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Sample records for repeat str analysis

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

    OpenAIRE

    Okamoto, Osamu; Yamamoto, Yuji; Inagaki, Sachiyo; Yoshitome, Kei; ishikawa, Takaki; Imabayashi, Kiyomi; Miyaishi, Satoru; Ishizu, Hideo

    2003-01-01

    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 di...

  2. 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)…

  3. Stutter analysis of complex STR MPS data

    DEFF Research Database (Denmark)

    Vilsen, Søren B; Tvedebrink, Torben; Eriksen, Poul Svante

    2018-01-01

    Stutters are common and well documented artefacts of amplification of short tandem repeat (STR) regions when using polymerase chain reaction (PCR) occurring as strands one or more motifs shorter or longer than the parental allele. Understanding the mechanism and rate by which stutters are created...... is especially important when the samples contain small amounts of DNA or DNA from multiple contributors. It has been shown that there is a linear relationship between the longest uninterrupted stretch (LUS) and the stutter ratio. This holds if there is only a single type of stutter variant. However...

  4. Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations.

    Science.gov (United States)

    Gilmore, Simon; Peakall, Rod; Robertson, James

    2003-01-09

    Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.

  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. MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis.

    Science.gov (United States)

    Asamura, H; Sakai, H; Kobayashi, K; Ota, M; Fukushima, H

    2006-05-01

    We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

  7. Analysis of the 19 Y-STR and 16 X-STR loci system in the Han population of Shandong province, China.

    Science.gov (United States)

    Gao, H M; Wang, C; Han, S Y; Sun, S H; Xiao, D J; Wang, Y S; Li, C T; Zhang, M X

    2017-03-30

    The sex-linked short tandem repeats (STR), Y-STR and X-STR, are important for autosomal STRs in forensic paternity testing. We evaluated the forensic parameters of 19 Y-STRs and 16 X-STRs in the Han population of Shandong province, China. A Goldeneye 20Y kit (DYS391, DYS389I, DYS390, DYS389II, DYS348, DYS456, Y-GATA-H4, DYS447, DYS19, DYS392, DYS393, DYS388, DYS439, DYS635, DYS448, DYS460, DYS458, DYS437, DYS385 a/b) was used to analyze the forensic parameters of 534 unrelated males. A Goldeneye17X system (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, DXS6810, amelogenin) was used to analyze 97 unrelated males and 214 females. In addition, we used the kits to examine 5 cases with abnormal amelogenin test results, as well as a male child with agenosomia typed by autosomal STR. We found 203 Y-STR haplotypes with allele frequencies ranging from 0.0019 to 0.7959, and GD ranging from 0.3429 to 0.9667. Expect in DXS6803, the allele frequencies of the other 15 X-STR loci showed no differences between females and males. PD F ranged from 0.5504 to 0.9638, while PD M ranged from 0.3176 to 0.8377. With the exception of DXS6803 and DXS6810, the allele frequencies of other X-STR loci were in accordance with Hardy-Weinberg equilibrium in females. One amelogenin negative case was characterized as a deletion of Y-DYS458. This paper provided data regarding the genetic polymorphism of Y-STRs and X-STRs in the Han population, and demonstrated the importance of Y-STR and X-STR in forensic autosomal STR analysis.

  8. Short tandem repeat (STR based genetic diversity and relationship of indigenous Niger cattle

    Directory of Open Access Journals (Sweden)

    M. Grema

    2017-11-01

    Full Text Available The diversity of cattle in Niger is predominantly represented by three indigenous breeds: Zebu Arabe, Zebu Bororo and Kuri. This study aimed at characterizing the genetic diversity and relationship of Niger cattle breeds using short tandem repeat (STR marker variations. A total of 105 cattle from all three breeds were genotyped at 27 STR loci. High levels of allelic and gene diversity were observed with an overall mean of 8.7 and 0.724 respectively. The mean inbreeding estimate within breeds was found to be moderate with 0.024, 0.043 and 0.044 in Zebu Arabe, Zebu Bororo and Kuri cattle respectively. The global F statistics showed low genetic differentiation among Niger cattle with about 2.6 % of total variation being attributed to between-breed differences. Neighbor-joining tree derived from pairwise allele sharing distance revealed Zebu Arabe and Kuri clustering together while Zebu Bororo appeared to be relatively distinct from the other two breeds. High levels of admixture were evident from the distribution of pairwise inter-individual allele sharing distances that showed individuals across populations being more related than individuals within populations. Individuals were assigned to their respective source populations based on STR genotypes, and the percent correct assignment of Zebu Bororo (87.5 to 93.8 % was consistently higher than Zebu Arabe (59.3 to 70.4 % and Kuri (80.0 to 83.3 % cattle. The qualitative and quantitative tests for mutation drift equilibrium revealed absence of genetic bottleneck events in Niger cattle in the recent past. High genetic diversity and poor genetic structure among indigenous cattle breeds of Niger might be due to historic zebu–taurine admixture and ongoing breeding practices in the region. The results of the present study are expected to help in formulating effective strategies for conservation and genetic improvement of indigenous Niger cattle breeds.

  9. Short tandem repeat analysis in Japanese population.

    Science.gov (United States)

    Hashiyada, M

    2000-01-01

    Short tandem repeats (STRs), known as microsatellites, are one of the most informative genetic markers for characterizing biological materials. Because of the relatively small size of STR alleles (generally 100-350 nucleotides), amplification by polymerase chain reaction (PCR) is relatively easy, affording a high sensitivity of detection. In addition, STR loci can be amplified simultaneously in a multiplex PCR. Thus, substantial information can be obtained in a single analysis with the benefits of using less template DNA, reducing labor, and reducing the contamination. We investigated 14 STR loci in a Japanese population living in Sendai by three multiplex PCR kits, GenePrint PowerPlex 1.1 and 2.2. Fluorescent STR System (Promega, Madison, WI, USA) and AmpF/STR Profiler (Perkin-Elmer, Norwalk, CT, USA). Genomic DNA was extracted using sodium dodecyl sulfate (SDS) proteinase K or Chelex 100 treatment followed by the phenol/chloroform extraction. PCR was performed according to the manufacturer's protocols. Electrophoresis was carried out on an ABI 377 sequencer and the alleles were determined by GeneScan 2.0.2 software (Perkin-Elmer). In 14 STRs loci, statistical parameters indicated a relatively high rate, and no significant deviation from Hardy-Weinberg equilibrium was detected. We apply this STR system to paternity testing and forensic casework, e.g., personal identification in rape cases. This system is an effective tool in the forensic sciences to obtain information on individual identification.

  10. 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

    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 the probabi......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...... the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace...... 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...

  11. Fetal gender determination through Y-STR analysis of maternal ...

    African Journals Online (AJOL)

    Hanaa M.H. Aal-Hamdan

    2014-10-01

    Oct 1, 2014 ... Fetal gender determination through Y-STR analysis of maternal plasma during the third trimester of pregnancy. Hanaa M.H. Aal-Hamdan, Ahmed M. Refaat *, Saranya R. Babu,. Abdul Rauf Choudhry. Department of Forensic Biology, College of Forensic Sciences, Naif Arab University for Security Sciences, ...

  12. [Observation and analysis on mutation of routine STR locus].

    Science.gov (United States)

    Li, Qiu-yang; Feng, Wei-jun; Yang, Qin-gen

    2005-05-01

    To observe and analyze the characteristic of mutation at STR locus. 27 mutant genes observed in 1211 paternity testing cases were checked by PAGE-silver stained and PowerPlex 16 System Kit and validated by sequencing. Mutant genes locate on 15 loci. The pattern of mutation was accord with stepwise mutation model. The mutation ratio of male-to-female was 8:1 and correlated to the age of father. Mutation rate is correlated to the geometric mean of the number of homogeneous repeats of locus. The higher the mean, the higher the mutation rate. These loci are not so appropriate for use in paternity testing.

  13. Stochastic filtering of quantitative data from STR DNA analysis

    DEFF Research Database (Denmark)

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

    due to the apparatus used for measurements). Pull-up effects (more systematic increase caused by overlap in the spectrum) Stutters (peaks located four basepairs before the true peak). We present filtering techniques for all three technical artifacts based on statistical analysis of data from......The quantitative data observed from analysing STR DNA is a mixture of contributions from various sources. Apart from the true allelic peaks, the observed signal consists of at least three components resulting from the measurement technique and the PCR amplification: Background noise (random noise...... controlled experiments conducted at The Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, Universityof Copenhagen, Denmark....

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

    OpenAIRE

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

    2016-01-01

    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 s...

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

    KAUST Repository

    Shimada, Makoto K.; Sanbonmatsu, Ryoko; Yamaguchi-Kabata, Yumi; Yamasaki, Chisato; Suzuki, Yoshiyuki; Chakraborty, Ranajit; Gojobori, Takashi; Imanishi, Tadashi

    2016-01-01

    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

  16. 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...

  17. Genetics analysis of 38 STR loci in Uygur population from Southern Xinjiang of China.

    Science.gov (United States)

    Yuan, Li; Liu, Haibo; Liao, Qinxiang; Xu, Xu; Chen, Wen; Hao, Shicheng

    2016-05-01

    The allele frequencies and statistical parameters of 38 autosomal short tandem repeat (STR) loci were analyzed in the Uygur population from Southern Xinjiang of China with 290 unrelated individuals. The results show these 38 STR loci have high or medium power of discrimination and probabilities of exclusion. All loci are in Hardy-Weinberg equilibrium. The genetic distances between the Uygur population and other Chinese populations were also estimated.

  18. Genetic Analysis of Eight X-Chromosomal Short Tandem Repeat ...

    African Journals Online (AJOL)

    X-Chromosome short tandem repeat (STR) typing can complement existing DNA profiling protocols and can also offer useful information in cases of complex kinship analysis. This is the first population study of 8 X-linked STRs in Iraq. The purpose of this work was to provide a basic data of allele and haplotype frequency for ...

  19. 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...

  20. STR melting curve analysis as a genetic screening tool for crime scene samples.

    Science.gov (United States)

    Nguyen, Quang; McKinney, Jason; Johnson, Donald J; Roberts, Katherine A; Hardy, Winters R

    2012-07-01

    In this proof-of-concept study, high-resolution melt curve (HRMC) analysis was investigated as a postquantification screening tool to discriminate human CSF1PO and THO1 genotypes amplified with mini-STR primers in the presence of SYBR Green or LCGreen Plus dyes. A total of 12 CSF1PO and 11 HUMTHO1 genotypes were analyzed on the LightScanner HR96 and LS-32 systems and were correctly differentiated based upon their respective melt profiles. Short STR amplicon melt curves were affected by repeat number, and single-source and mixed DNA samples were additionally differentiated by the formation of heteroduplexes. Melting curves were shown to be unique and reproducible from DNA quantities ranging from 20 to 0.4 ng and distinguished identical from nonidentical genotypes from DNA derived from different biological fluids and compromised samples. Thus, a method is described which can assess both the quantity and the possible probative value of samples without full genotyping. 2012 American Academy of Forensic Sciences. Published 2012. This article is a U.S. Government work and is in the public domain in the U.S.A.

  1. 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.

  2. STR analysis of artificially degraded DNA-results of a collaborative European exercise

    DEFF Research Database (Denmark)

    Schneider, Peter M; Bender, Klaus; Mayr, Wolfgang R

    2004-01-01

    Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect......, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European...... countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR...

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

    African Journals Online (AJOL)

    Yomi

    2012-03-15

    Mar 15, 2012 ... Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely .... Data analysis. The exact test of Hardy-Weinberg equilibrium was conducted with. Arlequin version 3.5 software (Computational and Molecular.

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. Analysis of 16 autosomal STR loci in Uyghur and Kazakh populations from Xinjiang, China

    DEFF Research Database (Denmark)

    Simayijiang, Halimurat; Pereira, Vania; Børsting, Claus

    2017-01-01

    from Hardy-Weinberg Equilibrium in any of the two populations. The forensic parameters indicated that the kit is suitable for personal identification, paternity testing, and complex kinship analysis in Uyghur and Kazakh populations. Allele frequency data for the STR loci were compared with other...

  9. My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.

    Science.gov (United States)

    Van Neste, Christophe; Vandewoestyne, Mado; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2014-03-01

    Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as molecular autopsy in legal medicine and in mitochondrial DNA research. Copyright © 2013 The Authors. Published by

  10. Current STR-based techniques in forensic science

    Directory of Open Access Journals (Sweden)

    Phuvadol Thanakiatkrai

    2013-01-01

    Full Text Available DNA analysis in forensic science is mainly based on short tandem repeat (STR genotyping. The conventional analysis is a three-step process of DNA extraction, amplification and detection. An overview of various techniques that are currently in use and are being actively researched for STR typing is presented. The techniques are separated into STR amplification and detection. New techniques for forensic STR analysis focus on increasing sensitivity, resolution and discrimination power for suboptimal samples. These are achieved by shifting primer-binding sites, using high-fidelity and tolerant polymerases and applying novel methods to STR detection. Examples in which STRs are used in criminal investigations are provided and future research directions are discussed.

  11. Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture, northwestern China.

    Science.gov (United States)

    Feng, Chunmei; Wang, Xin; Wang, Xiaolong; Yu, Hao; Zhang, Guohua

    2018-03-01

    We investigated the frequencies of 15 autosomal STR loci in the Kazak population of the Ili Kazak Autonomous Prefecture with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis. Genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analysed in 456 individuals of the Kazak population from Ili Kazakh Autonomous Prefecture, northwestern China. A total of 173 alleles at 15 autosomal STR loci were found; the allele frequencies ranged from 0.5022-0.0011. The combined power of discrimination and exclusion statistics for the 15 STR loci were 0.999 999 999 85 and 0.999 998 800 65, respectively. In addition, phylogenetic analysis involving the Ili Uygur population and other relevant populations was carried out. A neighbour-joining tree and multidimensional scaling plot were generated based on Nei's standard genetic distance. Results of the population comparison indicated that the Ili Uygur population was most closely related genetically to the Uygur populations from other regions in China. These findings are consistent with the historical and geographic backgrounds of these populations.

  12. Comparison of Variable Number Tandem Repeat and Short Tandem Repeat Genetic Markers for Qualitative and Quantitative Chimerism Analysis Post Allogeneic Stem Cell Transplantation

    International Nuclear Information System (INIS)

    Mossallam, G.I.; Smith, A.G.; Mcfarland, C.

    2005-01-01

    Analysis of donor chimerism has become a routine procedure for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation. Quantitative analysis of chimerism kinetics has been shown to predict graft failure or relapse. In this study, we compared the use of variable number tandem repeats (VNTR) and short tandem repeats (STR) as polymorphic genetic markers in chimerism analysis. This study included qualitative and quantitative assessment of both techniques to assess informative yield and sensitivity. Patients and Methods: We analyzed 206 samples representing 40 transplant recipients and their HLA identical sibling donors. A panel of six VNTR loci, 15 STR loci and 1 sex chromosome locus was used. Amplified VNTR products were visualized in an ethidium bromide stained gel. STR loci were amplified using fluorescent primers, and the products were analyzed by capillary electrophoresis. VNTR and STR analysis gave comparable qualitative results in the majority of cases. The incidence of mixed chimerism (Me) by STR analysis was 45% compared to 32% in cases evaluated by VNTR analysis. STR markers were more informative; several informative loci could be identified in all patients. Unique alleles for both patient and donor could be identified in all patients by STR versus 32/40 by VNTR analysis. The STR markers were also more sensitive in the detection of chimerism. The size of VNTR alleles and differences between the size of donor and recipient VNTR alleles affected the sensitivity of detection. With both techniques, quantitative assessment of chimerism showed some discrepancies between the estimated and the calculated percentage of donor DNA. Discordance between the two estimates was observed in 8/19 patients with Me. However, sequential monitoring of the relative band intensity of VNTR alleles offered some insight into the direction of change in engraftment over time. The higher yield of informative loci with STR and the automated measurement of

  13. 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.

  14. 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...... a laboratory-specific optimization process is indicated to reach a comparable sensitivity for the analysis of minute amounts of DNA....

  15. 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.

  16. 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.

  17. FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise.

    Science.gov (United States)

    Hoogenboom, Jerry; van der Gaag, Kristiaan J; de Leeuw, Rick H; Sijen, Titia; de Knijff, Peter; Laros, Jeroen F J

    2017-03-01

    Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions. FDSTools is an open-source software solution developed for this purpose. The level of stutter formation is influenced by various aspects of the sequence, such as the length of the longest uninterrupted stretch occurring in an STR. When MPS is used, STRs are evaluated as sequence variants that each have particular stutter characteristics which can be precisely determined. FDSTools uses a database of reference samples to determine stutter and other systemic PCR or sequencing artefacts for each individual allele. In addition, stutter models are created for each repeating element in order to predict stutter artefacts for alleles that are not included in the reference set. This information is subsequently used to recognise and compensate for the noise in a sequence profile. The result is a better representation of the true composition of a sample. Using Promega Powerseq™ Auto System data from 450 reference samples and 31 two-person mixtures, we show that the FDSTools correction module decreases stutter ratios above 20% to below 3%. Consequently, much lower levels of contributions in the mixed traces are detected. FDSTools contains modules to visualise the data in an interactive format allowing users to filter data with their own preferred thresholds. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  18. Automated forensic DNA purification optimized for FTA card punches and identifiler STR-based PCR analysis.

    Science.gov (United States)

    Tack, Lois C; Thomas, Michelle; Reich, Karl

    2007-03-01

    Forensic labs globally face the same problem-a growing need to process a greater number and wider variety of samples for DNA analysis. The same forensic lab can be tasked all at once with processing mixed casework samples from crime scenes, convicted offender samples for database entry, and tissue from tsunami victims for identification. Besides flexibility in the robotic system chosen for forensic automation, there is a need, for each sample type, to develop new methodology that is not only faster but also more reliable than past procedures. FTA is a chemical treatment of paper, unique to Whatman Bioscience, and is used for the stabilization and storage of biological samples. Here, the authors describe optimization of the Whatman FTA Purification Kit protocol for use with the AmpFlSTR Identifiler PCR Amplification Kit.

  19. [Analysis of genetic polymorphisms and mutations of 20 frequently used STR loci among ethnic Hans from Henan].

    Science.gov (United States)

    Wang, Hongdan; Kang, Bing; Gao, Yue; Huo, Xiaodong; Li, Tao; Guo, Qiannan; Zhu, Bofeng; Liao, Shixiu

    2017-04-10

    To study the genetic polymorphisms and mutations of 20 frequently used autosomal microsatellites among ethnic Hans from Henan. Peripheral blood samples of 2604 individuals were collected. DNA was amplified and genotyped using a PowerPlex(TM) 21 system. The frequencies, forensic parameters and mutation rates of the 20 short tandem repeat (STR) loci were analyzed. A total of 323 alleles were found in this population and the allelic frequencies have ranged from 0.0003 to 0.5144. Except for D3S1358, TH01 and TPOX, mutations have been found in all of the remaining 17 STR loci, which totaled 47, with mutation rates ranging from 0 to 3.46 × 10 -3 . The 20 STR loci selected by the PowerPlex(TM) 21 system are highly polymorphic among ethnic Hans from Henan, and may be of great value in forensic and human population studies. As no similar study has been carried out previously, above results may be of great value for individual discrimination and paternal testing.

  20. 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.

  1. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

    Science.gov (United States)

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

    2015-09-01

    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. The new guidelines for paternity analysis in Germany-how many STR loci are necessary when investigating duo cases?

    Science.gov (United States)

    Poetsch, Micaela; Preusse-Prange, Andrea; Schwark, Thorsten; von Wurmb-Schwark, Nicole

    2013-07-01

    The requirements in the new German guidelines for paternity analysis have not only changed according to the so-called Gendiagnostikgesetz, the new German law regulating human genetic as well as paternity analyses, but also regarding the minimal number of short tandem repeats (STRs) which should be investigated (15 STRs) and the minimal required average exclusion chance (99.999 %). Even in paternity analyses involving only two people (e.g., father and child or mother and child), this exclusion chance is mandatory. A retrospective analysis of 330 father-child cases from our routine investigations showed in 142 cases (43 %) an individual exclusion chance below 99.999 % when using 15 STRs as required, in our routine work provided by the Powerplex® 16 kit which is reported to have an average exclusion chance of 99.988 %. Therefore, these same 330 father-child pairs were additionally analysed using the Powerplex® 21 kit and 120 of these duos were additionally analysed using the Powerplex® ESX17 kit enabling the analysis of 20 or 16 loci respectively. Now, an individual exclusion chance of more than 99.999 % could be achieved in 95.5 % (Powerplex® 21; calculation without the results of D6S1043), 98.8 % (Powerplex® 21; calculation with the results of D6S1043, using allele frequencies established in this study for a German and a West African population) and 98.3 % (Powerplex® ESX17). These data clearly demonstrate that in duo cases, more than the required 15 STR loci have to be investigated to obtain sufficient results.

  3. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul

    2017-01-01

    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  4. Validation of the AmpFlSTR« SEfiler Plus(TM) PCR Amplification kit for forensic STR analysis

    DEFF Research Database (Denmark)

    Fredslund, Stine Frisk; Mogensen, Helle Smidt; Morling, Niels

    2009-01-01

    Validation of the AmpFlSTR« SEfiler Plus(TM) PCR Amplification kit with 29 and 30 PCR cycles for forensic STR analysis demonstrated that the kit had fewer artefacts than the AmpFlSTR« SGM Plus(TM) kit (28 PCR cycles). The SEfiler Plus kit was more sensitive and devoid of colour artefacts, but sho......, but showed more stutters, drop-ins, drop-outs and allelic imbalances...

  5. Genetic polymorphism of 21 non-CODIS STR loci in Chengdu Han population and its interpopulation analysis between 25 populations in China.

    Science.gov (United States)

    Li, Ye; Li, Hepei; He, Guanglin; Liang, Weibo; Luo, Haibo; Liao, Miao; Zhang, Ji; Yan, Jing; Li, Yingbi; Hou, Yiping; Wu, Jin

    2018-03-01

    AGCU 21+1 STR kit contains 21 non-combined DNA index system (non-CODIS) short tandem repeats (STR) loci and a sex-determining locus amelogenin. In this study, we evaluated the genetic diversity and forensically relevant population statistics of 21 non-CODIS loci in 210 Chinese Han individuals from Chengdu city, Sichuan province, Southwest China. No significant deviations from Hardy-Weinberg equilibrium were observed within the 21 non-CODIS STR loci. The combined power of discrimination (CPD) and combined power of exclusion (CPE) were 0.99999999999999999994278, 0.999999355 respectively. To reveal interpopulation differentiations of mainland population of China, a neighbor-joining (N-J) phylogenetic tree was constructed based on Nei's genetic distances among Chengdu Han and 25 published populations. The phylogenetic analyses indicated that Chengdu Han population keeps a close genetic relationship with other Han populations. Copyright © 2017. Published by Elsevier B.V.

  6. A Y-chromosome STR marker should be added to commercial multiplex STR kits.

    Science.gov (United States)

    Oz, Carla; Zaken, Neomi; Amiel, Merav; Zamir, Ashira

    2008-07-01

    Autosomal short tandem repeat (STR) analysis has become highly relevant in the identification of victims from mass disasters and terrorist attacks. In such events, gender misidentification can be of grave consequences, yet the list reporting amelogenin amplification failure using STR multiplex kits continues to grow. Presented here are three such examples. In the first case, we present two male suspects who demonstrated amelogenin Y-deficient results using two commercial kit procedures. The presence of their Y chromosomes was proven by obtaining a Y-haplotype. The second case demonstrated a profile from a third male suspect where only the Y homolog of the XY pair was amplified. In events such as mass disasters or terrorist attacks, timely and reliable high throughput DNA typing results are essential. As the number of reported cases of amplification failure at the amelogenin gene continues to grow, we suggest that the incorporation of a better gender identification tool in commercial kits is crucial.

  7. Digital repeat analysis; setup and operation.

    Science.gov (United States)

    Nol, J; Isouard, G; Mirecki, J

    2006-06-01

    Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

  8. Analysis of 17 STR data on 5362 southern Portuguese individuals-an update on reference database.

    Science.gov (United States)

    Cabezas Silva, Raquel; Ribeiro, Teresa; Lucas, Isabel; Porto, Maria João; Costa Santos, Jorge; Dario, Paulo

    2016-03-01

    The main objective of this work consisted of the updating of allele frequencies and other relevant forensic parameters for the 17 autosomal STR loci provided by the combination of the two types of kits used routinely in our laboratory casework: AmpF/STR Identifiler(®) and the Powerplex(®) 16 Systems. This aim was of significant importance, given that the last study on these kits within the southern Portuguese population dates back to 2006, and, as a consequence, it was necessary to correct the deviation caused by population evolution over the last ten years so that they might be better applied to our forensic casework. For this reason genetic data from 5362 unrelated Caucasian Portuguese individuals from the south of Portugal who were involved in paternity testing casework from 2005 to 2014 was used. Of all the markers, TPOX proved to be the least polymorphic, and Penta E the most. Secondly, this up-to-date southern Portuguese population was compared not only with the northern and central Portuguese populations, but also with that of southern Portugal in 2006, along with populations from Spain, Italy, Greece, Romania, Morocco, Angola and Korea in order to infer information about the relatedness of these respective populations, and the variation of the southern Portuguese population over time. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. 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.

  10. Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province, Central China.

    Science.gov (United States)

    Shi, Meisen; Liu, Yaju; Zhang, Juntao; Bai, Rufeng; Lv, Xiaojiao; Ma, Shuhua

    2015-07-01

    We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity. Copyright © 2015. Published by Elsevier Ireland Ltd.

  11. 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.

  12. Forensic characteristics and phylogenetic analysis of Hubei Han population in central China using 17 Y-STR loci.

    Science.gov (United States)

    Wang, Zheng; Du, Weian; He, Guanglin; Liu, Jing; Hou, Yiping

    2017-07-01

    Currently, the largest national database within the Y chromosome haplotype reference database (YHRD, https://yhrd.org, release 53) is China, which has approximately 38000 Y chromosomal 17-marker (Yfiler) haplotypes. These haplotype profiles derived from the vast majority of Chinese administrative divisions, but no haplotype data was available for Hubei province, which is located in the Central China region. Herein, 429 unrelated male Chinese Han individuals residing in Hubei province were recruited and genotyped with 17 Y-STR loci. 115 alleles were identified with corresponding allele frequencies spanned from 0.0023 to 07506. The gene diversity (GD) values ranged from 0.3988 at DYS438 to 0.9573 at DYS385a/b. A total of 410 distinct haplotypes were obtained with the overall haplotype diversity (HD) and discrimination capacity (DC) was 0.9995 and 0.9557, respectively. Additionally, genetic relationships along administrative (Han Chinese from different provinces) and ethnic divisions (minority ethnic groups) were analyzed using analysis of molecular variance (AMOVA) tests and visualized by multidimensional scaling plots (MDS). The Han ethnicity including the Hubei Han shows a high genetic homogeneity all across China and significant genetic differences existed between the Hubei Han and some ethnic groups, most prominently for the Kazakhs and the Tibetans. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. [The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks].

    Science.gov (United States)

    Chukhryaeva, M I; Ivanov, I O; Frolova, S A; Koshel, S M; Utevska, O M; Skhalyakho, R A; Agdzhoyan, A T; Bogunov, Yu V; Balanovska, E V; Balanovsky, O P

    2016-05-01

    STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.

  14. 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.

  15. Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China.

    Science.gov (United States)

    Zhao, Zhuo; Zhang, Jie; Wang, Hua; Liu, Zhi-Peng; Liu, Ming; Zhang, Yuan; Sun, Li; Zhang, Hui

    2015-09-01

    STR, short tandem repeats, are well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and average mutation rates had a positive correlation with paternal age, maternal age and the time of pregnancy respectively. Additionally, the average mutation rate of coastal areas was higher than that of inland areas.

  16. A comprehensive Y-STR portrait of Yousafzai's population.

    Science.gov (United States)

    Tabassum, Sadia; Ilyas, Muhammad; Ullah, Inam; Israr, Muhammad; Ahmad, Habib

    2017-09-01

    In the current study, 17 Y-Chromosomal short tandem repeats (Y-STRs) included in theAmpFlSTR Y-Filer amplification kit (Applied Biosystems, Foster City, USA) were investigated in 146 unrelated Yousafzai males residing in the Khyber Pakhtunkhwa Province of Pakistan. A total of 94 (89.52%) unique haplotypes were observed. Discrimination capacity was 71.92%. Haplotype diversity ranged from 0.354 (DYS456) to 0.663 (DYS458). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Yousafzais is significantly different from neighbouring populations.

  17. 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 <3%. In conclusion, the newly developed 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. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

  18. Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

    Science.gov (United States)

    Just, Rebecca S; Irwin, Jodi A

    2018-05-01

    Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools

  19. Development of the 16 X-STR loci typing system and genetic analysis in a Shanghai Han population from China.

    Science.gov (United States)

    Sun, Kuan; Zhao, Shumin; Tian, Huaizhou; Zhang, Suhua; Li, Chengtao

    2013-11-01

    This study developed a new multiplex PCR system that simultaneously amplifies 16 X-STR loci in the same PCR reaction, and the polymorphism and mutation rates of these 16 X-STR loci were explored in a Shanghai Han population from China. These loci included DXS10134, DXS10159, DXS6789, DXS6795, DXS6800, DXS6803, DXS6807, DXS6810, DXS7132, DXS7424, DXS8378, DXS9902, GATA165B12, GATA172D05, GATA31E08, and HPRTB. Samples from 591 unrelated individuals (293 males and 298 females) and 400 two-generation families were successfully analyzed using this multiplex system. Allele frequencies and mutation rates of the 16 loci were investigated, with the comparison of allele frequency distributions among different populations performed. Polymorphism information contents of these loci were all >0.6440 except the locus DXS6800 (0.4706). Nine cases of mutations were detected in the 16 loci from the investigation of 9232 meioses. Pairwise comparisons of allele frequency distributions showed significant differences for most loci among populations from different countries and ethnic groups but not among the Han population living in other areas of China. These results suggest that the 16 X-STR loci system provides highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China, as a complementary tool. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rockenbauer, Eszter

    2011-01-01

    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...

  1. Male DNA under female fingernails after scratching: transfer and persistence evaluation by RT-PCR analysis and Y-STR typing.

    Science.gov (United States)

    Iuvaro, Alessandra; Bini, Carla; Dilloo, Silvia; Sarno, Stefania; Pelotti, Susi

    2018-04-17

    The collection of biological debris beneath fingernails can be useful in forensic casework when a struggle between the victim and the offender is suspected. In the present study, we set up a controlled scratching experiment in which female volunteers scratched the male volunteers' forearms, simulating a defensive action during an assault. A total of 160 fingernail samples were collected: 80 "control samples" before the scratching, 40 samples immediately after the scratching (t = 0 h), and 40 samples 5 h after the scratching (t = 5 h). The aim was to evaluate, using a real-time PCR approach and Y-STR profiling, the transfer and the persistence of male DNA under female fingernails after scratching. A significant reduction in DNA yield was observed between fingernail samples collected immediately and those collected 5 h after scratching, with a corresponding decrease in Y-STR profile quality. Overall, 38/40 (95%) of the fingernail samples collected immediately (t = 0 h) and 24/40 (60%) of those collected 5 h later (t = 5 h) were suitable for comparison and the scratched male volunteers could not be excluded as donors of the foreign DNA from 37 (92.5%) of the t = 0 h and from 10 (25%) of the t = 5 h profiles. The analysis of male DNA under female fingernails showed that Y-chromosome STR typing may provide extremely valuable genetic information of the male contributor(s), although 5 h after scratching the profile of the scratched male was lost in three-quarters of samples.

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

    African Journals Online (AJOL)

    This study was carried out to investigate the genetic polymorphism of nine short tandem repeat (STR) loci including D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364 and D22GATA198B05 in Chinese Han population of Henan province and to assess its value in forensic science.

  3. X-Chromosome short tandem repeat, advantages and typing ...

    African Journals Online (AJOL)

    Microsatellites of the X-chromosome have been increasingly studied in recent years as a useful tool in forensic analysis. This review describes some details of X-chromosomal short tandem repeat (STR) analysis. Among them are: microsatellites, amplification using polymerase chain reaction (PCR) of STRs, PCR product ...

  4. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

    Science.gov (United States)

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-07-15

    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

  5. Repeatability study of replicate crash tests: A signal analysis approach.

    Science.gov (United States)

    Seppi, Jeremy; Toczyski, Jacek; Crandall, Jeff R; Kerrigan, Jason

    2017-10-03

    To provide an objective basis on which to evaluate the repeatability of vehicle crash test methods, a recently developed signal analysis method was used to evaluate correlation of sensor time history data between replicate vehicle crash tests. The goal of this study was to evaluate the repeatability of rollover crash tests performed with the Dynamic Rollover Test System (DRoTS) relative to other vehicle crash test methods. Test data from DRoTS tests, deceleration rollover sled (DRS) tests, frontal crash tests, frontal offset crash tests, small overlap crash tests, small overlap impact (SOI) crash tests, and oblique crash tests were obtained from the literature and publicly available databases (the NHTSA vehicle database and the Insurance Institute for Highway Safety TechData) to examine crash test repeatability. Signal analysis of the DRoTS tests showed that force and deformation time histories had good to excellent repeatability, whereas vehicle kinematics showed only fair repeatability due to the vehicle mounting method for one pair of tests and slightly dissimilar mass properties (2.2%) in a second pair of tests. Relative to the DRS, the DRoTS tests showed very similar or higher levels of repeatability in nearly all vehicle kinematic data signals with the exception of global X' (road direction of travel) velocity and displacement due to the functionality of the DRoTS fixture. Based on the average overall scoring metric of the dominant acceleration, DRoTS was found to be as repeatable as all other crash tests analyzed. Vertical force measures showed good repeatability and were on par with frontal crash barrier forces. Dynamic deformation measures showed good to excellent repeatability as opposed to poor repeatability seen in SOI and oblique deformation measures. Using the signal analysis method as outlined in this article, the DRoTS was shown to have the same or better repeatability of crash test methods used in government regulatory and consumer evaluation test

  6. 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

  7. Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases.

    Science.gov (United States)

    Purps, Josephine; Geppert, Maria; Nagy, Marion; Roewer, Lutz

    2015-11-01

    DNA testing is an established part of the investigation and prosecution of sexual assault. The primary purpose of DNA evidence is to identify a suspect and/or to demonstrate sexual contact. However, due to highly uneven proportions of female and male DNA in typical stains, routine autosomal analysis often fails to detect the DNA of the assailant. To evaluate the forensic efficiency of the combined application of autosomal and Y-chromosomal short tandem repeat (STR) markers, we present a large retrospective casework study of probative evidence collected in sexual-assault cases. We investigated up to 39 STR markers by testing combinations of the 16-locus NGMSElect kit with both the 23-locus PowerPlex Y23 and the 17-locus Yfiler kit. Using this dual approach we analyzed DNA extracts from 2077 biological stains collected in 287 cases over 30 months. To assess the outcome of the combined approach in comparison to stand-alone autosomal analysis we evaluated informative DNA profiles. Our investigation revealed that Y-STR analysis added up to 21% additional, highly informative (complete, single-source) profiles to the set of reportable autosomal STR profiles for typical stains collected in sexual-assault cases. Detection of multiple male contributors was approximately three times more likely with Y-chromosomal profiling than with autosomal STR profiling. In summary, 1/10 cases would have remained inconclusive (and could have been dismissed) if Y-STR analysis had been omitted from DNA profiling in sexual-assault cases. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  8. Estimating stutter rates for Y-STR alleles

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Olofsson, Jill Katharina; 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 AmpFlSTR Yfiler kit. We found that the stutter rates...

  9. Incremental Dynamic Analysis of Koyna Dam under Repeated Ground Motions

    Science.gov (United States)

    Zainab Nik Azizan, Nik; Majid, Taksiah A.; Nazri, Fadzli Mohamed; Maity, Damodar; Abdullah, Junaidah

    2018-03-01

    This paper discovers the incremental dynamic analysis (IDA) of concrete gravity dam under single and repeated earthquake loadings to identify the limit state of the dam. Seven ground motions with horizontal and vertical direction as seismic input considered in the nonlinear dynamic analysis based on the real repeated earthquake in the worldwide. All the ground motions convert to respond spectrum and scaled according to the developed elastic respond spectrum in order to match the characteristic of the ground motion to the soil type. The scaled was depends on the fundamental period, T1 of the dam. The Koyna dam has been selected as a case study for the purpose of the analysis by assuming that no sliding and rigid foundation, has been estimated. IDA curves for Koyna dam developed for single and repeated ground motions and the performance level of the dam identifies. The IDA curve of repeated ground motion shown stiffer rather than single ground motion. The ultimate state displacement for a single event is 45.59mm and decreased to 39.33mm under repeated events which are decreased about 14%. This showed that the performance level of the dam based on seismic loadings depend on ground motion pattern.

  10. 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 for ...... and kits. Sex and STR locus specific mutation rates were estimated with 95% confidence limits by the method of Clopper and Pearson (1934)....

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

    Directory of Open Access Journals (Sweden)

    Khan Faisal

    2005-09-01

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

  12. Y chromosome STR typing in crime casework.

    Science.gov (United States)

    Roewer, Lutz

    2009-01-01

    Since the beginning of the nineties the field of forensic Y chromosome analysis has been successfully developed to become commonplace in laboratories working in crime casework all over the world. The ability to identify male-specific DNA renders highly variable Y-chromosomal polymorphisms, the STR sequences, an invaluable addition to the standard panel of autosomal loci used in forensic genetics. The male-specificity makes the Y chromosome especially useful in cases of male/female cell admixture, namely in sexual assault cases. On the other hand, the haploidy and patrilineal inheritance complicates the interpretation of a Y-STR match, because male relatives share for several generations an identical Y-STR profile. Since paternal relatives tend to live in the geographic and cultural territory of their ancestors, the Y chromosome analysis has a potential to make inferences on the population of origin of a given DNA profile. This review addresses the fields of application of Y chromosome haplotyping, the interpretation of results, databasing efforts and population genetics aspects.

  13. [Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population].

    Science.gov (United States)

    Chen, Ling; Lu, Hui-Jie; DU, Wei-An; Qiu, Ping-Ming; Liu, Chao

    2016-02-20

    To evaluate the value of PowerPlex ® 21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex ® 21 System on 20 autosomal 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) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex ® 21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

  14. Conservative Sample Size Determination for Repeated Measures Analysis of Covariance.

    Science.gov (United States)

    Morgan, Timothy M; Case, L Douglas

    2013-07-05

    In the design of a randomized clinical trial with one pre and multiple post randomized assessments of the outcome variable, one needs to account for the repeated measures in determining the appropriate sample size. Unfortunately, one seldom has a good estimate of the variance of the outcome measure, let alone the correlations among the measurements over time. We show how sample sizes can be calculated by making conservative assumptions regarding the correlations for a variety of covariance structures. The most conservative choice for the correlation depends on the covariance structure and the number of repeated measures. In the absence of good estimates of the correlations, the sample size is often based on a two-sample t-test, making the 'ultra' conservative and unrealistic assumption that there are zero correlations between the baseline and follow-up measures while at the same time assuming there are perfect correlations between the follow-up measures. Compared to the case of taking a single measurement, substantial savings in sample size can be realized by accounting for the repeated measures, even with very conservative assumptions regarding the parameters of the assumed correlation matrix. Assuming compound symmetry, the sample size from the two-sample t-test calculation can be reduced at least 44%, 56%, and 61% for repeated measures analysis of covariance by taking 2, 3, and 4 follow-up measures, respectively. The results offer a rational basis for determining a fairly conservative, yet efficient, sample size for clinical trials with repeated measures and a baseline value.

  15. Haplotype and genetic relationship of 27 Y-STR loci in Han population of Chaoshan area of China

    Directory of Open Access Journals (Sweden)

    Qing-hua TIAN

    2017-04-01

    Full Text Available Objective  To investigate the genetic polymorphisms of 27 Y-chromosomal short tandem repeats (Y-STR loci included in Yfiler® Plus kit in Han population of Chaoshan area, and explore the population genetic relationships and evaluate its application value on forensic medicine. Methods  By detecting 795 unrelated Chaoshan Han males with Yfiler® Plus kit, haplotype frequencies and population genetics parameters of the 27 Y-STR loci were statistically analyzed and compared with available data of other populations from different races and regions for analyzing the genetic distance and clustering relation of Chaoshan Han population. Results  Seven hundred and eighty-seven different haplotypes were observed in 795 unrelated male individuals, of which 779 haplotypes were unique, and 8 haplotypes occurred twice. The haplotype diversity (HD was 0.999975 with discriminative capacity (DC of 98.99%. The gene diversity (GD at the 27 Y-STR loci ranged from 0.3637(DYS391 to 0.9559(DYS385a/b. Comparing with Asian reference populations, the genetic distance (Rst between Chaoshan Han and Guangdong Han was the smallest (0.0036, while it was relatively larger between Chaoshan Han and Gansu Tibetan population (0.0935. The multi-dimensional scaling (MDS plot based on Rst values was similar to the results of clustering analysis. Conclusion  Multiplex detection of the 27 Y-STR loci reveals a highly polymorphic genetic distribution in Chaoshan Han population, which demonstrates the important significance of Yfiler® Plus kit for establishing a Y-STR database, studying population genetics, and for good practice in forensic medicine. DOI: 10.11855/j.issn.0577-7402.2017.03.08

  16. Comparison of serum creatine kinase estimation with short tandem repeats based linkage analysis in carriers and affected children of duchenne muscular dystrophy

    International Nuclear Information System (INIS)

    Hashim, R.; Ahmad, S.; Sattar, A.; Khan, F.A.

    2011-01-01

    Background: Duchenne Muscular Dystrophy (DMD) is an X-linked recessive lethal, genetic disorder characterised by progressive weakness of skeletal muscles which is untreatable and transmitted to males by carrier females. Advances in laboratory techniques now focus direct mutational analysis as the most reliable and indirect analysis based on Short Tandem Repeats (STR) based linkage analysis as feasible, inexpensive, and efficient method for carrier detection and prenatal diagnosis. The objective of this study was to compare the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic efficiency of Serum Creatine Kinase (SCK) with Short Tandem Repeats (STR based linkage analysis in carriers and affected children of Duchenne Muscular Dystrophy. Methods: The study was carried out from Dec 2006 to Dec 2007 in families having index clinical cases of DMD who were referred from different hospitals for evaluation/workup of DMD. SCK was done as a preliminary investigation in all index cases. The PCR assay with STR based linkage analysis with Intron 44, 45, 49 and 50 of DMD gene were performed in all families. Six families were informative with Intron 44 of DMD gene and one family was non-informative with all four intronic markers of DMD. SCK analyses were done in all the family members and compared with PCR analysis in informative families. SCK was not performed on Chorionic villous sample (CVS) done for prenatal diagnosis of DMD, and CVS and non-informative family members were excluded from the study. Results: In carriers of DMD, the sensitivity and negative predictive value of SCK were 33.3%, and specificity and positive predictive were 100% with diagnostic efficiency of 50%. In affected cases of DMD the sensitivity and negative predictive value of SCK were 100%, and specificity and positive predictive were 91% and 88.8% respectively and diagnostic efficiency of 94.1%. Conclusion: The SCK is an excellent screening test for

  17. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit.

    Science.gov (United States)

    Hussing, C; Bytyci, R; Huber, C; Morling, N; Børsting, C

    2018-05-24

    Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.

  18. Genetic polymorphisms of 20 autosomal STR loci in the Vietnamese population from Yunnan Province, Southwest China.

    Science.gov (United States)

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

    2017-05-01

    The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated in 522 healthy unrelated Vietnamese from Yunnan, China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999999999999999999999991 26 and 0.999999975, respectively. Results suggested that the 20 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.

  19. A novel seven-octapeptide repeat insertion in the prion protein gene (PRNP) in a Dutch pedigree with Gerstmann-Sträussler-Scheinker disease phenotype: comparison with similar cases from the literature

    NARCIS (Netherlands)

    Jansen, Casper; Voet, Willem; Head, Mark W.; Parchi, Piero; Yull, Helen; Verrips, Aad; Wesseling, Pieter; Meulstee, Jan; Baas, Frank; van Gool, Willem A.; Ironside, James W.; Rozemuller, Annemieke J. M.

    2011-01-01

    Human prion diseases can be sporadic, inherited or acquired by infection and show considerable phenotypic heterogeneity. We describe the clinical, histopathological and pathological prion protein (PrP(Sc)) characteristics of a Dutch family with a novel 7-octapeptide repeat insertion (7-OPRI) in

  20. Allele frequency distribution for 21 autosomal STR loci in Nepal.

    Science.gov (United States)

    Kraaijenbrink, T; van Driem, G L; Opgenort, J R M L; Tuladhar, N M; de Knijff, P

    2007-05-24

    The allele frequency distributions of 21 autosomal loci contained in the AmpFlSTR Identifiler, the Powerplex 16 and the FFFL multiplex PCR kits, was studied in 953 unrelated individuals from Nepal. Several new alleles (i.e. not yet reported in the NIST Short Tandem Repeat DNA Internet DataBase [http://www.cstl.nist.gov/biotech/strbase/]) have been detected in the process.

  1. 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. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Analysis of positive control STR experiments reveals that results obtained for FGA, D3S1358, and D13S317 condition the success rate of the analysis of routine reference samples.

    Science.gov (United States)

    Murigneux, Valentine; Dufour, Anne-Béatrice; Lobry, Jean R; Pène, Laurent

    2014-07-01

    About 120,000 reference samples are analyzed each year in the Forensic Laboratory of Lyon. A total of 1640 positive control experiments used to validate and optimize the analytical method in the routine process were submitted to a multivariate exploratory data analysis approach with the aim of better understanding the underlying sources of variability. The peak heights of the 16 genetic markers targeted by the AmpFℓSTR(®) Identifiler(®) STR kit were used as variables of interest. Six different 3130xl genetic analyzers located in the same controlled environment were involved. Two major sources of variability were found: (i) the DNA load of the sample modulates all peak heights in a similar way so that the 16 markers are highly correlated, (ii) the genetic analyzer used with a locus-specific response for peak height and a better sensitivity for the most recently acquired. Three markers (FGA, D3S1358, and D13S317) were found to be of special interest to predict the success rate observed in the routine process. © 2014 American Academy of Forensic Sciences.

  3. Analysis of repeated measurement data in the clinical trials

    Science.gov (United States)

    Singh, Vineeta; Rana, Rakesh Kumar; Singhal, Richa

    2013-01-01

    Statistics is an integral part of Clinical Trials. Elements of statistics span Clinical Trial design, data monitoring, analyses and reporting. A solid understanding of statistical concepts by clinicians improves the comprehension and the resulting quality of Clinical Trials. In biomedical research it has been seen that researcher frequently use t-test and ANOVA to compare means between the groups of interest irrespective of the nature of the data. In Clinical Trials we record the data on the patients more than two times. In such a situation using the standard ANOVA procedures is not appropriate as it does not consider dependencies between observations within subjects in the analysis. To deal with such types of study data Repeated Measure ANOVA should be used. In this article the application of One-way Repeated Measure ANOVA has been demonstrated by using the software SPSS (Statistical Package for Social Sciences) Version 15.0 on the data collected at four time points 0 day, 15th day, 30th day, and 45th day of multicentre clinical trial conducted on Pandu Roga (~Iron Deficiency Anemia) with an Ayurvedic formulation Dhatrilauha. PMID:23930038

  4. Davis Strædet

    DEFF Research Database (Denmark)

    Råstofdirektoratet planlægger at udbyde flere licensområder med henblik på efterforskning og udvinding af olie og gas i den grønlandske del af Davis Stræde. Som en del af beslutningsgrundlaget har Råstofdirektoratet bedt DCE – Nationalt Center for Miljø og Energi og Grønlands Naturinstitut om at ...

  5. A massively parallel strategy for STR marker development, capture, and genotyping.

    Science.gov (United States)

    Kistler, Logan; Johnson, Stephen M; Irwin, Mitchell T; Louis, Edward E; Ratan, Aakrosh; Perry, George H

    2017-09-06

    Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci-97.3-99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

  6. Reject/repeat analysis and the effect prior film viewing has on a department's reject/repeat rate

    International Nuclear Information System (INIS)

    Clark, P.A.; Hogg, P.

    2003-01-01

    Purpose: Achieving cost-effectiveness within the NHS is an old initiative but one that has again been highlighted by recent government policies (The New NHS-Modern and Dependable, Stationary Office, London, 1997). It has been reiterated that it is the responsibility of individual Trusts to devise means to provide such a service. Reject/repeat analyses have long been the primary tool used to assess the cost-effectiveness of radiography departments (Quality Assurance in Diagnostic Radiology, WHO, Geneva, 1982). This research paper examines an in-house initiative (viewing patients' previous films) commonly employed in other Health Trusts in order to reduce departmental repeat/reject rates. Method: Three hundred orthopaedic patients with hip, knee and ankle prostheses were included in a reject/repeat analysis. The aim was to investigate whether or not viewing patient's previous relevant radiographs would be advantageous to the practicing radiographer. This was done through an audit cycle consisting of two audit periods each lasting for 3 months. The primary audit period recorded the baseline repeat/reject rate, with the secondary audit period recording the repeat/reject rate under an experimental condition of viewing the relevant radiographs. Results: The baseline audit revealed repeat rates of 33% in orthopaedic patients with hip, knee and ankle prostheses. The availability of prior film viewing to the radiographer reduced this repeat rate to 10.6%. Conclusion: Prior film viewing dramatically reduced the department's repeat/reject rate by 22.4%. This provides scope for significant patient dose reductions as well as reducing departmental film expenses. This is an underestimated initiative and should be used appropriately in routine clinical practice

  7. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

    Energy Technology Data Exchange (ETDEWEB)

    Salinero, Kennan Kellaris; Keller, Keith; Feil, William S.; Feil, Helene; Trong, Stephan; Di Bartolo, Genevieve; Lapidus, Alla

    2008-11-17

    Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. The a priori prediction that the D. aromatica genome would contain previously characterized 'central' enzymes involved in anaerobic aromatic degradation proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzyl succinyl synthase (bssABC) genes (responsible for formate addition to toluene) and the central benzoylCoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex with the somewhat rare exosortase (epsH), is also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and nitrogen fixation (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively). Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial

  8. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

    Directory of Open Access Journals (Sweden)

    Feil Helene

    2009-08-01

    Full Text Available Abstract Background Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. Results The a priori prediction that the D. aromatica genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (bssABC genes (responsible for fumarate addition to toluene and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively. Conclusion Analysis of the D. aromatica genome indicates there is much to be

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

    Science.gov (United States)

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

    2015-01-01

    For solving a maternity case, 19 autosomal short tandem repeats (STRs) were amplified using the AmpFℓSTR(®) Sinofiler(TM) 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 × 10(13), 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-STRs), 40 single nucleotide polymorphism (SNP) loci, and mitochondrial DNA (mtDNA) was carried out. The putative mother and the boy shared at least one allele at all 46 tested autosomal STR loci. But, according to the profile data of 20 X-STR and 40 SNP markers, different genotypes at 13 X-STR loci and five SNP loci excluded maternity. Mitochondrial profiles also clearly excluded the mother as a parent of the son because they have multiple differences. It was finally found that the putative mother is the sister of the biological father. Different kinds of genetic markers needfully supplement the use of autosomal STR loci in case where the putative parent is suspected to be related to the true parent.

  10. Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele.

    Science.gov (United States)

    Ye, Yi; Gao, Jingshang; Fan, Guangyao; Liao, Linchuan; Hou, Yiping

    2015-05-01

    Tibetan is one of 56 ethnic groups in China, where a level of genetic sub-structure might be expected. Although a global analysis of Y-chromosomal haplotype diversity for 23 STR loci and Y-STR databases with PPY23 kit were created with collaborative effort, there was a lack of data for Tibetan population. In this study we evaluated 248 unrelated male individuals of Chinese Tibetan living in the Tibet Autonomous Region to explore the underlying genetic structure of Tibetan populations. These samples 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) by using PPY23 kit. A total of 224 different haplotypes were found. Haplotype diversity was 0.9990. Both Rst pairwise analyses and multidimensional scaling plot showed the genetic structure of Tibetan population was significantly different from some of Chinese ethnic groups and neighboring populations. There were few interesting null features at DYS448 observed by PPY23 that deserved some comment. It revealed that PPY23 marker set provided substantially stronger discriminatory power in Tibetan population. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  11. 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.

  12. The case for repeatable analysis with energy economy optimization models

    International Nuclear Information System (INIS)

    DeCarolis, Joseph F.; Hunter, Kevin; Sreepathi, Sarat

    2012-01-01

    Energy economy optimization (EEO) models employ formal search techniques to explore the future decision space over several decades in order to deliver policy-relevant insights. EEO models are a critical tool for decision-makers who must make near-term decisions with long-term effects in the face of large future uncertainties. While the number of model-based analyses proliferates, insufficient attention is paid to transparency in model development and application. Given the complex, data-intensive nature of EEO models and the general lack of access to source code and data, many of the assumptions underlying model-based analysis are hidden from external observers. This paper discusses the simplifications and subjective judgments involved in the model building process, which cannot be fully articulated in journal papers, reports, or model documentation. In addition, we argue that for all practical purposes, EEO model-based insights cannot be validated through comparison to real world outcomes. As a result, modelers are left without credible metrics to assess a model's ability to deliver reliable insight. We assert that EEO models should be discoverable through interrogation of publicly available source code and data. In addition, third parties should be able to run a specific model instance in order to independently verify published results. Yet a review of twelve EEO models suggests that in most cases, replication of model results is currently impossible. We provide several recommendations to help develop and sustain a software framework for repeatable model analysis.

  13. A novel polymorphic repeat in the upstream regulatory region of the estrogen-induced gene EIG121 is not associated with the risk of developing breast or endometrial cancer.

    Science.gov (United States)

    Bolton, Katherine A; Holliday, Elizabeth G; Attia, John; Bowden, Nikola A; Avery-Kiejda, Kelly A; Scott, Rodney J

    2016-05-26

    The estrogen-induced gene 121 (EIG121) has been associated with breast and endometrial cancers, but its mechanism of action remains unknown. In a genome-wide search for tandem repeats, we found that EIG121 contains a short tandem repeat (STR) in its upstream regulatory region which has the potential to alter gene expression. The presence of this STR has not previously been analysed in relation to breast or endometrial cancer risk. In this study, the lengths of this STR were determined by PCR, fragment analysis and sequencing using DNA from 223 breast cancer patients, 204 endometrial cancer patients and 220 healthy controls to determine if they were associated with the risk of developing breast or endometrial cancer. We found this repeat to be highly variable with the number of copies of the AG motif ranging from 27 to 72 and having a bimodal distribution. No statistically significant association was identified between the length of this STR and the risk of developing breast or endometrial cancer or age at diagnosis. The STR in the upstream regulatory region of EIG121 is highly polymorphic, but is not associated with the risk of developing breast or endometrial cancer in the cohorts analysed here. While this polymorphic STR in the regulatory region of EIG121 appears to have no impact on the risk of developing breast or endometrial cancer, its association with disease recurrence or overall survival remains to be determined.

  14. Analysis of CR1 Repeats in the Zebra Finch Genome

    Directory of Open Access Journals (Sweden)

    George E. Liu

    2013-06-01

    Full Text Available Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1 repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

  15. Repeat profile analysis in an x-ray department

    International Nuclear Information System (INIS)

    Bassey, C.E.; Ojo, O.O.; Akpabio, I.

    1991-01-01

    The repeat profile of an x-ray department in a developing country was analysed monthly between July 1989 and June 1990. Results showed an average repeat rate of 3.7% for the period of study. The main causes of film repetition were: equipment fault, 33.9%; radiographer's fault, 27.4%; film fault, 19.3%; processing fault, 10.8% and patient's fault, 8.6%. The average repeat rate in the first 6 months of study reduced by 50% in the last 6 months. This was due to the effectiveness of implementation of corrective actions. The overall repeat rate was found to correlate well with both the equipment fault and radiographer's fault with correlation coefficients, r, of 0.94 and 0.91, respectively. It is expected that a further reduction in the repeat rate will be obtained after the introduction of quality assurance programmes. (author)

  16. 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.

  17. 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 AmpF?STR? 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...

  18. Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci.

    Science.gov (United States)

    Du, Weian; Feng, Peipei; Huang, Hongyan; Wu, Weibin; Zhang, Lei; Guo, Yulin; Liu, Changhui; Liu, Hong; Liu, Chao; Chen, Ling

    2018-05-30

    Y-chromosomal short tandem repeats (Y-STRs) have proven to be very useful in investigating sexual assault cases and in paternity lineage differentiation. However, currently available commercial Y-STR multiplex amplification systems bear the limitations in the identification of related males from the same paternal lineage due to there being an insufficient number of loci in any single amplification kit. The aim of this study was to establish and validate a novel 6-dye, 36-plex Y-STR multiplex amplification system that incorporated all of the loci present in the Yfiler™ Plus kit (DYS19, DYS385a/b, DYF387S1, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, Y_GATA_H4) as well as a further nine highly polymorphic Y-STR loci (DYS388, DYS444, DYS447, DYS522, DYS527a/b, DYS549, DYS596, DYS643). The novel system was optimized and validated by a series of studies that tested the effect of different PCR-based conditions as well as the species specificity, sensitivity, stability, stutter precision, suitability for use on DNA mixtures, reproducibility, and parallel testing of the system, as well as its performance on casework samples and population analysis, according to the SWGDAM developmental validation guidelines. A total of 246 haplotypes were found for the 36 Y-STRs among 247 Guangdong Han unrelated males. Collectively, the results demonstrate that the developed 36-plex Y-STR system is sensitive, robust, reliable, and highly informative for use in forensic genetics.

  19. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    1998). Cross- species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15:1275-1287.

  20. [Analysis of binary classification repeated measurement data with GEE and GLMMs using SPSS software].

    Science.gov (United States)

    An, Shengli; Zhang, Yanhong; Chen, Zheng

    2012-12-01

    To analyze binary classification repeated measurement data with generalized estimating equations (GEE) and generalized linear mixed models (GLMMs) using SPSS19.0. GEE and GLMMs models were tested using binary classification repeated measurement data sample using SPSS19.0. Compared with SAS, SPSS19.0 allowed convenient analysis of categorical repeated measurement data using GEE and GLMMs.

  1. Design and analysis of communication protocols for quantum repeater networks

    International Nuclear Information System (INIS)

    Jones, Cody; Kim, Danny; Rakher, Matthew T; Ladd, Thaddeus D; Kwiat, Paul G

    2016-01-01

    We analyze how the performance of a quantum-repeater network depends on the protocol employed to distribute entanglement, and we find that the choice of repeater-to-repeater link protocol has a profound impact on entanglement-distribution rate as a function of hardware parameters. We develop numerical simulations of quantum networks using different protocols, where the repeater hardware is modeled in terms of key performance parameters, such as photon generation rate and collection efficiency. These parameters are motivated by recent experimental demonstrations in quantum dots, trapped ions, and nitrogen-vacancy centers in diamond. We find that a quantum-dot repeater with the newest protocol (‘MidpointSource’) delivers the highest entanglement-distribution rate for typical cases where there is low probability of establishing entanglement per transmission, and in some cases the rate is orders of magnitude higher than other schemes. Our simulation tools can be used to evaluate communication protocols as part of designing a large-scale quantum network. (paper)

  2. Electromyographic analysis of repeated bouts of eccentric exercise.

    Science.gov (United States)

    McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W

    2001-03-01

    The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

  3. Analysis of unknown cause subarachnoid hemorrhage with repeated negative angiogram

    International Nuclear Information System (INIS)

    Fujii, Mutsumi; Takasato, Yoshio; Masaoka, Hiroyuki; Ohta, Yoshihisa; Hayakawa, Takanori; Honma, Masato

    2006-01-01

    Seven hundred and fifty five cases of acute non-traumatic subarachnoid hemorrhage (SAH) were admitted to the department of neurosurgery of our hospital from July, 1995 to March, 2004. In 555 patients cerebral angiography was conducted but initial angiography was negative in 30 patients. Except 10 general condition poor patients, in 20 initial angiogram-negative patients were undergone repeated angiography. The cause of SAH could not be demonstrated in 13 cases. The SAH in perimesencephalic and non-perimesencephalic cisturns was seen in 7 and 6 cases, respectively. Occipital and/or neck pain on admission was statistically more common among patients with perimesencephalic SAH than those with non-perimesencephalic SAH (p=0.029), and the prognosis of perimesencephalic SAH was good. We conclude that repeat angiography should not be recommended in patients with perimesencephalic SAH. Patients with non-perimesencephalic SAH had a higher rate of complication. In the non-perimesencephalic group, 3 patients developed hydrocephalus and 3 patients had vasospasm, which were found by repeated angiography. Therefore, repeated angiography is recommended for better clinical outcome by early detection and management of serious complications in this group of patients. (author)

  4. Short tandem repeat (STR) polymorphisms in Turkish population

    Indian Academy of Sciences (India)

    Research Note Volume 83 Issue 2 August 2004 pp 197-199 ... General Directory of Security, Criminal Police Laboratories, Biyoloji Bölümü, Aniteppe, Ankara, Turkey; Gazi University, Kirşehir Education Faculty, Kirşehir, Turkey; Ankara University, Faculty of Agriculture, Biometry-Genetics Unit, Ankara, Turkey; Gazi University ...

  5. Short tandem repeat (STR) polymorphisms in Turkish population

    Indian Academy of Sciences (India)

    Administrator

    4Gazi University, Faculty of Medicine, Department of Medical Biology and Genetics, Ankara, Turkey. Introduction ... by PCR-based method offers certain advantages over RFLP ... The combined PD, PE and PIC values of nine loci in Turk-.

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

    KAUST Repository

    D'Amato, Marí a Eugenia; Bajic, Vladimir B.; Davison, Sean P.

    2011-01-01

    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

  7. 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...

  8. Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

    Science.gov (United States)

    Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

    2010-12-01

    The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

  9. Repeatability analysis on LPFGs written by a CO2 laser

    Science.gov (United States)

    Nespereira, Marta; Castro Alves, D.; Coelho, João. M. P.; Monteiro, Fernando; Abreu, Manuel; Rebordão, J. M.

    2014-08-01

    The physical mechanisms involved in the writing process of long period fiber gratings (LPFG) using mid-infrared radiation emitted by CO2 lasers limit the obtained characteristics, in particular the minimum period that can be achieved. In order to evaluate the performances of a new methodology developed by us, we analyzed its capability to produce gratings with different periods (from 600 μm down to 300 μm). We also present a repeatability study on the obtained LPFG characteristics (mainly the resonant wavelength and grating length) for several values of the repetition period.

  10. Utility of repeat testing of critical values: a Q-probes analysis of 86 clinical laboratories.

    Science.gov (United States)

    Lehman, Christopher M; Howanitz, Peter J; Souers, Rhona; Karcher, Donald S

    2014-06-01

    A common laboratory practice is to repeat critical values before reporting the test results to the clinical care provider. This may be an unnecessary step that delays the reporting of critical test results without adding value to the accuracy of the test result. To determine the proportions of repeated chemistry and hematology critical values that differ significantly from the original value as defined by the participating laboratory, to determine the threshold differences defined by the laboratory as clinically significant, and to determine the additional time required to analyze the repeat test. Participants prospectively reviewed critical test results for 4 laboratory tests: glucose, potassium, white blood cell count, and platelet count. Participants reported the following information: initial and repeated test result; time initial and repeat results were first known to laboratory staff; critical result notification time; if the repeat result was still a critical result; if the repeat result was significantly different from the initial result, as judged by the laboratory professional or policy; significant difference threshold, as defined by the laboratory; the make and model of the instrument used for primary and repeat testing. Routine, repeat analysis of critical values is a common practice. Most laboratories did not formally define a significant difference between repeat results. Repeated results were rarely considered significantly different. Median repeated times were at least 17 to 21 minutes for 10% of laboratories. Twenty percent of laboratories reported at least 1 incident in the last calendar year of delayed result reporting that clinicians indicated had adversely affected patient care. Routine repeat analysis of automated chemistry and hematology critical values is unlikely to be clinically useful and may adversely affect patient care.

  11. [Analysis of variance of repeated data measured by water maze with SPSS].

    Science.gov (United States)

    Qiu, Hong; Jin, Guo-qin; Jin, Ru-feng; Zhao, Wei-kang

    2007-01-01

    To introduce the method of analyzing repeated data measured by water maze with SPSS 11.0, and offer a reference statistical method to clinical and basic medicine researchers who take the design of repeated measures. Using repeated measures and multivariate analysis of variance (ANOVA) process of the general linear model in SPSS and giving comparison among different groups and different measure time pairwise. Firstly, Mauchly's test of sphericity should be used to judge whether there were relations among the repeatedly measured data. If any (PSPSS statistical package is available to fulfil this process.

  12. Identification of variant alleles at AmpFlSTR SGM Plus STR loci in a ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-10-20

    Oct 20, 2008 ... origin. It is therefore important that forensic science community shares information on the occurrence of these variants and reduces complications during STR typing. In this study, we report 5 variant alleles at AmpFlSTR SGM. Plus loci in a sample population of Bangladesh. MATERIALS AND METHODS.

  13. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats.

    Science.gov (United States)

    Seman, Ali; Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-06-01

    Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84-1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data.

  14. Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.

    Science.gov (United States)

    Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

    2009-11-01

    Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.

  15. Performance testing of a semi-automatic card punch system, using direct STR profiling of DNA from blood samples on FTA™ cards.

    Science.gov (United States)

    Ogden, Samantha J; Horton, Jeffrey K; Stubbs, Simon L; Tatnell, Peter J

    2015-01-01

    The 1.2 mm Electric Coring Tool (e-Core™) was developed to increase the throughput of FTA(™) sample collection cards used during forensic workflows and is similar to a 1.2 mm Harris manual micro-punch for sampling dried blood spots. Direct short tandem repeat (STR) DNA profiling was used to compare samples taken by the e-Core tool with those taken by the manual micro-punch. The performance of the e-Core device was evaluated using a commercially available PowerPlex™ 18D STR System. In addition, an analysis was performed that investigated the potential carryover of DNA via the e-Core punch from one FTA disc to another. This contamination study was carried out using Applied Biosystems AmpflSTR™ Identifiler™ Direct PCR Amplification kits. The e-Core instrument does not contaminate FTA discs when a cleaning punch is used following excision of discs containing samples and generates STR profiles that are comparable to those generated by the manual micro-punch. © 2014 American Academy of Forensic Sciences.

  16. Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China.

    Science.gov (United States)

    Wu, Weiwei; Ren, Wenyan; Hao, Honglei; Nan, Hailun; He, Xin; Liu, Qiuling; Lu, Dejian

    2018-01-31

    Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1.0 × 10 -2 . DYS458, DYS630, and DYS518 were moderately mutating Y-STRs, with mutation rates ranging from 8 × 10 -3 to 1 × 10 -2 . Although the characteristics of the Y-STR mutations were consistent with those in previous studies, mutation rate differences between our data and previous published data were found at some rapidly mutating Y-STRs. The single-copy loci located on the short arm of the Y chromosome (Yp) showed relatively higher mutation rates more frequently than the multi-copy loci. These results will not only extend the data for Y-STR mutations but also be important for kinship analysis, paternal lineage identification, and family relationship reconstruction in forensic Y-STR analysis.

  17. The genetic analysis of repeated measures I: Simplex models

    NARCIS (Netherlands)

    Molenaar, P.C.M.; Boomsma, D.I.

    1987-01-01

    Extends the simplex model to a model that may be used for the genetic and environmental analysis of covariance (ANCOVA) structures. This "double" simplex structure can be specified as a linear structural relationships model. It is shown that data that give rise to a simplex correlation structure,

  18. Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences.

    Science.gov (United States)

    Claerhout, Sofie; Vandenbosch, Michiel; Nivelle, Kelly; Gruyters, Leen; Peeters, Anke; Larmuseau, Maarten H D; Decorte, Ronny

    2018-05-01

    Knowledge of Y-chromosomal short tandem repeat (Y-STR) mutation rates is essential to determine the most recent common ancestor (MRCA) in familial searching or genealogy research. Up to now, locus-specific mutation rates have been extensively examined especially for commercially available forensic Y-STRs, while haplogroup specific mutation rates have not yet been investigated in detail. Through 450 patrilineally related namesakes distributed over 212 deep-rooting genealogies, the individual mutation rates of 42 Y-STR loci were determined, including 27 forensic Y-STR loci from the Yfiler ® Plus kit and 15 additional Y-STR loci (DYS388, DYS426, DYS442, DYS447, DYS454, DYS455, DYS459a/b, DYS549, DYS607, DYS643, DYS724a/b and YCAIIa/b). At least 726 mutations were observed over 148,596 meiosis and individual Y-STR mutation rates varied from 2.83 × 10 -4 to 1.86 × 10 -2 . The mutation rate was significantly correlated with the average allele size, the complexity of the repeat motif sequence and the age of the father. Significant differences in average Y-STR mutations rates were observed when haplogroup 'I & J' (4.03 × 10 -3 mutations/generation) was compared to 'R1b' (5.35 × 10 -3 mutations/generation) and to the overall mutation rate (5.03 × 10 -3 mutations/generation). A difference in allele size distribution was identified as the only cause for these haplogroup specific mutation rates. The haplogroup specific mutation rates were also present within the commercially available Y-STR kits (Yfiler ® , PowerPlex ® Y23 System and Yfiler ® Plus). This observation has consequences for applications where an average Y-STR mutation rate is used, e.g. tMRCA estimations in familial searching and genealogy research. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Genetic analysis of repeated, biparental, diploid, hydatidiform moles

    DEFF Research Database (Denmark)

    Sunde, Lone; Vejerslev, Lars O.; Jensen, Mie Poulsen

    1993-01-01

    for the abnormal development can be envisaged, environmental as well as genetic. To conform to current ideas of molar pathogenesis, it is suggested that the present conceptuses might have arisen from imbalances in imprinted genomic regions. This could be a consequence of uniparental disomy in critical regions......A woman presented with five consecutive pregnancies displaying molar morphology. In the fifth pregnancy, a non-malformed, liveborn infant was delivered. Genetic analyses (RFLP analysis, cytogenetics, flow cytometry) were performed in pregnancies II-V. It was demonstrated that these pregnancies...... originated in separate conceptions, all conceptuses were diploid, and all had maternally as well as paternally derived genetic markers. By cytogenetic analysis, aberrant heteromorphisms were noted; no other abnormalities were observed in chromosome structure or in DNA sequence. Many different causes...

  20. Evaluation of 13 short tandem repeated loci for use in personal identification applications

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, H.A.; Caskey, C.T. (Baylor College of Medicine, Houston, TX (United States)); Jin, L.; Zhong, Y.; Chakraborty, R. (Univ. of Texas Graduate School of Biomedical Sciences, Houston, TX (United States))

    1994-07-01

    Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. The authors present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of [open quotes]match[close quotes] statistics. The authors have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching. 54 refs., 4 figs., 6 tabs.

  1. 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...

  2. How do repeat suicide attempters differ from first timers? An exploratory record based analysis

    Directory of Open Access Journals (Sweden)

    Vikas Menon

    2016-01-01

    Full Text Available Background: Evidence indicates that repeat suicide attempters, as a group, may differ from 1st time attempters. The identification of repeat attempters is a powerful but underutilized clinical variable. Aims: In this research, we aimed to compare individuals with lifetime histories of multiple attempts with 1st time attempters to identify factors predictive of repeat attempts. Setting and Design: This was a retrospective record based study carried out at a teaching cum Tertiary Care Hospital in South India. Methods: Relevant data was extracted from the clinical records of 1st time attempters (n = 362 and repeat attempters (n = 61 presenting to a single Tertiary Care Center over a 4½ year period. They were compared on various sociodemographic and clinical parameters. The clinical measures included Presumptive Stressful Life Events Scale, Beck Hopelessness Scale, Coping Strategies Inventory – Short Form, and the Global Assessment of Functioning Scale. Statistical Analysis Used: First time attempters and repeaters were compared using appropriate inferential statistics. Logistic regression was used to identify independent predictors of repeat attempts. Results: The two groups did not significantly differ on sociodemographic characteristics. Repeat attempters were more likely to have given prior hints about their act (χ2 = 4.500, P = 0.034. In the final regression model, beck hopelessness score emerged as a significant predictor of repeat suicide attempts (odds ratio = 1.064, P = 0.020. Conclusion: Among suicide attempters presenting to the hospital, the presence of hopelessness is a predictor of repeat suicide attempts, independent of clinical depression. This highlights the importance of considering hopelessness in the assessment of suicidality with a view to minimize the risk of future attempts.

  3. Improvement of recovery and repeatability in liquid chromatography-mass spectrometry analysis of peptides

    NARCIS (Netherlands)

    van Midwoud, Paul M.; Rieux, Laurent; Bischoff, Rainer; Verpoorte, Elisabeth; Niederlander, Harm A. G.

    2007-01-01

    Poor repeatability of peak areas is a problem frequently encountered in peptide analysis with nanoLiquid Chromatography coupled on-line with Mass Spectrometry (nanoLC-MS). As a result, quantitative analysis will be seriously hampered unless the observed variability can be corrected in some way.

  4. Repeat film analysis and its implications for quality assurance in dental radiology: An institutional case study

    Directory of Open Access Journals (Sweden)

    Shruthi Acharya

    2015-01-01

    Full Text Available Context: The goal of any radiologist is to produce the highest quality diagnostic radiographs, while keeping patient exposure as low as reasonably achievable (ALARA. Aims: The aim of this study was to describe the reasons for radiograph rejections through a repeat film analysis in an Indian dental school. Settings and Design: An observational study conducted in the Department of Oral Medicine and Radiology, Manipal College of Dental Sciences, Manipal. Materials and Methods: During a 6-month study period, a total of 9,495 intra-oral radiographs and 2339 extraoral radiographs taken in the Radiology Department were subjected to repeat film analysis. Statistical Analysis Used: SPSS Version 16. Descriptive analysis used. Results: The results showed that the repeat rates were 7.1% and 5.86% for intraoral and extraoral radiographs, respectively. Among the causes for errors reported, positioning error (38.7% was the most common, followed by improper angulations (26.1%, and improper film placement (11.2% for intra-oral radiographs. The study found that the maximum frequency of repeats among extraoral radiographs was for panoramic radiographs (49% followed by lateral cephalogram (33%, and paranasal sinus view (14%. It was also observed that repeat rate of intraoral radiographs was highest for internees (44.7%, and undergraduate students (28.2%. Conclusions: The study pointed to a need for more targeted interventions to achieve the goal of keeping patient exposure ALARA in a dental school setting.

  5. Power analysis for multivariate and repeated measures designs: a flexible approach using the SPSS MANOVA procedure.

    Science.gov (United States)

    D'Amico, E J; Neilands, T B; Zambarano, R

    2001-11-01

    Although power analysis is an important component in the planning and implementation of research designs, it is often ignored. Computer programs for performing power analysis are available, but most have limitations, particularly for complex multivariate designs. An SPSS procedure is presented that can be used for calculating power for univariate, multivariate, and repeated measures models with and without time-varying and time-constant covariates. Three examples provide a framework for calculating power via this method: an ANCOVA, a MANOVA, and a repeated measures ANOVA with two or more groups. The benefits and limitations of this procedure are discussed.

  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......, which can mask the male results when autosomal STRs are investigated. Sometimes, mixtures of Y-STRs are observed, e.g. in rape cases with multiple offenders. In such cases, Y-STR mixture analysis is required, e.g. by mixture deconvolution, to deduce the most likely DNA profiles from the contributors. We...... 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...

  7. The Potential of Cosmetic Applicators as a Source of DNA for Forensic Analysis.

    Science.gov (United States)

    Adamowicz, Michael S; Labonte, Renáe D; Schienman, John E

    2015-07-01

    Personal products, such as toothbrushes, have been used as both known reference and evidentiary samples for forensic DNA analysis. This study examined the viability of a broad selection of cosmetic applicators for use as targets for human DNA extraction and short tandem repeat (STR) analysis using standard polymerase chain reaction (PCR) conditions. Applicator types included eyeliner smudgers, pencils and crayons, eye shadow sponges, mascara wands, concealer wands, face makeup sponges, pads and brushes, lipsticks and balms, and lip gloss wands. The quantity and quality of DNA extracted from each type of applicator were examined by assessing the number of loci successfully amplified and the peak balance of the heterozygous alleles in each full STR profile. While degraded DNA, stochastic amplification, and PCR inhibition were observed for some items, full STR profiles were developed for 14 of 76 applicators. The face makeup sponge applicators yielded the highest proportional number of full STR profiles (4/7). © 2015 American Academy of Forensic Sciences.

  8. Repeatability of the Oxford Foot Model for Kinematic Gait Analysis of the Foot and Ankle

    NARCIS (Netherlands)

    van Hoeve, S.; Vos, J.; Weijers, P.; Verbruggen, J.; Willems, P.; Poeze, M.; Meijer, K.

    2015-01-01

    INTRODUCTION: Kinematic gait analysis via the multi-segmental Oxford foot model (OFM) may be a valuable addition to the biomechanical examination of the foot and ankle. The aim of this study is to assess the repeatability of the OFM in healthy subjects. METHODS: Nine healthy subjects, without a

  9. X-Chromosomal short tandem repeat loci in the Turkish population ...

    African Journals Online (AJOL)

    In this study, we aimed to demonstrate the importance and utility of polymorphic short tandem repeat (STR) found on the human X chromosome and to provide the first allelic frequency data of X-STR (X chromosomal) loci in the Turkish population. Blood samples were taken from unrelated individuals (135 males and 129 ...

  10. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    evaluating the deployment repeatability builds upon the testing or analysis of deployment kinematics (Chapter 6) and adds repetition. Introduction...material yield or failure during a test. For the purposes of this chapter, zero shift will refer to permanent changes in the structure, while reversible ...the content of other chapters in this book: Gravity Compensation (Chapter 4) and Deployment Kinematics and Dynamics (Chapter 6). Repeating the

  11. Bovine and equine forensic DNA analysis

    NARCIS (Netherlands)

    van de Goor, L.H.P.

    2011-01-01

    Animal forensic DNA analysis is being used for human criminal investigations (e.g traces from cats and dogs), wildlife management, breeding and food safety. The most common DNA markers used for such forensic casework are short tandem repeats (STR). Rules and guidelines concerning quality assurance

  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. Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

    International Nuclear Information System (INIS)

    Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

    2007-01-01

    The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

  14. 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

  15. Genetic polymorphism of 22 autosomal STR markers in a Han population of Southern China.

    Science.gov (United States)

    Liu, Qiu-Ling; Chen, Zi-Xiang; Chen, Chu-Guang; Lu, De-Jian

    2016-09-01

    Population genetic data and forensic statistics of 22 autosomal short tandem repeat (STR) loci (D1S1656, D2S1338, D3S3045, D4S2366, D5S2500, D6S477, D7S3048, D8S1132, D9S925, D10S1435, D11S2368, D12S391, D13S325, D14S608, D15S659, D16S539, D17S1290, D18S535, D19S253, D20S470, D21S1270 and GATA198B05) were determined for a sample of 515 unrelated individuals from Han population in Southern China. The expected heterozygosity and the discrimination power varied from 0.7358 to 0.8733 and 0.8915 to 0.9702, respectively. The probability of excluding an unrelated man as the true father (assuming no background relatedness in the population) for trios and for duos ranged from 0.5126 to 0.7415 and 0.3331 to 0.5864, respectively. The studied STRs appear to provide a significant improvement in the statistical power of kinship analysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. 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.

  17. Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

    Science.gov (United States)

    Liu, San-Xu; Hou, Wei; Zhang, Xue-Yan; Peng, Chang-Jun; Yue, Bi-Song; Fan, Zhen-Xin; Li, Jing

    2018-07-18

    The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (Pgenome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

  18. Repeatability and reproducibility of Population Viability Analysis (PVA and the implications for threatened species management

    Directory of Open Access Journals (Sweden)

    Clare Morrison

    2016-08-01

    Full Text Available Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost. Population Viability Analysis (PVA is frequently used in population focused conservation prioritizations. The critical nature of many of these management decisions requires that PVA models are repeatable and reproducible to reliably rank species and/or populations quantitatively. This paper assessed the repeatability and reproducibility of a subset of previously published PVA models. We attempted to rerun baseline models from 90 publicly available PVA studies published between 2000-2012 using the two most common PVA modelling software programs, VORTEX and RAMAS-GIS. Forty percent (n = 36 failed, 50% (45 were both repeatable and reproducible, and 10% (9 had missing baseline models. Repeatability was not linked to taxa, IUCN category, PVA program version used, year published or the quality of publication outlet, suggesting that the problem is systemic within the discipline. Complete and systematic presentation of PVA parameters and results are needed to ensure that the scientific input into conservation planning is both robust and reliable, thereby increasing the chances of making decisions that are both beneficial and defensible. The implications for conservation triage may be far reaching if population viability models cannot be reproduced with confidence, thus undermining their intended value.

  19. Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.

    Science.gov (United States)

    Hindle, K Lauren; Bella, Jordi; Lovell, Simon C

    2009-11-01

    Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/.

  20. Analysis of a kinetic multi-segment foot model. Part I: Model repeatability and kinematic validity.

    Science.gov (United States)

    Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

    2012-04-01

    Kinematic multi-segment foot models are still evolving, but have seen increased use in clinical and research settings. The addition of kinetics may increase knowledge of foot and ankle function as well as influence multi-segment foot model evolution; however, previous kinetic models are too complex for clinical use. In this study we present a three-segment kinetic foot model and thorough evaluation of model performance during normal gait. In this first of two companion papers, model reference frames and joint centers are analyzed for repeatability, joint translations are measured, segment rigidity characterized, and sample joint angles presented. Within-tester and between-tester repeatability were first assessed using 10 healthy pediatric participants, while kinematic parameters were subsequently measured on 17 additional healthy pediatric participants. Repeatability errors were generally low for all sagittal plane measures as well as transverse plane Hindfoot and Forefoot segments (median<3°), while the least repeatable orientations were the Hindfoot coronal plane and Hallux transverse plane. Joint translations were generally less than 2mm in any one direction, while segment rigidity analysis suggested rigid body behavior for the Shank and Hindfoot, with the Forefoot violating the rigid body assumptions in terminal stance/pre-swing. Joint excursions were consistent with previously published studies. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Analysis of oligonucleotide array experiments with repeated measures using mixed models

    Directory of Open Access Journals (Sweden)

    Getchell Thomas V

    2004-12-01

    Full Text Available Abstract Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease or absence (Control of the disease, and brain regions including olfactory bulb (OB or cerebellum (CER. In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. Results In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH procedure of controlling false discovery rate (FDR at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the α-level (αnew = 0.0033 determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD procedure at the level of αnew to control the family-wise error rate (FWER for each gene examined. Conclusions A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  2. In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

    Directory of Open Access Journals (Sweden)

    Evandro Vagner Tambarussi

    2009-01-01

    Full Text Available The availability of chloroplast genome (cpDNA sequences of Atropa belladonna, Nicotiana sylvestris, N.tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species,allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs incpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than geniccpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, pentaandhexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification ofnucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastomedatabase can be exploited for phylogenetic analysis and biotechnological approaches.

  3. Methodology for repeated load analysis of composite structures with embedded magnetic microwires

    Directory of Open Access Journals (Sweden)

    K. Semrád

    2017-01-01

    Full Text Available The article processes issue of strength of cyclically loaded composite structures with the possibility of contactless stress measuring inside a material. For this purpose a contactless tensile stress sensor using improved induction principle based on the magnetic microwires embedded in the composite structure has been developed. The methodology based on the E-N approach was applied for the analysis of the repeated load of the wing hinge connection, including finite element method (FEM fatigue strength analysis. The results proved that composites in comparison with the metal structures offer significant weight reduction of the small aircraft construction, whereas the required strength, stability and lifetime of the components are remained.

  4. [Variation of CAG repeats in coding region of ATXN2 gene in different ethnic groups].

    Science.gov (United States)

    Chen, Xiao-Chen; Sun, Hao; Mi, Dong-Qing; Huang, Xiao-Qin; Lin, Ke-Qin; Yi, Wen; Yu, Liang; Shi, Lei; Shi, Li; Yang, Zhao-Qing; Chu, Jia-You

    2011-04-01

    Toinvestigate CAG repeats variation of ATXN2 gene coding region in six ethnic groups that live in comparatively different environments, to evaluate whether these variations are under positive selection, and to find factors driving selection effects, 291 unrelated healthy individuals were collected from six ethnic groups and their STR geneotyping was performed. The frequencies of alleles and genotypes were counted and thereby Slatkin's linearized Fst values were calculated. The UPGMA tree against this gene was constructed. The MDS analysis among these groups was carried out as well. The results from the linearized Fst values indicated that there were significant evolutionary differences of the STR in ATXN2 gene between Hui and Yi groups, but not among the other 4 groups. Further analysis was performed by combining our data with published data obtained from other groups. These results indicated that there were significant differences between Japanese and other groups including Hui, Hani, Yunnan Mongolian, and Inner Mongolian. Both Hui and Mongolian from Inner Mongolia were significantly different from Han. In conclusion, the six ethnic groups had their own distribution characterizations of allelic frequencies of ATXN2 STR, and the potential cause of frequency changes in rare alleles could be the consequence of positive selection.

  5. Allele frequency distribution for 21 autosomal STR loci in Bhutan.

    Science.gov (United States)

    Kraaijenbrink, Thirsa; van Driem, George L; Tshering of Gaselô, Karma; de Knijff, Peter

    2007-07-20

    We studied the allele frequency distribution of 21 autosomal STR loci contained in the AmpFlSTR Identifiler (Applied Biosystems), the Powerplex 16 (Promega) and the FFFL (Promega) multiplex PCR kits among 936 individuals from the Royal Kingdom of Bhutan. As such these are the first published autosomal DNA results from this country.

  6. Repeatability of heart rate variability in congenital hypothyroidism as analysed by detrended fluctuation analysis

    International Nuclear Information System (INIS)

    Echeverría, J C; Solís, L I; Pérez, J E; Gaitán, M J; Mandujano, M; Sánchez, M C; González-Camarena, R; Rivera, I R

    2009-01-01

    The analysis of heart rate fluctuations, or heart rate variability (HRV), may be applied to explore children's neurodevelopment. However, previous studies have reported poor reliability (repeatability) of HRV measures in children at rest and during light exercise. Whether the reliability can be improved by controlling variables such as physical activity, breathing rate and tidal volume, or by selecting non-conventional techniques for analysing the data remains as an open question. We evaluated the short-term repeatability of RR-interval data from medicated children with congenital hypothyroidism (CH). The α 1 exponents, obtained by detrended fluctuation analysis (DFA), from the data of 21 children collected at two different sessions were compared. Elapsed days between sessions were 59 ± 33, and data were obtained during 10 min, trying to restrict the children's activity while being seated. We found statistical agreement between the means of α 1 exponents for each session (p = 0.94) and no bias with a low-coefficient variation (9.1%); an intraclass correlation coefficient ri = 0.48 ([0.14 0.72], 95% confidence interval) was also estimated. These findings, which were compared with results obtained by conventional time and frequency techniques, indicate the existence of agreement between the α 1 exponents obtained at each session, thereby providing support concerning the repeatability of HRV data as analysed by DFA in children with congenital hypothyroidism. Of particular interest was also the agreement found by using the central frequency of the high-frequency band and the parameter pNN20, both showing better or similar ri than α 1 (0.77 [0.57 0.89] and 0.51 [0.17 0.74], respectively), yet considerably better repeatability than other conventional time and frequency parameters

  7. Repeat participation in annual cross-sectional surveys of drug users and its implications for analysis.

    Science.gov (United States)

    Agius, P A; Aitken, C K; Breen, C; Dietze, P M

    2018-06-04

    We sought to establish the extent of repeat participation in a large annual cross-sectional survey of people who inject drugs and assess its implications for analysis. We used "porn star names" (the name of each participant's first pet followed by the name of the first street in which they lived) to identify repeat participation in three Australian Illicit Drug Reporting System surveys. Over 2013-2015, 2468 porn star names (96.2%) appeared only once, 88 (3.4%) twice, and nine (0.4%) in all 3 years. We measured design effects, based on the between-cluster variability for selected estimates, of 1.01-1.07 for seven key variables. These values indicate that the complex sample is (e.g.) 7% less efficient in estimating prevalence of heroin use (ever) than a simple random sample, and 1% less efficient in estimating number of heroin overdoses (ever). Porn star names are a useful means of tracking research participants longitudinally while maintaining their anonymity. Repeat participation in the Australian Illicit Drug Reporting System is low (less than 5% per annum), meaning point-prevalence and effect estimation without correction for the lack of independence in observations is unlikely to seriously affect population inference.

  8. High repeatability from 3D experimental platform for quantitative analysis of cellular branch pattern formations.

    Science.gov (United States)

    Hagiwara, Masaya; Nobata, Rina; Kawahara, Tomohiro

    2018-04-24

    Three-dimensional (3D) cell and tissue cultures more closely mimic biological environments than two-dimensional (2D) cultures and are therefore highly desirable in culture experiments. However, 3D cultures often fail to yield repeatable experimental results because of variation in the initial culture conditions, such as cell density and distribution in the extracellular matrix, and therefore reducing such variation is a paramount concern. Here, we present a 3D culture platform that demonstrates highly repeatable experimental results, obtained by controlling the initial cell cluster shape in the gel cube culture device. A micro-mould with the desired shape was fabricated by photolithography or machining, creating a 3D pocket in the extracellular matrix contained in the device. Highly concentrated human bronchial epithelial cells were then injected in the pocket so that the cell cluster shape matched the fabricated mould shape. Subsequently, the cubic device supplied multi-directional scanning, enabling high-resolution capture of the whole tissue structure with only a low-magnification lens. The proposed device significantly improved the repeatability of the developed branch pattern, and multi-directional scanning enabled quantitative analysis of the developed branch pattern formations. A mathematical simulation was also conducted to reveal the mechanisms of branch pattern formation. The proposed platform offers the potential to accelerate any research field that conducts 3D culture experiments, including tissue regeneration and drug development.

  9. Revisiting Slow Slip Events Occurrence in Boso Peninsula, Japan, Combining GPS Data and Repeating Earthquakes Analysis

    Science.gov (United States)

    Gardonio, B.; Marsan, D.; Socquet, A.; Bouchon, M.; Jara, J.; Sun, Q.; Cotte, N.; Campillo, M.

    2018-02-01

    Slow slip events (SSEs) regularly occur near the Boso Peninsula, central Japan. Their time of recurrence has been decreasing from 6.4 to 2.2 years from 1996 to 2014. It is important to better constrain the slip history of this area, especially as models show that the recurrence intervals could become shorter prior to the occurrence of a large interplate earthquake nearby. We analyze the seismic waveforms of more than 2,900 events (M≥1.0) taking place in the Boso Peninsula, Japan, from 1 April 2004 to 4 November 2015, calculating the correlation and the coherence between each pair of events in order to define groups of repeating earthquakes. The cumulative number of repeating earthquakes suggests the existence of two slow slip events that have escaped detection so far. Small transient displacements observed in the time series of nearby GPS stations confirm these results. The detection scheme coupling repeating earthquakes and GPS analysis allow to detect small SSEs that were not seen before by classical methods. This work brings new information on the diversity of SSEs and demonstrates that the SSEs in Boso area present a more complex history than previously considered.

  10. 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.

  11. Evaluation of two new STR loci 9q2h2 and wg3f12 in a Japanese population.

    Science.gov (United States)

    Mizutani, M; Huang, X L; Tamaki, K; Yoshimoto, T; Uchihi, R; Yamamoto, T; Katsumata, Y; Armour, J A

    1999-09-01

    Two short tandem repeat (STR) loci (9q2h2 and wg3f12) have been evaluated in a Japanese population. Ten and seven different alleles were observed in 9q2h2 and wg3f12 respectively. 9q2h2 displayed simple polymorphism in tetrameric repeat structure; by contrast, wg3f12 contained variable numbers of tetrameric repeats and a 30-bp deletion/insertion polymorphism. No "interalleles" were found. The expected heterozygosities of 9q2h2 and wg3fl2 were 0.749 and 0.574, respectively. No deviation from Hardy-Weinberg equilibrium was found.

  12. Characterization of Dutch Staphylococcus aureus from bovine mastitis using a Multiple Locus Variable Number Tandem Repeat Analysis

    NARCIS (Netherlands)

    Ikawaty, R.; Brouwer, E.C.; Jansen, M.D.; Duijkeren, van E.; Mevius, D.J.; Verhoef, J.; Fluit, A.C.

    2009-01-01

    Current typing methods for Staphylococcus aureus have important drawbacks. We evaluated a Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) scheme with 6 loci which lacks most drawbacks on 85 bovine mastitis isolates from The Netherlands. For each locus the number of repeat units (RU) was

  13. Y-STR frequency surveying method

    DEFF Research Database (Denmark)

    Willuweit, Sascha; Caliebe, Amke; Andersen, Mikkel Meyer

    2011-01-01

    Reasonable formalized methods to estimate the frequencies of DNA profiles generated from lineage markers have been proposed in the past years and were discussed in the forensic community. Recently, collections of population data on the frequencies of variations in Y chromosomal STR profiles have...... reached a new quality with the establishment of the comprehensive neatly quality-controlled reference database YHRD. Grounded on such unrivalled empirical material from hundreds of populations studies the core assumption of the Haplotype Frequency Surveying Method originally described 10 years ago can...... be tested and improved. Here we provide new approaches to calculate the parameters used in the frequency surveying method: a maximum likelihood estimation of the regression parameters (r1, r2, s1 and s2) and a revised Frequency Surveying framework with variable binning and a database preprocessing to take...

  14. On summary measure analysis of linear trend repeated measures data: performance comparison with two competing methods.

    Science.gov (United States)

    Vossoughi, Mehrdad; Ayatollahi, S M T; Towhidi, Mina; Ketabchi, Farzaneh

    2012-03-22

    The summary measure approach (SMA) is sometimes the only applicable tool for the analysis of repeated measurements in medical research, especially when the number of measurements is relatively large. This study aimed to describe techniques based on summary measures for the analysis of linear trend repeated measures data and then to compare performances of SMA, linear mixed model (LMM), and unstructured multivariate approach (UMA). Practical guidelines based on the least squares regression slope and mean of response over time for each subject were provided to test time, group, and interaction effects. Through Monte Carlo simulation studies, the efficacy of SMA vs. LMM and traditional UMA, under different types of covariance structures, was illustrated. All the methods were also employed to analyze two real data examples. Based on the simulation and example results, it was found that the SMA completely dominated the traditional UMA and performed convincingly close to the best-fitting LMM in testing all the effects. However, the LMM was not often robust and led to non-sensible results when the covariance structure for errors was misspecified. The results emphasized discarding the UMA which often yielded extremely conservative inferences as to such data. It was shown that summary measure is a simple, safe and powerful approach in which the loss of efficiency compared to the best-fitting LMM was generally negligible. The SMA is recommended as the first choice to reliably analyze the linear trend data with a moderate to large number of measurements and/or small to moderate sample sizes.

  15. A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.

    Science.gov (United States)

    Hauck, Yolande; Soler, Charles; Gérôme, Patrick; Vong, Rithy; Macnab, Christine; Appere, Géraldine; Vergnaud, Gilles; Pourcel, Christine

    2015-07-01

    Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. MULTIPLE-LOCUS VARIABLE-NUMBER TANDEM REPEAT ANALYSIS OF BRUCELLA ISOLATES FROM THAILAND.

    Science.gov (United States)

    Kumkrong, Khurawan; Chankate, Phanita; Tonyoung, Wittawat; Intarapuk, Apiradee; Kerdsin, Anusak; Kalambaheti, Thareerat

    2017-01-01

    Brucellosis-induced abortion can result in significant economic loss to farm animals. Brucellosis can be transmitted to humans during slaughter of infected animals or via consumption of contaminated food products. Strain identification of Brucella isolates can reveal the route of transmission. Brucella strains were isolated from vaginal swabs of farm animal, cow milk and from human blood cultures. Multiplex PCR was used to identify Brucella species, and owing to high DNA homology among Brucella isolates, multiple-locus variable-number tandem repeat analysis (MLVA) based on the number of tandem repeats at 16 different genomic loci was used for strain identification. Multiplex PCR categorized the isolates into B. abortus (n = 7), B. melitensis (n = 37), B. suis (n = 3), and 5 of unknown Brucella spp. MLVA-16 clustering analysis differentiated the strains into various genotypes, with Brucella isolates from the same geographic region being closely related, and revealed that the Thai isolates were phylogenetically distinct from those in other countries, including within the Southeast Asian region. Thus, MLVA-16 typing has utility in epidemiological studies.

  17. Usefulness of repeat coronary angiography 24 hours after balloon angioplasty to evaluate early lminal deterioration and facilitate quantitative analysis

    NARCIS (Netherlands)

    G.R. Heyndrickx (Guy); G-J. Laarman (GertJan); H. Suryapranata (Harry); F. Zijlstra (Felix); P.W.J.C. Serruys (Patrick); D.P. Foley (David); A.A. van den Bos (Arjan); J.W. Deckers (Jaap)

    1993-01-01

    textabstractBecause of the unavoidable occurrence of vessel disruption after successful coronary balloon angioplasty, the reliability of quantitative angiographic analysis in that setting has been questioned. For this reason and the suggested occurrence of delayed elastic recoil, repeat angiography

  18. Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis

    Directory of Open Access Journals (Sweden)

    Eriko Maeda-Mitani

    2016-01-01

    Full Text Available QUB11a is used as a locus for variable number of tandem repeats (VNTR analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp investigated contained IS6110 insertions and varied in the number of repeats (18 patterns and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

  19. 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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  20. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  1. "The devil's in the detail": Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide.

    Science.gov (United States)

    Phillips, C; Gettings, K Butler; King, J L; Ballard, D; Bodner, M; Borsuk, L; Parson, W

    2018-05-01

    The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. 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; Han, Myun Soo; Cho, Myung-Haing

    2016-09-30

    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.

  3. Repeatability, correlation and path analysis of physical and chemical characteristics of peach fruits

    Directory of Open Access Journals (Sweden)

    Rosana Gonçalves Pires Matias

    2014-12-01

    Full Text Available This study aimed to determine the number of measurements necessary to evaluate physical and chemical characteristics of peach fruits, study the relationships between them and their direct and indirect effects on the content of ascorbic acid and total carotenoids. The characteristics skin and pulp color, fruit weight, suture, equatorial and polar diameters, firmness, soluble solids (SS, titratable acidity (TA, SS/TA ratio, ascorbic acid and total carotenoids were evaluated in 39 cultivars of peach and 3 cultivars of nectarine from the orchard of the Universidade Federal de Viçosa. The repeatability coefficient was estimated by ANOVA and CPCOR. Phenotypic correlation coefficients (rf were estimated and, after the multicollinearity diagnostics, they were unfolded to direct and indirect effects of the explanatory variables on the response variable using path analysis. There was agreement on the magnitude of repeatability coefficients obtained by the two methods; however, they varied among the 14 characteristics. The highest correlations were found between FW, SD, ED and PD. Seven fruits are sufficient to evaluate the physical and chemical characteristics of peach with a correlation coefficient of 90%. The characteristics considered in the path diagrams (b* skin, hº skin, b* pulp, hº pulp, ED, PD, FIR, SS, SS/AT and TC are not the main determinants of the ascorbic acid. The yellow hue of the pulp (hº pulp has the potential to be used in indirect selection for total carotenoids.

  4. A multi locus variable number of tandem repeat analysis (MLVA scheme for Streptococcus agalactiae genotyping

    Directory of Open Access Journals (Sweden)

    Mereghetti Laurent

    2011-07-01

    Full Text Available Abstract Background Multilocus sequence typing (MLST is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR analysis (MLVA applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R. Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.

  5. Repeated attempted homicide by administration of drugs documented by hair analysis.

    Science.gov (United States)

    Baillif-Couniou, Valérie; Bartoli, Christophe; Sastre, Caroline; Chèze, Marjorie; Deveaux, Marc; Léonetti, Georges; Pélissier-Alicot, Anne-Laure

    2018-02-01

    Attempted murder by repeated poisoning is quite rare. The authors describe the case of a 62-year-old man who was admitted to an intensive care unit (ICU) for neurological disturbances complicated by inhalation pneumopathy. He presented a loss of consciousness while his wife was visiting him at the ICU (H0). Forty-eight hours later (H48), police officers apprehended the patient's wife pouring a liquid into his fruit salad at the hospital. Toxicological analyses of a blood sample and the infusion equipment (H0), as well as the fruit salad and its container (H48), confirmed the attempted poisoning with cyamemazine (H0) and hydrochloric acid (H48). In order to evaluate the anteriority of poisonings, hair analysis was requested and the medical records of the 6 previous months were also examined. Two 6-cm brown hair strands were sampled and the victim's medical record was seized in order to determine the treatments he had been given during the previous six months. Segmental hair testing on two 6-cm brown hair was conducted by GC-MS, LC-DAD and LC-MS/MS (0-2/2-4/4-6 cm; pg/mg). Haloperidol (9200/1391/227), amitriptyline (7450/1850/3260), venlafaxine (332/560/260), that had never been part of the victim's treatment were detected, as well as some benzodiazepines (alprazolam, bromazepam, nordazepam); cyamemazine was also detected in all the segments (9960/1610/2367) though only a single dose administration was reported in the medical records. The toxicological analyses performed at H0 and H48 confirmed the homicide attempts in the ICU. In addition, comparison of the results in hair analysis with the medical records confirmed repeated poisoning attempts over the previous six months, and thus explain the origin of the disorders presented by the victim. This case serves to remind us that repeated attempted murder can be difficult to diagnose and that hair analysis can be an effective way to detect such attempts. Copyright © 2018. Published by Elsevier Ltd.

  6. Cost-effectiveness analysis of repeat fine-needle aspiration for thyroid biopsies read as atypia of undetermined significance.

    Science.gov (United States)

    Heller, Michael; Zanocco, Kyle; Zydowicz, Sara; Elaraj, Dina; Nayar, Ritu; Sturgeon, Cord

    2012-09-01

    The 2007 National Cancer Institute (NCI) conference on Thyroid Fine-Needle Aspiration (FNA) introduced the category atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS). Repeat FNA in 3 to 6 months was recommended for low-risk patients. Compliance with these recommendations has been suboptimal. We hypothesized that repeat FNA would be more effective than diagnostic lobectomy, with decreased costs and improved rates of cancer detection. Cost-effectiveness analysis was performed in which we compared diagnostic lobectomy with repeat FNA. A Markov model was developed. Outcomes and probabilities were identified from literature review. Third-party payer costs were estimated in 2010 US dollars. Outcomes were weighted by use of the quality-of-life utility factors, yielding quality-adjusted life years (QALYs). Monte Carlo simulation and sensitivity analysis were used to examine the uncertainty of probability, cost, and utility estimates. The diagnostic lobectomy strategy cost $8,057 and produced 23.99 QALYs. Repeat FNA cost $2,462 and produced 24.05 QALYs. Repeat FNA was dominant until the cost of FNA increased to $6,091. Dominance of the repeat FNA strategy was not sensitive to the cost of operation or the complication rate. The NCI recommendations for repeat FNA regarding follow-up of AUS/FLUS results are cost-effective. Improving compliance with these guidelines should lead to less overall costs, greater quality of life, and fewer unnecessary operations. Copyright © 2012 Mosby, Inc. All rights reserved.

  7. Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus.

    Science.gov (United States)

    Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L

    2015-11-25

    Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

  8. Repeated Time-to-event Analysis of Consecutive Analgesic Events in Postoperative Pain

    DEFF Research Database (Denmark)

    Juul, Rasmus Vestergaard; Rasmussen, Sten; Kreilgaard, Mads

    2015-01-01

    BACKGROUND: Reduction in consumption of opioid rescue medication is often used as an endpoint when investigating analgesic efficacy of drugs by adjunct treatment, but appropriate methods are needed to analyze analgesic consumption in time. Repeated time-to-event (RTTE) modeling is proposed as a way...... to describe analgesic consumption by analyzing the timing of consecutive analgesic events. METHODS: Retrospective data were obtained from 63 patients receiving standard analgesic treatment including morphine on request after surgery following hip fracture. Times of analgesic events up to 96 h after surgery...... were extracted from hospital medical records. Parametric RTTE analysis was performed with exponential, Weibull, or Gompertz distribution of analgesic events using NONMEM®, version 7.2 (ICON Development Solutions, USA). The potential influences of night versus day, sex, and age were investigated...

  9. Multiple-locus variable-number tandem-repeat analysis of pathogenic Yersinia enterocolitica in China.

    Directory of Open Access Journals (Sweden)

    Xin Wang

    Full Text Available The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.

  10. Effects of Repeated-Sprint Training in Hypoxia on Sea-Level Performance: A Meta-Analysis.

    Science.gov (United States)

    Brocherie, Franck; Girard, Olivier; Faiss, Raphaël; Millet, Grégoire P

    2017-08-01

    Repeated-sprint training in hypoxia (RSH) is a recent intervention regarding which numerous studies have reported effects on sea-level physical performance outcomes that are debated. No previous study has performed a meta-analysis of the effects of RSH. We systematically reviewed the literature and meta-analyzed the effects of RSH versus repeated-sprint training in normoxia (RSN) on key components of sea-level physical performance, i.e., best and mean (all sprint) performance during repeated-sprint exercise and aerobic capacity (i.e., maximal oxygen uptake [[Formula: see text

  11. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences.

    Science.gov (United States)

    Zhang, Meiping; Rong, Ying; Lee, Mi-Kyung; Zhang, Yang; Stelly, David M; Zhang, Hong-Bin

    2015-10-01

    Cotton is the world's leading textile fiber crop and is also grown as a bioenergy and food crop. Knowledge of the phylogeny of closely related species and the genome origin and evolution of polyploid species is significant for advanced genomics research and breeding. We have reconstructed the phylogeny of the cotton genus, Gossypium L., and deciphered the genome origin and evolution of its five polyploid species by restriction fragment analysis of repeated sequences. Nuclear DNA of 84 accessions representing 35 species and all eight genomes of the genus were analyzed. The phylogenetic tree of the genus was reconstructed using the parsimony method on 1033 polymorphic repeated sequence restriction fragments. The genome origin of its polyploids was determined by calculating the diploid-polyploid restriction fragment correspondence (RFC). The tree is consistent with the morphological classification, genome designation and geographic distribution of the species at subgenus, section and subsection levels. Gossypium lobatum (D7) was unambiguously shown to have the highest RFC with the D-subgenomes of all five polyploids of the genus, while the common ancestor of Gossypium herbaceum (A1) and Gossypium arboreum (A2) likely contributed to the A-subgenomes of the polyploids. These results provide a comprehensive phylogenetic tree of the cotton genus and new insights into the genome origin and evolution of its polyploid species. The results also further demonstrate a simple, rapid and inexpensive method suitable for phylogenetic analysis of closely related species, especially congeneric species, and the inference of genome origin of polyploids that constitute over 70 % of flowering plants.

  12. 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.

  13. Developmental and internal validation of a novel 13 loci STR multiplex method for Cannabis sativa DNA profiling.

    Science.gov (United States)

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

    2017-05-01

    Marijuana (Cannabis sativa L.) is a plant cultivated and trafficked worldwide as a source of fiber (hemp), medicine, and intoxicant. The development of a validated method using molecular techniques such as short tandem repeats (STRs) could serve as an intelligence tool to link multiple cases by means of genetic individualization or association of cannabis samples. For this purpose, a 13 loci STR multiplex method was developed, optimized, and validated according to relevant ISFG and SWGDAM guidelines. The STR multiplex consists of 13 previously described C. sativa STR loci: ANUCS501, 9269, 4910, 5159, ANUCS305, 9043, B05, 1528, 3735, CS1, D02, C11, and H06. A sequenced allelic ladder consisting of 56 alleles was designed to accurately genotype 101 C. sativa samples from three seizures provided by a U.S. Customs and Border Protection crime lab. Using an optimal range of DNA (0.5-1.0ng), validation studies revealed well-balanced electropherograms (inter-locus balance range: 0.500-1.296), relatively balanced heterozygous peaks (mean peak height ratio of 0.83 across all loci) with minimal artifacts and stutter ratio (mean stutter of 0.021 across all loci). This multi-locus system is relatively sensitive (0.13ng of template DNA) with a combined power of discrimination of 1 in 55 million. The 13 STR panel was found to be species specific for C. sativa; however, non-specific peaks were produced with Humulus lupulus. The results of this research demonstrate the robustness and applicability of this 13 loci STR system for forensic DNA profiling of marijuana samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa.

    Science.gov (United States)

    Mouton, L; Ebert, D

    2008-05-01

    Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

  15. REPEATABILITY OF SPITZER/IRAC EXOPLANETARY ECLIPSES WITH INDEPENDENT COMPONENT ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Morello, G.; Waldmann, I. P.; Tinetti, G., E-mail: giuseppe.morello.11@ucl.ac.uk [Department of Physics and Astronomy, University College London, Gower Street, WC1E6BT (United Kingdom)

    2016-04-01

    The research of effective and reliable detrending methods for Spitzer data is of paramount importance for the characterization of exoplanetary atmospheres. To date, the totality of exoplanetary observations in the mid- and far-infrared, at wavelengths >3 μm, have been taken with Spitzer. In some cases, in past years, repeated observations and multiple reanalyses of the same data sets led to discrepant results, raising questions about the accuracy and reproducibility of such measurements. Morello et al. (2014, 2015) proposed a blind-source separation method based on the Independent Component Analysis of pixel time series (pixel-ICA) to analyze InfraRed Array Camera (IRAC) data, obtaining coherent results when applied to repeated transit observations previously debated in the literature. Here we introduce a variant to the pixel-ICA through the use of wavelet transform, wavelet pixel-ICA, which extends its applicability to low-signal-to-noise-ratio cases. We describe the method and discuss the results obtained over 12 eclipses of the exoplanet XO3b observed during the “Warm Spitzer” era in the 4.5 μm band. The final results are reported, in part, also in Ingalls et al. (2016), together with results obtained with other detrending methods, and over 10 synthetic eclipses that were analyzed for the “IRAC Data Challenge 2015.” Our results are consistent within 1σ with the ones reported in Wong et al. (2014) and with most of the results reported in Ingalls et al. (2016), which appeared on arXiv while this paper was under review. Based on many statistical tests discussed in Ingalls et al. (2016), the wavelet pixel-ICA method performs as well as or better than other state-of-art methods recently developed by other teams to analyze Spitzer/IRAC data, and, in particular, it appears to be the most repeatable and the most reliable, while reaching the photon noise limit, at least for the particular data set analyzed. Another strength of the ICA approach is its highest

  16. REPEATABILITY OF SPITZER/IRAC EXOPLANETARY ECLIPSES WITH INDEPENDENT COMPONENT ANALYSIS

    International Nuclear Information System (INIS)

    Morello, G.; Waldmann, I. P.; Tinetti, G.

    2016-01-01

    The research of effective and reliable detrending methods for Spitzer data is of paramount importance for the characterization of exoplanetary atmospheres. To date, the totality of exoplanetary observations in the mid- and far-infrared, at wavelengths >3 μm, have been taken with Spitzer. In some cases, in past years, repeated observations and multiple reanalyses of the same data sets led to discrepant results, raising questions about the accuracy and reproducibility of such measurements. Morello et al. (2014, 2015) proposed a blind-source separation method based on the Independent Component Analysis of pixel time series (pixel-ICA) to analyze InfraRed Array Camera (IRAC) data, obtaining coherent results when applied to repeated transit observations previously debated in the literature. Here we introduce a variant to the pixel-ICA through the use of wavelet transform, wavelet pixel-ICA, which extends its applicability to low-signal-to-noise-ratio cases. We describe the method and discuss the results obtained over 12 eclipses of the exoplanet XO3b observed during the “Warm Spitzer” era in the 4.5 μm band. The final results are reported, in part, also in Ingalls et al. (2016), together with results obtained with other detrending methods, and over 10 synthetic eclipses that were analyzed for the “IRAC Data Challenge 2015.” Our results are consistent within 1σ with the ones reported in Wong et al. (2014) and with most of the results reported in Ingalls et al. (2016), which appeared on arXiv while this paper was under review. Based on many statistical tests discussed in Ingalls et al. (2016), the wavelet pixel-ICA method performs as well as or better than other state-of-art methods recently developed by other teams to analyze Spitzer/IRAC data, and, in particular, it appears to be the most repeatable and the most reliable, while reaching the photon noise limit, at least for the particular data set analyzed. Another strength of the ICA approach is its highest

  17. D20S16 is a complex interspersed repeated sequence: Genetic and physical analysis of the locus

    Energy Technology Data Exchange (ETDEWEB)

    Bowden, D.W.; Krawchuk, M.D.; Howard, T.D. [Wake Forest Univ., Winston-Salem, NC (United States)] [and others

    1995-01-20

    The genomic structure of the D20S16 locus has been evaluated using genetic and physical methods. D20S16, originally detected with the probe CRI-L1214, is a highly informative, complex restriction fragment length polymorphism consisting of two separate allelic systems. The allelic systems have the characteristics of conventional VNTR polymorphisms and are separated by recombination ({theta} = 0.02, Z{sub max} = 74.82), as demonstrated in family studies. Most of these recombination events are meiotic crossovers and are maternal in origin, but two, including deletion of the locus in a cell line from a CEPH family member, occur without evidence for exchange of flanking markers. DNA sequence analysis suggests that the basis of the polymorphism is variable numbers of a 98-bp sequence tandemly repeated with 87 to 90% sequence similarity between repeats. The 98-bp repeat is a dimer of 49 bp sequence with 45 to 98% identity between the elements. In addition, nonpolymorphic genomic sequences adjacent to the polymorphic 98-bp repeat tracts are also repeated but are not polymorphic, i.e., show no individual to individual variation. Restriction enzyme mapping of cosmids containing the CRI-L1214 sequence suggests that there are multiple interspersed repeats of the CRI-L1214 sequence on chromosome 20. The results of dual-color fluorescence in situ hybridization experiments with interphase nuclei are also consistent with multiple repeats of an interspersed sequence on chromosome 20. 23 refs., 6 figs.

  18. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  19. An analysis of single amino acid repeats as use case for application specific background models

    Directory of Open Access Journals (Sweden)

    Sykacek Peter

    2011-05-01

    Full Text Available Abstract Background Sequence analysis aims to identify biologically relevant signals against a backdrop of functionally meaningless variation. Increasingly, it is recognized that the quality of the background model directly affects the performance of analyses. State-of-the-art approaches rely on classical sequence models that are adapted to the studied dataset. Although performing well in the analysis of globular protein domains, these models break down in regions of stronger compositional bias or low complexity. While these regions are typically filtered, there is increasing anecdotal evidence of functional roles. This motivates an exploration of more complex sequence models and application-specific approaches for the investigation of biased regions. Results Traditional Markov-chains and application-specific regression models are compared using the example of predicting runs of single amino acids, a particularly simple class of biased regions. Cross-fold validation experiments reveal that the alternative regression models capture the multi-variate trends well, despite their low dimensionality and in contrast even to higher-order Markov-predictors. We show how the significance of unusual observations can be computed for such empirical models. The power of a dedicated model in the detection of biologically interesting signals is then demonstrated in an analysis identifying the unexpected enrichment of contiguous leucine-repeats in signal-peptides. Considering different reference sets, we show how the question examined actually defines what constitutes the 'background'. Results can thus be highly sensitive to the choice of appropriate model training sets. Conversely, the choice of reference data determines the questions that can be investigated in an analysis. Conclusions Using a specific case of studying biased regions as an example, we have demonstrated that the construction of application-specific background models is both necessary and

  20. Determination of allele frequencies in nine short tandem repeat loci ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... out the human genome. These loci are a rich source of highly polymorphic markers that may be detected using the polymerase chain reaction (PCR). PCR is a mimic of the normal cellular process of replication of DNA molecules. Each STR is distinguished by the number of times a sequence is repeated, ...

  1. Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

    Directory of Open Access Journals (Sweden)

    Lam Connie

    2012-05-01

    Full Text Available Abstract Background Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs analysis (MLVA to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. Results MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. Conclusions MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.

  2. Genotypic characterization by multi locus variable number of tandem repeats analysis international Bordetella pertussis vaccine strains

    Directory of Open Access Journals (Sweden)

    M. Fatah Moghadam

    2017-10-01

    Full Text Available Background: In 1930's first whole cell pertussis vaccines became available to the public heralding a dramatic success in overcoming the global burden of the disease. To date only a handful of B. pertussis strains have been used by international/local pertussis vaccine manufacturers. Inevitable well-documented genetic changes in the world population of this pathogen have prompted serious questions on suitability of traditional vaccine strains protect human against currently circulating wild isolates of Bordetella pertussis. Objective: Analyzing the genetic diversity within the most frequently-used vaccine strains of B. pertussis in the world Methods: A recently developed multi locus variable number of tandem repeats analysis (MLVA genotyping system along with a bioinforamtic piece of analysis was conducted on 11 strain / substrains of B137, B203 (10536, C393, Cs, E476, Tohama I, J445 (134, B202 and J446 (509 plus 2 sub-strains of 134 and 509 that are used at Razi institute for preparation of pertussis vaccine. In this study have used 6 individual loci of VNTR1, VNTR3a, VNTR3b, VNTR4, VNTR5 and VNTR6. Findings: Six distinct genotypes were recognized among the examined strains by comparing our data with the Dutch MLVA databank. These were all new and not reported before in the database. Conclusion: This observation reiterates on necessity for detection of predominant native strains to include in vaccine preparations suitable for different countries.

  3. Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

    Directory of Open Access Journals (Sweden)

    Junjie Cui

    2017-06-01

    Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

  4. Choroba Gerstmanna-Sträusslera-Scheinkera

    Directory of Open Access Journals (Sweden)

    Paweł P. Liberski

    2011-04-01

    Full Text Available Choroba Gerstmanna-Sträusslera-Scheinkera (GSS jest genetycznie uwarunkowaną chorobą wywoływaną przez priony. Jest ona unikalna, ponieważ udało się przepasażować GSS na naczelne i gryzonie przynajmniej z mózgu obarczonego mutacją kodonu 102. Tym samym jest to jedyne schorzenie jednocześnie genetycznie uwarunkowane i zakaźne, aczkolwiek natura czynnika infekcyjnego (prionu nadal stanowi przedmiot dyskusji. W obrazie klinicznym GSS dominuje postępująca ataksja móżdżkowa z towarzyszącym otępieniem i objawami piramidowo-pozapiramidowymi. Jest to jednak choroba heterogenna, o różnym obrazie klinicznym u nosicieli różnych mutacji, a nawet u nosicieli tej samej mutacji. Obraz neuropatologiczny obejmuje obecność PrPd – immunododatnich złogów amyloidu pod postacią blaszek, zwłaszcza tzw. blaszek wielordzeniowych. Istnieje kilka modeli GSS. U myszy transgenicznych z nadekspresją zmutowanego genu kodującego PrP obserwuje się spontaniczną chorobę zwyrodnieniową, pasażowalną na myszy transgeniczne o niskiej liczbie transgenu. U myszy transgenicznych uzyskanych drogą wzajemnej rekombinacji, a więc bez nadeskpresji, nie występuje choroba spontaniczna, niemniej stają się one wrażliwe na zakażenie GSS.

  5. Imported brucellosis in Denmark: Molecular identification and multiple-locus variable number tandem repeat analysis (MLVA) genotyping of the bacteria

    DEFF Research Database (Denmark)

    Aftab, H.; Dargis, R.; Christensen, J. J.

    2011-01-01

    A polymerase chain reaction was used to identify Brucella species isolated from humans in Denmark. Consecutive analysis of referred bacteria and re-examination of historical isolates identified all as Brucella melitensis. Multiple-locus variable number tandem repeat analysis (MLVA) placed...... the isolates in the previously defined 'East Mediterranean' B. melitensis group....

  6. Molecular analysis of the eTG trinucleotide repeat in South African ...

    African Journals Online (AJOL)

    -4 When amplified, this trinucleotide repeat is responsible for DNA instability and molecular pathology. A similar mechanism of trinucleotide repeat expansion has been described in fragile X mental retardation syndrome. (CGG):·· spinobulbar muscular atrophy (CAG)' and, more. MRC Human Ecogenetics Research Unit, ...

  7. Allele frequencies of 18 autosomal STR loci in the Uyghur population living in Kashgar Prefecture, Northwest China.

    Science.gov (United States)

    Zhang, Jian; Li, Zhenghui; Mo, Xiaoting; Ma, Wenhua; Zhang, Hantao; Lin, Ziqing; Ye, Jian

    2018-03-10

    There is currently no large population data-based data set in Kashgar Prefecture Uyghur. The allele frequencies of 18 autosomal short tandem repeat (STR) loci included in the DNATyper™ 19 kit were evaluated in 2600 Uyghur individuals living in Kashgar Prefecture, Northwest China. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) of all 18 autosomal STR loci were 0.99999999999999999998235 and 0.99999998670, respectively. Phylogenetic analyses revealed that the Uyghur population has a closer relationship with the Xinjiang-Kazakh, Inner Mongolia-Mongolian, and other three Uyghur populations. In addition, our results are consistent with the hypothesis that Uyghur population is an admixture of Eastern Asian and European populations.

  8. Allele Frequency Data for 17 Short Tandem Repeats in a Czech Population Sample

    Czech Academy of Sciences Publication Activity Database

    Šimková, H.; Faltus, Václav; Marván, Richard; Pexa, T.; Stenzl, V.; Brouček, J.; Hořínek, A.; Mazura, Ivan; Zvárová, Jana

    2009-01-01

    Roč. 4, č. 1 (2009), e15-e17 ISSN 1872-4973 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : short tandem repeat (STR) * allelic frequency * PowerPlex 16 System * AmpflSTR Identifiler * population genetics * Czech Republic Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.421, year: 2009

  9. Resolution of a serum sample mix-up through the use of short tandem repeat DNA typing.

    Science.gov (United States)

    Allen, Robert W; Pritchard, Jane K

    2004-12-01

    A sample mix-up occurred in a tissue procurement laboratory in which aliquots of serum from two tissue donors were accidentally mislabeled. The clues to the apparent mixup involved discrepant Hepatitis C test results. In an attempt to resolve the apparent mix up, DNA typing was performed using serum samples as a possible source of genomic DNA. Two hundred microliter aliquots of two reference sera and aliquots prepared from them were subjected to DNA extraction. PCR amplification of 9 STR loci was performed on the extracts and amplicons were analyzed by capillary electrophoresis. About 1 microg/ml of DNA was recovered from all serum samples and was of sufficient quality to direct the amplification of most, if not all STR loci allowing the mislabeled specimens to be traced to the proper tissue donor. Serum is a useful source of genomic DNA for STR analysis in situations in which such samples are the only source of DNA for testing. Interestingly, one of the tissue donors on life support and repeatedly receiving blood products, exhibited a mixed DNA profile indicative of the presence of DNA from multiple individuals in the bloodstream.

  10. [Analytical procedure of variable number of tandem repeats (VNTR) analysis and effective use of analysis results for tuberculosis control].

    Science.gov (United States)

    Hachisu, Yushi; Hashimoto, Ruiko; Kishida, Kazunori; Yokoyama, Eiji

    2013-12-01

    Variable number of tandem repeats (VNTR) analysis is one of the methods for molecular epidemiological studies of Mycobacterium tuberculosis. VNTR analysis is a method based on PCR, provides rapid highly reproducible results and higher strain discrimination power than the restriction fragment length polymorphism (RFLP) analysis widely used in molecular epidemiological studies of Mycobacterium tuberculosis. Genetic lineage compositions of Mycobacterium tuberculosis clinical isolates differ among the regions from where they are isolated, and allelic diversity at each locus also differs among the genetic lineages of Mycobacterium tuberculosis. Therefore, the combination of VNTR loci that can provide high discrimination capacity for analysis is not common in every region. The Japan Anti-Tuberculosis Association (JATA) 12 (15) reported a standard combination of VNTR loci for analysis in Japan, and the combination with hypervariable (HV) loci added to JATA12 (15), which has very high discrimination capacity, was also reported. From these reports, it is thought that data sharing between institutions and construction of a nationwide database will progress from now on. Using database construction of VNTR profiles, VNTR analysis has become an effective tool to trace the route of tuberculosis infection, and also helps in decision-making in the treatment course. However, in order to utilize the results of VNTR analysis effectively, it is important that each related organization cooperates closely, and analysis should be appropriately applied in the system in which accurate control and private information protection are ensured.

  11. Image analysis as a non-destructive method to assess regrowth of weeds after repeated flame weeding

    DEFF Research Database (Denmark)

    Rask, Anne Merete; Kristoffersen, Palle; Andreasen, Christian

    2013-01-01

    picture of the long-term effect of repeated treatments. Image analysis was most useful for assessing the effect of repeated treatments when weed cover was relatively low (below 40%) and when plots contained relatively much withered plant material. However, when weed cover is close to 100%, dry weight......, and therefore it may influence the long-term effect of repeated treatments. Visual assessment of weed cover or image analysis do not affect the remaining parts of the weed plants after treatment, but the methods may have other disadvantages. In order to evaluate and compare three methods we measured changes...... in vegetation cover of perennial ryegrass after flaming by (1) a simple image analysis programme counting green pixels, (2) visual assessment of images and (3) by taking biomass samples. Plants were flame treated with eight different dosages (0, 20, 30, 35, 45, 60, 90 and 180 kg propane ha-1) and with various...

  12. Post-Mortem Identification of a Fire Carbonized Body by STR Genotyping.

    Science.gov (United States)

    Dumache, Raluca; Muresan, Camelia; Ciocan, Veronica; Rogobete, Alexandru F; Enache, Alexandra

    2016-10-01

    Identification of bodies of unknown identity that are victims of exposure to very high temperatures, resulting from fires, plane crashes, and terrorist attacks, represents one of the most difficult sides of forensic genetics, because of the advanced state of decomposition. The aim of this study was the identification of the carbonized cadaver of a fire victim through STR genotyping. We used blood samples obtained from the iliac artery during the autopsy examination as biological samples from the unidentified victim. After DNA isolation and quantification, we proceeded to its amplification using the multiplex PCR kit AmpFlSTR Identifiler. The DNA products were separated using an ABI 3500 genetic analyzer. Further analysis of the data was done using Gene Mapper ID-X version 1.4 software. In this case, it was possible to obtain a complete DNA profile from the biological samples. Due to the fact that the amelogenin gene presented two alleles, X and Y, we concluded that the victim was a man. We conclude that STR profiling of unidentified bodies (carbonized, decomposed) represents a powerful method of human identification in forensic medicine.

  13. Improving complex kinship analyses with additional STR loci.

    Science.gov (United States)

    Carboni, Ilaria; Iozzi, Sara; Nutini, Anna Lucia; Torricelli, Francesca; Ricci, Ugo

    2014-11-01

    In a standard paternity testing, mother, child, and alleged father are analyzed with STR markers using commercially available kits. Since Italian civil legislation does not have thresholds to confirm a paternity, paternity is practically proven when likelihood ratio increases prior probability of paternity to posterior, accepted by court as sufficient. However, in some cases the number of markers included in a commercial kit may be insufficient to conclusively prove or disprove a relationship between individuals, especially when complex family scenarios are suspected or indirect analyses are required. Additional genetic information can increase the values of the likelihood ratio regarding the detection of true parental relationships in a pedigree, while reducing the chances of false attributions (e.g. false paternities). In these cases the introduction of a 26Plex amplification system allows to examine 23-26 additional markers depending on the commercial kit used, thus increasing the statistical power of the kinship analysis. The PCR conditions were optimized for a multiplex amplification system and a new generation CE instrument. In order to demonstrate the utility of additional STRs markers, four complex kinship cases are presented. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Testing Mean Differences among Groups: Multivariate and Repeated Measures Analysis with Minimal Assumptions.

    Science.gov (United States)

    Bathke, Arne C; Friedrich, Sarah; Pauly, Markus; Konietschke, Frank; Staffen, Wolfgang; Strobl, Nicolas; Höller, Yvonne

    2018-03-22

    To date, there is a lack of satisfactory inferential techniques for the analysis of multivariate data in factorial designs, when only minimal assumptions on the data can be made. Presently available methods are limited to very particular study designs or assume either multivariate normality or equal covariance matrices across groups, or they do not allow for an assessment of the interaction effects across within-subjects and between-subjects variables. We propose and methodologically validate a parametric bootstrap approach that does not suffer from any of the above limitations, and thus provides a rather general and comprehensive methodological route to inference for multivariate and repeated measures data. As an example application, we consider data from two different Alzheimer's disease (AD) examination modalities that may be used for precise and early diagnosis, namely, single-photon emission computed tomography (SPECT) and electroencephalogram (EEG). These data violate the assumptions of classical multivariate methods, and indeed classical methods would not have yielded the same conclusions with regards to some of the factors involved.

  15. [An analysis of industrial accidents in the working field with a particular emphasis on repeated accidents].

    Science.gov (United States)

    Wakisaka, I; Yanagihashi, T; Tomari, T; Sato, M

    1990-03-01

    The present study is based on an analysis of routinely submitted reports of occupational accidents experienced by the workers of industrial enterprises under the jurisdiction of Kagoshima Labor Standard Office during a 5-year period 1983 to 1987. Officially notified injuries serious enough to keep employees away from their job for work at least 4 days were utilized in this study. Data was classified so as to give an observed frequency distribution for workers having any specified number of accidents. Also, the accident rate which is an indicator of the risk of accident was compared among different occupations, between age groups and between the sexes. Results obtained are as follows; 1) For the combined total of 6,324 accident cases for 8 types of occupation (Construction, Transportation, Mining & Quarrying, Forestry, Food manufacture, Lumber & Woodcraft, Manufacturing industry and Other business), the number of those who had at least one accident was 6,098, of which 5,837 were injured only once, 208 twice, 21 three times and 2 four times. When occupation type was fixed, however, the number of workers having one, two, three and four times of accidents were 5,895, 182, 19 and 2, respectively. This suggests that some workers are likely to have experienced repeated accidents in more than one type of occupation.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

    Science.gov (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

    2014-04-08

    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

  17. Discovery and analysis of an active long terminal repeat-retrotransposable element in Aspergillus oryzae.

    Science.gov (United States)

    Jie Jin, Feng; Hara, Seiichi; Sato, Atsushi; Koyama, Yasuji

    2014-01-01

    Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.

  18. Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients.

    Science.gov (United States)

    Messina, Francesco; Finocchio, Andrea; Akar, Nejat; Loutradis, Aphrodite; Michalodimitrakis, Emmanuel I; Brdicka, Radim; Jodice, Carla; Novelletto, Andrea

    2018-02-01

    Tetranucleotide Short Tandem Repeats (STRs) for human identification and common use in forensic cases have recently been used to address the population genetics of the North-Eastern Mediterranean area. However, to gain confidence in the inferences made using STRs, this kind of analysis should be challenged with changes in three main aspects of the data, i.e. the sizes of the samples, their distance across space and the genetic background from which they are drawn. To test the resilience of the gradients previously detected in the North-Eastern Mediterranean to the enlargement of the surveyed area and population set, using revised data. STR genotype profiles were obtained from a publicly available database (PopAffilietor databank) and a dataset was assembled including >7000 subjects from the Arabian Peninsula to Scandinavia, genotyped at eight loci. Spatial principal component analysis (sPCA) was applied and the frequency maps of the nine alleles which contributed most strongly to sPC1 were examined in detail. By far the greatest part of diversity was summarised by a single spatial principal component (sPC1), oriented along a SouthEast-to-NorthWest axis. The alleles with the top 5% squared loadings were TH01(9.3), D19S433(14), TH01(6), D19S433(15.2), FGA(20), FGA(24), D3S1358(14), FGA(21) and D2S1338(19). These results confirm a clinal pattern over the whole range for at least four loci (TH01, D19S433, FGA, D3S1358). Four of the eight STR loci (or even alleles) considered here can reproducibly capture continental arrangements of diversity. This would, in principle, allow for the exploitation of forensic data to clarify important aspects in the formation of local gene pools.

  19. Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

    Directory of Open Access Journals (Sweden)

    Chermette René

    2010-12-01

    Full Text Available Abstract Background Multiple-locus variable-number tandem repeat (VNTR analysis (MLVA is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8 of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89. The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST. The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a

  20. [Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

    Science.gov (United States)

    Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

    2015-04-01

    This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

  1. Position Paper: Applying Machine Learning to Software Analysis to Achieve Trusted, Repeatable Scientific Computing

    Energy Technology Data Exchange (ETDEWEB)

    Prowell, Stacy J [ORNL; Symons, Christopher T [ORNL

    2015-01-01

    Producing trusted results from high-performance codes is essential for policy and has significant economic impact. We propose combining rigorous analytical methods with machine learning techniques to achieve the goal of repeatable, trustworthy scientific computing.

  2. Isolation and characterization of repeat elements of the oak genome and their application in population analysis

    International Nuclear Information System (INIS)

    Fluch, S.; Burg, K.

    1998-01-01

    Four minisatellite sequence elements have been identified and isolated from the genome of the oak species Quercus petraea and Quercus robur. Minisatellites 1 and 2 are putative members of repeat families, while minisatellites 3 and 4 show repeat length variation among individuals of test populations. A 590 base pair (bp) long element has also been identified which reveals individual-specific autoradiographic patterns when used as probe in Southern hybridisations of genomic oak DNA. (author)

  3. Strömende Flüssigkeiten und Gase

    Science.gov (United States)

    Heintze, Joachim

    Die Bemerkung über die Probleme eines allgemeingültigen Ansatzes, die wir zu Anfang von Kap. 1 machten, gilt in noch höherem Maße für die Mechanik von strömenden Flüssigkeiten; dort erreicht man sogar ziemlich rasch die Grenze der Leistungsfähigkeit der heutigen Mathematik, d. h. wir können zwar - ausgehend von den Newtonschen Gesetzen (Bd. I/3) - eine Differentialgleichung für die Strömung von Flüssigkeiten aufstellen, die sog. Navier-Stokes-Gleichung, es sind aber keine allgemein anwendbaren Lösungsverfahren für diese Gleichung bekannt. Ein Blick in die Natur und auf die vielfältigen Strömungsphänomene zeigt, dass diese Tatsache nicht verwunderlich ist.

  4. Power analysis for multivariate and repeated measurements designs via SPSS: correction and extension of D'Amico, Neilands, and Zambarano (2001).

    Science.gov (United States)

    Osborne, Jason W

    2006-05-01

    D'Amico, Neilands, and Zambarano (2001) published SPSS syntax to perform power analyses for three complex procedures: ANCOVA, MANOVA, and repeated measures ANOVA. Unfortunately, the published SPSS syntax for performing the repeated measures analysis needed some minor revision in order to perform the analysis correctly. This article presents the corrected syntax that will successfully perform the repeated measures analysis and provides some guidance on modifying the syntax to customize the analysis.

  5. Genetic distribution of 15 autosomal STR markers in the Punjabi population of Pakistan.

    Science.gov (United States)

    Shan, Muhammad Adnan; Hussain, Manzoor; Shafique, Muhammad; Shahzad, Muhammad; Perveen, Rukhsana; Idrees, Muhammad

    2016-11-01

    Genetic diversity of 15 autosomal short tandem repeat (STR) loci was evaluated in 713 unrelated individual samples of a Punjabi population of Pakistan. These loci were scrutinized to establish allelic frequencies and statistical parameters of forensic and paternity interests. A total of 165 alleles were observed with the corresponding allele frequencies ranging from 0.001 to 0.446. D2S1338 was found as the most informative locus while TPOX (0.611) was the least discriminating locus. The combined power of discrimination (CPD), the combined probability of exclusion (CPE), and cumulative probability of matching (CPM) were found equaled to 0.999999999999999998606227424808, 0.999995777557989, and 1.37543 × 10-18, respectively. All the loci followed the Hardy-Weinberg equilibrium after the Bonferroni correction (p < 0.0033) except one locus D3S1358. The study revealed that these STR loci are highly polymorphic, suitable for forensic and parentage analyses. In comparison to different populations (Asians and non-Asians), significant differences were recorded for these loci.

  6. Spoligotyping and variable number tandem repeat analysis of Mycobacterium bovis isolates from cattle in Brazil

    Directory of Open Access Journals (Sweden)

    Patrícia Martins Parreiras

    2012-02-01

    Full Text Available We performed spoligotyping and 12-mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTRs typing to characterise Mycobacterium bovis isolates collected from tissue samples of bovines with lesions suggestive for tuberculosis during slaughter inspection procedures in abattoirs in Brazil. High-quality genotypes were obtained with both procedures for 61 isolates that were obtained from 185 bovine tissue samples and all of these isolates were identified as M. bovis by conventional identification procedures. On the basis of the spoligotyping, 53 isolates were grouped into nine clusters and the remaining eight isolates were unique types, resulting in 17 spoligotypes. The majority of the Brazilian M. bovis isolates displayed spoligotype patterns that have been previously observed in strains isolated from cattle in other countries. MIRU-VNTR typing produced 16 distinct genotypes, with 53 isolates forming eight of the groups, and individual isolates with unique VNTR profiles forming the remaining eight groups. The allelic diversity of each VNTR locus was calculated and only two of the 12-MIRU-VNTR loci presented scores with either a moderate (0.4, MIRU16 or high (0.6, MIRU26 discriminatory index (h. Both typing methods produced similar discriminatory indexes (spoligotyping h = 0.85; MIRU-VNTR h = 0.86 and the combination of the two methods increased the h value to 0.94, resulting in 29 distinct patterns. These results confirm that spoligotyping and VNTR analysis are valuable tools for studying the molecular epidemiology of M. bovis infections in Brazil.

  7. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

    Science.gov (United States)

    Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

    2010-02-01

    A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

  8. Pilot study for early prognosis of Azoospermia in relation to Y-STR Profiling

    Directory of Open Access Journals (Sweden)

    Ahmed M. Refaat

    2016-01-01

    Conclusion: There was a significant correlation of Y-STR Profiling results and the prevalence of Azoospermia condition, which supports the idea of using Y-STR Profiling in early prognosis of Azoospermia.

  9. Population data and mutation rates of 19 STR loci in seven provinces from China based on Goldeneye™ DNA ID System 20A.

    Science.gov (United States)

    Liu, Qiu-Ling; Chen, Ye-Fei; Huang, Xiao-Ling; Liu, Kai-Yan; Zhao, Hu; Lu, De-Jian

    2017-05-01

    Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated. Furthermore, population stratification of Southern China Han nationality among seven provinces was established. The multidimensional scaling (MDS) plot based on genetic distances (Fst) showed that the studied populations can be clustered into two major groups. However, relationships among populations were weak (Fst < 0.0043). A total of 376 cases of mutation were detected from the 19 selected loci in 15,396 meioses. The average mutation rate for the 19 loci was estimated to be 1.3 × 10 -3 per meiosis. The mutation was mainly single step; the paternal mutation rate was higher than the maternal; and paternal mutation rate increases with paternal age.

  10. [Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

    Science.gov (United States)

    Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

    2009-11-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

  11. [The mutation analysis of PAH gene and prenatal diagnosis in classical phenylketonuria family].

    Science.gov (United States)

    Yan, Yousheng; Hao, Shengju; Yao, Fengxia; Sun, Qingmei; Zheng, Lei; Zhang, Qinghua; Zhang, Chuan; Yang, Tao; Huang, Shangzhi

    2014-12-01

    To characterize the mutation spectrum of phenylalanine hydroxylase (PAH) gene and perform prenatal diagnosis for families with classical phenylketonuria. By stratified sequencing, mutations were detected in the exons and flaking introns of PAH gene of 44 families with classical phenylketonuria. 47 fetuses were diagnosed by combined sequencing with linkage analysis of three common short tandem repeats (STR) (PAH-STR, PAH-26 and PAH-32) in the PAH gene. Thirty-one types of mutations were identified. A total of 84 mutations were identified in 88 alleles (95.45%), in which the most common mutation have been R243Q (21.59%), EX6-96A>G (6.82%), IVS4-1G>A (5.86%) and IVS7+2T>A (5.86%). Most mutations were found in exons 3, 5, 6, 7, 11 and 12. The polymorphism information content (PIC) of these three STR markers was 0.71 (PAH-STR), 0.48 (PAH-26) and 0.40 (PAH-32), respectively. Prenatal diagnosis was performed successfully with the combined method in 47 fetuses of 44 classical phenylketonuria families. Among them, 11 (23.4%) were diagnosed as affected, 24 (51.1%) as carriers, and 12 (25.5%) as unaffected. Prenatal diagnosis can be achieved efficiently and accurately by stratified sequencing of PAH gene and linkage analysis of STR for classical phenylketonuria families.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Jun Yao

    Full Text Available 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.

  14. Repeated CT scans in trauma transfers: An analysis of indications, radiation dose exposure, and costs

    International Nuclear Information System (INIS)

    Hinzpeter, Ricarda; Sprengel, Kai; Wanner, Guido A.; Mildenberger, Peter; Alkadhi, Hatem

    2017-01-01

    Highlights: • Repetition of CT in trauma patients occurs relatively often. • Repetition of CT is mainly caused by inadequate image data transfer. • Potentially preventable CT examinations add radiation dose to patients. • Repeated CT is associated with excess costs to the health care system. - Abstract: Objectives: To identify the number of CT scans repeated in acute trauma patients receiving imaging before being referred to a trauma center, to define indications, and to assess radiation doses and costs of repeated CT. Methods: This retrospective study included all adult trauma patients transferred from other hospitals to a Level-I trauma center during 2014. Indications for repeated CT scans were categorized into: inadequate CT image data transfer, poor image quality, repetition of head CT after head injury together with completion to whole-body CT (WBCT), and follow-up of injury known from previous CT. Radiation doses from repeated CT were determined; costs were calculated using a nation-wide fee schedule. Results: Within one year, 85/298 (28.5%) trauma patients were transferred from another hospital because of severe head injury (n = 45,53%) and major body trauma (n = 23;27%) not manageable in the referring hospital, repatriation from a foreign country (n = 14;16.5%), and no ICU-capacity (n = 3;3.5%). Of these 85 patients, 74 (87%) had repeated CT in our center because of inadequate CT data transfer (n = 29;39%), repetition of head CT with completion to WBCT (n = 24;32.5%), and follow-up of known injury (n = 21;28.5%). None occurred because of poor image quality. Cumulative dose length product (DLP) and annual costs of potential preventable, repeated CT (inadequate data transfer) was 631mSv (81′304mGy*cm) and 35′233€, respectively. Conclusion: A considerable number of transferred trauma patients undergo potentially preventable, repeated CT, adding radiation dose to patients and costs to the health care system.

  15. Repeated CT scans in trauma transfers: An analysis of indications, radiation dose exposure, and costs

    Energy Technology Data Exchange (ETDEWEB)

    Hinzpeter, Ricarda, E-mail: Ricarda.Hinzpeter@usz.ch [Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Raemistr. 100, Zurich CH-8091 (Switzerland); Sprengel, Kai, E-mail: Kai.Sprengel@usz.ch [Division of Trauma Surgery, Department of Surgery, University Hospital Zurich, University of Zurich, Raemistr. 100, CH-8091 Zurich (Switzerland); Wanner, Guido A., E-mail: Guido.Wanner@sbk-vs.de [Division of Trauma Surgery, Department of Surgery, University Hospital Zurich, University of Zurich, Raemistr. 100, CH-8091 Zurich (Switzerland); Department of General Surgery, Schwarzwald-Baar Klinikum, University of Freiburg, Klinikstr. 11, D-78052 Villingen-Schwenningen (Germany); Mildenberger, Peter, E-mail: peter.mildenberger@unimedizin-mainz.de [Department of Diagnostic and Interventional Radiology, University Hospital of Mainz, Langenbeckstr. 1, D-55131 Mainz (Germany); Alkadhi, Hatem, E-mail: hatem.alkadhi@usz.ch [Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Raemistr. 100, Zurich CH-8091 (Switzerland)

    2017-03-15

    Highlights: • Repetition of CT in trauma patients occurs relatively often. • Repetition of CT is mainly caused by inadequate image data transfer. • Potentially preventable CT examinations add radiation dose to patients. • Repeated CT is associated with excess costs to the health care system. - Abstract: Objectives: To identify the number of CT scans repeated in acute trauma patients receiving imaging before being referred to a trauma center, to define indications, and to assess radiation doses and costs of repeated CT. Methods: This retrospective study included all adult trauma patients transferred from other hospitals to a Level-I trauma center during 2014. Indications for repeated CT scans were categorized into: inadequate CT image data transfer, poor image quality, repetition of head CT after head injury together with completion to whole-body CT (WBCT), and follow-up of injury known from previous CT. Radiation doses from repeated CT were determined; costs were calculated using a nation-wide fee schedule. Results: Within one year, 85/298 (28.5%) trauma patients were transferred from another hospital because of severe head injury (n = 45,53%) and major body trauma (n = 23;27%) not manageable in the referring hospital, repatriation from a foreign country (n = 14;16.5%), and no ICU-capacity (n = 3;3.5%). Of these 85 patients, 74 (87%) had repeated CT in our center because of inadequate CT data transfer (n = 29;39%), repetition of head CT with completion to WBCT (n = 24;32.5%), and follow-up of known injury (n = 21;28.5%). None occurred because of poor image quality. Cumulative dose length product (DLP) and annual costs of potential preventable, repeated CT (inadequate data transfer) was 631mSv (81′304mGy*cm) and 35′233€, respectively. Conclusion: A considerable number of transferred trauma patients undergo potentially preventable, repeated CT, adding radiation dose to patients and costs to the health care system.

  16. Apraxia of Speech: Perceptual Analysis of Trisyllabic Word Productions across Repeated Sampling Occasions

    Science.gov (United States)

    Mauszycki, Shannon C.; Wambaugh, Julie L.; Cameron, Rosalea M.

    2012-01-01

    Purpose: Early apraxia of speech (AOS) research has characterized errors as being variable, resulting in a number of different error types being produced on repeated productions of the same stimuli. Conversely, recent research has uncovered greater consistency in errors, but there are limited data examining sound errors over time (more than one…

  17. Genome-wide analysis of tandem repeats in plants and green algae

    Science.gov (United States)

    Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang

    2014-01-01

    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...

  18. Device-independent secret-key-rate analysis for quantum repeaters

    Science.gov (United States)

    Holz, Timo; Kampermann, Hermann; Bruß, Dagmar

    2018-01-01

    The device-independent approach to quantum key distribution (QKD) aims to establish a secret key between two or more parties with untrusted devices, potentially under full control of a quantum adversary. The performance of a QKD protocol can be quantified by the secret key rate, which can be lower bounded via the violation of an appropriate Bell inequality in a setup with untrusted devices. We study secret key rates in the device-independent scenario for different quantum repeater setups and compare them to their device-dependent analogon. The quantum repeater setups under consideration are the original protocol by Briegel et al. [Phys. Rev. Lett. 81, 5932 (1998), 10.1103/PhysRevLett.81.5932] and the hybrid quantum repeater protocol by van Loock et al. [Phys. Rev. Lett. 96, 240501 (2006), 10.1103/PhysRevLett.96.240501]. For a given repeater scheme and a given QKD protocol, the secret key rate depends on a variety of parameters, such as the gate quality or the detector efficiency. We systematically analyze the impact of these parameters and suggest optimized strategies.

  19. Design and analysis of effects of triplet repeat oligonucleotides in cell models for myotonic dystrophy

    NARCIS (Netherlands)

    Gonzalez-Barriga, A.; Mulders, S.A.M.; Giessen, J. van der; Hooijer, J.D.; Bijl, S.; Kessel, I.D.G. van; Beers, J. van; Deutekom, J.C. van; Fransen, J.A.M.; Wieringa, B.; Wansink, D.G.

    2013-01-01

    Myotonic dystrophy type 1 (DM1) is caused by DM protein kinase (DMPK) transcripts containing an expanded (CUG)n repeat. Antisense oligonucleotide (AON)-mediated suppression of these mutant RNAs is considered a promising therapeutic strategy for this severe disorder. Earlier, we identified a

  20. Nonparametric modeling and analysis of association between Huntington's disease onset and CAG repeats.

    Science.gov (United States)

    Ma, Yanyuan; Wang, Yuanjia

    2014-04-15

    Huntington's disease (HD) is a neurodegenerative disorder with a dominant genetic mode of inheritance caused by an expansion of CAG repeats on chromosome 4. Typically, a longer sequence of CAG repeat length is associated with increased risk of experiencing earlier onset of HD. Previous studies of the association between HD onset age and CAG length have favored a logistic model, where the CAG repeat length enters the mean and variance components of the logistic model in a complex exponential-linear form. To relax the parametric assumption of the exponential-linear association to the true HD onset distribution, we propose to leave both mean and variance functions of the CAG repeat length unspecified and perform semiparametric estimation in this context through a local kernel and backfitting procedure. Motivated by including family history of HD information available in the family members of participants in the Cooperative Huntington's Observational Research Trial (COHORT), we develop the methodology in the context of mixture data, where some subjects have a positive probability of being risk free. We also allow censoring on the age at onset of disease and accommodate covariates other than the CAG length. We study the theoretical properties of the proposed estimator and derive its asymptotic distribution. Finally, we apply the proposed methods to the COHORT data to estimate the HD onset distribution using a group of study participants and the disease family history information available on their family members. Copyright © 2013 John Wiley & Sons, Ltd.

  1. Large scale analysis of small repeats via mining of the human genome

    NARCIS (Netherlands)

    van den Berg, I.; Bosnacki, D.; Hilbers, P.A.J.

    2009-01-01

    Small repetitive sequences, called tandem repeats, are abundant throughout the human genome, both in coding and in non-coding regions. Their role is still mostly unknown, but at least 20 of those repetitive sequences have been related to neurodegenerative disorders. The mutational process that is

  2. Factors influencing repeated teenage pregnancy: a review and meta-analysis.

    Science.gov (United States)

    Maravilla, Joemer C; Betts, Kim S; Couto E Cruz, Camila; Alati, Rosa

    2017-11-01

    Existing evidence of predictors of repeated teenage pregnancy has not been assessed rigorously. This systematic review provides a comprehensive evaluation of protective and risk factors that are associated with repeated teenage pregnancy through a metaanalytical consensus. We used PubMed, EMBASE, CINAHL, ProQuest, PsychINFO, ScienceDirect, Scopus, and Web of Science databases from 1997-2015 and the reference list of other relevant research papers and related reviews. Eligibility criteria included (1) epidemiologic studies that analyzed factors associated with repeated pregnancy or birth among adolescents pregnancy, and (2) experimental studies with an observational component that was adjusted for the intervention. We performed narrative synthesis of study characteristics, participant characteristics, study results, and quality assessment. We also conducted random-effects and quality-effects metaanalyses with meta-regression to obtain pooled odds ratios of identified factors and to determine sources of between-study heterogeneity. Twenty-six eligible epidemiologic studies, most from the United States (n=24), showed >47 factors with no evidence of publication bias for each metaanalysis. Use of contraception (pooled odds ratio, 0.60; 95% confidence interval, 0.35-1.02), particularly long-acting reversible contraceptives (pooled odds ratio, 0.19; 95% confidence interval, 0.08-0.45), considerably reduced repeated teenage pregnancy risk. Among studies about contraception, the number of follow-up visits (adjusted coefficient, 0.72; P=.102) and country of study (unadjusted coefficient, 2.57; permuted P=.071) explained between-study heterogeneity. Education-related factors, which included higher level of education (pooled odds ratio, 0.74; 95% confidence interval, 0.60-0.91) and school continuation (pooled odds ratio, 0.53; 95% confidence interval, 0.33-0.84), were found to be protective. Conversely, depression (pooled odds ratio, 1.46; 95% confidence interval, 1

  3. Association analysis of a highly polymorphic CAG Repeat in the human potassium channel gene KCNN3 and migraine susceptibility

    Directory of Open Access Journals (Sweden)

    Ovcaric Mick

    2005-09-01

    Full Text Available Abstract Background Migraine is a polygenic multifactorial disease, possessing environmental and genetic causative factors with multiple involved genes. Mutations in various ion channel genes are responsible for a number of neurological disorders. KCNN3 is a neuronal small conductance calcium-activated potassium channel gene that contains two polyglutamine tracts, encoded by polymorphic CAG repeats in the gene. This gene plays a critical role in determining the firing pattern of neurons and acts to regulate intracellular calcium channels. Methods The present association study tested whether length variations in the second (more 3' polymorphic CAG repeat in exon 1 of the KCNN3 gene, are involved in susceptibility to migraine with and without aura (MA and MO. In total 423 DNA samples from unrelated individuals, of which 202 consisted of migraine patients and 221 non-migraine controls, were genotyped and analysed using a fluorescence labelled primer set on an ABI310 Genetic Analyzer. Allele frequencies were calculated from observed genotype counts for the KCNN3 polymorphism. Analysis was performed using standard contingency table analysis, incorporating the chi-squared test of independence and CLUMP analysis. Results Overall, there was no convincing evidence that KCNN3 CAG lengths differ between Caucasian migraineurs and controls, with no significant difference in the allelic length distribution of CAG repeats between the population groups (P = 0.090. Also the MA and MO subtypes did not differ significantly between control allelic distributions (P > 0.05. The prevalence of the long CAG repeat (>19 repeats did not reach statistical significance in migraineurs (P = 0.15, nor was there a significant difference between the MA and MO subgroups observed compared to controls (P = 0.46 and P = 0.09, respectively, or between MA vs MO (P = 0.40. Conclusion This association study provides no evidence that length variations of the second polyglutamine array in

  4. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-02-01

    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  5. 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......Abstract Estimating the weight of evidence in forensic genetics is often done in terms of a likelihood ratio, LR. The LR evaluates the probability of the observed evidence under competing hypotheses. Most often, probabilities used in the LR only consider the evidence from the genomic variation...... 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...

  6. Genetic data for 15 STR loci in a Kadazan-Dusun population from East Malaysia.

    Science.gov (United States)

    Kee, B P; Lian, L H; Lee, P C; Lai, T X; Chua, K H

    2011-04-26

    Allele frequencies of 15 short tandem repeat (STR) loci, namely D5S818, D7S820, D13S317, D16S539, TH01, TPOX, Penta D, Penta E, D3S1358, D8S1179, D18S51, D21S11, CSF1PO, vWA, and FGA, were determined for 154 individuals from the Kadazan-Dusun tribe, an indigenous population of East Malaysia. All loci were amplified by polymerase chain reaction, using the Powerplex 16 system. Alleles were typed using a gene analyzer and the Genemapper ID software. Various statistical parameters were calculated and the combined power of discrimination for the 15 loci in the population was calculated as 0.999999999999999. These loci are thus, informative and can be used effectively in forensic and genetic studies of this indigenous population.

  7. Multilocus Variable-Number Tandem-Repeat Analysis, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Patterns in Discrimination of Sporadic and Outbreak-Related Strains of Yersinia enterocolitica

    Directory of Open Access Journals (Sweden)

    Skurnik Mikael

    2011-02-01

    Full Text Available Abstract Background We assessed the potential of multilocus variable-number tandem-repeat analysis (MLVA, pulsed-field gel electrophoresis (PFGE, and antimicrobial susceptibility testing for discriminating 104 sporadic and outbreak-related Yersinia enterocolitica (YE bio/serotype 3-4/O:3 and 2/O:9 isolates. MLVA using six VNTR markers was performed in two separate multiplex PCRs, and the fluorescently labeled PCR products were accurately sized on an automated DNA sequencer. Results MLVA discriminated 82 sporadic YE 3-4/O:3 and 2/O:9 strains into 77 types, whereas PFGE with the restriction enzyme NotI discriminated the strains into 23 different PFGE pulsotypes. The discriminatory index for a sporadic strain was 0.862 for PFGE and 0.999 for MLVA. MLVA confirmed that a foodborne outbreak in the city of Kotka, Finland in 2003 had been caused by a multiresistant YE 4/O:3 strain that was distinctly different from those of epidemiologically unrelated strains with an identical PFGE pulsotype. The multiresistance of Y. enterocolitica strains (19% of the sporadic strains correlated significantly (p = 0.002 with travel abroad. All of the multiresistant Y. enterocolitica strains belonged to four PFGE pulsotypes that did not contain any susceptible strains. Resistance to nalidixic acid was related to changes in codons 83 or 87 that stemmed from mutations in the gyrA gene. The conjugation experiments demonstrated that resistance to CHL, STR, and SUL was carried by a conjugative plasmid. Conclusions MLVA using six loci had better discriminatory power than PFGE with the NotI enzyme. MLVA was also a less labor-intensive method than PFGE and the results were easier to analyze. The conjugation experiments demonstrated that a resistance plasmid can easily be transferred between Y. enterocolitica strains. Antimicrobial multiresistance of Y. enterocolitica strains was significantly associated with travel abroad.

  8. An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system.

    Directory of Open Access Journals (Sweden)

    Erin K Hanson

    Full Text Available In forensic casework, Y chromosome short tandem repeat markers (Y-STRs are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12-17 loci are currently used in forensic casework (Promega's PowerPlex Y and Applied Biosystems' AmpFlSTR Yfiler. Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used 'core' Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572 indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR Yfiler kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary

  9. Filipino DNA variation at 12 X-chromosome short tandem repeat markers.

    Science.gov (United States)

    Salvador, Jazelyn M; Apaga, Dame Loveliness T; Delfin, Frederick C; Calacal, Gayvelline C; Dennis, Sheila Estacio; De Ungria, Maria Corazon A

    2018-06-08

    Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator ® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq ™ DNA Signature Prep kit of the MiSeq ® FGx ™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Determinants and Experiences of Repeat Pregnancy among HIV-Positive Kenyan Women--A Mixed-Methods Analysis.

    Directory of Open Access Journals (Sweden)

    Victor Akelo

    Full Text Available To identify factors associated with repeat pregnancy subsequent to an index pregnancy among women living with HIV (WLWH in western Kenya who were enrolled in a 24-month phase-II clinical trial of triple-ART prophylaxis for prevention of mother-to-child transmission, and to contextualize social and cultural influences on WLWH's reproductive decision making.A mixed-methods approach was used to examine repeat pregnancy within a 24 month period after birth. Counselor-administered questionnaires were collected from 500 WLWH. Forty women (22 with a repeat pregnancy; 18 with no repeat pregnancy were purposively selected for a qualitative interview (QI. Simple and multiple logistic regression analyses were performed for quantitative data. Thematic coding and saliency analysis were undertaken for qualitative data.Eighty-eight (17.6% women had a repeat pregnancy. Median maternal age was 23 years (range 15-43 years and median gestational age at enrollment was 34 weeks. In multiple logistic regression analyses, living in the same compound with a husband (adjusted odds ratio (AOR: 2.33; 95% confidence interval (CI: 1.14, 4.75 was associated with increased odds of repeat pregnancy (p ≤ 0.05. Being in the 30-43 age group (AOR: 0.25; 95% CI: 0.07, 0.87, having talked to a partner about family planning (FP use (AOR: 0.53; 95% CI: 0.29, 0.98, and prior usage of FP (AOR: 0.45; 95% CI: 0.25, 0.82 were associated with a decrease in odds of repeat pregnancy. QI findings centered on concerns about modern contraception methods (side effects and views that they 'ruined the womb' and a desire to have the right number of children. Religious leaders, family, and the broader community were viewed as reinforcing cultural expectations for married women to have children. Repeat pregnancy was commonly attributed to contraception failure or to lack of knowledge about post-delivery fertility.In addition to cultural context, reproductive health programs for WLWH may need to

  11. CAG repeat polymorphisms in the androgen receptor and breast cancer risk in women: a meta-analysis of 17 studies

    Directory of Open Access Journals (Sweden)

    Mao Q

    2015-08-01

    Full Text Available Qixing Mao,1–3,* Mantang Qiu,1–3,* Gaochao Dong,3 Wenjie Xia,1–3 Shuai Zhang,1,3 Youtao Xu,1,3 Jie Wang,3 Yin Rong,1,3 Lin Xu,1,3 Feng Jiang1,3 1Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, 2Fourth Clinical College of Nanjing Medical University, 3Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People’s Republic of China *These authors contributed equally to this work Abstract: The association between polymorphic CAG repeats in the androgen receptor gene in women and breast cancer susceptibility has been studied extensively. However, the conclusions regarding this relationship remain conflicting. The purpose of this meta-analysis was to identify whether androgen receptor CAG repeat lengths were related to breast cancer susceptibility. The MEDLINE, PubMed, and EMBASE databases were searched through to December 2014 to identify eligible studies. Data and study quality were rigorously assessed by two investigators according to the Newcastle-Ottawa Quality Assessment Scale. The publication bias was assessed by the Begg’s test. Seventeen eligible studies were included in this meta-analysis. The overall analysis suggested no association between CAG polymorphisms and breast cancer risk (odds ratio [OR] 1.031, 95% confidence interval [CI] 0.855–1.245. However, in the subgroup analysis, we observed that long CAG repeats significantly increased the risk of breast cancer in the Caucasian population (OR 1.447, 95% CI 1.089–1.992. Additionally, the risk was significantly increased in Caucasian women carrying two alleles with CAG repeats ≥22 units compared with those with two shorter alleles (OR 1.315, 95% CI 1.014–1.707. These findings suggest that long CAG repeats increase the risk of breast cancer in Caucasian women. However, larger scale case-control studies are needed to validate our results. Keywords: androgen, CAG repeat polymorphism, women

  12. REPEATED MEASURES ANALYSIS OF CHANGES IN PHOTOSYNTHETIC EFFICIENCY IN SOUR CHERRY DURING WATER DEFICIT

    Directory of Open Access Journals (Sweden)

    Marija Viljevac

    2012-06-01

    Full Text Available The objective of this study was to investigate changes in photosynthetic efficiency applying repeated measures ANOVA using the photosynthetic performance index (PIABS of the JIP-test as a vitality parameter in seven genotypes of sour cherry (Prunus cerasus, L. during 10 days of continuous water deficit. Both univariate and multivariate ANOVA repeated measures revealed highly significant time effect (Days and its subsequent interactions with genotype and water deficit. However, the multivariate Pillai’s trace test detected the interaction Time × Genotype × Water deficit as not significant. According to the Tukey’s Studentized Range (HSD test, differences between the control and genotypes exposed to water stress became significant on the fourth day of the experiment, indicating that the plants on the average, began to lose their photosynthetic efficiency four days after being exposed to water shortage. It corroborates previous findings in other species that PIABS is very sensitive tool for detecting drought stress.

  13. Multielemental segregation analysis of the thallium bromide impurities purified by repeated Bridgman technique

    International Nuclear Information System (INIS)

    Santos, Robinson A. dos; Hamada, Margarida M.; Costa, Fabio E. da; Gennari, Roseli F.; Martins, Joao F.T.; Marcondes, Renata M.; Mesquita, Carlos H. de

    2011-01-01

    TlBr crystals were purified and grown by the repeated Bridgman method from two commercial TlBr salts and characterized to be used as radiation detectors. To evaluate the purification efficiency, measurements of the impurity concentration were made after each growth, analyzing the trace impurities by inductively coupled plasma mass spectroscopy (ICP-MS). A significant decrease of the impurity concentration resulting from the purification number was observed. To evaluate the crystal as a radiation semiconductor detector, measurements of its resistivity and gamma-ray spectroscopy were carried out. The radiation response depended on the crystal purity. The repeated Bridgman technique improved the TlBr crystal quality used as a radiation detector. A compartmental model was proposed to fit the impurity concentration as a function of the repetition number of the Bridgman growth. (author)

  14. Hysteresis analysis of graphene transistor under repeated test and gate voltage stress

    International Nuclear Information System (INIS)

    Yang Jie; Jia Kunpeng; Su Yajuan; Zhao Chao; Chen Yang

    2014-01-01

    The current transport characteristic is studied systematically based on a back-gate graphene field effect transistor, under repeated test and gate voltage stress. The interface trapped charges caused by the gate voltage sweep process screens the gate electric field, and results in the neutral point voltage shift between the forth and back sweep direction. In the repeated test process, the neutral point voltage keeps increasing with test times in both forth and back sweeps, which indicates the existence of interface trapped electrons residual and accumulation. In gate voltage stress experiment, the relative neutral point voltage significantly decreases with the reducing of stress voltage, especially in −40 V, which illustrates the driven-out phenomenon of trapped electrons under negative voltage stress. (semiconductor devices)

  15. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models

    International Nuclear Information System (INIS)

    Teng, S.; Tebby, C.; Barcellini-Couget, S.; De Sousa, G.; Brochot, C.; Rahmani, R.; Pery, A.R.R.

    2016-01-01

    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro – in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. - Highlights: • We could predict cell response over repeated exposure to mixtures of cosmetics. • Compounds acted independently on the cells. • Metabolic interactions impacted exposure concentrations to the compounds.

  16. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models

    Energy Technology Data Exchange (ETDEWEB)

    Teng, S.; Tebby, C. [Models for Toxicology and Ecotoxicology Unit, INERIS, Parc Technologique Alata, BP 2, 60550 Verneuil-en-Halatte (France); Barcellini-Couget, S. [ODESIA Neosciences, Sophia Antipolis, 400 route des chappes, 06903 Sophia Antipolis (France); De Sousa, G. [INRA, ToxAlim, 400 route des Chappes, BP, 167 06903 Sophia Antipolis, Cedex (France); Brochot, C. [Models for Toxicology and Ecotoxicology Unit, INERIS, Parc Technologique Alata, BP 2, 60550 Verneuil-en-Halatte (France); Rahmani, R. [INRA, ToxAlim, 400 route des Chappes, BP, 167 06903 Sophia Antipolis, Cedex (France); Pery, A.R.R., E-mail: alexandre.pery@agroparistech.fr [AgroParisTech, UMR 1402 INRA-AgroParisTech Ecosys, 78850 Thiverval Grignon (France); INRA, UMR 1402 INRA-AgroParisTech Ecosys, 78850 Thiverval Grignon (France)

    2016-08-15

    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro – in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. - Highlights: • We could predict cell response over repeated exposure to mixtures of cosmetics. • Compounds acted independently on the cells. • Metabolic interactions impacted exposure concentrations to the compounds.

  17. Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

    Science.gov (United States)

    M.N. lslam-Faridi; C.D. Nelson; S.P. DiFazio; L.E. Gunter; G.A. Tuskan

    2009-01-01

    The 185-285 rDNA and 55 rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 185-285 rDNA sites and one 55 rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones...

  18. High-Dimensional Multivariate Repeated Measures Analysis with Unequal Covariance Matrices

    Science.gov (United States)

    Harrar, Solomon W.; Kong, Xiaoli

    2015-01-01

    In this paper, test statistics for repeated measures design are introduced when the dimension is large. By large dimension is meant the number of repeated measures and the total sample size grow together but either one could be larger than the other. Asymptotic distribution of the statistics are derived for the equal as well as unequal covariance cases in the balanced as well as unbalanced cases. The asymptotic framework considered requires proportional growth of the sample sizes and the dimension of the repeated measures in the unequal covariance case. In the equal covariance case, one can grow at much faster rate than the other. The derivations of the asymptotic distributions mimic that of Central Limit Theorem with some important peculiarities addressed with sufficient rigor. Consistent and unbiased estimators of the asymptotic variances, which make efficient use of all the observations, are also derived. Simulation study provides favorable evidence for the accuracy of the asymptotic approximation under the null hypothesis. Power simulations have shown that the new methods have comparable power with a popular method known to work well in low-dimensional situation but the new methods have shown enormous advantage when the dimension is large. Data from Electroencephalograph (EEG) experiment is analyzed to illustrate the application of the results. PMID:26778861

  19. Analysis of the Effect of Radio Frequency Interference on Repeat Track Airborne InSAR System

    Directory of Open Access Journals (Sweden)

    Ding Bin

    2012-03-01

    Full Text Available The SAR system operating at low frequency is susceptible to Radio Frequency Interference (RFI from television station, radio station, and some other civil electronic facilities. The presence of RFI degrades the SAR image quality, and obscures the targets in the scene. Furthermore, RFI can cause interferometric phase error in repeat track InSAR system. In order to analyze the effect of RFI on interferometric phase of InSAR, real measured RFI signal are added on cone simulated SAR echoes. The imaging and interferometric processing results of both the RFI-contaminated and raw data are given. The effect of real measured RFI signal on repeat track InSAR system is analyzed. Finally, the imaging and interferometric processing results of both with and without RFI suppressed of the P band airborne repeat track InSAR real data are presented, which demonstrates the efficiency of the RFI suppression method in terms of decreasing the interferometric phase errors caused by RFI.

  20. Dynamic changes in cellular infiltrates with repeated cutaneous vaccination: a histologic and immunophenotypic analysis

    Directory of Open Access Journals (Sweden)

    Schaefer Jochen T

    2010-08-01

    Full Text Available Abstract Background Melanoma vaccines have not been optimized. Adjuvants are added to activate dendritic cells (DCs and to induce a favourable immunologic milieu, however, little is known about their cellular and molecular effects in human skin. We hypothesized that a vaccine in incomplete Freund's adjuvant (IFA would increase dermal Th1 and Tc1-lymphocytes and mature DCs, but that repeated vaccination may increase regulatory cells. Methods During and after 6 weekly immunizations with a multipeptide vaccine, immunization sites were biopsied at weeks 0, 1, 3, 7, or 12. In 36 participants, we enumerated DCs and lymphocyte subsets by immunohistochemistry and characterized their location within skin compartments. Results Mature DCs aggregated with lymphocytes around superficial vessels, however, immature DCs were randomly distributed. Over time, there was no change in mature DCs. Increases in T and B-cells were noted. Th2 cells outnumbered Th1 lymphocytes after 1 vaccine 6.6:1. Eosinophils and FoxP3+ cells accumulated, especially after 3 vaccinations, the former cell population most abundantly in deeper layers. Conclusions A multipeptide/IFA vaccine may induce a Th2-dominant microenvironment, which is reversed with repeat vaccination. However, repeat vaccination may increase FoxP3+T-cells and eosinophils. These data suggest multiple opportunities to optimize vaccine regimens and potential endpoints for monitoring the effects of new adjuvants. Trail Registration ClinicalTrials.gov Identifier: NCT00705640

  1. 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…

  2. Y-Chromosome Haplogroups in the Bosnian-Herzegovinian Population Based on 23 Y-STR Loci.

    Science.gov (United States)

    Doğan, Serkan; Ašić, Adna; Doğan, Gulsen; Besic, Larisa; Marjanovic, Damir

    2016-07-01

    In a study of the Bosnian-Herzegovinian (B&H) population, Y-chromosome marker frequencies for 100 individuals, generated using the PowerPlex Y23 kit, were used to perform Y-chromosome haplogroup assignment via Whit Athey's Haplogroup Predictor. This algorithm determines Y-chromosome haplogroups from Y-chromosome short tandem repeat (Y-STR) data using a Bayesian probability-based approach. The most frequent haplogroup appeared to be I2a, with a prevalence of 49%, followed by R1a and E1b1b, each accounting for 17% of all haplogroups within the population. Remaining haplogroups were J2a (5%), I1 (4%), R1b (4%), J2b (2%), G2a (1%), and N (1%). These results confirm previously published preliminary B&H population data published over 10 years ago, especially the prediction about the B&H population being a part of the Western Balkan area, which served as the Last Glacial Maximum refuge for the Paleolithic human European population. Furthermore, the results corroborate the hypothesis that this area was a significant stopping point on the "Middle East-Europe highway" during the Neolithic farmer migrations. Finally, since these results are almost completely in accordance with previously published data on B&H and neighboring populations generated by Y-chromosome single nucleotide polymorphism analysis, it can be concluded that in silico analysis of Y-STRs is a reliable method for approximation of the Y-chromosome haplogroup diversity of an examined population.

  3. Fingerprint enhancement revisited and the effects of blood enhancement chemicals on subsequent profiler Plus fluorescent short tandem repeat DNA analysis of fresh and aged bloody fingerprints.

    Science.gov (United States)

    Frégeau, C J; Germain, O; Fourney, R M

    2000-03-01

    This study was aimed at determining the effect of seven blood enhancement reagents on the subsequent Profiler Plus fluorescent STR DNA analysis of fresh or aged bloody fingerprints deposited on various porous and nonporous surfaces. Amido Black, Crowle's Double Stain. 1,8-diazafluoren-9-one (DFO), Hungarian Red, leucomalachite green, luminol and ninhydrin were tested on linoleum, glass, metal, wood (pine, painted white), clothing (85% polyester/15% cotton, 65% polyester/35% cotton, and blue denim) and paper (Scott 2-ply and Xerox-grade). Preliminary experiments were designed to determine the optimal blood dilutions to use to ensure a DNA typing result following chemical enhancement. A 1:200 blood dilution deposited on linoleum and enhanced with Crowle's Double Stain generated enough DNA for one to two rounds of Profiler Plus PCR amplification. A comparative study of the DNA yields before and after treatment indicated that the quantity of DNA recovered from bloody fingerprints following enhancement was reduced by a factor of 2 to 12. Such a reduction in the DNA yields could potentially compromise DNA typing analysis in the case of small stains. The blood enhancement chemicals selected were also evaluated for their capability to reveal bloodmarks on the various porous and nonporous surfaces chosen in this study. Luminol. Amido Black and Crowle's Double Stain showed the highest sensitivity of all seven chemicals tested and revealed highly diluted (1:200) bloody fingerprints. Both luminol and Amido Black produced excellent results on both porous and nonporous surfaces, but Crowle's Double Stain failed to produce any results on porous substrates. Hungarian Red, DFO, leucomalachite green and ninhydrin showed lower sensitivities. Enhancement of bloodmarks using any of the chemicals selected, and short-term exposure to these same chemicals (i.e., less than 54 days), had no adverse effects on the PCR amplification of the nine STR systems surveyed (D3S 1358, HumvWA, Hum

  4. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models.

    Science.gov (United States)

    Teng, S; Tebby, C; Barcellini-Couget, S; De Sousa, G; Brochot, C; Rahmani, R; Pery, A R R

    2016-08-15

    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro - in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

    Directory of Open Access Journals (Sweden)

    Ana Gutiérrez-Preciado

    2017-04-01

    Full Text Available We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

  6. Analysis of the finescale timing of repeated signals: does shell rapping in hermit crabs signal stamina?

    Science.gov (United States)

    Briffa; Elwood

    2000-01-01

    Hermit crabs, Pagurus bernhardus, sometimes exchange shells after a period of shell rapping, when the initiating or attacking crab brings its shell rapidly and repeatedly into contact with the shell of the noninitiator or defender in a series of bouts. Bouts are separated by pauses, and raps within bouts are separated by very short periods called 'gaps'. Since within-contest variation is missed when signals are studied by averaging performance rates over entire contests, we analysed the fine within-bout structure of this repeated, aggressive signal. We found that the pattern is consistent with high levels of fatigue in initiators. The duration of the gaps between individual raps increased both within bouts and from bout to bout, and we conclude that this activity is costly to perform. Furthermore, long pauses between bouts is correlated with increased vigour of rapping in the subsequent bout, which suggests that the pause allows for recovery from fatigue induced by rapping. These between-bout pauses may be assessed by noninitiators and provide a signal of stamina. Copyright 2000 The Association for the Study of Animal Behaviour.

  7. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

    2013-04-01

    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  8. Variability and repeatability analysis of plantar pressure during gait in older people.

    Science.gov (United States)

    Franco, Pedro S; Silva, Caio Borella P da; Rocha, Emmanuel S da; Carpes, Felipe P

    2015-01-01

    Repeatability and variability of the plantar pressure during walking are important components in the clinical assessment of the elderly. However, there is a lack of information on the uniformity of plantar pressure patterns in the elderly. To analyze the repeatability and variability in plantar pressure considering mean, peak and asymmetries during aged gait. Plantar pressure was monitored in four different days for ten elderly subjects (5 female), with mean±standard-deviation age of 73±6 years, walking barefoot at preferred speed. Data were compared between steps for each day and between different days. Mean and peak plantar pressure values were similar between the different days of evaluation. Asymmetry indexes were similar between the different days evaluated. Plantar pressure presented a consistent pattern in the elderly. However, the asymmetry indexes observed suggest that the elderly are exposed to repetitive asymmetric loading during locomotion. Such result requires further investigation, especially concerning the role of these asymmetries for development of articular injuries. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

  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

    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......) 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...

  10. Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

    Directory of Open Access Journals (Sweden)

    Marwa H Saied

    Full Text Available Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6 with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001. We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R(2 = 0.7. We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array.

  11. One-time versus repeated abutment connection for platform-switched implant: A systematic review and meta-analysis.

    Science.gov (United States)

    Wang, Qing-Qing; Dai, Ruoxi; Cao, Chris Ying; Fang, Hui; Han, Min; Li, Quan-Li

    2017-01-01

    This review aims to compare peri-implant tissue changes in terms of clinical and radiographic aspects of implant restoration protocol using one-time abutment to repeated abutment connection in platform switched implant. A structured search strategy was applied to three electronic databases, namely, Pubmed, Embase and Web of Science. Eight eligible studies, including seven randomised controlled studies and one controlled clinical study, were identified in accordance with inclusion/exclusion criteria. Outcome measures included peri-implant bone changes (mm), peri-implant soft tissue changes (mm), probing depth (mm) and postsurgical complications. Six studies were pooled for meta-analysis on bone tissue, three for soft tissue, two for probing depth and four for postsurgical complications. A total of 197 implants were placed in one-time abutment group, whereas 214 implants were included in repeated abutment group. The implant systems included Global implants, Ankylos, JDEvolution (JdentalCare), Straumann Bone level and Conelog-Screwline. One-time abutment group showed significantly better outcomes than repeated abutment group, as measured in the standardised differences in mean values (fixed- and random-effect model): vertical bone change (0.41, 3.23) in 6 months, (1.51, 14.81) in 12 months and (2.47, 2.47) in 3 years and soft tissue change (0.21, 0.23). No significant difference was observed in terms of probing depth and complications. Our meta-analysis revealed that implant restoration protocol using one-time abutment is superior to repeated abutment for platform switched implant because of less bone resorption and soft tissue shifts in former. However, future randomised clinical trials should be conducted to further confirm these findings because of the small samples and the limited quality of the original research.

  12. TGC repeat expansion in the TCF4 gene increases the risk of Fuchs' endothelial corneal dystrophy in Australian cases.

    Directory of Open Access Journals (Sweden)

    Abraham Kuot

    Full Text Available Fuchs' endothelial corneal dystrophy (FECD is a progressive, vision impairing disease. Common single nucleotide polymorphisms (SNPs and a trinucleotide repeat polymorphism, thymine-guanine-cytosine (TGC, in the TCF4 gene have been associated with the risk of FECD in some populations. We previously reported association of SNPs in TCF4 with FECD risk in the Australian population. The aim of this study was to determine whether TGC repeat polymorphism in TCF4 is associated with FECD in the Australian population. In 189 unrelated Australian cases with advanced late-onset FECD and 183 matched controls, the TGC repeat polymorphism located in intron 3 of TCF4 was genotyped using a short tandem repeat (STR assay. The repeat length was verified by direct sequencing in selected homozygous carriers. We found significant association between the expanded TGC repeat (≥ 40 repeats in TCF4 and advanced FECD (P = 2.58 × 10-22; OR = 15.66 (95% CI: 7.79-31.49. Genotypic analysis showed that 51% of cases (97 compared to 5% of controls (9 were heterozygous or homozygous for the expanded repeat allele. Furthermore, the repeat expansion showed stronger association than the most significantly associated SNP, rs613872, in TCF4, with the disease in the Australian cohort. This and haplotype analysis of both the polymorphisms suggest that considering both the polymorphisms together rather than either of the two alone would better predict susceptibility to FECD in the Australian population. This is the first study to report association of the TGC trinucleotide repeat expansion in TCF4 with advanced FECD in the Australian population.

  13. NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes.

    Science.gov (United States)

    Duewer, David L; Kline, Margaret C; Redman, Janette W; Butler, John M

    2004-12-01

    Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

  14. M13 multiple stellar populations seen with the eyes of Strömgren photometry

    Science.gov (United States)

    Savino, A.; Massari, D.; Bragaglia, A.; Dalessandro, E.; Tolstoy, E.

    2018-03-01

    We present a photometric study of M13 multiple stellar populations over a wide field of view, covering approximately 6.5 half-light radii, using archival Isaac Newton Telescope observations to build an accurate multiband Strömgren catalogue. The use of the Strömgren index cy permits us to separate the multiple populations of M13 on the basis of their position on the red giant branch. The comparison with medium and high resolution spectroscopic analysis confirms the robustness of our selection criterion. To determine the radial distribution of stars in M13, we complemented our data set with Hubble Space Telescope observations of the cluster core, to compensate for the effect of incompleteness affecting the most crowded regions. From the analysis of the radial distributions, we do not find any significant evidence of spatial segregation. Some residuals may be present in the external regions where we observe only a small number of stars. This finding is compatible with the short dynamical time-scale of M13 and represents, to date, one of the few examples of fully spatially mixed multiple populations in a massive globular cluster.

  15. [Clinical outcomes and economic analysis of two ovulation induction protocols in patients undergoing repeated IVF/ICSI cycles].

    Science.gov (United States)

    Chen, Xiao; Geng, Ling; Li, Hong

    2014-04-01

    To compare the clinical outcomes and cost-effectiveness of luteal phase down-regulation with gonadotrophin-releasing hormone (GnRH) agonist protocol and GnRH antagonist protocol in patients undergoing repeated in vitro fertilization and intracytoplasmic sperm injection (IVF-ICSI) cycles. A retrospective analysis of clinical outcomes and costs was conducted among 198 patients undergoing repeated IVF-ICSI cycles, including 109 receiving luteal phase down-regulation with GnRH agonist protocol (group A) and 89 receiving GnRH antagonist protocol (group B). The numbers of oocytes retrieved and good embryos, clinical pregnancy rate, abortion rate, the live birth rate, mean total cost, and the cost-effective ratio were compared between the two groups. In patients undergoing repeated IVF-ICSI cycles, the two protocols produced no significant differences in the number of good embryos, clinical pregnancy rate, abortion rate, or twin pregnancy rate. Compared with group B, group A had better clinical outcomes though this difference was not statistically significant. The number of retrieved oocytes was significantly greater and live birth rate significantly higher in group A than in group B (9.13=4.98 vs 7.11=4.74, and 20.2% vs 9.0%, respectively). Compared with group B, group A had higher mean total cost per cycle but lower costs for each oocyte retrieved (2729.11 vs 3038.60 RMB yuan), each good embryo (8867.19 vs 9644.85 RMB yuan), each clinical pregnancy (77598.06 vs 96139.85 RMB yuan). For patients undergoing repeated IVF/ICSI cycle, luteal phase down-regulation with GnRH agonist protocol produces good clinical outcomes with also good cost-effectiveness in spite an unsatisfactory ovarian reserve.

  16. Multiple-locus variable-number tandem repeat analysis of Neisseria meningitidis yields groupings similar to those obtained by multilocus sequence typing.

    NARCIS (Netherlands)

    Schouls, Leo M; Ende, Arie van der; Damen, Marjolein; Pol, Ingrid van de

    2006-01-01

    We identified many variable-number tandem repeat (VNTR) loci in the genomes of Neisseria meningitidis serogroups A, B, and C and utilized a number of these loci to develop a multiple-locus variable-number tandem repeat analysis (MLVA). Eighty-five N. meningitidis serogroup B and C isolates obtained

  17. 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 (peastern African ethnic groups, and suggests caution in the use of country-based haplotype frequency distributions for forensic inferences in this region. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Molecular characterization of Leptospira sp by multilocus variable number tandem repeat analysis (MLVA from clinical samples: a case report

    Directory of Open Access Journals (Sweden)

    Hélène Pailhoriès

    2015-08-01

    Full Text Available Leptospirosis is a zoonotic infection for which diagnosis is difficult. It has appeared as a global emerging infectious disease over recent years. Genotype determination often requires a Leptospira strain obtained by culture, which is a long and fastidious technique. A method based on multilocus variable number tandem repeat analysis (MLVA to determine the genotype of Leptospira interrogans, performed directly on blood or urine samples, is proposed. This method was applied to a fatal case of leptospirosis for which the geographical origin of infection was unknown. This technique will allow a genotype to be obtained for L. interrogans, even when cultures remain negative.

  19. Theoretical conformational analysis of the tetrasaccharide repeating units of the O-antigenic polysaccharide of Shigella flexneri

    International Nuclear Information System (INIS)

    Lipkind, G.M.; Kochetkov, N.K.

    1986-01-01

    A theoretical conformational analysis has been made of the four tetrasaccharide repeating units of the polysaccharide of Shigella flexneri, serotype Y. The interdependence of the conformation states of the neighboring disaccharide units and the oligosaccharides has been investigated. The distribution of the tetrasaccharides over the conformations in solution obtained by calculating the free energies of the optimum structures is given. It has been shown that a substantial correction of the results relating to oligosaccharide chains is achieved when the entropy factors is taken into account

  20. Recommendations for analysis of repeated-measures designs: testing and correcting for sphericity and use of manova and mixed model analysis.

    Science.gov (United States)

    Armstrong, Richard A

    2017-09-01

    A common experimental design in ophthalmic research is the repeated-measures design in which at least one variable is a within-subject factor. This design is vulnerable to lack of 'sphericity' which assumes that the variances of the differences among all possible pairs of within-subject means are equal. Traditionally, this design has been analysed using a repeated-measures analysis of variance (RM-anova) but increasingly more complex methods such as multivariate anova (manova) and mixed model analysis (MMA) are being used. This article surveys current practice in the analysis of designs incorporating different factors in research articles published in three optometric journals, namely Ophthalmic and Physiological Optics (OPO), Optometry and Vision Science (OVS), and Clinical and Experimental Optometry (CXO), and provides advice to authors regarding the analysis of repeated-measures designs. Of the total sample of articles, 66% used a repeated-measures design. Of those articles using a repeated-measures design, 59% and 8% analysed the data using RM-anova or manova respectively and 33% used MMA. The use of MMA relative to RM-anova has increased significantly since 2009/10. A further search using terms to select those papers testing and correcting for sphericity ('Mauchly's test', 'Greenhouse-Geisser', 'Huynh and Feld') identified 66 articles, 62% of which were published from 2012 to the present. If the design is balanced without missing data then manova should be used rather than RM-anova as it gives better protection against lack of sphericity. If the design is unbalanced or with missing data then MMA is the method of choice. However, MMA is a more complex analysis and can be difficult to set up and run, and care should be taken first, to define appropriate models to be tested and second, to ensure that sample sizes are adequate. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

  1. Simple Sequence Repeat Analysis of Selected NSIC-registered Coffee Varieties in the Philippines

    Directory of Open Access Journals (Sweden)

    Daisy May C. Santos

    2016-06-01

    Full Text Available Coffee (Coffea sp. is an important commercial crop worldwide. Three species of coffee are used as beverage, namely Coffea arabica, C. canephora, and C. liberica. Coffea arabica L. is the most cultivated among the three coffee species due to its taste quality, rich aroma, and low caffeine content. Despite its inferior taste and aroma, C. canephora Pierre ex A. Froehner, which has the highest caffeine content, is the second most widely cultivated because of its resistance to coffee diseases. On the other hand, C. liberica W.Bull ex Hierncomes is characterized by its very strong taste and flavor. The Philippines used to be a leading exporter of coffee until coffee rust destroyed the farms in Batangas, home of the famous Kapeng Barako. The country has been attempting to revive the coffee industry by focusing on the production of specialty coffee with registered varieties on the National Seed Industry Council (NSIC. Correct identification and isolation of pure coffee beans are the main factors that determine coffee’s market value. Local farms usually misidentify and mix coffee beans of different varieties, leading to the depreciation of their value. This study used simple sequence repeat (SSR markers to evaluate and distinguish Philippine NSIC-registered coffee species and varieties. The neighbor-joining tree generated using PAUP showed high bootstrap support, separating C. arabica, C. canephora, and C. liberica from each other. Among the twenty primer pairs used, seven were able to distinguish C. arabica, nine for C. liberica, and one for C. canephora.

  2. Identification of the sequence variations of 15 autosomal STR loci in a Chinese population.

    Science.gov (United States)

    Chen, Wenjing; Cheng, Jianding; Ou, Xueling; Chen, Yong; Tong, Dayue; Sun, Hongyu

    2014-01-01

    DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected. In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci. Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced. A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01. Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.

  3. Neural network modeling of drying of rice in BAU-STR dryer

    Science.gov (United States)

    Alam, Md. Ashraful; Saha, Chayan Kumer; Alam, Md. Monjurul; Ashraf, Md. Ali; Bala, Bilash Kanti; Harvey, Jagger

    2018-05-01

    The experimental performance and artificial neural network modeling of rice drying in BAU-STR dryer is presented in this paper. The dryer consists of a biomass stove as a heat source, a perforated inner bin and a perforated outer bin with annular space for grains, and a blower (1 hp) to supply heated air. The dryer capacity was 500 kg of freshly harvested rice. Twenty experimental runs were conducted to investigate the experimental performance of the dryer for drying of rice. An independent multilayer neural network approach was used to predict the performance of the BAU-STR dryer for drying of rice. Ten sets of experimental data were used for training using back propagation algorithm and another ten sets of data were used for testing the artificial neural network model. The prediction of the performance of the dryer was found to be excellent after it was adequately trained. The statistical analysis showed that the errors (MSE and RMSE) were within and acceptable range of ±5% with a coefficient of determination (R2) of 99%. The model can be used to predict the potential of the dryer for different locations, and can also be used in a predictive optimal control algorithm.

  4. 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).

  5. Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer

    International Nuclear Information System (INIS)

    Spink, Barbara C.; Bloom, Michael S.; Wu, Susan; Sell, Stewart; Schneider, Erasmus; Ding, Xinxin; Spink, David C.

    2015-01-01

    The aryl hydrocarbon receptor (AhR) regulates expression of numerous genes, including those of the CYP1 gene family. With the goal of determining factors that control AHR gene expression, our studies are focused on the role of the short tandem repeat polymorphism, (GGGGC) n , located in the proximal promoter of the human AHR gene. When luciferase constructs containing varying GGGGC repeats were transfected into cancer cell lines derived from the lung, colon, and breast, the number of GGGGC repeats affected AHR promoter activity. The number of GGGGC repeats was determined in DNA from 327 humans and from 38 samples representing 5 species of non-human primates. In chimpanzees and 3 species of macaques, only (GGGGC) 2 alleles were observed; however, in western gorilla, (GGGGC) n alleles with n = 2, 4, 5, 6, 7, and 8 were identified. In all human populations examined, the frequency of (GGGGC) n was n = 4 > 5 ≫ 2, 6. When frequencies of the (GGGGC) n alleles in DNA from patients with lung, colon, or breast cancer were evaluated, the occurrence of (GGGGC) 2 was found to be 8-fold more frequent among lung cancer patients in comparison with its incidence in the general population, as represented by New York State neonates. Analysis of matched tumor and non-tumor DNA samples from the same individuals provided no evidence of microsatellite instability. These studies indicate that the (GGGGC) n short tandem repeats are inherited, and that the (GGGGC) 2 allele in the AHR proximal promoter region should be further investigated with regard to its potential association with lung cancer susceptibility. - Highlights: • The AHR proximal promoter contains a polymorphism, (GGGGC) n , where n = 4 > 5 ≫ 2, 6 • Matched tumor and non-tumor DNA did not show (GGGGC) n microsatellite instability • AHR promoter activity of a construct with (GGGGC) 2 was lower than that of (GGGGC) 4 • The frequency of (GGGGC) 2 in lung cancer patients was 8-fold higher than in neonates • The

  6. Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer

    Energy Technology Data Exchange (ETDEWEB)

    Spink, Barbara C. [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Bloom, Michael S. [Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Wu, Susan [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Sell, Stewart; Schneider, Erasmus [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Ding, Xinxin [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Spink, David C., E-mail: spink@wadsworth.org [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States)

    2015-01-01

    The aryl hydrocarbon receptor (AhR) regulates expression of numerous genes, including those of the CYP1 gene family. With the goal of determining factors that control AHR gene expression, our studies are focused on the role of the short tandem repeat polymorphism, (GGGGC){sub n}, located in the proximal promoter of the human AHR gene. When luciferase constructs containing varying GGGGC repeats were transfected into cancer cell lines derived from the lung, colon, and breast, the number of GGGGC repeats affected AHR promoter activity. The number of GGGGC repeats was determined in DNA from 327 humans and from 38 samples representing 5 species of non-human primates. In chimpanzees and 3 species of macaques, only (GGGGC){sub 2} alleles were observed; however, in western gorilla, (GGGGC){sub n} alleles with n = 2, 4, 5, 6, 7, and 8 were identified. In all human populations examined, the frequency of (GGGGC){sub n} was n = 4 > 5 ≫ 2, 6. When frequencies of the (GGGGC){sub n} alleles in DNA from patients with lung, colon, or breast cancer were evaluated, the occurrence of (GGGGC){sub 2} was found to be 8-fold more frequent among lung cancer patients in comparison with its incidence in the general population, as represented by New York State neonates. Analysis of matched tumor and non-tumor DNA samples from the same individuals provided no evidence of microsatellite instability. These studies indicate that the (GGGGC){sub n} short tandem repeats are inherited, and that the (GGGGC){sub 2} allele in the AHR proximal promoter region should be further investigated with regard to its potential association with lung cancer susceptibility. - Highlights: • The AHR proximal promoter contains a polymorphism, (GGGGC){sub n}, where n = 4 > 5 ≫ 2, 6 • Matched tumor and non-tumor DNA did not show (GGGGC){sub n} microsatellite instability • AHR promoter activity of a construct with (GGGGC){sub 2} was lower than that of (GGGGC){sub 4} • The frequency of (GGGGC){sub 2} in lung

  7. Deformation analysis of the repeated positional surveys in the undermined localities using web applications and WMS map services

    Directory of Open Access Journals (Sweden)

    Milan Talich

    2007-06-01

    Full Text Available The XML web application for on-line calculations of deformation analysis from the repeated positional surveys using Internet service and data is described. Parameters of deformation field (strain tensors, total dilatations are determined in a grid network covering the zone of interest. Displacement vectors from repeated measurements at given points of a geodetic network represent the imput data of calculation. The calculation is based on application of the theory of continuum mechanics and its fundamental prerequisite is homogeneity of the researched territory.The application currently utilizes the Web Map Services - WMS for the graphic presentation of calculated results as GIS. This service for example enables on-line thematic map composition as defined by the user in the window of Internet explorer based on data given by servers of WMS service. Thus the user does not need to own any geographic data to create his/her GIS.Furthermore there are also given application examples of the repeated geodetic surveys used in the field at localities in the forefront of ČSA giant quarry at Komořany and in the undermined territory in Ostrava region. The examples show the independence of calculated values of tensors from rotation and translation of the coordinate systems in practise. This fact gives the evidence that the deformation analysis is more objective dynamic indicator in the researched area and not only the calculus and representation of point displacement vectors. After registration this application is at all interested persons disposal to on-line calculations via the Internet.

  8. Repeating Marx

    DEFF Research Database (Denmark)

    Fuchs, Christian; Monticelli, Lara

    2018-01-01

    This introduction sets out the context of the special issue “Karl Marx @ 200: Debating Capitalism & Perspectives for the Future of Radical Theory”, which was published on the occasion of Marx’s bicentenary on 5 May 2018. First, we give a brief overview of contemporary capitalism’s development...... and its crises. Second, we argue that it is important to repeat Marx today. Third, we reflect on lessons learned from 200 years of struggles for alternatives to capitalism. Fourth, we give an overview of the contributions in this special issue. Taken together, the contributions in this special issue show...... that Marx’s theory and politics remain key inspirations for understanding exploitation and domination in 21st-century society and for struggles that aim to overcome these phenomena and establishing a just and fair society. We need to repeat Marx today....

  9. Deployment Repeatability

    Science.gov (United States)

    2016-08-31

    large cohort of trials to spot unusual cases. However, deployment repeatability is inherently a nonlinear phenomenon, which makes modeling difficult...and GEMS tip position were both tracked during ground testing by a laser target tracking system. Earlier SAILMAST testing in 2005 [8] used...recalls the strategy used by SRTM, where a constellation of lights was installed at the tip of the boom and a modified star tracker was used to track tip

  10. Modelling noise in second generation sequencing forensic genetics STR data using a one-inflated (zero-truncated) negative binomial model

    DEFF Research Database (Denmark)

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

    2015-01-01

    We present a model fitting the distribution of non-systematic errors in STR second generation sequencing, SGS, analysis. The model fits the distribution of non-systematic errors, i.e. the noise, using a one-inflated, zero-truncated, negative binomial model. The model is a two component model...

  11. Development and validation of a single-tube multiple-locus variable number tandem repeat analysis for Klebsiella pneumoniae.

    Directory of Open Access Journals (Sweden)

    Antoinette A T P Brink

    Full Text Available Genotyping of Klebsiella pneumoniae is indispensable for management of nosocomial infections, monitoring of emerging strains--including extended-spectrum beta-lactamase (ESBL producers-, and general epidemiology. Such objectives require a high-resolution genotyping method with a fixed scheme that allows (1 long-term retrospective and prospective assessment, (2 objective result readout and (3 library storage for database development and exchangeable results. We have developed a multiple-locus variable number tandem repeat analysis (MLVA using a single-tube fluorescently primed multiplex PCR for 8 Variable Number Tandem Repeats (VNTRs and automated fragment size analysis. The type allocation scheme was optimized using 224 K. pneumoniae clinical isolates, which yielded 101 MLVA types. The method was compared to the gold standard multilocus sequence typing (MLST using a subset of these clinical isolates (n = 95 and found to be highly concordant, with at least as high a resolution but with considerably less hands-on time. Our results position this MLVA scheme as an appropriate, high-throughput and relatively low-cost tool for K. pneumoniae epidemiology.

  12. Experimental Analysis for Factors Affecting the Repeatability of Plastics Injection Molding Tests on the Self-developed Apparatus

    Directory of Open Access Journals (Sweden)

    Yugang Huang

    2013-06-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 To improve the repeatability of the injection molding test result, the affecting factors were investigated by means of experiments. Besides the traditional processing parameter, the factors of test conditions were also considered. In order to focus on the molding process rather than the molded part, the curve measurement of the melt pressure at the entrance to the nozzle was used as the output characteristic. Experiments for polypropylene (PP showed that the injected volume was the key processing parameter. Within the test conditions, the injection number is the most important factor. According to the analysis the operating procedure was improved effectively. Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Doi: 10.12777/ijse.5.1.6-11 [How to cite this article: Huang, Y., Li, D., Liu, Y. (2013. Experimental Analysis for Factors Affecting the Repeatability of Plastics Injection Molding Tests on the Self-developed Apparatus. International Journal of Science and Engineering, 5(1,6-11. Doi: 10.12777/ijse.5.1.6-11]

  13. Z3str3: A String Solver with Theory-aware Branching

    OpenAIRE

    Berzish, Murphy; Zheng, Yunhui; Ganesh, Vijay

    2017-01-01

    We present a new string SMT solver, Z3str3, that is faster than its competitors Z3str2, Norn, CVC4, S3, and S3P over a majority of three industrial-strength benchmarks, namely Kaluza, PISA, and IBM AppScan. Z3str3 supports string equations, linear arithmetic over length function, and regular language membership predicate. The key algorithmic innovation behind the efficiency of Z3str3 is a technique we call theory-aware branching, wherein we modify Z3's branching heuristic to take into account...

  14. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

    Directory of Open Access Journals (Sweden)

    Ciervo Alessandra

    2006-04-01

    Full Text Available Abstract Background The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR Analysis (MLVA assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. Results Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. Conclusion In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the

  15. Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system

    Science.gov (United States)

    Yang, Chun; Zhang, Jianqiu

    2017-01-01

    In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population. PMID:28704439

  16. Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system.

    Directory of Open Access Journals (Sweden)

    Huipin Wang

    Full Text Available In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population.

  17. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Directory of Open Access Journals (Sweden)

    Charlotte Rehm

    Full Text Available 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.

  18. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

    Science.gov (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

    2014-11-01

    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  19. A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

    Science.gov (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

    2017-07-17

    Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

  20. Cyclic elastic analysis of a PWR nozzle subjected to a repeated thermal shock

    International Nuclear Information System (INIS)

    Locci, J.M.; Prost, J.P.

    1979-01-01

    In the primary piping system of a PWR nuclear power plant, some nozzles are subjected to strong thermal shocks due to sudden thermal variations in the internal water flow. The thermal gradients are sufficiently high to induce general elastic plastic behaviour. The design of these nozzles using the simplified elastic plastic analysis given in the ASME III Code NB-3200 generally leads to a very high usage factor. The aim of this work is to show by giving an example that a complete cyclic elastic plastic analysis makes it possible to considerably reduce the usage factor. (orig.)

  1. The genetic analysis of repeated measures II: The Karhunen-Loeve expansion.

    NARCIS (Netherlands)

    Molenaar, P.C.M.; Boomsma, D.I.

    1987-01-01

    Outlines the Karhunen-Loeve (N. Ahmed and K. R. Rao, 1975) approach to the genetic analysis of time series of arbitrary length and with arbitrary covariance function. This approach is based on the simultaneous eigenvalue decomposition of the covariance matrices of the original time series obtained

  2. Rule-of-thumb adjustment of sample sizes to accommodate dropouts in a two-stage analysis of repeated measurements.

    Science.gov (United States)

    Overall, John E; Tonidandel, Scott; Starbuck, Robert R

    2006-01-01

    Recent contributions to the statistical literature have provided elegant model-based solutions to the problem of estimating sample sizes for testing the significance of differences in mean rates of change across repeated measures in controlled longitudinal studies with differentially correlated error and missing data due to dropouts. However, the mathematical complexity and model specificity of these solutions make them generally inaccessible to most applied researchers who actually design and undertake treatment evaluation research in psychiatry. In contrast, this article relies on a simple two-stage analysis in which dropout-weighted slope coefficients fitted to the available repeated measurements for each subject separately serve as the dependent variable for a familiar ANCOVA test of significance for differences in mean rates of change. This article is about how a sample of size that is estimated or calculated to provide desired power for testing that hypothesis without considering dropouts can be adjusted appropriately to take dropouts into account. Empirical results support the conclusion that, whatever reasonable level of power would be provided by a given sample size in the absence of dropouts, essentially the same power can be realized in the presence of dropouts simply by adding to the original dropout-free sample size the number of subjects who would be expected to drop from a sample of that original size under conditions of the proposed study.

  3. At what price? A cost-effectiveness analysis comparing trial of labour after previous caesarean versus elective repeat caesarean delivery.

    Directory of Open Access Journals (Sweden)

    Christopher G Fawsitt

    Full Text Available BACKGROUND: Elective repeat caesarean delivery (ERCD rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland. METHODS: Using a decision analytic model, a cost-effectiveness analysis (CEA was performed where the measure of health gain was quality-adjusted life years (QALYs over a six-week time horizon. A review of international literature was conducted to derive representative estimates of adverse maternal health outcomes following a trial of labour after caesarean (TOLAC and ERCD. Delivery/procedure costs derived from primary data collection and combined both "bottom-up" and "top-down" costing estimations. RESULTS: Maternal morbidities emerged in twice as many cases in the TOLAC group than the ERCD group. However, a TOLAC was found to be the most-effective method of delivery because it was substantially less expensive than ERCD (€ 1,835.06 versus € 4,039.87 per women, respectively, and QALYs were modestly higher (0.84 versus 0.70. Our findings were supported by probabilistic sensitivity analysis. CONCLUSIONS: Clinicians need to be well informed of the benefits and risks of TOLAC among low risk women. Ideally, clinician-patient discourse would address differences in length of hospital stay and postpartum recovery time. While it is premature advocate a policy of TOLAC across maternity units, the results of the study prompt further analysis and repeat iterations, encouraging future studies to synthesis previous research and new and relevant evidence under a single

  4. Kinematic Analysis of a Six-Degrees-of-Freedom Model Based on ISB Recommendation: A Repeatability Analysis and Comparison with Conventional Gait Model.

    Science.gov (United States)

    Żuk, Magdalena; Pezowicz, Celina

    2015-01-01

    Objective. The purpose of the present work was to assess the validity of a six-degrees-of-freedom gait analysis model based on the ISB recommendation on definitions of joint coordinate systems (ISB 6DOF) through a quantitative comparison with the Helen Hays model (HH) and repeatability assessment. Methods. Four healthy subjects were analysed with both marker sets: an HH marker set and four marker clusters in ISB 6DOF. A navigated pointer was used to indicate the anatomical landmark position in the cluster reference system according to the ISB recommendation. Three gait cycles were selected from the data collected simultaneously for the two marker sets. Results. Two protocols showed good intertrial repeatability, which apart from pelvic rotation did not exceed 2°. The greatest differences between protocols were observed in the transverse plane as well as for knee angles. Knee internal/external rotation revealed the lowest subject-to-subject and interprotocol repeatability and inconsistent patterns for both protocols. Knee range of movement in transverse plane was overestimated for the HH set (the mean is 34°), which could indicate the cross-talk effect. Conclusions. The ISB 6DOF anatomically based protocol enabled full 3D kinematic description of joints according to the current standard with clinically acceptable intertrial repeatability and minimal equipment requirements.

  5. Structural analysis within the Rožná and Olší uranium deposits (Strážek Moldanubicum) for the estimation of deformation and stress conditions of underground gas storage

    Czech Academy of Sciences Publication Activity Database

    Ptáček, Jiří; Melichar, R.; Hájek, Antonín; Koníček, Petr; Souček, Kamil; Staš, Lubomír; Kříž, P.; Lazárek, J.

    2013-01-01

    Roč. 10, č. 2 (2013), s. 237-246 ISSN 1214-9705 Institutional support: RVO:68145535 Keywords : structural analysis * deformation * stress * underground gas storage Subject RIV: DH - Mining, incl. Coal Mining Impact factor: 0.667, year: 2013 http://www.irsm.cas.cz/materialy/acta_content/2013_02/acta_170_13_Ptacek_237-246.pdf

  6. The relationship between visitor spending and repeat visits: An analysis of spectators at the Old Mutual Two Oceans Marathon

    Directory of Open Access Journals (Sweden)

    M. Kruger

    2012-12-01

    Full Text Available Purpose: The purpose of this research is to determine the relationship between visitor spending patterns, and previous and planned return visits as well as demographic and trip characteristics of supporters to the Old Mutual Two Oceans Marathon held annually in Cape Town. Problem investigated: Spectator sport is a significant segment of the tourism industry which also has a considerable economic impact on host communities. For this reason, communities and destinations have recognised and attempt to capitalise on hosting large sporting events. In this regard visitor spending is crucial since information concerning the latter can provide sport event organisers to focus their marketing efforts to attract optimal economic benefits. In addition, the relationship of previous visits to a sport event and intended re-visits to visitor spending has received increasing attention since it is believed that repeat visitation is associated with higher levels of expenditure. However limited attention is currently being paid to the relationship between spectator spending patterns and previous and planned return visits in a South African sport spectator context even though the latter has a direct impact on the future sustainability of an event. Methodology: A supporter survey was done for the first time in 2010 (30 March - 2 April 2010 at the event and 430 questionnaires were completed. Factor analysis and regression analysis are used to analyse the data and to identify the relationship between repeat visits and visitor spending patterns. Findings: Results from this study shows that it is predominantly socio-demographic variables that influence travel behaviour. The significant socio-demographic determinants that influence spending per person are gender, language and province of origin while the only behavioural determinant was group size. The results also revealed that there is no significant relationship between spectator spending, repeat attendance and

  7. In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

    Directory of Open Access Journals (Sweden)

    Andrea Vásquez

    2014-01-01

    Full Text Available We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp. It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.

  8. Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers.

    Science.gov (United States)

    Xue, Huiling; Xiao, Yao; Jin, Yanling; Li, Xinbo; Fang, Yang; Zhao, Hai; Zhao, Yun; Guan, Jiafa

    2012-01-01

    Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.

  9. Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations.

    Science.gov (United States)

    Soltyszewski, Ireneusz; Plocienniczak, Andrzej; Fabricius, Hans Ake; Kornienko, Igor; Vodolazhsky, Dmitrij; Parson, Walther; Hradil, Roman; Schmitter, Hermann; Ivanov, Pavel; Kuzniar, Piotr; Malyarchuk, Boris A; Grzybowski, Tomasz; Woźniak, Marcin; Henke, Jurgen; Henke, Lotte; Olkhovets, Sergiv; Voitenko, Vladimir; Lagus, Vita; Ficek, Andrej; Minárik, Gabriel; de Knijff, Peter; Rebała, Krzysztof; Wysocka, Joanna; Kapińska, Ewa; Cybulska, Lidia; Mikulich, Alexei I; Tsybovsky, Iosif S; Szczerkowska, Zofia; Krajewski, Paweł; Ploski, Rafał

    2008-06-01

    The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.

  10. Genetic polymorphisms in 18 autosomal STR loci in the Tibetan population living in Tibet Chamdo, Southwest China.

    Science.gov (United States)

    Li, Zhenghui; Zhang, Jian; Zhang, Hantao; Lin, Ziqing; Ye, Jian

    2018-05-01

    Short tandem repeats (STRs) play a vitally important role in forensics. Population data is needed to improve the field. There is currently no large population data-based data set in Chamdo Tibetan. In our study, the allele frequencies and forensic statistical parameters of 18 autosomal STR loci (D5S818, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, VWA, D8S1179, D16S539, PentaE, TPOX, TH01, D19S433, D18S51, FGA, D6S1043, D13S317, and D12S391) included in the DNATyper™19 kit were investigated in 2249 healthy, unrelated Tibetan subjects living in Tibet Chamdo, Southwest China. The combined power of discrimination and the combined probability of exclusion of all 18 loci were 0.9999999999999999999998174 and 0.99999994704, respectively. Furthermore, the genetic relationship between our Tibetan group and 33 previously published populations was also investigated. Phylogenetic analyses revealed that the Chamdo Tibetan population is more closely related genetically with the Lhasa Tibetan group. Our results suggest that these autosomal STR loci are highly polymorphic in the Tibetan population living in Tibet Chamdo and can be used as a powerful tool in forensics, linguistics, and population genetic analyses.

  11. Population data and mutation rates of 20 autosomal STR loci in a Chinese Han population from Yunnan Province, Southwest China.

    Science.gov (United States)

    Zhang, Xiufeng; Liu, Linlin; Xie, Runfang; Wang, Guiyi; Shi, Yuan; Gu, Tao; Hu, Liping; Nie, Shengjie

    2018-07-01

    The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated from 2068 unrelated, healthy individuals from the Chinese Han population of Yunnan Province in southwest China. All of the loci reached Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationships among the Yunnan Han and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.99999999999999999999999126 and 0.999999975, respectively. In addition, mutation rates from 4363 parentage cases (2215 trios and 2148 duos) were investigated in this study. A total of 164 mutations were observed in 6578 meioses from the 20 loci. The highest mutation rate was observed in D12S391 (0.30%), and the lowest mutation rates were observed in D13S317 (0.03%) and TPOX (0.03%). The average mutation rate for the 20 loci was estimated to be 1.246 × 10 -3 per meiosis. The mutations were primarily single-step and paternal mutations.

  12. 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

  13. 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...

  14. 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.

    2017-12-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) 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 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 Glenn Research Center (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 has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  15. Variable Number of Tandem Repeats (VNTR) analysis of Flavobacterium psychrophilum from salmonids in Chile and Norway.

    Science.gov (United States)

    Apablaza, Patricia; Brevik, Øyvind J; Mjøs, Svein; Valdebenito, Samuel; Ilardi, Pedro; Battaglia, Juan; Dalsgaard, Inger; Nylund, Are

    2015-07-14

    Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of different isolates of this bacterium could play an important role in the development of good management strategies. The aim of this study was to identify genetic markers for discrimination between isolates. A selection of eight VNTRs from 53 F. psychrophilum isolates from Norway, Chile, Denmark and Scotland were analyzed. The results were compared with previous work on the same pathogen using MLST for genetic differentiation. The VNTR analysis gave a separation between the F. psychrophilum isolates supporting the results of previous MLST work. A higher diversity was found among the Chilean isolates compared to those from Norway, which suggests a more homogenous reservoir in Norway. Transgenerational transmission of F. psychrophilum from other countries, exporting salmon embryos to Chile, may explain the differences in diversity. The same transmission mechanisms could also explain the wide geographical distribution of identical isolates in Norway. But, this could also be a result of movement of smolts and embryos. The selected VNTRs are stable genetic markers and no variation was observed after several passages on agar plates at different temperatures. These VNTRs are important additions for genotyping of F. psychrophilum isolates. Future studies on VNTRs of F. psychrophilum should include isolates from more host species from a wider geographical area. To get a more robust genotyping the VNTRs should be used in concert with MLST. Future studies of isolates with high and low virulence should focus on identifying virulence markers using VTNRs and MLST.

  16. Måling på ikke sinusformede AC strømme og spændinger

    DEFF Research Database (Denmark)

    Nielsen, Arne Hejde

    1998-01-01

    Målinger på en- og trefasede spændinger og strømme i elforsyningen. Specielt gennemgås forholdene ved ikke symetriske systemer med overtoner i spændinger og strømme.......Målinger på en- og trefasede spændinger og strømme i elforsyningen. Specielt gennemgås forholdene ved ikke symetriske systemer med overtoner i spændinger og strømme....

  17. NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana.

    Science.gov (United States)

    Xu, Shenyuan; Ni, Shuisong; Kennedy, Michael A

    2017-05-23

    At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown. Given its unusual structure, we investigated the biophysical properties of At2g44920 as a representative of the β-helix family to determine if it had exceptional global stability, backbone dynamics, or amide hydrogen exchange rates. Circular dichroism measurements yielded a melting point of 62.8°C, indicating unexceptional global thermal stability. Nuclear spin relaxation measurements indicated that the Rfr-fold core was rigid with order parameters ranging from 0.7 to 0.9. At2g44920 exhibited a striking range of amide hydrogen exchange rates spanning 10 orders of magnitude, with lifetimes ranging from minutes to several months. A weak correlation was found among hydrogen exchange rates, hydrogen bonding energies, and amino acid solvent-accessible areas. Analysis of contributions from fast (approximately picosecond to nanosecond) backbone dynamics to amide hydrogen exchange rates revealed that the average order parameter of amides undergoing fast exchange was significantly smaller compared to those undergoing slow exchange. Importantly, the activation energies for amide hydrogen exchange were found to be generally higher for the slowest exchanging amides in the central Rfr coil and decreased toward the terminal coils. This could be explained by assuming that the concerted motions of two preceding or following coils required for hydrogen bond disruption and amide hydrogen exchange have a higher activation energy

  18. Overcrowding in Italian Jails. A Quantitative Analysis of Foreigners (Supraaglomerarea în închisorile italiene. O analiză cantitativă asupra străinilor

    Directory of Open Access Journals (Sweden)

    Stefania GIRONE

    2013-11-01

    Full Text Available Victims of prison-overcrowding in Italy are part of a structural and systemic problem which is still struggling to find plausible solutions. When natives and foreigners are separately considered, the overcrowding phenomenon assumes a perspective that goes beyond the mere Italian attribute and, therefore, better focalises on the ones who, having the status of foreigner, are somehow in a weaker position in comparison with the native ones. As a matter of fact, the combination foreign prisoner-overcrowding has allowed to address the prison issue in accordance with a more specific approach that compares the Italian native component and the foreign one. This highlights that the overcrowding phenomenon in Italy is not an aspect suffered mainly by foreign prisoners, but it is equally endured by most of the native ones. Additionally, this analysis takes into account, on the one hand, the most outstanding foreign nationalities housed in Italian prisons and, on the other hand, the Regions having the highest rates of overcrowding, foreign inmates, and prison capacities. The outcomes reveal that Moroccans, Romanians, Tunisians and Albanians are the ones at increased risk of prison overcrowding since, in fact, they represent 60.0% of the total foreign presence in the Italian jails. However, there is a sort of “equal overcrowding distress” that comes out of this context: actually, the four major foreign presences are housed at the same percentage by the six selected Regions (the most overcrowded by foreigners, circumstance that generates a kind of homogeneity of the unlivable conditions in prisons.

  19. Paroxysmal nocturnal hemoglobinuria first described in 1882 by Paul Strübing: an example of cooperation between clinical and basic research.

    Science.gov (United States)

    Wilmanns, J C

    1982-12-01

    The 100th anniversary of the first description of paroxysmal nocturnal hemoglobinuria by Paul Strübing presents an opportunity to analyze the premises valid for the description of this disease in addition to an attempt at an extensive pathophysiological analysis. Strübing's two papers of 1882 were way ahead of his time, when pathophysiology was just at its beginning, particularly considering the fact that neither Marchiafava, who is still commonly credited wit the first description of this disease (1911) and its recognition as a clinical entity (1928), nor his student Micheli analyzed the PNH syndrome in pathophysiological terms as carefully as Strübing. Both of the former names were given to the disease, which is generally referred to as the Marchiafava-Micheli Anemia. William Crosby, who in 1951 in a historical review of PHN first pointed out the pioneering achievement of Strübing, suggested that it was mainly due to the lack of the right "intellectual climate" at the time that so little attention was paid to his work. Still another important aspect of the early history of PNH will be described in the present paper. The analysis of Strübing's publications leads to the conclusion that he was only able to make his important contribution to medical science because he not only had the appropriate clinical setting but also the scientific backup of the famous physiologist Leonhard Landois and his institute at the University of Greifswald, which is an excellent example of scientific progress through cooperation between a clinician and a research scientist.

  20. [Usefulness of the variable numbers of tandem repeats (VNTR) analysis for complex infections of Mycobacterium avium and Mycobacterium intracellulare].

    Science.gov (United States)

    Tsunematsu, Noriko; Goto, Mieko; Saiki, Yumiko; Baba, Michiko; Udagawa, Tadashi; Kazumi, Yuko

    2008-09-01

    The bacilli which were isolated from a patient suspected of the mixed infections with Mycobacterium avium and Mycobacterium intracellulare, were analyzed. The genotypes of M. avium in the sedimented fractions of treated sputum and in some colonies isolated from Ogawa medium were compared by the Variable Numbers of Tandem Repeats (VNTR). A woman, aged 57. Mycobacterial species isolated from some colonies by culture in 2004 and 2006 and from the treated sputum in 2006, were determined by DNA sequencing analysis of the 16S rRNA gene. Also, by using VNTR, the genotype of mycobacteria was analyzed. [Results] (1) The colony isolated from Ogawa medium in 2004 was monoclonal M. avium. (2) By VNTR analyses of specimens in 2006, multiple acid-fast bacteria were found in the sputum sediment and in isolated bacteria from Ogawa medium. (3) By analyses of 16S rRNA DNA sequence, M. avium and M. intracellulare were found in the colonies isolated from the sputum sediment and the Ogawa medium in 2006. (4) The same VNTR patterns were obtained in M. avium in 2004 and 2006 when single colony was analyzed. (5) From the showerhead and culvert of the bathroom in the patient's house, M. avium was not detected. By VNTR analyses, it was considered that the mixed infections of M. avium and M. intracellulare had been generated during treatment in this case. Therefore, in the case of suspected complex infection, VNTR analysis would be a useful genotyping method in M. avium complex infection.

  1. Assessment of repeatability of composition of perfumed waters by high-performance liquid chromatography combined with numerical data analysis based on cluster analysis (HPLC UV/VIS - CA).

    Science.gov (United States)

    Ruzik, L; Obarski, N; Papierz, A; Mojski, M

    2015-06-01

    High-performance liquid chromatography (HPLC) with UV/VIS spectrophotometric detection combined with the chemometric method of cluster analysis (CA) was used for the assessment of repeatability of composition of nine types of perfumed waters. In addition, the chromatographic method of separating components of the perfume waters under analysis was subjected to an optimization procedure. The chromatograms thus obtained were used as sources of data for the chemometric method of cluster analysis (CA). The result was a classification of a set comprising 39 perfumed water samples with a similar composition at a specified level of probability (level of agglomeration). A comparison of the classification with the manufacturer's declarations reveals a good degree of consistency and demonstrates similarity between samples in different classes. A combination of the chromatographic method with cluster analysis (HPLC UV/VIS - CA) makes it possible to quickly assess the repeatability of composition of perfumed waters at selected levels of probability. © 2014 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

  2. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

    Directory of Open Access Journals (Sweden)

    Perumal Sampath

    Full Text Available Miniature inverted-repeat transposable elements (MITEs are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5 were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1 were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.

  3. Genetic diversity analysis of cyanogenic potential (CNp) of root among improved genotypes of cassava using simple sequence repeat markers.

    Science.gov (United States)

    Moyib, O K; Mkumbira, J; Odunola, O A; Dixon, A G

    2012-12-01

    Cyanogenic potential (CNp) of cassava constitutes a serious problem for over 500 million people who rely on the crop as their main source of calories. Genetic diversity is a key to successful crop improvement for breeding new improved variability for target traits. Forty-three improved genotypes of cassava developed by International Institute of Tropical Agriculture (ITA), Ibadan, were characterized for CNp trait using 35 Simple Sequence.Repeat (SSR) markers. Essential colorimetry picric test was used for evaluation of CNp on a color scale of 1 to 14. The CNp scores obtained ranged from 3 to 9, with a mean score of 5.48 (+/- 0.09) based on Statistical Analysis System (SAS) package. TMS M98/ 0068 (4.0 +/- 0.25) was identified as the best genotype with low CNp while TMS M98/0028 (7.75 +/- 0.25) was the worst. The 43 genotypes were assigned into 7 phenotypic groups based on rank-sum analysis in SAS. Dissimilarity analysis representatives for windows generated a phylogenetic tree with 5 clusters which represented hybridizing groups. Each of the clusters (except 4) contained low CNp genotypes that could be used for improving the high CNp genotypes in the same or near cluster. The scatter plot of the genotypes showed that there was little or no demarcation for phenotypic CNp groupings in the molecular groupings. The result of this study demonstrated that SSR markers are powerful tools for the assessment of genetic variability, and proper identification and selection of parents for genetic improvement of low CNp trait among the IITA cassava collection.

  4. Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan

    Directory of Open Access Journals (Sweden)

    Zhang Jinyong

    2011-09-01

    Full Text Available Abstract Background H. pylori (Helicobacter pylori is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

  5. Population data of 19 autosomal STR loci in the Li population from Hainan Province in southernmost China.

    Science.gov (United States)

    Fan, Haoliang; Wang, Xiao; Ren, Zheng; He, Guanglin; Long, Ren; Liang, Anwen; Song, Tao; Deng, Jianqiang

    2018-03-20

    In the present study, population data of 19 autosomal STR loci included in the Goldeneye™ DNA ID System 20A in 653 Li individuals was obtained and population genetic relationships among 13 populations were investigated. MDS and phylogenetic analysis suggested that the Hainan Li population kept a close genetic relationship with the Chinese Han populations, especially for Southern Han populations (Guangdong Han, Sichuan Han, and Hunan Han). Our results indicated that the 19 autosomal STRs are highly discriminative and polymorphic in the Hainan Li population suitable for personal forensic identification and paternity testing.

  6. Analysis of genetic relationships and identification of lily cultivars based on inter-simple sequence repeat markers.

    Science.gov (United States)

    Cui, G F; Wu, L F; Wang, X N; Jia, W J; Duan, Q; Ma, L L; Jiang, Y L; Wang, J H

    2014-07-29

    Inter-simple sequence repeat (ISSR) markers were used to discriminate 62 lily cultivars of 5 hybrid series. Eight ISSR primers generated 104 bands in total, which all showed 100% polymorphism, and an average of 13 bands were amplified by each primer. Two software packages, POPGENE 1.32 and NTSYSpc 2.1, were used to analyze the data matrix. Our results showed that the observed number of alleles (NA), effective number of alleles (NE), Nei's genetic diversity (H), and Shannon's information index (I) were 1.9630, 1.4179, 0.2606, and 0.4080, respectively. The highest genetic similarity (0.9601) was observed between the Oriental x Trumpet and Oriental lilies, which indicated that the two hybrids had a close genetic relationship. An unweighted pair-group method with arithmetic means dendrogram showed that the 62 lily cultivars clustered into two discrete groups. The first group included the Oriental and OT cultivars, while the Asiatic, LA, and Longiflorum lilies were placed in the second cluster. The distribution of individuals in the principal component analysis was consistent with the clustering of the dendrogram. Fingerprints of all lily cultivars built from 8 primers could be separated completely. This study confirmed the effect and efficiency of ISSR identification in lily cultivars.

  7. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

    Science.gov (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

    2016-08-05

    Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

  8. Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013.

    Science.gov (United States)

    Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun

    2017-05-02

    Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

  9. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  10. Repeat syphilis has a different immune response compared with initial syphilis: an analysis of biomarker kinetics in two cohorts.

    Science.gov (United States)

    Kenyon, Chris; Tsoumanis, Achilleas; Osbak, Kara; Van Esbroeck, Marjan; Florence, Eric; Crucitti, Tania; Kestens, Luc

    2017-10-11

    We aimed to asses if there are differences in the clinical presentation and immune response of repeat as compared with initial syphilis. Prospective study: we prospectively recruited all patients with a new diagnosis of syphilis and tested their plasma for a range of cytochemokines and rapid plasma reagin (RPR) at baseline pretreatment and 6 months following therapy. Retrospective study: we compared RPR assay response kinetics between initial and repeat syphilis in persons attending our HIV/STI clinic from 1993 to 2016. Prospective study: a total of 91 individuals, 36 with initial syphilis and 55 with repeat syphilis, were included in the study. At baseline visit, those with initial syphilis were more likely to be symptomatic and have higher levels of interleukin-10 than repeaters. At baseline, median RPR titres were higher in the repeat than the initial infection groups. Repeaters were less likely than those with initial infections to serorevert to a negative RPR and be serofast (<4-fold RPR titre decline) at 6 months.Retrospective study: syphilis was diagnosed in 1027/43 870 individuals tested. At diagnosis, repeaters had higher RPR titres and a stepwise increase in RPR titre with number of syphilis episodes. They had a different RPR test response kinetic: they were less likely to be serofast and to serorevert than initial syphilis at 6 and 12 months. No individuals with four or more previous episodes of syphilis seroreverted. Repeat syphilis has a different clinical presentation and immunological response to initial infection. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  11. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

    Science.gov (United States)

    Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin

    2014-05-01

    Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Analysis of tandem repeat units of the promoter of capsanthin/capsorubin synthase (Ccs) gene in pepper fruit.

    Science.gov (United States)

    Tian, Shi-Lin; Li, Zheng; Li, Li; Shah, S N M; Gong, Zhen-Hui

    2017-07-01

    Capsanthin/capsorubin synthase ( Ccs ) gene is a key gene that regulates the synthesis of capsanthin and the development of red coloration in pepper fruits. There are three tandem repeat units in the promoter region of Ccs , but the potential effects of the number of repetitive units on the transcriptional regulation of Ccs has been unclear. In the present study, expression vectors carrying different numbers of repeat units of the Ccs promoter were constructed, and the transient expression of the β-glucuronidase ( GUS ) gene was used to detect differences in expression levels associated with the promoter fragments. These repeat fragments and the plant expression vector PBI121 containing the 35s CaMV promoter were ligated to form recombinant vectors that were transfected into Agrobacterium tumefaciens GV3101. A fluorescence spectrophotometer was used to analyze the expression associated with the various repeat units. It was concluded that the constructs containing at least one repeat were associated with GUS expression, though they did not differ from one another. This repeating unit likely plays a role in transcription and regulation of Ccs expression.

  13. Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

    DEFF Research Database (Denmark)

    Litrup, E.; Christensen, H.; Nordentoft, Steen

    2010-01-01

    To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients. A total...

  14. Pilot study for early prognosis of Azoospermia in relation to Y-STR ...

    African Journals Online (AJOL)

    Ahmed M. Refaat

    2015-07-06

    Jul 6, 2015 ... Azoospermia condition, which supports the idea of using Y-STR Profiling in early prognosis of ... feedback loop is interrupted (lack of feedback inhibition on. FSH). ..... From the statistical results represented in Tables 1–12, we.

  15. Repeatability of quantitative 18F-FLT uptake measurements in solid tumors: an individual patient data multi-center meta-analysis.

    Science.gov (United States)

    Kramer, G M; Liu, Y; de Langen, A J; Jansma, E P; Trigonis, I; Asselin, M-C; Jackson, A; Kenny, L; Aboagye, E O; Hoekstra, O S; Boellaard, R

    2018-06-01

    3'-deoxy-3'-[ 18 F]fluorothymidine ( 18 F-FLT) positron emission tomography (PET) provides a non-invasive method to assess cellular proliferation and response to antitumor therapy. Quantitative 18 F-FLT uptake metrics are being used for evaluation of proliferative response in investigational setting, however multi-center repeatability needs to be established. The aim of this study was to determine the repeatability of 18 F-FLT tumor uptake metrics by re-analyzing individual patient data from previously published reports using the same tumor segmentation method and repeatability metrics across cohorts. A systematic search in PubMed, EMBASE.com and the Cochrane Library from inception-October 2016 yielded five 18 F-FLT repeatability cohorts in solid tumors. 18 F-FLT avid lesions were delineated using a 50% isocontour adapted for local background on test and retest scans. SUV max , SUV mean , SUV peak , proliferative volume and total lesion uptake (TLU) were calculated. Repeatability was assessed using the repeatability coefficient (RC = 1.96 × SD of test-retest differences), linear regression analysis, and the intra-class correlation coefficient (ICC). The impact of different lesion selection criteria was also evaluated. Images from four cohorts containing 30 patients with 52 lesions were obtained and analyzed (ten in breast cancer, nine in head and neck squamous cell carcinoma, and 33 in non-small cell lung cancer patients). A good correlation was found between test-retest data for all 18 F-FLT uptake metrics (R 2  ≥ 0.93; ICC ≥ 0.96). Best repeatability was found for SUV peak (RC: 23.1%), without significant differences in RC between different SUV metrics. Repeatability of proliferative volume (RC: 36.0%) and TLU (RC: 36.4%) was worse than SUV. Lesion selection methods based on SUV max  ≥ 4.0 improved the repeatability of volumetric metrics (RC: 26-28%), but did not affect the repeatability of SUV metrics. In multi-center studies

  16. Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

    Directory of Open Access Journals (Sweden)

    Benner Steven A

    2005-03-01

    Full Text Available Abstract Background Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs. Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting because they may represent recent adaptive events, or potential future adaptive opportunities within the human lineage. Sequence analysis tools are needed, however, to decide whether these interpretations are likely, whether a particular set of LCRs represents nearly neutral drift creating junk DNA, or whether the appearance of LCRs reflects assembly error. Here we investigate an LCR family containing the sulfotransferase (SULT 1A genes involved in drug metabolism, cancer, hormone regulation, and neurotransmitter biology as a first step for defining the problems that those tools must manage. Results Sequence analysis here identified a fourth sulfotransferase gene, which may be transcriptionally active, located on human chromosome 16. Four regions of genomic sequence containing the four human SULT1A paralogs defined a new LCR family. The stem hominoid SULT1A progenitor locus was identified by comparative genomics involving complete human and rodent genomes, and a draft chimpanzee genome. SULT1A expansion in hominoid genomes was followed by positive selection acting on specific protein sites. This episode of adaptive evolution appears to be responsible for the dopamine sulfonation function of some SULT enzymes. Each of the conclusions that this bioinformatic analysis generated using data that has uncertain reliability (such as that from the chimpanzee genome sequencing project has been confirmed experimentally or by a "finished" chromosome 16 assembly, both of which were published after the submission of this manuscript. Conclusion SULT1A genes expanded from one to four copies in hominoids during intra-chromosomal LCR duplications, including (apparently one after the divergence of chimpanzees and humans. Thus, LCRs may

  17. Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

    Science.gov (United States)

    Ma, S J; Sa, K J; Hong, T K; Lee, J K

    2017-09-21

    In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

  18. [Association of aggressive behaviors of schizophrenia with short tandem repeats loci].

    Science.gov (United States)

    Yang, Chun; Ba, Huajie; Tan, Xingqi; Zhao, Hanqing; Zhang, Shuyou; Yu, Haiying

    2017-12-10

    To assess the association of short tandem repeats (STRs) loci with aggressive behaviors of schizophrenia. Blood samples from 123 schizophrenic patients with aggressive behaviors and 489 schizophrenic patients without aggressive behaviors were collected. DNA from all samples was amplified with a PowerPlex 21 system and separated by electrophoresis to determine the genotypes and allelic frequencies of 20 STR loci including D3S1368, D1S1656, D6S1043, D13S317, Penta E, D16S639, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, and FGA. All of the 20 STR loci have reached Hardy-Weinberg equilibrium in both groups. A significant difference was found in allelic and genotypic frequencies of loci Penta D between the two groups (alleles: P=0.042; genotypes: P=0.014) but not for the remaining 19 loci (P> 0.05). Univariate analysis also showed a significant difference for allele 10 and genotypes 10-12 of Penta D between the two groups (P=0.0027, P=0.0001), with the OR being 1.81 (95%CI: 1.22-2.67) and 4.33 (95%CI: 1.95-9.59), respectively. Penta D may be associated with aggressive behaviors of schizophrenia. Allele 10 and genotypes 10-12 of Penta D may confer a risk for the disease.

  19. Repeat prenatal corticosteroid prior to preterm birth: a systematic review and individual participant data meta-analysis for the PRECISE study group (prenatal repeat corticosteroid international IPD study group: assessing the effects using the best level of evidence - study protocol

    Directory of Open Access Journals (Sweden)

    Crowther Caroline A

    2012-02-01

    Full Text Available Abstract Background The aim of this individual participant data (IPD meta-analysis is to assess whether the effects of repeat prenatal corticosteroid treatment given to women at risk of preterm birth to benefit their babies are modified in a clinically meaningful way by factors related to the women or the trial protocol. Methods/Design The Prenatal Repeat Corticosteroid International IPD Study Group: assessing the effects using the best level of Evidence (PRECISE Group will conduct an IPD meta-analysis. The PRECISE International Collaborative Group was formed in 2010 and data collection commenced in 2011. Eleven trials with up to 5,000 women and 6,000 infants are eligible for the PRECISE IPD meta-analysis. The primary study outcomes for the infants will be serious neonatal outcome (defined by the PRECISE International IPD Study Group as one of death (foetal, neonatal or infant; severe respiratory disease; severe intraventricular haemorrhage (grade 3 and 4; chronic lung disease; necrotising enterocolitis; serious retinopathy of prematurity; and cystic periventricular leukomalacia; use of respiratory support (defined as mechanical ventilation or continuous positive airways pressure or other respiratory support; and birth weight (Z-scores. For the children, the primary study outcomes will be death or any neurological disability (however defined by trialists at childhood follow up and may include developmental delay or intellectual impairment (developmental quotient or intelligence quotient more than one standard deviation below the mean, cerebral palsy (abnormality of tone with motor dysfunction, blindness (for example, corrected visual acuity worse than 6/60 in the better eye or deafness (for example, hearing loss requiring amplification or worse. For the women, the primary outcome will be maternal sepsis (defined as chorioamnionitis; pyrexia after trial entry requiring the use of antibiotics; puerperal sepsis; intrapartum fever requiring the use

  20. Social instigation and repeated aggressive confrontations in male Swiss mice: analysis of plasma corticosterone, CRF and BDNF levels in limbic brain areas

    Directory of Open Access Journals (Sweden)

    Paula Madeira Fortes

    2017-06-01

    Full Text Available Abstract Introduction: Agonistic behaviors help to ensure survival, provide advantage in competition, and communicate social status. The resident-intruder paradigm, an animal model based on male intraspecific confrontations, can be an ethologically relevant tool to investigate the neurobiology of aggressive behavior. Objectives: To examine behavioral and neurobiological mechanisms of aggressive behavior in male Swiss mice exposed to repeated confrontations in the resident intruder paradigm. Methods: Behavioral analysis was performed in association with measurements of plasma corticosterone of mice repeatedly exposed to a potential rival nearby, but inaccessible (social instigation, or to 10 sessions of social instigation followed by direct aggressive encounters. Moreover, corticotropin-releasing factor (CRF and brain-derived neurotrophic factor (BNDF were measured in the brain of these animals. Control mice were exposed to neither social instigation nor aggressive confrontations. Results: Mice exposed to aggressive confrontations exhibited a similar pattern of species-typical aggressive and non-aggressive behaviors on the first and the last session. Moreover, in contrast to social instigation only, repeated aggressive confrontations promoted an increase in plasma corticosterone. After 10 aggressive confrontation sessions, mice presented a non-significant trend toward reducing hippocampal levels of CRF, which inversely correlated with plasma corticosterone levels. Conversely, repeated sessions of social instigation or aggressive confrontation did not alter BDNF concentrations at the prefrontal cortex and hippocampus. Conclusion: Exposure to repeated episodes of aggressive encounters did not promote habituation over time. Additionally, CRF seems to be involved in physiological responses to social stressors.

  1. Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

    Science.gov (United States)

    Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

    2011-08-01

    Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

  2. Analysis of the repeatability of the exhaust pollutants emission research results for cold and hot starts under controlled driving cycle conditions.

    Science.gov (United States)

    Jaworski, Artur; Kuszewski, Hubert; Ustrzycki, Adam; Balawender, Krzysztof; Lejda, Kazimierz; Woś, Paweł

    2018-04-20

    Measurement of car engines exhaust pollutants emissions is very important because of their harmful effects on the environment. This article presents the assessment of repeatability of the passenger car engine exhaust pollutants emission research results obtained in the conditions of a chassis dynamometer. The research was conducted in a climate chamber, enabling the temperature conditions to be determined from - 20 to + 30 °C. The emission of CO, CH 4 , CO 2 , NO X , THC, and NMHC was subjected to the analysis. The aim of the research is to draw attention to the accuracy of the pollutant emission research results in driving cycles, and the comparison of pollutant emission results and their repeatability obtained in successive NEDC cycles under cold and hot start conditions. The results of the analysis show that, in the case of a small number of measurements, the results repeatability analysis is necessary for a proper interpretation of the pollutant emission results on the basis of the mean value. According to the authors' judgment, it is beneficial to determine the coefficient of variation for a more complete assessment of exhaust emission result repeatability obtained from a small number of measurements. This parameter is rarely presented by the authors of papers on exhaust components emission research.

  3. Diversity of Salmonella enterica serovar Typhi strains collected from india using variable number tandem repeat (VNTR)-PCR analysis.

    Science.gov (United States)

    Sankar, Sathish; Kuppanan, Suresh; Nandagopal, Balaji; Sridharan, Gopalan

    2013-08-01

    Typhoid fever is endemic in India, and a seasonal increase of cases is observed annually. In spite of effective therapies and the availability of vaccines, morbidity is widespread owing to the circulation of multiple genetic variants, frequent migration of asymptomatic carriers, unhygienic food practices and the emergence of multidrug resistance and thus continues to be a major public health problem in developing countries, particularly in India. Classical methods of strain typing such as pulsed-field gel electrophoresis, ribotyping, random amplification of polymorphic DNA and amplified fragment length polymorphism are either laborious and technically complicated or less discriminatory. We investigated the molecular diversity of Indian strains of Salmonella enterica serovar Typhi (S. Typhi) isolated from humans from different parts of India to establish the molecular epidemiology of the organism using the variable number tandem repeat (VNTR)-PCR analysis. The electrophoretic band pattern was analysed using the GelCompar II software program. Of the 94 strains tested for three VNTRs loci, 75 VNTR genotypes were obtained. Of the three VNTRs tested in this study, VNTR1 was amplified in all the strains except one and found to be predominant. VNTR2 was amplified only in 57 strains with a Simpson diversity index of 0.93 indicating the high variability of this region within the strains. VNTR3 was amplified in 90 strains. The discriminatory power of this typing tool has been greatly enhanced by this VNTR2 region as the other two regions could not discriminate strains significantly. In our study, about 55 % of the strains amplified all three VNTR regions and 39 % of the strains lacked the VNTR2 region. Among the three VNTR regions tested, the majority of the strains produced similar banding pattern for any two regions grouped into a cluster. The strains grouped as a genotype were from the same geographical location. Strains collected from each geographical region were also

  4. DNA typing of birch: Development of a forensic STR system for Betula pendula and Betula pubescens.

    Science.gov (United States)

    Wesselink, Monique; Dragutinović, Aleksandar; Noordhoek, Jeroen W; Bergwerff, Leonie; Kuiper, Irene

    2018-04-07

    Although botanical trace evidence is often encountered in case investigations, the utilization of such traces in forensic investigations is still limited. Development of a forensic STR system for the two species of Betula (birch) indigenous to and abundant in North West Europe is a step in enhancing the applicability of traces from these species. We describe six microsatellite markers developed for birch species in detail, including repeat structure, and we propose a nomenclature for the encountered alleles. To assess the population characteristics, the genetic composition of wild, planted and intermediate populations of Betula pendula (a diploid species) and Betula pubescens (a tetraploid species) were investigated. The genetic differences between these two species were larger than the differences between populations of one species, even when both species co-occurred at one location. Therefore allele frequencies were estimated for both species separately. General, conservative random match probabilities were estimated for wild trees based on these allele frequencies (5∙10 -6 for the diploid B. pendula and 1∙10 -13 for the tetraploid B. pubescens), illustrating the potential relevance if trace evidence secured from a suspect is found to match a birch tree growing on or near a crime scene. Apart from wild trees, planted Betula trees also occur that may not originate from seeds, but may have been propagated through cloning. Based on the studied Betula trees, the random match probability of a potentially planted profile might be as high as 1.4∙10 -2 . Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Probabilistic peak detection in CE-LIF for STR DNA typing.

    Science.gov (United States)

    Woldegebriel, Michael; van Asten, Arian; Kloosterman, Ate; Vivó-Truyols, Gabriel

    2017-07-01

    In this work, we present a novel probabilistic peak detection algorithm based on a Bayesian framework for forensic DNA analysis. The proposed method aims at an exhaustive use of raw electropherogram data from a laser-induced fluorescence multi-CE system. As the raw data are informative up to a single data point, the conventional threshold-based approaches discard relevant forensic information early in the data analysis pipeline. Our proposed method assigns a posterior probability reflecting the data point's relevance with respect to peak detection criteria. Peaks of low intensity generated from a truly existing allele can thus constitute evidential value instead of fully discarding them and contemplating a potential allele drop-out. This way of working utilizes the information available within each individual data point and thus avoids making early (binary) decisions on the data analysis that can lead to error propagation. The proposed method was tested and compared to the application of a set threshold as is current practice in forensic STR DNA profiling. The new method was found to yield a significant improvement in the number of alleles identified, regardless of the peak heights and deviation from Gaussian shape. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Boston Type 1 Keratoprosthesis versus Repeat Donor Keratoplasty for Corneal Graft Failure: A Systematic Review and Meta-analysis.

    Science.gov (United States)

    Ahmad, Sumayya; Mathews, Priya M; Lindsley, Kristina; Alkharashi, Majed; Hwang, Frank S; Ng, Sueko M; Aldave, Anthony J; Akpek, Esen Karamursel

    2016-01-01

    To compare repeat penetrating keratoplasty (PK) with Boston type I keratoprosthesis (KPro) implantation for full-thickness donor corneal graft failure. Previous donor graft failure is a common indication for both PK and KPro implantation. Selection of the surgical procedure is entirely dependent on the surgeon because there are no studies available for guidance. Therefore, a systematic review was undertaken to examine vision, device retention, graft clarity, and postoperative glaucoma and infection outcomes after repeat PK versus KPro implantation. Articles with data regarding repeat PK published between 1990 and 2014 were identified in PubMed, EMBASE, the Latin American and Caribbean Health Sciences Literature Database, and the Cochrane Central Register of Controlled Trials and were reviewed. Results were compared with a retrospective review of consecutive, nonrandomized, longitudinal case series of KPro implantations performed at 5 tertiary care centers in the United States. Visual acuity at 2 years was the primary outcome measure. The proportion of clear grafts in the repeat PK group, device retention in the KPro group, and the development of postoperative glaucoma and infection were secondary outcome measures. The search strategy identified 17 128 articles in the PK analysis. After screening, 26 studies (21 case series and 5 cohort studies) were included in the review. Pooled analysis of the 26 unique studies demonstrated a 42% (95% confidence interval [CI], 30%-56%) likelihood of maintaining 20/200 or better at 2 years after repeat PK, compared with an 80% (95% CI, 68%-88%) probability with KPro implantation. The probability of maintaining a clear graft at 5 years was 47% (95% CI, 40%-54%) after repeat PK, whereas the probability of retention of the KPro at 5 years was 75% (95% CI, 64%-84%). The rate of progression of glaucoma at 3 years was 25% (95% CI, 10%-44%) after repeat PK and 30% in the KPro cohort. These results demonstrate favorable outcomes of KPro

  7. Elective repeat cesarean delivery compared with trial of labor after a prior cesarean delivery: a propensity score analysis

    NARCIS (Netherlands)

    Kok, N.; Ruiter, L.; Lindeboom, R.; de Groot, C.; Pajkrt, E.; Mol, B. W.; Kazemier, B. M.

    2015-01-01

    To determine neonatal and short term maternal outcomes according to intentional mode of delivery following a cesarean delivery (CD). Women pregnant after CD between January 2000 and December 2007 were categorized according to whether they had an elective repeat CD (ERCD) or a Trial of Labor (TOL).

  8. The method of purging applied to repeated cross-sectional data: Practical applications using logistic and linear regression analysis

    NARCIS (Netherlands)

    Grotenhuis, H.F. te; Eisinga, R.N.; Scheepers, P.L.H.

    2004-01-01

    In cross-sectional survey research, it is quite common to estimate the(standardized) effect of independent variable(s) on a dependent variable. However, if repeated cross-sectional data are available, much is to be gained if the consequences of these effects on longitudinal social change are

  9. Structure-Function Analysis of Cf-9, a Receptor-Like Protein with Extracytoplasmic Leucine-Rich Repeats

    NARCIS (Netherlands)

    Hoorn, van der R.A.L.; Wulff, B.B.H.; Rivas, S.; Durrant, M.C.; Ploeg, van der A.; Wit, de P.J.G.M.; Jones, J.D.G.

    2005-01-01

    The tomato (Lycopersicon pimpinellifolium) resistance protein Cf-9 belongs to a large class of plant proteins with extracytoplasmic Leu-rich repeats (eLRRs). eLRR proteins play key roles in plant defense and development, mainly as receptor-like proteins or receptor-like kinases, conferring

  10. Analysis of Dextromethorphan and Dextrorphan in Skeletal Remains Following Differential Microclimate Exposure: Comparison of Acute vs. Repeated Drug Exposure.

    Science.gov (United States)

    Morrison, Lucas M; Unger, Kirk A; Watterson, James H

    2017-07-01

    Analysis of dextromethorphan (DXM) and its metabolite dextrorphan (DXT) in skeletal remains of rats following acute (ACU, 75 mg/kg, IP, n = 10) or three repeated (REP, 25 mg/kg, IP, n = 10, 40-min interval) doses of DXM is described. Following dosing and euthanasia, rats decomposed outdoors to skeleton in two different microclimate environments (n = 5 ACU and n = 5 REP at each site): Site A (shaded forest microenvironment) and Site B (rocky substrate exposed to direct sunlight, 600 m from Site A). Two drug-free rats at each site served as negative controls. Skeletal elements (vertebrae, ribs, pelvic girdles, femora, tibiae, skulls and scapulae) were recovered, pulverized and underwent methanolic microwave assisted extraction (MAE). Extracts were analyzed by GC-MS following clean-up by solid-phase extraction (SPE). Drug levels, expressed as mass-normalized response ratios and the ratios of DXT and DXM levels (RRDXT/RRDXM) were compared between drug exposures, microclimate sites, and across skeletal elements. DXM levels differed significantly (P < 0.05) between corresponding bone elements across exposure groups (5/7-site A; 4/7-site B), but no significant differences in DXT levels were observed between corresponding elements. RRDXT/RRDXM differed significantly (P < 0.05) between corresponding bone elements across exposure groups (6/7-site A; 5/7-site B). No significant differences were observed in levels of DXM, DXT or RRDXT/RRDXM between corresponding elements from either group between sites. When data from all bone elements was pooled, levels of DXM and RRDXT/RRDXM differed significantly between exposure groups at each site, while those of DXT did not. For both exposure groups, comparison of pooled data between sites showed no significant differences in levels of DXM, DXT or RRDXT/RRDXM. Different decomposition microclimates did not impede the discrimination of DXM exposure patterns from the analyses of DXM, DXT and RRDXT/RRDXM in bone samples. © The Author 2017

  11. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    Science.gov (United States)

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. 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.

  13. Population data and phylogenetic structure of Han population from Jiangsu province of China on GlobalFiler STR loci.

    Science.gov (United States)

    Adnan, Atif; Zhan, Xiaoni; Kasim, Kadirya; Rakha, Allah; Xin, Xing Jia

    2018-03-02

    Forensic statistical parameters based on allelic frequencies of commonly used short tandem repeats were estimated for the Han population of Jiangsu province from P.R. China. The 6-dye GlobalFiler™ PCR amplification kit incorporates 21 autosomal STRs, providing reliable DNA typing results with enhanced the power of discrimination. Here, we analyzed the GlobalFiler™ STR loci in 516 unrelated individuals from Jiangsu Han population. A total of 256 alleles were observed ranging between 5 and 35.2 repeat units, and SE33 showed the greatest power of discrimination (34 alleles) in Jiangsu Han population. Most of the loci were found to be in the Hardy-Weinberg equilibrium after the Bonferroni correction with the exception of D3S1358. The combined power of exclusion (CPE) was 0.999999996353609, and the combined match probability (CMP) was 3.64 × 10 -25 . Phylogenetic parameters including pairwise genetic distances showed that Han population living in Jiangsu had closest genetic relationship with other East Asian populations. The present study provides precise reference database for forensic applications and population genetic studies.

  14. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Legionella pneumophila and Development of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿

    Science.gov (United States)

    Pourcel, Christine; Visca, Paolo; Afshar, Baharak; D'Arezzo, Silvia; Vergnaud, Gilles; Fry, Norman K.

    2007-01-01

    The utility of a genotypic typing assay for Legionella pneumophila was investigated. A multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) scheme using PCR and agarose gel electrophoresis is proposed based on eight minisatellite markers. Panels of well-characterized strains were examined in a multicenter analysis to validate the assay and to compare its performance to that of other genotyping assays. Excellent typeability, reproducibility, stability, and epidemiological concordance were observed. The MLVA type or profile is composed of a string of allele numbers, corresponding to the number of repeats at each VNTR locus, separated by commas, in a predetermined order. A database containing information from 99 L. pneumophila serogroup 1 strains and four strains of other serogroups and their MLVA profiles, which can be queried online, is available from http://bacterial-genotyping.igmors.u-psud.fr/. PMID:17251393

  15. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.

    Directory of Open Access Journals (Sweden)

    Andrew J Alverson

    2011-01-01

    Full Text Available The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean, and show that despite its unexceptional size (401,262 nt, the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38-297 nt repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

  16. Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method

    OpenAIRE

    Vergnaud Gilles; Moissenet Didier; Corvol Harriet; Fauroux Brigitte; Corbineau Gaëlle; Hormigos Katia; Vu-Thien Hoang; Pourcel Christine

    2010-01-01

    Abstract Background Staphylococcus aureus infection in patients with cystic fibrosis (CF) is frequent and may be due to colonization by a few pathogenic lineages. Systematic genotyping of all isolates, methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) is necessary to identify such lineages and follow their evolution in patients. Multiple-locus variable-number tandem repeat analysis (MLVA/VNTR) was used to survey S. aureus clinical isolates in a French ...

  17. Film repeats in radiology department

    International Nuclear Information System (INIS)

    Suwan, A. Z.; Al-Shakharah, A. I

    1997-01-01

    During a one year period, 4910 radiographs of 55780 films were repeated. The objective of our study was to analyse and to classify the causes in order to minimize the repeats, cut the expenses and to provide optimal radiographs for accurate diagnosis. Analysis of the different factors revealed that, 43.6% of film repeats in our service were due to faults in exposure factors, centering comprises 15.9% of the repeats, while too much collimation was responsible for 7.6% of these repeats. All of which can be decreased by awareness and programmed training of technicians. Film blurring caused by patient motion was also responsible for 4.9% for radiographs reexamination, which can be minimized by detailed explanation to the patient and providing the necessary privacy. Fogging of X-Ray films by improper storage or inadequate handling or processing faults were responsible for 14.5% in repeats in our study. Methods and criteria for proper storage and handling of films were discussed. Recommendation for using modern day-light and laser processor has been high lighted. Artefacts are noticeably high in our cases, due to spinal dresses and frequent usage of precious metals for c osmotic purposes in this part of the world. The repeated films comprise 8.8% of all films We conclude that, the main factor responsible for repeats of up to 81.6% of cases was the technologists, thus emphasizing the importance of adequate training of the technologists. (authors). 15 refs., 9 figs., 1 table

  18. Determination of combined sibship indices "gray zone" using 15 STR loci for central Bosnian human population.

    Science.gov (United States)

    Musanovic, Jasmin; Filipovska-Musanovic, Marijana; Kovacevic, Lejla; Buljugic, Dzenisa; Dzehverovic, Mirela; Avdic, Jasna; Marjanovic, Damir

    2012-05-01

    In our previous population studies of Bosnia and Herzegovina human population, we have used autosomal STR, Y-STR, and X-STR loci, as well as Y-chromosome NRY biallelic markers. All obtained results were included in Bosnian referent database. In order of future development of applied population molecular genetics researches of Bosnia and Herzegovina human population, we have examined the effectiveness of 15 STR loci system in determination of sibship by using 15 STR loci and calculating different cut-off points of combined sibship indices (CSI) and distribution of sharing alleles. From the perspective of its application, it is very difficult and complicated to establish strict CSI cut-off values for determination of the doubtless sibship. High statistically significant difference between the means of CSI values and in distribution of alleles sharing in siblings and non-siblings was noticed (P < 0.0001). After constructing the "gray zone", only one false positive result was found in three CSI cut-off levels with the highest percent of determined sibship/non-sibship at the CSI = 0.067, confirming its practical benefit. Concerning the distribution of sharing alleles, it is recommended as an informative estimator for its usage within Bosnia and Herzegovina human population.

  19. 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

    -going in the area at Strømfjordshavn. The C14 datings of marine shells collected on the marine clay terraces at level 300kPa. Clay minerals were weathered causing moderate to high activity and plasticity despite the formation age of only 7000 years. (b) The "River Bank Erosion Cut" 2 km east of the Airport Terminal...... level with Upper Marine Limit (UML) varying from +120 to +140m at the West Coast to +40 at Kangerlussuaq. This retreat is well documented through C14-dating in the local area near to Kangerlussuaq Airport related to Fjord Stages F2 (+60m/8300 y BC) and F3 (+40m/8100 y BC) and Mt. Keglen stage (+40m/7200....... We studied a frozen marine clay deposit at +35 m with stratified ice layers under sandy gravel top layer. During laboratory analysis using fall cone testing a thawed clay sample was found to be quick (St>700) due to dilution of pore water salts. Multidisciplinary approach was necessary for this study....

  20. Genetic diversity of 21 autosomal STR loci in the Han population from Sichuan province, Southwest China.

    Science.gov (United States)

    He, Guanglin; Li, Ye; Wang, Zheng; Liang, Weibo; Luo, Haibo; Liao, Miao; Zhang, Ji; Yan, Jing; Li, Yingbi; Hou, Yiping; Wu, Jin

    2017-11-01

    Exploration of the ethnic origin and genetic differentiation of 56 Chinese officially recognized nationalities populations played a fundamental role in the research field of population genetics, forensic science, linguistics, anthropology, and archaeology. In the present study, population data of 21 autosomal STR loci (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D2S441, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, Penta D, Penta E, TH01, TPOX, and vWA) included in the AGCU EX22 kit in 2793 Southwest Han Chinese individuals was obtained and population genetic relationships among 28 Chinese populations were investigated. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Sichuan Han population and can be used as a powerful tool in the routine forensic usage. MDS and phylogenetic analysis suggested that the Sichuan Han population kept a close genetic relationship with the southwest populations. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  2. At what price? A cost-effectiveness analysis comparing trial of labour after previous Caesarean versus elective repeat Caesarean delivery.

    LENUS (Irish Health Repository)

    Fawsitt, Christopher G

    2013-01-01

    Elective repeat caesarean delivery (ERCD) rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland.

  3. Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs

    Directory of Open Access Journals (Sweden)

    Halling Shirley M

    2003-07-01

    Full Text Available Abstract Background Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. Results An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. Conclusion This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among

  4. Economic analysis of human papillomavirus triage, repeat cytology, and immediate colposcopy in management of women with minor cytological abnormalities in Sweden.

    Science.gov (United States)

    Ostensson, Ellinor; Fröberg, Maria; Hjerpe, Anders; Zethraeus, Niklas; Andersson, Sonia

    2010-10-01

    To assess the cost-effectiveness of using human papillomavirus testing (HPV triage) in the management of women with minor cytological abnormalities in Sweden. An economic analysis based on a clinical trial, complemented with data from published meta-analyses on accuracy of HPV triage. The study takes perspective of the Swedish healthcare system. The Swedish population-based cervical cancer screening program. A decision analytic model was constructed to evaluate cost-effectiveness of HPV triage compared to repeat cytology and immediate colposcopy with biopsy, stratifying by index cytology (ASCUS = atypical squamous cells of undetermined significance, and LSIL = low-grade squamous intraepithelial lesion) and age (23-60 years, cytological abnormalities. Today, immediate colposcopy with biopsy is a cost-effective alternative compared to HPV triage and repeat cytology.

  5. The application of mathematical transformation in order to define edges of pluton Valja Strž

    Directory of Open Access Journals (Sweden)

    Ignjatović Snežana M.

    2014-01-01

    Full Text Available The Timok Magmatic Complex (TMC belongs to the East Serbian and is the largest volcanic area in our country. The largest pluton in this area is Valja Strž. This pluton is situated in the northwestern part of the complex. Applying different methods of mathematical transformation on aeromagnetic data facilitated outlining of pluton edges in subsurface of surrounding rocks. In this paper we used mathematical transformation on anomaly values of the magnetic field, obtained from processing of aeromagnetic data. In order to detect the edges of pluton Valja Strž we used following set of mathematical transformation: first vertical derivative, the total horizontal derivative, tilt derivative, upward continuation, and combination of upward continuation and tilt derivative. Results of application of mathematical transformation showed that outspread of the pluton Valja Strž in the subsurface is larger than its extend on the surface.

  6. Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics

    Directory of Open Access Journals (Sweden)

    Janet M. Doolittle-Hall

    2015-11-01

    Full Text Available Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV, hepatitis B virus (HBV or Merkel cell polyomavirus (MCPyV. These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures.

  7. Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junin arenavirus envelope glycoprotein

    International Nuclear Information System (INIS)

    York, Joanne; Agnihothram, Sudhakar S.; Romanowski, Victor; Nunberg, Jack H.

    2005-01-01

    The G2 fusion subunit of the Junin virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins, four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell-cell fusion. Taken together, our results indicate that α-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever

  8. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  9. Grasshoppers (Orthoptera: Caelifera and crickets (Orthoptera: Ensifera from slopes of Macošská stráň and Vilémovická stráň (Moravský kras Protected landscape area, Czech Republic

    Directory of Open Access Journals (Sweden)

    Jana Niedobová

    2011-01-01

    Full Text Available In 2008 we found 21 species of grasshoppers and crickets on Macošská stráň slope and 18 species on Vilémovická stráň slope. Both slopes are located in the northern part of the Moravský kras Protected landscape area and have xerothermic character. Both slopes are influenced by pasture management. For the most comprehensive picture of Orthoptera we used a standard method (sweeping of vegetation and nonstandard methods (pitfall traps and Möricke yellow cups. Termophilous species of Orthoptera on Macošská stráň (47% were dominating. On Vilémovická stráň mezophilous species (46% were dominating. The most common species were Stenobothrus lineatus (Panzer, 1796 on Macošská stráň slope and Chorthippus parallelus (Zetterstedt, 1821, Stenobothrus lineatus, Chorthippus bigutulus (Linné, 1758 and Chorthippus dorsatus (Zetterstedt, 1821 on Vilémovická stráň slope. Rare species of this assemblage were Stenobothrus nigromaculatus (Herrich-Schaffer, 1840 which was on Macošská stráň slope only and Tetrix bipunctata (Linnaeus, 1758 which has much bigger abundances also on Macošská stráň slope.

  10. 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

    /child pairs were analyzed. Significant differences were observed between the distribution of fragments ('alleles'), whereby allele number 7 was considerably more frequent in Eskimos (0.687) than in Danes (0.201). The distributions of HUMTH01 phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo...

  11. Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China).

    Science.gov (United States)

    Zhang, Yu-Dang; Shen, Chun-Mei; Meng, Hao-Tian; Guo, Yu-Xin; Dong, Qian; Yang, Guang; Yan, Jiang-Wei; Liu, Yao-Shun; Mei, Ting; Huang, Rui-Zhe; Zhu, Bo-Feng

    2016-07-01

    X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Temperatur- og tøjningsmålinger i Østrør - Limfjordstunnel

    DEFF Research Database (Denmark)

    Hansen, Lars Pilegaard

    Laboratoriet for Bærende Konstruktioner, Instituttet for Bygningsteknik, Aalborg Universitetscenter har i samarbejde med Rambøll og Hannemann A/S, Nørresundby udført temperatur- og tøjningsmålinger på en tunnelvæg i østrøret af Limfjordstunnellen.......Laboratoriet for Bærende Konstruktioner, Instituttet for Bygningsteknik, Aalborg Universitetscenter har i samarbejde med Rambøll og Hannemann A/S, Nørresundby udført temperatur- og tøjningsmålinger på en tunnelvæg i østrøret af Limfjordstunnellen....

  13. 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

  14. Repeatability of road pavement condition assessment based on three-dimensional analysis of linear accelerations of vehicles

    Science.gov (United States)

    Staniek, Marcin

    2018-05-01

    The article provides a discussion concerning a tool used for road pavement condition assessment based on signals of linear accelerations recorded with high sampling frequency for typical vehicles traversing the road network under real-life road traffic conditions. Specific relationships have been established for the sake of road pavement condition assessment, including identification of road sections of poor technical condition. The data thus acquired have been verified with regard to repeatability of estimated road pavement assessment indices. The data make it possible to describe the road network status against an area in which users of the system being developed move. What proves to be crucial in the assessment process is the scope of the data set based on multiple transfers within the road network.

  15. Development of new multilocus variable number of tandem repeat analysis (MLVA) for Listeria innocua and its application in a food processing plant.

    Science.gov (United States)

    Takahashi, Hajime; Ohshima, Chihiro; Nakagawa, Miku; Thanatsang, Krittaporn; Phraephaisarn, Chirapiphat; Chaturongkasumrit, Yuphakhun; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2014-01-01

    Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE). The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

  16. Development of new multilocus variable number of tandem repeat analysis (MLVA for Listeria innocua and its application in a food processing plant.

    Directory of Open Access Journals (Sweden)

    Hajime Takahashi

    Full Text Available Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE. The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

  17. The SCA1 (Spinocerebellar ataxia type 1 and MJD (Machado-Joseph disease CAG repeats in normal individuals: segregation analysis and allele frequencies

    Directory of Open Access Journals (Sweden)

    Cláudia Emília Vieira Wiezel

    2003-01-01

    Full Text Available Spinocerebellar ataxia type 1 (SCA1 and Machado-Joseph disease (MJD/SCA3 are autosomal dominant neurodegenerative diseases caused by expansions of a CAG trinucleotide repeat in the SCA1 and MJD genes. These expanded sequences are unstable upon transmission, leading to an intergeneration increase in the number of repeats (dynamic mutation. The transmission of the CAG repeat was studied in normal mother-father-child trios, referred for paternity testing (SCA1, n = 367; MJD, n = 879. No segregation distortion was detected. The CAG allele frequencies were determined in 330 unrelated individuals (fathers from couples tested for paternity. The allele frequency distributions did not differ from those previously reported for European populations. The estimated values for the statistic parameters indicating diversity at the SCA1 locus did not differ much from those reported previously for other STRs in the Brazilian population, while those for the MJD locus were close to or higher than the maximum values of previous reports. This shows that SCA1 and MJD are highly informative loci for applications in genetic and population studies and for forensic analysis.

  18. Repeated intravenous administration of gadobutrol does not lead to increased signal intensity on unenhanced T1-weighted images - a voxel-based whole brain analysis

    Energy Technology Data Exchange (ETDEWEB)

    Langner, Soenke; Kromrey, Marie-Luise [University Medicine Greifswald, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany); Kuehn, Jens-Peter [University Medicine Greifswald, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany); University Hospital, Carl Gustav Carus University Dresden, Institute for Radiology, Dresden (Germany); Grothe, Matthias [University Medicine Greifswald, Department of Neurology, Greifswald (Germany); Domin, Martin [University Medicine Greifswald, Functional Imaging Unit, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany)

    2017-09-15

    To identify a possible association between repeated intravenous administration of gadobutrol and increased signal intensity in the grey and white matter using voxel-based whole-brain analysis. In this retrospective single-centre study, 217 patients with a clinically isolated syndrome underwent baseline brain magnetic resonance imaging and at least one annual follow-up examination with intravenous administration of 0.1 mmol/kg body weight of gadobutrol. Using the ''Diffeomorphic Anatomical Registration using Exponentiated Lie algebra'' (DARTEL) normalisation process, tissue templates for grey matter (GM), white matter (WM), and cerebrospinal fluid (CSF) were calculated, as were GM-CSF and WM-CSF ratios. Voxel-based whole-brain analysis was used to calculate the signal intensity for each voxel in each data set. Paired t-test was applied to test differences to baseline MRI for significance. Voxel-based whole-brain analysis demonstrated no significant changes in signal intensity of grey and white matter after up to five gadobutrol administrations. There was no significant change in GM-CSF and grey WM-CSF ratios. Voxel-based whole-brain analysis did not demonstrate increased signal intensity of GM and WM on unenhanced T1-weighted images after repeated gadobutrol administration. The molecular structure of gadolinium-based contrast agent preparations may be an essential factor causing SI increase on unenhanced T1-weighted images. (orig.)

  19. Grå strækninger på det overordnede vejnet i det åbne land

    DEFF Research Database (Denmark)

    Sørensen, Michael

    2006-01-01

    udviklet konkrete metoder til udpegning, analyse og udbedring af grå strækninger. I ph.d.-afhandlingen “Grå strækninger i det åbne land – Udvikling, anvendelse og vurdering af alvorlighedsbaseret metode til udpegning, analyse og udbedring af grå strækninger” er der derfor blevet formuleres en overordnet...... filosofi for det grå strækningsarbejde samtidig med, at der med fokus på udpegning udvikles metoder til udpegning, analyse og udbedring af grå strækninger på det overordnede vejnet i det åbne land. Formålet har specifikt været at udvikle metoder, som er både uheldsteoretisk velfunderede og anvendelige i...

  20. Calibration of micro-thermal analysis for the detection of glass transition temperatures and melting points: repeatability and reproducibility

    NARCIS (Netherlands)

    Fischer, H.R.

    2008-01-01

    Micro-thermal analysis (μTATM) is a technique in which thermal analysis is performed on surfaces of test specimens on a small (ca. 2×2 μm) scale. Like any thermal analysis technique, interpretation of results benefits from accurate temperature information and knowledge of the precision of the

  1. Analysis of three variable number terminal repeat loci is sufficient to characterize the deoxyribonucleic acid fingerprints of a panel of human tumor cell lines.

    Science.gov (United States)

    Anding, Allyson L; Reiss, Tanika; Germain, Glen S

    2003-01-01

    Using primers for the MCT118, YNZ22, and COL2A1 loci in polymerase chain reaction analysis we could distinguish among the approximately 20 cell lines routinely maintained in our laboratory. We also demonstrated that the cell line NB-1691 (a neuroblastoma) and its xenograft had an identical number of repeats at two loci. Rh30 (a rhabdomyosarcoma) made resistant to rapamycin was identical to its parent line and to a subline that had reverted to sensitivity after it was cultured without rapamycin in the medium.

  2. DEVELOPMENT OF A MULTIPLE-LOCUS VARIABLE NUMBER OF TANDEM REPEAT ANALYSIS (MLVA FOR HELICOBACTER PYLORI AND ITS APPLICATION TO HELICOBACTER PYLORI ISOLATES FROM ROSTOV REGION,RUSSIA

    Directory of Open Access Journals (Sweden)

    Sorokin VM

    2012-09-01

    Full Text Available Stomach infection with Helicobacter pylori (H. pylori is the second most common infectious disease of humans. The severe pathological consequences of this infection include gastric and duodenal ulcer disease, the development of gastric mucosal atrophy, gastric carcinoma, and, more rarely, malignant tumors of the lymphoma. H. pylori infections cause very high morbidity and mortality and are of particular concern in developing countries, where H. pylori prevalences as high as 90% have been reported. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-Locus of Variable number of tandem repeat Analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori isolates in Russia. MLVA of 4 VNTR loci with high discrimination power based on 10 candidates were performed on a collection of 22 strains of H. pylori which originated from Rostov region of Russia. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made.

  3. The relationship of sugar to population-level diabetes prevalence: an econometric analysis of repeated cross-sectional data.

    Science.gov (United States)

    Basu, Sanjay; Yoffe, Paula; Hills, Nancy; Lustig, Robert H

    2013-01-01

    While experimental and observational studies suggest that sugar intake is associated with the development of type 2 diabetes, independent of its role in obesity, it is unclear whether alterations in sugar intake can account for differences in diabetes prevalence among overall populations. Using econometric models of repeated cross-sectional data on diabetes and nutritional components of food from 175 countries, we found that every 150 kcal/person/day increase in sugar availability (about one can of soda/day) was associated with increased diabetes prevalence by 1.1% (p <0.001) after testing for potential selection biases and controlling for other food types (including fibers, meats, fruits, oils, cereals), total calories, overweight and obesity, period-effects, and several socioeconomic variables such as aging, urbanization and income. No other food types yielded significant individual associations with diabetes prevalence after controlling for obesity and other confounders. The impact of sugar on diabetes was independent of sedentary behavior and alcohol use, and the effect was modified but not confounded by obesity or overweight. Duration and degree of sugar exposure correlated significantly with diabetes prevalence in a dose-dependent manner, while declines in sugar exposure correlated with significant subsequent declines in diabetes rates independently of other socioeconomic, dietary and obesity prevalence changes. Differences in sugar availability statistically explain variations in diabetes prevalence rates at a population level that are not explained by physical activity, overweight or obesity.

  4. Development of systematic evaluation method on nonlinear behavior of the constructions using repeated finite element method analysis

    International Nuclear Information System (INIS)

    Kasahara, Naoto

    1997-01-01

    Supposing that the nuclear reactor stops on any reason, the temperature of flown out coolant from the reactor core will decrease and the temperature of elements touched with the coolant in the nuclear plant equipments also decreases on response to this. On the other hand, temperature pursuit at non-touched portions is delayed to form a thermal stress due to their temperature difference. In particular, a stress over its yield value at discontinuous portion of structure due to stress concentration generates, which could be thought of possibility to form a creep fatigue crack if repeating such thermal stress under high temperature. The Power Reactor and Nuclear Fuel Development Corporation has developed the transient thermal stress real time simulation code for calculating thermal stress formed within a construction in accompany with temperature changes of the coolant once and at high speed since 1994 FY, and after 1995 FY the development of FEM simulation technique from macroscopic region to microscopic region which set an objective regions from construction level to material texture has been promoted. In future, development of total simulation technique connected both and optimum design technique due to its results will be planned. (G.K.)

  5. Feiing og salting i Strømsås-tunnelen mars 2004: innledende analyse

    OpenAIRE

    Aldrin, Magne

    2004-01-01

    I mars 2004 blei det gjennomført forsøk med vasking og salting i Strømsåstunnelen, med sikte på å redusere konsentrasjonen av svevestøv. Samtidig blei det gjort målinger av PM10, meteorologi og trafikkvolum.

  6. 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

    -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...

  7. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

    Science.gov (United States)

    Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

    2011-01-01

    Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

  8. Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

    Directory of Open Access Journals (Sweden)

    Norio Matsushima

    2015-08-01

    Full Text Available The NOD-like receptors (NLRs and Toll-like receptors (TLRs are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids. The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.

  9. Multiple-locus variant-repeat assay (MLVA) is a useful tool for molecular epidemiologic analysis of Streptococcus agalactiae strains causing bovine mastitis.

    Science.gov (United States)

    Radtke, Andreas; Bruheim, Torkjel; Afset, Jan Egil; Bergh, Kåre

    2012-06-15

    Group B streptococci (GBS) were considered a major cause of mastitis in cattle until preventive measures succeeded in controlling the disease in the 1970s and 1980s. During the last 5-6 years an increasing number of cases have been observed in some Scandinavian countries. A total of 187 GBS isolates from mastitis cases were collected from 119 animals in 34 Norwegian farms in the period from April 2007 to November 2010. 133 (71%) of the isolates were from farms with automated milking systems. The strains underwent typing of capsular polysaccharides (CPS) and surface proteins, and were analyzed by multi-locus variable repeat assay (MLVA) to investigate the epidemiological relationship of strains within and between farms. The GBS strains were differentiated into 12 types by CPS and surface protein analysis, with CPS types V (54%) and IV (34%) predominating. MLVA was superior to CPS and protein typing for strain differentiation, resolving the 187 strains into 37 types. In 29 of 34 farms all GBS strains had identical MLVA profiles specific for each farm. However, in one farm represented with 48 isolates, four MLVA variants with differences in one repeat locus were observed during the almost 3-year long collection period. Similar variations were observed at four other farms. This might reflect the stability of repeat loci under in vivo conditions. Farms with automated milking systems were overrepresented in this material. In conclusion, the five-loci MLVA allowed rapid high-resolution genotyping of the bovine GBS strains within and between farms. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Development of QSAR models using artificial neural network analysis for risk assessment of repeated-dose, reproductive, and developmental toxicities of cosmetic ingredients.

    Science.gov (United States)

    Hisaki, Tomoka; Aiba Née Kaneko, Maki; Yamaguchi, Masahiko; Sasa, Hitoshi; Kouzuki, Hirokazu

    2015-04-01

    Use of laboratory animals for systemic toxicity testing is subject to strong ethical and regulatory constraints, but few alternatives are yet available. One possible approach to predict systemic toxicity of chemicals in the absence of experimental data is quantitative structure-activity relationship (QSAR) analysis. Here, we present QSAR models for prediction of maximum "no observed effect level" (NOEL) for repeated-dose, developmental and reproductive toxicities. NOEL values of 421 chemicals for repeated-dose toxicity, 315 for reproductive toxicity, and 156 for developmental toxicity were collected from Japan Existing Chemical Data Base (JECDB). Descriptors to predict toxicity were selected based on molecular orbital (MO) calculations, and QSAR models employing multiple independent descriptors as the input layer of an artificial neural network (ANN) were constructed to predict NOEL values. Robustness of the models was indicated by the root-mean-square (RMS) errors after 10-fold cross-validation (0.529 for repeated-dose, 0.508 for reproductive, and 0.558 for developmental toxicity). Evaluation of the models in terms of the percentages of predicted NOELs falling within factors of 2, 5 and 10 of the in-vivo-determined NOELs suggested that the model is applicable to both general chemicals and the subset of chemicals listed in International Nomenclature of Cosmetic Ingredients (INCI). Our results indicate that ANN models using in silico parameters have useful predictive performance, and should contribute to integrated risk assessment of systemic toxicity using a weight-of-evidence approach. Availability of predicted NOELs will allow calculation of the margin of safety, as recommended by the Scientific Committee on Consumer Safety (SCCS).

  11. Association Analysis of Simple Sequence Repeat (SSR Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb..

    Directory of Open Access Journals (Sweden)

    Yanhong Lou

    Full Text Available Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia, were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR markers. The panel displayed significant variation in spike count per plant (SCP and spike weight (SW. However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single

  12. Coordination in continuously repeated games

    NARCIS (Netherlands)

    Weeren, A.J.T.M.; Schumacher, J.M.; Engwerda, J.C.

    1995-01-01

    In this paper we propose a model to describe the effectiveness of coordination in a continuously repeated two-player game. We study how the choice of a decision rule by a coordinator affects the strategic behavior of the players, resulting in more or less cooperation. Our model requires the analysis

  13. Comparison of the capillary and agarose electrophoresis based multiple locus VNTR (variable number of tandem repeats) analysis (MLVA) on Mycobacterium bovis isolates.

    Science.gov (United States)

    Jenkins, A O; Venter, E H; Hutamo, K; Godfroid, J

    2010-09-28

    Electrophoretic techniques that can be used for genotyping of bacterial pathogens ranges from manual, low-cost, agarose gels to high-throughput capillary electrophoresis sequencing machines. These two methods are currently employed in the electrophoresis of PCR products used in multiple locus VNTR (variable number of tandem repeats) analysis (MLVA), i.e. the agarose electrophoresis (AE) and the capillary electrophoresis (CE). Some authors have suggested that clusters generated by AE are less reliable than those generated by CE and that the latter is a more sensitive technique than the former when typing Mycobacterium tuberculosis complex (MTC) isolates. Because such a claim could have significant consequences for investigators in this field, a comparison was made on 19 Belgian Mycobacterium bovis strains which had previously been genotyped using CE VNTR analysis. The VNTR profiles of the CE VNTR analysis were compared with those obtained by AE VNTR analysis at 14 VNTR loci. Our results indicated that there were no differences in copy numbers at all loci tested when the copy numbers obtained by the AE VNTR analysis were compared with those obtained by CE VNTR analysis. The use of AE VNTR analysis in mycobacterial genotyping does not alter the sensitivity of the MLVA technique compared with the CE VNTR analysis. The AE VNTR can therefore be regarded as a viable alternative in moderately equipped laboratories that cannot afford the expensive equipment required for CE VNTR analysis and data obtained by AE VNTR analysis can be shared between laboratories which use the CE VNTR method. (c) 2010 Elsevier B.V. All rights reserved.

  14. Discontinuous Patterns of Cigarette Smoking From Ages 18 to 50 in the United States: A Repeated-Measures Latent Class Analysis.

    Science.gov (United States)

    Terry-McElrath, Yvonne M; O'Malley, Patrick M; Johnston, Lloyd D

    2017-12-13

    Effective cigarette smoking prevention and intervention programming is enhanced by accurate understanding of developmental smoking pathways across the life span. This study investigated within-person patterns of cigarette smoking from ages 18 to 50 among a US national sample of high school graduates, focusing on identifying ages of particular importance for smoking involvement change. Using data from approximately 15,000 individuals participating in the longitudinal Monitoring the Future study, trichotomous measures of past 30-day smoking obtained at 11 time points were modeled using repeated-measures latent class analyses. Sex differences in latent class structure and membership were examined. Twelve latent classes were identified: three characterized by consistent smoking patterns across age (no smoking; smoking developing effective smoking prevention and intervention programming. This study examined cigarette smoking among a national longitudinal US sample of high school graduates from ages 18 to 50 and identified distinct latent classes characterized by patterns of movement between no cigarette use, light-to-moderate smoking, and the conventional definition of heavy smoking at 11 time points via repeated-measures latent class analysis. Membership probabilities for each smoking class were estimated, and critical ages of susceptibility to change in smoking behaviors were identified. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. The Utility of Repeat Culture in Fungal Corneal Ulcer Management: A Secondary Analysis of the MUTT-I Randomized Clinical Trial.

    Science.gov (United States)

    Ray, Kathryn J; Lalitha, Prajna; Prajna, N Venkatesh; Rajaraman, Revathi; Krishnan, Tiruvengada; Srinivasan, Muthiah; Ryg, Peter; McLeod, Stephen; Acharya, Nisha R; Lietman, Thomas M; Rose-Nussbaumer, Jennifer

    2017-06-01

    To determine whether patients who had a positive repeated culture was predictive of worse clinical outcome than those who achieved microbiological cure at 6 days in the Mycotic Ulcer Treatment Trial I (MUTT-I). Secondary analysis from a multicenter, double-masked, randomized clinical trial. setting: Multiple hospital sites of the Aravind Eye Care System, India. Patients with culture-positive filamentous fungal ulcers and visual acuity of 20/40 to 20/400 reexamined 6 days after initiation of treatment. Corneal scraping and cultures were obtained from study participants at day 6 after enrollment. We assessed 3-month best spectacle-corrected visual acuity (BSCVA), 3-month infiltrate/scar size, corneal perforation, and re-epithelialization rates stratified by culture positivity at day 6. Of the 323 patients with smear-positive ulcers enrolled in MUTT-I, 299 (92.6%) were scraped and cultured 6 days after enrollment. Repeat culture positivity was 31% (92/299). Among patients who tested positive at enrollment, those with positive 6-day cultures had significantly worse 3-month BSCVA (0.39 logMAR; 95% confidence interval [CI]: 0.24-0.44; P cure on culture is a predictor of clinical response to treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter pittii and Development of an Optimized Multiple-Locus VNTR Analysis Typing Scheme.

    Science.gov (United States)

    Hu, Yuan; Li, Bo Qing; Jin, Da Zhi; He, Li Hua; Tao, Xiao Xia; Zhang, Jian Zhong

    2015-12-01

    To develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing. Polymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates. Ten VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination. Compared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  17. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, M; Fuentes, J L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Rodriguez, N N; Cueto, J [Max Planck Institut fur Zuchtungsforschung (MPIZ), Koln (Germany); Becker, D; Rohde, W [Instituto de Investigaciones en Fruticultura Tropical (IIFT). C. Habana (Cuba)

    2001-07-01

    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed.

  18. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    International Nuclear Information System (INIS)

    Ramirez, M; Fuentes, J. L.; Rodriguez, N.N.; Cueto, J.; Becker, D.; Rohde, W.

    2001-01-01

    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed

  19. The PCA3 test for guiding repeat biopsy of prostate cancer and its cut-off score: a systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Yong Luo

    2014-06-01

    Full Text Available The specificity of prostate-specific antigen (PSA for early intervention in repeat biopsy is unsatisfactory. Prostate cancer antigen 3 (PCA3 may be more accurate in outcome prediction than other methods for the early detection of prostate cancer (PCa. However, the results were inconsistent in repeated biopsies. Therefore, we performed a systematic review and meta-analysis to evaluate the role of PCA3 in outcome prediction. A systematic bibliographic search was conducted for articles published before April 2013, using PubMed, Medline, Web of Science, Embase and other databases from health technology assessment agencies. The quality of the studies was assessed on the basis of QUADAS criteria. Eleven studies of diagnostic tests with moderate to high quality were selected. A meta-analysis was carried out to synthesize the results. The results of the meta-analyses were heterogeneous among studies. We performed a subgroup analysis (with or without inclusion of high-grade prostatic intraepithelial neoplasia (HGPIN and atypical small acinar proliferation (ASAP. Using a PCA3 cutoff of 20 or 35, in the two sub-groups, the global sensitivity values were 0.93 or 0.80 and 0.79 or 0.75, specificities were 0.65 or 0.44 and 0.78 or 0.70, positive likelihood ratios were 1.86 or 1.58 and 2.49 or 1.78, negative likelihood ratios were 0.81 or 0.43 and 0.91 or 0.82 and diagnostic odd ratios (ORs were 5.73 or 3.45 and 7.13 or 4.11, respectively. The areas under the curve (AUCs of the summary receiver operating characteristic curve were 0.85 or 0.72 and 0.81 or 0.69, respectively. PCA3 can be used for repeat biopsy of the prostate to improve accuracy of PCa detection. Unnecessary biopsies can be avoided by using a PCa cutoff score of 20.

  20. Objectivity of two methods of differentiating fibre types and repeatability of measurements by application of the TEMA image analysis system.

    Science.gov (United States)

    Henckel, P; Ducro, B; Oksbjerg, N; Hassing, L

    1998-01-01

    The objectivity of two of the most widely used methods for differentiation of fibre types, i.e. 1) the myosin ATP-ase method (Brooke and Kaiser, 1970a,b) and 2) the combined method, by which the myosin ATP-ase reaction is used to differentiate between fast and slow twitch fibres and NADH-tetrazolium reductase activity is used to identify the subgroups of fast twitch fibres (Ashmore and Doerr, 1970, Peter et al., 1972), was assessed in muscle samples from horses, calves and pigs. We also assessed the objectivity of the alpha-amylase-PAS preparation for the visualisation of capillaries (Andersen, 1975) in these species. For the purpose of reducing the time costs of histochemical analysis of muscle samples, we have developed an interactive image analysis system which is described. All analyses are performed on this system. In accordance with several other investigations, differences between the two methods of differentiating fibre types were found only for the relative distribution of the fast-twitch fibre subgroups (p 87%), the impact of differences in pre-requisites (varied degrees of overlap between the fibre types) for performing the differentiation by the combined method raises a question of the reliability of this method. Apparently, no general rules for comparison of results of distribution of the two subgroups of fast twitch fibres by the two methods are applicable. The alpha-amylase-PAS method was found to be a fairly objective method to identify capillaries in muscles from horses, calves and pigs. However, as capillarity described in combination with other traits to give an indication of diffusion characteristics is significantly influenced by person, it is recommended that the same person perform all the analysis of a project. In addition to the methodological results in this study, we have shown that by application of the TEMA image analysis system, which is more rapid compared with the time-consuming traditional method for evaluation of histochemical

  1. Population data of 17 short tandem repeat loci in 2923 individuals from the Han population of Nantong in East China.

    Science.gov (United States)

    Yang, Min; Li, Liming; Han, Haijun; Jin, Li; Jia, Dongtao; Li, Shilin

    2016-09-01

    Nantong is located in mid-eastern China, and the Han population in Nantong may be greatly affected by population admixture between northern and southern Han Chinese populations. In this study, we analyzed 17 autosomal short tandem repeat (STR) loci on 2923 unrelated individuals collected from the Han population of Nantong. No significant deviation from Hardy-Weinberg equilibrium was observed at all STR loci, and the expected heterozygosity ranged from 0.6184 to 0.9187. The combined match probability (CMP) was 3.87 × 10(-21), and the combined power of discrimination (CPD) was 99.999999999999999999613 %. No significant difference of allele frequencies was observed between Nantong and other Han populations at all STR loci, as well as Dai, Mongolian, and Tibetan. Significant differences were only observed between Nantong Han and Uyghur at TH01, as well as Nantong Han and Dong at CSF1PO and FGA. Nantong Han showed significant differences between She, Bouyei, and Miao at multiple STR loci.

  2. Developmental validation of the PowerPlex(®) ESI 16 and PowerPlex(®) ESI 17 Systems: STR multiplexes for the new European standard.

    Science.gov (United States)

    Tucker, Valerie C; Hopwood, Andrew J; Sprecher, Cynthia J; McLaren, Robert S; Rabbach, Dawn R; Ensenberger, Martin G; Thompson, Jonelle M; Storts, Douglas R

    2011-11-01

    In response to the ENFSI and EDNAP groups' call for new STR multiplexes for Europe, Promega(®) developed a suite of four new DNA profiling kits. This paper describes the developmental validation study performed on the PowerPlex(®) ESI 16 (European Standard Investigator 16) and the PowerPlex(®) ESI 17 Systems. The PowerPlex(®) ESI 16 System combines the 11 loci compatible with the UK National DNA Database(®), contained within the AmpFlSTR(®) SGM Plus(®) PCR Amplification Kit, with five additional loci: D2S441, D10S1248, D22S1045, D1S1656 and D12S391. The multiplex was designed to reduce the amplicon size of the loci found in the AmpFlSTR(®) SGM Plus(®) kit. This design facilitates increased robustness and amplification success for the loci used in the national DNA databases created in many countries, when analyzing degraded DNA samples. The PowerPlex(®) ESI 17 System amplifies the same loci as the PowerPlex(®) ESI 16 System, but with the addition of a primer pair for the SE33 locus. Tests were designed to address the developmental validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), and those of the DNA Advisory Board (DAB). Samples processed include DNA mixtures, PCR reactions spiked with inhibitors, a sensitivity series, and 306 United Kingdom donor samples to determine concordance with data generated with the AmpFlSTR(®) SGM Plus(®) kit. Allele frequencies from 242 white Caucasian samples collected in the United Kingdom are also presented. The PowerPlex(®) ESI 16 and ESI 17 Systems are robust and sensitive tools, suitable for the analysis of forensic DNA samples. Full profiles were routinely observed with 62.5pg of a fully heterozygous single source DNA template. This high level of sensitivity was found to impact on mixture analyses, where 54-86% of unique minor contributor alleles were routinely observed in a 1:19 mixture ratio. Improved sensitivity combined with the robustness afforded by smaller amplicons

  3. A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients.

    Science.gov (United States)

    Lunestad, B T; Truong, T T T; Lindstedt, B-A

    2013-10-01

    The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

  4. The STR/ort mouse model of spontaneous osteoarthritis - an update.

    Science.gov (United States)

    Staines, K A; Poulet, B; Wentworth, D N; Pitsillides, A A

    2017-06-01

    Osteoarthritis is a degenerative joint disease and a world-wide healthcare burden. Characterized by cartilage degradation, subchondral bone thickening and osteophyte formation, osteoarthritis inflicts much pain and suffering, for which there are currently no disease-modifying treatments available. Mouse models of osteoarthritis are proving critical in advancing our understanding of the underpinning molecular mechanisms. The STR/ort mouse is a well-recognized model which develops a natural form of osteoarthritis very similar to the human disease. In this Review we discuss the use of the STR/ort mouse in understanding this multifactorial disease with an emphasis on recent advances in its genetics and its bone, endochondral and immune phenotypes. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. The Origin of Workerless Parasites in Leptothorax (S. Str. (Hymenoptera: Formicidae

    Directory of Open Access Journals (Sweden)

    Jürgen Heinze

    1995-01-01

    Full Text Available The evolutionary origin of workerless parasitic ants parasitizing colonies of Leptothorax (s.str. is investigated using data on morphology, chromosome number, and allozyme phenotype of both social parasites and their hosts. Of the three previously proposed pathways, the evolution of workerless parasites from guest ants or slave-makers is unlikely, at least according to a phenogram obtained by UPGMA clustering of Nei's similarities based on seven enzymes, lntraspecific evolution of the workerless parasites Doronomyrmex goesswaldi, D. kutteri, and D. pacis from their common host, Leptothorax acervorum cannot be excluded with the present data. The workerless parasite L. paraxenus, however, clearly differs from its host, L. cf. canadensis, in morphology and biochemistry, and most probably did not evolve from the latter species. It is proposed to synonymize Doronomyrmex under Leptothorax (s.str..

  6. Computerized Analysis of Verbal Fluency: Normative Data and the Effects of Repeated Testing, Simulated Malingering, and Traumatic Brain Injury.

    Directory of Open Access Journals (Sweden)

    David L Woods

    Full Text Available In verbal fluency (VF tests, subjects articulate words in a specified category during a short test period (typically 60 s. Verbal fluency tests are widely used to study language development and to evaluate memory retrieval in neuropsychiatric disorders. Performance is usually measured as the total number of correct words retrieved. Here, we describe the properties of a computerized VF (C-VF test that tallies correct words and repetitions while providing additional lexical measures of word frequency, syllable count, and typicality. In addition, the C-VF permits (1 the analysis of the rate of responding over time, and (2 the analysis of the semantic relationships between words using a new method, Explicit Semantic Analysis (ESA, as well as the established semantic clustering and switching measures developed by Troyer et al. (1997. In Experiment 1, we gathered normative data from 180 subjects ranging in age from 18 to 82 years in semantic ("animals" and phonemic (letter "F" conditions. The number of words retrieved in 90 s correlated with education and daily hours of computer-use. The rate of word production declined sharply over time during both tests. In semantic conditions, correct-word scores correlated strongly with the number of ESA and Troyer-defined semantic switches as well as with an ESA-defined semantic organization index (SOI. In phonemic conditions, ESA revealed significant semantic influences in the sequence of words retrieved. In Experiment 2, we examined the test-retest reliability of different measures across three weekly tests in 40 young subjects. Different categories were used for each semantic ("animals", "parts of the body", and "foods" and phonemic (letters "F", "A", and "S" condition. After regressing out the influences of education and computer-use, we found that correct-word z-scores in the first session did not differ from those of the subjects in Experiment 1. Word production was uniformly greater in semantic than

  7. Effect of repeated transsphenoidal surgery in recurrent or residual pituitary adenomas: A systematic review and meta-analysis

    Science.gov (United States)

    Heringer, Lindolfo Carlos; de Oliveira, Matheus Fernandes; Rotta, José Marcus; Botelho, Ricardo Vieira

    2016-01-01

    Background: Recurrent or residual pituitary adenomas previously treated by transsphenoidal surgery are not uncommon. There are no strongly established guidelines to perform treatment of such cases. The objective of this study is to elucidate the effect of transsphenoidal reoperation in residual or recurrent pituitary adenomas. Methods: We made a systematic review of the literature to elucidate this effect through electronic search in MEDLINE/PubMed and Cochrane Central database. PRISMA statement was used as a basis for this systematic review and analysis of the risk of bias was made according to the Grading of Recommendations, Assessment, Development and Evaluation recommendations. Results: In this review, fifteen studies were finally pooled analyzed. Although remission rates (RRs) and follow-up periods varied widely, from 149 patients with growth hormone-secreting tumors the mean RR was 44.5%, from 273 patients with adrenocorticotropic hormone-secreting tumors the mean RR was 55.5% and among 173 patients with nonsecreting tumors, RR was 76.1%. There was significant higher RR in nonsecreting tumors. Mean follow-up was 32.1 months. No difference was found between microscopic and endoscopic techniques. Conclusions: A second transsphenoidal surgery is accompanied by a chance of remission in approximately half of cases with secreting tumors. In nonsecreting ones, success is higher. PMID:26958420

  8. 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.

  9. Population genetic data for 15 STR loci (Identifiler kit) in Honduras.

    Science.gov (United States)

    Matamoros, Mireya; Pinto, Yessica; Inda, Francisco Javier; García, Oscar

    2008-09-01

    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 198 unrelated individuals from Honduras, Central America.

  10. El subgénero Trigona S. Str. Jurine 1808 (Hymenoptera: Apidae: Meliponinae) en Colombia

    OpenAIRE

    Édgar Javier Hernández Martínez; Guiomar Nates Parra

    2004-01-01

    Para Colombia se registran 28 de los 29 taxones descritos para el subgénero Trigona s. str. T. (T.) albipennis Almeida, 1992; T. (T.) amalthea Olivier, 1789; T. (T.) hyalinata var. amazonensis Ducke, 1916; T. (T.) hyalinata var. branneri Cockerell, 1912; T. (T.) chanchamayoënsis Schwarz, 1948; T. (T.) cilipes Fabricius, 1804; T. (T.) corvina Cockerell, 1913; T. (T.) crassipes Fabricius, 1793; T. (T.) dallatorreana Friese, 1900; T. (T.) dimidiata var. venezuelana Schwarz, 1948; T. (T.) dimi...

  11. El subgénero Trigona S. Str. Jurine 1808 (Hymenoptera: Apidae: Meliponinae) en Colombia

    OpenAIRE

    Hernández Martínez Édgar Javier; Nates Parra Guiomar

    2004-01-01

    Para Colombia se registran 28 de los 29 taxones descritos para el subgénero Trigona s. str. T. (T.) albipennis Almeida, 1992; T. (T.) amalthea Olivier, 1789; T. (T.) hyalinata var. amazonensis
    Ducke, 1916; T. (T.) hyalinata var. branneri Cockerell, 1912; T. (T.) chanchamayoënsis Schwarz, 1948; T. (T.) cilipes Fabricius, 1804; T. (T.) corvina Cockerell, 1913; T. (T.) crassipes Fabricius, 1793; T. (T.) dallatorreana Friese, 1900; T. (T.) dimidiata var. venezuelana Schwarz, 1948; T. (...

  12. Topical problems connected with the German act on electricity from renewable energy sources (StrEG)

    International Nuclear Information System (INIS)

    Pohlmann, M.

    1998-01-01

    The German act (StrEG) intended to enhance the use of renewable energy sources for electricity generation and to promote the relevant technologies raises some problems in connection with constitutional law that still await judicial review by the German Federal Constitutional Court. In addition, doubts as to the lawfulness of provisions of the act have been emerging in connection with EC laws governing the regime of subsidies and state aid. The article here summarizes the current situation. (orig./CB) [de

  13. Demographic and practice factors predicting repeated non-attendance in primary care: a national retrospective cohort analysis

    Directory of Open Access Journals (Sweden)

    David A Ellis, PhD

    2017-12-01

    Full Text Available Summary: Background: Addressing the causes of low engagement in health care is a prerequisite for reducing health inequalities. People who miss multiple appointments are an under-researched group who might have substantial unmet health needs. Individual-level patterns of missed general practice appointments might thus provide a risk marker for vulnerability and poor health outcomes. We sought to ascertain the contributions of patient and practice factors to the likelihood of missing general practice appointments. Methods: For this national retrospective cohort analysis, we extracted UK National Health Service general practice data that were routinely collected across Scotland between Sept 5, 2013, and Sept 5, 2016. We calculated the per-patient number of missed appointments from individual appointments and investigated the risk of missing a general practice appointment using a negative binomial model offset by number of appointments made. We then analysed the effect of patient-level factors (including age, sex, and socioeconomic status and practice-level factors (including appointment availability and geographical location on the risk of missing appointments. Findings: The full dataset included information from 909 073 patients, of whom 550 083 were included in the analysis after processing. We observed that 104 461 (19·0% patients missed more than two appointments in the 3 year study period. After controlling for the number of appointments made, patterns of non-attendance could be differentiated, with patients who were aged 16–30 years (relative risk ratio [RRR] 1·21, 95% CI 1·19–1·23 or older than 90 years (2·20, 2·09–2·29, and of low socioeconomic status (Scottish Index of Multiple Deprivation decile 1: RRR 2·27, 2·22–2·31 significantly more likely to miss multiple appointments. Men missed fewer appointments overall than women, but were somewhat more likely to miss appointments

  14. Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

    Science.gov (United States)

    Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

    2018-01-01

    Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Analysis of 8 X-chromosomal markers in the population of central Croatia

    Science.gov (United States)

    Gršković, Branka; Zidkova, Anastassiya; Stenzl, Vlastimil; Popović, Maja; Primorac, Dragan; Mršić, Gordan

    2013-01-01

    Aim To analyze 8 X-linked short tandem repeat (STR) markers in the population of central Croatia and to evaluate their forensic efficiency. Methods We carried out a statistical analysis of the data from previously performed genetic analyses, collected during routine forensic work by the Forensic Science Centre ‘‘Ivan Vučetić.’’ Mentype® Argus X-8 PCR amplification kit was used for typing the data of 99 unrelated healthy women and 78 men from central Croatia. Haplotype frequencies were calculated only in male samples. Arlequin 3.5 software was used to assess Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), observed and expected heterozygosity. Power of discrimination (PD) for men and women, polymorphism information content (PIC), power of exclusion, and mean exclusion chance for deficiency cases, normal trios, and duos were determined using online database ChrX-STR.org. Results In female samples, deviations from HWE (P = 0.006) for each locus were not found. LD test performed both on female and male samples revealed no significant association between markers (P = 0.002). DXS10135 was the most polymorphic locus (PIC = 0.931). PD varied from 0.692 to 0.935 in male and from 0.845 to 0.992 in female samples. Combined PD reached 99.999999% in men and 99.9999999999% in women. Conclusion Performed analyses revealed that the studied marker set contained polymorphic markers with high power of discrimination. We can conclude that Mentype® Argus X-8 PCR kit is suitable for application in the population of central Croatia. Results of this study, together with collected allele and haplotype frequencies, are the first step in establishing a national reference X-STR database based on 8 X-STR loci. PMID:23771754

  16. 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.

  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. Analysis of the a genome genetic diversity among brassica napus, b. rapa and b. juncea accessions using specific simple sequence repeat markers

    International Nuclear Information System (INIS)

    Tian, H.; Yan, J.; Zhang, R.; Guo, Y.; Hu, S.; Channa, S.A.

    2017-01-01

    This investigation was aimed at evaluating the genetic diversity of 127 accessions among Brassica napus, B. rapa, and B. juncea by using 15 pairs of the A genome specific simple sequence repeat primers. These 127 accessions could be clearly separated into three groups by cluster analysis, principal component analysis, and population structure analysis separately, and the results analyzed by the three methods were very similar. Group I comprised of mainly B. napus accessions and the most of B. juncea accessions formed Group II, Group III included nearly all of the B. rapa accessions. The result showed that 36.86% of the variance was due to significant differences among populations of species, indicated that abundance genetic diversity existed among the A genome of B. napus, B. rapa, and B. juncea accessions. B. napus, B. rapa, and B. juncea have the abundant genetic diversity in the A genome, and some elite genes can be used to broaden the genetic base of them, especially for B. napus, in future rapeseed breeding program. (author)

  19. Quantum repeated games revisited

    International Nuclear Information System (INIS)

    Frąckiewicz, Piotr

    2012-01-01

    We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the 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 proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable. (paper)

  20. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).

    Science.gov (United States)

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

    2014-06-04

    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

    Directory of Open Access Journals (Sweden)

    Shirasawa Kenta

    2012-06-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp.

  2. Minimal sharing of Y-chromosome STR haplotypes among five endogamous population groups from western and southwestern India.

    Science.gov (United States)

    Das, Birajalaxmi; Chauhan, P S; Seshadri, M

    2004-10-01

    We attempt to address the issue of genetic variation and the pattern of male gene flow among and between five Indian population groups of two different geographic and linguistic affiliations using Y-chromosome markers. We studied 221 males at three Y-chromosome biallelic loci and 184 males for the five Y-chromosome STRs. We observed 111 Y-chromosome STR haplotypes. An analysis of molecular variance (AMOVA) based on Y-chromosome STRs showed that the variation observed between the population groups belonging to two major regions (western and southwestern India) was 0.17%, which was significantly lower than the level of genetic variance among the five populations (0.59%) considered as a single group. Combined haplotype analysis of the five STRs and the biallelic locus 92R7 revealed minimal sharing of haplotypes among these five ethnic groups, irrespective of the similar origin of the linguistic and geographic affiliations; this minimal sharing indicates restricted male gene flow. As a consequence, most of the haplotypes were population specific. Network analysis showed that the haplotypes, which were shared between the populations, seem to have originated from different mutational pathways at different loci. Biallelic markers showed that all five ethnic groups have a similar ancestral origin despite their geographic and linguistic diversity.

  3. Large Diversity of Porcine Yersinia enterocolitica 4/O:3 in Eight European Countries Assessed by Multiple-Locus Variable-Number Tandem-Repeat Analysis.

    Science.gov (United States)

    Alakurtti, Sini; Keto-Timonen, Riikka; Virtanen, Sonja; Martínez, Pilar Ortiz; Laukkanen-Ninios, Riikka; Korkeala, Hannu

    2016-06-01

    A total of 253 multiple-locus variable-number tandem-repeat analysis (MLVA) types among 634 isolates were discovered while studying the genetic diversity of porcine Yersinia enterocolitica 4/O:3 isolates from eight different European countries. Six variable-number tandem-repeat (VNTR) loci V2A, V4, V5, V6, V7, and V9 were used to study the isolates from 82 farms in Belgium (n = 93, 7 farms), England (n = 41, 8 farms), Estonia (n = 106, 12 farms), Finland (n = 70, 13 farms), Italy (n = 111, 20 farms), Latvia (n = 66, 3 farms), Russia (n = 60, 10 farms), and Spain (n = 87, 9 farms). Cluster analysis revealed mainly country-specific clusters, and only one MLVA type consisting of two isolates was found from two countries: Russia and Italy. Also, farm-specific clusters were discovered, but same MLVA types could also be found from different farms. Analysis of multiple isolates originating either from the same tonsils (n = 4) or from the same farm, but 6 months apart, revealed both identical and different MLVA types. MLVA showed a very good discriminatory ability with a Simpson's discriminatory index (DI) of 0.989. DIs for VNTR loci V2A, V4, V5, V6, V7, and V9 were 0.916, 0.791, 0.901, 0.877, 0.912, and 0.785, respectively, when studying all isolates together, but variation was evident between isolates originating from different countries. Locus V4 in the Spanish isolates and locus V9 in the Latvian isolates did not differentiate (DI 0.000), and locus V9 in the English isolates showed very low discriminatory power (DI 0.049). The porcine Y. enterocolitica 4/O:3 isolates were diverse, but the variation in DI demonstrates that the well discriminating loci V2A, V5, V6, and V7 should be included in MLVA protocol when maximal discriminatory power is needed.

  4. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

  5. Repeat migration and disappointment.

    Science.gov (United States)

    Grant, E K; Vanderkamp, J

    1986-01-01

    This article investigates the determinants of repeat migration among the 44 regions of Canada, using information from a large micro-database which spans the period 1968 to 1971. The explanation of repeat migration probabilities is a difficult task, and this attempt is only partly successful. May of the explanatory variables are not significant, and the overall explanatory power of the equations is not high. In the area of personal characteristics, the variables related to age, sex, and marital status are generally significant and with expected signs. The distance variable has a strongly positive effect on onward move probabilities. Variables related to prior migration experience have an important impact that differs between return and onward probabilities. In particular, the occurrence of prior moves has a striking effect on the probability of onward migration. The variable representing disappointment, or relative success of the initial move, plays a significant role in explaining repeat migration probabilities. The disappointment variable represents the ratio of actural versus expected wage income in the year after the initial move, and its effect on both repeat migration probabilities is always negative and almost always highly significant. The repeat probabilities diminish after a year's stay in the destination region, but disappointment in the most recent year still has a bearing on the delayed repeat probabilities. While the quantitative impact of the disappointment variable is not large, it is difficult to draw comparisons since similar estimates are not available elsewhere.

  6. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    Science.gov (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  7. Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea).

    Science.gov (United States)

    Sharma, Ranu; Rawat, Vimal; Suresh, C G

    2017-12-01

    The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four cis -regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.

  8. Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Yuan Tong

    2010-01-01

    Full Text Available Abstract Background Transmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs, representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. Results As a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs of 194 LRR-RLKs were cloned into the GatewayR donor vector pDONR/ZeoR and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into GatewayR destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC at Ohio State University for full accessibility by the Arabidopsis research community. Conclusions Most of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family.

  9. IL1 receptor antagonist gene IL1-RN variable number of tandem repeats polymorphism and cancer risk: a literature review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Ying Zhang

    Full Text Available IL1 receptor antagonist (IL1RA and IL1beta (IL1β, members of the pro-inflammatory cytokine interleukin-1 (IL1 family, play a potential role against infection and in the pathogenesis of cancers. The variable number of tandem repeats (VNTR polymorphism in the second intron of the IL1 receptor antagonist gene (IL1-RN and a polymorphism in exon 5 of IL1B (IL1B+3954C>T, rs1143634 have been suggested in predisposition to cancer risk. However, studies have shown inconsistent results. To validate any association, a meta-analysis was performed with 14,854 cases and 19,337 controls from 71 published case-control studies for IL1-RN VNTR and 33 eligible studies contained 7,847 cases and 8917 controls for IL1B +3954. Odds ratios (ORs with 95% confidence intervals (CIs were calculated from comparisons to assess the strength of the association. There was significant association between the IL1-RN VNTR polymorphism and the risk of cancer for any overall comparison. Furthermore, cancer type stratification analysis revealed that there were significantly increased risks of gastric cancer, bladder cancer and other cancer groups. Infection status analysis indicated that the H. pylori or HBV/HCV infection and IL1-RN VNTR genotypes were independent factors for developing gastric or hepatocellular cancers. In addition, a borderline significant association was observed between IL1B+3954 polymorphism and the increased cancer risk. Although some modest bias could not be eliminated, this meta-analysis suggested that the IL1-RN VNTR polymorphisms may contribute to genetic susceptibility to gastric cancer. More studies are needed to further evaluate the role of the IL1B+3954 polymorphism in the etiology of cancer.

  10. Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross between Gossypium hirsutum and G. mustelinum

    Directory of Open Access Journals (Sweden)

    Baohua Wang

    2017-10-01

    Full Text Available The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum (Upland cotton was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. The BC3F2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC3-derived families were phenotyped for fiber strength (STR and fineness (Micronaire, MIC. A total of 42 quantitative trait loci (QTLs were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses. Alleles from G. mustelinum increased STR for eight of 15 and reduced MIC for 15 of 27 QTLs. Significant among-family genotypic effects (P < 0.001 were detected in 13 and 10 loci for STR and MIC respectively, and five loci showed significant (P < 0.001 genotype × family interaction for MIC. These results support the hypothesis that fiber quality improvement for Upland cotton could be realized by introgressing G. mustelinum alleles although complexities due to the different effects of genetic background on introgressed chromatin might be faced. Building on prior work with G. barbadense, G. tomentosum, and G. darwinii, QTL mapping involving introgression of G. mustelinum alleles offers new allelic variation to Upland cotton germplasm.

  11. Specific multilocus variable-number tandem-repeat analysis genotypes of Mycoplasma pneumoniae are associated with diseases severity and macrolide susceptibility.

    Directory of Open Access Journals (Sweden)

    Jiuxin Qu

    Full Text Available Clinical relevance of multilocus variable-number tandem-repeat (VNTR analysis (MLVA in patients with community-acquired pneumonia (CAP by Mycoplasma pneumoniae (M. pneumoniae is unknown. A multi-center, prospective study was conducted from November 2010 to April 2012. Nine hundred and fifty-four CAP patients were consecutively enrolled. M. pneumoniae clinical isolates were obtained from throat swabs. MLVA typing was applied to all isolates. Comparison of pneumonia severity index (PSI and clinical features among patients infected with different MLVA types of M. pneumoniae were conducted. One hundred and thirty-six patients were positive with M. pneumoniae culture. The clinical isolates were clustered into 18 MLVA types. One hundred and fourteen (88.3% isolates were resistant to macrolide, covering major MLVA types. The macrolide non-resistant rate of M. pneumoniae isolates with Mpn13-14-15-16 profile of 3-5-6-2 was significantly higher than that of other types (p ≤ 0.001. Patients infected with types U (5-4-5-7-2 and J (3-4-5-7-2 had significantly higher PSI scores (p<0.001 and longer total duration of cough (p = 0.011. Therefore it seems that there is a correlation between certain MLVA types and clinical severity of disease and the presence of macrolide resistance.

  12. Development of a spatial analysis method using ground-based repeat photography to detect changes in the alpine treeline ecotone, Glacier National Park, Montana, U.S.A.

    Science.gov (United States)

    Roush, W.; Munroe, Jeffrey S.; Fagre, D.B.

    2007-01-01

    Repeat photography is a powerful tool for detection of landscape change over decadal timescales. Here a novel method is presented that applies spatial analysis software to digital photo-pairs, allowing vegetation change to be categorized and quantified. This method is applied to 12 sites within the alpine treeline ecotone of Glacier National Park, Montana, and is used to examine vegetation changes over timescales ranging from 71 to 93 years. Tree cover at the treeline ecotone increased in 10 out of the 12 photo-pairs (mean increase of 60%). Establishment occurred at all sites, infilling occurred at 11 sites. To demonstrate the utility of this method, patterns of tree establishment at treeline are described and the possible causes of changes within the treeline ecotone are discussed. Local factors undoubtedly affect the magnitude and type of the observed changes, however the ubiquity of the increase in tree cover implies a common forcing mechanism. Mean minimum summer temperatures have increased by 1.5??C over the past century and, coupled with variations in the amount of early spring snow water equivalent, likely account for much of the increase in tree cover at the treeline ecotone. Lastly, shortcomings of this method are presented along with possible solutions and areas for future research. ?? 2007 Regents of the University of Colorado.

  13. The prognostic role of Leucine-rich repeat-containing G-protein-coupled receptor 5 in gastric cancer: A systematic review with meta-analysis.

    Science.gov (United States)

    Huang, Tianchen; Qiu, Xinguang; Xiao, Jianan; Wang, Qingbing; Wang, Yanjun; Zhang, Yong; Bai, Dongxiao

    2016-04-01

    The prognostic value of Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) in gastric cancer remains controversial. To further investigate this relationship, we performed meta-analyses to systematically review the association between LGR5 expression and various clinical parameters in gastric cancer patients. Eligible studies from PubMed, Embase, Web of Science, CNKI (Chinese National Knowledge Infrastructure), Wangfang (Database of Chinese Ministry of Science & Technology) and CBM (China Biological Medicine) databases were evaluated to investigate the association of LGR5 expression with overall survival (OS) and clinicopathological features of gastric cancer. LGR5 overexpression was significantly associated with poor OS in patients with gastric cancer (HR 1.66, 95% CI 1.02-2.69). LGR5 overexpression was also significantly associated with TNM stage (TIII/TIV vs TI/TII: OR 5.42, 95% CI 1.02-28.72) and lymph node metastasis (positive vs negative: OR 2.30, 95% CI 1.06-5.0). Our meta-analysis indicates that LGR5 may be a predictive factor for invasion and metastasis, and poor prognosis in patients with gastric cancer. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  14. Genetic diversity of Neisseria meningitidis serogroup C ST-4821 in China based on multiple-locus variable number tandem repeat analysis.

    Directory of Open Access Journals (Sweden)

    Xiaoying Shan

    Full Text Available Neisseria meningitidis sequence type (ST-4821 was first reported in China in 2003, and a new hyper-virulent lineage has been designated as the ST-4821 complex. A large number of N. meningitidis ST-4821 strains have been identified in China since 2003; however, the microevolution characteristics of this complex are unclear. Different combinations of variable number of tandem repeats (VNTR loci were used in multiple-locus VNTR analysis (MLVA to analyze 118 N. meningitidis serogroup C ST-4821 strains isolated from seventeen provinces between 2003 and 2012. Additionally, MLVA with five VNTR loci was performed due to its high discriminatory power. One hundred and eighteen isolates were found to comprise 112 subtypes based on MLVA, and 16 outbreak-associated strains were clustered into one group. These data indicate a high level of diversity for N. meningitidis ST-4821 due to microevolution in the last decade. In addition, the results revealed high similarity between isolates from the same geographic origins, which is helpful when monitoring the spread of N. meningitidis serogroup C ST-4821 and will provide valuable information for the control and prevention of bacterial meningitis in China.

  15. Comparative analysis of transcriptomic responses to repeated-dose exposure to 2-MCPD and 3-MCPD in rat kidney, liver and testis.

    Science.gov (United States)

    Buhrke, Thorsten; Schultrich, Katharina; Braeuning, Albert; Lampen, Alfonso

    2017-08-01

    3-Chloro-1,2-propanediol (3-MCPD) and its isomer 2-chloro-1,3-propanediol (2-MCPD) are heat-induced food contaminants present in oil- and fat-containing foodstuff. Kidney and testes are among the main target organs of 3-MCPD. Almost no data on 2-MCPD toxicity are available. Here, transcriptomic responses following repeated-dose exposure of rats to non-toxic doses of 10 mg/kg body weight per day 2-MCPD or 3-MCPD for 28 days were characterized by microarray analysis of kidney, liver, and testes. 3-MCPD exerted more pronounced effects than 2-MCPD in all organs. The limited overlap between the datasets indicates that 2-MCPD and 3-MCPD do not share the same molecular mechanisms of toxicity. By combining transcriptomic data with datasets on proteomic regulation by 3-MCPD, a comprehensive view on 3-MCPD-induced regulation of glucose utilization and oxidative stress response was developed. Bioinformatic analyses revealed that Nrf2 (nuclear factor (erythroid-derived 2)-like 2) signaling is likely to be involved in mediating the oxidative stress response to 3-MCPD. In summary, this study for the first time presents data on alterations in global gene expression by two important food contaminants, 2-MCPD and 3-MCPD. Data demonstrate profound differences between the effects of the two compounds and substantially broaden our knowledge on molecular details of 3-MCPD-induced disturbance of glucose utilization and redox balance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Evaluation of a highly discriminating multiplex multi-locus variable-number of tandem-repeats (MLVA) analysis for Vibrio cholerae.

    Science.gov (United States)

    Olsen, Jaran S; Aarskaug, Tone; Skogan, Gunnar; Fykse, Else Marie; Ellingsen, Anette Bauer; Blatny, Janet M

    2009-09-01

    Vibrio cholerae is the etiological agent of cholera and may be used in bioterror actions due to the easiness of its dissemination, and the public fear for acquiring the cholera disease. A simple and highly discriminating method for connecting clinical and environmental isolates of V. cholerae is needed in microbial forensics. Twelve different loci containing variable numbers of tandem-repeats (VNTRs) were evaluated in which six loci were polymorphic. Two multiplex reactions containing PCR primers targeting these six VNTRs resulted in successful DNA amplification of 142 various environmental and clinical V. cholerae isolates. The genetic distribution inside the V. cholerae strain collection was used to evaluate the discriminating power (Simpsons Diversity Index=0.99) of this new MLVA analysis, showing that the assay have a potential to differentiate between various strains, but also to identify those isolates which are collected from a common V. cholerae outbreak. This work has established a rapid and highly discriminating MLVA assay useful for track back analyses and/or forensic studies of V. cholerae infections.

  17. FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome.

    Science.gov (United States)

    Rajan-Babu, Indhu-Shree; Lian, Mulias; Cheah, Felicia S H; Chen, Min; Tan, Arnold S C; Prasath, Ethiraj B; Loh, Seong Feei; Chong, Samuel S

    2017-07-19

    Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification. The assay was optimised and validated on single lymphoblasts isolated from fragile X reference cell lines, and applied to a simulated PGD case and a clinical in vitro fertilisation (IVF)-PGD case. In the simulated PGD case, definitive diagnosis of the expected results was achieved for all 'embryos'. In the clinical IVF-PGD case, delivery of a healthy baby girl was achieved after transfer of an expansion-negative blastocyst. FMR1 TP-PCR reliably detects presence of expansion mutations and obviates reliance on informative normal alleles for determining expansion status in female embryos. Together with multi-marker haplotyping and gender determination, misdiagnosis and diagnostic ambiguity due to allele dropout is minimised, and couple-specific assay customisation can be avoided.

  18. Allele frequencies data and statistic parameters for 16 STR loci—D19S433, D2S1338, CSF1PO, D16S539, D7S820, D21S11, D18S51, D13S317, D5S818, FGA, Penta E, TH01, vWA, D8S1179, TPOX, D3S1358—in the Rio de Janeiro population, Brazil

    OpenAIRE

    Góes, Andrea Carla de Souza; Silva, Dayse Aparecida da; Gil, Érica Helena Fonseca; Silva, Márcia Teixeira Desidério; Pereira, Rinaldo Wellerson; Carvalho, Elizeu Fagundes de

    2004-01-01

    Allele frequencies for 16 short tandem repeats (STR) loci were determined with a sample of 230–300 unrelated individuals from the population of Rio de Janeiro, Brazil. The loci are the most commonly used in forensic and paternity testing, being analysed by the Identifiler (Applied Biosystems) and PowerPlex 2.1 (Promega) commercial kits. It was proved that Penta E and D18S51 are the most polymorphic loci.

  19. New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

    Science.gov (United States)

    Guinard, Jérémy; Latreille, Anne; Guérin, Fabien; Poussier, Stéphane

    2016-01-01

    ABSTRACT Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations. IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the

  20. The Pentapeptide Repeat Proteins

    OpenAIRE

    Vetting, Matthew W.; Hegde, Subray S.; Fajardo, J. Eduardo; Fiser, Andras; Roderick, Steven L.; Takiff, Howard E.; Blanchard, John S.

    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 Myc...

  1. Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations

    DEFF Research Database (Denmark)

    Meldgaard, Michael; Morling, N

    1997-01-01

    Detection on automated DNA sequencers of polymerase chain reaction (PCR) products of tetra- and penta-nucleotide short tandem repeat (STR) loci frequently reveals one or more extra peaks along with the true, major allele peak. The most frequent extra peak pattern is a single smaller peak which...... is one repeat unit shorter than the true allele peak. The existence of such artificial peaks is of special importance when the methods are used for forensic investigations because the artificial extra peaks may simulate true alleles when samples containing mixtures of DNA from different individuals...... are analyzed. We have investigated the relative levels of formation of extra peaks in 14 STR marker systems. We found that not only the parameters of the PCR but also factors determining the stringency during the post-PCR and pre-electrophoresis handling of samples were of importance for the formation of extra...

  2. Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes.

    Science.gov (United States)

    Sun, Jiangmei; Li, Leiting; Wang, Peng; Zhang, Shaoling; Wu, Juyou

    2017-10-10

    Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively. All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%. Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

  3. Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

    Science.gov (United States)

    Iakhiaeva, Elena; Howard, Susan T.; Brown Elliott, Barbara A.; McNulty, Steven; Newman, Kristopher L.; Falkinham, Joseph O.; Williams, Myra; Kwait, Rebecca; Lande, Leah; Vasireddy, Ravikiran; Turenne, Christine

    2016-01-01

    “Mycobacterium avium subsp. hominissuis” is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilm M. avium isolates underwent molecular identification. Testing for IS901 was done to separate M. avium subsp. avium from M. avium subsp. hominissuis. VNTR types were defined using VNTR loci, and subtyping was performed using 3′ hsp65 and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes of M. avium subsp. hominissuis (IS901 negative) were identified among 416 isolates of M. avium from 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3′ hsp65 sequence code (sequevar). A total of 44 isolates belonging to four M. avium subsp. hominissuis VNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901 PCR primers. By sequencing, all 44 amplicons were not IS901 but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis of M. avium subsp. hominissuis isolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates of M. avium subsp. avium were identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. PMID:26739155

  4. Some remarks on the influence of temperature-variations, non-linearities, repeatability and ageing on modal-analysis for structural health monitoring of real bridges

    Directory of Open Access Journals (Sweden)

    Maas Stefan

    2015-01-01

    Full Text Available Structural Health Monitoring (SHM intends to identify damage by changes of characteristics as for instance the modal parameters. The eigenfrequencies, mode-shapes and damping-values are either directly used as damage indicators or the changes of derived parameters are analysed, such as e.g. flexibilities or updated finite element models. One common way is a continuous monitoring under environmental excitation forces, such as wind or traffic, i.e. the so-called output-only modal analysis. Alternatively, a forced measured external excitation in distinct time-intervals may be used for input-output modal analysis. Both methods are limited by the precision or the repeatability under real-life conditions at site. The paper will summarize several field tests of artificially step-by-step damaged bridges prior to their final demolishment and it will show the changes of eigenfrequencies due to induced artificial damage. Additionally, some results of a monitoring campaign of a healthy bridge in Luxembourg are presented. Reinforced concrete shows non-linear behaviour in the sense that modal parameters depend on the excitation force amplitude, i.e. higher forces lead often to lower eigenfrequencies than smaller forces. Furthermore, the temperature of real bridges is neither constant in space nor in time, while for instance the stiffness of asphalt is strongly dependant on it. Finally, ageing as such can also change a bridge’s stiffness and its modal parameters, e.g. because creep and shrinkage of concrete or ageing of elastomeric bearing pads influence their modulus of elasticity. These effects cannot be considered as damage, though they influence the measurement of modal parameters and hinder damage detection.

  5. Effect of exposure to evening light on sleep initiation in the elderly: a longitudinal analysis for repeated measurements in home settings.

    Science.gov (United States)

    Obayashi, Kenji; Saeki, Keigo; Iwamoto, Junko; Okamoto, Nozomi; Tomioka, Kimiko; Nezu, Satoko; Ikada, Yoshito; Kurumatani, Norio

    2014-05-01

    Epidemiologic data have demonstrated associations of sleep-onset insomnia with a variety of diseases, including depression, dementia, diabetes and cardiovascular diseases. Sleep initiation is controlled by the suprachiasmatic nucleus of the hypothalamus and endogenous melatonin, both of which are influenced by environmental light. Exposure to evening light is hypothesized to cause circadian phase delay and melatonin suppression before bedtime, resulting in circadian misalignment and sleep-onset insomnia; however, whether exposure to evening light disturbs sleep initiation in home settings remains unclear. In this longitudinal analysis of 192 elderly individuals (mean age: 69.9 years), we measured evening light exposure and sleep-onset latency for 4 days using a wrist actigraph incorporating a light meter and an accelerometer. Mixed-effect linear regression analysis for repeated measurements was used to evaluate the effect of evening light exposure on subsequent sleep-onset latency. The median intensity of evening light exposure and the median sleep-onset latency were 27.3 lux (interquartile range, 17.9-43.4) and 17 min (interquartile range, 7-33), respectively. Univariate models showed significant associations between sleep-onset latency and age, gender, daytime physical activity, in-bed time, day length and average intensity of evening and nighttime light exposures. In a multivariate model, log-transformed average intensity of evening light exposure was significantly associated with log-transformed sleep-onset latency independent of the former potential confounding factors (regression coefficient, 0.133; 95% CI, 0.020-0.247; p = 0.021). Day length and nighttime light exposure were also significantly associated with log-transformed sleep-onset latency (p = 0.001 and p < 0.001, respectively). In conclusion, exposure to evening light in home setting prolongs subsequent sleep-onset latency in the elderly.

  6. A novel PRNP Y218N mutation in Gerstmann-Sträussler-Scheinker disease with neurofibrillary degeneration.

    Science.gov (United States)

    Alzualde, Ainhoa; Indakoetxea, Begoña; Ferrer, Isidre; Moreno, Fermin; Barandiaran, Myriam; Gorostidi, Ana; Estanga, Ainara; Ruiz, Irune; Calero, Miguel; van Leeuwen, Fred W; Atares, Begoña; Juste, Ramón; Rodriguez-Martínez, Ana Belén; López de Munain, Adolfo

    2010-08-01

    Gerstmann-Sträussler-Scheinker (GSS) disease is a prion disease associated with prion protein gene (PRNP) mutations. We report a novel PRNP mutation (Y218N) associated with GSS disease in a pathologically confirmed case and in two other affected family members. The clinical features of these cases met criteria for possible Alzheimer disease and possible frontotemporal dementia. Neuropathologic analysis revealed deposition of proteinase K-resistant prion protein (PrP(res)), widespread hyperphosphorylated tau pathology, abnormal accumulation of mitochondria in the vicinity of PrP deposits, and expression of mutant ubiquitin (UBB(+1)) in neurofibrillary tangles and dystrophic neurites. Prion protein immunoblotting using 3F4 and 1E4 antibodies disclosed multiple bands ranging from approximately 20 kd to 80 kd and lower bands of 15 kd and approximately 10 kd, the latter only seen after a long incubation. These bands were partially resistant to proteinase K pretreatment. This pattern differs from those seen in Creutzfeldt-Jakob disease andresembles those reported in other GSS cases. The approximately 10kd band was recognized with anti-PrP C-terminus antibodies but not with anti-N terminus antibodies, suggesting PrP truncation at the N terminal. This new mutation extends the list of known mutations responsible for GSS disease and reinforces its clinical heterogeneity. Genetic examination of the PRNP gene should be included in the workup of patients with poorly classifiable dementia.

  7. Quantitative, functional MRI and neurophysiological markers in a case of Gerstmann-Sträussler-Scheinker syndrome.

    Science.gov (United States)

    Marino, Silvia; Morabito, Rosa; De Salvo, S; Bonanno, L; Bramanti, A; Pollicino, P; Giorgianni, R; Bramanti, Placido

    Gerstmann-Sträussler-Scheinker syndrome (GSS) is an inherited autosomal dominant prion disease, caused by a codon 102 proline to leucine substitution (P102L) in the prion protein gene (PRNP). We describe the case of a 40-year-old male, affected by a slowly progressive gait disturbance, leg weakness and cognitive impairment. Genomic DNA revealed a point mutation of PRNP at codon 102, resulting in P102L, and the diagnosis of GSS was confirmed. Somatosensory evoked potentials showed alterations of principal parameters, particularly in the right upper and lower limbs. Laser-evoked potentials were indicative of nociceptive system impairment, especially in the right upper and lower limbs. Conventional magnetic resonance imaging (MRI) revealed marked atrophy of the vermis and cerebellar hemispheres and mild atrophy of the middle cerebellar peduncles and brainstem, as confirmed by a brain volume automatic analysis. Resting-state functional MRI showed increased functional connectivity in the bilateral visual cortex, and decreased functional connectivity in the bilateral frontal pole and supramarginal and precentral gyrus. Albeit limited to a single case, this is the first study to assess structural and functional connectivity in GSS using a multimodal approach.

  8. 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...

  9. Neutrality of miniSTR D22S1045 marker by Ewing's sarcoma phenotype.

    Science.gov (United States)

    Silva, Deborah S B S; Raimann, Paulo E; Moro, Tatiane; Picanço, Juliane B; Abujamra, Ana L; de Farias, Caroline B; Roesler, Rafael; Brunetto, Algemir L; Alho, Clarice S

    2013-11-01

    Neutrality investigations of markers with forensic use are important to see if a phenotypic trait is being expressed in relation to the alleles of the marker. MiniSTR marker D22S1045 (locus 22q12.3) is localized near the breakpoint region of the EWS gene (22q12.2), which leads to the development of Ewing's Sarcoma. Analyzing allele frequencies and linkage disequilibrium in Ewing's sarcoma patients and non-affected populations, we found that the marker mD22S1045 was neutral when related to Ewing's Sarcoma. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  10. A novel magnet based 3D printed marker wand as basis for repeated in-shoe multi segment foot analysis: a proof of concept.

    Science.gov (United States)

    Eerdekens, Maarten; Staes, Filip; Pilkington, Thomas; Deschamps, Kevin

    2017-01-01

    Application of in-shoe multi-segment foot kinematic analyses currently faces a number of challenges, including: (i) the difficulty to apply regular markers onto the skin, (ii) the necessity for an adequate shoe which fits various foot morphologies and (iii) the need for adequate repeatability throughout a repeated measure condition. The aim of this study therefore was to design novel magnet based 3D printed markers for repeated in-shoe measurements while using accordingly adapted modified shoes for a specific multi-segment foot model. Multi-segment foot kinematics of ten participants were recorded and kinematics of hindfoot, midfoot and forefoot were calculated. Dynamic trials were conducted to check for intra and inter-session repeatability when combining novel markers and modified shoes in a repeated measures design. Intraclass correlation coefficients were calculated to determine reliability. Both repeatability and reliability were proven to be good to excellent with maximum joint angle deviations of 1.11° for intra-session variability and 1.29° for same-day inter-session variability respectively and ICC values of >0.91. The novel markers can be reliably used in future research settings using in-shoe multi-segment foot kinematic analyses with multiple shod conditions.

  11. Repeated Causal Decision Making

    Science.gov (United States)

    Hagmayer, York; Meder, Bjorn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  12. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  13. Phenylketonuria mutation analysis in Northern Ireland: A rapid stepwise approach

    Energy Technology Data Exchange (ETDEWEB)

    Zschocke, J.; Graham, C.A.; Nevin, N.C. [Queen`s Univ., Belfast (Australia)] [and others

    1995-12-01

    We present a multistep approach for the rapid analysis of phenylketonuria (PKU) mutations. In the first step, three common mutations and a polymorphic short tandem repeat (STR) system are rapidly analyzed with a fluorescent multiplex assay. In the second step, minihaplotypes combining STR and VNTR data are used to determine rare mutations likely to be present in an investigated patient, which are then confirmed by restriction enzyme analysis. The remaining mutations are analyzed with denaturant gradient-gel electrophoresis and sequencing. The first two steps together identify both mutations in 90%-95% of PKU patients, and results can be obtained within 2 d. We have investigated 121 Northern Irish families with hyperphenylalaninemia, including virtually all patients born since 1972, and have found 34 different mutations on 241 of the 242 mutant alleles. Three mutations (R408W, 165T, and F39L) account for 57.5% of mutations, while 14 mutations occur with a frequency of 1%-6%. The present analysis system is efficient and inexpensive and is particularly well suited to routine mutation analysis in a diagnostic setting. 19 refs., 5 tabs.

  14. Evaluation of the Repeatability of the Delta Q Duct Leakage Testing TechniqueIncluding Investigation of Robust Analysis Techniques and Estimates of Weather Induced Uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Dickerhoff, Darryl; Walker, Iain

    2008-08-01

    The DeltaQ test is a method of estimating the air leakage from forced air duct systems. Developed primarily for residential and small commercial applications it uses the changes in blower door test results due to forced air system operation. Previous studies established the principles behind DeltaQ testing, but raised issues of precision of the test, particularly for leaky homes on windy days. Details of the measurement technique are available in an ASTM Standard (ASTM E1554-2007). In order to ease adoption of the test method, this study answers questions regarding the uncertainty due to changing weather during the test (particularly changes in wind speed) and the applicability to low leakage systems. The first question arises because the building envelope air flows and pressures used in the DeltaQ test are influenced by weather induced pressures. Variability in wind induced pressures rather than temperature difference induced pressures dominates this effect because the wind pressures change rapidly over the time period of a test. The second question needs to answered so that DeltaQ testing can be used in programs requiring or giving credit for tight ducts (e.g., California's Building Energy Code (CEC 2005)). DeltaQ modeling biases have been previously investigated in laboratory studies where there was no weather induced changes in envelope flows and pressures. Laboratory work by Andrews (2002) and Walker et al. (2004) found biases of about 0.5% of forced air system blower flow and individual test uncertainty of about 2% of forced air system blower flow. The laboratory tests were repeated by Walker and Dickerhoff (2006 and 2008) using a new ramping technique that continuously varied envelope pressures and air flows rather than taking data at pre-selected pressure stations (as used in ASTM E1554-2003 and other previous studies). The biases and individual test uncertainties for ramping were found to be very close (less than 0.5% of air handler flow) to those

  15. Methods for analysing cardiovascular studies with repeated measures

    NARCIS (Netherlands)

    Cleophas, T. J.; Zwinderman, A. H.; van Ouwerkerk, B. M.

    2009-01-01

    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies

  16. Impact of the 2008 global financial crisis on the health of Canadians: repeated cross-sectional analysis of the Canadian Community Health Survey, 2007-2013.

    Science.gov (United States)

    Nour, Sabrina; Labonté, Ronald; Bancej, Christina

    2017-04-01

    Despite a clear impact on the Canadian economy, little is known about the subsequent health impacts of the 2008 global financial crisis (GFC) in this country. This study fills this gap in knowledge by conducting a repeated cross-sectional analysis of the Canadian Community Health Survey (CCHS). Data from 7 cycles (2007-2013) of the CCHS were combined to form a large data set representative of the Canadian working-age population (15-64 years) residing in 1 of 10 provinces. A logistic regression model was used to determine whether exposure to various periods of the GFC resulted in increased odds of reporting poor mental health. Exposure was categorised into 4 periods based on political and economic indicators, as follows: precrisis period (baseline), initial crisis period, stimulus period and austerity period. Other outcomes investigated included: anxiety disorders (AD), mood disorders (MD), poor physical health and health-related behaviours (heavy alcohol drinking (HAD) and decreased fruit/vegetable consumption (FVC)). A significant increased odds of reporting poor mental health was observed during the austerity period compared with the precrisis period (OR=1.26 (1.16 to 1.32)); findings remain significant when adjusted for sex, marital status and education. Exposure to the austerity period was also significantly associated with increased odds of reporting AD, MD, HAD and decreased odds of FVC. No significant associations were observed for the poor self-perceived physical health variable. Statistically significant associations were observed between several negative health outcomes and the austerity period when compared with the precrisis period. Austerity has been linked to worsening health in other studies and represents an example of how the policy response can have greater detrimental impact on health than the financial crisis itself. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to

  17. Multiple-locus variable-number tandem repeat analysis of Leptospira interrogans and Leptospira borgpetersenii isolated from small feral and wild mammals in East Asia.

    Science.gov (United States)

    Koizumi, Nobuo; Izumiya, Hidemasa; Mu, Jung-Jung; Arent, Zbigniew; Okano, Shou; Nakajima, Chie; Suzuki, Yasuhiko; Mizutani Muto, Maki; Tanikawa, Tsutomu; Taylor, Kyle R; Komatsu, Noriyuki; Yoshimatsu, Kumiko; Thi Thu Ha, Hoang; Ohnishi, Makoto

    2015-12-01

    Leptospira spp. are the causative agents of a worldwide zoonosis, leptospirosis, maintained by various mammals. Each Leptospira serovar is frequently associated with a particular maintenance host, and recently, Leptospira genotype-host association has also been suggested to limit serovars to restricted areas. We investigated the molecular characteristics of L. interrogans and L. borgpetersenii which were isolated from small feral and wild animals in four East Asian states using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA using 11 loci was performed on 110 L. interrogans serogroups from Japan (79 strains of 5 serogroups from 3 animal species), Philippines (21; 3; 2), Taiwan (7; 2; 3), and Vietnam (3; 1; 1). A MLVA method using 4 loci for L. borgpetersenii was established and performed on 52 isolates from Japan (26; 3; 7), Philippines (13; 1; 2), and Taiwan (13; 1; 3). In L. interrogans, serogroups Autumnalis and Hebdomadis appeared more genetically diverse than serogroups Bataviae, Grippotyphosa, Icterohaemorrhagiae, Pomona, or Pyrogenes. The former serogroup strains with the exception of one Hebdomadis strain were isolated from Apodemus speciosus while all the latter serogroup strains with the exception of Grippotyphosa were isolated from Rattus norvegicus. L. borgpetersenii was isolated from at least 11 animal species while L. interrogans was isolated from five species, which might suggest a wider host range for L. borgpetersenii. Broad host preference in a single genotype was also observed, which colonized not only different species of the same genera but also multiple animal genera. This study demonstrates that there may be variability in the range of genetic diversity among different Leptospira serogroups, which may be attributed to maintenance host animals and environmental factors. Copyright © 2015. Published by Elsevier B.V.

  18. 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.

  19. Latvijas strādājošo jauniešu attieksme pret naudu

    OpenAIRE

    Stigeviča, Inga

    2010-01-01

    Ar naudu šobrīd nākas saskarties ikvienam Latvijas iedzīvotājam, jo bez naudas cilvēks nav spējīgs pilnvērtīgi eksistēt. Tādā gadījumā arī katram indivīdam ir izveidojusies noteikta attieksme pret naudu, kas spējīga izpausties noteiktās darbībās un nozīmes. Autore savā bakalaura darbā vēlas saprast, kāda ir tieši Latvijas strādājošo jauniešu attieksme pret savu nopelnīto naudu un naudas fenomenu kopumā. Par pētījuma objektu tika izvēlēti strādājošie jaunieši Latvijā, jo publiski pieejamu pētī...

  20. Strömgren uvby photometry of the peculiar globular cluster NGC 2419

    Science.gov (United States)

    Frank, Matthias J.; Koch, Andreas; Feltzing, Sofia; Kacharov, Nikolay; Wilkinson, Mark I.; Irwin, Mike

    2015-09-01

    NGC 2419 is a peculiar Galactic globular cluster offset from the others in the size-luminosity diagram, and showing several chemical abundance anomalies. Here, we present Strömgren uvby photometry of the cluster. Using the gravity- and metallicity-sensitive c1 and m1 indices, we identify a sample of likely cluster members extending well beyond the formal tidal radius. The estimated contamination by cluster non-members is only one per cent, making our catalogue ideally suited for spectroscopic follow-up. We derive photometric [Fe/H] of red giants, and depending on which metallicity calibration from the literature we use, we find reasonable to excellent agreement with spectroscopic [Fe/H], both for the cluster mean metallicity and for individual stars. We demonstrate explicitly that the photometric uncertainties are not Gaussian and this must be accounted for in any analysis of the metallicity distribution function. Using a realistic, non-Gaussian model for the photometric uncertainties, we find a formal internal [Fe/H] spread of σ=0.11+0.02-0.01 dex. This is an upper limit to the cluster's true [Fe/H] spread and may partially, and possibly entirely, reflect the limited precision of the photometric metallicity estimation and systematic effects. The lack of correlation between spectroscopic and photometric [Fe/H] of individual stars is further evidence against a [Fe/H] spread on the 0.1 dex level. Finally, the CN-sensitive δ4, among other colour indices, anti-correlates strongly with magnesium abundance, indicating that the second-generation stars are nitrogen enriched. The absence of similar correlations in some other CN-sensitive indices supports the second generation being enriched in He, which in these indices approximately compensates the shift due to CN. Compared to a single continuous distribution with finite dispersion, the observed δ4 distribution of red giants is slightly better fit by two distinct populations with no internal spread, with the nitrogen

  1. The characterization of a new set of EST-derived simple sequence repeat (SSR markers as a resource for the genetic analysis of Phaseolus vulgaris

    Directory of Open Access Journals (Sweden)

    Borba Tereza CO

    2011-05-01

    Full Text Available Abstract Background Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats, specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested. Results From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11% showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%, Vigna (25.9%, Glycine (19.8%, Medicago (10.2%, Dipterix (6% and Arachis (1.8% genera. The average PIC (Polymorphism Information Content varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558 population, 24% (76 were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5% were mapped to 14 linkage groups, resulting in a map length of 1,157 cM. Conclusions A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity

  2. Prevalence, antimicrobial resistance and multiple-locus variable-number tandem-repeat analysis profiles of diarrheagenic Escherichia coli isolated from different retail foods.

    Science.gov (United States)

    Wang, Lili; Nakamura, Hiromi; Kage-Nakadai, Eriko; Hara-Kudo, Yukiko; Nishikawa, Yoshikazu

    2017-05-16

    Diarrheagenic E. coli (DEC) isolates were recovered from local retail markets and the Osaka Municipal Central Wholesale Market in Japan. Retail food samples were collected for analysis in Osaka Japan from 2005 to 2008 and consisted of 32 beef, 28 pork, 20 poultry, 136 fish, 66 fruits and vegetables and 51 ready-to-eat (RTE) food samples. A total of 82 DEC strains were recovered from 64 (19%) food samples with the highest prevalence in poultry (100%, 20/20), followed by pork (54%, 15/28), beef (28%, 9/32), fruits and vegetables (12%, 8/66), fish (6.6%, 9/136) and RTE foods (5.9%, 3/51). Most of the strains belonged to E. coli possessing the enteroaggregative E. coli (EAEC) heat-stable enterotoxin 1 (EAST1) gene (EAST1EC; n=62, P3 antimicrobial agents. Isolates resistant to >5 antimicrobials were only found in the meat samples, while isolates from the fruits and vegetables as well as RTE foods showed resistance to only 1 or 2 antimicrobial agents. Sixty one percent of EAST1EC, 56% of EPEC and all of the EAEC and ETEC were resistant to at least 1 antimicrobial agent. Multiple-locus variable-number tandem repeat analysis (MLVA) was used in this study for genotyping of DEC. The 82 isolates collected for this study showed 77 distinct MLVA profiles located among 3 branches. The Simpson's Index of Diversity (D) was 99.9% at its highest. The high diversity of these food strains would suggest their originating from a variety of sources and environments. In conclusion, retail food samples in Japan were contaminated with DEC; EAST1EC, a putative DEC, were detected at high rates in poultry, pork and beef. Isolates resistant to >3 antimicrobials were found only in raw meat and fish. Food animals may act as the reservoir for multi-resistant bacteria. Due to the finding that nearly 1/3 of EAST1EC strains were resistant to >3 antimicrobials, additional surveillance for EAST1EC should be initiated. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA

    Directory of Open Access Journals (Sweden)

    Sintchenko Vitali

    2012-03-01

    Full Text Available Abstract Background Prospective typing of Salmonella enterica serovar Typhimurium (STM by multiple-locus variable-number tandem-repeat analysis (MLVA can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance. Methods During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW state public health surveillance program. Results A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates, DT135 (13.9%, DT9 (10.8%, DT44 (4.5% and DT126 (4.5%. There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed. Conclusions Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance. A part of this study was presented at the MEEGID

  4. Stereotactic body radiotherapy (SBRT) for multiple pulmonary oligometastases: Analysis of number and timing of repeat SBRT as impact factors on treatment safety and efficacy.

    Science.gov (United States)

    Klement, R J; Hoerner-Rieber, J; Adebahr, S; Andratschke, N; Blanck, O; Boda-Heggemann, J; Duma, M; Eble, M J; Eich, H C; Flentje, M; Gerum, S; Hass, P; Henkenberens, C; Hildebrandt, G; Imhoff, D; Kahl, K H; Klass, N D; Krempien, R; Lohaus, F; Petersen, C; Schrade, E; Wendt, T G; Wittig, A; Guckenberger, M

    2018-03-03

    Stereotactic body radiotherapy (SBRT) for oligometastatic disease is characterized by an excellent safety profile; however, experiences are mostly based on treatment of one single metastasis. It was the aim of this study to evaluate safety and efficacy of SBRT for multiple pulmonary metastases. This study is based on a retrospective database of the DEGRO stereotactic working group, consisting of 637 patients with 858 treatments. Cox regression and logistic regression were used to analyze the association between the number of SBRT treatments or the number and the timing of repeat SBRT courses with overall survival (OS) and the risk of early death. Out of 637 patients, 145 patients were treated for multiple pulmonary metastases; 88 patients received all SBRT treatments within one month whereas 57 patients were treated with repeat SBRT separated by at least one month. Median OS for the total patient population was 23.5 months and OS was not significantly influenced by the overall number of SBRT treatments or the number and timing of repeat SBRT courses. The risk of early death within 3 and 6 months was not increased in patients treated with multiple SBRT treatments, and no grade 4 or grade 5 toxicity was observed in these patients. In appropriately selected patients, synchronous SBRT for multiple pulmonary oligometastases and repeat SBRT may have a comparable safety and efficacy profile compared to SBRT for one single oligometastasis. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

    Science.gov (United States)

    Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

    2016-09-01

    The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

  6. Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: Evidence for differences and commonalities in size distributions and size restrictions

    NARCIS (Netherlands)

    M. Schaap (Michiel); R.J.L.F. Lemmers (Richard); R. Maassen (Roel); P.J. van der Vliet (Patrick); L.F. Hoogerheide (Lennart); H.K. van Dijk (Herman); N. Basturk (Nalan); P. de Knijff (Peter); S.M. van der Maarel (Silvère)

    2013-01-01

    textabstractBackground: Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and

  7. Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions

    NARCIS (Netherlands)

    Schaap, M.; Lemmers, R.J.L.F.; Maassen, R.; van der Vliet, P.J.; Hoogerheide, L.F.; van Dijk, H.K.; Basturk, N.; de Knijff, P.; van der Maarel, S.M.

    2013-01-01

    Background: Macrosatellite repeats (MSRs), usually spanning hundreds of kilobases of genomic DNA, comprise a significant proportion of the human genome. Because of their highly polymorphic nature, MSRs represent an extreme example of copy number variation, but their structure and function is largely

  8. Meta-analysis of the effect of overexpression of C-repeat/dehydration-responsive element binding family genes on temperature stress tolerance and related responses

    Science.gov (United States)

    C-repeat/dehydration-responsive element binding proteins are transcription factors that play a critical role in plant response to temperature stress. Over-expression of CBF/DREB genes has been demonstrated to enhance temperature stress tolerance. A series of physiological and biochemical modificat...

  9. Serological analysis of human anti-human antibody responses in colon cancer patients treated with repeated doses of humanized monoclonal antibody A33.

    Science.gov (United States)

    Ritter, G; Cohen, L S; Williams, C; Richards, E C; Old, L J; Welt, S

    2001-09-15

    Mouse monoclonal antibody A33 (mAb A33) recognizes a M(r) 43,000 cell surface glycoprotein (designated A33) expressed in human colonic epithelium and colon cancer but absent from most other normal tissues. In patients, mAb A33 localizes with high specificity to colon cancer and is retained for up to 6 weeks in the cancer but cleared rapidly from normal colon (5-6 days). As a carrier of (125)I or (131)I, mAb A33 has shown antitumor activity. Induction of strong human anti-mouse antibody (immunoglobulin; HAMA) responses in patients, however, limits the use of the murine mAb A33 to very few injections. A humanized version of this antibody (huAb A33) has been prepared for Phase I and II clinical studies in patients with colon cancer. In those studies, immunogenicity of huAb A33 has been monitored using a novel, highly sensitive BIACORE method, which allows measurement of human anti-human antibodies (HAHAs) without the use of secondary reagents. We found that 63% (26 of 41) of the patients treated with repeated doses of huAb A33 developed HAHAs against a conformational antigenic determinant located in the V(L) and V(H) regions of huAb A33. Detailed serological analysis showed two distinct types of HAHAs. HAHA of type I (49% of patients) was characterized by an early onset with peak HAHA levels after 2 weeks of treatment, which declined with ongoing huAb A33 treatment. HAHA of type II (17% of patients) was characterized by a typically later onset of HAHA than in type I and by progressively increasing HAHA levels with each subsequent huAb A33 administration. Colon cancer patients with type I HAHAs did not develop infusion-related adverse events. In contrast, HAHA of type II was indicative of infusion-related adverse events. By using this new method, we were able to distinguish these two types of HAHAs in patients while on antibody treatment, allowing patients to be removed from study prior to the onset of severe infusion-related adverse events.

  10. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Science.gov (United States)

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  11. Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

    Science.gov (United States)

    Zhou, Anju; Wu, Weiwei; Liu, Qiuling; Wu, Yeda; Lu, Dejian

    2013-03-01

    Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

  12. FvSTR1, a striatin orthologue in Fusarium virguliforme, is required for asexual development and virulence.

    Science.gov (United States)

    Islam, Kazi T; Bond, Jason P; Fakhoury, Ahmad M

    2017-08-01

    The soil-borne fungus Fusarium virguliforme causes sudden death syndrome (SDS), one of the most devastating diseases of soybean in North and South America. Despite the importance of SDS, a clear understanding of the fungal pathogenicity factors that affect the development of this disease is still lacking. We have identified FvSTR1, a F. virguliforme gene, which encodes a protein similar to a family of striatin proteins previously reported to regulate signalling pathways, cell differentiation, conidiation, sexual development, and virulence in filamentous fungi. Striatins are multi-domain proteins that serve as scaffolding units in the striatin-interacting phosphatase and kinase (STRIPAK) complex in fungi and animals. To address the function of a striatin homologue in F. virguliforme, FvSTR1 was disrupted and functionally characterized using a gene knock out strategy. The resulting Fvstr1 mutants were largely impaired in conidiation and pigmentation, and displayed defective conidia and conidiophore morphology compared to the wild-type and ectopic transformants. Greenhouse virulence assays revealed that the disruption of FvSTR1 resulted in complete loss of virulence in F. virguliforme. Microtome studies using fluorescence microscopy showed that the Fvstr1 mutants were defective in their ability to colonize the vascular system. The Fvstr1 mutants also showed a reduced transcript level of genes involved in asexual reproduction and in the production of secondary metabolites. These results suggest that FvSTR1 has a critical role in asexual development and virulence in F. virguliforme.

  13. 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.

  14. Oligomerisation of C. elegans Olfactory Receptors, ODR-10 and STR-112, in Yeast

    KAUST Repository

    Tehseen, Muhammad; Liao, Chunyan; Dacres, Helen; Dumancic, Mira; Trowell, Stephen; Anderson, Alisha

    2014-01-01

    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.

  15. [Polymorphism of PentaD and PentaE STR locus in five Chinese Han population].

    Science.gov (United States)

    Liu, Qiu-ling; Lu, Hui-ling; Lü, De-jian

    2003-01-01

    To obtain the genetic polymorphism data of Guangxi, Hunan, Henan, Sichuan, Taiwang Chinese Han population and compare the polymorphism of PentaD and PentaE STR locus. The two loci was analyzed by using the PowerPlex 16 System. 10 alleles of PentaD and 19 alleles of PentaE were found in the five Han population. PentaD and PentaE have the expected heterozygosity values of 0.7746-0.8047 and 0.9005-0.9219, the polymorphism information content values of 0.7710-0.8025 and 0.8969-0.9176, the discrimination power values of 0.9223-0.9341 and 0.9471-0.9782, the power of exclusion values of 0.5435-0.6325 and 0.6785-0.8465, respectively. The result showed that these two loci were highly informative and suitable for forensic application.

  16. Strømmålinger for ny forbindelse over Limfjorden i Lindholmlinien ved Aalborg

    DEFF Research Database (Denmark)

    Burcharth, Hans F.; Larsen, Torben

    På foranledning af "Undersøgelsesgruppen af 1. maj 1975", repræsenteret ved Rambøll og Hannemann A/S, Nørresundby har laboratoriet i november og december udført en række strømmålinger i området mellem Egholm og jernbanebroen i Limfjorden ved Aalborg med henblik på at fremskaffe et grundlag...... for vurderingen af besejlingsforholdene ved en kommende ny forbindelse over limfjorden ved lindholmlinien. Ved undersøgelsens planlægning har medvirket civilingeniør J. C. Schmidt, Rambøll og Hannemann A/S, ingeniørdocent H. F. Burchart og civilingeniør Torben Larsen. Herværende rapport er udarbejdet af Torben...

  17. First evidence of multiple populations along the AGB from Strömgren photometry

    Science.gov (United States)

    Gruyters, Pieter; Casagrande, Luca; Milone, Antonino P.; Hodgkin, Simon T.; Serenelli, Aldo; Feltzing, Sofia

    2017-07-01

    Spectroscopic studies have demonstrated that nearly all Galactic globular clusters (GCs) harbour multiple stellar populations with different chemical compositions. Moreover, colour-magnitude diagrams based exclusively on Strömgrem photometry have allowed us to identify and characterise multiple populations along the RGB of a large number of clusters. In this paper we show for the first time that Strömgren photometry is also very efficient at identifying multiple populations along the AGB, and demonstrate that the AGB of M 3, M 92, NGC 362, NGC 1851, and NGC 6752 are not consistent with a single stellar population. We also provide a catalogue of RGB and AGB stars photometrically identified in these clusters for further spectroscopic follow-up studies. We combined photometry and elemental abundances from the literature for RGB and AGB stars in NGC 6752 where the presence of multiple populations along the AGB has been widely debated. We find that, while the MS, SGB, and RGB host three stellar populations with different helium and light element abundances, only two populations of AGB stars are present in the cluster. These results are consistent with standard evolutionary theory. Based on observations made with the Isaac Newton Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.Full Tables B.1 and B.2 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/603/A37

  18. Preimplantation genetic diagnosis of X-linked diseases examined by indirect linkage analysis.

    Science.gov (United States)

    Borgulova, I; Putzova, M; Soldatova, I; Krautova, L; Pecnova, L; Mika, J; Kren, R; Potuznikova, P; Stejskal, D

    2015-01-01

    Many centers of assisted reproduction in the Czech Republic offer preimplantation genetic diagnosis with fluorescent in situ hybridization (FISH) to couples requiring preimplantation genetic diagnosis (PGD) of X-linked diseases. However, this process results in discarding all male embryos and is not able to distinguish a carrier or healthy female embryo in X-linked recessive disorders. The main aim of this study was to summarize a six-year period of PGD of X-linked monogenic diseases using indirect linkage analysis. We wanted to accentuate the advantage indirect analysis of PGD using multiple displacement amplification (MDA) followed by short tandem repeat (STR) analysis. We present forty-six PGD cycles, including pre-case haplotyping (PGH) panel, for fifteen X-linked diseases. Embryo transfer was made thirty-eight times and gravidity was confirmed in thirteen female probands with a success rate of pregnancy calculated at 42 %. PGD procedure using MDA amplification followed by STR analysis provides help in identifying genetic defects within embryos prior to implantation. The reliability of the method was also supported by high pregnancy rate compared to other publications, which commonly achieved a 30-35 % success rate (Tab. 2, Fig. 1, Ref. 33).

  19. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

    Science.gov (United States)

    Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

    2015-10-01

    Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

  20. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-05-23

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

  1. Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

    Science.gov (United States)

    Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

    2016-01-01

    Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample

  2. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  3. 78 FR 65594 - Vehicular Repeaters

    Science.gov (United States)

    2013-11-01

    ... coordinators estimate the effect on coordination fees? Does the supposed benefit that mobile repeater stations... allow the licensing and operation of vehicular repeater systems and other mobile repeaters by public... email: [email protected] or phone: 202-418- 0530 or TTY: 202-418-0432. For detailed instructions for...

  4. Telomerase Repeated Amplification Protocol (TRAP).

    Science.gov (United States)

    Mender, Ilgen; Shay, Jerry W

    2015-11-20

    Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

  5. The influence of preirradiation history of E. coli WP2 cells on the residual fixation of mutations in rpsL. (strA) locus

    International Nuclear Information System (INIS)

    Filippov, V.D.

    1986-01-01

    The values of residual fixation of strA mutations in E.coli culture, irradiated by UV-light (6.8 J/m 2 ) in different physiological states and conforming to different in depth strA mutation frequency decrease in postirradiation incubation under conditions unfavourable for protein synthesis are determined. By residual fixation one should mean accumulation of strA mutations stable to antimutagenous effect of photoreactivating light in cell population incubated in buffer after UV radiation. It is established that residual fixation is small in cultures, conforming to deep decrease, and is a factor (about 40% of strA mutations is fixed) in a culture, conforming to moderate decrease (about 60% of strA mutations disappears) of mutation frequency in incubation under conditions unfavourable for protein synthesis. The conclusion is made that the depth of strA mutation frequency decrease, taking place under the influence of mfd system, depends on the level of residual fixation of this mutations. It is supposed that residual fixation is caused by rpsL (strA) locus introduction in replication cycle initiated after radiation

  6. Influence of preirradiation history of E. coli WP2 cells on the residual fixation of mutations in rpsL. (strA) locus

    Energy Technology Data Exchange (ETDEWEB)

    Filippov, V D

    1986-07-01

    The values of residual fixation of strA mutations in E.coli culture, irradiated by UV-light (6.8 J/m/sup 2/) in different physiological states and conforming to different in depth strA mutation frequency decrease in postirradiation incubation under conditions unfavourable for protein synthesis are determined. By residual fixation one should mean accumulation of strA mutations stable to antimutagenous effect of photoreactivating light in cell population incubated in buffer after UV radiation. It is established that residual fixation is small in cultures, conforming to deep decrease, and is a factor (about 40% of strA mutations is fixed) in a culture, conforming to moderate decrease (about 60% of strA mutations disappears) of mutation frequency in incubation under conditions unfavourable for protein synthesis. The conclusion is made that the depth of strA mutation frequency decrease, taking place under the influence of mfd system, depends on the level of residual fixation of this mutations. It is supposed that residual fixation is caused by rpsL (strA) locus introduction in replication cycle initiated after radiation.

  7. Hematopoietic stem cell transplantation monitoring in childhood. Hematological diseases in Serbia: STR-PCR techniques

    Directory of Open Access Journals (Sweden)

    Krstić Aleksandra D.

    2007-01-01

    Full Text Available Hematopoietic stem cell transplantation (HSCT is a very successful method of treatment for children with different aquired or inborn diseases. The main goal of post-transplantation chimerism monitoring in HSCT is to predict negative events (such as disease relapse and graft rejection, in order to intervene with appropriate therapy and improve the probability of long-term DFS (disease free survival. In this context, by quantifying the relative amounts of donor and recipient cells present in the peripheral blood sample, it can be determined if engraftment has taken place at all, or if full or mixed chimerism exists. In a group of patients who underwent hematopoietic stem cell transplantation at the Mother and Child Health Care Institute, we decided to use standard human identfication tests based on multiplex PCR analyses of short tandem repeats (STRs, as they are highly informative, sensitive, and fast and therefore represent an optimal methodological approach to engraftment analysis.

  8. Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues.

    Science.gov (United States)

    Barallon, Rita; Bauer, Steven R; Butler, John; Capes-Davis, Amanda; Dirks, Wilhelm G; Elmore, Eugene; Furtado, Manohar; Kline, Margaret C; Kohara, Arihiro; Los, Georgyi V; MacLeod, Roderick A F; Masters, John R W; Nardone, Mark; Nardone, Roland M; Nims, Raymond W; Price, Paul J; Reid, Yvonne A; Shewale, Jaiprakash; Sykes, Gregory; Steuer, Anton F; Storts, Douglas R; Thomson, Jim; Taraporewala, Zenobia; Alston-Roberts, Christine; Kerrigan, Liz

    2010-10-01

    Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues.

  9. Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

    Science.gov (United States)

    Barallon, Rita; Bauer, Steven R.; Butler, John; Capes-Davis, Amanda; Dirks, Wilhelm G.; Furtado, Manohar; Kline, Margaret C.; Kohara, Arihiro; Los, Georgyi V.; MacLeod, Roderick A. F.; Masters, John R. W.; Nardone, Mark; Nardone, Roland M.; Nims, Raymond W.; Price, Paul J.; Reid, Yvonne A.; Shewale, Jaiprakash; Sykes, Gregory; Steuer, Anton F.; Storts, Douglas R.; Thomson, Jim; Taraporewala, Zenobia; Alston-Roberts, Christine; Kerrigan, Liz

    2010-01-01

    Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues. PMID:20614197

  10. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Tomaszkiewicz, Marta; Campos-Sánchez, Rebeca; Eckert, Kristin A; DeGiorgio, Michael; Makova, Kateryna D

    2016-10-01

    Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA-DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Repeated causal decision making.

    Science.gov (United States)

    Hagmayer, York; Meder, Björn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in such situations and how they use their knowledge to adapt to changes in the decision context. Our studies show that decision makers' behavior is strongly contingent on their causal beliefs and that people exploit their causal knowledge to assess the consequences of changes in the decision problem. A high consistency between hypotheses about causal structure, causally expected values, and actual choices was observed. The experiments show that (a) existing causal hypotheses guide the interpretation of decision feedback, (b) consequences of decisions are used to revise existing causal beliefs, and (c) decision makers use the experienced feedback to induce a causal model of the choice situation even when they have no initial causal hypotheses, which (d) enables them to adapt their choices to changes of the decision problem. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  12. Performance Analysis of Measurement Inaccuracies of IMU/GPS on Airborne Repeat-pass Interferometric SAR in the Presence of Squint

    Directory of Open Access Journals (Sweden)

    Deng Yuan

    2014-08-01

    Full Text Available In the MOtion COmpensation (MOCO approach to airborne repeat-pass interferometric Synthetic Aperture Radar (SAR based on motion measurement data, the measurement inaccuracies of Inertial Measurement Unit/Global Positioning System (IMU/GPS and the positioning errors of the target, which may contribute to the residual uncompensated motion errors, affect the imaging result and interferometric measurement. Considering the effects of the two types of error, this paper builds a mathematical model of residual motion errors in presence of squint, and analyzes the effects on the residual motion errors induced by the measurement inaccuracies of IMU/GPS and the positioning errors of the target. In particular, the effects of various measurement inaccuracies of IMU/GPS on interferometric SAR image quality, interferometric phase, and digital elevation model precision are disscussed. Moreover, the paper quantitatively researches the effects of residual motion errors on airborne repeat-pass interferometric SAR through theoretical and simulated analyses and provides theoretical bases for system design and signal processing.

  13. Structural Analysis and Anticoagulant Activities of the Novel Sulfated Fucan Possessing a Regular Well-Defined Repeating Unit from Sea Cucumber

    Directory of Open Access Journals (Sweden)

    Mingyi Wu

    2015-04-01

    Full Text Available Sulfated fucans, the complex polysaccharides, exhibit various biological activities. Herein, we purified two fucans from the sea cucumbers Holothuria edulis and Ludwigothurea grisea. Their structures were verified by means of HPGPC, FT-IR, GC–MS and NMR. As a result, a novel structural motif for this type of polymers is reported. The fucans have a unique structure composed of a central core of regular (1→2 and (1→3-linked tetrasaccharide repeating units. Approximately 50% of the units from L. grisea (100% for H. edulis fucan contain sides of oligosaccharides formed by nonsulfated fucose units linked to the O-4 position of the central core. Anticoagulant activity assays indicate that the sea cucumber fucans strongly inhibit human blood clotting through the intrinsic pathways of the coagulation cascade. Moreover, the mechanism of anticoagulant action of the fucans is selective inhibition of thrombin activity by heparin cofactor II. The distinctive tetrasaccharide repeating units contribute to the anticoagulant action. Additionally, unlike the fucans from marine alga, although the sea cucumber fucans have great molecular weights and affluent sulfates, they do not induce platelet aggregation. Overall, our results may be helpful in understanding the structure-function relationships of the well-defined polysaccharides from invertebrate as new types of safer anticoagulants.

  14. Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

    Science.gov (United States)

    Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

    2016-09-01

    Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

  15. Efficacy of Repeated Botulinum Toxin Type A Injections for Spastic Equinus in Children with Cerebral Palsy-A Secondary Analysis of the Randomized Clinical Trial.

    Science.gov (United States)

    Hong, Bo Young; Chang, Hyun Jung; Lee, Sang-Jee; Lee, Soyoung; Park, Joo Hyun; Kwon, Jeong-Yi

    2017-08-21

    Botulinum toxin A is considered an important tool to control spasticity in children with cerebral palsy. Several factors are known to affect the efficacy of botulinum toxin, such as dosage, appropriate muscle selection and application, age, and accompanying therapy. A multicenter, double-blind, randomized, prospective phase III clinical trial of botulinum toxin A for the treatment of dynamic equinus in 144 children with cerebral palsy was performed to compare the efficacies of letibotulinumtoxin A and onabotulinumtoxin A. Secondary analyses were performed to evaluate factors that affected the outcome, focusing on the number of times injections were repeated. Effectiveness was defined as a change of 2 or more in the physician's rating scale. Multivariate regression analyses were performed with multiple variables. The first injection of botulinum toxin A significantly improved D subscale of Gross Motor Function Measure-88 scores at 3 months compared to repeated injections ( p < 0.05). After 6 months, patients who had one injection or none before the study showed significantly better outcomes than those who had more than one injection in terms of observational gait scores.

  16. A Further Analysis of the Relationship between Yellow Ripe-Fruit Color and the Capsanthin-Capsorubin Synthase Gene in Pepper (Capsicum sp.) Indicated a New Mutant Variant in C. annuum and a Tandem Repeat Structure in Promoter Region

    Science.gov (United States)

    Gui, Xiao-Ling; Chang, Xiao-Bei; Gong, Zhen-Hui

    2013-01-01

    Mature pepper (Capsicum sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs), we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production. PMID:23637942

  17. [Axel Ström--pioneer of social medicine and administrator].

    Science.gov (United States)

    Sundby, Per

    2002-01-10

    Dr Axel Strøm (1901-85), professor in the University of Oslo from 1940 to 1970, was a leader in Norwegian medicine in the latter half of the 20th century. He qualified in 1926 and in 1936 gained a doctorate with a dissertation on the toxin production of the Corynebacterium diphtheriae. His first appointment as a professor was in hygiene. In 1951 he moved on to public health, a field that he pioneered in Norway and the other Scandinavian countries. As a professor during the German occupation of Norway in the Second World War, he joined the university's resistance against the Nazi authorities' attempts at taking control. When the war was over he became deeply involved in research on the impact of war on health. At a time when the study of the impact of lifestyle factors was still in its infancy, he suggested that the war-induced reduction in dietary fat consumption might be the cause of observed lower cardiovascular mortality. Of more practical importance were the studies he initiated of the mainly psychological late-onset effects of traumas suffered by prisoners in German camps, seamen, soldiers and other exposed groups. In this area, too, he was an early explorer, of what has come to be known as post-traumatic stress disorder. His efforts led to improved war pension entitlements for the victims. Over the years, exposed groups became his major professional interest as a public health specialist. In his academic work, dr Strøm also pioneered medical ethics, care for the elderly, legislation on abortion, and the rapidly expanding field of the medical basis for social security benefits. As a practising physician he was in the vanguard of occupational medicine and other kinds of preventive medicine. What brought him most recognition was, however, his leading role over many years in the Norwegian Medical Association and in the University of Oslo. He served as chairman of the Junior Hospital Doctors Association, president of the Norwegian Medical Association and

  18. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.26134, Lat: 23.76895 (WGS84); Sensor Depth: 4.57m; Data Range: 20080915-20100908.

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    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, FFS; Long: -166.27510, Lat: 23.85623 (WGS84); Sensor Depth: 7.62m; Data Range: 20080915-20091009.

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    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); NWHI, FFS; Long: -166.17967, Lat: 23.63883 (WGS84); Sensor Depth: 11.28m; Data Range: 20060906-20070930.

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    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); NWHI, FFS; Long: -166.16683, Lat: 23.73815 (WGS84); Sensor Depth: 2.01m; Data Range: 20040918-20060905.

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    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, FFS; Long: -166.26132, Lat: 23.76897 (WGS84); Sensor Depth: 3.96m; Data Range: 20040917-20060905.

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  3. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.26197, Lat: 23.76887 (WGS84); Sensor Depth: 10.06m; Data Range: 20080915-20090614.

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  4. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27163, Lat: 23.85675 (WGS84); Sensor Depth: 7.92m; Data Range: 20061112-20070924.

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    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); NWHI, FFS; Long: -166.16685, Lat: 23.73815 (WGS84); Sensor Depth: 2.13m; Data Range: 20060906-20081008.

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  6. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27506, Lat: 23.85620 (WGS84); Sensor Depth: 0.30m; Data Range: 20091009-20100907.

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  7. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.16747, Lat: 23.73812 (WGS84); Sensor Depth: 3.05m; Data Range: 20081008-20100908.

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    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); NWHI, FFS; Long: -166.27185, Lat: 23.85682 (WGS84); Sensor Depth: 7.90m; Data Range: 20040918-20051009.

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    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, FFS; Long: -166.26135, Lat: 23.76892 (WGS84); Sensor Depth: 4.57m; Data Range: 20070930-20080915.

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    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); NWHI, FFS; Long: -166.21990, Lat: 23.86595 (WGS84); Sensor Depth: 2.10m; Data Range: 20040919-20060905.

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    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, FFS; Long: -166.21970, Lat: 23.86607 (WGS84); Sensor Depth: 3.05m; Data Range: 20080916-20100907.

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    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); NWHI, FFS; Long: -166.17971, Lat: 23.63880 (WGS84); Sensor Depth: 10.36m; Data Range: 20080915-20100910.

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    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, FFS; Long: -166.21967, Lat: 23.86611 (WGS84); Sensor Depth: 2.00m; Data Range: 20030716-20040918.

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  14. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27513, Lat: 23.85626 (WGS84); Sensor Depth: 7.92m; Data Range: 20091009-20100907.

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  15. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.26140, Lat: 23.76891 (WGS84); Sensor Depth: 4.00m; Data Range: 20021005-20030715.

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  16. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.16685, Lat: 23.73815 (WGS84); Sensor Depth: 2.00m; Data Range: 20030717-20040916.

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  17. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.21967, Lat: 23.86611 (WGS84); Sensor Depth: 2.00m; Data Range: 20020912-20030714.

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  18. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.27154, Lat: 23.85652 (WGS84); Sensor Depth: 6.10m; Data Range: 20070925-20071110.

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  19. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.18554, Lat: 23.63507 (WGS84); Sensor Depth: 23.80m; Data Range: 20100514-20100909.

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  20. CRED Subsurface Temperature Recorder (STR); NWHI, FFS; Long: -166.17377, Lat: 23.64516 (WGS84); Sensor Depth: 2.13m; Data Range: 20070930-20080915.

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    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...