in the genome of the M. genitalium type strain G37 and identified 18 loci containing STRs. In addition to one previously studied locus, MG309, we chose two others, MG307 and MG338, for further study. Based on an analysis of 74 unrelated patient specimens from New Orleans and Scandinavia, the discriminatory indices (DIs for these three markers were 0.9153, 0.7381 and 0.8730, respectively. Two other previously described markers, including single nucleotide polymorphisms (SNPs in the rRNA genes (rRNA-SNPs and SNPs in the MG191 gene (MG191-SNPs were found to have DIs of 0.5820 and 0.9392, respectively. A combination of MG309-STRs and MG191-SNPs yielded almost perfect discrimination (DI = 0.9894. An additional finding was that the rRNA-SNPs distribution pattern differed significantly between Scandinavia and New Orleans. Finally we applied multi-locus typing to further confirm sexual transmission using specimens from 74 unrelated patients and 31 concurrently infected couples. Analysis of multi-locus genotype profiles using the five variable loci described above revealed 27 of the couples had concordant genotype profiles compared to only four examples of concordance among the 74 unrelated randomly selected patients. Conclusion We propose that a combination of the MG309-STRs and MG191-SNPs is

  4. 新疆昌吉维吾尔族17个Y-STR基因座遗传多态性%Genetic polymorphisms of seventeen Y-chromosomeal STR loci in XinJiang Changji Uygur Population

    Institute of Scientific and Technical Information of China (English)

    张丽萍; 陈健刚; 蒲红伟; 付志敏; 杨昊

    2012-01-01

    目的 调查17个Y染色体短串联重复序列(Y-STR)基因座及其单倍型在新疆昌吉地区维吾尔族人群中的分布情况.方法 采用AmpFlSTR YfilerTM荧光标记复合扩增系统,对154名维吾尔族无关男性个体血样进行17个Y-STR位点的复合扩增,用ABI 3130XL遗传分析仪对扩增产物进行检测分析.结果 DYS456、DYS389Ⅰ、DYS390、DYS389Ⅱ、DYS458、DYS19、DYS385a/b、DYS393、DYS391、DYS439、DYS635、DYS392、Y-GATA-H4、DYS437、DYS438、DYS448各位点遗传多样性(GD值)分布在0.529 7~0.959 9之间;17个Y-STR位点共观察到单倍型151种,其单倍型多样性GD值为0.999 7.结论 新疆昌吉地区维吾尔族17个Y-STR位点具有丰富的遗传多样性,可为父权鉴定和父系进化研究提供有价值的遗传学资料.%Objective To investigate the allelic and haplotype frequency distribution of seventeen short tandem repeat loci of Y chromosome in Xinjiang Uygur population in Changji. Methods Seventeen Y-STR loci of which the template DNAs were extracted from blood samples of 154 unrelated male individuals in Uygur population, were amplified by using the AmpFlSTR YfilerTM. The PCR products were analyzed and genotyped with ABI3130XL Sequencer. Results The gene diversity ranged from 0. 529 7 to 0. 959 9 at DYS456,DYS389 I ,DYS390,DYS389 II ,DYS458,DYS19 ,DYS385a/b,DYS393,DYS391 ,DYS439 ,DYS635 ,DYS392, Y-G∧T∧-H4,DYS4 37,DYS438, and DYS448. A total of 151 different haplotypes were observed. The haplotype diversity value calculated from all 17 loci was 0. 999 7. Conclusion The 17th Y-STR loci in Xinjiang Uygur population in Changji are highly affluent genetic polymorphic and can offer valuable genetic datas for paternity testing and paternal genetic lineages evolution.

  5. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  6. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  7. All-photonic quantum repeaters

    Science.gov (United States)

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  8. Repeatability and Reproducibility of Virtual Subjective Refraction.

    Science.gov (United States)

    Perches, Sara; Collados, M Victoria; Ares, Jorge

    2016-10-01

    To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

  9. A multifluorescent STR-PCR for prenatal gene diagnosis of hemophilia A carriers%多重荧光STR-PCR方法在血友病A携带者产前基因诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    李少英; 马晓燕; 张慧敏; 王晓蔓; 黎青

    2011-01-01

    Objective To establish a reliable method for prenatal diagnosis of hemophilia A hy genetic linkage analysis. Method Multifluorescent STR-PCR method was used to analyze 50 normal females and 20 hemophilia A families. Result The heterozygote rate of DXS15 , DXS9901 , G6PD , DXS1073 , DXS1108 and F8Civs13 were 88% , 84% , 20o/e , 62% , 22% and 30%. Twenty hemophilia A carriers were successfully identified by these six STRs loci. Conclusion Multifluorescent STR-PCR is a convenient and efficient method for prenatal diagnosis of hemophilia A.%目的:通过血友病A家系遗传连锁分析,建立血友病A携带者产前诊断方法.方法:采用多重荧光STR-PCR方法对50例正常女性进行检测和20个血友病A家系进行连锁分析.结果:DXS15、DXS9901、G6PD、DXS1073、DXS1108和F8Civs13的杂合率分别为88%、84%、20%、62%、22%和30%;用这6个位点提供的遗传信息成功为20个血友病A携带者进行了产前诊断.结论:多重荧光STR-PCR方法是一种快速、简便、实用的血友病A产前诊断方法.

  10. CRED Subsurface Temperature Recorder (STR); PRIA, WAK; Long: 166.63805, Lat: 19.30092 (WGS84); Sensor Depth: 1.22m; Data Range: 20070505-20090324.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series...

  11. CRED Subsurface Temperature Recorder (STR); AMSM, OFU; Long: -169.65220, Lat: -14.18020 (WGS84); Sensor Depth: 6.10m; Data Range: 20060228-20080228.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  12. CRED Subsurface Temperature Recorder (STR); MHI, LAN; Long: -156.96869, Lat: 20.73729 (WGS84); Sensor Depth: 8.23m; Data Range: 20050804-20060806.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series...

  13. CRED Subsurface Temperature Recorder (STR); PRIA, PAL; Long: -162.08588, Lat: 05.88625 (WGS84); Sensor Depth: 3.30m; Data Range: 20060325-20071115.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  14. CRED Subsurface Temperature Recorder (STR); NWHI, LAY; Long: -171.73891, Lat: 25.77957 (WGS84); Sensor Depth: 1.22m; Data Range: 20060911-20070411.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  15. CRED Subsurface Temperature Recorder (STR); AMSM, SWA; Long: -171.09092, Lat: -11.05855 (WGS84); Sensor Depth: 14.00m; Data Range: 20060211-20080116.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  16. CRED Subsurface Temperature Recorder (STR); NWHI, MAR; Long: -170.53972, Lat: 25.38417 (WGS84); Sensor Depth: 1.50m; Data Range: 20030720-20040920.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  17. CRED Subsurface Temperature Recorder (STR); PRIA, WAK; Long: 166.59801, Lat: 19.31633 (WGS84); Sensor Depth: 24.08m; Data Range: 20051023-20070430.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  18. CRED Subsurface Temperature Recorder (STR); CNMI, MAU; Long: 145.20714, Lat: 20.01792 (WGS84); Sensor Depth: 31.39m; Data Range: 20070531-20080516.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  19. CRED Subsurface Temperature Recorder (STR); NWHI, LIS; Long: -173.96097, Lat: 26.06337 (WGS84); Sensor Depth: 0.61m; Data Range: 20060925-20081005.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  20. CRED Subsurface Temperature Recorder (STR); AMSM, OFU; Long: -169.65265, Lat: -14.17770 (WGS84); Sensor Depth: 1.22m; Data Range: 20080228-20100311.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  1. CRED Subsurface Temperature Recorder (STR); PRIA, PAL; Long: -162.04503, Lat: 05.87029 (WGS84); Sensor Depth: 1.21m; Data Range: 20060326-20070618.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  2. CRED Subsurface Temperature Recorder (STR); CNMI, SAI; Long: 145.72256, Lat: 15.23749 (WGS84); Sensor Depth: 5.49m; Data Range: 20070521-20090414.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  3. CRED Subsurface Temperature Recorder (STR); NWHI, LIS; Long: -173.91583, Lat: 25.96762 (WGS84); Sensor Depth: 10.36m; Data Range: 20081004-20090910.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  4. CRED Subsurface Temperature Recorder (STR); CNMI, FDP; Long: 144.90023, Lat: 20.53725 (WGS84); Sensor Depth: 31.70m; Data Range: 20070603-20090428.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  5. CRED Subsurface Temperature Recorder (STR); MHI, HAW; Long: -155.50222, Lat: 19.13291 (WGS84); Sensor Depth: 14.90m; Data Range: 20060816-20081031.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  6. CRED Subsurface Temperature Recorder (STR); PRIA, JAR; Long: -159.99665, Lat: -00.38183 (WGS84); Sensor Depth: 10.06m; Data Range: 20080327-20100403.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  7. CRED Subsurface Temperature Recorder (STR); NWHI, PHR; Long: -175.86345, Lat: 27.94234 (WGS84); Sensor Depth: 24.69m; Data Range: 20080923-20100915.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  8. CRED Subsurface Temperature Recorder (STR); PRIA, BAK; Long: -176.48881, Lat: 00.19171 (WGS84); Sensor Depth: 16.80m; Data Range: 20040124-20050627.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  9. CRED Subsurface Temperature Recorder (STR); AMSM, TUT; Long: -170.62375, Lat: -14.25194 (WGS84); Sensor Depth: 5.80m; Data Range: 20040220-20051111.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  10. CRED Subsurface Temperature Recorder (STR); CNMI, GUG; Long: 145.83140, Lat: 17.30733 (WGS84); Sensor Depth: 5.80m; Data Range: 20030911-20050712.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  11. CRED Subsurface Temperature Recorder (STR); NWHI, KUR; Long: -178.34453, Lat: 28.41852 (WGS84); Sensor Depth: 10.06m; Data Range: 20060917-20080929.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  12. CRED Subsurface Temperature Recorder (STR); PRIA, JAR; Long: -159.97450, Lat: -00.37545 (WGS84); Sensor Depth: 12.20m; Data Range: 20040328-20060320.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  13. CRED Subsurface Temperature Recorder (STR); PRIA, JAR; Long: -159.97228, Lat: -00.37500 (WGS84); Sensor Depth: 33.22m; Data Range: 20080328-20100403.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  14. Hudvård- och sårbehandling till patienter i samband med extern strålbehandling. En litteraturstudie.

    OpenAIRE

    2015-01-01

    Bakgrund: Strålbehandling är en vanlig behandlingsform vid cancersjukdom och hälften av alla cancerpatienter får någon form av strålbehandling, antingen extern eller intern strålbehandling. Hudreaktioner vid strålbehandling kan inte undvikas men med rätt omvårdnadsåtgärder kan man minska symptomen. Hudbiverkningar kan vara till stort besvär och förorsaka obehag hos patienten. Det finns fortfarande oklarheter i hur dessa bäst kan förebyggas och, när de uppstår, bäst lindras. Syfte: Syftet var ...

  15. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27506, Lat: 23.85620 (WGS84); Sensor Depth: 0.30m; Data Range: 20091009-20100907.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  16. CRED Subsurface Temperature Recorder (STR); AMSM, OFU; Long: -169.68165, Lat: -14.17364 (WGS84); Sensor Depth: 7.92m; Data Range: 20060301-20080228.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  17. CRED Subsurface Temperature Recorder (STR); NWHI, GAR; Long: -167.99958, Lat: 24.99883 (WGS84); Sensor Depth: 10.36m; Data Range: 20040920-20060705.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  18. CRED Subsurface Temperature Recorder (STR); NWHI, GAR; Long: -167.99952, Lat: 24.99883 (WGS84); Sensor Depth: 10.40m; Data Range: 20030719-20040919.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  19. CRED Subsurface Temperature Recorder (STR); PRIA, HOW; Long: -176.62134, Lat: 00.80661 (WGS84); Sensor Depth: 3.05m; Data Range: 20080207-20100203.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  20. CRED Subsurface Temperature Recorder (STR); PRIA, KIN; Long: -162.38180, Lat: 06.42888 (WGS84); Sensor Depth: 5.18m; Data Range: 20080407-20100415.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  1. CRED Subsurface Temperature Recorder (STR); AMSM, ROS; Long: -168.16019, Lat: -14.55129 (WGS84); Sensor Depth: 3.40m; Data Range: 20040210-20060307.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  2. CRED Subsurface Temperature Recorder (STR); NWHI, KUR; Long: -178.36845, Lat: 28.42927 (WGS84); Sensor Depth: 0.61m; Data Range: 20041008-20060917.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  3. CRED Subsurface Temperature Recorder (STR); AMSM, ROS; Long: -168.16883, Lat: -14.54871 (WGS84); Sensor Depth: 31.40m; Data Range: 20080313-20100303.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  4. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27505, Lat: 23.85625 (WGS84); Sensor Depth: 7.62m; Data Range: 20070924-20080915.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  5. CRED Subsurface Temperature Recorder (STR); MHI, LAN; Long: -156.83701, Lat: 20.87187 (WGS84); Sensor Depth: 13.10m; Data Range: 20060805-20081019.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  6. CRED Subsurface Temperature Recorder (STR); NWHI, PHR; Long: -175.88112, Lat: 27.78202 (WGS84); Sensor Depth: 23.16m; Data Range: 20060913-20060922.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  7. CRED Subsurface Temperature Recorder (STR); MHI, KAU; Long: -159.44752, Lat: 21.86888 (WGS84); Sensor Depth: 7.01m; Data Range: 20060809-20081107.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  8. CRED Subsurface Temperature Recorder (STR); MHI, OAH; Long: -158.21747, Lat: 21.46010 (WGS84); Sensor Depth: 7.32m; Data Range: 20050723-20070305.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  9. CRED Subsurface Temperature Recorder (STR); NWHI, KUR; Long: -178.36847, Lat: 28.42927 (WGS84); Sensor Depth: 0.91m; Data Range: 20080930-20100918.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  10. CRED Subsurface Temperature Recorder (STR); MHI, LAN; Long: -156.83705, Lat: 20.87186 (WGS84); Sensor Depth: 13.11m; Data Range: 20081019-20101021.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  11. CRED Subsurface Temperature Recorder (STR); NWHI, LIS; Long: -173.88414, Lat: 25.94299 (WGS84); Sensor Depth: 21.34m; Data Range: 20081004-20100922.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  12. CRED Subsurface Temperature Recorder (STR); AMSM, ROS; Long: -168.16019, Lat: -14.55126 (WGS84); Sensor Depth: 7.90m; Data Range: 20040210-20050923.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  13. CRED Subsurface Temperature Recorder (STR); NWHI, KUR; Long: -178.36842, Lat: 28.42927 (WGS84); Sensor Depth: 0.60m; Data Range: 20030805-20041006.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  14. CRED Subsurface Temperature Recorder (STR); PRIA, PAL; Long: -162.04044, Lat: 05.87450 (WGS84); Sensor Depth: 5.18m; Data Range: 20080402-20100409.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  15. CRED Subsurface Temperature Recorder (STR); PRIA, BAK; Long: -176.47588, Lat: 00.20543 (WGS84); Sensor Depth: 16.76m; Data Range: 20080210-20100207.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  16. CRED Subsurface Temperature Recorder (STR); PRIA, HOW; Long: -176.62172, Lat: 00.80645 (WGS84); Sensor Depth: 18.89m; Data Range: 20060128-20080205.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  17. CRED Subsurface Temperature Recorder (STR); MHI, OAH; Long: -158.13684, Lat: 21.35467 (WGS84); Sensor Depth: 17.68m; Data Range: 20090206-20090902.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  18. CRED Subsurface Temperature Recorder (STR); PRIA, PAL; Long: -162.03065, Lat: 05.86423 (WGS84); Sensor Depth: 9.14m; Data Range: 20060327-20080302.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  19. CRED Subsurface Temperature Recorder (STR); PRIA, PAL; Long: -162.12722, Lat: 05.89647 (WGS84); Sensor Depth: 10.06m; Data Range: 20090916-20100408.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...

  20. CRED Subsurface Temperature Recorder (STR); MHI, HAW; Long: -155.50220, Lat: 19.13292 (WGS84); Sensor Depth: 14.94m; Data Range: 20050305-20060816.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Coral Reef Ecosystem Division (CRED), NOAA Pacific Islands Fisheries Science Center (PIFSC) Subsurface Temperature Recorders (STR) provide a time series of...