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Sample records for g-rich short tandem

  1. Short Tandem Repeat DNA Internet Database

    National Institute of Standards and Technology Data Gateway

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

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

    PubMed Central

    2013-01-01

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

  3. [Polymorphic loci and polymorphism analysis of short tandem repeats within XNP gene].

    PubMed

    Liu, Qi-Ji; Gong, Yao-Qin; Guo, Chen-Hong; Chen, Bing-Xi; Li, Jiang-Xia; Guo, Yi-Shou

    2002-01-01

    To select polymorphic short tandem repeat markers within X-linked nuclear protein (XNP) gene, genomic clones which contain XNP gene were recognized by homologous analysis with XNP cDNA. By comparing the cDNA with genomic DNA, non-exonic sequences were identified, and short tandem repeats were selected from non-exonic sequences by using BCM search Launcher. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five short tandem repeats were identified from XNP gene, two of which were polymorphic. Four and 11 alleles were observed in Chinese population for XNPSTR1 and XNPSTR4, respectively. Heterozygosities were 47% for XNPSTR1 and 70% for XNPSTR4. XNPSTR1 and XNPSTR4 localized within 3' end and intron 10, respectively. Two polymorphic short tandem repeats have been identified within XNP gene and will be useful for linkage analysis and gene diagnosis of XNP gene. PMID:12182071

  4. Evolutionary Footprints of Short Tandem Repeats in Avian Promoters

    PubMed Central

    Abe, Hideaki; Gemmell, Neil J.

    2016-01-01

    Short tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs within promoters have evolved in avian lineages under mutation-selection balance, more than 400 evolutionary conserved STRs (ecSTRs) were identified in this study by comparing the 2 kb upstream promoter sequences of chicken against those of other birds (turkey, duck, zebra finch, and flycatcher). The rate of conservation was significantly higher in AG dinucleotide repeats than in AC or AT repeats, with the expansion of AG motifs being noticeably constrained in passerines. Analysis of the relative distance between ecSTRs and TFBSs revealed a significantly higher rate of conserved TFBSs in the vicinity of ecSTRs in both chicken-duck and chicken-passerine comparisons. Our comparative study provides a novel insight into which intrinsic factors have influenced the degree of constraint on repeat expansion/contraction during avian promoter evolution. PMID:26766026

  5. Microchip-based forensic short tandem repeat genotyping.

    PubMed

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

    2015-08-01

    Micro total analysis system (μTAS) or lab-on-a-chip (LOC) technology has advanced over decades, and the high performance for chemical and biological analysis has been well demonstrated with advantages of low sample consumption, rapid analysis time, high-throughput screening, and portability. In particular, μTAS or LOC based genetic applications have been extensively explored, and the short tandem repeat (STR) typing on a chip has garnered attention in the forensic community due to its special use for human identification in the field of mass disaster and missing person investigation, paternity testing, and perpetrator identification. The STR typing process consists of sample collection, DNA extraction, DNA quantitation, STR loci amplification, capillary electrophoretic separation, and STR profiling. Recent progress of microtechnology shows its ability to substitute the conventional analytical tools, and furthermore demonstrates total integration of the whole STR processes on a single wafer for on-site STR typing. In this review article, we highlighted some representative results for fluorescence labeling techniques, microchip-based DNA purification, on-chip polymerase chain reaction (PCR), a capillary electrophoretic microdevice, and a fully integrated microdevice for STR typing. PMID:25963560

  6. Hybrid de novo tandem repeat detection using short and long reads

    PubMed Central

    2015-01-01

    Background As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases. Many methods designed for tandem repeat detection on reference sequences obtain high quality results. However, in the case of a de novo context, where no reference sequence is available, tandem repeat detection remains a difficult problem. The short reads obtained with the second-generation sequencing methods are not long enough to span regions that contain long repeats. This length limitation was tackled by the long reads obtained with the third-generation sequencing platforms such as Pacific Biosciences technologies. Nevertheless, the gain on the read length came with a significant increase of the error rate. The main objective of nowadays studies on long reads is to handle the high error rate up to 16%. Methods In this paper we present MixTaR, the first de novo method for tandem repeat detection that combines the high-quality of short reads and the large length of long reads. Our hybrid algorithm uses the set of short reads for tandem repeat pattern detection based on a de Bruijn graph. These patterns are then validated using the long reads, and the tandem repeat sequences are constructed using local greedy assemblies. Results MixTaR is tested with both simulated and real reads from complex organisms. For a complete analysis of its robustness to errors, we use short and long reads with different error rates. The results are then analysed in terms of number of tandem repeats detected and the length of their patterns. Conclusions Our method shows high precision and sensitivity. With low false positive rates even for highly erroneous reads, MixTaR is able to detect accurate tandem repeats with pattern lengths varying within a significant interval. PMID:26399998

  7. Child abuse in medical setting presenting as gross hematuria: diagnosis by DNA short tandem repeats.

    PubMed

    Tsai, Hsin-Lin; Yang, Ling-Yu; Chin, Tai-Wai; Chen, Po-Hon; Yen, Hsiu-Ju; Liu, Chin-Su; Wang, Hsin-Hui; Chang, Jei-Wen

    2012-07-01

    Two sisters, aged 15 and 13 years, had previous epithelioid angiomyolipoma of the kidney and suspected thin basement membrane disease, respectively. They presented with 2 years of gross hematuria and new-onset heavy proteinuria. Extensive investigations failed to find an overt cause of their urinary manifestations. The diagnosis of child abuse in a medical setting was confirmed by DNA short tandem repeats analysis, which are the first documented cases in which factitious hematuria was thus diagnosed. Complex forms of child abuse in a medical setting may require forensic tests such as DNA short tandem repeats analysis for diagnosis. PMID:22732177

  8. US forensic Y-chromosome short tandem repeats database.

    PubMed

    Ge, Jianye; Budowle, Bruce; Planz, John V; Eisenberg, Arthur J; Ballantyne, Jack; Chakraborty, Ranajit

    2010-11-01

    A forensic Y-STR database generated in the US was compiled with profiles containing a portion or complete typing of 16 STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4. There were 17,447 samples in the version of database in which 77% and 20% were collected in North America and Asia, respectively. The database was separated into six general populations, African American, Asian, Caucasian, Hispanic, Indian, and Native American. Each population was further classified into subgroups according to geographic regions. Some subgroups were tested, found to be homogenous and merged together. Allele and haplotype frequencies, as well as sample sizes were summarized. Of the full haplotypes (i.e., 16 STRs without missing data), 93.7% in total population were distinct, 92.9% were population specific, and 89.3% were only observed once. The majority of shared haplotypes were found among North American populations as a result of admixture lasting the past few hundred years. The power of discrimination (PD), coancestry coefficient (F(st)), and coefficient of gene differentiation (G(st)) at locus and haplotype levels were also calculated. The most polymorphic marker was DYS385; this marker contains a tandem duplication and actually is composed of two loci. Both G(st) and F(st) estimates were very small with haplotypes composed of a high number of STRs haplotypes (e.g., 10-16 markers), although G(st) is slightly more conservative for these extended haplotypes. With Native American removed from the total population data set, the G(st) and F(st) estimates reduce further. PD was 0.9998 for the total population dataset for all 16 Y-STR markers. Three measures of Y-STR profile frequency were calculated: (1) unconditional haplotype frequency, (2) population substructure adjusted frequency, and (3) binomial upper bound of the haplotype frequency. The binomial upper bound is the most

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

    PubMed Central

    Madsen, Bo Eskerod; Villesen, Palle; Wiuf, Carsten

    2008-01-01

    Background In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions), are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats) are known to be hypermutable (indel-rich), but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect) tandem repeats (STRs) which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%), 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp) and the limited length of STR regions. PMID:18789129

  10. gRICH68 and gRICH70 are 2',3'-cyclic-nucleotide 3'-phosphodiesterases induced during goldfish optic nerve regeneration.

    PubMed

    Ballestero, R P; Wilmot, G R; Agranoff, B W; Uhler, M D

    1997-04-25

    Biochemical characterization of changes in gene expression that accompany optic nerve regeneration has led to the identification of proteins that may play key roles in the regeneration process. In this report, a cDNA encoding gRICH70, a novel isoform of the regeneration-induced gRICH68 protein, has been identified and characterized in goldfish. Both gRICH68 and gRICH70 show significant homology (34-36%) to mammalian 2',3'-cyclic-nucleotide 3'-phosphodiesterases (CNPases), hence the name goldfish regeneration-induced CNPase homolog (gRICH). The predicted 431-amino acid gRICH70 protein is 88% homologous to gRICH68, and the retinal mRNA for gRICH70 is coordinately induced with gRICH68 mRNA during optic nerve regeneration. Enzymatic analysis of recombinant proteins confirms that both gRICH proteins possess CNPase activity. Despite the relatively limited sequence homology, the kinetic constants obtained suggest that both gRICH proteins are at least as efficient as recombinant mouse CNP1 in catalyzing the hydrolysis of 2',3'-cAMP. Immunoprecipitation studies indicate that gRICH proteins are responsible for the majority of the CNPase activity detected in regenerating goldfish retinas. The evidence presented demonstrates that gRICH68 and gRICH70 correspond to a previously described doublet of acidic proteins that are selectively induced in the goldfish retina during optic nerve regeneration. Thus, CNPase enzyme activity is implicated for the first time in the process of nerve regeneration. PMID:9111061

  11. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

    PubMed Central

    2013-01-01

    Background Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes. Results The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression. Conclusions STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome. PMID:24228761

  12. Abundant contribution of short tandem repeats to gene expression variation in humans

    PubMed Central

    Gymrek, Melissa; Willems, Thomas; Guilmatre, Audrey; Zeng, Haoyang; Markus, Barak; Georgiev, Stoyan; Daly, Mark J.; Price, Alkes L.; Pritchard, Jonathan; Sharp, Andrew

    2016-01-01

    The contribution of repetitive elements to quantitative human traits is largely unknown. Here, we report a genome-wide survey of the contribution of Short Tandem Repeats (STRs), one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from linked SNPs and indels and found that eSTRs contribute 10%–15% of the cis-heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, co-localize with regulatory elements, and can modulate certain histone modifications. By analyzing known GWAS hits and searching for new associations in 1,685 deeply-phenotyped whole-genomes, we found that eSTRs are enriched in various clinically-relevant conditions. These results highlight the contribution of short tandem repeats to the genetic architecture of quantitative human traits. PMID:26642241

  13. A continuous linkage map of 22 short tandem repeat polymorphisms on human chromosome 12

    SciTech Connect

    Dawson, E.; Shaikh, S.; Powell, J.F.; Gill, M. ); Weber, J.L.; Wang, Z. ); Weissenbach, J. )

    1993-07-01

    A continuous linkage map consisting of 22 short tandem repeat polymorphisms has been constructed for human chromosome 12 using 23 non-CEPH pedigrees. The markers were distributed at an average distance of 9.35 cM (3.1-33.9 cM). Eighteen of the markers could be positioned uniquely with a likelihood of >1000:1. The physical locations of some of the markers suggest that the map covers 85-95% of the chromosome. This framework map of 18 markers has a female length of 213 cM and a male length of 131 cM. Female recombination frequencies were greater than male recombination frequencies except in the distal portion of the short arm. The map provides confirmatory evidence for orders established previously on CEPH pedigrees and uniquely positions 4 additional markers (CD4, ATPSB, D12S56, PLA2). 19 refs., 1 fig., 1 tab.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25823460

  15. A study of allelic polymorphism of four short tandem repeats in the population of northwestern Russia

    SciTech Connect

    Aseev, M.V.; Skakun, V.N.; Baranov, V.S.

    1995-06-01

    Characteristics of the allelic polymorphisms of the trimeric AGC repeat of the androgen receptor gene (Xq11-12), exon 1 (AR); the tetrameric ATCT repeat of the von Willebrand factor gene (12p12), intron 40 (vWF); the AGAT repeat of the hypoxanthine phosphoribosyltransferase gene (Xq26) (HPRT); and the AGAT repeat of anonymous DNA sequences of the short arm of chromosome X (STRX1) were studied in 160 DNA samples from unrelated inhabitants of northwestern Russia using the method of polymerase chain reaction. Seventeen, ten, eight, and nine alleles were revealed electrophoretically for short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The heterozygosity indices for these repeats were 0.80, 0.70, 0.54, and 0.58, respectively. The values for AR and vWF correlated with those expected according to the Hardy-Weinberg equilibrium, whereas the values for HPRT and STRX1 differed significantly from those theoretically expected. The individualization potentials were 0.045, 0.135, 0.095, and 0.061 for the short tandem repeats of AR, vWF, HPRT, and STRX1, respectively. The distribution of genotypes for the set of these four loci in the population studied was determined. The possibilities of using the studied polymorphic marker systems in molecular diagnosis of the corresponding monogenic diseases - spinal and bulbar muscle atrophy (AR), Lesch-Nyhan disease (HPRT), and von Willebrand disease (vWF) - as well as in population human genetics, testing of personal identity, and molecular approaches to the estimation of mutagenic activity are discussed. 17 refs., 2 figs., 6 tabs.

  16. Inferring short tandem repeat variation from paired-end short reads

    PubMed Central

    Cao, Minh Duc; Tasker, Edward; Willadsen, Kai; Imelfort, Michael; Vishwanathan, Sailaja; Sureshkumar, Sridevi; Balasubramanian, Sureshkumar; Bodén, Mikael

    2014-01-01

    The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats. PMID:24353318

  17. Establishing the robustness of short-tandem-repeat statistics for forensic applications.

    PubMed Central

    Evett, I. W.; Gill, P. D.; Scrange, J. K.; Weir, B. S.

    1996-01-01

    Before the introduction of a four-locus multiplex short-tandem-repeat (STR) system into casework, an extensive series of tests were carried out to determine robust procedures for assessing the evidential value of a match between crime and suspect samples. Twelve databases were analyzed from the three main ethnic groups encountered in casework in the United Kingdom: Caucasians, Afro-Caribbeans, and Asians from the Indian subcontinent. Independence tests resulted in a number of significant results, and the impact that these might have on forensic casework was investigated. It is demonstrated that previously published methods provide a simple procedure for correcting allele frequencies--and that this leads to conservative casework estimates of evidential value. PMID:8571967

  18. [Detection of short tandem repeat (STR) polymorphisms by microchip electrophoresis for individual identification of cattle].

    PubMed

    Yamaguchi, Akihiro; Shimizu, Kaori; Mishima, Takashi; Hattori, Hideki; Katsuda, Shin-ichi; Sato, Hidetaka; Ueda, Nobuo; Sato, Noriyuki

    2006-12-01

    A simple and rapid detection of short tandem repeat (STR) markers was studied as a screening test for individual identification of cattle. DNAs were extracted from eight commercial beef samples by a proteinase K-boil method followed by purification with 2-propanol precipitation. Five STR markers, known to be highly polymorphic, were amplified by PCR and analyzed both by a conventional sequencing analysis (SEQ) and by a proposed microchip electrophoresis (MEP). Every marker revealed high polymorphism, such as 5-9 alleles in SEQ analysis, and 4-6 alleles in MEP analysis. This simple and rapid MEP analysis is expected to be an effective screening tool with use of confirmatory SEQ analysis. PMID:17228791

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

    PubMed

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

    2016-09-01

    In order to find out the characteristics of genetic mutations in 15 short tandem repeat (STR) loci, 3734 parentage cases were analyzed using AmpFlSTR Sinofiler kit. The allele source, mutation rate, and mutation rule of the STR loci were determined. Seventy mutations were observed in all cases for paternity testing. Among 15 STR loci, the highest mutation rate was observed in D12S391 (0.21 %), but the D5S818 gene mutation rate was relatively low (0.02 %). One-step mutation cases accounted for 95.7 % of all of the cases monitored. And the mutations in this study mainly showed paternal mutation (64/70). The research results are of great significance for identification and paternity tests and for the improvement of genetic studies on Chinese population in the future. PMID:26223683

  20. Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany.

    PubMed

    Benecke, M; Knopf, M; Voll, W; Oesterreich, W; Jacobi, Y; Edelmann, J

    1998-10-01

    Applied DNA typing in medico-legal investigations, in criminalistic practice, and in paternity cases often relies on high inclusion and exclusion probabilities. For that reason, the short autosomal tandem repeat locus D8D306 was validated for forensic use and incorporated into a nonoverlapping multiplex reaction with HUMDHFRP2 and HUMCD4: The allele frequencies of D8S306 in four different regions of Germany (n = 1220 alleles) were determined for use in a population database; the allele distributions did not significantly deviate from each other. The hererozygosity of D8S306 is 83%, expected exclusion chance in stain cases is 96% (paternity cases: 69%), the lowest amount of successfully amplified DNA was 30 pg. The alleles are in Hardy-Weinberg equilibrium. PMID:9820956

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

    SciTech Connect

    Hammond, H.A.; Caskey, C.T. ); Jin, L.; Zhong, Y.; Chakraborty, R. )

    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.

  2. Success Rates of Nuclear Short Tandem Repeat Typing from Different Skeletal Elements

    PubMed Central

    Miloš, Ana; Selmanović, Arijana; Smajlović, Lejla; Huel, René L.M.; Katzmarzyk, Cheryl; Rizvić, Adi; Parsons, Thomas J.

    2007-01-01

    Aim To evaluate trends in DNA typing success rates of different skeletal elements from mass graves originating from conflicts that occurred in the former Yugoslavia (Bosnia and Herzegovina and Kosovo) during the 1990s, and to establish correlation between skeletal sample age and success of high throughput short tandem repeat (STR) typing in the large data set of the International Commission on Missing Persons. Method DNA extraction and short tandem repeat (STR) typing have been attempted on over 25 000 skeletal samples. The skeletal samples originated from different geographical locations where the conflicts occurred and from different time periods from 1992 to 1999. DNA preservation in these samples was highly variable, but was often significantly degraded and of limited quantity. For the purpose of this study, processed samples were categorized according to skeletal sample type, sample age since death, and success rates tabulated. Results Well-defined general trends in success rates of DNA analyses were observed with respect to the type of bone tested and sample age. The highest success rates were observed with samples from dense cortical bone of weight-bearing leg bones (femur 86.9%), whereas long bones of the arms showed significantly lower success (humerus 46.2%, radius 24.5%, ulna 22.8%). Intact teeth also exhibited high success rates (teeth 82.7%). DNA isolation from other skeletal elements differed considerably in success, making bone sample selection an important factor influencing success. Conclusion The success of DNA typing is related to the type of skeletal sample. By carefully evaluating skeletal material available for forensic DNA testing with regard to sample age and type of skeletal element available, it is possible to increase the success and efficiency of forensic DNA testing. PMID:17696303

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

    ERIC Educational Resources Information Center

    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)…

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

    PubMed

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

    2009-08-01

    The molecular genotyping of individuals and reconstruction of kinship through short and highly polymorphic DNA markers, so called short tandem repeats (STR), has become one of the important and efficient methods in anthropology studies and forensic science. Although many populations have been analyzed, no study has yet been carried out on Sadat populations who are putative descendents of Prophet Mohammad (peace be upon him). Polymorphisms of 6 Y-STR loci (DYS19, DYS385a/b, DYS389II, DYS390, DYS392, and DYS393) have been studied in an unrelated population of Sadat males. The aim of this study was to find possible similarities within Sadat males, resided in Iran. Among Sadat, DYS385b was proved to be the most polymorphic (GD = 0.8588), and DYS392 showed the lowest polymorphism (GD = 0.3527). In 50 samples, 45 different haplotypes were found, of which 39 haplotypes were unique. In the study, three samples had multi-allelic patterns. Haplotype diversity, in regard to these 7 markers was 0.9942. PMID:19769300

  5. Population data for 17 short tandem repeat loci on Y chromosome in northern Croatia.

    PubMed

    Gršković, Branka; Mršić, Gordan; Polašek, Ozren; Vrdoljak, Andro; Merkaš, Siniša; Anđelinović, Simun

    2011-03-01

    Human Y-short tandem repeats (STRs) are tandem repeat arrays of two to seven base pair units on non-recombining region (NRY) of the human Y chromosome. Studies on Y-STR are interesting in both population genetics and forensics. The aim of this study was to investigate the population genetic properties of 17 STR loci on Y chromosome in the northern Croatia region. We carried out a statistical analysis of the data from previously performed genetic analysis collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from northern Croatia were selected for the purpose of this study. Genomic DNA was extracted using Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 210 haplotypes were identified, 200 of which were unique. Total haplotype diversity was 0.995. Locus diversity varied from 0.331 for DYS392 to 0.783 for DYS385 locus. Allele frequencies diversity was 0.662. Discrimination capacity was 95.7%. The use of European minimal haplotype set indicated the most resemblance of this population to the Croatian capital of Zagreb, with modest resemblance to Bosnia and Herzegovina, Serbia and Hungary. This article provides the first overview of the Y chromosome STR variability in northern Croatia, thus providing the referent point for any future forensic and genetic epidemiology efforts in this region. PMID:20859689

  6. G-rich, a Drosophila selenoprotein, is a Golgi-resident type III membrane protein

    SciTech Connect

    Chen, Chang Lan; Shim, Myoung Sup; Chung, Jiyeol; Yoo, Hyun-Seung; Ha, Ji Min; Kim, Jin Young; Choi, Jinmi; Zang, Shu Liang; Hou, Xiao; Carlson, Bradley A.; Hatfield, Dolph L.; Lee, Byeong Jae . E-mail: imbglmg@plaza.snu.ac.kr

    2006-10-06

    G-rich is a Drosophila melanogaster selenoprotein, which is a homologue of human and mouse SelK. Subcellular localization analysis using GFP-tagged G-rich showed that G-rich was localized in the Golgi apparatus. The fusion protein was co-localized with the Golgi marker proteins but not with an endoplasmic reticulum (ER) marker protein in Drosophila SL2 cells. Bioinformatic analysis of G-rich suggests that this protein is either type II or type III transmembrane protein. To determine the type of transmembrane protein experimentally, GFP-G-rich in which GFP was tagged at the N-terminus of G-rich, or G-rich-GFP in which GFP was tagged at the C-terminus of G-rich, were expressed in SL2 cells. The tagged proteins were then digested with trypsin, and analyzed by Western blot analysis. The results showed that the C-terminus of the G-rich protein was exposed to the cytoplasm indicating it is a type III microsomal membrane protein. G-rich is First selenoprotein identified in the Golgi apparatus.

  7. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.

    PubMed

    Sun, Guangyun; McGarvey, Stephen T; Bayoumi, Riad; Mulligan, Connie J; Barrantes, Ramiro; Raskin, Salmo; Zhong, Yixi; Akey, Joshua; Chakraborty, Ranajit; Deka, Ranjan

    2003-01-01

    We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended. PMID:12529704

  8. Use of short tandem repeat analysis in unusual presentations of trophoblastic tumors and their mimics.

    PubMed

    Aranake-Chrisinger, John; Huettner, Phyllis C; Hagemann, Andrea R; Pfeifer, John D

    2016-06-01

    Gestational trophoblastic tumors can be difficult to distinguish from nongestational neoplasms. Somatic and germ cell tumors can mimic gestational choriocarcinoma, and epithelioid trophoblastic tumor (ETT) is known for its histologic, and sometimes clinical, resemblance to squamous cell carcinoma. Short tandem repeat (STR) analysis can separate gestational from nongestational neoplasms and can provide useful information about the type of causative conceptus. We present a series of cases which demonstrate the utility of STR analysis in the evaluation of gestational choriocarcinoma, epithelioid trophoblastic tumor, and their mimics. Samples from normal tissue and tumor were microdissected. DNA was extracted, and STR analysis was performed. Five cases were identified in which there was clinical and/or histologic concern for a gestational trophoblastic neoplasm. Case 1 is a choriocarcinoma presenting concurrently with a 16-week gestation. STR testing on the tumor, mother, and fetus showed that the tumor arose from a previous occult complete hydatidiform mole. Case 2 is an ETT presenting as multiple masses in bilateral kidneys, initially diagnosed as urothelial carcinoma. However, because of an elevated human chorionic gonadotropin, additional workup was performed which showed that the tumor was most likely an ETT. STR analysis showed that the tumor arose from a nonmolar pregnancy. Cases 3-5 illustrate somatic carcinomas mimicking gestational neoplasia. In those cases, STR confirmed a somatic origin. STR can be useful in distinguishing gestational from nongestational neoplasms, particularly in unusual settings. Also, STR analysis can add clinically useful information that is not available from clinical or histologic evaluation. PMID:26980014

  9. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    PubMed Central

    2012-01-01

    Background Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH), obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91), k-Modes-RVF (0.81), New Fuzzy k-Modes (0.80), k-Modes (0.76), k-Modes-Hybrid 1 (0.76), k-Modes-Hybrid 2 (0.75), Fuzzy k-Modes (0.74), and k-Modes-UAVM (0.70). Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k)) and considered to be linear. PMID:23039132

  10. Genetic diversity of 17 Y-short tandem repeats in Indian population.

    PubMed

    Ghosh, Tania; Kalpana, D; Mukerjee, Sanjukta; Mukherjee, Meeta; Sharma, Anil Kumar; Nath, Subhankar; Rathod, Varsha Rajesh; Thakar, Mukesh Kumar; Jha, Ganga Nath

    2011-08-01

    Seventeen short tandem repeats (DYS389I, DYS390, DYS389II, DYS19, DYS385a/b, DYS393, DYS391, DYS392, DYS439, DYS438, DYS456, DYS458, DYS635, Y(GATA)H4, DYS437, and DYS448) from the non-recombining region of the human Y-chromosome were analyzed in 750 unrelated males representing four major linguistic families of India using AmpFlSTR(®) Yfiler(®) PCR Amplification kit. A total of 612 distinct haplotypes were observed, of which 545 were unique. Rare alleles for the loci DYS456, DYS458, DYS635, Y(GATA)H4, and duplication at the loci DYS389I and DYS389II were also observed. To understand the genetic diversity of the Indian population, and utility of Y-STRs in forensics, the locus diversity, haplotype diversity, and discrimination capacity in all populations was determined. MDS plot based on pairwise Φ(st) and AMOVA revealed the high genetic heterogeneity among the Indian populations due to linguistic diversity and social stratification. PMID:21277272

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

    PubMed Central

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

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  12. Genetic analysis of a Sicilian population using 15 short tandem repeats.

    PubMed

    Calò, C M; Garofano, L; Mameli, A; Pizzamiglio, M; Vona, G

    2003-04-01

    The genetic structure of the population of Alia (Sicily, Italy) was analyzed using 15 short tandem repeats: TPOX, D2S1338, D3S1358, FIBRA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D19S433, and D21S11. Two of these markers, D2S1338 and D19S433, have never before been used in research on population genetics and only recently have they been put to use in forensic medicine. Results of the analysis underline the genetic isolation of the Alia population and show it to be a recent bottleneck as a consequence of a cholera epidemic in 1837. While comparing the Alia population with other populations from Sicily, a genetic heterogeneity within Sicily was uncovered, thus confirming previous results obtained from the analysis of classical markers. This heterogeneity underlines the existence of genetic boundaries within the island. Comparisons with other Italian, Mediterranean, and European populations highlight the differentiation of the Sicilian population, reflecting the presence of a genetic boundary that separates Sicily from northern and central Italy and from the western Mediterranean basin. PMID:12943156

  13. Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci.

    PubMed

    Li, Shi-Lin; Yamamoto, Toshimichi; Yoshimoto, Takashi; Uchihi, Rieko; Mizutani, Masaki; Kurimoto, Yukihide; Tokunaga, Katsushi; Jin, Feng; Katsumata, Yoshinao; Saitou, Naruya

    2006-02-01

    We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K> or =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed. PMID:16315063

  14. Improvement of short tandem repeat analysis of samples highly contaminated by humic acid.

    PubMed

    Seo, Seung Bum; Jin, Hong Xuan; Lee, Hye Young; Ge, Jianye; King, Jonathan L; Lyoo, Sung Hee; Shin, Dong Hoon; Lee, Soong Deok

    2013-10-01

    We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick(®) PCR Purification, QIAamp(®) DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX(®) Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold(®) DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX(®) Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples. PMID:24112347

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

    PubMed

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

    2015-08-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  16. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

    PubMed

    Darby, Brian J; Erickson, Shay F; Hervey, Samuel D; Ellis-Felege, Susan N

    2016-07-01

    High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data. PMID:27386092

  17. Short tandem repeats haplotyping of the HLA region in preimplantation HLA matching.

    PubMed

    Fiorentino, Francesco; Kahraman, Semra; Karadayi, Hüseyin; Biricik, Anil; Sertyel, Semra; Karlikaya, Güvenc; Saglam, Yaman; Podini, Daniele; Nuccitelli, Andrea; Baldi, Marina

    2005-08-01

    Recently, preimplantation genetic diagnosis (PGD) has been considered for several indications beyond its original purpose, not only to test embryos for genetic disease but also to select embryos for a nondisease trait, such as specific human leukocyte antigen (HLA) genotypes, related to immune compatibility with an existing affected child in need of a haematopoetic stem cell (HSC) transplant. We have optimized an indirect single-cell HLA typing protocol based on a multiplex fluorescent polymerase chain reaction (PCR) of short tandem repeat (STR) markers scattered throughout the HLA complex. The assay was clinically applied in 60 cycles from 45 couples. A conclusive HLA-matching diagnosis was achieved in 483/530 (91.1%) of the embryos tested. In total, 74 (15.3%) embryos revealed an HLA match with the affected siblings, 55 (11.4%) of which resulted unaffected and 46 (9.5%) have been transferred to the patients. Nine pregnancies were achieved, five healthy HLA-matched children have already been delivered and cord blood HSCs, were transplanted to three affected siblings, resulting in a successful haematopoietic reconstruction. PMID:15886713

  18. Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system.

    PubMed

    Mendoza, Maria A; Mills, DeEtta K; Lata, Hemant; Chandra, Suman; ElSohly, Mahmoud A; Almirall, Jose R

    2009-01-01

    Cannabis sativa is the most frequently used of all illicit drugs in the USA. Cannabis has been used throughout history for its stems in the production of hemp fiber, seed for oil and food, and buds and leaves as a psychoactive drug. Short tandem repeats (STRs) were chosen as molecular markers owing to their distinct advantages over other genetic methods. STRs are codominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power, and can be multiplexed. In this study, six STR markers previously described for C. sativa were multiplexed into one reaction. The multiplex reaction was able to individualize 98 cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 states of the USA) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single-reaction sixplex and apply it to the analysis of almost 100 cannabis samples of known geographic origin. PMID:19066867

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

    PubMed

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

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation. PMID:27108803

  20. Validation of a Short Tandem Repeat Multiplex Typing System for Genetic Individualization of Domestic Cat Samples

    PubMed Central

    Coomber, Nikia; David, Victor A.; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

    2007-01-01

    Aim To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples. Methods To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n = 13). Additional studies were performed to evaluate the system’s species’ specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation rates for the 11 loci were directly examined in a large multi-generation domestic cat pedigree (n = 263). Results Our studies confirm that the multiplex system was species-specific for feline DNA and amplified robustly with as little as 125 picograms of genomic template DNA, demonstrating good product balance. The multiplex generated all components of a two DNA mixture when the minor component was one tenth of the major component at a threshold of 50 relative fluorescence units. The multiplex was reproducible in multiple tissue types of the same individual. Mutation rates for the 11 STR were within the range of sex averaged rates observed for Combined DNA Index System (CODIS) loci. Conclusion The cat STR multiplex typing system is a robust and reliable tool for the use of forensic DNA analysis of domestic cat samples. PMID:17696310

  1. Detection of maternal DNA in umbilical cord plasma by fluorescent PCR amplification of short tandem repeat sequences.

    PubMed

    Bauer, M; Orescovic, I; Schoell, W M; Bianchi, D W; Pertl, B

    2001-09-01

    Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short tandem repeat (STR) markers to detect maternal DNA in umbilical cord plasma. PMID:11708473

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

    PubMed

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

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes. PMID:20102040

  3. Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population.

    PubMed

    Gršković, Branka; Mršić, Gordan; Polašek, Ozren; Vrdoljak, Andro; Merkaš, Siniša; Anđelinović, Simun

    2011-06-01

    In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. 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". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies. PMID:21279707

  4. Core promoter short tandem repeats as evolutionary switch codes for primate speciation.

    PubMed

    Ohadi, Mina; Valipour, Elaheh; Ghadimi-Haddadan, Saeed; Namdar-Aligoodarzi, Pegah; Bagheri, Abouzar; Kowsari, Ali; Rezazadeh, Maryam; Darvish, Hossein; Kazeminasab, Somayeh

    2015-01-01

    Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥ 6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. PMID:25099915

  5. Exceptionally long 5' UTR short tandem repeats specifically linked to primates.

    PubMed

    Namdar-Aligoodarzi, P; Mohammadparast, S; Zaker-Kandjani, B; Talebi Kakroodi, S; Jafari Vesiehsari, M; Ohadi, M

    2015-09-10

    We have previously reported genome-scale short tandem repeats (STRs) in the core promoter interval (i.e. -120 to +1 to the transcription start site) of protein-coding genes that have evolved identically in primates vs. non-primates. Those STRs may function as evolutionary switch codes for primate speciation. In the current study, we used the Ensembl database to analyze the 5' untranslated region (5' UTR) between +1 and +60 of the transcription start site of the entire human protein-coding genes annotated in the GeneCards database, in order to identify "exceptionally long" STRs (≥5-repeats), which may be of selective/adaptive advantage. The importance of this critical interval is its function as core promoter, and its effect on transcription and translation. In order to minimize ascertainment bias, we analyzed the evolutionary status of the human 5' UTR STRs of ≥5-repeats in several species encompassing six major orders and superorders across mammals, including primates, rodents, Scandentia, Laurasiatheria, Afrotheria, and Xenarthra. We introduce primate-specific STRs, and STRs which have expanded from mouse to primates. Identical co-occurrence of the identified STRs of rare average frequency between 0.006 and 0.0001 in primates supports a role for those motifs in processes that diverged primates from other mammals, such as neuronal differentiation (e.g. APOD and FGF4), and craniofacial development (e.g. FILIP1L). A number of the identified STRs of ≥5-repeats may be human-specific (e.g. ZMYM3 and DAZAP1). Future work is warranted to examine the importance of the listed genes in primate/human evolution, development, and disease. PMID:26022613

  6. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.

    PubMed

    Zhang, Zhou; Zheng, Yinan; Zhang, Xu; Liu, Cong; Joyce, Brian Thomas; Kibbe, Warren A; Hou, Lifang; Zhang, Wei

    2016-02-01

    Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits. PMID:26714498

  7. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

    PubMed Central

    Ballantyne, Kaye N; Ralf, Arwin; Aboukhalid, Rachid; Achakzai, Niaz M; Anjos, Maria J; Ayub, Qasim; Balažic, Jože; Ballantyne, Jack; Ballard, David J; Berger, Burkhard; Bobillo, Cecilia; Bouabdellah, Mehdi; Burri, Helen; Capal, Tomas; Caratti, Stefano; Cárdenas, Jorge; Cartault, François; Carvalho, Elizeu F; Carvalho, Monica; Cheng, Baowen; Coble, Michael D; Comas, David; Corach, Daniel; D'Amato, Maria E; Davison, Sean; de Knijff, Peter; De Ungria, Maria Corazon A; Decorte, Ronny; Dobosz, Tadeusz; Dupuy, Berit M; Elmrghni, Samir; Gliwiński, Mateusz; Gomes, Sara C; Grol, Laurens; Haas, Cordula; Hanson, Erin; Henke, Jürgen; Henke, Lotte; Herrera-Rodríguez, Fabiola; Hill, Carolyn R; Holmlund, Gunilla; Honda, Katsuya; Immel, Uta-Dorothee; Inokuchi, Shota; Jobling, Mark A; Kaddura, Mahmoud; Kim, Jong S; Kim, Soon H; Kim, Wook; King, Turi E; Klausriegler, Eva; Kling, Daniel; Kovačević, Lejla; Kovatsi, Leda; Krajewski, Paweł; Kravchenko, Sergey; Larmuseau, Maarten H D; Lee, Eun Young; Lessig, Ruediger; Livshits, Ludmila A; Marjanović, Damir; Minarik, Marek; Mizuno, Natsuko; Moreira, Helena; Morling, Niels; Mukherjee, Meeta; Munier, Patrick; Nagaraju, Javaregowda; Neuhuber, Franz; Nie, Shengjie; Nilasitsataporn, Premlaphat; Nishi, Takeki; Oh, Hye H; Olofsson, Jill; Onofri, Valerio; Palo, Jukka U; Pamjav, Horolma; Parson, Walther; Petlach, Michal; Phillips, Christopher; Ploski, Rafal; Prasad, Samayamantri P R; Primorac, Dragan; Purnomo, Gludhug A; Purps, Josephine; Rangel-Villalobos, Hector; Rębała, Krzysztof; Rerkamnuaychoke, Budsaba; Gonzalez, Danel Rey; Robino, Carlo; Roewer, Lutz; Rosa, Alexandra; Sajantila, Antti; Sala, Andrea; Salvador, Jazelyn M; Sanz, Paula; Schmitt, Cornelia; Sharma, Anil K; Silva, Dayse A; Shin, Kyoung-Jin; Sijen, Titia; Sirker, Miriam; Siváková, Daniela; Škaro, Vedrana; Solano-Matamoros, Carlos; Souto, Luis; Stenzl, Vlastimil; Sudoyo, Herawati; Syndercombe-Court, Denise; Tagliabracci, Adriano; Taylor, Duncan; Tillmar, Andreas; Tsybovsky, Iosif S; Tyler-Smith, Chris; van der Gaag, Kristiaan J; Vanek, Daniel; Völgyi, Antónia; Ward, Denise; Willemse, Patricia; Yap, Eric PH; Yong, Rita YY; Pajnič, Irena Zupanič; Kayser, Manfred

    2014-01-01

    Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. PMID:24917567

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

    PubMed

    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. PMID:20927602

  9. Y-Short Tandem Repeat Multiplex Systems - Y-PLEX™ 6 and Y-PLEX™ 5.

    PubMed

    Shewale, J G

    2003-07-01

    Y-Chromosome short tandem repeats (Y-STRs) have become a very useful tool in forensic casework, paternity, and male lineage studies. In forensic casework, one can obtain the male profile from a mixture sample containing male and female DNA. Two Y-STR genotyping systems, Y-PLEX™ 6 and Y-PLEX™ 5, have been developed for use in human identification. Y-PLEX™ 6 enables simultaneous amplification of DYS393, DYS19, DYS389II, DYS390, DYS391, and DYS385; Y-PLEX™ 5 enables simultaneous amplification of DYS389I, DYS389II, DYS439, DYS438, and DYS392 loci. The Y-PLEX™ 6 and Y-PLEX™ 5 systems together provide analysis of all nine Y-STR loci generating minimal haplotype and two additional loci, DYS438 and DYS439. These systems also provide analysis for all 11 Y-STR loci recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM) for forensic casework and population database studies. Both the systems were validated following the Federal Bureau of Investigation (FBI) Director's Quality Assurance Standards. Allelic ladders, which serve as a reference in genotyping, were generated. The nucleotide sequence of alleles in the allelic ladder was determined and the nomenclature is in accord with the recommendations of the International Society of Forensic Genetics (ISFG). The minimum sensitivity of the Y-PLEX™ 6 and Y-PLEX™ 5 systems was 0.2 and 0.1 ng of male DNA, respectively. The nonhuman study revealed that the primers in the Y-PLEX™ 6 and Y-PLEX™ 5 systems were specific for the DNA from humans and some higher primates. Mean stutter values ranged from 3.6 to 11.9%. The Y-PLEX™ 6 and Y-PLEX™ 5 systems were used in several forensic cases. The results from these multiplex systems have been admitted in various U.S. Courts. Thus, Y-PLEX™ 6 and Y-PLEX™ 5 genotyping systems are sensitive, reliable, and robust for use in human forensic and male lineage identification studies. PMID:26256728

  10. Study of the Function of G-Rich Aptamers Selected for Lung Adenocarcinoma.

    PubMed

    Hu, Jun; Zhao, Zilong; Liu, Qiaoling; Ye, Mao; Hu, Bingqiang; Wang, Jing; Tan, Weihong

    2015-07-01

    Guanine (G)-rich oligonucleotides have attracted considerable interest as therapeutic agents. Two G-rich aptamers were selected against epidermal growth factor receptor (EGFR)-transfected A549 cells, and their G-rich domains (S13 and S50) were identified to account for the binding of parental aptamers. Circular dichroism (CD) spectra showed that S13 and S50 bound to their targets by forming parallel quadruplexes. Their binding, internalization, and antiproliferation activity in cancer and noncancer cells were investigated by flow cytometry and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay, and compared with those of nucleolin-binding AS1411 and thrombin-binding aptamer. The two truncated aptamers (S13 and S50) have good binding and internalization in cancer cells and noncancer cells; however, only S50, similar to AS1411, shows potent antiproliferation against cancer cells. Our data suggest that tumor-selective antiproliferation of G-rich oligonucleotides does not directly depend on the binding of the G-rich aptamer to cells. PMID:25864879

  11. Effects of Short-term Exposure to Inhalable Particulate Matter on DNA Methylation of Tandem Repeats

    PubMed Central

    Guo, Liqiong; Byun, Hyang-Min; Zhong, Jia; Motta, Valeria; Barupal, Jitendra; Zheng, Yinan; Dou, Chang; Zhang, Feiruo; McCracken, John P.; Diaz, Anaité; Marco, Sanchez-Guerra; Colicino, Silvia; Schwartz, Joel; Wang, Sheng; Hou, Lifang; Baccarelli, Andrea A.

    2015-01-01

    There is compelling evidence that particulate matter (PM) increases lung cancer risk by triggering systemic inflammation, and leukocyte DNA hypomethylation. However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which display a greater propensity to mutate, and are often hypomethylated in cancer patients, have never been investigated in individuals exposed to PM. We measured methylation of three tandem repeats (SATα, NBL2, D4Z4) by polymerase chain reaction–pyrosequencing on blood samples from truck drivers and office workers (60 per group) in Beijing, China. We used lightweight monitors to measure personal PM2.5 (PM with aerodynamic diameter ≤2.5 µm) and elemental carbon (EC, a tracer of PM from vehicular traffic). Ambient PM10 data were obtained from air quality measuring stations. Overall, an interquartile increase in personal PM2.5 and ambient PM10 levels was associated with a significant covariate-adjusted decrease in SATα methylation (−1.35% 5-methyl cytosine [5mC], P = 0.01; and −1.33%5mC; P = 0.01, respectively). Effects from personal PM2.5 and ambient PM10 on SATα methylation were stronger in truck drivers (−2.34%5mC, P = 0.02; −1.44%5mC, P = 0.06) than office workers (−0.95%5mC, P = 0.26; −1.25%5mC, P = 0.12, respectively). Ambient PM10 was negatively correlated with NBL2 methylation in truck drivers (−1.38%5mC, P = 0.03) but not in office workers (1.04%5mC, P = 0.13). Our result suggests that PM exposure is associated with hypomethylation of selected tandem repeats. Measuring tandem-repeat hypomethylation in easy-to-obtain blood specimens might identify individuals with biological effects and potential cancer risk from PM exposure. PMID:24436168

  12. G-quadruplex formation between G-rich PNA and homologous sequences in oligonucleotides and supercoiled plasmid DNA.

    PubMed

    Gaynutdinov, Timur I; Englund, Ethan A; Appella, Daniel H; Onyshchenko, Mykola I; Neumann, Ronald D; Panyutin, Igor G

    2015-04-01

    Guanine (G)-rich DNA sequences can adopt four-stranded quadruplex conformations that may play a role in the regulation of genetic processes. To explore the possibility of targeted molecular recognition of DNA sequences with short G-rich peptide nucleic acids (PNA) and to assess the strand arrangement in such complexes, we used PNA and DNA with the Oxytricha nova telomeric sequence d(G4T4G4) as a model. PNA probes were complexed with DNA targets in the following forms: single-stranded oligonucleotides, a loop of DNA in a hairpin conformation, and as supercoiled plasmid with the (G4T4G4)/(C4A4C4) insert. Gel-shift mobility assays demonstrated formation of stable hybrid complexes between the homologous G4T4G4 PNA and DNA with multiple modes of binding. Chemical and enzymatic probing revealed sequence-specific and G-quadruplex dependent binding of G4T4G4 PNA to dsDNA. Spectroscopic and electrophoretic analysis of the complex formed between PNA and the synthetic DNA hairpin containing the G4T4G4 loop showed that the stoichiometry of a prevailing complex is three PNA strands per one DNA strand. We speculate how this new PNA-DNA complex architecture can help to design more selective, quadruplex-specific PNA probes. PMID:25650982

  13. Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua.

    PubMed

    Arnason, E; Rand, D M

    1992-09-01

    The mitochondrial DNA of the Atlantic cod (Gadus morhua) contains a tandem array of 40-bp repeats in the D-loop region of the molecule. Variation among molecules in the copy number of these repeats results in mtDNA length variation and heteroplasmy (the presence of more than one form of mtDNA in an individual). In a sample of fish collected from different localities around Iceland and off George's Bank, each individual was heteroplasmic for two or more mtDNAs ranging in repeat copy number from two (common) to six (rare). An earlier report on mtDNA heteroplasmy in sturgeon (Acipenser transmontanus) presented a competitive displacement model for length mutations in mtDNAs containing tandem arrays and the cod data deviate from this model. Depending on the nature of putative secondary structures and the location of D-loop strand termination, additional mechanisms of length mutation may be needed to explain the range of mtDNA length variants maintained in these populations. The balance between genetic drift and mutation in maintaining this length polymorphism is estimated through a hierarchical analysis of diversity of mtDNA length variation in the Iceland samples. Eighty percent of the diversity lies within individuals, 8% among individuals and 12% among localities. An estimate of theta = 2N(eo) mu greater than 1 indicates that this system is characterized by a high mutation rate and is governed primarily by deterministic dynamics. The sequences of repeat arrays from fish collected in Norway, Iceland and George's Bank show no nucleotide variation suggesting that there is very little substructuring to the North Atlantic cod population. PMID:1356884

  14. Detection of a novel X-chromosomal short tandem repeat marker in Xq28 in four ethnic groups.

    PubMed

    Nishi, Takeki; Nakamura, Takako; Honda, Katuya

    2016-03-01

    DNA testing of X-chromosomal short tandem repeat (X-STR) polymorphisms has been the focus of attention in several studies, mainly due to its applicability in the investigation of complex kinship cases. Studies of X-STR in analyses of DNA sequences, population studies and DNA testing applications have been reported. We performed detection and population genetic study of a novel tetranucleotide X-STR locus in the present study. We identified a unique X-STR locus consisting of two tetranucleotides in Xq28. Although the STR is a simple tetranucleotide, its polymorphism was comparatively high [polymorphism information content (PIC)=0.7140] in Japanese subjects. In addition, the STR varied in structure among ethnic groups. We conclude that this locus will be useful for forensic DNA testing and anthropological studies. PMID:26980253

  15. A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

    PubMed Central

    Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

    2011-01-01

    Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

  16. Effective Small RNA Destruction by the Expression of a Short Tandem Target Mimic in Arabidopsis[C][W

    PubMed Central

    Yan, Jun; Gu, Yiyou; Jia, Xiaoyun; Kang, Wenjun; Pan, Shangjin; Tang, Xiaoqing; Chen, Xuemei; Tang, Guiliang

    2012-01-01

    MicroRNAs (miRNAs) and other endogenous small RNAs act as sequence-specific regulators of the genome, transcriptome, and proteome in eukaryotes. The interrogation of small RNA functions requires an effective, widely applicable method to specifically block small RNA function. Here, we report the development of a highly effective technology that targets specific endogenous miRNAs or small interfering RNAs for destruction in Arabidopsis thaliana. We show that the expression of a short tandem target mimic (STTM), which is composed of two short sequences mimicking small RNA target sites, separated by a linker of an empirically determined optimal size, leads to the degradation of targeted small RNAs by small RNA degrading nucleases. The efficacy of the technology was demonstrated by the strong and specific developmental defects triggered by STTMs targeting three miRNAs and an endogenous siRNA. In summary, we developed an effective approach for the destruction of endogenous small RNAs, thereby providing a powerful tool for functional genomics of small RNA molecules in plants and potentially animals. PMID:22345490

  17. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing. PMID:25450788

  18. Accurate mass determination of short-lived isotopes by a tandem Penning-trap mass spectrometer

    SciTech Connect

    Stolzenberg, H.; Becker, S.; Bollen, G.; Kern, F.; Kluge, H.; Otto, T.; Savard, G.; Schweikhard, L. ); Audi, G. ); Moore, R.B. ); The ISOLDE Collaboration

    1990-12-17

    A mass spectrometer consisting of two Penning traps has been set up for short-lived isotopes at the on-line mass separator ISOLDE at CERN. The ion beam is collected and cooled in the first trap. After delivery to the second trap, high-accuracy direct mass measurements are made by determining the cyclotron frequency of the stored ions. Measurements have been performed for {sup 118}Cs--{sup 137}Cs. A resolving power of over 10{sup 6} and an accuracy of 1.4{times}10{sup {minus}7} have been achieved, corresponding to about 20 keV.

  19. Population data of 17 short tandem repeat loci in 2923 individuals from the Han population of Nantong in East China.

    PubMed

    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. PMID:26932871

  20. Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers

    SciTech Connect

    Wang, Y.; Ju, J.; Carpenter, B.A.; Atherton, J.M.; Sensabaugh, G.F.; Mathies, R.A.

    1995-04-01

    Genetic typing of the short tandem repeat (STR) polymorphism HUMTHO1 has been performed using capillary array electroporesis and energy-transfer fluorescent dye-labeled polymerase chain reaction primers. Target alleles were amplified by use of primers labeled with one fluorescein at the 5` end and another fluorescein at the position of the 15th (modified) base to produce fragments that fluoresce in the green ({lambda}{sub max} = 525 nm). Unknown alleles were electrophoretically separated together with a standard ladder made up of alleles having 6, 7, 8, and 9 four-base pair repeats, each of which was amplified with an energy-transfer primer having a donor fluorescein at the 5` end and a rhodamine acceptor at the position of the 7th (modified) base to produce standard fragments fluorescing in the red (>590 nm). Separations are complete in less than 20 min and allow sizing with an absolute error or accuracy of less than 0.4 base pair and an average standard deviation of nearly 0.5 base pair with no correction for mobility shift and cross-talk between the fluorescence channels. This work establishes feasibility of high-speed, high-throughput STR typing of double-stranded DNA fragments using capillary array electrophoresis. 27 refs., 7 figs., 1 tab.

  1. The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

    PubMed

    Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

    2015-07-01

    Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. PMID:25950598

  2. Von Willebrand gene tracking by single-tube automated fluorescent analysis of four short tandem repeat polymorphisms.

    PubMed

    Vidal, Francisco; Julià, Antoni; Altisent, Carme; Puig, Lluís; Gallardo, Doinique

    2005-05-01

    Molecular diagnosis of von Willebrand disease (VWD) has been hampered by the large size and complex genomic characteristics of the gene involved. For this reason, indirect methods using intragenic polymorphic markers described along the von Willebrand factor (VWF) gene are valuable tools for gene monitoring and linkage analysis. Several studies have demonstrated the four commonly utilized short tandem repeats (STRs), three located in intron 40 and one in the promoter region of the VWF gene, to be highly informative for this task. Our objective was t o develop a rapid, automated method to simultaneously analyze these four STRs for VWF gene tracking. Amplification of the four loci is achieved in a single multiplex fluorescent PCR which is then analyzed in the same run by capillary electrophoresis. Data processing with GeneScan and Genotyper software has simplified management and tabulation of the resulting haplotypes. Analysis of the VWF gene in DNA from 102 individuals (204 chromosomes) revealed that the three STRs within intron 40 showed significant linkage disequilibrium against each other but not against the VWP locus. Moreover, the combination of the four markers offers a high heterozygosity rate (>99%) that improves tracing VWF gene inheritance. In conclusion, the automated fluorescent capillary electrophoresis method presented here is an extremely rapid, simple and highly informative technique for association studies between VWD and the VWF gene in addition to genetic counseling and prenatal diagnosis by precise linkage analysis in VWD-affected families. PMID:15886817

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

    PubMed Central

    Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-01-01

    Abstract 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. PMID:25945508

  4. Variant Alleles, Triallelic Patterns, and Point Mutations Observed in Nuclear Short Tandem Repeat Typing of Populations in Bosnia and Serbia

    PubMed Central

    Huel, René L. M.; Bašić, Lara; Madacki-Todorović, Kamelija; Smajlović, Lejla; Eminović, Izet; Berbić, Irfan; Miloš, Ana; Parsons, Thomas J.

    2007-01-01

    Aim To present a compendium of off-ladder alleles and other genotyping irregularities relating to rare/unexpected population genetic variation, observed in a large short tandem repeat (STR) database from Bosnia and Serbia. Methods DNA was extracted from blood stain cards relating to reference samples from a population of 32 800 individuals from Bosnia and Serbia, and typed using Promega’s PowerPlex®16 STR kit. Results There were 31 distinct off-ladder alleles were observed in 10 of the 15 STR loci amplified from the PowerPlex®16 STR kit. Of these 31 alleles, 3 have not been previously reported. Furthermore, 16 instances of triallelic patterns were observed in 9 of the 15 loci. Primer binding site mismatches that affected amplification were observed in two loci, D5S818 and D8S1179. Conclusion Instances of deviations from manufacturer’s allelic ladders should be expected and caution taken to properly designate the correct alleles in large DNA databases. Particular care should be taken in kinship matching or paternity cases as incorrect designation of any of these deviations from allelic ladders could lead to false exclusions. PMID:17696304

  5. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.

    PubMed

    van der Gaag, Kristiaan J; de Leeuw, Rick H; Hoogenboom, Jerry; Patel, Jaynish; Storts, Douglas R; Laros, Jeroen F J; de Knijff, Peter

    2016-09-01

    Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts. PMID:27347657

  6. Genetic polymorphism of the 26 short tandem repeat loci in the Chinese Hebei Han population using two commercial forensic kits.

    PubMed

    Lei, Liang; Xu, Jie; Du, Qingqing; Fu, Lihong; Zhang, Xiaojing; Yu, Feng; Ma, Chunling; Cong, Bin; Li, Shujin

    2015-01-01

    We determined the allele frequencies and forensic parameters for the 26 short tandem repeat (STR) autosomal markers in two commercial kits (the Investigator HDplex and AmpFLSTR(®) Identifiler(®) systems) for 183 unrelated individuals from the Han population of the Hebei Province of China. The 26 STRs were all in Hardy-Weinberg equilibrium. No linkage disequilibrium was detected between any pair of loci. The combined power of discrimination and the combined power of exclusion for the 26 STR loci were 1-7.74E-31 and 1-1.21E-11, respectively. Six rare alleles of D10S2325 were identified and named 20, 21, 22, 23, 24, and 31. All the length of the six rare alleles were out of the range of allelic ladder. We calculated the population pairwise genetic distance based on the allele frequencies, using published population data including German, central Polish, south Dutch, northeastern Polish, south Brazilian, Korean, Sichuan Han of China, and Shanghai Han of China. Also we examined the population pairwise genetic distance of loci included in Identifiler system between Hebei Han and other ethnic population of China. These 26 autosomal STR loci could provide highly informative polymorphic data for paternity testing and forensic identification in the Hebei Han population in China. Because they are all in linkage equilibrium, they could be used together to solve deficient kinship cases or cases with mutations. PMID:25262358

  7. Characterisation of novel and rare Y-chromosome short tandem repeat alleles in self-declared South Australian Aboriginal database.

    PubMed

    Collins, Tegan E; Ottens, Renee; Ballantyne, Kaye N; Nagle, Nano; Henry, Julianne; Taylor, Duncan; Gardner, Michael G; Fitch, Alison J; Goodman, Amanda; van Oorschot, Roland A H; Mitchell, R John; Linacre, Adrian

    2014-01-01

    Y-chromosome short tandem repeats (Y-STRs) are used in forensic science laboratories all over the world, as their application is wide and often vital in solving casework. Analysis of an in-house database of South Australian self-declared Aboriginal males held by Forensic Science South Australia (FSSA) using the Applied Biosystem's AmpFℓSTR® Yfiler™ PCR Amplification Kit revealed 43 variant Y-STR alleles at 6 of the 17 loci. All variant alleles were sequenced to determine the exact repeat structure for each. As a high level of admixture has previously been found within the SA Aboriginal database, samples were haplogrouped using Y-SNPs to determine their likely geographical origin. Although a number of variant alleles were associated with non-Aboriginal Y-haplogroups, a high frequency was observed within the Australian K-M9 lineage. Detailed knowledge of these variant alleles may have further application in the development of new DNA markers for identification purposes, and in population and evolutionary studies of Australian Aborigines. PMID:24048501

  8. Analysis of Short Tandem Repeat and Single Nucleotide Polymorphism Loci From Single-Source Samples Using a Custom HaloPlex Target Enrichment System Panel.

    PubMed

    Wendt, Frank R; Zeng, Xiangpei; Churchill, Jennifer D; King, Jonathan L; Budowle, Bruce

    2016-06-01

    Short tandem repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short tandem repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE. With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing custom-selected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 short tandem repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment. PMID:27075592

  9. Discovery and Development of the G-rich Oligonucleotide AS1411 as a Novel Treatment for Cancer

    PubMed Central

    Bates, Paula J.; Laber, Damian A.; Miller, Donald M.; Thomas, Shelia D.; Trent, John O.

    2009-01-01

    Certain guanine-rich (G-rich) DNA and RNA molecules can associate intermolecularly or intramolecularly to form four stranded or “quadruplex” structures, which have unusual biophysical and biological properties. Several synthetic G-rich quadruplex-forming oligodeoxynucleotides have recently been investigated as therapeutic agents for various human diseases. We refer to these biologically active G-rich oligonucleotides as aptamers because their activities arise from binding to protein targets via shape-specific recognition (analogous to antibody-antigen binding). As therapeutic agents, the G-rich aptamers may have some advantages over monoclonal antibodies and other oligonucleotide-based approaches. For example, quadruplex oligonucleotides are non-immunogenic, heat stable and they have increased resistance to serum nucleases and enhanced cellular uptake compared to unstructured sequences. In this review, we describe the characteristics and activities of G-rich oligonucleotides. We also give a personal perspective on the discovery and development of AS1411, an antiproliferative G-rich phosphodiester oligonucleotide that is currently being tested as an anticancer agent in Phase II clinical trials. This molecule functions as an aptamer to nucleolin, a multifunctional protein that is highly expressed by cancer cells, both intracellularly and on the cell surface. Thus, the serendipitous discovery of the G-rich oligonucleotides also led to the identification of nucleolin as a new molecular target for cancer therapy. PMID:19454272

  10. A Systematic Evaluation of Short Tandem Repeats in Lipid Candidate Genes: Riding on the SNP-Wave

    PubMed Central

    Lamina, Claudia; Haun, Margot; Coassin, Stefan; Kloss-Brandstätter, Anita; Gieger, Christian; Peters, Annette; Grallert, Harald; Strauch, Konstantin; Meitinger, Thomas; Kedenko, Lyudmyla; Paulweber, Bernhard; Kronenberg, Florian

    2014-01-01

    Structural genetic variants as short tandem repeats (STRs) are not targeted in SNP-based association studies and thus, their possible association signals are missed. We systematically searched for STRs in gene regions known to contribute to total cholesterol, HDL cholesterol, LDL cholesterol and triglyceride levels in two independent studies (KORA F4, n = 2553 and SAPHIR, n = 1648), resulting in 16 STRs that were finally evaluated. In a combined dataset of both studies, the sum of STR alleles was regressed on each phenotype, adjusted for age and sex. The association analyses were repeated for SNPs in a 200 kb region surrounding the respective STRs in the KORA F4 Study. Three STRs were significantly associated with total cholesterol (within LDLR, the APOA1/C3/A4/A5/BUD13 gene region and ABCG5/8), five with HDL cholesterol (3 within CETP, one in LPL and one inAPOA1/C3/A4/A5/BUD13), three with LDL cholesterol (LDLR, ABCG5/8 and CETP) and two with triglycerides (APOA1/C3/A4/A5/BUD13 and LPL). None of the investigated STRs, however, showed a significant association after adjusting for the lead or adjacent SNPs within that gene region. The evaluated STRs were found to be well tagged by the lead SNP within the respective gene regions. Therefore, the STRs reflect the association signals based on surrounding SNPs. In conclusion, none of the STRs contributed additionally to the SNP-based association signals identified in GWAS on lipid traits. PMID:25050552

  11. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

    PubMed

    Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

    2015-12-01

    The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds. PMID:26341181

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

    PubMed

    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. PMID:24444463

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

    PubMed

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

    2015-05-01

    Monozygotic twins can be co-identified by genotyping of short tandem repeats (STRs); however, for distinguishing them, STR genotyping is ineffective, especially in the case of murder. Here, a rarely occurring tri-allelic pattern in the vWA locus (16, 18, 19) was identified only in the DNA of one identical twin, which could help to exonerate the innocent twin in a murder charge. This mutation was defined as primary through genotyping of the family and could be detected in blood, buccal and semen samples from the individual; however, two alternative allele-balanced di-allelic patterns (16, 18 or 16, 19) were detected in hair root sheath cells. Such a kind of segregation indicates a one-step mutation occurs in cell mitosis, which is after embryonic zygote formation and during the early development of the individual after the division of the blastocyte. Sequencing revealed the insertion between the allele 18 and 19 is a repeat unit of TAGA/TCTA (plus/minus strand), which belongs to "AGAT/ATCT"-based core repeats identified from all tri-allelic pattern reports recorded in the STR base and a detailed model was proposed for STR repeat length variation caused by false priming during DNA synthesis. Our model illustrates the possible origination of allele-balanced and unbalanced tri-allelic pattern, clarifies that the genotypes of parent-child mismatches, aberrant di-allelic patterns, and type 1 or 2 tri-allelic patterns should be considered as independent, but interconnected forms of STR mutation. PMID:25732248

  14. Evaluation of factor VIII polymorphic short tandem repeat markers in linkage analysis for carrier diagnosis of hemophilia A

    PubMed Central

    Shrestha, Sabina; Dong, Sufang; Li, Zuhua; Huang, Zhuliang; Zheng, Fang

    2016-01-01

    Hemophilia A (HA) is the most common inherited X-linked recessive bleeding disorder caused by heterogeneous mutations in the factor VIII gene (FVIII). Diagnosis of the carrier is critical for preventing the birth of children affected by this coagulation disorder, which ultimately facilitates its management. Due to the heterogeneous nature of mutations, the large inversions and the complexity of the FVIII gene, direct recognition of the disease-associated mutation in HA is complex. Indirect linkage analysis using highly informative heterozygous polymorphic markers is an alternative method for determining the co-segregation of the mutant gene within a family for carrier detection of HA. The aim of the present study was to perform carrier diagnosis in a family with HA. Rapid multifluorescent polymerase chain reaction (PCR) was performed with six extragenic short tandem repeats (STRs), DXS1073, DXS15, DXS8091, DXS1227, DXS991, DXS993 and one intragenic marker, STR22 for linkage analysis in the HA family. All the STR markers employed in the present study were informative for linkages of pathogenic and healthy haplotypes among family members, particularly STR22, DXS1073 and DXS15. The STR marker, STR22, is within the FVIII gene while the DXS1073 and DXS15 markers are very close to the FVIII gene, where the chances of recombination are comparatively low, and provided the most accurate interpretation analysis, indicating that the proband's sister may have been the HA carrier. Rapid multifluorescent PCR using STR markers and linkage analysis was identified to be a simple method for performing HA carrier diagnosis. PMID:27446547

  15. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing.

    PubMed

    Jin, Bo; Su, Qin; Luo, Haibo; Li, Yingbi; Wu, Jin; Yan, Jing; Hou, Yiping; Liang, Weibo; Zhang, Lin

    2016-07-01

    Mutation rates and 95% CI of 33 short tandem repeat (STR) loci (D1S2142, D2S1338, D2S441, D3S1358, D3S1754, D5S818, D6S1043, D7S3048, D7S820, D8S1132, D8S1179, D10S1248, D11S2368, D12S391, D13S1492, D13S317, D13S325, D14S306, D15S659, D16S539, D18S1364, D18S51, D19S433, D20S161, D21S11, D22GATA198B05, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA) were investigated through more than 424,000 parent-child meiotic transfers obtained from 10636 trios parentage testing cases in southwest Chinese Han population. Overall, 297, including 292 single-step, 4 double-step and 1 triple-step mutation events were observed. The average mutation rate was 0.70×10(-3). Most of the locus-specific mutation rates (varied from 0.20×10(-3) to 1.96×10(-3)) were lower than the other datasets (p<0.05). Mutations of 7 loci are reported for the first time. Mutation rates varied with population from different ethnicities and geographical regions. There was no significant difference between mutation expansion and contraction (∼1.04:1). Paternal origin mutations occurred more frequently than maternal origin ones (∼5.02:1). In addition, mutation rates indicated positive correlation with the expected heterozygosity (He) and geometric mean of longest run of perfect repeats (LRPR), respectively. Short alleles showed a trend toward mutation gain while long alleles trended toward mutation loss. A credible forensic dataset for locus-specific mutation rates of 33 loci has been established based upon strict inclusion criteria of large-sized parents/child-trio cases. PMID:27045978

  16. Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region.

    PubMed

    Seio, Kohji; Tokugawa, Munefumi; Tsunoda, Hirosuke; Ohkubo, Akihiro; Arisaka, Fumio; Sekine, Mitsuo

    2013-12-15

    The structural properties of a DNA/RNA duplex having a pyrene residue at the 5' end of DNA and a G-rich single strand region at the 3' end of RNA were studied in detail. Fluorescence and ultracentrifugation analyses indicated the formation of a complex containing four DNA/RNA duplexes, which required a pyrene residue, G-rich sequence, RNA-type backbone, and high salt concentration. PMID:24183539

  17. Haplotype frequencies of 17 Y-chromosomal short tandem repeat loci from the Cukurova region of Turkey

    PubMed Central

    Serin, Ayse; Canan, Husniye; Alper, Behnan; Sertdemir, Yasar

    2011-01-01

    Aim To investigate the distribution of 17 Y-short tandem repeat (STR) loci in the population of the Cukurova region of Turkey. Methods In the period between 2009 and 2010, we investigated the distribution of 17 Y-STRs in a sample of 249 unrelated healthy men from the Cukurova region of Turkey. Genomic DNA was extracted with InstaGene matrix and Y-STRs were determined using the AmpFISTR Yfiler PCR amplification kit. Gene and haplotype diversity values were estimated using the Arlequin software. To compare our data to other populations, population pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Web site software. Results At 17 Y-STR loci we detected 148 alleles. The lowest gene diversity in this region was 0.51 for DYS391 and the highest 0.95 for DYS385a/b. Haplotype diversity was 0.9997 ± 0.0004. We compared our data with haplotype data of other Turkish populations and no significant differences were found, except with Ankara population (Φst = 0.025, P = 0.018). Comparisons were also made with the neighboring populations using analysis of molecular variance of the Y-STR loci genetic structure and our population was nearest to Lenkoran-Azerbaijani (Φst = 0.012, P = 0.068) and Iranian Ahvaz population (Φst = 0.007, P = 0.173), followed by Greek (Φst = 0.026, P = 0.000) and Russian (Φst = 0.048, P = 0.000) population. Other countries like Portugal, Spain, Italy, Egypt, Israel (Palestinian Authority Area), and Taiwan showed a high genetic distance from our population. Conclusion Our study showed that Y-STR polymorphisms were a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations. PMID:22180269

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

    PubMed

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

    2016-03-01

    Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently. PMID:26432330

  19. Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior

    PubMed Central

    Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

    2013-01-01

    Background Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Objective Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. Methods The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR® Identifiler™ kits. Results Compared to controls, the average frequencies of the following alleles were significantly lower in individuals with a history of violent behavior: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). Conclusions To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship. PMID:24991178

  20. Reduced aggregation and improved specificity of G-rich oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine bases

    PubMed Central

    Kutyavin, Igor V.; Lokhov, Sergey G.; Afonina, Irina A.; Dempcy, Robert; Gall, Alexander A.; Gorn, Vladimir V.; Lukhtanov, Eugene; Metcalf, Mark; Mills, Alan; Reed, Michael W.; Sanders, Sylvia; Shishkina, Irina; Vermeulen, Nicolaas M. J.

    2002-01-01

    Guanine (G)-rich oligodeoxyribonucleotides (ODNs) can form undesired complexes by self association through non-Watson–Crick interactions. These aggregates can compromise performance of DNA probes and make genetic analysis unpredictable. We found that the 8-aza-7-deazaguanine (PPG), a pyrazolo[3,4-d]pyrimidine analog, reduces guanine self association of G-rich ODNs. In the PPG heterocycle, the N-7 and C-8 atoms of G are interposed. This leaves the ring system with an electron density similar to G, but prevents Hoogsteen-bonding associated with N-7. ODNs containing multiple PPG bases were easily prepared using a dimethylformamidine-protected phosphoramidite reagent. Substitution of PPG for G in ODNs allowed formation of more stable DNA duplexes. When one or more PPGs were substituted for G in ODNs containing four or more consecutive Gs, G aggregation was eliminated. Substitution of PPG for G also improved discrimination of G/A, G/G and G/T mismatches in Watson–Crick hybrids. Use of PPG in fluorogenic minor groove binder probes was also explored. PPG prevented aggregation in MGB probes (MGBTM is a trademark of Epoch Biosciences) and allowed use of G-rich sequences. An increased signal was observed in 5′-PPG probes due to reduced quenching of fluorescein by PPG. In summary, substitution of PPG for G enhances affinity, specificity, sensitivity and predictability of G-rich DNA probes. PMID:12433999

  1. Allelic ladder characterization of the short tandem repeat polymorphism located in the 5{prime} flanking region to the human coagulation factor XIII A subunit gene

    SciTech Connect

    Puers, C.; Lins, A.M.; Sprecher, C.J.

    1994-09-01

    The short tandem repeat (STR) polymorphism present within the 5{prime} untranslated region of the human coagulation factor XIII A subunit gene, HUM-F13A01 [AAAG]{sub n}, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population. 27 refs., 2 figs., 1 tab.

  2. A new variant of endemic pemphigus foliaceus in El-Bagre, Colombia: the Hardy-Weinberg-Castle law and linked short tandem repeats

    PubMed Central

    Abreu-Velez, Ana María; Robles, Edinson Villa; Howard, Michael S.

    2009-01-01

    Background: We reported a new variant of endemic pemphigus foliaceus in El Bagre, Colombia. Aims: Our study performed Complex Segregation Analysis (CSA) and short tandem repeats to discriminate between environmental and/or genetic factors in this disorder. Materials and Methods: The CSA analysis was carried out according to the unified model, implemented using the transmission probabilities implemented in the computer program POINTER, and evaluated by using a software package for population genetic data analysis (GDA), Arlequin. We performed pedigree analyses by using Cyrillic 2.1 software, with a total of 30 families with 50 probands (47 males and 3 females) tested. In parallel to the CSA, we tested for the presence of short tandem repeats from HLA class II, DQ alpha 1, involving the gene locus D6S291 by using the Hardy-Weinberg- Castle law. Results Our results indicate that the best model of inheritance in this disease is a mixed model, with multifactorial effects within a recessive genotype. Two types of possible segregation patterns were found; one with strong recessive penetrance in families whose phenotype is more Amerindian-like, and another of possible somatic mutations. Conclusion: The penetrance of 10% or less in female patients 60 years of age or older indicates that hormones could protect younger females. The greatest risk factor for men being affected by the disorder was the NN genotype. These findings are only possible due to somatic mutations, and/or strong environmental effects. We also found a protective role for two genetic loci (D6S1019 AND D6S439) in the control group. PMID:22666691

  3. Diversity of Y-short tandem repeats in the representative sample of the population of Canton Sarajevo residents, Bosnia and Herzegovina.

    PubMed

    Cenanović, Merisa; Pojskić, Naris; Kovacević, Lejla; Dzehverović, Mirela; Cakar, Jasmina; Musemić, Dzenisa; Marjanović, Damir

    2010-06-01

    In our previous population study, we have used twelve Y-chromosomal short tandem repeats loci incorporated in the PowerPlex Y System to determine Y-STR diversity in B&H human population. With intent to obtain additional verification of the previously obtained results as well as to establish specific reference for a local B&H population, we have decided to test DNA samples collected from 100 unrelated healthy male Canton Sarajevo residents (from Sarajevo region) for the same twelve Y-linked short tandem repeats loci. Qiagen DNeasy Tissue Kit (Qiagen, GmbH, Hilden, Germany) was used for DNA extraction from buccal swabs and PowerPlex Y System (Promega Corp., Madison, WI) has been used to simultaneously amplify Y-STR loci by PCR. PowerPlex Y System includes 12 STR loci: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. The total PCR reaction volume was 5 microL. PCR amplifications were carried out in PE GeneAmp PCR System Thermal Cycler (ABI). Electrophoresis of the amplification products was preformed on an ABI PRISM 310 genetic analyzer (ABI, Foster City, CA) according to the manufacturer's recommendations. The raw data were compiled and analyzed using the accessory software: ABI PRISM Data Collection Software and Genemapper version 3.2. In addition, we have compared the obtained "Sarajevo" dataset with the data previously generated for the entire Bosnian and Herzegovinian population, as well as with the available data on geographically close (neighboring) European populations. The results of this study will be used as guidelines in additional improving of research into genetic relationship among recent local B&H populations, both isolated and open, which is a long-term project in our country. PMID:20698129

  4. Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects

    PubMed Central

    Palladino, Andrew A.; Chen, Jie; Kallish, Staci; Stanley, Charles A.; Bennett, Michael J.

    2013-01-01

    The primary accumulating metabolites in fatty acid oxidation defects are intramitochondrial acyl-CoAs. Typically, secondary metabolites such as acylcarnitines, acylglycines and dicarboxylic acids are measured to study these disorders. Methods have not been adapted for tissue acyl-CoA measurement in defects with primarily acyl-CoA accumulation. Our objective was to develop a method to measure fatty acyl-CoA species that are present in tissues of mice with fatty acid oxidation defects using flow-injection tandem mass spectrometry. Following the addition of internal standards of [13C2] acetyl-CoA, [13C8] octanoyl-CoA, and [C17] heptadecanoic CoA, acyl-CoA’s are extracted from tissue samples and are injected directly into the mass spectrometer. Data is acquired using a 506.9 neutral loss scan and multiple reaction-monitoring (MRM). This method can identify all long, medium and short-chain acyl-CoA species in wild type mouse liver including predicted 3-hydroxyacyl-CoA species. We validated the method using liver of the short-chain-acyl-CoA dehydrogenase (SCAD) knock-out mice. As expected, there is a significant increase in [C4] butyryl-CoA species in the SCAD −/− mouse liver compared to wild type. We then tested the assay in liver from the short-chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD) deficient mice to determine the profile of acyl-CoA accumulation in this less predictable model. There was more modest accumulation of medium chain species including 3-hydroxyacyl-CoA’s consistent with the known chain-length specificity of the SCHAD enzyme. PMID:23117082

  5. Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

    PubMed Central

    Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

    2014-01-01

    Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

  6. Towards Improvements in the Estimation of the Coalescent: Implications for the Most Effective Use of Y Chromosome Short Tandem Repeat Mutation Rates

    PubMed Central

    Bird, Steven C.

    2012-01-01

    Over the past two decades, many short tandem repeat (STR) microsatellite loci on the human Y chromosome have been identified together with mutation rate estimates for the individual loci. These have been used to estimate the coalescent age, or the time to the most recent common ancestor (TMRCA) expressed in generations, in conjunction with the average square difference measure (ASD), an unbiased point estimator of TMRCA based upon the average within-locus allele variance between haplotypes. The ASD estimator, in turn, depends on accurate mutation rate estimates to be able to produce good approximations of the coalescent age of a sample. Here, a comparison is made between three published sets of per locus mutation rate estimates as they are applied to the calculation of the coalescent age for real and simulated population samples. A novel evaluation method is developed for estimating the degree of conformity of any Y chromosome STR locus of interest to the strict stepwise mutation model and specific recommendations are made regarding the suitability of thirty-two commonly used Y-STR loci for the purpose of estimating the coalescent. The use of the geometric mean for averaging ASD and across loci is shown to improve the consistency of the resulting estimates, with decreased sensitivity to outliers and to the number of STR loci compared or the particular set of mutation rates selected. PMID:23119076

  7. Forensic and population genetic analysis of Xinjiang Uyghur population on 21 short tandem repeat loci of 6-dye GlobalFiler™ PCR Amplification kit.

    PubMed

    Zhang, Honghua; Xia, Mingying; Qi, Lijie; Dong, Lei; Song, Shuang; Ma, Teng; Yang, Shuping; Jin, Li; Li, Liming; Li, Shilin

    2016-05-01

    Estimating the allele frequencies and forensic statistical parameters of commonly used short tandem repeat (STR) loci of the Uyghur population, which is the fifth largest group in China, provides a more precise reference database for forensic investigation. The 6-dye GlobalFiler™ Express PCR Amplification kit incorporates 21 autosomal STRs, which have been proven that could provide reliable DNA typing results and enhance the power of discrimination. Here we analyzed the GlobalFiler STR loci on 1962 unrelated individuals from Chinese Uyghur population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were detected within and between the GlobalFiler STR loci. SE33 showed the greatest power of discrimination in Uyghur population, whereas TPOX showed the lowest. The combined power of discrimination was 99.999999999999999999999998746%. No significant difference was observed between Uyghur and the other two Uyghur populations at all tested STRs, as well as Dai and Mongolian. Significant differences were only observed between Uyghur and other Chinese populations at TH01, as well as Central-South Asian at D13S317, East Asian at TH01 and VWA. The phylogenetic analysis showed that Uyghur is genetically close to Chinese populations, as well as East Asian and Central-South Asian. PMID:26809046

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

    PubMed

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

    1999-11-01

    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group. PMID:10582369

  9. An Empirical Comparison of Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs) for Relatedness Estimation in Chinese Rhesus Macaques (Macaca mulatta)

    PubMed Central

    Ross, Cody T.; Weise, Jessica A.; Bonnar, Sarah; Nolin, David; Trask, Jessica Satkoski; Smith, David Glenn; Ferguson, Betsy; Ha, James; Kubisch, H. Michael; Vinson, Amanda; Kanthaswamy, Sree

    2015-01-01

    We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller and Goodnight [1994] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management. PMID:24273109

  10. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. PMID:27352221

  11. Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats.

    PubMed

    Tsuchimochi, Tsukasa; Iwasa, Mineo; Maeno, Yoshitaka; Koyama, Hiroyoshi; Inoue, Hiroyuki; Isobe, Ichiro; Matoba, Ryoji; Yokoi, Motoo; Nagao, Masataka

    2002-09-01

    A procedure utilizing Chelex 100, chelating resin, was adapted to extract DNA from dental pulp. The procedure was simple and rapid, involved no organic solvents, and did not require multiple tube transfers. The extraction of DNA from dental pulp using this method was as efficient, or more so, than using proteinase K and phenol-chloroform extraction. In this study, the Chelex method was used with amplification and typing at Y-chromosomal loci to determine the effects of temperature on the sex determination of the teeth. The extracted teeth were incinerated in a dental furnace for 2 minutes at 100 degrees C, 200 degrees C, 300 degrees C, 400 degrees C, and 500 degrees C. After the isolation of DNA from the dental pulp by the Chelex method, alphoid repeats, and short tandem repeats, the human Y chromosome (DYZ3), DYS19, SYS389, DYS390, and DYS393 could be amplified and typed in all samples incinerated at up to 300 degrees C for 2 minutes. The DYS389 locus in some samples could not be amplified at 300 degrees C for 2 minutes. An autopsy case is described in which genotypings of DYS19, DYS390, and DYS393 from dental pulp obtained from a burned body were needed. The data presented in this report suggest that Chelex 100-based DNA extraction, amplification, and typing are possible in burned teeth in forensic autopsy cases. PMID:12198355

  12. Determination of landiolol, an ultra-short-acting β₁-receptor antagonist, in human plasma by liquid chromatography-tandem mass spectrometry.

    PubMed

    He, Qun; Shi, Meiyun; Liu, Xidong; Sun, Yantong; Hu, Lianghai; Yang, Yan; Fawcett, J Paul; Gu, Jingkai; Zhao, Limei

    2012-04-01

    A method for the determination of landiolol, an ultra-short-acting β₁-adrenoreceptor antagonist, in human plasma has been developed and validated. With the addition of pyridostigmine bromide to stabilize landiolol in the blood/plasma samples, and bisoprolol as internal standard, plasma samples were subjected to liquid-liquid extraction with diethyl ether:dicholoromethane (60:40, v/v) prior to assay by liquid chromatography-tandem mass spectrometry. Separation was performed on a TC-C₁₈ column (150 mm × 4.6 mm, 5 μm) using a mobile phase of methanol:10 mM ammonium acetate containing 1% formic acid (65:35, v/v) in a run time of 3.5 min. Detection involved electrospray ionization in the positive ion mode followed by multiple reaction monitoring of the precursor-to-product ion transitions of landiolol at m/z 510.1→157.2 and bisoprolol at m/z 326.3→116.1. The method was linear over the concentration range 0.5-500 ng/ml with a lower limit of quantitation of 0.5 ng/ml. Intra- and inter-day precisions (as relative standard deviation, RSD) were <4.4% and <10.0%, respectively, with accuracy (as relative error, RE) <10.0%. The method was successfully applied to a clinical pharmacokinetic study involving a continuous infusion of landiolol hydrochloride to healthy Chinese volunteers. PMID:22418070

  13. GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences.

    PubMed

    Kostadinov, Rumen; Malhotra, Nishtha; Viotti, Manuel; Shine, Robert; D'Antonio, Lawrence; Bagga, Paramjeet

    2006-01-01

    Guanine-rich nucleic acids are known to form highly stable G-quadruplex structures, also known as G-quartets. Recently, there has been a tremendous amount of interest in studying G-quadruplexes owing to the realization of their biological importance. G-rich sequences (GRSs) capable of forming G-quadruplexes are found in the vicinity of polyadenylation regions and are involved in regulating 3' end processing of mammalian pre-mRNAs. G-rich motifs are also known to play an important role in alternative, tissue-specific splicing by interacting with hnRNP H protein subfamily. Whether quadruplex structure directly plays a role in regulating RNA processing events requires further investigation. To date there has not been a comprehensive effort to study G-quadruplexes near RNA processing sites. We have applied a computational approach to map putative Quadruplex forming GRSs within the transcribed regions of a large number of alternatively processed human and mouse gene sequences that were obtained as fully annotated entries from GenBank and RefSeq. We have used the computed data to build the GRSDB database that provides a unique avenue for studying G-quadruplexes in the context of RNA processing sites. GRSDB website offers visual comparison of G-quadruplex distribution patterns among all the alternative RNA products of a gene with the help of dynamic graphics. At present, GRSDB contains data from 1310 human and mouse genes, of which 1188 are alternatively processed. It has a total of 379,223 predicted G-quadruplexes, of which 54,252 are near RNA processing sites. GRSDB is a good resource for researchers interested in investigating the functional relevance of G-quadruplexes, especially in the context of alternative RNA processing. It can be accessed at http://bioinformatics.ramapo.edu/grsdb/. PMID:16381828

  14. GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences

    PubMed Central

    Kostadinov, Rumen; Malhotra, Nishtha; Viotti, Manuel; Shine, Robert; D'Antonio, Lawrence; Bagga, Paramjeet

    2006-01-01

    Guanine-rich nucleic acids are known to form highly stable G-quadruplex structures, also known as G-quartets. Recently, there has been a tremendous amount of interest in studying G-quadruplexes owing to the realization of their biological importance. G-rich sequences (GRSs) capable of forming G-quadruplexes are found in the vicinity of polyadenylation regions and are involved in regulating 3′ end processing of mammalian pre-mRNAs. G-rich motifs are also known to play an important role in alternative, tissue-specific splicing by interacting with hnRNP H protein subfamily. Whether quadruplex structure directly plays a role in regulating RNA processing events requires further investigation. To date there has not been a comprehensive effort to study G-quadruplexes near RNA processing sites. We have applied a computational approach to map putative Quadruplex forming GRSs within the transcribed regions of a large number of alternatively processed human and mouse gene sequences that were obtained as fully annotated entries from GenBank and RefSeq. We have used the computed data to build the GRSDB database that provides a unique avenue for studying G-quadruplexes in the context of RNA processing sites. GRSDB website offers visual comparison of G-quadruplex distribution patterns among all the alternative RNA products of a gene with the help of dynamic graphics. At present, GRSDB contains data from 1310 human and mouse genes, of which 1188 are alternatively processed. It has a total of 379 223 predicted G-quadruplexes, of which 54 252 are near RNA processing sites. GRSDB is a good resource for researchers interested in investigating the functional relevance of G-quadruplexes, especially in the context of alternative RNA processing. It can be accessed at . PMID:16381828

  15. Separation of isomeric short-chain acyl-CoAs in plant matrices using ultra-performance liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Purves, Randy W; Ambrose, Stephen J; Clark, Shawn M; Stout, Jake M; Page, Jonathan E

    2015-02-01

    Acyl coenzyme A (acyl-CoA) thioesters are important intermediates in cellular metabolism and being able to distinguish among them is critical to fully understanding metabolic pathways in plants. Although significant advances have been made in the identification and quantification of acyl-CoAs using liquid chromatography tandem mass spectrometry (LC-MS/MS), separation of isomeric species such as isobutyryl- and n-butyrl-CoA has remained elusive. Here we report an ultra-performance liquid chromatography (UPLC)-MS/MS method for quantifying short-chain acyl-CoAs including isomeric species n-butyryl-CoA and isobutyryl-CoA as well as n-valeryl-CoA and isovaleryl-CoA. The method was applied to the analysis of extracts of hop (Humulus lupulus) and provided strong evidence for the existence of an additional structural isomer of valeryl-CoA, 2-methylbutyryl-CoA, as well as an unexpected isomer of hexanoyl-CoA. The results showed differences in the acyl-CoA composition among varieties of Humulus lupulus, both in glandular trichomes and cone tissues. When compared with the analysis of hemp (Cannabis sativa) extracts, the contribution of isobutyryl-CoAs in hop was greater as would be expected based on the downstream polyketide products. Surprisingly, branched chain valeryl-CoAs (isovaleryl-CoA and 2-methylbutyryl-CoA) were the dominant form of valeryl-CoAs in both hop and hemp. The capability to separate these isomeric forms will help to understand biochemical pathways leading to specialized metabolites in plants. PMID:25553535

  16. Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

    PubMed

    Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

    2016-04-15

    A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer. PMID:26657593

  17. Evidence for human meiotic recombination interference obtained through construction of a short tandem repeat-polymorphism linkage map of chromosome 19

    SciTech Connect

    Weber, J.L.; Wang, Z.; Hansen, K.; Stephenson, M.; Kappel, C.; Salzman, S.; Wilkie, P.J. ); Keats, B. ); Dracopoli, N.C. ); Brandriff, B.F.; Olsen, A.S. )

    1993-11-01

    An improved linkage map for human chromosome 19 containing 35 short tandem repeat polymorphisms (STRPs) and one VNTR (D19S20) was constructed. The map included 12 new (GATA)[sub n] tetranucleotide STRPs. Although total lengths of the male (114 cM) and female (128 cM) maps were similar, at both ends of the chromosome male recombination exceeded female recombination, while in the interior portion of the map female recombination was in excess. Cosmid clones containing the STRP sequences were identified and were positioned along the chromosome by fluorescent in situ hybridization. Four rounds of careful checking and removal of genotyping errors allowed biologically relevant conclusions to be made concerning the numbers and distributions of recombination events on chromosome 19. The average numbers of recombinations per chromosome matched closely the lengths of the genetic maps computed by using the program CRIMAP. Significant numbers of chromosomes with zero, one, two, or three recombinations were detected as products of both female and male meioses. On the basis of the total number of observed pairs of recombination events in which only a single informative marker was situated between the two recombinations, a maximal estimate for the rate of meiotic STRP [open quotes]gene[close quotes] conversion without recombination was calculated as 3 [times] 10[sup [minus]4]/meiosis. For distances up to 30 cM between recombinations, many fewer chromosomes which had undergone exactly two recombinations were observed than were expected on the basis of the assumption of independent recombination locations. This strong new evidence for human meiotic interference will help to improve the accuracy of interpretation of clinical DNA test results involving polymorphisms flanking a genetic abnormality. 61 refs., 2 figs., 5 tabs.

  18. Multifunctional G-Rich and RRM-Containing Domains of TbRGG2 Perform Separate yet Essential Functions in Trypanosome RNA Editing

    PubMed Central

    Foda, Bardees M.; Downey, Kurtis M.; Fisk, John C.

    2012-01-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3′-to-5′ progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain. PMID:22798390

  19. Multifunctional G-rich and RRM-containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing.

    PubMed

    Foda, Bardees M; Downey, Kurtis M; Fisk, John C; Read, Laurie K

    2012-09-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3'-to-5' progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain. PMID:22798390

  20. Short tandem repeat (STR) genotyping of keratinised hair. Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles.

    PubMed

    McNevin, Dennis; Wilson-Wilde, Linzi; Robertson, James; Kyd, Jennelle; Lennard, Chris

    2005-10-29

    A feasibility study of short tandem repeat (STR) genotyping of telogen phase hairs in particular, and hair shaft in general, is presented. A number of extraction procedures in common use were investigated and the quantities of nuclear DNA (nuDNA) delivered were quantified via a real-time PCR assay. The extracts were subjected to two variations on AmpFlSTR Profiler Plus PCR amplification strategies (extended cycles, two rounds of PCR) and the genotypes compared. Nuclear DNA was found to persist in human hair shafts, albeit at very low levels. Full Profiler Plus profiles consistent with the hair donor were obtained from 100 mg hair shaft samples (bleached and unbleached). These were, however, mixed profiles, indicating low copy number (LCN) contamination in the extracts. Single telogen hair clubs and single hair shafts delivered partial profiles with usually only one allele of heterozygous loci. Telogen phase hairs yielded the same amount of nuDNA (and no more) as hair shafts (either anagen or telogen). Whether hair shafts dissolved or not in lysis buffer had no effect on either the quantitated yield of DNA or on the chance of obtaining a correct genotype. These results provide evidence that genomic DNA resides on the exterior of the hair shaft and we use this information to suggest an optimal procedure for nuDNA extraction from keratinised hair samples: soaking hairs in simple digestion buffers containing Tris-HCl, a salt and a chelating agent without prior cleaning of the hair shafts. It is proposed that cleaning removes most of the recoverable DNA. This procedure was applied to obtain genotypes from 3 cm hair shafts which matched reference profiles from the donors at up to 9 out of 10 AmpFlSTR Profiler Plus STR loci. When the genotyping success was measured by counting the number of matches between the two dominant alleles at each locus for each extract with the reference DNA profile of the hair donor, the success was found to be highly dependent on the donor. The

  1. Identification of Skeletal Remains of Communist Armed Forces Victims During and After World War II: Combined Y-chromosome Short Tandem Repeat (STR) and MiniSTR Approach

    PubMed Central

    Marjanović, Damir; Durmić-Pašić, Adaleta; Kovačević, Lejla; Avdić, Jasna; Džehverović, Mirela; Haverić, Sanin; Ramić, Jasmin; Kalamujić, Belma; Bilela, Lada Lukić; Škaro, Vedrana; Projić, Petar; Bajrović, Kasim; Drobnič, Katja; Davoren, Jon; Primorac, Dragan

    2009-01-01

    Aim To report on the use of STR, Y-STRs, and miniSTRs typing methods in the identification of victims of revolutionary violence and crimes against humanity committed by the Communist Armed Forces during and after World War II in which bodies were exhumed from mass and individual graves in Slovenia. Methods Bone fragments and teeth were removed from human remains found in several small and closely located hidden mass graves in the Škofja Loka area (Lovrenska Grapa and Žolšče) and 2 individual graves in the Ljubljana area (Podlipoglav), Slovenia. DNA was isolated using the Qiagen DNA extraction procedure optimized for bone and teeth. Some DNA extracts required additional purification, such as N-buthanol treatment. The QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. Initially, PowerPlex 16 kit was used to simultaneously analyze 15 short tandem repeat (STR) loci. The PowerPlex S5 miniSTR kit and AmpFℓSTR® MiniFiler PCR Amplification Kit was used for additional analysis if preliminary analysis yielded weak partial or no profiles at all. In 2 cases, when the PowerPlex 16 profiles indicated possible relatedness of the remains with reference samples, but there were insufficient probabilities to call the match to possible male paternal relatives, we resorted to an additional analysis of Y-STR markers. PowerPlex® Y System was used to simultaneously amplify 12 Y-STR loci. Fragment analysis was performed on an ABI PRISM 310 genetic analyzer. Matching probabilities were estimated using the DNA-View software. Results Following the Y-STR analysis, 1 of the “weak matches” previously obtained based on autosomal loci, was confirmed while the other 1 was not. Combined standard STR and miniSTR approach applied to bone samples from 2 individual graves resulted in positive identifications. Finally, using the same approach on 11 bone samples from hidden mass grave Žološče, we were able to obtain 6 useful DNA profiles. Conclusion The results of

  2. Effect of G-rich oligonucleotides on the proliferation of leukemia cells and its relationship with p53 expression.

    PubMed

    Zhi, Lei; Zhang, Jianwei; Jia, Yujiao; Shan, Shilong; Li, Yan; Wang, Donghai; Wang, Min; Rao, Qing; Xing, Haiyan; Tang, Kejing; Tian, Zheng; Wang, Jianxiang; Mi, Yingchang

    2011-02-01

    G-rich oligonucleotides (GROs) can inhibit cell proliferation by inducing cell cycle arrest at S phase in tumor cell lines. GROs bind specific cellular proteins, such as nucleolin, a crucial protein interacting with P53; however, little is known about the relationship between GROs and P53. In this study, we have shown that GROs inhibited the proliferation of U937 cells (a human monocytic leukemia cell line without P53 expression) by inducing S-phase arrest. We also showed that GRO colocalized with nucleolin in U937 cells. GRO treatment induced alteration of a series of cell cycle regulatory proteins in U937 cells. Increased Cdk2 expression might promote the cells to enter S phase and subsequent decrease of Cdk2 might induce cell cycle arrest in S phase. Transfection of U937 cells with a wild-type p53 gene caused the formation of nucleolin-P53 complex, which alleviated the effect of GRO on leukemia cells. This alleviated effect is probably due to the decreased uptake of GRO. PMID:21247336

  3. Thermal stability of G-rich anti-parallel DNA triplexes upon insertion of LNA and α-L-LNA.

    PubMed

    Kosbar, Tamer R; Sofan, Mamdouh A; Abou-Zeid, Laila; Pedersen, Erik B

    2015-05-14

    G-rich anti-parallel DNA triplexes were modified with LNA or α-L-LNA in their Watson-Crick and TFO strands. The triplexes were formed by targeting a pyrimidine strand to a putative hairpin formed by Hoogsteen base pairing in order to use the UV melting method to evaluate the stability of the triplexes. Their thermal stability was reduced when the TFO strand was modified with LNA or α-L-LNA. The same trend was observed when the TFO strand and the purine Watson-Crick strand both were modified with LNA. When all triad components were modified with α-L-LNA and LNA in the middle of the triplex, the thermal melting was increased. When the pyrimidine sequence was modified with a single insertion of LNA or α-L-LNA the ΔTm increased. Moreover, increasing the number of α-L-LNA in the pyrimidine target sequence to six insertions, leads to a high increase in the thermal stability. The conformational S-type structure of α-L-LNA in anti-parallel triplexes is preferable for triplex stability. PMID:25833006

  4. 5meCpG Epigenetic Marks Neighboring a Primate-Conserved Core Promoter Short Tandem Repeat Indicate X-Chromosome Inactivation

    PubMed Central

    Machado, Filipe Brum; Machado, Fabricio Brum; Faria, Milena Amendro; Lovatel, Viviane Lamim; Alves da Silva, Antonio Francisco; Radic, Claudia Pamela; De Brasi, Carlos Daniel; Rios, Álvaro Fabricio Lopes; de Sousa Lopes, Susana Marina Chuva; da Silveira, Leonardo Serafim; Ruiz-Miranda, Carlos Ramon; Ramos, Ester Silveira; Medina-Acosta, Enrique

    2014-01-01

    X-chromosome inactivation (XCI) is the epigenetic transcriptional silencing of an X-chromosome during the early stages of embryonic development in female eutherian mammals. XCI assures monoallelic expression in each cell and compensation for dosage-sensitive X-linked genes between females (XX) and males (XY). DNA methylation at the carbon-5 position of the cytosine pyrimidine ring in the context of a CpG dinucleotide sequence (5meCpG) in promoter regions is a key epigenetic marker for transcriptional gene silencing. Using computational analysis, we revealed an extragenic tandem GAAA repeat 230-bp from the landmark CpG island of the human X-linked retinitis pigmentosa 2 RP2 promoter whose 5meCpG status correlates with XCI. We used this RP2 onshore tandem GAAA repeat to develop an allele-specific 5meCpG-based PCR assay that is highly concordant with the human androgen receptor (AR) exonic tandem CAG repeat-based standard HUMARA assay in discriminating active (Xa) from inactive (Xi) X-chromosomes. The RP2 onshore tandem GAAA repeat contains neutral features that are lacking in the AR disease-linked tandem CAG repeat, is highly polymorphic (heterozygosity rates approximately 0.8) and shows minimal variation in the Xa/Xi ratio. The combined informativeness of RP2/AR is approximately 0.97, and this assay excels at determining the 5meCpG status of alleles at the Xp (RP2) and Xq (AR) chromosome arms in a single reaction. These findings are relevant and directly translatable to nonhuman primate models of XCI in which the AR CAG-repeat is monomorphic. We conducted the RP2 onshore tandem GAAA repeat assay in the naturally occurring chimeric New World monkey marmoset (Callitrichidae) and found it to be informative. The RP2 onshore tandem GAAA repeat will facilitate studies on the variable phenotypic expression of dominant and recessive X-linked diseases, epigenetic changes in twins, the physiology of aging hematopoiesis, the pathogenesis of age-related hematopoietic

  5. Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree

    PubMed Central

    Myres, Natalie M.; Ritchie, Kathleen H.; Lin, Alice A.; Hughes, Robert H.; Woodward, Scott R.; Underhill, Peter A.

    2009-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. Results We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Conclusions Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and Y-STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context. PMID:19480020

  6. Y-chromosome Short Tandem Repeat DYS458.2 Non-consensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405

    PubMed Central

    Myres, Natalie M.; Ekins, Jayne E.; Lin, Alice A.; Cavalli-Sforza, L. Luca; Woodward, Scott R.; Underhill, Peter A.

    2007-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of non-consensus DYS458.2 short tandem repeat alleles and evaluate their phylogenetic substructure and frequency in representative samples from the Middle East, Europe, and Pakistan. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci, including DYS388 to construct haplotypes. DNA sequencing of the DYS458 locus and median-joining network analyses were used to evaluate Y-chromosome lineages displaying the DYS458.2 motif. Results We showed that the DYS458.2 allelic innovation arose independently on at least two distinctive binary haplogroup backgrounds and possibly a third as well. The partial allele length pattern was fixed in all haplogroup J1 chromosomes examined, including its known rare sub-haplogroups. Within the alternative R1b3 associated M405 defined sub-haplogroup, both DYS458.0 and DYS458.2 allele classes occurred. A single chromosome also allocated to the R1b3-M269*(xM405) classification. The physical position of the partial insertion/deletion occurrence within the normal tetramer tract differed distinctly in each haplogroup context. Conclusions While unusual DYS458.2 alleles are informative, additional information for other linked polymorphic loci is required when using such non-conforming alleles to infer haplogroup background and common ancestry. PMID:17696299

  7. Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

    PubMed

    Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

    2014-01-29

    We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression. PMID:24392825

  8. Tandem betatron accelerator

    NASA Astrophysics Data System (ADS)

    Keinigs, Rhon K.

    1991-04-01

    1407_50The tandem betatron is a compact, high-current induction accelerator that has the capability to accelerate electrons to an energy of order one gigavolt. Based upon the operating principle of a conventional betatron, the tandem betatron employs two synchronized induction cores operating 180 degrees out of phase. Embedded within the cores are the vacuum chambers, and these are connected by linear transport sections to allow for moving the beam back and forth between the two betatrons. The 180 degree phase shift between the core fluxes permits the circumvention of the flux swing constraint that limits the maximum energy gain of a conventional betatron. By transporting the beam between the synchronized cores, an electron can access more than one acceleration cycle, and thereby continue to gain energy. This added degree of freedom also permits a significant decrease in the size of the magnet system. Biasing coils provide independent control of the confining magnetic field. Provided that efficient beam switching can be performed, it appears feasible that a one gigavolt electron beam can be generated and confined. At this energy, a high current electron beam circulating in a one meter radius orbit could provide a very intense source of short wavelength ((lambda) < 10 nm) synchrotron radiation. This has direct application to the emerging field of x-ray lithography. At more modest energies (10 MeV-30 MeV) a compact tandem betatron could be employed in the fields of medical radiation therapy, industrial radiography, and materials processing.

  9. Tandem betatron

    DOEpatents

    Keinigs, Rhonald K.

    1992-01-01

    Two betatrons are provided in tandem for alternately accelerating an electron beam to avoid the single flux swing limitation of conventional betatrons and to accelerate the electron beam to high energies. The electron beam is accelerated in a first betatron during a period of increasing magnetic flux. The eletron beam is extracted from the first betatron as a peak magnetic flux is reached and then injected into a second betatron at a time of minimum magnetic flux in the second betatron. The cycle may be repeated until the desired electron beam energy is obtained. In one embodiment, the second betatron is axially offset from the first betatron to provide for electron beam injection directly at the axial location of the beam orbit in the second betatron.

  10. Indole-3-acetic acid biosensor based on G-rich DNA labeled AuNPs as chemiluminescence probe coupling the DNA signal amplification

    NASA Astrophysics Data System (ADS)

    Hun, Xu; Mei, Zhenghua; Wang, Zhouping; He, Yunhua

    2012-09-01

    A highly sensitive chemiluminescence (CL) method for detection of phytohormone indole-3-acetic acid (IAA) was developed by using G-rich DNA labeled gold nanoparticles (AuNPs) as CL probe coupling the DNA signal amplification technology. The IAA antibody was immobilized on carboxyl terminated magnetic beads (MBs). In the presence of IAA, antibody labeled AuNPs were captured by antibody functionalized MBs. The DNA on AuNPs is released by a ligand exchange process induced by the addition of DTT. The released DNA is then acted as the linker and hybridized with the capture DNA on MBs and probe DNA on AuNPs CL probe. The CL signal is obtained via the instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxyl-phenylglyoxal (TMPG), and the G-rich DNA on AuNPs CL probe. IAA can be detected in the concentration range from 0.02 ng/mL to 30 ng/mL, and the limit of detection is 0.01 ng/mL.

  11. DNA methyltransferase activity detection based on fluorescent silver nanocluster hairpin-shaped DNA probe with 5'-C-rich/G-rich-3' tails.

    PubMed

    Liu, Wenting; Lai, Han; Huang, Rong; Zhao, Chuntao; Wang, Yimo; Weng, Xiaocheng; Zhou, Xiang

    2015-06-15

    DNA methylation has received a large amount of attention due to its close relationship to a wide range of biological phenomena, such as gene activation, gene imprinting, and chromatin stability. Herein, we have designed a hairpin-shaped DNA probe with 5'-C-rich/G-rich-3' tails and developed a simple and reliable fluorescence turn-off assay for DNA adenine methylation (Dam) methyltransferase (MTase) detection combining site recognition and the fluorescence enhancement of DNA-templated silver nanoclusters (DNA-AgNCs) by guanine-rich DNA sequences. A designed hairpin probe with 5' CCCTTACCCC and 3' GGGTGGGGTGGGGTGGGG displays a bright red emission after reacting with AgNO3 and NaBH4. In the presence of Dam MTase, the methylation-sensitive restriction endonuclease Dpn I which has the same recognition site with the Dam MTase can split the probe, freeing the G-rich sequence from the C-rich sequence, thus quenching the fluorescence of DNA-AgNCs. Compared to traditional fluorescent-based methods, this strategy is simple and inexpensive. A linear response to concentrations of Dam MTase which range from 1 U/mL to 100 U/mL and a detection limit of 1 U/mL are obtained without any amplification steps. In addition, we also demonstrate the method can be used for evaluation and screening of inhibitors for Dam MTase. PMID:25682501

  12. Highly sensitive electrochemical sensor using a MWCNTs/GNPs-modified electrode for lead (II) detection based on Pb(2+)-induced G-rich DNA conformation.

    PubMed

    Zhu, Yuan; Zeng, Guang-ming; Zhang, Yi; Tang, Lin; Chen, Jun; Cheng, Min; Zhang, Li-hua; He, Ling; Guo, Yuan; He, Xiao-xiao; Lai, Ming-yong; He, Yi-bin

    2014-10-01

    A sensitive electrochemical lead ion (Pb(2+)) sensor based on carboxylic acid group functionalized multi-walled carbon nanotubes (MWNTs-COOH) and direct electrodeposited gold nanoparticles (GNPs) was developed for Pb(2+) detection. The DNA capture probe was self-assembled onto the surface of the modified electrode for hybridizing with the guanine-rich (G-rich) aptamer probe and for forming the DNA double helix structure. When Pb(2+) was added in, the DNA duplex unwound and formed a stabilized G-quadruplex (G4) due to the Pb(2+)-induced G-rich DNA conformation. Also, methylene blue (MB) was selected as the G4-binding indicator. Compared with previous Pb(2+) sensors, the proposed sensor had better sensitivity, because the modified MWCNTs/GNPs could provide a large surface area and good charge-transport capacity to dramatically improve the DNA attachment quantity and sensor performance. The sensor could detect Pb(2+) in a range from 5.0 × 10(-11) to 1.0 × 10(-14) M, with a detection of 4.3 × 10(-15) M. PMID:25105175

  13. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs.

    PubMed

    Abdelmohsen, Kotb; Tominaga, Kumiko; Lee, Eun Kyung; Srikantan, Subramanya; Kang, Min-Ju; Kim, Mihee M; Selimyan, Roza; Martindale, Jennifer L; Yang, Xiaoling; Carrier, France; Zhan, Ming; Becker, Kevin G; Gorospe, Myriam

    2011-10-01

    RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3'-untranslated region (UTR), but also in the coding region (CR) and 5'-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation. PMID:21737422

  14. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs

    PubMed Central

    Abdelmohsen, Kotb; Tominaga, Kumiko; Lee, Eun Kyung; Srikantan, Subramanya; Kang, Min-Ju; Kim, Mihee M.; Selimyan, Roza; Martindale, Jennifer L.; Yang, Xiaoling; Carrier, France; Zhan, Ming; Becker, Kevin G.; Gorospe, Myriam

    2011-01-01

    RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3′-untranslated region (UTR), but also in the coding region (CR) and 5′-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation. PMID:21737422

  15. Tandem Couture

    PubMed Central

    Ericksen, Spencer S.; Boileau, Andrew J.

    2008-01-01

    Receptor subunits in the Cys-loop superfamily assemble to form channels as homopentamers or heteropentamers, expanding functional diversity through modularity. Expression of two or more compatible subunit types can lead to various receptor assemblies or subtypes. However, what may be good for diversity in vivo may be undesirable for the bench scientist, because we often wish to reduce our analyses to a single receptor subtype. By linking two or more subunits, creating tandems or concatamers, we can control stoichiometry and limit expression to exactly one receptor subtype. In this fashion, receptors with mixed subunit subtypes and heterozygous mutations can be separated from a mixture and can be described in detail. However, several recent studies have shown that this may be more easily conceived than accomplished, because several unforeseen problems have arisen. Concatamers can degrade, linkers can sometimes be clipped after or during translation, and one subunit may “loop out” or even become part of a second (now linked) pentamer with different characteristics. Some strategies have been developed to overcome these drawbacks, and the resultant new information that has begun to emerge has revitalized the study of these receptors in heterologous expression systems. PMID:17519509

  16. Precision and accuracy in fluorescent short tandem repeat DNA typing: assessment of benefits imparted by the use of allelic ladders with the AmpF/STR Profiler Plus kit.

    PubMed

    Leclair, Benoît; Frégeau, Chantal J; Bowen, Kathy L; Fourney, Ron M

    2004-03-01

    Base-calling precision of short tandem repeat (STR) allelic bands on dynamic slab-gel electrophoresis systems was evaluated. Data was collected from over 6000 population database allele peaks generated from 468 population database samples amplified with the AmpF/STR Profiler Plus (PP) kit and electrophoresed on ABD 377 DNA sequencers. Precision was measured by way of standard deviations and was shown to be essentially the same, whether using fixed or floating bin genotyping. However, the allelic ladders have proven more sensitive to electrophoretic variations than database samples, which have caused some floating bins of D18S51 to shift on occasion. This observation prompted the investigation of polyacrylamide gel formulations in order to stabilize allelic ladder migration. The results demonstrate that, although alleles comprised in allelic ladders and questioned samples run on the same gel should migrate in an identical manner, this premise needs to be verified for any given electrophoresis platform and gel formulation. We show that the compilation of base-calling data is a very informative and useful tool for assessing the performance stability of dynamic gel electrophoresis systems, stability on which depends genotyping result quality. PMID:15004837

  17. AmpFlSTR profiler Plus short tandem repeat DNA analysis of casework samples, mixture samples, and nonhuman DNA samples amplified under reduced PCR volume conditions (25 microL).

    PubMed

    Frégeau, Chantal J; Bowen, Kathy L; Leclair, Benoît; Trudel, Isabelle; Bishop, Lucy; Fourney, Ron M

    2003-09-01

    As part of the validation of the AmpFlSTR Profiler Plus short tandem repeat (STR) system, under reduced polymerase chain reaction (PCR) volume conditions (i.e., 25 microL), a total of 275 casework samples were processed. Examples of profiles are presented along with amplification conditions to improve the odds of obtaining balanced and complete profiles for samples showing partial results or profiles with a descending slope. Data collected and used to develop our interpretation guidelines are included. From the mixture studies, full profiles were obtained for minor contributors, using 2 ng of DNA, with ratios of 10:1 or 1:20 and using 1 ng of DNA, with ratios of 10:1 and 1:8. The specificity of the Profiler Plus amplification reaction performed in 25 microL was examined and confirmed using a large spectrum of nonhuman DNAs. This report supports the use of the AmpFlSTR Profiler Plus STR system for casework DNA typing under reduced PCR volume conditions. PMID:14535664

  18. Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) Founder Mutation: Clues from Haplotyping of Short Tandem Repeats on Chromosome 17p

    PubMed Central

    Paskulin, Diego Davila; Giacomazzi, Juliana; Achatz, Maria Isabel; Costa, Sandra; Reis, Rui Manoel; Hainaut, Pierre; dos Santos, Sidney Emanuel Batista; Ashton-Prolla, Patricia

    2015-01-01

    Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial history. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Iberic origin, distant in about 72–84 generations (2000 years assuming a 25 years intergenerational distance) and thus pre-dating European migration to Brazil. So far, the founder p.Arg337His haplotype has not been detected outside Brazil, with the exception of two residents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil. PMID:26618902

  19. Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging

    PubMed Central

    Chu, Michelle W; Siegmund, Kimberly D; Eckstam, Carrie L; Kim, Jung Yeon; Yang, Allen S; Kanel, Gary C; Tavaré, Simon; Shibata, Darryl

    2007-01-01

    Background Cell division occurs during normal human development and aging. Despite the likely importance of cell division to human pathology, it has been difficult to infer somatic cell mitotic ages (total numbers of divisions since the zygote) because direct counting of lifetime numbers of divisions is currently impractical. Here we attempt to infer relative mitotic ages with a molecular clock hypothesis. Somatic genomes may record their mitotic ages because greater numbers of replication errors should accumulate after greater numbers of divisions. Mitotic ages will vary between cell types if they divide at different times and rates. Methods Age-related increases in DNA methylation at specific CpG sites (termed "epigenetic molecular clocks") have been previously observed in mitotic human epithelium like the intestines and endometrium. These CpG rich sequences or "tags" start unmethylated and potentially changes in methylation during development and aging represent replication errors. To help distinguish between mitotic versus time-associated changes, DNA methylation tag patterns at 8–20 CpGs within three different genes, two on autosomes and one on the X-chromosome were measured by bisulfite sequencing from heart, brain, kidney and liver of autopsies from 21 individuals of different ages. Results Levels of DNA methylation were significantly greater in adult compared to fetal or newborn tissues for two of the three examined tags. Consistent with the relative absence of cell division in these adult tissues, there were no significant increases in tag methylation after infancy. Conclusion Many somatic methylation changes at certain CpG rich regions or tags appear to represent replication errors because this methylation increases with chronological age in mitotic epithelium but not in non-mitotic organs. Tag methylation accumulates differently in different tissues, consistent with their expected genealogies and mitotic ages. Although further studies are necessary

  20. 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.

    PubMed

    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

  1. Comprehensive profiling of mercapturic acid metabolites from dietary acrylamide as short-term exposure biomarkers for evaluation of toxicokinetics in rats and daily internal exposure in humans using isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry.

    PubMed

    Zhang, Yu; Wang, Qiao; Cheng, Jun; Zhang, Jingshun; Xu, Jiaojiao; Ren, Yiping

    2015-09-24

    Mercapturic acid metabolites from dietary acrylamide are important short-term exposure biomarkers for evaluating the in vivo toxicity of acrylamide. Most of studies have focused on the measurement of two metabolites, N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA) and N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA). Thus, the comprehensive profile of acrylamide urinary metabolites cannot be fully understood. We developed an isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of all four mercapturic acid adducts of acrylamide and its primary metabolite glycidamide under the electroscopy ionization negative (ESI-) mode in the present study. The limit of detection (LOD) and limit of quantification (LOQ) of the analytes ranged 0.1-0.3 ng/mL and 0.4-1.0 ng/mL, respectively. The recovery rates with low, intermediate and high spiking levels were calculated as 95.5%-105.4%, 98.2%-114.0% and 92.2%-108.9%, respectively. Acceptable within-laboratory reproducibility (RSD<7.0%) substantially supported the use of current method for robust analysis. Rapid pretreatment procedures and short run time (8 min per sample) ensured good efficiency of metabolism profiling, indicating a wide application for investigating short-term internal exposure of dietary acrylamide. Our proposed UHPLC-MS/MS method was successfully applied to the toxicokinetic study of acrylamide in rats. Meanwhile, results of human urine analysis indicated that the levels of N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), which did not appear in the mercapturic acid metabolites in rodents, were more than the sum of GAMA and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Thus, AAMA-sul may alternatively become a specific biomarker for investigating the acrylamide exposure in humans. Current proposed method provides a substantial methodology support for comprehensive profiling of

  2. High-sensitivity mass spectrometry with a tandem accelerator

    SciTech Connect

    Henning, W.

    1983-01-01

    The characteristic features of accelerator mass spectrometry are discussed. A short overview is given of the current status of mass spectrometry with high-energy (MeV/nucleon) heavy-ion accelerators. Emphasis is placed on studies with tandem accelerators and on future mass spectrometry of heavier isotopes with the new generation of higher-voltage tandems.

  3. GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs

    PubMed Central

    Kikin, Oleg; Zappala, Zachary; D’Antonio, Lawrence; Bagga, Paramjeet S.

    2008-01-01

    G-quadruplex motifs in the RNA play significant roles in key cellular processes and human disease. While sequences capable of forming G-quadruplexes in the pre-mRNA are involved in regulation of polyadenylation and splicing events in mammalian transcripts, the G-quadruplex motifs in the UTRs may help regulate mRNA expression. GRSDB2 is a second-generation database containing information on the composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in ∼29 000 eukaryotic pre-mRNA sequences, many of which are alternatively processed. The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries with the help of an improved version of the QGRS Mapper program. The database allows complex queries with a wide variety of parameters, including Gene Ontology terms. The data is displayed in a variety of formats with several additional computational capabilities. We have also developed a new database, GRS_UTRdb, containing information on the composition and distribution patterns of putative QGRS in the 5′- and 3′-UTRs of eukaryotic mRNA sequences. The goal of these experiments has been to build freely accessible resources for exploring the role of G-quadruplex structure in regulation of gene expression at post-transcriptional level. The databases can be accessed at the G-Quadruplex Resource Site at: http://bioinformatics.ramapo.edu/GQRS/. PMID:18045785

  4. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA

    PubMed Central

    Munroe, Stephen H.; Morales, Christopher H.; Duyck, Tessa H.; Waters, Paul D.

    2015-01-01

    The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3’ end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3’splice site of TRα2 mRNA and antisense to the 3’UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

  5. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA.

    PubMed

    Munroe, Stephen H; Morales, Christopher H; Duyck, Tessa H; Waters, Paul D

    2015-01-01

    The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3' end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3'splice site of TRα2 mRNA and antisense to the 3'UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

  6. Tandem mobile robot system

    DOEpatents

    Buttz, James H.; Shirey, David L.; Hayward, David R.

    2003-01-01

    A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

  7. Monolithic Parallel Tandem Organic Photovoltaic Cell with Transparent Carbon Nanotube Interlayer

    NASA Technical Reports Server (NTRS)

    Tanaka, S.; Mielczarek, K.; Ovalle-Robles, R.; Wang, B.; Hsu, D.; Zakhidov, A. A.

    2009-01-01

    We demonstrate an organic photovoltaic cell with a monolithic tandem structure in parallel connection. Transparent multiwalled carbon nanotube sheets are used as an interlayer anode electrode for this parallel tandem. The characteristics of front and back cells are measured independently. The short circuit current density of the parallel tandem cell is larger than the currents of each individual cell. The wavelength dependence of photocurrent for the parallel tandem cell shows the superposition spectrum of the two spectral sensitivities of the front and back cells. The monolithic three-electrode photovoltaic cell indeed operates as a parallel tandem with improved efficiency.

  8. Tandem Air Propellers - II

    NASA Technical Reports Server (NTRS)

    Lesley, E. P.

    1939-01-01

    Tests of three-blade, adjustable-pitch counterrotating tandem model propellers, adjusted to absorb equal power at maximum efficiency of the combination, were made at Stanford University. The aerodynamic characteristics, for blade-angle settings of 15, 25, 35, 45, 55, and 65 degrees at 0.75R of the forward propeller and for diameters spacings of 8-1/2, 15 and 30% were compared with those of three-blade and six-blade propellers of the same blade form. It was found that, in order to realize the condition of equal power at maximum efficiency, the blade angles for the rear propeller must be generally less than for the forward propeller, the difference increasing the blade angle. The tests showed that, at maximum efficiency, the tandem propellers absorb about double the power of three-blade propellers and about 8% more power than six-blade propellers having the pitch of the forward propeller of the tandem combination. The maximum efficiency of the tandem propellers was found to be from 2-15% greater than for six-blade propellers, the difference varying directly with blade angle. It was also found that the maximum efficiency of the tandem propellers was greater than that of a three-blade propeller for blade angles at 0.75R of 25 degrees or more. The difference in maximum efficiency again varied directly with blade angle, being about 9% for 65 degrees at 0.75R.

  9. Advances in Tandem Mirror fusion power reactors

    SciTech Connect

    Perkins, L.J.; Logan, B.G.

    1986-05-20

    The Tandem Mirror exhibits several distinctive features which make the reactor embodiment of the principle very attractive: Simple low-technology linear central cell; steady-state operation; high-..beta.. operation; no driven current or disruptions; divertorless operation; direction conversion of end-loss power; low-surface heat loads; and advanced fusion fuel capability. In this paper, we examine these features in connection with two tandem mirror reactor designs, MARS and MINIMARS, and several advanced reactor concepts including the wall-stabilized reactor and the field-reversed mirror. With a novel compact end plug scheme employing octopole stabilization, MINIMARS is expressly designed for short construction times, factory-built modules, and a small (600 MWe) but economic reactor size. We have also configured the design for low radioactive afterheat and inherent/passive safety under LOCA/LOFA conditions, thereby obviating the need for expensive engineered safety systems. In contrast to the complex and expensive double-quadrupole end-cell of the MARS reactor, the compact octopole end-cell of MINIMARS enables ignition to be achieved with much shorter central cell lengths and considerably improves the economy of scale for small (approx.250 to 600 MWe) tandem mirror reactors. Finally, we examine the prospects for realizing the ultimate potential of the tandem mirror with regard to both innovative configurations and novel neutron energy conversion schemes, and stress that advanced fuel applications could exploit its unique reactor features.

  10. Tandem mirror fusion research

    SciTech Connect

    Baldwin, D.E.

    1983-12-02

    The tandem mirror program has evolved considerably in the last decade. Of significance is the viable reactor concept embodied in the MARS design. An aggressive experimental program, culminating in the operation of MFTF-B in late 1986, will provide a firm basis for refining the MARS design as necessary for constructing a reactor prototype in the 1990s.

  11. Tandem BRCT Domains

    PubMed Central

    Mesquita, Rafael D.; Woods, Nicholas T.; Seabra-Junior, Eloy S.; Monteiro, Alvaro N.A.

    2010-01-01

    The cell’s ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell’s genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor–interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as “readers” of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response. PMID:21533002

  12. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, I.J.; Wendt, J.R.

    1994-09-06

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors. 8 figs.

  13. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, Ian J.; Wendt, Joel R.

    1994-01-01

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors.

  14. Flute waves in a tandem mirror

    SciTech Connect

    Mikhailovskaya, L.V.

    1984-03-01

    Stability conditions are derived for flute waves in a short tandem mirror stabilized by end cells with a min B. The frequency spectrum of the flute waves is analyzed. Those conditions under which the resonant excitation of waves by ions and electrons must be taken into account are found. When end cells without a min B are added to a central mirror system, the system becomes destabilized as the result of resonant excitation of waves at a frequency near the precession frequency of ions having a finite energy distribution.

  15. Monolithic tandem solar cell

    DOEpatents

    Wanlass, M.W.

    1994-06-21

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. 9 figs.

  16. Monolithic tandem solar cell

    DOEpatents

    Wanlass, Mark W.

    1991-01-01

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, and (c) a second photoactive subcell on the first subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. The solar cell can be provided as a two-terminal device or a three-terminal device.

  17. Quadruplex formation by both G-rich and C-rich DNA strands of the C9orf72 (GGGGCC)8•(GGCCCC)8 repeat: effect of CpG methylation

    PubMed Central

    Zamiri, Bita; Mirceta, Mila; Bomsztyk, Karol; Macgregor, Robert B.; Pearson, Christopher E.

    2015-01-01

    Unusual DNA/RNA structures of the C9orf72 repeat may participate in repeat expansions or pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded repeats are CpG methylated with unknown consequences. Typically, quadruplex structures form by G-rich but not complementary C-rich strands. Using CD, UV and electrophoresis, we characterized the structures formed by (GGGGCC)8 and (GGCCCC)8 strands with and without 5-methylcytosine (5mCpG) or 5-hydroxymethylcytosine (5hmCpG) methylation. All strands formed heterogenous mixtures of structures, with features of quadruplexes (at pH 7.5, in K+, Na+ or Li+), but no feature typical of i-motifs. C-rich strands formed quadruplexes, likely stabilized by G•C•G•C-tetrads and C•C•C•C-tetrads. Unlike G•G•G•G-tetrads, some G•C•G•C-tetrad conformations do not require the N7-Guanine position, hence C9orf72 quadruplexes still formed when N7-deazaGuanine replace all Guanines. 5mCpG and 5hmCpG increased and decreased the thermal stability of these structures. hnRNPK, through band-shift analysis, bound C-rich but not G-rich strands, with a binding preference of unmethylated > 5hmCpG > 5mCpG, where methylated DNA-protein complexes were retained in the wells, distinct from unmethylated complexes. Our findings suggest that for C-rich sequences interspersed with G-residues, one must consider quadruplex formation and that methylation of quadruplexes may affect epigenetic processes. PMID:26432832

  18. Quadruplex formation by both G-rich and C-rich DNA strands of the C9orf72 (GGGGCC)8•(GGCCCC)8 repeat: effect of CpG methylation.

    PubMed

    Zamiri, Bita; Mirceta, Mila; Bomsztyk, Karol; Macgregor, Robert B; Pearson, Christopher E

    2015-11-16

    Unusual DNA/RNA structures of the C9orf72 repeat may participate in repeat expansions or pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded repeats are CpG methylated with unknown consequences. Typically, quadruplex structures form by G-rich but not complementary C-rich strands. Using CD, UV and electrophoresis, we characterized the structures formed by (GGGGCC)8 and (GGCCCC)8 strands with and without 5-methylcytosine (5mCpG) or 5-hydroxymethylcytosine (5hmCpG) methylation. All strands formed heterogenous mixtures of structures, with features of quadruplexes (at pH 7.5, in K(+), Na(+) or Li(+)), but no feature typical of i-motifs. C-rich strands formed quadruplexes, likely stabilized by G•C•G•C-tetrads and C•C•C•C-tetrads. Unlike G•G•G•G-tetrads, some G•C•G•C-tetrad conformations do not require the N7-Guanine position, hence C9orf72 quadruplexes still formed when N7-deazaGuanine replace all Guanines. 5mCpG and 5hmCpG increased and decreased the thermal stability of these structures. hnRNPK, through band-shift analysis, bound C-rich but not G-rich strands, with a binding preference of unmethylated > 5hmCpG > 5mCpG, where methylated DNA-protein complexes were retained in the wells, distinct from unmethylated complexes. Our findings suggest that for C-rich sequences interspersed with G-residues, one must consider quadruplex formation and that methylation of quadruplexes may affect epigenetic processes. PMID:26432832

  19. A robust and cost-effective integrated process for nitrogen and bio-refractory organics removal from landfill leachate via short-cut nitrification, anaerobic ammonium oxidation in tandem with electrochemical oxidation.

    PubMed

    Wu, Li-Na; Liang, Da-Wei; Xu, Ying-Ying; Liu, Ting; Peng, Yong-Zhen; Zhang, Jie

    2016-07-01

    A cost-effective process, consisting of a denitrifying upflow anaerobic sludge blanket (UASB), an oxygen-limited anoxic/aerobic (A/O) process for short-cut nitrification, and an anaerobic reactor (ANR) for anaerobic ammonia oxidation (anammox), followed by an electrochemical oxidation process with a Ti-based SnO2-Sb2O5 anode, was developed to remove organics and nitrogen in a sewage diluted leachate. The final chemical oxygen demand (COD), ammonia nitrogen (NH4(+)-N) and total nitrogen (TN) of 70, 11.3 and 39 (all in mg/L), respectively, were obtained. TN removal in UASB, A/O and ANR were 24.6%, 49.6% and 16.1%, respectively. According to the water quality and molecular biology analysis, a high degree of anammox besides short-cut nitrification and denitrification occurred in A/O. Counting for 16.1% of TN removal in ANR, at least 43.2-49% of TN was removed via anammox. The anammox bacteria in A/O and ANR, were in respective titers of (2.5-5.9)×10(9) and 2.01×10(10)copy numbers/(gSS). PMID:27115616

  20. Advancing tandem solar cells by spectrally selective multilayer intermediate reflectors.

    PubMed

    Hoffmann, Andre; Paetzold, Ulrich W; Zhang, Chao; Merdzhanova, Tsvetelina; Lambertz, Andreas; Ulbrich, Carolin; Bittkau, Karsten; Rau, Uwe

    2014-08-25

    Thin-film silicon tandem solar cells are composed of an amorphous silicon top cell and a microcrystalline silicon bottom cell, stacked and connected in series. In order to match the photocurrents of the top cell and the bottom cell, a proper photon management is required. Up to date, single-layer intermediate reflectors of limited spectral selectivity are applied to match the photocurrents of the top and the bottom cell. In this paper, we design and prototype multilayer intermediate reflectors based on aluminum doped zinc oxide and doped microcrystalline silicon oxide with a spectrally selective reflectance allowing for improved current matching and an overall increase of the charge carrier generation. The intermediate reflectors are successfully integrated into state-of-the-art tandem solar cells resulting in an increase of overall short-circuit current density by 0.7 mA/cm(2) in comparison to a tandem solar cell with the standard single-layer intermediate reflector. PMID:25322181

  1. Fueling of tandem mirror reactors

    SciTech Connect

    Gorker, G.E.; Logan, B.G.

    1985-01-01

    This paper summarizes the fueling requirements for experimental and demonstration tandem mirror reactors (TMRs), reviews the status of conventional pellet injectors, and identifies some candidate accelerators that may be needed for fueling tandem mirror reactors. Characteristics and limitations of three types of accelerators are described; neutral beam injectors, electromagnetic rail guns, and laser beam drivers. Based on these characteristics and limitations, a computer module was developed for the Tandem Mirror Reactor Systems Code (TMRSC) to select the pellet injector/accelerator combination which most nearly satisfies the fueling requirements for a given machine design.

  2. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 3 2014-10-01 2014-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching...

  3. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching...

  4. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  5. Condensin Promotes Position Effects within Tandem DNA Repeats via the RITS complex

    PubMed Central

    He, Haijin; Zhang, Shu; Wang, Danni; Hochwagen, Andreas; Li, Fei

    2016-01-01

    Summary Tandem repetitive DNA is highly abundant in eukaryotic genomes, and contributes to transcription control and genome stability. However, how the individual sequences within tandem repeats behave remains largely unknown. Here we develop a collection of fission yeast strains with a reporter gene inserted at different units in a tandem repeat array. We show that, contrary to what is usually assumed, transcriptional silencing and replication timing among the individual repeats differ significantly. RNAi-mediated H3K9 methylation is essential for the silencing position effect. A short hairpin RNA of ura4+ induces silencing in trans within the tandem array in a position-dependent manner. Importantly, the position effect depends on the condensin subunit, cut3+. Cut3 promotes the position effect via interaction with the RNA-induced transcriptional silencing (RITS) complex. This study reveals variations in silencing within tandem DNA repeats and provides mechanistic insights into how DNA repeats at the individual level are regulated. PMID:26832414

  6. Tandem Cylinder Noise Predictions

    NASA Technical Reports Server (NTRS)

    Lockhard, David P.; Khorrami, Mehdi R.; CHoudhari, Meelan M.; Hutcheson, Florence V.; Brooks, Thomas F.; Stead, Daniel J.

    2007-01-01

    In an effort to better understand landing-gear noise sources, we have been examining a simplified configuration that still maintains some of the salient features of landing-gear flow fields. In particular, tandem cylinders have been studied because they model a variety of component level interactions. The present effort is directed at the case of two identical cylinders spatially separated in the streamwise direction by 3.7 diameters. Experimental measurements from the Basic Aerodynamic Research Tunnel (BART) and Quiet Flow Facility (QFF) at NASA Langley Research Center (LaRC) have provided steady surface pressures, detailed off-surface measurements of the flow field using Particle Image Velocimetry (PIV), hot-wire measurements in the wake of the rear cylinder, unsteady surface pressure data, and the radiated noise. The experiments were conducted at a Reynolds number of 166 105 based on the cylinder diameter. A trip was used on the upstream cylinder to insure a fully turbulent shedding process and simulate the effects of a high Reynolds number flow. The parallel computational effort uses the three-dimensional Navier-Stokes solver CFL3D with a hybrid, zonal turbulence model that turns off the turbulence production term everywhere except in a narrow ring surrounding solid surfaces. The current calculations further explore the influence of the grid resolution and spanwise extent on the flow and associated radiated noise. Extensive comparisons with the experimental data are used to assess the ability of the computations to simulate the details of the flow. The results show that the pressure fluctuations on the upstream cylinder, caused by vortex shedding, are smaller than those generated on the downstream cylinder by wake interaction. Consequently, the downstream cylinder dominates the noise radiation, producing an overall directivity pattern that is similar to that of an isolated cylinder. Only calculations based on the full length of the model span were able to

  7. Dual analyte detection using tandem flash luminescence.

    PubMed

    Adamczyk, Maciej; Moore, Jeffrey A; Shreder, Kevin

    2002-02-11

    A heterogeneous, dual analyte-binding assay which makes use of the flash luminescence from both aequorin and an acridinium-9-carboxamide label is presented. The signal generating species were triggered both differentially and sequentially using Ca(2+) followed by basic peroxide. Both signals were resolved readily using a single photomultiplier tube without the need for multiwavelength detection. To demonstrate the tandem luminescence concept in a model assay system, dose-response curves for two analytes, biotinylated BSA and myoglobin, were generated using a competitive binding format. Because of the relatively short assay time and the well-resolved signals, this format will be useful in the development of dual analyte high-throughput assays. PMID:11814805

  8. Short stature

    MedlinePlus

    Idiopathic short stature; Non-growth hormone deficient short stature ... Turner syndrome Williams syndrome Other reasons include: Growth hormone deficiency Infections of the developing baby before birth ...

  9. Tandem-structured, hot electron based photovoltaic cell with double Schottky barriers

    PubMed Central

    Lee, Young Keun; Lee, Hyosun; Park, Jeong Young

    2014-01-01

    We demonstrate a tandem-structured, hot electron based photovoltaic cell with double Schottky barriers. The tandem-structured, hot electron based photovoltaic cell is composed of two metal/semiconductor interfaces. Two types of tandem cells were fabricated using TiO2/Au/Si and TiO2/Au/TiO2, and photocurrent enhancement was detected. The double Schottky barriers lead to an additional pathway for harvesting hot electrons, which is enhanced through multiple reflections between the two barriers with different energy ranges. In addition, light absorption is improved by the band-to-band excitation of both semiconductors with different band gaps. Short-circuit current and energy conversion efficiency of the tandem-structured TiO2/Au/Si increased by 86% and 70%, respectively, compared with Au/Si metal/semiconductor nanodiodes, showing an overall solar energy conversion efficiency of 5.3%. PMID:24694838

  10. Efficiently-designed hybrid tandem photovoltaic with organic and inorganic single cells

    NASA Astrophysics Data System (ADS)

    Vincent, Premkumar; Bae, Jin-Hyuk; Kim, Hyeok

    2016-05-01

    Conjugated polymers for solar-cell applications have been extensively studied and have proven highly beneficial in tandem solar-cell structures. This study focuses on achieving power conversion efficiencies of greater than 10% when in tandem with a highly efficient copper indium gallium diselenide (CIGS) solar cell. The optimal design is suggested based on the result of optical simulations on the organic-CIGS tandem structure. This is one of the first reports to show theoretically an organic-CIGS tandem solar cell to obtain an efficiency of greater than 10%. The best PCE was at a thickness of 200 nm for PTB7:PCBM, the active layer of the organic solar cell, and 400 nm for CIGS active layer. Our best datum showed an efficiency of 11.41% with a short-circuit current density of 11.56 mA/cm2 and a good spectral response at our optimized thicknesses.

  11. MINIMARS: an attractive small tandem mirror fusion reactor

    SciTech Connect

    Perkins, L.J.; Logan, B.G.; Doggett, J.N.; Devoto, R.S.; Nelson, W.D.; Lousteau, D.C.; Kulcinski, G.L.; Santarius, J.F.; Gordon, J.D.; Campbell, R.B.

    1985-11-13

    Through the innovative design of a novel end plug scheme employing octopole MHD stabilization, we present the conceptual design of ''MIMIMARS'', a small commercial fusion reactor based on the tandem mirror principle. The current baseline for MINIMARS has a net electric output of 600 MWe and we have configured the design for short construction times, factory-built modules, inherently safe blanket systems, and multiplexing in station sizes of approx. 600 to 2400 MWe. We demonstrate that the compact octopole end cell provides a number of advantages over the more conventional quadrupole (yin-yang) end cell encountered in the MARS tandem mirror reactor study, and enables ignition to be achieved with much shorter central cell lengths. Accordingly, being economic in small sizes, MINIMARS provides an attractive alternative to the more conventional larger conceptual fusion reactors encountered to date, and would contribute significantly to the lowering of utility financial risk in a developing fusion economy.

  12. Nanopyramid structure for ultrathin c-Si tandem solar cells.

    PubMed

    Li, Guijun; Li, He; Ho, Jacob Y L; Wong, Man; Kwok, Hoi Sing

    2014-05-14

    Recently, ultrathin crystalline silicon solar cells have gained tremendous interest because they are deemed to dramatically reduce material usage. However, the resulting conversion efficiency is still limited by the incomplete light absorption in such ultrathin devices. In this letter, we propose ultrathin a-Si/c-Si tandem solar cells with an efficient light trapping design, where a nanopyramid structure is introduced between the top and bottom cells. The superior light harvesting results in a 48% and 35% remarkable improvement of the short-circuit current density for the top and bottom cells, respectively. Meanwhile, the use of SiOx mixed-phase nanomaterial helps to provide the maximum light trapping without paying the price of reduced electrical performance, and conversion efficiencies of up to 13.3% have been achieved for the ultrathin tandem cell employing only 8 μm of silicon, which is 29% higher than the result obtained for the planar cell. PMID:24730470

  13. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.

    PubMed

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  14. Versatile communication strategies among tandem WW domain repeats

    PubMed Central

    Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

    2015-01-01

    Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

  15. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

    PubMed Central

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  16. Nanocrystal assembly for tandem catalysis

    DOEpatents

    Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

    2014-10-14

    The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

  17. "Nanocrystal bilayer for tandem catalysis"

    SciTech Connect

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  18. Detecting long tandem duplications in genomic sequences

    PubMed Central

    2012-01-01

    Background Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. Results In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,a we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. Conclusions ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations. PMID:22568762

  19. The characterization of tandem and corrugated wings

    NASA Astrophysics Data System (ADS)

    Lian, Yongsheng; Broering, Timothy; Hord, Kyle; Prater, Russell

    2014-02-01

    Dragonfly wings have two distinct features: a tandem configuration and wing corrugation. Both features have been extensively studied with the aim to understand the superior flight performance of dragonflies. In this paper we review recent development of tandem and corrugated wing aerodynamics. With regards to the tandem configuration, this review will focus on wing/wing and wing/vortex interactions at different flapping modes and wing spacing. In addition, the aerodynamics of tandem wings under gusty conditions will be reviewed and compared with isolated wings to demonstrate the gust resistance characteristics of flapping wings. Regarding corrugated wings, we review their structural and aerodynamic characteristics.

  20. Recent Activities at Tokai Tandem Accelerator

    SciTech Connect

    Ishii, Tetsuro

    2010-05-12

    Recent activities at the JAEA-Tokai tandem accelerator facility are presented. The terminal voltage of the tandem accelerator reached 19.1 MV by replacing acceleration tubes. The multi-charged positive-ion injector was installed in the terminal of the tandem accelerator, supplying high-current noble-gas ions. A superconducting cavity for low-velocity ions was developed. Radioactive nuclear beams of {sup 8,9}Li and fission products, produced by the tandem accelerator and separated by the ISOL, were supplied with experiment. Recent results of nuclear physics experiments are reported.

  1. Tandem mirror technology demonstration facility

    SciTech Connect

    Not Available

    1983-10-01

    This report describes a facility for generating engineering data on the nuclear technologies needed to build an engineering test reactor (ETR). The facility, based on a tandem mirror operating in the Kelley mode, could be used to produce a high neutron flux (1.4 MW/M/sup 2/) on an 8-m/sup 2/ test area for testing fusion blankets. Runs of more than 100 h, with an average availability of 30%, would produce a fluence of 5 mW/yr/m/sup 2/ and give the necessary experience for successful operation of an ETR.

  2. Improved monolithic tandem solar cell

    SciTech Connect

    Wanlass, M.W.

    1991-04-23

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surf ace of the InP substrate, (c) a second photoactive subcell on the first subcell; and (d) an optically transparent prismatic cover layer over the second subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched.

  3. Transcriptome annotation using tandem SAGE tags

    PubMed Central

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  4. Tandem junction amorphous silicon solar cells

    DOEpatents

    Hanak, Joseph J.

    1981-01-01

    An amorphous silicon solar cell has an active body with two or a series of layers of hydrogenated amorphous silicon arranged in a tandem stacked configuration with one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon arranged in tandem configuration can have the same bandgap or differing bandgaps.

  5. 33 CFR 401.41 - Tandem lockage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Tandem lockage. 401.41 Section 401.41 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT OF TRANSPORTATION SEAWAY REGULATIONS AND RULES Regulations Seaway Navigation § 401.41 Tandem lockage. Where two...

  6. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases

    PubMed Central

    2012-01-01

    Background Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters. Results In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases. Conclusions By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability. We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our

  7. Highly efficient photoelectrochemical water splitting by a hybrid tandem perovskite solar cell.

    PubMed

    Bin, Abd Rashid; Yusoff, Mohd; Jang, Jin

    2016-04-30

    Herein, we show that graphene can be fully utilized to function as an electrocatalyst in highly efficient photoelectrochemical water splitting. Combining a solution-processed organic photovoltaic and the state-of-the-art perovskite solar cell in a tandem architecture yields a stable short-circuit water splitting photocurrent of ∼7.25 mA cm(-2) under 1 sun illumination. The ∼7.25 mA cm(-2) photocurrent corresponds to a solar-to-hydrogen efficiency of 9.02%, which is the highest efficiency yet reported for water splitting based on a hybrid tandem perovskite solar cell. PMID:27035707

  8. Label-free electrochemical nucleic acid biosensing by tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme amplification.

    PubMed

    Liu, Shufeng; Gong, Hongwei; Wang, Yanqun; Wang, Li

    2016-03-15

    Owing to the intrinsic importance of nucleic acid as bio-targets, the achievement of its simple and sensitive detection with high confidence is very essential for biological studies and diagnostic purposes. Herein, a label-free, isothermal, and ultrasensitive electrochemical detection of target DNA was developed by using a tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme releasing amplification strategy. Upon sensing of the nucleic acid analyte for the assembled hairpin-like probe DNA on the electrode, the DNA polymerase guided the target recycling and simultaneously triggered the lambda exonuclease cleavage, accompanied by the cascade recycling of the released new complementary strand and the amplified liberation of the G-rich sequence of the HRP-mimicking DNAzyme. The electrocatalytic reduction of H2O2 by the generated hemin/G-quadruplex DNAzyme was used for the signal readout and further amplification toward target response. Such tandem functional operation by DNA polymerase, lambda exonuclease and DNAzyme endows the developed biosensor with a high sensitivity and also a high confidence. A low detection limit of 5 fM with an excellent selectivity toward target DNA could be achieved. It also exhibits the distinct advantages of simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus may offer a promising avenue for the applications in disease diagnosis and clinical biomedicine. PMID:26513289

  9. Short bones

    MedlinePlus

    Short bones in the human body are often cube-like, their length, width, and height are all about the same. Short bones include the carpal bones of the hands and wrist, and the tarsal bones of the feet and ankles.

  10. The TandemHeart pVAD in the treatment of acute fulminant myocarditis.

    PubMed

    Khalife, Wissam I; Kar, Biswajit

    2007-01-01

    Acute fulminant myocarditis commonly manifests itself as severe, rapidly progressive hemodynamic deterioration and circulatory collapse that may be resistant to high doses of inotropic agents and steroids and to mechanical support by intra-aortic balloon pump. Acute myocarditis has a high mortality rate and may necessitate heart transplantation. The best short-term therapy available to support the patient may be a percutaneous left ventricular assist device. One such unit, the TandemHeart percutaneous ventricular assist device, can enable patients to recover in a few days. Two of our patients who experienced profound, therapy-resistant heart failure arising from acute myocarditis were successfully supported by the TandemHeart. To the best of our knowledge, these are the 1st reported cases in which the TandemHeart percutaneous ventricular assist device served as a bridge to recovery from acute fulminant myocarditis. PMID:17622371

  11. Tandem Mirror Reactor Systems Code (Version I)

    SciTech Connect

    Reid, R.L.; Finn, P.A.; Gohar, M.Y.; Barrett, R.J.; Gorker, G.E.; Spampinaton, P.T.; Bulmer, R.H.; Dorn, D.W.; Perkins, L.J.; Ghose, S.

    1985-09-01

    A computer code was developed to model a Tandem Mirror Reactor. Ths is the first Tandem Mirror Reactor model to couple, in detail, the highly linked physics, magnetics, and neutronic analysis into a single code. This report describes the code architecture, provides a summary description of the modules comprising the code, and includes an example execution of the Tandem Mirror Reactor Systems Code. Results from this code for two sensitivity studies are also included. These studies are: (1) to determine the impact of center cell plasma radius, length, and ion temperature on reactor cost and performance at constant fusion power; and (2) to determine the impact of reactor power level on cost.

  12. Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

    PubMed

    Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

    2014-12-01

    YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

  13. Ligand Binding to WW Tandem Domains of YAP2 Transcriptional Regulator Is Under Negative Cooperativity

    PubMed Central

    Schuchardt, Brett J.; Mikles, David C.; Hoang, Lawrence M.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

    2014-01-01

    YAP2 transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well-documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

  14. Tandem balloon catheter for coronary angioplasty.

    PubMed

    Finci, L; Meier, B; Steffenino, G; Rutishauser, W

    1986-01-01

    The Tandem balloon catheter is a triple lumen steerable catheter for coronary angioplasty with two separately inflatable balloons of different diameters. Indications and results of 26 consecutive patients treated with a Tandem balloon catheter are reviewed. Adequate distal pressure measurements were obtained in 71% of the cases. In ten patients, the Tandem balloon catheter was selected for two stenoses in different segments of the same coronary artery. Angioplasty was successful for all lesions in five and for at least the strategic lesions in five patients (in one only after changing to a single-balloon catheter). In the seven patients with stenoses in two different coronary arteries of various calibers, angioplasty was successful for both vessels in three and for one vessel in four patients. In the six patients with a very tight stenosis, where the Tandem balloon catheter was selected to predilate with the small balloon, the procedure was technically successful in all, but there was a myocardial infarction in one patient. In the three patients with a chronic total occlusion, where the stiffness of the Tandem balloon was the reason for selection, one recanalization was successful. The Tandem balloon catheter provides a handy tool for complex coronary angioplasty. It offers comparable ease in manipulation and pressure transmission and may save time, money, and radiation exposure by avoiding catheter exchanges. PMID:2949848

  15. A Comparison of Tandem Walk Performance Between Bed Rest Subjects and Astronauts

    NASA Technical Reports Server (NTRS)

    Miller, Chris; Peters, Brian; Kofman, Igor; Philips, Tiffany; Batson, Crystal; Cerisano, Jody; Fisher, Elizabeth; Mulavara, Ajitkumar; Feiveson, Alan; Reschke, Millard; Bloomberg, Jacob

    2015-01-01

    Astronauts experience a microgravity environment during spaceflight, which results in a central reinterpretation of both vestibular and body axial-loading information by the sensorimotor system. Subjects in bed rest studies lie at 6deg head-down in strict bed rest to simulate the fluid shift and gravity-unloading of the microgravity environment. However, bed rest subjects still sense gravity in the vestibular organs. Therefore, bed rest isolates the axial-unloading component, thus allowing for the direct study of its effects. The Tandem Walk is a standard sensorimotor test of dynamic postural stability. In a previous abstract, we compared performance on a Tandem Walk test between bed rest control subjects, and short- and long-duration astronauts both before and after flight/bed rest using a composite index of performance, called the Tandem Walk Parameter (TWP), that takes into account speed, accuracy, and balance control. This new study extends the previous data set to include bed rest subjects who performed exercise countermeasures. The purpose of this study was to compare performance during the Tandem Walk test between bed rest subjects (with and without exercise), short-duration (Space Shuttle) crewmembers, and long-duration International Space Station (ISS) crewmembers at various time points during their recovery from bed rest or spaceflight.

  16. Gyrokinetic equilibrium and stability in quadrupole tandem mirrors

    SciTech Connect

    Bulmer, R.H.; Kaiser, T.B.; Nevins, W.M.; Newcomb, W.A.; Pearlstein, L.D.; Strauss, H.R.; Wollman, S.; Wakatani, M.

    1982-08-02

    This paper discusses recent theoretical work on the equilibrium and stability of quadrupole tandem mirrors in the paraxial limit. It reviews calculations of three-dimensional equilibria by means of a ..beta..-expansion technique which lead to an understanding of the important role played by parallel currents and the corollary importance of careful design of the structure of the vacuum geodesic curvature. The previously predicted scaling with central-cell length of the finite-..beta.. distortion of vacuum flux surfaces is shown to saturate because of finite orbit effects. An adaptation to tandem geometries of the reduced MHD technique for calculating high-..beta.. three-dimensional equilibria is described. This approach uses the paraxial expansion to resolve the time-dependent relaxation to equilibrium into three distinct timescales on which the motion can be followed independently. Regarding stability, it is shown that kinetic effects suppress ballooning modes of short-to-moderate perpendicular wavelength; in the limit that such effects are dominant only rigid modes are possible. The stability of the latter modes is investigated within the context of the energy principle. Results of equilibrium and stability calculations for the TMX-U and MFTF-B experiments at Livermore are presented.

  17. Optimizing a tandem disk model

    SciTech Connect

    Healey, J.V.

    1983-07-01

    A very simple physicomathematical model, in which thin straight blades with zero drag skim across a plane rectangular disk, shows that the maximum power coefficient attains the classical maximum of 0.593 over a range of T and a zero or small negative value of alpha/sub 0/. This maximum appears independent of sigma and there are values of T and alpha/sub 0/ for which the speed through the disk becomes complex and the model breaks down. Extending this model to a tandem disk system leads to a difficulty in defining the power coefficient. Attempts to optimize the system output based on reference areas A/sub 1/, A/sub 2/, and A/sub 4/ prove futile and the sum of the coefficients is chosen for this purpose. For thin blades and zero drag the analytic solution is available and it shows that the maximum value of 2 X 0.593 is attained over a narrow range of slightly negative alpha/sub 0/ (blade nose in) and medium values of T. The maximum is independent of sigma. As T is increased, the model breaks down either after C /SUB psum/ becomes large and negative or after backflow through the downwind disk occurs. There appears to be no requirement on load distribution between the disks. By comparison, modeling a machine with NACA 0012 blades at Re = 1.34 X 10/sup 6/ shows that the maximum value of C /SUB psum/ depends on the solidity. For example, at sigma = 0.4, the maximum value of C /SUB psum/ is 83% of 2 X 0.593. At such high values of sigma, however, the ranges of alpha/sub 0/ and T over which solutions are available become very limited.

  18. Tandem Catalysis Utilizing Olefin Metathesis Reactions.

    PubMed

    Zieliński, Grzegorz K; Grela, Karol

    2016-07-01

    Since olefin metathesis transformation has become a favored synthetic tool in organic synthesis, more and more distinct non-metathetical reactions of alkylidene ruthenium complexes have been developed. Depending on the conditions applied, the same olefin metathesis catalysts can efficiently promote isomerization reactions, hydrogenation of C=C double bonds, oxidation reactions, and many others. Importantly, these transformations can be carried out in tandem with olefin metathesis reactions. Through addition of one portion of a catalyst, a tandem process provides structurally advanced products from relatively simple substrates without the need for isolation of the intermediates. These aspects not only make tandem catalysis very attractive from a practical point of view, but also open new avenues in (retro)synthetic planning. However, in the literature, the term "tandem process" is sometimes used improperly to describe other types of multi-reaction sequences. In this Concept, a number of examples of tandem catalysis involving olefin metathesis are discussed with an emphasis on their synthetic value. PMID:27203528

  19. Titan and Enceladus mission (TANDEM)

    NASA Astrophysics Data System (ADS)

    Coustenis, A.

    2007-08-01

    Our understanding of Titan's atmosphere and surface has recently been enhanced by the data returned by the Cassini-Huygens mission. The Cassini orbiter will continue to be operational for about 3 more years during its extended mission. After this mission, any unanswered questions will forever remain unknown, unless we go back with an optimized orbital tour and advanced instrumentation. Considering the complementary nature of the geological, chemical and evolutionary history of Titan and Enceladus, we propose to carry out studies for a mission to perform an in situ exploration of these two objects in tandem. In our proposal we determine key science measurements, the types of samples that would be needed and the instrument suites for achieving the science goals. In particular, we develop conceptual designs for delivering the science payload, including orbiters, aerial platforms and probes, and define a launch/delivery/communication management architecture. This mission will require new technologies and capabilities so that the science goals can be achieved within the cost cap and acceptable risks. International participation will play a key role in achieving all the science goals of this mission. We will build this mission concept around a central core of single orbiter, a single Titan aerial probe and a core group of category 1 instruments. Aerobraking with Titan's atmosphere will be given serious consideration to minimize resource requirements and risk. This approach will allow a single orbiter to be used for both Enceladus science and Titan science with final orbit around Titan and later release of aerial probe(s) into Titan's atmosphere. The Titan aerial probe may be a Montgolfière balloon concept that will use the waster heat ~ 1000 watts from a single RTG power system. There will be a release of penetrator(s) on Enceladus also. This proposal addresses directly several of the scientific questions highlighted in the ESA Cosmic Vision 2015-2025 call, particularly

  20. Alpha particle confinement in tandem mirrors

    SciTech Connect

    Devoto, R.S.; Ohnishi, M.; Kerns, J.; Woo, J.T.

    1980-10-10

    Mechanisms leading to loss of alpha particles from non-axisymmetric tandem mirrors are considered. Stochastic diffusion due to bounce-drift resonances, which can cause rapid radial losses of high-energy alpha particles, can be suppressed by imposing a 20% rise in axisymmetric fields before the quadrupole transition sections. Alpha particles should then be well-confined until thermal energies when they enter the resonant plateau require. A fast code for computation of drift behavior in reactors is described. Sample calculations are presented for resonant particles in a proposed coil set for the Tandem Mirror Next Step.

  1. High performance polymer tandem solar cell

    NASA Astrophysics Data System (ADS)

    da Silva, Wilson Jose; Schneider, Fabio Kurt; Mohd Yusoff, Abd. Rashid Bin; Jang, Jin

    2015-12-01

    A power conversion efficiency of 9.02% is obtained for a fully solution-processed polymer tandem solar cell, based on the diketopyrrolopyrrole unit polymer as a low bandgap photoactive material in the rear subcell, in conjunction with a new robust interconnecting layer. This interconnecting layer is optically transparent, electrically conductive, and physically strong, thus, the charges can be collected and recombined in the interconnecting layer under illumination, while the charge is generated and extracted under dark conditions. This indicates that careful interface engineering of the charge-carrier transport layer is a useful approach to further improve the performance of polymer tandem solar cells.

  2. Homicidal tandem bullet wound of the chest.

    PubMed

    Bentley, A J; Busuttil, A; Clifton, B; Sibbald, P

    1997-03-01

    An unusual case of a homicidal gunshot wound to the chest is reported in which two bullets were fired in unison as tandem bullets from a handgun. At autopsy, two intact bullets were retrieved from the body of the victim, yet there was only one entrance wound and a single bullet track across the chest wall and thoracic organs. An examination of the weapon and ammunition supported the likelihood of tandem bullets and suggested the probable mechanism for this event. Very few similar cases have been documented. PMID:9095302

  3. High performance polymer tandem solar cell

    PubMed Central

    da Silva, Wilson Jose; Schneider, Fabio Kurt; Mohd Yusoff, Abd. Rashid bin; Jang, Jin

    2015-01-01

    A power conversion efficiency of 9.02% is obtained for a fully solution-processed polymer tandem solar cell, based on the diketopyrrolopyrrole unit polymer as a low bandgap photoactive material in the rear subcell, in conjunction with a new robust interconnecting layer. This interconnecting layer is optically transparent, electrically conductive, and physically strong, thus, the charges can be collected and recombined in the interconnecting layer under illumination, while the charge is generated and extracted under dark conditions. This indicates that careful interface engineering of the charge-carrier transport layer is a useful approach to further improve the performance of polymer tandem solar cells. PMID:26669577

  4. Tandem transformation of glycerol to esters.

    PubMed

    Sotenko, Maria V; Rebroš, Martin; Sans, Victor S; Loponov, Konstantin N; Davidson, Matthew G; Stephens, Gill; Lapkin, Alexei A

    2012-12-31

    Tandem transformation of glycerol via microbial fermentation and enzymatic esterification is presented. The reaction can be performed with purified waste glycerol from biodiesel production in a continuous mode, combining continuous fermentation with membrane-supported enzymatic esterification. Continuous anaerobic fermentation was optimized resulting in the productivity of 2.4 g L⁻¹ h⁻¹ of 1,3-propanediol. Biphasic esterification of 1,3-propanediol was optimized to achieve ester yield of up to 75%. A hollow fibre membrane contactor with immobilized Rhizomucor miehei lipase was demonstrated for the continuous tandem fermentation-esterification process. PMID:22796408

  5. High voltage series connected tandem junction solar battery

    DOEpatents

    Hanak, Joseph J.

    1982-01-01

    A high voltage series connected tandem junction solar battery which comprises a plurality of strips of tandem junction solar cells of hydrogenated amorphous silicon having one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon, arranged in a tandem configuration, can have the same bandgap or differing bandgaps. The tandem junction strip solar cells are series connected to produce a solar battery of any desired voltage.

  6. Large-scale analysis of tandem repeat variability in the human genome

    PubMed Central

    Duitama, Jorge; Zablotskaya, Alena; Gemayel, Rita; Jansen, An; Belet, Stefanie; Vermeesch, Joris R.; Verstrepen, Kevin J.; Froyen, Guy

    2014-01-01

    Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats. PMID:24682812

  7. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Canard or tandem wing configurations. 23.302 Section 23.302 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem...

  8. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Canard or tandem wing configurations. 23.302 Section 23.302 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem...

  9. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Canard or tandem wing configurations. 23.302 Section 23.302 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem...

  10. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Canard or tandem wing configurations. 23.302 Section 23.302 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem...

  11. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Canard or tandem wing configurations. 23.302 Section 23.302 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem...

  12. Tandem mirror fusion-fission hybrid studies

    NASA Astrophysics Data System (ADS)

    Lee, J. D.

    1980-04-01

    The concept of combining nuclear fusion and nuclear fission techniques is discussed. Initial tandem mirror hybrid studies predict the ability to produce large amounts of fissile fuel (2 to 7 tons U233 per year from a 4000 MW plant) at a cost that adds less than 25% to the cost of power from a light water reactor.

  13. Status of BINP proton tandem accelerator

    NASA Astrophysics Data System (ADS)

    Burdakov, A.; Davydenko, V.; Dolgushin, V.; Dranichnikov, A.; Ivanov, A.; Farrell, J. P.; Khilchenko, A.; Kobets, V.; Konstantinov, S.; Krivenko, A.; Kudryavtsev, A.; Tiunov, M.; Savkin, V.; Shirokov, V.; Sorokin, I.

    2007-08-01

    The status of a unique 2.0 MeV, 10 mA proton tandem accelerator with vacuum insulation is presented. The accelerator is intended to be used in facilities generating resonant gamma rays for explosives detection and epithermal neutrons for boron neutron-capture therapy of brain tumors. A magnetically coupled DC voltage multiplier derived from an industrial ELV-type electron accelerator is used as a high voltage source for the accelerator. A dc high current negative ion source has been developed for injection into the tandem. In the tandem accelerator there is set of nested potential electrodes with openings which form a channel for accelerating the negative hydrogen ion beam and subsequently accelerating the proton beam after stripping in the gas target. The electrodes are connected to a high voltage feedthrough insulator to which required potentials are applied from the high voltage power supply by means of a resistor voltage divider. In the paper the first experimental results obtained with the vacuum insulated tandem accelerator are also given.

  14. Tandem oligonucleotide synthesis using linker phosphoramidites

    PubMed Central

    Pon, Richard T.; Yu, Shuyuan

    2005-01-01

    Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated. PMID:15814811

  15. 25 MV tandem accelerator at Oak Ridge

    SciTech Connect

    Jones, C.M.

    1980-01-01

    A new heavy-ion accelerator facility is under construction at the Oak Ridge National Laboratory. A brief description of the scope and status of this project is presented with emphasis on the first operational experience with the 25 MV tandem accelerator.

  16. Modelling of tandem cell temperature coefficients

    SciTech Connect

    Friedman, D.J.

    1996-05-01

    This paper discusses the temperature dependence of the basic solar-cell operating parameters for a GaInP/GaAs series-connected two-terminal tandem cell. The effects of series resistance and of different incident solar spectra are also discussed.

  17. Organic Tandem Solar Cells: Design and Formation

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Chao

    In the past decade, research on organic solar cells has gone through an important development stage leading to major enhancements in power conversion efficiency, from 4% to 9% in single-junction devices. During this period, there are many novel processing techniques and device designs that have been proposed and adapted in organic solar-cell devices. One well-known device architecture that helps maximize the solar cell efficiency is the multi-junction tandem solar-cell design. Given this design, multiple photoactive absorbers as subcells are stacked in a monolithic fashion and assembled via series connection into one complete device, known as the tandem solar cell. Since multiple absorbers with different optical energy bandgaps are being applied in one tandem solar-cell device, the corresponding solar cell efficiency is maximized through expanded absorption spectrum and reduced carrier thermalization loss. In Chapter 3, the architecture of solution-processible, visibly transparent solar cells is introduced. Unlike conventional organic solar-cell devices with opaque electrodes (such as silver, aluminum, gold and etc.), the semi-transparent solar cells rely on highly transparent electrodes and visibly transparent photoactive absorbers. Given these two criteria, we first demonstrated the visibly transparent single-junction solar cells via the polymer absorber with near-infrared absorption and the top electrode based on solution-processible silver nanowire conductor. The highest visible transparency (400 ˜ 700 nm) of 65% was achieved for the complete device structure. More importantly, power conversion efficiency of 4% was also demonstrated. In Chapter 4, we stacked two semi-transparent photoactive absorbers in the tandem architecture in order to realize the semi-transparent tandem solar cells. A noticeable performance improvement from 4% to 7% was observed. More importantly, we modified the interconnecting layers with the incorporation of a thin conjugated

  18. Technology for large tandem mirror experiments

    SciTech Connect

    Thomassen, K.I.

    1980-09-04

    Construction of a large tandem mirror (MFTF-B) will soon begin at Lawrence Livermore National Laboratory (LLNL). Designed to reach break-even plasma conditions, the facility will significantly advance the physics and technology of magnetic-mirror-based fusion reactors. This paper describes the objectives and the design of the facility.

  19. Tandem mirror next step conceptual design

    SciTech Connect

    Doggett, J.N.; Damm, C.C.; Bulmer, R.H.

    1980-10-14

    A study was made to define the features of the experimental mirror fusion device - The Tandem Mirror Next Step, or TMNS - that will bridge the gap between present mirror confinement experiments and a power-producing reactor. We outline the project goals, describe some initial device parameters, and relate the technological requirements to ongoing development programs.

  20. Vortex interaction between two tandem flexible propulsors

    NASA Astrophysics Data System (ADS)

    Park, Sung Goon; Sung, Hyung Jin; Flow Control Laboratory Team

    2015-11-01

    Schooling behaviors of flying and swimming animals are widespread phenomena in nature. Inspired by schooling behaviors of swimming jellyfish, self-propelling flexible bodies with a paddling-based locomotion were modeled in a tandem configuration. The interactions between surrounding fluids and propulsors were considered by using the immersed boundary method. The hydrodynamic patterns generated by the interactions between tandem flexible propulsors were analyzed in the presen study. As a result of the flow-mediated interactions between them, stable configurations were formed spontaneously in which the gap distance between propulsors increased and decreased during the contraction and relaxation phases of the upstream propulsor. The stable configuration was not affected by the initial gap distance but influenced by the phase difference in the flapping frequency between them. Both tandem propulsors benefited from the tandem configuration in terms of the locomotion as compared with an isolated propulsor. This study was supported by the Creative Research Initiatives (No. 2015-001828) program of the National Research Foundation of Korea (MSIP).

  1. Inverted Three-Junction Tandem Thermophotovoltaic Modules

    NASA Technical Reports Server (NTRS)

    Wojtczuk, Steven

    2012-01-01

    An InGaAs-based three-junction (3J) tandem thermophotovoltaic (TPV) cell has been investigated to utilize more of the blackbody spectrum (from a 1,100 C general purpose heat source GPHS) efficiently. The tandem consists of three vertically stacked subcells, a 0.74-eV InGaAs cell, a 0.6- eV InGaAs cell, and a 0.55-eV InGaAs cell, as well as two interconnecting tunnel junctions. A greater than 20% TPV system efficiency was achieved by another group with a 1,040 C blackbody using a single-bandgap 0.6- eV InGaAs cell MIM (monolithic interconnected module) (30 lateral junctions) that delivered about 12 V/30 or 0.4 V/junction. It is expected that a three-bandgap tandem MIM will eventually have about 3 this voltage (1.15 V) and about half the current. A 4 A/cm2 would be generated by a single-bandgap 0.6-V InGaAs MIM, as opposed to the 2 A/cm2 available from the same spectrum when split among the three series-connected junctions in the tandem stack. This would then be about a 50% increase (3xVoc, 0.5xIsc) in output power if the proposed tandem replaced the single- bandgap MIM. The advantage of the innovation, if successful, would be a 50% increase in power conversion efficiency from radioisotope heat sources using existing thermophotovoltaics. Up to 50% more power would be generated for radioisotope GPHS deep space missions. This type of InGaAs multijunction stack could be used with terrestrial concentrator solar cells to increase efficiency from 41 to 45% or more.

  2. Numerical modeling of GaInP/GaAs monolithic tandem solar cells

    NASA Astrophysics Data System (ADS)

    Mahfoud, Abderrezak; Fathi, Mohamed; Belghachi, Abderrahmane; Djahli, Farid

    2016-07-01

    In this work, we present simulation of a monolithic tandem GaInP/GaAs solar cell made from a top GaInP cell and a bottom GaAs cell. For this purpose we used one dimensional simulation program tool called Solar Cell Capacitance Simulator in one Dimension (SCAPS-1D), the proposed methodology consists of simulating each cell separately. For enhanced electric characteristics of a tandem solar cell, the current-match condition between the top and bottom cells should be satisfied, which in turn requires careful design of the tandem parameters. To fulfill this condition, the top cell base thickness of (GaInP) is adjusted accordingly. The solar spectrum reaching the lower cell is computed by subtracting the top cell spectrum from the total solar spectrum. The optimal value of the short circuit current density corresponds to a top cell's base thickness of 0.7 μm; this results in an open circuit voltage of 2.397 V, a short circuit current density of 13.87 mA/cm2, an efficiency of 29.83 % and a fill factor of 89.74 % under the AM1.5G solar spectrum.

  3. Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

    SciTech Connect

    Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata; Leavis, Paul C.; Navaza, Jorge; Dominguez, Roberto

    2013-11-20

    Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin {beta}4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin {beta}4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  4. Application of CBZ dimer, C343 and SQ dye as photosensitizers for pn-tandem DSCs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Hyi; Park, Ji Young; Thogiti, Suresh; Cheruku, Rajesh; Kim, Jae Hong

    2016-07-01

    A pn-tandem dye-sensitized solar cell ( pn-DSC) was prepared with three different sensitized dyes CBZ Dimer (CBZD), C343, and SQ in two different compartments of the n-type or p-type cells. The constructed tandem solar cell was exhibited considerable improvement in experimental pn-DSCs parameters, open-circuit voltage, short-circuit current, fill factor, etc. These results were achieved under air mass 1.5 illumination with three different sensitized dyes in the upper and lower compartment of the pn-DSCs. These results demonstrate a complementary absorption among the two photoelectrodes in the pn-DSCs is a good approach to the efficient and low cost pn-DSCs. [Figure not available: see fulltext.

  5. Tritium measurements with a tandem accelerator

    NASA Astrophysics Data System (ADS)

    Middleton, R.; Klein, J.; Fink, D.

    1990-06-01

    Tritium concentrations ( 3H: 2H) of less than 10 -15 are readily measurable with almost any tandem accelerator and with an overall detection efficiency as high as 4.5%. The isobar, 3He, and other potential sources of interference (mainly 6Li, 2H and 1H) can all be removed by an absorber in front of the triton detector, so there is little need for analyzing elements other than the negative-and positive-ion magnets found on most tandems. The technique is particularly well suited for detecting tritium in deuterium absorbed in a metal and testing for cold fusion. We caution that tritium can occur in commercial deuterium and heavy water from sources other than cold fusion; one sample was observed to have a tritium-to-deuterium ratio of 10 -10.

  6. Locomotion by Tandem and Parallel Wings

    NASA Astrophysics Data System (ADS)

    Tanida, Yoshimichi

    A two-dimensional analysis was carried out on the locomotion by tandem and parallel wings in relation to the free flight of dragonflies and beetles, remarking the mutual interference between fore and hind wings. The results obtained are summarized as follows: In the case of tandem wings, (1)High thrust and propulsive efficiency can be achieved when the forewing oscillates with a definite phase lag behind the hindwing, as in the case of real dragonflies, (2)Somewhat smaller amplitude of hindwing leads to optimum condition for work sharing of two wings, (3)The hard forewing does not serve for the thrust and propulsive efficiency, whereas the hard hindwing does for the augmentation of them; In the case of parallel wings, (4)The hard wing placed near the soft wing acts nearly as an infinite plate, as for the ground effect, increasing both thrust and propulsive efficiency.

  7. Tandem microwave waste remediation and decontamination system

    DOEpatents

    Wicks, George G.; Clark, David E.; Schulz, Rebecca L.

    1999-01-01

    The invention discloses a tandem microwave system consisting of a primary chamber in which microwave energy is used for the controlled combustion of materials. A second chamber is used to further treat the off-gases from the primary chamber by passage through a susceptor matrix subjected to additional microwave energy. The direct microwave radiation and elevated temperatures provide for significant reductions in the qualitative and quantitative emissions of the treated off gases. The tandem microwave system can be utilized for disinfecting wastes, sterilizing materials, and/or modifying the form of wastes to solidify organic or inorganic materials. The simple design allows on-site treatment of waste by small volume waste generators.

  8. Nucleic acid recognition by tandem helical repeats.

    PubMed

    Rubinson, Emily H; Eichman, Brandt F

    2012-02-01

    Protein domains constructed from tandem α-helical repeats have until recently been primarily associated with protein scaffolds or RNA recognition. Recent crystal structures of human mitochondrial termination factor MTERF1 and Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA revealed two new superhelical tandem repeat architectures capable of wrapping around the double helix in unique ways. Unlike DNA sequence recognition motifs that rely mainly on major groove read-out, MTERF and ALK motifs locate target sequences and aberrant nucleotides within DNA by resculpting the double-helix through extensive backbone contacts. Comparisons between MTERF and ALK repeats, together with recent advances in ssRNA recognition by Pumilio/FBF (PUF) domains, provide new insights into the fundamental principles of protein-nucleic acid recognition. PMID:22154606

  9. Electron irradiation of tandem junction solar cells

    NASA Technical Reports Server (NTRS)

    Anspaugh, B. E.; Miyahira, T. F.; Scott-Monck, J. A.

    1979-01-01

    The electrical behavior of 100 micron thick tandem junction solar cells manufactured by Texas Instruments was studied as a function of 1 MeV electron fluence, photon irradiation, and 60 C annealing. These cells are found to degrade rapidly with radiation, the most serious loss occurring in the blue end of the cell's spectral response. No photon degradation was found to occur, but the cells did anneal a small amount at 60 C.

  10. Current and lattice matched tandem solar cell

    DOEpatents

    Olson, Jerry M.

    1987-01-01

    A multijunction (cascade) tandem photovoltaic solar cell device is fabricated of a Ga.sub.x In.sub.1-x P (0.505.ltoreq.X.ltoreq.0.515) top cell semiconductor lattice matched to a GaAs bottom cell semiconductor at a low-resistance heterojunction, preferably a p+/n+ heterojunction between the cells. The top and bottom cells are both lattice matched and current matched for high efficiency solar radiation conversion to electrical energy.

  11. DDES and IDDES of tandem cylinders.

    SciTech Connect

    Balakrishnan, R.; Garbaruk, A.; Shur, M.; Strelets, M.; Spalart, P.; New Technologies and Services - Russia; St.-Peterburg State Polytechnic Univ.; Boeing Commercial Airplanes

    2010-09-09

    The paper presents an overview of the authors contribution to the BANC-I Workshop on the flow past tandem cylinders (Category 2). It includes an outline of the simulation approaches, numerics, and grid used, the major results of the simulations, their comparison with available experimental data, and some preliminary conclusions. The effect of varying the spanwise period in the simulations is strong for some quantities, and not others.

  12. Cold Climate Heat Pumps Using Tandem Compressors

    SciTech Connect

    Shen, Bo; Abdelaziz, Omar; Rice, C Keith; Baxter, Van D

    2016-01-01

    In cold climate zones, e.g. ASHRAE climate regions IV and V, conventional electric air-source heat pumps (ASHP) do not work well, due to high compressor discharge temperatures, large pressure ratios and inadequate heating capacities at low ambient temperatures. Consequently, significant use of auxiliary strip heating is required to meet the building heating load. We introduce innovative ASHP technologies as part of continuing efforts to eliminate auxiliary strip heat use and maximize heating COP with acceptable cost-effectiveness and reliability. These innovative ASHP were developed using tandem compressors, which are capable of augmenting heating capacity at low temperatures and maintain superior part-load operation efficiency at moderate temperatures. Two options of tandem compressors were studied; the first employs two identical, single-speed compressors, and the second employs two identical, vapor-injection compressors. The investigations were based on system modeling and laboratory evaluation. Both designs have successfully met the performance criteria. Laboratory evaluation showed that the tandem, single-speed compressor ASHP system is able to achieve heating COP = 4.2 at 47 F (8.3 C), COP = 2.9 at 17 F (-8.3 C), and 76% rated capacity and COP = 1.9 at -13 F (-25 C). This yields a HSPF = 11.0 (per AHRI 210/240). The tandem, vapor-injection ASHP is able to reach heating COP = 4.4 at 47 F, COP = 3.1 at 17 F, and 88% rated capacity and COP = 2.0 at -13 F. This yields a HSPF = 12.0. The system modeling and further laboratory evaluation are presented in the paper.

  13. Expression of tandem gene duplicates is often greater than twofold

    PubMed Central

    Loehlin, David W.; Carroll, Sean B.

    2016-01-01

    Tandem gene duplication is an important mutational process in evolutionary adaptation and human disease. Hypothetically, two tandem gene copies should produce twice the output of a single gene, but this expectation has not been rigorously investigated. Here, we show that tandem duplication often results in more than double the gene activity. A naturally occurring tandem duplication of the Alcohol dehydrogenase (Adh) gene exhibits 2.6-fold greater expression than the single-copy gene in transgenic Drosophila. This tandem duplication also exhibits greater activity than two copies of the gene in trans, demonstrating that it is the tandem arrangement and not copy number that is the cause of overactivity. We also show that tandem duplication of an unrelated synthetic reporter gene is overactive (2.3- to 5.1-fold) at all sites in the genome that we tested, suggesting that overactivity could be a general property of tandem gene duplicates. Overactivity occurs at the level of RNA transcription, and therefore tandem duplicate overactivity appears to be a previously unidentified form of position effect. The increment of surplus gene expression observed is comparable to many regulatory mutations fixed in nature and, if typical of other genomes, would shape the fate of tandem duplicates in evolution. PMID:27162370

  14. TandEM: Titan and Enceladus mission

    USGS Publications Warehouse

    Coustenis, A.; Atreya, S.K.; Balint, T.; Brown, R.H.; Dougherty, M.K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R.A.; Griffith, C.A.; Gurvits, L.I.; Jaumann, R.; Langevin, Y.; Leese, M.R.; Lunine, J.I.; McKay, C.P.; Moussas, X.; Muller-Wodarg, I.; Neubauer, F.; Owen, T.C.; Raulin, F.; Sittler, E.C.; Sohl, F.; Sotin, C.; Tobie, G.; Tokano, T.; Turtle, E.P.; Wahlund, J.-E.; Waite, J.H.; Baines, K.H.; Blamont, J.; Coates, A.J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R.D.; Morse, A.; Porco, C.C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J.C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D.H.; Benilan, Y.; Bertucci, C.; Bezard, B.; Bjoraker, G.L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M.T.; Chassefiere, E.; Coll, P.; Combes, M.; Cooper, J.F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I.A.; de Angelis, E.; De Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F.M.; Fortes, A.D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Kuppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le, Mouelic S.; Lebonnois, S.; Ledvina, S.; Li, J.; Livengood, T.A.; Lopes, R.M.; Lopez-Moreno, J. -J.; Luz, D.; Mahaffy, P.R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Salvan, C.M.; Milillo, A.; Mitchell, D.G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, C.D.; Nixon, C.A.; Mvondo, D.N.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F.T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Bermejo, M.R.; Sarris, E.T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L.J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D.F.; Szego, K.; Szopa

    2009-01-01

    TandEM was proposed as an L-class (large) mission in response to ESA's Cosmic Vision 2015-2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini-Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini-Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfi??re) and possibly several landing probes to be delivered through the atmosphere. ?? Springer Science + Business Media B.V. 2008.

  15. Organic Light-Emitting Devices with Tandem Structure.

    PubMed

    Chiba, Takayuki; Pu, Yong-Jin; Kido, Junji

    2016-06-01

    Tandem organic light-emitting devices (OLEDs) have attracted considerable attention for solid-state lighting and flat panel displays because their tandem architecture enables high efficiency and long operational lifetime simultaneously. In the tandem OLED structure, plural light-emitting units (LEUs) are stacked in series through a charge generation layer (CGL) and an electron injection layer (EIL). In this chapter, we focus on the key features of tandem OLEDs for high efficiency and long operational lifetimes. We also demonstrate the effect of the CGL comprising a Lewis acid, an n-type semiconductor metal oxide, and an organic electron-accepting material. We discuss the two types of EILs in tandem OLEDs: alkali metals containing n-type compounds and ultra-thin metals. Finally, we focus on the recent progress of the state-of-the-art solution-processed tandem OLEDs. PMID:27573273

  16. [Tandem repeats in rodents genome and their mapping].

    PubMed

    Ostromyshenskii, D I; Kuznetsova, L S; Komissarov, A S; Kartavtseva, I V; Podgornaya, L

    2015-01-01

    Tandemly-repeated sequences represent a unique class of eukaryotic DNA. Their content in the genome of higher eukaryotes mounts to tens of percents. However, the evolution of this class of sequences is poorly-studied. In our paper, 62 families of Mus musculus tandem repeats are analyzed by bioinformatic methods, and 7 of them are analyzed by fluorescence in situ hybridization. It is shown that the same tandem repeat sets co-occure only in closely related species of mice. But even in such species we observe differences in localization on the chromosomes and the number of individual tandem repeats. With increasing evolutionary distance only some of the tandem repeat families remain common for different species. It is shown, that the use of a combination of bioinformatics and molecular biology techniques is very perspective for further studies of the evolution of tandem repeats. PMID:26035967

  17. Effects of practicing tandem gait with and without vibrotactile biofeedback in subjects with unilateral vestibular loss

    PubMed Central

    Dozza, Marco; Wall, Conrad; Peterka, Robert J.; Chiari, Lorenzo; Horak, Fay B.

    2008-01-01

    Subjects with unilateral vestibular loss exhibit motor control impairments as shown by body and limb deviation during gait. Biofeedback devices have been shown to improve stance postural control, especially when sensory information is limited by environmental conditions or pathologies such as unilateral vestibular loss. However, the extent to which biofeedback could improve motor performance or learning while practicing a dynamic task such as narrow gait is still unknown. In this cross-over design study, 9 unilateral vestibular loss subjects practiced narrow gait with and without wearing a trunk-tilt, biofeedback device in 2 practice sessions. The biofeedback device informed the subjects of their medial-lateral angular tilt and tilt velocity during gait via vibration of the trunk. From motion analysis and tilt data, the performance of the subjects practicing tandem gait were compared over time with and without biofeedback. By practicing tandem gait, subjects reduced their trunk-tilt, center of mass displacement, medial-lateral feet distance, and frequency of stepping error. In both groups, use of tactile biofeedback consistently increased postural stability during tandem gait, beyond the effects of practice alone. However, one single session of practice with biofeedback did not result in conclusive short-term after-effects consistent with short-term retention of motor performance without this additional biofeedback. Results from this study support the hypothesis that tactile biofeedback acts similar to natural sensory feedback to improve dynamic motor performance but does not facilitate a recalibration of motor performance to improve function after short-term use. PMID:18525145

  18. Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome

    PubMed Central

    Shimada, Makoto K.; Sasaki-Haraguchi, Noriko; Mayeda, Akila

    2015-01-01

    According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism. PMID:25961948

  19. Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome.

    PubMed

    Shimada, Makoto K; Sasaki-Haraguchi, Noriko; Mayeda, Akila

    2015-01-01

    According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37-65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism. PMID:25961948

  20. Flexible and fragmentable tandem photosensitive nanocrystal skins

    NASA Astrophysics Data System (ADS)

    Akhavan, S.; Uran, C.; Bozok, B.; Gungor, K.; Kelestemur, Y.; Lesnyak, V.; Gaponik, N.; Eychmüller, A.; Demir, H. V.

    2016-02-01

    We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm-2 at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion.We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of

  1. A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome.

    PubMed

    Darrow, Emily M; Seberg, Andrew P; Das, Sunny; Figueroa, Debbie M; Sun, Zhuo; Moseley, Shawn C; Chadwick, Brian P

    2014-09-01

    Euchromatic features are largely absent from the human inactive X chromosome (Xi), with the exception of several large tandem repeats that can be detected as euchromatin bands at metaphase. Despite residing megabases apart, these tandem repeats make frequent inactive X-specific interactions. The mouse homologue has been reported for at least one of the tandem repeats, but whether the mouse Xi is also characterized by distinct bands of euchromatin remains unknown. We examined the mouse Xi for the presence of euchromatin bands by examining the pattern of histone H3 dimethylated at lysine 4 and detected two major signals. The first band resides in the subtelomeric region of band XF5 and may correspond to the pseudoautosomal region. The second band localizes to XE3 and coincides with an extensive complex repeat composed of a large tandem and inverted repeat segment as well as several large short interspersed nuclear element (SINE)-rich tandem repeats. Fluorescence in situ hybridization reveals that sequences with homology to the repeat region are scattered along the length of the Y chromosome. Immunofluorescence analysis of histone H3 trimethylated at lysine 9 on metaphase chromosomes indicates that the repeat region corresponds to a band of constitutive heterochromatin on the male X and female active X chromosomes, whereas the euchromatin signal appears to be female specific. These data suggest that the band of euchromatin observed at XE3 is unique to the mouse Xi, comparable to the chromatin arrangement of several large tandem repeats located on the human X chromosome. PMID:24821208

  2. Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission

    PubMed Central

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of ‘Candidatus Liberibacter’ among which ‘Ca. Liberibacter asiaticus’ has the widest distribution. ‘Ca. L. asiaticus’ is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of ‘Ca. L. asiaticus’ were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a ‘Ca. L. asiaticus’ strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of ‘Ca. L. asiaticus’ change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively. PMID:26402645

  3. Changes in Variable Number of Tandem Repeats in 'Candidatus Liberibacter asiaticus' through Insect Transmission.

    PubMed

    Katoh, Hiroshi; Inoue, Hiromitsu; Iwanami, Toru

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' has the widest distribution. 'Ca. L. asiaticus' is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of 'Ca. L. asiaticus' were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a 'Ca. L. asiaticus' strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of 'Ca. L. asiaticus' change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively. PMID:26402645

  4. Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases.

    PubMed

    Feschenko, Vladimir V; Rajman, Luis A; Lovett, Susan T

    2003-02-01

    Rearrangements between tandemly repeated DNA sequences are a common source of genetic instability. Such rearrangements underlie several human genetic diseases. In many organisms, the mismatch-repair (MMR) system functions to stabilize repeats when the repeat unit is short or when sequence imperfections are present between the repeats. We show here that the action of single-stranded DNA (ssDNA) exonucleases plays an additional, important role in stabilizing tandem repeats, independent of their role in MMR. For perfect repeats of approximately 100 bp in Escherichia coli that are not susceptible to MMR, exonuclease (Exo)-I, ExoX, and RecJ exonuclease redundantly inhibit deletion. Our data suggest that >90% of potential deletion events are avoided by the combined action of these three exonucleases. Imperfect tandem repeats, less prone to rearrangements, are stabilized by both the MMR-pathway and ssDNA-specific exonucleases. For 100-bp repeats containing four mispairs, ExoI alone aborts most deletion events, even in the presence of a functional MMR system. By genetic analysis, we show that the inhibitory effect of ssDNA exonucleases on deletion formation is independent of the MutS and UvrD proteins. Exonuclease degradation of DNA displaced during the deletion process may abort slipped misalignment. Exonuclease action is therefore a significant force in genetic stabilization of many forms of repetitive DNA. PMID:12538867

  5. Flexible and fragmentable tandem photosensitive nanocrystal skins.

    PubMed

    Akhavan, S; Uran, C; Bozok, B; Gungor, K; Kelestemur, Y; Lesnyak, V; Gaponik, N; Eychmüller, A; Demir, H V

    2016-02-18

    We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm(-2) at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion. PMID:26498487

  6. Tandem robot control system and method for controlling mobile robots in tandem

    DOEpatents

    Hayward, David R.; Buttz, James H.; Shirey, David L.

    2002-01-01

    A control system for controlling mobile robots provides a way to control mobile robots, connected in tandem with coupling devices, to navigate across difficult terrain or in closed spaces. The mobile robots can be controlled cooperatively as a coupled system in linked mode or controlled individually as separate robots.

  7. Recurrent simple tandem repeat mutations during human Y-chromosome radiation in Caucasian subpopulations.

    PubMed

    Ciminelli, B M; Pompei, F; Malaspina, P; Hammer, M; Persichetti, F; Pignatti, P F; Palena, A; Anagnou, N; Guanti, G; Jodice, C

    1995-12-01

    The haplotypes at four polymorphic loci of the Y chromosome were determined in 245 Caucasian males from 12 subpopulations. The data show that haplotype radiation occurred among Caucasians. Haplotype radiation was accompanied by recurrent mutations at STR loci that caused partial randomization of haplotype structure. The present distribution of alleles at short tandem repeats (STRs) can be explained by a mutation pattern similar to those described for autosomal STRs. The degree of variation among groups of subpopulations was assayed by using the Analysis of Molecular Variance. The results confirm a faster divergence of the Y chromosome as compared to the rest of the genome. PMID:8587142

  8. The Naples University 3 MV tandem accelerator

    SciTech Connect

    Campajola, L.; Brondi, A.

    2013-07-18

    The 3 MV tandem accelerator of the Naples University is used for research activities and applications in many fields. At the beginning of operation (1977) the main utilization was in the field of nuclear physics. Later, the realization of new beam lines allowed the development of applied activities as radiocarbon dating, ion beam analysis, biophysics, ion implantation etc. At present, the availability of different ion sources and many improvements on the accelerator allow to run experiments in a wide range of subjects. An overview of the characteristics and major activities of the laboratory is presented.

  9. Reduction of radial losses in tandem mirrors

    NASA Astrophysics Data System (ADS)

    Myra, J. R.; Dippolito, D. A.; Catto, P. J.

    1982-07-01

    The conditions for omnigenous magnetic fields are generalized to determine the fields which give the smallest mean square neoclassical step size consistent with given boundary conditions and constraints. This transport minimization produces less restrictive field configurations than omnigenity, and a wider class of practical applications is possible. An explicit set of ordinary differential equations is obtained for the transport minimizing vacuum fields in long thin tandem mirror geometry. The constraint, for these configurations no parallel current flows into the center cell (due to the Stupakov effect), is imposed naturally.

  10. HRIBF Tandem Accelerator Radiation Safety System Upgrade

    SciTech Connect

    Blankenship, J.L.; Juras, R.C.

    1998-11-04

    The HRIBF Tandem Accelerator Radiation Safety System was designed to permit experimenters and operations staff controlled access to beam transport and experiment areas with accelerated beam present. Neutron-Gamma detectors are mounted in eaeh area at points of maximum dose rate and the resulting signals are integrated by redundan~ circuitry; beam is stopped if dose rate or integrated dose exceeds established limits. This paper will describe the system, in use for several vears at the HRIBF, and discuss changes recently made to modernize the system and to make the system compliant with DOE Order 5480.25 and related ORNL updated safety rules.

  11. A Hybrid Approach To Tandem Cylinder Noise

    NASA Technical Reports Server (NTRS)

    Lockard, David P.

    2004-01-01

    Aeolian tone generation from tandem cylinders is predicted using a hybrid approach. A standard computational fluid dynamics (CFD) code is used to compute the unsteady flow around the cylinders, and the acoustics are calculated using the acoustic analogy. The CFD code is nominally second order in space and time and includes several turbulence models, but the SST k - omega model is used for most of the calculations. Significant variation is observed between laminar and turbulent cases, and with changes in the turbulence model. A two-dimensional implementation of the Ffowcs Williams-Hawkings (FW-H) equation is used to predict the far-field noise.

  12. Method of fabricating bifacial tandem solar cells

    SciTech Connect

    Wojtczuk, Steven J; Chiu, Philip T; Zhang, Xuebing; Gagnon, Edward; Timmons, Michael

    2014-10-07

    A method of fabricating on a semiconductor substrate bifacial tandem solar cells with semiconductor subcells having a lower bandgap than the substrate bandgap on one side of the substrate and with subcells having a higher bandgap than the substrate on the other including, first, growing a lower bandgap subcell on one substrate side that uses only the same periodic table group V material in the dislocation-reducing grading layers and bottom subcells as is present in the substrate and after the initial growth is complete and then flipping the substrate and growing the higher bandgap subcells on the opposite substrate side which can be of different group V material.

  13. HRIBF Tandem Accelerator Radiation Safety System Upgrade

    NASA Astrophysics Data System (ADS)

    Juras, R. C.; Blankenship, J. L.

    1999-06-01

    The HRIBF Tandem Accelerator Radiation Safety System was designed to permit experimenters and operations staff controlled access to beam transport and experiment areas with accelerated beam present. Neutron-Gamma detectors are mounted in each area at points of maximum dose rate and the resulting signals are integrated by redundant circuitry; beam is stopped if dose rate or integrated dose exceeds established limits. This paper will describe the system, in use for several years at the HRIBF, and discuss changes recently made to modernize the system and to make the system compliant with DOE Order 5480.25 and related ORNL updated safety rules.

  14. The role of variable DNA tandem repeats in bacterial adaptation.

    PubMed

    Zhou, Kai; Aertsen, Abram; Michiels, Chris W

    2014-01-01

    DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date. PMID:23927439

  15. Progress in the tandem mirror program

    SciTech Connect

    Fowler, T.K.; Borchers, R.R.

    1981-09-13

    Experimental results in TMX have confirmed the basic principles of the tandem-mirror concept. A center-cell particle confinement parameter eta tau approx. 10/sup 11/ cm/sup -3/ s has been obtained at ion temperatures around 100 eV, which is a hundred-fold improvement over single mirrors at the same temperatures. For TMX these results have been obtained at peak beta values in the center cell in the range 10 to 40%, not yet limited by MHD activity; and ion-cyclotron resonant heating (ICRH) in the Phaedrus tandem-mirror experiment has produced beta values approx. 25%, which is several times the ideal MHD limit for that device. In addition, it has been demonstrated that the end fan chambers of TMX simultaneously isolate the hot electrons from the end walls, provide adequate pumping and conveniently dispose of the exhaust plasma energy either by thermal deposition on the end wall or by direct conversion to electricity (at 48% efficiency in agreement with calculations). Also, evidence was obtained for inherent divertor action in TMX, presumably in part responsible for the observed low impurity level (<0.5% low-Z ions in the center cell).

  16. Tandem mass spectrometry for sequencing proanthocyanidins.

    PubMed

    Li, Hui-Jing; Deinzer, Max L

    2007-02-15

    Proanthocyanidins (PAs) are a group of bioflavonoids consisting of oligomers based on catechin monomeric units. These polyphenolic compounds are widely distributed in higher plants and are an integral part of the human diet. A sensitive LC-tandem mass spectrometric (LC/ESI-MS(n)) method in the positive ion mode for sequencing these ubiquitous and highly beneficial antioxidants is described. The hydroxylation patterns and interflavanoid linkage for A- and B-type PAs were determined by fragment ions derived from a retro-Diels-Alder (RDA) fission, heterocyclic ring fission (HRF), a novel benzofuran-forming (BFF) fission described here for the first time, and a quinone methide (QM) fission. The subunit sequence of the PAs was determined by diagnostic ions derived from HRF/RDA fission, HRF/BFF fission, and RDA/HRF fission together with QM fission. A total of 26 PAs were reliably sequenced by the newly established tandem mass spectrometric protocol. It is shown that the protocol based on a combination of these different fragmentation patterns allows for uniquely identifying PA oligomers. PMID:17297981

  17. A tandem-based compact dual-energy gamma generator

    SciTech Connect

    Persaud, A.; Kwan, J.W.; Leitner, M.; Leung, K.N.; Ludewigt, B.; Tanaka, N.; Waldron, W.; Wilde, S.; Antolak, A.J.; Morse, D.H.; Raber, T.

    2009-11-11

    A dual-energy tandem-type gamma generator has been developed at E.O. Lawrence Berkeley National Laboratory and Sandia National Laboratories. The tandem accelerator geometry allows higher energy nuclear reactions to be reached, thereby allowing more flexible generation of MeV-energy gammas for active interrogation applications.

  18. Thermal-barrier production and indentification in a tandem mirror

    SciTech Connect

    Grubb, D.P.; Allen, S.L.; Casper, T.A.; Clauser, J.F.; Coensgen, F.H.; Correll, D.L.; Cummins, W.F.; Damm, C.C.; Foote, J.H.; Goodman, R.K.; Hill, D.N.; Hooper,Jr., E.B.; Hornady, R.S.; Hunt, A.L.; Kerr, R.G.; Leppelmeier, G.W.; Marilleau, J.; Moller, J.M.; Molvik, A.W.; Nexsen, W.E.; Pickles, W.L.; Porter, G.D.; Poulsen, P.; Silver, E.H.; Simonen, T.C.; Stallard, B.W.; Turner, W.C.; Hsu, W.L.; Yu, T.L.; Barter, J.D.; Christensen, T.; Dimonte, G.; Romesser, T.W.; Ellis, R.F.; James, R.A.; Lasnier, C.J.; Berzins, L.V.; Carter, M.R.; Clower, C.A.; Failor, B.H.; Falabella, S.; Flammer, M.; Nash, T.

    1984-08-20

    In thermal-barrier experiments in the tandem mirror experiment upgrade axial confinement times of 50 to 100 ms have been achieved. During enhanced confinement we measured the thermal-barrier potential profile using a neutral-particle-beam probe. The experimental data agree qualitatively and quantitatively with the theory of thermal-barrier formation in a tandem mirror.

  19. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 2 2011-01-01 2011-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a...

  20. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 2 2013-01-01 2013-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a...

  1. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 2 2012-01-01 2012-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a...

  2. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 2 2014-01-01 2014-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a...

  3. Tandem-type pulse tube refrigerator without reservoir

    NASA Astrophysics Data System (ADS)

    Ki, Taekyung; Jeong, Sangkwon; Ko, Junseok; Park, Jiho

    2015-12-01

    In this paper, a tandem-type pulse tube refrigerator without a reservoir is discussed and investigated. For its practical application a tandem-type compressor is designed to generate two pulsating pressure waves with opposite phases, simultaneously. A tandem-type pulse tube refrigerator consists of a tandem-type compressor and two identical pulse tube refrigerators. The two identical pulse tube refrigerators share the same heat exchangers and one can be connected with the other by an inertance tube without a reservoir. In this proposed configuration, the mechanical vibration and temperature oscillations in the cold-end heat exchanger can be internally suppressed due to its intrinsic opposite-characteristic operation. To examine the quantitative evaluation of the tandem feature which does not require a reservoir in the pulse tube, an evolutionary approach has been attempted. A general structure of a pulse tube refrigerator is modified into tandem Stirling-type and GM-type machines and the transformed configuration has been simulated for tandem operation. The simulation results clearly demonstrate that a properly designed tandem-type pulse tube refrigerator without a reservoir can function favorably.

  4. Shortness of Breath

    MedlinePlus

    ... Body & lifestyle changes > Shortness of breath Shortness of breath E-mail to a friend Please fill in ... oxygen your baby gets. Causes of shortness of breath during pregnancy Early pregnancy In the first few ...

  5. Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

    PubMed Central

    Nunes, D P; Keates, A C; Afdhal, N H; Offner, G D

    1995-01-01

    Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids. Images Figure 4 Figure 5 Figure 6 PMID:7646470

  6. The physiological effects of cycling on tandem and single bicycles

    PubMed Central

    Seifert, J; Bacharach, D; Burke, E; Langenfeld, M; Snyder, A

    2003-01-01

    Objective: The purpose of this field study was to compare the physiological responses from cycling on a tandem road bicycle to those from cycling on a single road bicycle. Methods: Nine pairs of experienced, recreational tandem cyclists rode a tandem or their single bicycle for 5 min at each velocity of 19.3, 22.5, 25.8, and 29.0 kph on a flat, paved surface. Heart rate (HR), rating of perceived exertion (RPE), and lactic acid (LA) data were collected after each interval. Results: Riding a tandem resulted in lower HR, RPE, and LA mean values across the four velocities compared to the single bicycle. Mean (SD) HR, RPE, and LA for tandem and single bicycles were 126 (20.7) v 142 (20.1) bpm, 10.1 (1.7) v 11.3 (2.6), and 1.46 (1.0) mM/L v 2.36 (1.7) mM/L, respectively. No position differences were observed between the captain and stoker (front and rear positions) when both were on the tandem. Stokers had significantly lower HR, LA, and RPE values when they rode a tandem compared to a single bicycle. No statistical differences were observed between bicycles for the captains. When on the single bicycle, captains exhibited significantly lower HR, RPE, and LA values than stokers. Conclusion: Cycling on a tandem resulted in lower physiological stress than when cycling at the same velocity on a single bicycle. Cyclists were able to ride from 4.8–8.0 kph faster on a tandem than on a single bicycle at similar physiological stress. Apparently, stokers can add to power output on a tandem without adding significantly to wind resistance. PMID:12547743

  7. Electronic Tandem Language Learning (eTandem): A Third Approach to Second Language Learning for the 21st Century

    ERIC Educational Resources Information Center

    Cziko, Gary A.

    2004-01-01

    Tandem language learning occurs when two learners of different native languages work together to help each other learn the other language. First used in face-to-face contexts, Tandem is now increasingly being used by language-learning partners located in different countries who are linked via various forms of electronic communication, a context…

  8. Axisymmetric Tandem Mirrors: Stabilization and Confinement Studies

    SciTech Connect

    Post, R F; Fowler, T K; Bulmer, R; Byers, J; Hua, D; Tung, L

    2004-07-15

    The 'Kinetic Stabilizer' has been proposed as a means of MHD stabilizing an axisymmetric tandem mirror system. The K-S concept is based on theoretical studies by Ryutov, confirmed experimentally in the Gas Dynamic Trap experiment in Novosibirsk. In the K-S beams of ions are directed into the end of an 'expander' region outside the outer mirror of a tandem mirror. These ions, slowed, stagnated, and reflected as they move up the magnetic gradient, produce a low-density stabilizing plasma. At the Lawrence Livermore National Laboratory we have been conducting theoretical and computational studies of the K-S Tandem Mirror. These studies have employed a low-beta code written especially to analyze the beam injection/stabilization process, and a new code SYMTRAN (by Hua and Fowler) that solves the coupled radial and axial particle and energy transport in a K-S TM. Also, a 'legacy' MHD stability code, FLORA, has been upgraded and employed to benchmark the injection/stabilization code and to extend its results to high beta values. The FLORA code studies so far have confirmed the effectiveness of the K-S in stabilizing high-beta (40%) plasmas with stabilizer plasmas the peak pressures of which are several orders of magnitude smaller than those of the confined plasma. Also the SYMTRAN code has shown D-T plasma ignition from alpha particle energy deposition in T-M regimes with strong end plugging. Our studies have confirmed the viability of the K-S-T-M concept with respect to MHD stability and radial and axial confinement. We are continuing these studies in order to optimize the parameters and to examine means for the stabilization of possible residual instability modes, such as drift modes and 'trapped-particle' modes. These modes may in principle be controlled by tailoring the stabilizer plasma distribution and/or the radial potential distribution. In the paper the results to date of our studies are summarized and projected to scope out possible fusion-power versions of the K

  9. Axisymmetric Tandem Mirrors: Stabilization and Confinement Studies

    SciTech Connect

    Post, R.F.; Fowler, T.K.; Bulmer, R.; Byers, J.; Hua, D.; Tung, L.

    2005-01-15

    The 'Kinetic Stabilizer' has been proposed as a means of MHD stabilizing an axisymmetric tandem mirror system. The K-S concept is based on theoretical studies by Ryutov, confirmed experimentally in the Gas Dynamic Trap experiment in Novosibirsk. In the K-S beams of ions are directed into the end of an 'expander' region outside the outer mirror of a tandem mirror. These ions, slowed, stagnated, and reflected as they move up the magnetic gradient, produce a low-density stabilizing plasma.At the Lawrence Livermore National Laboratory we have been conducting theoretical and computational studies of the K-S Tandem Mirror. These studies have employed a low-beta code written especially to analyze the beam injection/stabilization process,and a new code SYMTRAN (by Hua and Fowler)that solves the coupled radial and axial particle and energy transport in a K-S T-M. Also, a 'legacy' MHD stability code, FLORA, has been upgraded and employed to benchmark the injection/stabilization code and to extend its results to high beta values.The FLORA code studies so far have confirmed the effectiveness of the K-S in stabilizing high-beta (40%) plasmas with stabilizer plasmas the peak pressures of which are several orders of magnitude smaller than those of the confined plasma.Also the SYMTRAN code has shown D-T plasma ignition from alpha particle energy deposition in T-M regimes with strong end plugging.Our studies have confirmed the viability of the K-S T-M concept with respect to MHD stability and radial and axial confinement. We are continuing these studies in order to optimize the parameters and to examine means for the stabilization of possible residual instability modes, such as drift modes and 'trapped-particle' modes. These modes may in principle be controlled by tailoring the stabilizer plasma distribution and/or the radial potential distribution.In the paper the results to date of our studies are summarized and projected to scope out possible fusion-power versions of the K-S T-M.

  10. Negative deuterium ions for tandem mirror next step and tandem mirror reactors

    SciTech Connect

    Hamilton, G.W.

    1980-09-25

    Recent designs for mirror fusion reactors with good power balance include ambipolar potential plugs to reduce end losses and thermal barriers to maintain a difference in electron temperature between the large-volume central cell plasma and the confining end plugs. These designs led to several new requirements for D/sup 0/ neutral beams derived from negative ions at energies of 150 to 200 keV and possibly higher. Such beams are required for injection of fat ions into the plugs and the barrier and for charge-exchange pumping of thermal ions diffusing into the barrier. Negative ions are preferred for these purposes because of their relatively high efficiency of neutralization and their high purity of single-energy D/sup -/. Examples of injector designs for Tandem Mirror Next Step (TMNS) and Tandem Mirror Reactors (TMR) are presented.