WorldWideScience

Sample records for based insertion polymorphism

  1. MULTINDELS-BOV: Zebu traceback method based on DNA insertion-deletion polymorphisms.

    Science.gov (United States)

    Groenner-Penna, M; Croce, E F D; Pimenta, C G; Bicalho, H M S; Pena, S D J

    2014-01-01

    Brazil is a major producer and exporter of beef, with a herd of approximately 210 million animals. For the meat industry, a reliable animal traceback from its origin to the consumer market is paramount. Of all available identification systems, DNA is the only one that survives the slaughterhouse and reaches the dish of the consumer. DNA polymorphisms are already used for cattle traceback, but primarily for the subspecies Bos taurus taurus. However, in Brazil, another subspecies, B. taurus indicus predominates. We describe here the development of a DNA traceback method designed primarily for B. taurus indicus (Zebu), without leaving B. taurus taurus aside. We used insertion/deletion (indel) polymorphisms, which have the advantage of being simple and easily automatable, since in most cases, the variable loci are biallelic. We studied 94 indels, with a difference of two or more base pairs, in DNA pools of 60 Zebu and 60 taurine animals. A set of 22 indels with heterozygosity greater than 0.3 were selected and used to construct two multiplex PCRs. On the basis of the allelic frequency of these indels, the probability of random match was calculated to be 1.12 x 10(-8) for B. taurus indicus and 1.60 x 10(-6) for B. taurus taurus. Moreover, we estimated that an analysis would cost less than US$15.00 per animal. Thus, this system (MULTINDELS-BOV) is perfectly suited for building large genetic databases and offering viable prospects of a national system for cattle traceback DNA in Brazil. PMID:25501139

  2. Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane

    Science.gov (United States)

    Metcalfe, Cushla J.; Oliveira, Sarah G.; Gaiarsa, Jonas W.; Aitken, Karen S.; Carneiro, Monalisa S.; Zatti, Fernanda; Van Sluys, Marie-Anne

    2015-01-01

    Sugarcane is the main source of the world’s sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum. PMID:26093024

  3. The genetic diversity and evolution of field pea (Pisum studied by high throughput retrotransposon based insertion polymorphism (RBIP marker analysis

    Directory of Open Access Journals (Sweden)

    Smýkal Petr

    2010-02-01

    Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture

  4. Fast high-throughput screening of angiotensin-converting enzyme insertion/deletion polymorphism by variable programmed electric field strength-based microchip electrophoresis.

    Science.gov (United States)

    Sun, Yucheng; Kim, Su-Kang; Zhang, Peng; Woo, Nain; Kang, Seong Ho

    2016-08-15

    An insertion (I)/deletion (D) polymorphism in angiotensin-converting enzyme (ACE) has been associated with susceptibility to various diseases in numerous studies. Traditionally, slab gel electrophoresis (SGE) after polymerase chain reaction (PCR) has been used to genotype this ACE I/D polymorphism. In this study, single- and multi-channel microchip electrophoresis (ME) methods based on variable programmed electric field strength (PEFS) (i.e., low constant, high constant, (+)/(-) staircase, and random electric field strengths) were developed for fast high-throughput screening of this specific polymorphism. The optimum PEFS conditions were set as 470V/cm for 0-9s, 129V/cm for 9-13s, 470V/cm for 13-13.9s, 294V/cm for 13.9-16s, and 470V/cm for 16-20s for single-channel ME, and 615V/cm for 0-22.5s, 231V/cm for 22.5-28.5s, and 615V/cm for 28.5-40s for multi-channel ME, respectively. In the multi-channel PEFS-ME, target ACE I/D polymorphism DNA fragments (D=190bp and I=490bp) were identified within 25s without loss of resolving power, which was ∼300 times faster than conventional SGE. In addition, PCR products of the ACE gene from human blood samples were detected after only 10 cycles by multi-channel PEFS-ME, but not by SGE. This parallel detection multichannel-based PEFS-ME method offers a powerful tool for fast high-throughput ACE I/D polymorphism screening with high sensitivity. PMID:27322633

  5. Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

    OpenAIRE

    Riju, Aykkal; Chandrasekar, Arumugam; Arunachalam, Vadivel

    2007-01-01

    The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into co...

  6. Genotyping of the 19-bp insertion/deletion polymorphism in the 5' flank of beta-hydroxylase gene by dissociation analysis of allele-specific PCR products

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2005-01-01

    The 19-bp insertion/deletion polymorphism in the 5' flank of the dopamine beta-hydroxylase (DBH) gene has been associated with psychiatric disorders. We have developed a simple, reliable and inexpensive closed-tube assay for genotyping of this polymorphism based upon T(m) determination of amplified...

  7. Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm.

    Science.gov (United States)

    Riju, Aykkal; Chandrasekar, Arumugam; Arunachalam, Vadivel

    2007-01-01

    The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies. PMID:21670789

  8. A rapid detection method for PAI-1 promoter insertion/deletion polymorphism (4G/5G

    Directory of Open Access Journals (Sweden)

    Annichino-Bizzacchi Joyce M.

    1998-01-01

    Full Text Available Plasminogen activator inhibitor-1 (PAI-1 is an important inhibitor of fibrinolysis, and increased levels of PAI-1 are associated with atheroma and myocardial infarction. A common 4G/5G insertion/deletion polymorphism located in the promoter region of PAI-1 gene has been described associated with PAI-1 activity in plasma levels. Genotyping of this polymorphism is commonly conducted with an allele-specific oligonucleotide melting technique. In the present study, we describe a quick, easy method for genotyping 4G/5G polymorphism in the promoter region of the PAI-1 gene.

  9. Insertion/deletion polymorphism of the ACE gene and adherence to ACE inhibitors

    NARCIS (Netherlands)

    H. Schelleman (Hedi); O.H. Klungel (Olaf); C.M. van Duijn (Cock); J.C.M. Witteman (Jacqueline); A. Hofman (Albert); A. de Boer (Anthonius); B.H.Ch. Stricker (Bruno)

    2005-01-01

    textabstractAims: We investigated whether the insertion/deletion (I/D) polymorphism of the ACE gene modified the adherence to ACE inhibitors as measured by the discontinuation of an ACE inhibitor, or addition of another antihypertensive drug. Methods: This was a cohort study among 239 subjects who s

  10. Insertion/deletion polymorphism of the ACE gene and adherence to ACE inhibitors

    NARCIS (Netherlands)

    Schelleman, H; Klungel, O H; van Duijn, C M; Witteman, J C M; Hofman, A; de Boer, A; Stricker, B H Ch

    2005-01-01

    AIMS: We investigated whether the insertion/deletion (I/D) polymorphism of the ACE gene modified the adherence to ACE inhibitors as measured by the discontinuation of an ACE inhibitor, or addition of another antihypertensive drug. METHODS: This was a cohort study among 239 subjects who started ACE i

  11. Alkali metal insertion into TiO2 polymorphs for battery applications

    Czech Academy of Sciences Publication Activity Database

    Zukalová, Markéta; Pitňa Lásková, Barbora; Kavan, Ladislav

    Dubai: EMN Dubai, 2016. s. 13-14. [EMN Dubai Meeting. Energy Materials Nanotechnology . 01.04.2016-04.04.2016, Dubai] R&D Projects: GA ČR GA15-06511S Institutional support: RVO:61388955 Keywords : TiO2 polymorphs * alkali metal insertion * LTO Subject RIV: CG - Electrochemistry

  12. Variations in angiotensin-converting enzyme gene insertion/deletion polymorphism in Indian populations of different ethnic origins

    Indian Academy of Sciences (India)

    M A Qadar Pasha; Amjad P Khan; Ratan Kumar; Rekh B Ram; Surinder K Grover; Kaushal K Srivastava; William Selvamurthy; Samir K Brahmachari

    2002-02-01

    The pattern of angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism in the Indian population is poorly known. In order to determine the status of the polymorphism, young unrelated male army recruits were screened. The population had cultural and linguistic differences and lived in an environment that varied significantly from one region to another. Analysis of the genotype, showed higher frequency of the insertion allele in four of the five groups i.e. I allele frequency was significantly higher ( < 0.05) in Dogras, Assamese and Kumaonese. The deletion allele frequency was comparatively higher in the fifth group that belonged to Punjab. A correlation was observed between the genotype and enzyme activity. Involvement of a single D allele in the genotype enhanced the activity up to 37.56 ± 3.13%. The results suggested ethnic heterogeneity with a significant gene cline with higher insertion allele frequency. Such population-based data on various polymorphisms can ultimately be exploited in pharmacogenomics.

  13. Association of an HLA-G 14-bp Insertion/Deletion polymorphism with high HBV replication in chronic hepatitis.

    Science.gov (United States)

    Laaribi, A B; Zidi, I; Hannachi, N; Ben Yahia, H; Chaouch, H; Bortolotti, D; Zidi, N; Letaief, A; Yacoub, S; Boudabous, A; Rizzo, R; Boukadida, J

    2015-10-01

    Identification of an HLA-G 14-bp Insertion/Deletion (Ins/Del) polymorphism at the 3' untranslated region of HLA-G revealed its importance in HLA-G mRNA stability and HLA-G protein level variation. We evaluated the association between the HLA-G 14-bp Ins/Del polymorphism in patients with chronic Hepatitis B virus (HBV) infection in a case-control study. Genomic DNA was extracted from 263 patients with chronic HBV hepatitis and 246 control subjects and was examined for the HLA-G 14-bp Ins/Del polymorphism by PCR. The polymorphic variants were genotyped in chronic HBV seropositive cases stratified according to HBV DNA levels, fibrosis stages and in a control population. There was no statistical significant association between the 14-bp Ins/Del polymorphism and increased susceptibility to HBV infection neither for alleles (P = 0.09) nor for genotypes (P = 0.18). The stratification of HBV patients based on HBV DNA levels revealed an association between the 14-bp Ins/Del polymorphism and an enhanced HBV activity with high HBV DNA levels. In particular, the Ins allele was significantly associated with high HBV DNA levels (P = 0.0024, OR = 1.71, 95% CI 1.2-2.4). The genotype Ins/Ins was associated with a 2.5-fold (95% CI, 1.29-4.88) increased risk of susceptibility to high HBV replication compared with the Del/Del and Ins/Del genotypes. This susceptibility is linked to the presence of two Ins alleles. No association was observed between the 14-bp Ins/Del polymorphism and fibrosis stage of HBV infection. We observed an association between the 14-bp Ins/Del polymorphism and high HBV replication characterized by high HBV DNA levels in chronic HBV patients. These results suggest a potential prognostic value for disease outcome evaluation. PMID:25619305

  14. Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site.

    Science.gov (United States)

    Monden, Yuki; Fujii, Nobuyuki; Yamaguchi, Kentaro; Ikeo, Kazuho; Nakazawa, Yoshiko; Waki, Takamitsu; Hirashima, Keita; Uchimura, Yosuke; Tahara, Makoto

    2014-05-01

    Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. PMID:25072847

  15. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

    DEFF Research Database (Denmark)

    Pereira, Rui; Pereira, Vania; Gomes, Iva;

    2012-01-01

    Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of......-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian....... Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers....

  16. Angiotensin-converting enzyme gene (ACE) insertion/deletion polymorphism in Mexican populations.

    Science.gov (United States)

    Vargas-Alarcón, Gilberto; Hernández-Pacheco, Guadalupe; Rodríguez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Pavón, Zinnia; Fragoso, José Manuel; Juarez-Cedillo, Teresa; Villarreal-Garza, Cynthia; Granados, Julio

    2003-12-01

    The angiotensin-converting enzyme gene (ACE) insertion/deletion polymorphism was determined in 211 Mexican healthy individuals belonging to different Mexican ethnic groups (98 Mestizos, 64 Teenek, and 49 Nahuas). ACE polymorphism differed among Mexicans with a high frequency of the D allele and the D/D genotype in Mexican Mestizos. The D/D genotype was absent in Teenek and present in only one Nahua individual (2.0%). When comparisons were made, we observed that Caucasian, African, and Asian populations presented the highest frequencies of the D allele, whereas Amerindian (Teenek and Pima) and Australian Aboriginals showed the highest frequencies of the I allele. The distribution of I/D genotype was heterogeneous in all populations: Australian Aboriginals presented the lowest frequency (4.9%), whereas Nahuas presented the highest (73.4%). The present study shows the frequencies of a polymorphism not analyzed previously in Mexican populations and establishes that this polymorphism distinguishes the Amerindian populations of other groups. On the other hand, since ACE alleles have been associated with genetic susceptibility to developing cardiovascular diseases and hypertension, knowledge of the distribution of these alleles could help to define the true significance of ACE polymorphism as a genetic susceptibility marker in the Amerindian populations. PMID:15018037

  17. Instrumentation for continuous array genotyping of short insertion/deletion polymorphisms

    Science.gov (United States)

    Rusch, Terry L.; Dickinson, William; Che, Jian; Fieweger, Kim; Chudyk, Jon; Doktycz, Mitchel J.; Yu, Adong; Weber, James L.

    2003-07-01

    Methods for DNA testing are abundant, however, there is still a need for lower cost, higher-throughput genotyping. Much emphasis has been placed on short tandem repeat polymorphisms (STRPs) and single nucleotide polymorphisms (SNPs). Another important polymorphism is the diallelic short insertion/deletion (indel). Our laboratory is using a continuous reel of 384 well arrays on polypropylene tape to genotype indel polymorphisms. The reel of arrays allows low cost automation, and an opportunity to decrease reaction volumes. The diallelic indel is typed by tagging allele-specific PCR primers with a FAM or JOE molecular beacon uniprimer. Our most recent array pattern contains wells that hold a maximum of 1.1 microliters with reaction volumes of 800 nanoliters. Because micro array tape (microtape) is unique, commercial equipment is not yet available. A series of instruments were developed in-house to handle the tape. A pipetting instrument was developed to deliver the DNA samples or other reagents. A solenoid micro-valve aspirating and jetting unit was developed for dispensing a common reaction mix. The arrays are sealed with commercially available microtiter plate seal material prior to polymerase chain reaction (PCR) within a custom built waterbath thermal cycler. The arrays are scanned using an epi-fluorescence detection unit designed to read FAM and JOE fluorescent dyes. The detector uses an argon ion laser for excitation and two photomultiplier tubes (PMTs) for detection. The resulting images are processed using custom software.

  18. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina.

    Science.gov (United States)

    Trigiano, Robert N; Wadl, Phillip A; Dean, Deborah; Hadziabdic, Denita; Scheffler, Brian E; Runge, Fabian; Telle, Sabine; Thines, Marco; Ristaino, Jean; Spring, Otmar

    2012-01-01

    Ten polymorphic microsatellite loci for the obligate biotrophic, oomycete pathogen of tobacco, Peronospora tabacina, were identified from a small insert genomic library enriched for GT motifs. Eighty-five percent of the 162 loci identified were composed of dinucleotide repeats, whereas only 4% and 11% were tri-and tetra-nucleotide repeats respectively. About 82% of all the microsatellites were perfect and within the library; only about 7% of the loci were duplicated. Primers were designed for 63 loci; 10 loci were polymorphic, 19 were monomorphic and 34 either failed to amplify or produced ambiguous/inconsistent results. The 10 polymorphic loci were characterized with 44 isolates of P. tabacina collected from tobacco plants growing in Europe, the Near East and North and South America. The number of alleles per locus was either three or four with a mean of 3.2, and the mean number of genotypes per locus was 3.6. Observed heterozygosity was 0.32-0.95, whereas expected heterozygosity was 0.44-0.69 for these loci. All loci except PT054 did not conform to the Hardy-Weinberg distribution. Polymorphic information content (PIC) for the loci was 0.35-0.69 with a mean of 0.50. These microsatellite loci provide a set of markers sufficient to perform genetic diversity and population studies of P. tabacina, and possibly other species of Peronospora. PMID:22241615

  19. ACE Gene Insertion/Deletion Polymorphism and Type-2 Diabetic Nephropathy in Eastern Indian Population

    Directory of Open Access Journals (Sweden)

    Mithun Sikdar

    2013-02-01

    Full Text Available Background: Nephropathy is one of the major complications among the patients having type 1 or long term Type 2 diabetes and there are various studies that suggest its genetic predisposition. A 287 bp insertion/deletion (I/D polymorphism of the gene encoding angiotensin-I converting enzyme (ACE is shown to have association with diabetic nephropathy. Aim: To identify the association of ACE I/D polymorphism with subjects having diabetic nephropathy.Materials and methods: The present study examined the prevalence of ACE insertion/deletion polymorphism among 91 Bengali individuals from Eastern India. Among them 30 individuals belong to diabetic nephropathy (DN, 30 individuals having diabetes without nephropathy (DM and 31 normal controls. The DNA samples of studied subjects were genotyped using polymerase chain reaction.Results: The frequency of DD, ID and II genotypes in patients having diabetic nephropathy (DN were found to be 26.7%, 53.3% and 20.0% respectively, whereas the same for only diabetic patients (DM were 26.7%, 50.0%and 23.3% respectively. The frequencies of the same genotypes among the normal controls were found to be 9.68%, 64.5% and 25.8% respectively. Inspite of a slightly higher odds ratio for DD genotypes among DM and DN subjects in comparison to the normal group the distribution pattern of DD genotype did not differ significantly within the three cohorts. The frequency of D allele among the patients having diabetic nephropathy, diabetic without nephropathy and control subjects was found to be 0.533, 0.516 and 0.420 respectively. This distribution pattern also did not differ significantly (χ2=1.859, p>0.05.Conclusion: No significant association was found between ACE I/D polymorphism with diabetic nephropathy patients from Bengali caste population.

  20. Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions

    Directory of Open Access Journals (Sweden)

    Blouin Christian

    2007-11-01

    Full Text Available Abstract Background In protein evolution, the mechanism of the emergence of novel protein domain is still an open question. The incremental growth of protein variable regions, which was produced by stochastic insertions, has the potential to generate large and complex sub-structures. In this study, a deterministic methodology is proposed to reconstruct phylogenies from protein structures, and to infer insertion events in protein evolution. The analysis was performed on a broad range of SCOP domain families. Results Phylogenies were reconstructed from protein 3D structural data. The phylogenetic trees were used to infer ancestral structures with a consensus method. From these ancestral reconstructions, 42.7% of the observed insertions are nested insertions, which locate in previous insert regions. The average size of inserts tends to increase with the insert rank or total number of insertions in the variable regions. We found that the structures of some nested inserts show complex or even domain-like fold patterns with helices, strands and loops. Furthermore, a basal level of structural innovation was found in inserts which displayed a significant structural similarity exclusively to themselves. The β-Lactamase/D-ala carboxypeptidase domain family is provided as an example to illustrate the inference of insertion events, and how the incremental growth of a variable region is capable to generate novel structural patterns. Conclusion Using 3D data, we proposed a method to reconstruct phylogenies. We applied the method to reconstruct the sequences of insertion events leading to the emergence of potentially novel structural elements within existing protein domains. The results suggest that structural innovation is possible via the stochastic process of insertions and rapid evolution within variable regions where inserts tend to be nested. We also demonstrate that the structure-based phylogeny enables the study of new questions relating to the

  1. Genotyping of the 19-bp insertion/deletion polymorphism in the 5' flank of beta-hydroxylase gene by dissociation analysis of allele-specific PCR products

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2005-01-01

    The 19-bp insertion/deletion polymorphism in the 5' flank of the dopamine beta-hydroxylase (DBH) gene has been associated with psychiatric disorders. We have developed a simple, reliable and inexpensive closed-tube assay for genotyping of this polymorphism based upon T(m) determination of amplified...... DNA fragments. Mistyping of heterozygote samples due to preferential allele amplification was prevented by use of an optimized concentration of Mg(2+), addition of dimethyl sulfoxide and annealing/extension at an appropriate temperature. Comparison of results achieved by the closed-tube assay and a...... conventional approach based upon agarose gel electrophoresis of amplified fragments revealed complete concordance between the two procedures. The insights obtained in this study may be utilized to develop assays based upon dissociation analysis of PCR products for genotyping of other insertion...

  2. Association of NOD1 (CARD4) insertion/deletion polymorphism with susceptibility to IBD: A meta-analysis

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM: To find evidences about whether NOD1/CARD4 insertion/deletion polymorphism is associated with inflammatory bowel disease by meta-analysis. METHODS: We surveyed the studies on the association of NOD1/CARD4 insertion/deletion polymorphism with inflammatory bowel disease in PubMed. Meta-analysis was performed for genotypes GG/T vs T/T, GG/GG vs T/T, GG/T + GG/GG vs T/T, GG/GG vs T/T + GG/T, and GG allele vs T allele in a fixed/random effect model. RESULTS: We identified 8 studies (6439 cases and 4798 cont...

  3. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms.

    Directory of Open Access Journals (Sweden)

    Rita Rebollo

    2011-09-01

    Full Text Available The "arms race" relationship between transposable elements (TEs and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE-induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness.

  4. Positive Selection on a Regulatory Insertion-Deletion Polymorphism in FADS2 Influences Apparent Endogenous Synthesis of Arachidonic Acid.

    Science.gov (United States)

    Kothapalli, Kumar S D; Ye, Kaixiong; Gadgil, Maithili S; Carlson, Susan E; O'Brien, Kimberly O; Zhang, Ji Yao; Park, Hui Gyu; Ojukwu, Kinsley; Zou, James; Hyon, Stephanie S; Joshi, Kalpana S; Gu, Zhenglong; Keinan, Alon; Brenna, J Thomas

    2016-07-01

    Long chain polyunsaturated fatty acids (LCPUFA) are bioactive components of membrane phospholipids and serve as substrates for signaling molecules. LCPUFA can be obtained directly from animal foods or synthesized endogenously from 18 carbon precursors via the FADS2 coded enzyme. Vegans rely almost exclusively on endogenous synthesis to generate LCPUFA and we hypothesized that an adaptive genetic polymorphism would confer advantage. The rs66698963 polymorphism, a 22-bp insertion-deletion within FADS2, is associated with basal FADS1 expression, and coordinated induction of FADS1 and FADS2 in vitro. Here, we determined rs66698963 genotype frequencies from 234 individuals of a primarily vegetarian Indian population and 311 individuals from the US. A much higher I/I genotype frequency was found in Indians (68%) than in the US (18%). Analysis using 1000 Genomes Project data confirmed our observation, revealing a global I/I genotype of 70% in South Asians, 53% in Africans, 29% in East Asians, and 17% in Europeans. Tests based on population divergence, site frequency spectrum, and long-range haplotype consistently point to positive selection encompassing rs66698963 in South Asian, African, and some East Asian populations. Basal plasma phospholipid arachidonic acid (ARA) status was 8% greater in I/I compared with D/D individuals. The biochemical pathway product-precursor difference, ARA minus linoleic acid, was 31% and 13% greater for I/I and I/D compared with D/D, respectively. This study is consistent with previous in vitro data suggesting that the insertion allele enhances n-6 LCPUFA synthesis and may confer an adaptive advantage in South Asians because of the traditional plant-based diet practice. PMID:27188529

  5. Association of kinase insert domain-containing receptor (KDR) gene polymorphism/ haplotypes with recurrent spontaneous abortion and genetic structure

    Science.gov (United States)

    Shahsavari, Shiva; Noormohammadi, Zahra; Zare Karizi, Shohreh

    2015-01-01

    Background: Recurrent spontaneous abortion is one of the diseases that can lead to physical, psychological, and, economical problems for both individuals and society. Recently a few numbers of genetic polymorphisms in kinase insert domain-containing receptor (KDR) gene are examined that can endanger the life of the fetus in pregnant women. Objective: The risk of KDR gene polymorphisms was investigated in Iranian women with idiopathic recurrent spontaneous abortion (RSA). Materials and Methods: A case controlled study was performed. One hundred idiopathic recurrent spontaneous abortion patients with at least two consecutive pregnancy losses before 20 weeks of gestational age with normal karyotypes were included in the study. Also, 100 healthy women with at least one natural pregnancy were studied as control group. Two functional SNPs located in KDR gene; rs1870377 (Q472H), and rs2305948 (V297I) as well as one tag SNP in the intron region (rs6838752) were genotyped by using PCR based restriction fragment length polymorphism (PCR-RFLP) technique. Haplotype frequency was determined for these three SNPs’ genotypes. Analysis of genetic STRUCTURE and K means clustering were performed to study genetic variation. Results: Functional SNP (rs1870377) was highly linked to tag SNP (rs6838752) (D´ value=0. 214; χ2 = 16.44, p<0. 001). K means clustering showed that k = 8 as the best fit for the optimal number of genetic subgroups in our studied materials. This result was in agreement with Neighbor Joining cluster analysis. Conclusion: In our study, the allele and genotype frequencies were not associated with RSA between patient and control individuals. Inconsistent results in different populations with different allele frequencies among RSA patients and controls may be due to ethnic variation and used sample size. PMID:27141535

  6. A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla

    Directory of Open Access Journals (Sweden)

    Crouau-Roy Brigitte

    2008-10-01

    Full Text Available Abstract Background The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia. There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields. Results and discussion We report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants. This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species. When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion. The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region. Conclusion The gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.

  7. Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform

    OpenAIRE

    Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

    2014-01-01

    In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LI...

  8. An angiotensin I-converting enzyme insertion/deletion polymorphism is associated with Pakistani asthmatic cases and controls

    Indian Academy of Sciences (India)

    NUSRAT SABA; OSMAN YUSUF; SADIA REHMAN; SAEEDA MUNIR; SHEERAZ AHMAD; ATIKA MANSOOR; GHAZALA K RAJA

    2016-09-01

    Asthma is a chronic disease due to inflammation of the airways of lungs that is clinically characterized by variablesymptoms including wheezing, coughing and shortness of breath. Angiotensin I-converting enzyme (ACE) plays a majorrole in fibrous tissue formation and is highly expressed in lungs. The main aim of this research work was to study the roleof ACE insertion/deletion (I/D) polymorphism, rs4646994, in asthma in Pakistani patients. A total of 854 subjects,including 333 asthma patients and 521 ethnically matched controls, were studied. The ACE (I/D) polymorphism wasgenotyped using polymerase chain reaction (PCR). Chi-square, Fisher’s exact and Hardy–Weinberg equilibrium testswere used to compare groups. Homozygous insertion genotype II ($p \\ lt 0.0001$, $OR=3.38$) and insertion allele (I) wassignificantly more frequent in Pakistani asthmatics than in healthy controls ($p=0.0007, OR=1.40$). The ID genotype ($p \\lt 0.0001$, $OR=0.43$) and the deletion allele (D) were associated with protection of disease in Pakistani patients($p=0.0007, OR=0.71$). These data suggest the involvement of ACE I/D polymorphism in asthma risk in the Pakistanipopulation. This marker may be an important indication in the molecular mechanism of asthma and can become a usefultool in risk assessment and help in designing strategy to combat disease.

  9. A new insertion/deletion fragment polymorphism of inhibin-α gene associated with follicular cysts in Large White sows.

    Science.gov (United States)

    Li, Wanhong; Chen, Shuxiong; Li, Hongjiao; Liu, Zhuo; Zhao, Yun; Chen, Lu; Zhou, Xu; Li, Chunjing

    2016-05-18

    Ovarian follicular cysts are anovulatory follicular structures that lead to infertility. Hormones play key roles in the formation and persistence of cysts. Inhibins are heterodimeric gonadal glycoprotein hormones that belong to the transforming growth factor-β superfamily. These hormones suppress the secretion of follicle-stimulating hormone. In this report, partial fragment of inhibin-α (INHA) subunit gene of Large White pig was detected from the genomic DNA by polymerase chain reaction. The sequence showed a 283 bp fragment insertion/deletion (I/D) polymorphism in INHA subunit gene. A total of 49 Large White sows with cystic follicles and 152 normal sows were screened for this polymorphism. The relationship of INHA I/D polymorphisms with follicular cysts was investigated. The distribution of I/D was significantly different between cystic and normal sows, thereby suggesting that the INHA subunit gene might be a potential biological marker for breeding programs in pig. PMID:26521695

  10. Insertion/deletion polymorphism in intron 16 of ACE gene in idiopathic recurrent spontaneous abortion: case-control study, systematic review and meta-analysis.

    Science.gov (United States)

    Pereza, Nina; Ostojić, Saša; Zdravčević, Matea; Volk, Marija; Kapović, Miljenko; Peterlin, Borut

    2016-02-01

    The insertion/deletion (I/D) polymorphism in intron 16 of the angiotensin I-converting enzyme gene (ACE) has been extensively studied as a predisposing factor for idiopathic recurrent spontaneous abortion (IRSA). A case-control study including 149 women with ≥3 spontaneous abortions and 149 controls was performed to test the association of ACE I/D polymorphism with IRSA. A systematic review was conducted of previous case-control studies, with strict selection criteria for meta-analyses. We also aimed to evaluate the potential differences in summary estimates between studies defining IRSA as ≥2 and ≥3 spontaneous abortions. Genotyping was performed by PCR, and systematic review conducted using PubMed and Scopus. There was no association of the polymorphism with IRSA in Slovenian women. Sixteen case-control studies, showing substantial differences regarding IRSA definition and selection criteria for women were identified. Meta-analysis was performed and included four studies defining IRSA as ≥2 spontaneous abortions and the current study, which defined IRSA as ≥3 spontaneous abortions. Based on random effects model, meta-analysis conducted on 1192 patients and 736 controls showed no association with IRSA under dominant(DD+IDvsII) and recessive(DDvsID+II) genetic models. Well-designed studies are needed to evaluate the role of ACE I/D polymorphism in IRSA defined as ≥3 spontaneous abortions. PMID:26673102

  11. Can the occurrence of rare insertion/deletion polymor-phisms in human mtDNA beverified from phylogeny?

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Due to its specific characteristics, such as maternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occurring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distinguished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the fragment with the indel is the best and the most reliable way for confirmation.

  12. Mechanism of alkali metal insertion into TiO2 polymorphs

    Czech Academy of Sciences Publication Activity Database

    Zukalová, Markéta; Lásková, Barbora; Kavan, Ladislav

    Toulouse: Phantoms Foundation, 2015. s. 139-139. [TNT2015. Trends in Nanotechnology /16./. 07.09.2015-11.09.2015, Toulouse] R&D Projects: GA ČR GA13-07724S; GA ČR(CZ) GA15-06511S Institutional support: RVO:61388955 Keywords : TiO2 * alkali metal insertion Subject RIV: CG - Electrochemistry

  13. Automated Genotyping of Biobank Samples by Multiplex Amplification of Insertion/Deletion Polymorphisms

    OpenAIRE

    Lucy Mathot; Elin Falk-Sörqvist; Lotte Moens; Marie Allen; Tobias Sjöblom; Mats Nilsson

    2012-01-01

    The genomic revolution in oncology will entail mutational analyses of vast numbers of patient-matched tumor and normal tissue samples. This has meant an increased risk of patient sample mix up due to manual handling. Therefore, scalable genotyping and sample identification procedures are essential to pathology biobanks. We have developed an efficient alternative to traditional genotyping methods suited for automated analysis. By targeting 53 prevalent deletions and insertions found in human p...

  14. Association between sHLA-G and HLA-G 14-bp deletion/insertion polymorphism in Crohn's disease.

    Science.gov (United States)

    Zidi, Inès; Ben Yahia, Hamza; Bortolotti, Daria; Mouelhi, Leila; Laaribi, Ahmed Baligh; Ayadi, Shema; Zidi, Nour; Houissa, Fatma; Debbech, Radhouane; Boudabous, Abdellatif; Najjar, Taoufik; Di Luca, Dario; Rizzo, Roberta

    2015-06-01

    The aim of this study was to evaluate the association between the HLA-G 14-bp deletion/insertion (Del/Ins) polymorphism and soluble (s) HLA-G production in patients with Crohn's disease (CD). We analyzed also the sHLA-G molecules by ELISA and western blot in plasma samples. Among unselected patients, the 14-bp Del/Ins polymorphism was not significantly associated with increased CD risk neither for alleles (P = 0.371) nor for genotypes (P = 0.625). However, a significant association was reported between the 14-bp Del/Ins polymorphism and CD, in particular in young-onset CD patients for alleles [P = 0.020, odds ratio (OR) = 2.438, 95% confidence interval (CI): 1.13-5.25] but not with adult-onset CD patients. A significant association was reported concerning the genotype Ins/Ins for young-onset CD patients (P = 0.029, OR = 3.257, 95% CI: 1.08-9.77). We observed also a significant increase in sHLA-G measured by ELISA in CD patients compared to controls (P = 0.002). The 14-bp Del/Del and 14-bp Del/Ins genotypes are the high HLA-G producers. Among sHLA-G(positive) patients, 43% of subjects present dimers of HLA-G. The presence of dimers seems to be related to the advanced stages of the disease. The 14-bp Del/Ins polymorphism is associated with an increased risk of CD particularly in young-onset CD patients and controls sHLA-G plasma levels. Dimers of sHLA-G are frequent in advanced disease stages. The above findings indicate that the genetic 14-bp Del/Ins polymorphism in exon 8 of the HLA-G gene is associated with the risk of CD and suggest a role for sHLA-G as a prognostic marker for progressive disease. PMID:25577194

  15. The association between the HLA-G 14-bp insertion/deletion polymorphism and type 1 diabetes.

    Science.gov (United States)

    Silva, H P V; Ururahy, M A G; Souza, K S C; Loureiro, M B; Oliveira, Y M C; Oliveira, G H M; Luchessi, A D; Carvalho, K T C; Freitas, J C O C; Donadi, E A; Hirata, R D C; Almeida, M G; Arrais, R F; Hirata, M H; Rezende, A A

    2016-01-01

    Type 1 diabetes (T1D) is a multifactorial disease that has a strong genetic component. The HLA-G is a nonclassical HLA class I locus that is associated with immunomodulatory functions, including downregulation of innate and adaptive immune responses and induction of immune tolerance. However, there is currently limited information about the involvement of HLA-G in T1D susceptibility. This case-control study aims to investigate the T1D susceptibility association of alleles and genotypes of a widely investigated 14-bp insertion/deletion polymorphism in the HLA-G and to provide further evidence of the frequency distribution of class II HLA-DR-DQ-risk genotypes in T1D children and adolescents in the Brazilian population. The deletion allele and the homozygous deletion genotype are associated with susceptibility to T1D and the insertion allele and the heterozygous deletion/insertion genotype are associated with protection from T1D. We also confirm that genetic susceptibility to T1D is associated with the DRB1*03:01-DQA1*05:01-DQB1*02:01 and DRB1*04-DQA1*03:01-DQB1*03:02 haplotypes in Brazilian northeast region. The DR3-DQ2/DR4-DQ8 genotype conferred the highest detected risk for T1D. Our results identify a novel association of the 14-bp deletion allele and the homozygous deletion genotype with T1D development and provide additional evidence of the importance of HLA class II heterozygous DR3-DQ2/DR4-DQ8 genotype in T1D susceptibility. PMID:26492519

  16. Mortality in patients with hypertension on angiotensin-I converting enzyme (ACE)-inhibitor treatment is influenced by the ACE insertion/deletion polymorphism

    NARCIS (Netherlands)

    Bleumink, GS; Schut, Anna F.C.; Sturkenboom, MCJM; van Duijn, CM; Deckers, JW; Hofman, A; Kingma, J. Herre; Witteman, JCM; Stricker, BHC

    2005-01-01

    Background The response to angiotensin-l converting enzyme (ACE)-inhibitor therapy is highly variable. Residual ACE activity during treatment, potentially modified by the ACE insertion/deletion (I/D) polymorphism, may explain part of this variability. We studied the possible interaction between ACE-

  17. Cache Replacement Policy Using Map-based Adaptive Insertion

    OpenAIRE

    Ishii,Yasuo; Inaba, Mary; Hiraki, Kei

    2010-01-01

    International audience In this paper, we propose a map-based adaptive insertion policy (MAIP) for a novel cache replacement. The MAIP estimates the data reuse possibility on the basis of data reuse history. To track data reuse history, the MAIP employs a bitmap data structure, which we call memory access map. The memory access map holds all memory accessed locations in a fixed sized memory area to detect the data reuse. It can cover a large memory area that is compared to the size of a lar...

  18. Association between insertion/deletion polymorphism in angiotensin-converting enzyme gene and acute lung injury/acute respiratory distress syndrome: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Matsuda Akihisa

    2012-08-01

    Full Text Available Abstract Background A previous meta-analysis reported a positive association between an insertion/deletion (I/D polymorphism in the angiotensin-converting enzyme gene (ACE and the risk of acute lung injury (ALI/acute respiratory distress syndrome (ARDS. Here, we updated this meta-analysis and additionally assessed the association of this polymorphism with ALI/ARDS mortality. Methods We searched electronic databases through October 2011 for the terms “angiotensin-converting enzyme gene”, “acute lung injury”, and “acute respiratory distress syndrome,” and reviewed all studies that reported the relationship of the I/D polymorphism in ACE with ALI/ARDS in humans. Seven studies met the inclusion criteria, comprising 532 ALI/ARDS patients, 3032 healthy controls, and 1432 patients without ALI/ARDS. We used three genetic models: the allele, dominant, and recessive models. Results The ACE I/D polymorphism was not associated with susceptibility to ALI/ARDS for any genetic model. However, the ACE I/D polymorphism was associated with the mortality risk of ALI/ARDS in Asian subjects ( Pallele Pdominant = 0.001, Precessive = 0.002. This finding remained significant after correction for multiple comparisons. Conclusions There is a possible association between the ACE I/D polymorphism genotype and the mortality risk of ALI/ARDS in Asians.

  19. Distribution of Angiotensin-1 Converting Enzyme Insertion/Deletion and α-Actinin-3 Codon 577 Polymorphisms in Turkish Male Soccer Players.

    Science.gov (United States)

    Ulucan, Korkut; Sercan, Canan; Biyikli, Türker

    2015-01-01

    Angiotensin-1 converting enzyme (ACE) gene and α-actinin-3 (ACTN3) gene polymorphisms are considered to be the most important candidate genes for genetic predisposition to human athletic performance. In the present study, we aimed to analyze the distribution of ACE and ACTN3 polymorphisms for the first time in male Turkish soccer players. In this prospective study, our cohort consisted of 25 professional players, all with Turkish ancestry. Polymerase chain reaction (PCR)-restriction length polymorphism was used for the characterization of the genotype of ACTN3 and single PCR for ACE. For ACE genotype, 16%, 44%, and 40% of the players had insertion/insertion (II), insertion/deletion (ID), and deletion/deletion (DD) genotypes, respectively, whereas 20% had XX, 36% had RX, and 44% had RR genotypes for ACTN3. When we examined the allelic percentages, for ACE, D allele was recorded as 62 and I as 38, and for ACTN3, R allele was 62 and X was 38. Our results were in agreement with the previous reports, indicating the presence of ACTN3 D and ACE X allele in soccer players. We suggest that ACE and ACTN3 genotypes are important biomarkers for genetic counseling for the individuals who are prone to be successful soccer players. PMID:26448692

  20. The Angiotensin Converting Enzyme Insertion/Deletion Polymorphism Modifies Exercise-Induced Muscle Metabolism.

    Directory of Open Access Journals (Sweden)

    David Vaughan

    Full Text Available A silencer region (I-allele within intron 16 of the gene for the regulator of vascular perfusion, angiotensin-converting enzyme (ACE, is implicated in phenotypic variation of aerobic fitness and the development of type II diabetes. We hypothesised that the reportedly lower aerobic performance in non-carriers compared to carriers of the ACE I-allele, i.e. ACE-DD vs. ACE-ID/ACE-II genotype, is associated with alterations in activity-induced glucose metabolism and capillarisation in exercise muscle.Fifty-three, not-specifically trained Caucasian men carried out a one-legged bout of cycling exercise to exhaustion and/or participated in a marathon, the aim being to identify and validate genotype effects on exercise metabolism. Respiratory exchange ratio (RER, serum glucose and lipid concentration, glycogen, and metabolite content in vastus lateralis muscle based on ultra-performance lipid chromatography-mass spectrometry (UPLC-MS, were assessed before and after the cycling exercise in thirty-three participants. Serum metabolites were measured in forty subjects that completed the marathon. Genotype effects were assessed post-hoc.Cycling exercise reduced muscle glycogen concentration and this tended to be affected by the ACE I-allele (p = 0.09. The ACE-DD genotype showed a lower maximal RER and a selective increase in serum glucose concentration after exercise compared to ACE-ID and ACE-II genotypes (+24% vs. +2% and -3%, respectively. Major metabolites of mitochondrial metabolism (i.e. phosphoenol pyruvate, nicotinamide adenine dinucleotide phosphate, L-Aspartic acid, glutathione were selectively affected in vastus lateralis muscle by exercise in the ACE-DD genotype. Capillary-to-fibre ratio was 24%-lower in the ACE-DD genotype. Individuals with the ACE-DD genotype demonstrated an abnormal increase in serum glucose to 7.7 mM after the marathon.The observations imply a genetically modulated role for ACE in control of glucose import and oxidation in

  1. Effects of Laser Peripheral Iridotomy in Subgroups of Primary Angle Closure Based on Iris Insertion

    OpenAIRE

    Sung-Cheol Yun; Ji Wook Hong; Kyung Rim Sung; Jin Young Lee

    2015-01-01

    Purpose. To investigate the effect of laser peripheral iridotomy (LPI) in subgroups of primary angle closure based on iris insertion configuration. Methods. Anterior segment optical coherence tomography (AS-OCT) images were obtained before and two weeks after LPI. Qualitative classification of angle closure eyes according to iris insertion (basal insertion group (BG) and nonbasal insertion group (NBG)) was performed. Anterior chamber depth (ACD), lens vault (LV), iris curvature, iris area, ir...

  2. The -271 G>A polymorphism of kinase insert domain-containing receptor gene regulates its transcription level in patients with non-small cell lung cancer

    International Nuclear Information System (INIS)

    Kinase insert domain-containing receptor (KDR) plays a critical role in the metastasis of cancer and is used as a molecular target in cancer therapy. We investigated the characteristics of the -271 G>A polymorphism of the KDR gene to gain information that may benefit the development of individualized therapies for patients with non-small cell lung cancer (NSCLC). The -271 G>A polymorphism of the KDR gene in 106 lung cancer patients and 203 healthy control individuals was analyzed by polymerase chain reaction (PCR) and DNA sequencing methods. Real-time quantitative PCR and immunohistochemical methods were used to evaluate KDR mRNA and protein expression levels, respectively, in frozen tumor specimens. The -271 G>A polymorphism was associated with the mRNA expression level of the KDR gene in tumor tissues (t = 2.178, P = 0.032, independent samples t-test). Compared with the AG/GG genotype, the AA genotype was associated with higher KDR mRNA expression in tumor tissues. We found no relationship between the genotype and the KDR protein expression level and no significant difference in the distribution of the KDR gene polymorphism genotypes between lung cancer patients and the control group (χ2 = 1.269, P = 0.264, Fisher's exact test). This study is the first to show that the -271 G>A polymorphism of the KDR gene may be a functional polymorphism related to the regulation of gene transcription. These findings may have important implications for therapies targeting KDR in patients with NSCLC

  3. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

    Directory of Open Access Journals (Sweden)

    Voorrips Roeland E

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. Results We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. Conclusion QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at

  4. Angiotensin-converting enzyme insertion/deletion polymorphism does not influence the restenosis rate after coronary stent implantation

    OpenAIRE

    Ferrari, Markus; Mudra, Harald; Grip, Lars; Voudris, Vassilis; Schächinger, Volker; de Jaegere, Peter; Rieber, Johannes; Hausmann, Dirk; Rothman, Martin; Koschyk, Dietmar H.; Figulla, Hans R

    2002-01-01

    Background. Experimental studies have shown an activation of the angiotensin-converting enzyme (ACE) system as a response to endothelial injury. Recent publications have elucidated the hypothesis that the ACE gene polymorphism may influence the level of late luminal loss after coronary stent implantation. It is still unclear whether the polymorphism of the angiotensin gene is a major predictor of the extent of neointimal hyperplasia. In this multicenter study, we therefore tested the relation...

  5. In vitro microbiological evaluation of polyvinyl alcohol-based ocular inserts of Ciprofloxacin hydrochloride

    Directory of Open Access Journals (Sweden)

    Balasubramaniam J

    2006-01-01

    Full Text Available Soluble inserts of ciprofloxacin hydrochloride using high and low molecular weight polyvinyl alcohol alone and in various combinations were fabricated by a casting technique. The in vitro drug release from the prepared inserts was studied using a continuous flow-through model, developed in our laboratory. The antimicrobial efficacies of the prepared inserts against common ocular pathogens, viz., Staphylococcus aureus ATCC 25923 and Pseudomonas aeruginosa ATCC 27853, were evaluated using a modified in vitro microbiological model. Ciprofloxacin hydrochloride release from the inserts followed matrix diffusion kinetics showing an anomalous release mechanism (erosion-controlled based on the calculated release exponent (n values. Drug release increased with an increase in the proportion of high molecular weight polyvinyl alcohol in the inserts. The in vitro microbiological model demonstrated the effectiveness of the inserts against the two microorganisms. Further, the results of the in vitro release studies correlated well with that of the antimicrobial studies.

  6. Association between angiotensin converting enzyme gene insertion/deletion polymorphism and renal scar risk in children vesicoureteral reflex: a reappraise meta-analysis

    Science.gov (United States)

    Ai, Jin-Wei; Zeng, Xian-Tao; Liu, Ying; Fu, Yu; Liu, Tong-Zu; Pei, Bin

    2016-01-01

    Vesicoureteral reflex(VUR) is a common disease in children. Some studies indicated that the angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism associated with the renal scar in VUR, but not all researchers agreed with it. To clarify the effect of ACE I/D polymorphism on renal scar risk in children with VUR, we performed the present meta-analysis. PubMed, CNKI, CBM, and Embase databases were searched for studies that examined the relationship between ACE I/D polymorphism and renal scar risk in children with VUR. The Stata 12.0 software was used for statistical analyses. 11 case-control studies with 1,032 VUR patients were analyzed. The results showed that the DD genotype and D allele were associated with renal scar risk in overall VUR patients, DD vs. DI + II: OR = 1.61, 95% CI = 1.04–2.49, P = 0.03; DD vs. II: OR = 1.78, 95% CI = 1.20–2.65, P < 0.01; D vs. I: OR = 1.38, 95% CI = 1.02–1.86, P = 0.04. Similar results were revealed in Turks, but not in Caucasians and Asians. Our meta-analysis indicated that the ACE DD genotype may increase the risk of renal scar in children with VUR. PMID:27506878

  7. Association of deletion allele of insertion/deletion polymorphism in α2B adrenoceptor gene and hypertension with or without type 2 diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Tayel SI

    2012-12-01

    Full Text Available Safaa I Tayel,1 Heba F Khader,1 Nesreen G El-Helbawy,1 Waleed A Ibrahim21Department of Medical Biochemistry, 2Department of Cardiology, Faculty of Medicine, Menoufiya University, Shebin Elkom, EgyptBackground: Vascular α2B-adrenoreceptors have the potential to increase blood pressure by mediating vasoconstriction. A nine-nucleotide deletion in the receptor enhances vasoconstriction and exacerbates hypertension. The aim of this study was to determine the association between insertion/deletion (I/D polymorphism of the α2B-adrenoceptor and hypertension with and without diabetes.Methods: The study was carried out in 35 hypertensive patients with diabetes, 35 hypertensive patients without diabetes, and 30 healthy controls. Clinical data, blood lipid profiles, and I/D polymorphism were assessed.Results: Hypertensive patients were significantly older, with significantly higher systolic/diastolic blood pressures and worse plasma lipid profiles than controls. The frequency of the DD genotype was significantly higher in both hypertensive patients with (77.14%, P < 0.01 and without (71.43%, P < 0.05 diabetes versus controls (40%. Also, the D allele was significantly more common in both hypertensive patients with (84.29%, P < 0.01 and without (80%, P < 0.05 diabetes versus controls (58.33%. Hypertensive patients were more likely to have the D allele with (3.83-fold and without (2.85-fold diabetes. The frequencies of the DD genotype and the D allele were not significantly (P > 0.05 different between the patient groups. The DD genotype was associated with significantly lower high-density lipoprotein (P = 0.001 and significantly higher low-density lipoprotein (P = 0.017 levels versus the II and ID genotypes in the hypertensive group without diabetes.Conclusion: A marked and statistically significant association between DD genotype and D allele of I/D polymorphism in the α2B-adrenoceptor gene may be a risk factor for hypertension ± diabetes. The association

  8. Developmental validation of an X-Insertion/Deletion polymorphism panel and application in HAN population of China

    Science.gov (United States)

    Zhang, Suhua; Sun, Kuan; Bian, Yingnan; Zhao, Qi; Wang, Zheng; Ji, Chaoneng; Li, Chengtao

    2015-01-01

    InDels are short-length polymorphisms characterized by low mutation rates, high inter-population diversity, short amplicon strategy and simplicity of laboratory analysis. This work describes the developmental validation of an X-InDels panel amplifying 18 bi-allelic markers and Amelogenin in one single PCR system. Developmental validation indicated that this novel panel was reproducible, accurate, sensitive and robust for forensic application. Sensitivity testing of the panel was such that a full profile was obtainable even with 125 pg of human DNA with intra-locus balance above 70%. Specificity testing was demonstrated by the lack of cross-reactivity with a variety of commonly encountered animal species and microorganisms. For the stability testing in cases of PCR inhibition, full profiles have been obtained with hematin (≤1000 μM) and humic acid (≤150 ng/μL). For the forensic investigation of the 18 X-InDels in the HAN population of China, no locus deviated from the Hardy–Weinberg equilibrium and linkage disequilibrium. Since they are independent from each other, the CDPfemale was 0.999999726 and CDPmale was 0.999934223. The forensic parameters suggested that this X-Indel panel is polymorphic and informative, which provides valuable X-linked information for deficient relationship cases where autosomal markers are uninformative. PMID:26655948

  9. iMembrane: homology-based membrane-insertion of proteins

    OpenAIRE

    Kelm, Sebastian; Shi, Jiye; Deane, Charlotte M

    2009-01-01

    Summary: iMembrane is a homology-based method, which predicts a membrane protein's position within a lipid bilayer. It projects the results of coarse-grained molecular dynamics simulations onto any membrane protein structure or sequence provided by the user. iMembrane is simple to use and is currently the only computational method allowing the rapid prediction of a membrane protein's lipid bilayer insertion. Bilayer insertion data are essential in the accurate structural modelling of membrane...

  10. Tendon insertion at the base of the proximal phalanx of the hallux: surgical implications.

    Science.gov (United States)

    Becerro de Bengoa Vallejo, Ricardo; Losa Iglesias, Marta Elena; Jules, Kevin T

    2012-01-01

    Hallux valgus, limitus, and rigidus are conditions affecting the first metatarsophalangeal joint that can be treated by arthroplasty. Excessive arthroplasty can compromise the insertion of the tendons at the base of the proximal phalanx of the hallux, leading to first metatarsophalangeal joint plantarflexion weakness, cock-up toe deformity, and altered forefoot loading. The present study investigated the anatomic length of insertion of the medial and lateral flexor hallucis brevis, extensor hallucis brevis, abductor hallucis, and adductor hallucis tendons into the base of the hallux proximal phalanx and the amount of bone that can be safely resected without compromising the insertional limits. A total of 43 specimens (22 right and 21 left) from 22 embalmed cadavers (11 male and 11 female) were dissected. The insertion lengths of the 5 tendons were measured, along with the dimensions of the hallux proximal phalanx. No statistically significant differences were found in any proximal phalanx measurements or tendon insertion lengths according to side (p > .05). Significant differences were found between the genders in most dimensions of the hallux proximal phalanx (p hallux proximal phalanx resection should not exceed 3 mm. Resection of the tendons is ensured by removal of more than 7.88 mm and 9.37 mm in females and males, respectively. When performing hallux arthroplasty of the first metatarsophalangeal joint, we recommend calculating the length of the tendon insertions, instead of the length of the hallux proximal phalanx. PMID:22789484

  11. Iron based Li-ion insertion materials for battery applications

    OpenAIRE

    Blidberg, Andreas

    2016-01-01

    Li-ion batteries are currently the most efficient technology available for electrochemical energy storage. The technology has revolutionized the portable electronics market and is becoming a corner stone for large scale applications, such as electric vehicles. It is therefore important to develop materials in which the energy storage relies on abundant redox active species, such as iron. In this thesis, new iron based electrode materials for positive electrodes in Li-ion batteries were invest...

  12. A functional 12T-insertion polymorphism in the ATP1A1 promoter confers decreased susceptibility to hypertension in a male Sardinian population.

    Directory of Open Access Journals (Sweden)

    Victoria L Herrera

    Full Text Available Identification of susceptibility genes for essential hypertension in humans has been a challenge due to its multifactorial pathogenesis complicated by gene-gene and gene-environment interactions, developmental programing and sex specific differences. These concurrent features make identification of causal hypertension susceptibility genes with a single approach difficult, thus requiring multiple lines of evidence involving genetic, biochemical and biological experimentation to establish causal functional mutations. Here we report experimental evidence encompassing genetic, biochemical and in vivo modeling that altogether support ATP1A1 as a hypertension susceptibility gene in males in Sardinia, Italy. ATP1A1 encodes the α1Na,K-ATPase isoform, the sole sodium pump in vascular endothelial and renal tubular epithelial cells. DNA-sequencing detected a 12-nucleotide long thymidine (12T insertion(ins/deletion(del polymorphism within a poly-T sequence (38T vs 26T in the ATP1A1 5'-regulatory region associated with hypertension in a male Sardinian population. The 12T-insertion allele confers decreased susceptibility to hypertension (P = 0.035; OR = 0.50 [0.28-0.93] accounting for 12.1 mmHg decrease in systolic BP (P = 0.02 and 6.6 mmHg in diastolic BP (P = 0.046. The ATP1A1 promoter containing the 12T-insertion exhibited decreased transcriptional activity in in vitro reporter-assay systems, indicating decreased α1Na,K-ATPase expression with the 12T-insertion, compared with the 12T-deletion ATP1A1 promoter. To test the effects of decreased α1Na,K-ATPase expression on blood pressure, we measured blood pressure by radiotelemetry in three month-old, highly inbred heterozygous knockout ATP1A1+/- male mice with resultant 58% reduction in ATP1A1 protein levels. Male ATP1A1+/- mice showed significantly lower blood pressure (P < 0.03 than age-matched male wild-type littermate controls. Concordantly, lower ATP1A1 expression is expected to lower Na

  13. Screening of mitochondrial mutations and insertion-deletion polymorphism in gestational diabetes mellitus in the Asian Indian population.

    Science.gov (United States)

    Khan, Imran Ali; Shaik, Noor Ahmad; Pasupuleti, Nagarjuna; Chava, Srinivas; Jahan, Parveen; Hasan, Qurratulain; Rao, Pragna

    2015-05-01

    In this study we scrutinized the association between the A8344G/A3243G mutations and a 9-bp deletion polymorphism with gestational diabetes mellitus (GDM) in an Asian Indian population. The A3243G mutation in the mitochondrial tRNA(Leu(UUR)) causes mitochondrial encephalopathy myopathy, lactic acidosis, and stroke-like episodes (MELAS), while the A8344G mutation in tRNA(Lys) causes myoclonus epilepsy with ragged red fibers (MERRF). We screened 140 pregnant women diagnosed with GDM and 140 non-GDM participants for these mutations by PCR-RFLP analysis. Both A3243G and A8344G were associated with GDM (A3243: OR-3.667, 95% CI = 1.001-13.43, p = 0.03; A8344G: OR-11.00, 95% CI = 0.6026-200.8, p = 0.04). Mitochondrial DNA mutations contribute to the development of GDM. Our results conclude that mitochondrial mutations are associated with the GDM women in our population. Thus it is important to screen other mitochondrial mutations in the GDM women. PMID:25972744

  14. Prevalence of angiotensin converting enzyme (ACE gene insertion/deletion polymorphism in South Indian population with hypertension and chronic kidney disease

    Directory of Open Access Journals (Sweden)

    R Shanmuganathan

    2015-01-01

    Full Text Available Context: Chronic Kidney Disease (CKD is associated with a high risk of developing further severe complications such as, cardiovascular disease and eventually End Stage Renal Disease (ESRD leading to death. Hypertension plays a key role in the progression of renal failure and is also a chief risk factor for the occurrence of End Stage Renal Disease (ESRD. Aim: This study investigates the possible association of insertion (I and deletion (D polymorphism of ACE gene in patients of Chronic Kidney Disease (CKD with and without hypertension (HT. Settings and Design: Total 120 participants with 30 members in each group (Control, HT, CKD and CKD-HT were chosen followed by informed consent. Materials and Methods: Blood samples were collected and subjected to biochemical analyses and nested PCR amplification was performed to genotype the DNA, for ACE I/D using specific primers. Statistical Analysis: Statistical analyses were performed using SPSS version 13. Allele and genotypic frequency was calculated by direct gene counting method. Comparison of the different genotypes was done by using Chi square test. Odd′s ratios were calculated with a 95% confidence interval limit. Results: The ACE genotype were distributed as II, 27 (90%; DD, 2 (6.67% and ID, 1 (3.33% in control, II, 1 (3.33%; DD, 5 (16.67% and ID, 24 (80% in HT, II, 4 (13.33%; DD, 24 (80% and ID, 2 (6.67% in CKD and II, 0 (0%; DD, 2 (6.67% and ID, 28 (93.33% in CKD-HT group. Conclusions: D allele of ACE gene confers a greater role in genetic variations underlying CKD and hypertension. This result suggest that CKD patients should be offered analysis for defects in ACE I/D polymorphisms, especially if they are hypertensive.

  15. Habitat-based polymorphism is common in stream fishes.

    Science.gov (United States)

    Senay, Caroline; Boisclair, Daniel; Peres-Neto, Pedro R

    2015-01-01

    Morphological differences (size and shape) across habitats are common in lake fish where differences relate to two dominant contrasting habitats: the pelagic and littoral habitat. Repeated occurrence of littoral and pelagic morphs across multiple populations of several lake fish species has been considered as important evidence that polymorphism is adaptive in these systems. It has been suggested that these habitat-based polymorphic differences are due to the temporal stability of the differences between littoral and pelagic habitats. Although streams are spatially heterogeneous, they are also more temporally dynamic than lakes and it is still an open question whether streams provide the environmental conditions that promote habitat-based polymorphism. We tested whether fish from riffle, run and pool habitats, respectively, differed consistently in their morphology. Our test compared patterns of morphological variation (size and shape) in 10 fish species from the three stream habitat types in 36 separate streams distributed across three watersheds. For most species, body size and shape (after controlling for body size) differed across riffle, run and pool habitats. Unlike many lake species, the nature of these differences was not consistent across species, possibly because these species use these habitat types in different ways. Our results suggest that habitat-based polymorphism is an important feature also in stream fishes despite the fact that streams are temporally variable in contrast to lake systems. Future research is required to assess whether the patterns of habitat-based polymorphism encountered in streams have a genetic basis or they are simply the result of within generation phenotypic plasticity. PMID:25041645

  16. Effects of Laser Peripheral Iridotomy in Subgroups of Primary Angle Closure Based on Iris Insertion

    Directory of Open Access Journals (Sweden)

    Sung-Cheol Yun

    2015-01-01

    Full Text Available Purpose. To investigate the effect of laser peripheral iridotomy (LPI in subgroups of primary angle closure based on iris insertion configuration. Methods. Anterior segment optical coherence tomography (AS-OCT images were obtained before and two weeks after LPI. Qualitative classification of angle closure eyes according to iris insertion (basal insertion group (BG and nonbasal insertion group (NBG was performed. Anterior chamber depth (ACD, lens vault (LV, iris curvature, iris area, iris thickness (IT750, and angle opening distance (AOD750 750 microns from scleral spur were calculated. Uni- and multivariate regression analysis was carried out to evaluate factors associated with AOD750 before and after LPI. Results. Ninety-two eyes of 92 subjects were categorized as NBG (39 eyes or BG (53 eyes. The mean change after LPI was not significantly different between two groups in all parameters. In both groups, AOD750 was affected by ACD (p<0.001, p=0.044 before LPI. AOD750 was affected by LV (p=0.012 in NBG, but by ACD (p<0.001 and IT750 (p=0.039 in BG after LPI. Conclusions. The outcomes of LPI are not significantly different between angle closure subgroups with different iris insertions. However, factors affecting AOD750 show differences between two subgroups after LPI.

  17. A comparative study of insertion/deletion polymorphisms applied among Southwest, South and Northwest Chinese populations using Investigator(®) DIPplex.

    Science.gov (United States)

    Wang, Li; Lv, Meili; Zaumsegel, Daniel; Zhang, Lushun; Liu, Fengji; Xiang, Jihua; Li, Jun; Schneider, Peter M; Liang, Weibo; Zhang, Lin

    2016-03-01

    The low mutation rates, short amplicon sizes and length variation characteristics of biallelic insertion/deletion polymorphisms (INDELs) are features that allow combining advantages of both STR and SNP markers for genetic analysis. The Qiagen Investigator DIPplex kit contains 30 biallelic autosomal INDELs plus Amelogenin for forensic personal identification and parentage testing. This study compares general performances, forensic and population data collected in 7 Chinese ethnic populations (Han, Tibetan, Yi, Zhuang, Dong, Miao and Uyghur) from three areas (Southwest, South and Northwest) of China by DIPplex kit. There were no significant departures from Hardy-Weinberg equilibrium (HWE) of the 30 markers in all the tested populations after Bonferroni correction. The combined matching probabilities ranged from 1.4273×10(-10) for the Dong minority to 1.2817×10(-12) for the Uyghur minority. The combined power of paternity exclusion was from 0.9854 to 0.9968. All pairwise genetic differences (FST) between the seven ethnic groups were less than 0.05, and the results of STRUCTURE analysis did not indicate the presence of substructures suggesting genetic similarity among the populations in these three areas. The DIPplex kit can be used as a good additional tool for forensic personal identification in these three areas of China. PMID:26656953

  18. Does the Angiotensin-converting enzyme (ACE gene insertion/deletion polymorphism modify the response to ACE inhibitor therapy? – A systematic review

    Directory of Open Access Journals (Sweden)

    Perna Annalisa

    2005-10-01

    Full Text Available Abstract Background Pharmacogenetic testing to individualize ACE inhibitor therapy remains controversial. We conducted a systematic review to assess the effect modification of the insertion/deletion (I/D polymorphism of the ACE gene on any outcome in patients treated with ACE inhibitors for cardiovascular and/or renal disease. Methods Our systematic review involved searching six electronic databases, then contacting the investigators (and pharmaceutical industry representatives responsible for the creation of these databases. Two reviewers independently selected relevant randomized, placebo-controlled trials and abstracted from each study details on characteristics and quality. Results Eleven studies met our inclusion criteria. Despite repeated efforts to contact authors, only four of the eleven studies provided sufficient data to quantify the effect modification by genotypes. We observed a trend towards better response to ACE inhibitors in Caucasian DD carriers compared to II carriers, in terms of blood pressure, proteinuria, glomerular filtration rate, ACE activity and progression to end-stage renal failure. Pooling of the results was inappropriate, due to heterogeneity in ethnicity, clinical domains and outcomes. Conclusion Lack of sufficient genetic data from the reviewed studies precluded drawing any convincing conclusions. Better reporting of genetic data are needed to confirm our preliminary observations concerning better response to ACE inhibitors among Caucasian DD carriers as compared to II carriers.

  19. Insertion stability of poly(ethylene glycol)-cholesteryl-based lipid anchors in liposome membranes.

    Science.gov (United States)

    Molnar, Daniel; Linders, Jürgen; Mayer, Christian; Schubert, Rolf

    2016-06-01

    Liposomes consist of a hydrophilic core surrounded by a phospholipid (PL) bilayer. In human blood, the half-life of such artificial vesicles is limited. To prolong their stability in the circulation, liposomal bilayers can be modified by inserting poly(ethylene glycol) (PEG) molecules using either PL or sterols as membrane anchors. This establishes a hydrophilic steric barrier, reducing the adsorption of serum proteins, recognition and elimination by cells of the immune system. In addition, targeting ligands (such as antibodies) are frequently coupled to the distal end of the PEG chains to direct the vesicles (then called 'immuno-liposomes') to specific cell types, such as tumor cells. To our knowledge, experiments on the stability of ligand anchoring have so far only been conducted with PL-based PEGs and not with sterol-based PEGs after insertion via the sterol-based post-insertion technique (SPIT). Therefore, our study examines the insertion stability of PEG-cholesteryl ester (Chol-PEG) molecules with PEG chains of 1000, 1500 and 2000Da molecular mass which have been inserted into the membranes of liposomes using SPIT. For this study we used different acceptor media and multiple analytical techniques, including pulsed-field-gradient nuclear magnetic resonance (PFG-NMR), free-flow electrophoresis, size exclusion chromatography and ultracentrifugation. The obtained data consistently showed that a higher molar mass of PEG chains positively correlates with higher release from the liposome membranes. Furthermore, we could detect and quantify the migration of Chol-PEG molecules from radioactively double-labeled surface-modified liposomes to negatively charged acceptor liposomes via free-flow electrophoresis. Insertion of Chol-PEG molecules into the membrane of preformed liposomes using SPIT is an essential step for the functionalization of liposomes with the aim of specific targeting. For the first time, we present a kinetic analysis of this insertion process using PFG

  20. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila.

    Science.gov (United States)

    Hacker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A

    2003-06-24

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are P element-based and can therefore not be combined with the use of P elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-P element transposons. An enhanced yellow fluorescent protein-marked piggyBac-based mutator element was mobilized by a piggyBac specific transposase source expressed from a Hermes-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798 piggyBac insertions on FRT bearing third chromosomes of which 9% have sustained a putatively piggyBac-related lethal hit. The FRTs present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no P element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the Drosophila genome. The system is Drosophila nonspecific and potentially applicable in a broad spectrum of nonmodel organisms. PMID:12802016

  1. Dopaminergic Genetic Polymorphisms Predict Rule-based Category Learning.

    Science.gov (United States)

    Byrne, Kaileigh A; Davis, Tyler; Worthy, Darrell A

    2016-07-01

    Dopaminergic genes play an important role in cognitive function. DRD2 and DARPP-32 dopamine receptor gene polymorphisms affect striatal dopamine binding potential, and the Val158Met single-nucleotide polymorphism of the COMT gene moderates dopamine availability in the pFC. Our study assesses the role of these gene polymorphisms on performance in two rule-based category learning tasks. Participants completed unidimensional and conjunctive rule-based tasks. In the unidimensional task, a rule along a single stimulus dimension can be used to distinguish category members. In contrast, a conjunctive rule utilizes a combination of two dimensions to distinguish category members. DRD2 C957T TT homozygotes outperformed C allele carriers on both tasks, and DARPP-32 AA homozygotes outperformed G allele carriers on both tasks. However, we found an interaction between COMT and task type where Met allele carriers outperformed Val homozygotes in the conjunctive rule task, but both groups performed equally well in the unidimensional task. Thus, striatal dopamine binding may play a critical role in both types of rule-based tasks, whereas prefrontal dopamine binding is important for learning more complex conjunctive rule tasks. Modeling results suggest that striatal dopaminergic genes influence selective attention processes whereas cortical genes mediate the ability to update complex rule representations. PMID:26918585

  2. -141C insertion/deletion polymorphism of the dopamine D2 receptor gene is associated with schizophrenia in Chinese Han population: Evidence from an ethnic group-specific meta-analysis.

    Science.gov (United States)

    Zhao, Xiaofeng; Huang, Yinglin; Chen, Kaiyuan; Li, Duolu; Han, Chao; Kan, Quancheng

    2016-09-01

    Accumulate evidence has implicated dopamine D2 receptor gene polymorphisms in the etiology of schizophrenia. A single nucleotide polymorphism, -141C insertion/deletion (Ins/Del) (rs1799732), in the promoter region of the dopamine D2 receptor gene has been linked to schizophrenia; however, the data are inconclusive. This study investigated whether the -141C polymorphism is associated with the risk of schizophrenia in different ethnic groups by performing a meta-analysis. A total of 24 case-control studies examining the association between -141C Ins/Del polymorphism and schizophrenia were identified according to established inclusion criteria. Significant association was revealed between -141C Ins/Del polymorphism and schizophrenia risk in dominant genetic model (Ins/Ins + Ins/Del versus Del/Del) (odds ratio = 0.33, 95% confidence interval = 0.14-0.81, z = 2.41, P = 0.02) in Chinese Han but not in Caucasian, Japanese or India populations. Our results indicate that -141C Ins/Del polymorphism might be a susceptibility factor for schizophrenia in Chinese Han population. PMID:26346037

  3. Lyophilized Chitosan/xanthan Polyelectrolyte Complex Based Mucoadhesive Inserts for Nasal Delivery of Promethazine Hydrochloride

    OpenAIRE

    G Dehghan, Mohamed Hassan; Marzuka, Marzuka

    2014-01-01

    The objective of this investigation was the development of chitosan/xanthan polyelectrolyte complex based mucoadhesive nasal insert of promethazine hydrochloride a drug used in the treatment of motion sickness. A 32 factorial design was applied for preparing chitosan/xanthan polyelectrolyte complex and to study the effect of independent variables i.e. concentration of xanthan [X1] and concentration of chitosan [X2] on various responses i.e. viscosity of polyelectrolyte complex solution, water...

  4. Nasal inserts containing ondansetron hydrochloride based on Chitosan-gellan gum polyelectrolyte complex: In vitro-in vivo studies.

    Science.gov (United States)

    Sonje, Ashish G; Mahajan, Hitendra S

    2016-07-01

    The aim of this study was the production of ondansetron hydrochloride loaded lyophilized insert for nasal delivery. The nasal insert was prepared by the lyophilisation technique using Chitosan-gellan gum polyelectrolyte complex as the polymer matrix. The ondansetron loaded inserts were evaluated with respect to water uptake, bioadhesion, drug release kinetic study, ex vivo permeation study, and in vivo study. Lyophilised nasal inserts were characterized by differential scanning calorimetry, scanning electron microscopy and X-ray diffraction study. Scanning electron microscopy confirmed the porous sponge like structure of inserts whereas release kinetic model revealed that drug release followed non-fickian case II diffusion. The nasal delivery showed improved bioavailability as compared to oral delivery. In conclusion, the ondansetron containing nasal inserts based on Chitosan-gellan gum complex with potential muco-adhesive potential is suitable for nasal delivery. PMID:27127060

  5. Alu Insertions and Genetic Diversity: A Preliminary Investigation by an Undergraduate Bioinformatics Class

    Science.gov (United States)

    Elwess, Nancy L.; Duprey, Stephen L.; Harney, Lindesay A.; Langman, Jessie E.; Marino, Tara C.; Martinez, Carolina; McKeon, Lauren L.; Moss, Chantel I. E.; Myrie, Sasha S.; Taylor, Luke Ryan

    2008-01-01

    "Alu"-insertion polymorphisms were used by an undergraduate Bioinformatics class to study how these insertion sites could be the basis for an investigation in human population genetics. Based on the students' investigation, both allele and genotype "Alu" frequencies were determined for African-American and Japanese populations as well as a…

  6. Postoperative Astigmatic Outcomes Based on the Haptic Axis of Intraocular Lenses Inserted in Cataract Surgery

    OpenAIRE

    Kim, In-Tae; Park, Hae-Young Lopilly; Kim, Hyun-Seung

    2011-01-01

    Purpose This study was conducted to compare post-operative astigmatic outcomes of two groups, with-the-rule (WTR) and against-the-rule (ATR) astigmatism patients, according to the haptic axis of intraocular lenses (IOLs) inserted in cataract surgery. Methods Seventy-two eyes with WTR astigmatism and 79 eyes with ATR astigmatism had cataract surgery through a clear corneal temporal incision. These two groups of eyes were then each divided into 2 groups based on whether the haptic axis of the i...

  7. Insertion/deletion polymorphism of the angiotensin-converting enzyme gene and the risk of hypertension among residents of two cities, South-South Nigeria

    Directory of Open Access Journals (Sweden)

    Mary Esien Kooffreh

    2014-01-01

    Conclusion: The I/D polymorphism of the angiotensin-converting enzyme gene was a risk factor for hypertension in the sample population of Calabar and Uyo. This research will form baseline information for subsequent molecular studies in this population.

  8. Distribution of Angiotensin-1 Converting Enzyme Insertion/Deletion and α-Actinin-3 Codon 577 Polymorphisms in Turkish Male Soccer Players

    OpenAIRE

    Korkut Ulucan; Canan Sercan; Türker Biyikli

    2015-01-01

    Angiotensin-1 converting enzyme (ACE) gene and α-actinin-3 (ACTN3) gene polymorphisms are considered to be the most important candidate genes for genetic predisposition to human athletic performance. In the present study, we aimed to analyze the distribution of ACE and ACTN3 polymorphisms for the first time in male Turkish soccer players. In this prospective study, our cohort consisted of 25 professional players, all with Turkish ancestry. Polymerase chain reaction (PCR)-restriction length po...

  9. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    Science.gov (United States)

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries. PMID:19935925

  10. A novel perfusion-based method for cochlear implant electrode insertion

    OpenAIRE

    Kale, Sushrut; Cervantes, Vanessa M.; Wu, Mailing R.; Pisano, Dominic V.; Sheth, Nakul; Olson, Elizabeth S.

    2014-01-01

    A cochlear implant (CI) restores partial hearing to profoundly deaf individuals. CI electrodes are inserted manually in the cochlea and surgeons rely on tactile feedback from the implant to determine when to stop the insertion. This manual insertion method results in a large degree of variability in surgical outcomes and intra-cochlear trauma. Additionally, implants often span only the basal turn. In the present study we report on the development of a new method to assist CI electrode inserti...

  11. Calibration and stability of a SiPM-based simultaneous PET/MR insert

    International Nuclear Information System (INIS)

    On behalf of the HYPER Image project, a Silicon photomultiplier (SiPM) based preclinical PET insert for a commercial human 3 T MRI scanner was built. In this contribution we report on the stability of imaging performance of the PET scanner and MR hardness and compatibility. From data sets that were acquired during the last 7 months we extracted SiPM gain values and their annual drift, the mean energy resolution and the energy resolution drift, spatial resolution and spatial resolution drift, and photo peak position and their annual drift. Further, a point source and a hot rod phantom was imaged fully simultaneously with the MRI scanner and the PET scanner. No interference between either modality was observed

  12. Calibration and stability of a SiPM-based simultaneous PET/MR insert

    Energy Technology Data Exchange (ETDEWEB)

    Lerche, Christoph W., E-mail: christoph.lerche@philips.com [Philips Research, Europe, Eindhoven (Netherlands); Mackewn, Jane [Kings College London (United Kingdom); Goldschmidt, Benjamin [Philips Research, Europe, Eindhoven (Netherlands); RWTH University Aachen (Germany); Salomon, Andre; Gebbhardt, Pierre; Weissler, Bjoern; Ayres, Richard [Philips Research, Europe Eindhoven (Netherlands); Kings College London (United Kingdom); Marsden, Paul [Kings College London (United Kingdom); Schulz, Volkmar [Philips Research, Europe, Eindhoven (Netherlands); RWTH University Aachen (Germany)

    2013-02-21

    On behalf of the HYPER Image project, a Silicon photomultiplier (SiPM) based preclinical PET insert for a commercial human 3 T MRI scanner was built. In this contribution we report on the stability of imaging performance of the PET scanner and MR hardness and compatibility. From data sets that were acquired during the last 7 months we extracted SiPM gain values and their annual drift, the mean energy resolution and the energy resolution drift, spatial resolution and spatial resolution drift, and photo peak position and their annual drift. Further, a point source and a hot rod phantom was imaged fully simultaneously with the MRI scanner and the PET scanner. No interference between either modality was observed.

  13. Two single base polymorphisms in introns 41 and 16 of the NF1 gene

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Ming Hong; Upadhyaya, M. [Univ. of Wales, Cardiff (United Kingdom)

    1995-04-24

    We have characterized two intragenic polymorphisms in the neurofibromatosis type 1 (NF1) gene by direct sequencing of PCR products. The variants for these polymorphisms were initially detected on Hydrolink gels. One of the polymorphisms involves a G to A transition in intron 41 at the 28th base upstream of exon 42 with an observed {open_quote}G{close_quote}/{open_quote}A{close_quote} heterozygosity of 0.42. The other polymorphism is a T to C transition in intron 16 at the 16th base upstream of exon 17 with an observed {open_quote}T{close_quote}/{open_quote}C{close_quote} heterozygosity of 0.09. In combination with other documented polymorphisms in the NF1 gene, these variants should assist in genetic analysis of NF1 families. 24 refs., 3 figs.

  14. A complex insertion/deletion polymorphism in the compositionally biased region of the ZFHX3 gene in patients with coronary heart disease in a Chinese population

    OpenAIRE

    Sun, Shunchang; Zhang, Wenwu; Chen, Xi; Peng, Yunsheng; Chen, Qunrong

    2015-01-01

    Coronary heart disease (CHD) is a leading cause of morbidity and mortality around the world and has both genetic and environmental precipitants. Genetic factors are significant in determining the level of risk factors in individuals. Variants in ZFHX3 gene are associated with atrial fibrillation in individuals of European ancestry. The aim of this study was to analyze the polymorphisms in the compositionally biased region of the ZFHX3 gene in patients with coronary heart disease in a Chinese ...

  15. A Six-nucleotide insertion-deletion polymorphism in the CASP8 promoter is associated with risk of coal workers' pneumoconiosis

    Energy Technology Data Exchange (ETDEWEB)

    Ni, C.H.; Ye, Y.; Wang, M.L.; Qian, H.Y.; Song, Z.F.; Jia, X.M.; Zhou, J.W. [Nanjing Medical University, Nanjing (China). Dept. of Occupational Medicine

    2009-07-01

    Coal workers' pneumoconiosis (CWP) is a chronic interstitial lung disease with a complex etiology that can occur after cumulative dust exposure. A case-control study was conducted to test the hypothesis that single-nucleotide polymorphisms (SNP) within CASPASE-8 (CASP8) promoter involved in resolution of inflammatory processes modulate the risk of CWP development. The study population consisted of 619 underground coal miners in the 5 coal mines of Xuzhou Mining Business Group Co. Ltd., China, of whom 315 were diagnosed with CWP. The association study between CASP8-652 6N ins/del polymorphism with CWP by multiple logistic regression analysis showed a significant association of the genotype del/del with CWP compared with to ins/ins genotypes, and showed that the risk was significantly higher for stage I CWP. Further analysis showed that in subjects with the del/del genotype there was significantly increased risk for CWP occurrence among younger individuals (66 yr) or those with longer duration dust exposure (26 yr). These findings suggested that CASP8-652 6N ins/del polymorphism may contribute to the genetic susceptibility for CWP development.

  16. WISP1 Polymorphisms Contribute to Platinum-Based Chemotherapy Toxicity in Lung Cancer Patients

    OpenAIRE

    Juan Chen; Jiye Yin; Xiangping Li; Ying Wang; Yi Zheng; Chenyue Qian; Ling Xiao; Ting Zou; Zhan Wang; Junyan Liu; Wei Zhang; Honghao Zhou; Zhaoqian Liu

    2014-01-01

    Platinum-based chemotherapy toxicity is always one of the serious problems from which lung cancer patients suffer. The genetic polymorphism of WISP1 was revealed to be associated with susceptibility and platinum-based chemotherapy response in our previous studies. In this study, we aimed to investigate the relationship of WISP1 genetic polymorphisms with platinum-based chemotherapy toxicity in lung cancer patients. A total of 412 lung cancer patients were enrolled in this study, and 28 polym...

  17. A novel perfusion-based method for cochlear implant electrode insertion.

    Science.gov (United States)

    Kale, Sushrut; Cervantes, Vanessa M; Wu, Mailing R; Pisano, Dominic V; Sheth, Nakul; Olson, Elizabeth S

    2014-08-01

    A cochlear implant (CI) restores partial hearing to profoundly deaf individuals. CI electrodes are inserted manually in the cochlea and surgeons rely on tactile feedback from the implant to determine when to stop the insertion. This manual insertion method results in a large degree of variability in surgical outcomes and intra-cochlear trauma. Additionally, implants often span only the basal turn. In the present study we report on the development of a new method to assist CI electrode insertion. The design objectives are (1) an automated and standardized insertion technique across patients with (2) more apical insertion than is possible by the contemporary methods, while (3) minimizing insertion trauma. The method relies on a viscous fluid flow through the cochlea to carry the electrode array with it. A small cochleostomy (∼100-150 um in diameter) is made in scala vestibuli (SV) and the round window (RW) membrane is opened. A flow of diluted Sodium Hyaluronate (also known as Hyaluronic Acid, (HA)) is set up from the RW to the SV opening using a perfusion pump that sets up a unidirectional flow. Once the flow is established an implant is dropped into the ongoing flow. Here we present a proof-of-concept study where we used this technique to insert silicone implants all the way to the cochlear apex in rats and gerbils. In light-microscopic histology, the implantation occurred without cochlear trauma. To further assess the ototoxicity of the HA perfusion, we measured compound action potential (CAP) thresholds following the perfusion of HA, and found that the CAP thresholds were substantially elevated. Thus, at this point the method is promising, and requires further development to become clinically viable. PMID:24882641

  18. Sleeping Beauty transposon insertional mutagenesis based mouse models for cancer gene discovery

    Science.gov (United States)

    Moriarity, Branden S; Largaespada, David A

    2016-01-01

    Large-scale genomic efforts to study human cancer, such as the cancer gene atlas (TCGA), have identified numerous cancer drivers in a wide variety of tumor types. However, there are limitations to this approach, the mutations and expression or copy number changes that are identified are not always clearly functionally relevant, and only annotated genes and genetic elements are thoroughly queried. The use of complimentary, nonbiased, functional approaches to identify drivers of cancer development and progression is ideal to maximize the rate at which cancer discoveries are achieved. One such approach that has been successful is the use of the Sleeping Beauty (SB) transposon-based mutagenesis system in mice. This system uses a conditionally expressed transposase and mutagenic transposon allele to target mutagenesis to somatic cells of a given tissue in mice to cause random mutations leading to tumor development. Analysis of tumors for transposon common insertion sites (CIS) identifies candidate cancer genes specific to that tumor type. While similar screens have been performed in mice with the PiggyBac (PB) transposon and viral approaches, we limit extensive discussion to SB. Here we discuss the basic structure of these screens, screens that have been performed, methods used to identify CIS. PMID:26051241

  19. Basic Study for Ultrasound-Based Navigation for Pedicle Screw Insertion Using Transmission and Backscattered Methods

    Science.gov (United States)

    Chen, Ziqiang; Wu, Bing; Zhai, Xiao; Bai, Yushu; Zhu, Xiaodong; Luo, Beier; Chen, Xiao; Li, Chao; Yang, Mingyuan; Xu, Kailiang; Liu, Chengcheng; Wang, Chuanfeng; Zhao, Yingchuan; Wei, Xianzhao; Chen, Kai; Yang, Wu; Ta, Dean; Li, Ming

    2015-01-01

    The purpose of this study was to understand the acoustic properties of human vertebral cancellous bone and to study the feasibility of ultrasound-based navigation for posterior pedicle screw fixation in spinal fusion surgery. Fourteen human vertebral specimens were disarticulated from seven un-embalmed cadavers (four males, three females, 73.14 ± 9.87 years, two specimens from each cadaver). Seven specimens were used to measure the transmission, including tests of attenuation and phase velocity, while the other seven specimens were used for backscattered measurements to inspect the depth of penetration and A-Mode signals. Five pairs of unfocused broadband ultrasonic transducers were used for the detection, with center frequencies of 0.5 MHz, 1 MHz, 1.5 MHz, 2.25 MHz, and 3.5 MHz. As a result, good and stable results were documented. With increased frequency, the attenuation increased (P0.05). At about 0.6 cm away from the cortical bone, warning signals were easily observed from the backscattered measurements. In conclusion, the ultrasonic system proved to be an effective, moveable, and real-time imaging navigation system. However, how ultrasonic navigation will benefit pedicle screw insertion in spinal surgery needs to be determined. Therefore, ultrasound-guided pedicle screw implantation is theoretically effective and promising. PMID:25861053

  20. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  1. Relationship between Angiotensin-Converting Enzyme Insertion/Deletion Gene Polymorphism and Susceptibility of Minimal Change Nephrotic Syndrome: A Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Tian-Biao Zhou

    2011-01-01

    Africans: D: =.81, DD: =.49. Furthermore, the II genotype seemed not to play a protective role against MCNS risk for Asians, Caucasians and Africans (=.12, =.09, =.76, resp.. Interestingly, there was also significant association between ACE I/D gene polymorphism and MCNS susceptibility in overall populations (D: =.007, DD: =.04, II: =.03. Conclusion. D allele or DD genotype might be a significant genetic molecular marker for MCNS susceptibility in Asians and overall populations, but not for Caucasians and Africans. More larger and rigorous genetic epidemiological investigations are required to further explore this association.

  2. Optimizing design of triplexer chip with low insert loss and high isolation based on planar lightwave circuit

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Design optimization of a novel integrated triplexer based on planar lightwave circuit (PLC) for fiber-to-the-home applications is described. The two-mode interference coupler and Mach-Zehnder interference are used to construct the filter chip.Simulation results of high isolation and low insertion loss are gotten for proposed design. Technique tolerance is improved for fabricating device.

  3. FRET-based localization of fluorescent protein insertions within the ryanodine receptor type 1.

    Directory of Open Access Journals (Sweden)

    Shweta A Raina

    Full Text Available Fluorescent protein (FP insertions have often been used to localize primary structure elements in mid-resolution 3D cryo electron microscopic (EM maps of large protein complexes. However, little is known as to the precise spatial relationship between the location of the fused FP and its insertion site within a larger protein. To gain insights into these structural considerations, Förster resonance energy transfer (FRET measurements were used to localize green fluorescent protein (GFP insertions within the ryanodine receptor type 1 (RyR1, a large intracellular Ca(2+ release channel that plays a key role in skeletal muscle excitation contraction coupling. A series of full-length His-tagged GFP-RyR1 fusion constructs were created, expressed in human embryonic kidney (HEK-293T cells and then complexed with Cy3NTA, a His-tag specific FRET acceptor. FRET efficiency values measured from each GFP donor to Cy3NTA bound to each His tag acceptor site were converted into intermolecular distances and the positions of each inserted GFP were then triangulated relative to a previously published X-ray crystal structure of a 559 amino acid RyR1 fragment. We observed that the chromophoric centers of fluorescent proteins inserted into RyR1 can be located as far as 45 Å from their insertion sites and that the fused proteins can also be located in internal cavities within RyR1. These findings should prove useful in interpreting structural results obtained in cryo EM maps using fusions of small fluorescent proteins. More accurate point-to-point distance information may be obtained using complementary orthogonal labeling systems that rely on fluorescent probes that bind directly to amino acid side chains.

  4. WISP1 Polymorphisms Contribute to Platinum-Based Chemotherapy Toxicity in Lung Cancer Patients

    Directory of Open Access Journals (Sweden)

    Juan Chen

    2014-11-01

    Full Text Available Platinum-based chemotherapy toxicity is always one of the serious problems from which lung cancer patients suffer. The genetic polymorphism of WISP1 was revealed to be associated with susceptibility and platinum-based chemotherapy response in our previous studies. In this study, we aimed to investigate the relationship of WISP1 genetic polymorphisms with platinum-based chemotherapy toxicity in lung cancer patients. A total of 412 lung cancer patients were enrolled in this study, and 28 polymorphisms of the WISP1 gene were genotyped by SequenomMassARRAY. We found that WISP1 polymorphisms (rs2929965, rs2929969, rs2929970, rs2929973 and rs754958 were related to the overall chemotherapy toxicity of lung cancer in subgroup analyses. Rs16904853, rs2929970, rs2977549 and rs2977551 (p = 0.021, 0.028, 0.024, 0.048, respectively polymorphisms were significantly associated with hematologic toxicity. Rs2929946, rs2929970, rs2977519, rs2977536, rs3739262 and rs754958 (p = 0.031, 0.046, 0.029, 0.016, 0.042, 0.035, respectively polymorphisms were significantly associated with the gastrointestinal toxicity of lung cancer. Genotypes of WISP1 may be novel and useful biomarkers for predicting platinum-based chemotherapy toxicity in lung cancer patients.

  5. WISP1 Polymorphisms Contribute to Platinum-Based Chemotherapy Toxicity in Lung Cancer Patients

    Science.gov (United States)

    Chen, Juan; Yin, Jiye; Li, Xiangping; Wang, Ying; Zheng, Yi; Qian, Chenyue; Xiao, Ling; Zou, Ting; Wang, Zhan; Liu, Junyan; Zhang, Wei; Zhou, Honghao; Liu, Zhaoqian

    2014-01-01

    Platinum-based chemotherapy toxicity is always one of the serious problems from which lung cancer patients suffer. The genetic polymorphism of WISP1 was revealed to be associated with susceptibility and platinum-based chemotherapy response in our previous studies. In this study, we aimed to investigate the relationship of WISP1 genetic polymorphisms with platinum-based chemotherapy toxicity in lung cancer patients. A total of 412 lung cancer patients were enrolled in this study, and 28 polymorphisms of the WISP1 gene were genotyped by SequenomMassARRAY. We found that WISP1 polymorphisms (rs2929965, rs2929969, rs2929970, rs2929973 and rs754958) were related to the overall chemotherapy toxicity of lung cancer in subgroup analyses. Rs16904853, rs2929970, rs2977549 and rs2977551 (p = 0.021, 0.028, 0.024, 0.048, respectively) polymorphisms were significantly associated with hematologic toxicity. Rs2929946, rs2929970, rs2977519, rs2977536, rs3739262 and rs754958 (p = 0.031, 0.046, 0.029, 0.016, 0.042, 0.035, respectively) polymorphisms were significantly associated with the gastrointestinal toxicity of lung cancer. Genotypes of WISP1 may be novel and useful biomarkers for predicting platinum-based chemotherapy toxicity in lung cancer patients. PMID:25405734

  6. Effect of ACE insertion/deletion and 12 other polymorphisms on clinical outcomes and response to treatment in the life study

    DEFF Research Database (Denmark)

    2010-01-01

    OBJECTIVE: This pharmacogenetics substudy from the Losartan Intervention for Endpoint reduction in Hypertension study in patients with hypertension and left ventricular hypertrophy (LVH) treated with the angiotensin receptor blocker losartan versus the beta-blocker atenolol for 4.8 years tested....... These polymorphisms were chosen because they could affect blood pressure control or the pharmacological action of losartan or atenolol. METHODS: We genotyped 3503 patients, 1774 on losartan and 1729 on atenolol. RESULTS: ACE and the 12 other genotypes did not affect the reduction in systolic blood...... pressure, diastolic blood pressure, pulse pressure, mean arterial pressure, or heart rate, or treatment differences between losartan and atenolol on these endpoints, as assessed by general linear models. Also, ACE and the 12 other genotypes did not affect risk of the primary composite endpoint or its...

  7. Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus

    OpenAIRE

    Wei Lu; Shi Wang; Xiaoyu Mu; Meilin Tian; Huixia Du; Zhenmin Bao; Jingjing Yan

    2012-01-01

    Single nucleotide polymorphisms (SNPs) are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM) genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for the aquaculture industry in East Asian countries. HRM analysis revealed that all the loci showed polymorphisms when evaluated using 40 A. japonicus individuals col...

  8. Association Study between BDNF Gene Polymorphisms and Autism by Three-Dimensional Gel-Based Microarray

    OpenAIRE

    Zuhong Lu; Yunfei Bai; Xiaoyan Ke; Beili Sun; Lu Cheng; Pengfeng Xiao; Qinyu Ge

    2009-01-01

    Single nucleotide polymorphisms (SNPs) are important markers which can be used in association studies searching for susceptible genes of complex diseases. High-throughput methods are needed for SNP genotyping in a large number of samples. In this study, we applied polyacrylamide gel-based microarray combined with dual-color hybridization for association study of four BDNF polymorphisms with autism. All the SNPs in both patients and controls could be analyzed quickly and correctly. Among four ...

  9. Association between two single base polymorphisms of intercellular adhesion molecule 1 gene and inflammatory bowel disease

    Science.gov (United States)

    Habibi, Manijeh; Naderi, Nosratllah; Farnood, Alma; Balaii, Hedieh; Dadaei, Tahereh; Almasi, Shohreh; Zojaji, Homayoun; Asadzadeh Aghdae, Hamid; Zali, Mohammad Reza

    2016-01-01

    Aim: The present study evaluated the association between G241R and K469E polymorphisms of intercellular adhesion molecule 1 gene and inflammatory bowel disease in Iranian population. Background: Inflammatory bowel disease including ulcerative colitis and Crohn’s disease, is a chronic idiopathic inflammatory disease of the gastrointestinal tract. There are two single base polymorphisms of intercellular adhesion molecule 1gene, G241R and K469E, reported to be associated with inflammatory disorders. Patients and methods: In this case-control study, 156 inflammatory bowel disease patients (110 ulcerative colitis and 46 Crohn’s disease patients) and 131 healthy controls were enrolled. Two polymorphisms of intercellular adhesion molecule 1 gene, including G241R and K469E, were assessed by polymerase chain reaction followed by restriction fragment length polymorphism. Results: The E469 allele of K469E polymorphism was significantly more frequent in Crohn’s disease patients compared to controls (P< 0.05, OR= 1.83; 95% CI: 1.13 to 2.96). The mutant homozygote genotype of K469E polymorphism (E/E) was also significantly more frequent in Crohn’s disease patients compared to controls (P< 0.05, OR= 4.23; 95% CI: 1.42 to 12.59). No difference was observed in the frequency of K469E polymorphism among ulcerative colitis patients compared to controls. There were no significant differences in genotype and allele frequencies of G241R polymorphism among ulcerative colitis and Crohn’s disease patients compared to control subjects. Conclusion: According to our findings, K469E polymorphism of intercellular adhesion molecule 1 gene may probably participate in the pathogenesis of Crohn’s disease in Iran. PMID:27099667

  10. Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution

    OpenAIRE

    H??naff, Elizabeth; Zapata Ortiz, Luis; Casacuberta, Josep M.; Ossowski, Stephan

    2015-01-01

    Background Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases. Results Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping ...

  11. Calorimeter insertion

    CERN Multimedia

    2006-01-01

    Calorimeter insertion between toroids in the ATLAS experiment detector Calorimeters are surrounding the inner detector. Calorimeters will absorb and measure the energies of the most charged and neutral particles after the collisions. The saved energy in the calorimeter is detected and converted to signals that are taken out with data taking electronics.

  12. Lexis in Chinese-English Translation of Drug Package Inserts: Corpus-based Error Analysis and Its Translation Strategies

    OpenAIRE

    Ying, Lin; Yumei, Zhou

    2010-01-01

    Error analysis (EA) has been broadly applied to the researches of writing, speaking, second language acquisition (SLA) and translation. This study was carried out based on Carl James’ error taxonomy to investigate the distribution of lexical errors in Chinese-English (C-E) translation of drug package inserts (DPIs)(1), explore the underlying causes and propose some translation strategies for correction and reduction of lexical errors in DPIs. A translation corpus consisting of 25 DPIs transla...

  13. Dynamic emulation based modeling and detection of polymorphic shellcode at the network level

    Institute of Scientific and Technical Information of China (English)

    WANG LanJia; DUAN HaiXin; LI Xing

    2008-01-01

    It is a promising way to detect polymorphic shellcode using emulation method. However, previous emulation-based approaches are limited in their performance and resilience against evasions. A new enhanced emulation-based detection ap proach is proposed, including an automaton-based model of the dynamic behavior of olymorphic shellcode and a detection algorithm, the detection criterion of which is derived from that model and ensures high detection accuracy. The algorithm also contains several optimization techniques, highly improving the running performance and the resilience against detection evasion shellcode. We have implemented a prototype system for our approach. The advantages of our algorithmare validated by the experiments with real network data, polymorphic shellcode samples generated by available polymorphic engines and hand-crafted detection evasion shellcode.

  14. Insertion sequences.

    OpenAIRE

    Mahillon, Jacques; Chandler, M.

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryoti...

  15. Hybrid plasmonic waveguide-based ultra-low insertion loss transverse electric-pass polarizer.

    Science.gov (United States)

    Sun, X; Mojahedi, M; Aitchison, J S

    2016-09-01

    We have designed and experimentally demonstrated an integrated transverse electric (TE)-pass polarizer on silicon-on-insulator platform. The polarizer consists of an asymmetric coupling section where only the transverse magnetic (TM) mode is coupled to the cross-hybrid plasmonic waveguide and attenuated. The TE mode does not couple and passes through the polarizer. The polarizer was fabricated on the silicon-on-insulator platform. The device is 30 μm long, has a high extinction ratio of more than 28 dB over 150 nm bandwidth, and has a good fabrication tolerance. Most important, the proposed polarizer has an ultra-low insertion loss of less than 0.04 dB for the TE mode. PMID:27607962

  16. A backing device based on an embedded stiffener and retractable insertion tool for thin-film cochlear arrays

    Science.gov (United States)

    Tewari, Radheshyam

    Intracochlear trauma from surgical insertion of bulky electrode arrays and inadequate pitch perception are areas of concern with current hand-assembled commercial cochlear implants. Parylene thin-film arrays with higher electrode densities and lower profiles are a potential solution, but lack rigidity and hence depend on manually fabricated permanently attached polyethylene terephthalate (PET) tubing based bulky backing devices. As a solution, we investigated a new backing device with two sub-systems. The first sub-system is a thin poly(lactic acid) (PLA) stiffener that will be embedded in the parylene array. The second sub-system is an attaching and detaching mechanism, utilizing a poly(N-vinylpyrrolidone)-block-poly(d,l-lactide) (PVP-b-PDLLA) copolymer-based biodegradable and water soluble adhesive, that will help to retract the PET insertion tool after implantation. As a proof-of-concept of sub-system one, a microfabrication process for patterning PLA stiffeners embedded in parylene has been developed. Conventional hot-embossing, mechanical micromachining, and standard cleanroom processes were integrated for patterning fully released and discrete stiffeners coated with parylene. The released embedded stiffeners were thermoformed to demonstrate that imparting perimodiolar shapes to stiffener-embedded arrays will be possible. The developed process when integrated with the array fabrication process will allow fabrication of stiffener-embedded arrays in a single process. As a proof-of-concept of sub-system two, the feasibility of the attaching and detaching mechanism was demonstrated by adhering 1x and 1.5x scale PET tube-based insertion tools and PLA stiffeners embedded in parylene using the copolymer adhesive. The attached devices survived qualitative adhesion tests, thermoforming, and flexing. The viability of the detaching mechanism was tested by aging the assemblies in-vitro in phosphate buffer solution. The average detachment times, 2.6 minutes and 10 minutes

  17. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  18. DIFFERENTIATION OF BARLEY GENOTYPES BASED ON DNA POLYMORPHISM

    Directory of Open Access Journals (Sweden)

    Marián Tomka

    2013-02-01

    Full Text Available Identification and characterization of genotypes is essential for improving the quality of cultivated varieties in breeding programs. Information about the origin of varieties can help farmers in selecting appropriate varieties to specific growing conditions or end use of crops. A set of ten microsatellite markers was used to describe genetic diversity in a sample of 30 barley (Hordeum vulgare L. genotypes. A total of 55 different alleles were amplified using ten SSR markers localized on chromosomes 1H, 2H, 3H, 5H, 6H, 7H with an average number of 5.5 alleles per locus. On the basis of allele frequencies we have calculated diversity index, polymorphic information content and index of probability, which have mean values of 0.664; 0.643 and 0.126 respectively. These values indicate high differentiation ability of SSR markers. In the created dendrogram using hierarchical cluster analysis using UPGMA algorithm we were able to differentiate all 30 barley genotypes. The results show that DNA markers are suitable for the identification and differentiation of genotypes and indicated the effectiveness of microsatellite markers to describe genetic diversity.

  19. Development of a web services based system for dissemination of single nucleotide polymorphism data

    Science.gov (United States)

    Single nucleotide polymorphisms (SNPs) can be used to generate DNA-based fingerprints for individual identification. The efficiency of DNA fingerprinting is greatest when the frequency of both SNP alleles is near 0.50. A number of SNPs have been identified in cattle populations with minor allele f...

  20. ENDOSCOPIC GROMMET INSERTION OUR EXPERIENCE

    Directory of Open Access Journals (Sweden)

    Balasubramanian Thiagarajan

    2012-03-01

    Full Text Available Grommet insertion the commonest surgical procedure next only to circumcision is usually performed using an operating microscope 1. Authors have been using 4 mm 0 degree nasalendoscopes to perform this procedure during the last 5 years. This is a report of their experience in using endoscope inlieu of microscope in performing this surgery. This study makes a comparative analysis of Endoscopic Grommet insertion viz a viz Microscopic Grommet insertion. For this comparative analysis one year (2009 data base of Government Stanley Medical College Chennai India was used. This study reveals that Endoscopic Grommet insertion compared favorably with Microscopic Grommet insertion in all aspects with certain obvious advantages.

  1. Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus

    OpenAIRE

    Chen, Chunxian; Gmitter Jr, Fred G

    2013-01-01

    Background Single nucleotide polymorphisms (SNPs), the most abundant variations in a genome, have been widely used in various studies. Detection and characterization of citrus haplotype-based expressed sequence tag (EST) SNPs will greatly facilitate further utilization of these gene-based resources. Results In this paper, haplotype-based SNPs were mined out of publicly available citrus expressed sequence tags (ESTs) from different citrus cultivars (genotypes) individually and collectively for...

  2. Genetic contributions to avoidance-based decisions: striatal D2 receptor polymorphisms.

    Science.gov (United States)

    Frank, M J; Hutchison, K

    2009-11-24

    Individuals differ in their tendencies to seek positive decision outcomes or to avoid negative ones. At the neurobiological level, our model suggests that phasic changes in dopamine support learning to reinforce good decisions via striatal D1 receptors, and to avoid maladaptive choices via striatal D2 receptors. Accordingly, in a previous study individual differences in positive and negative learning were strongly modulated by two genetic polymorphisms factors related to striatal D1 and D2 function, respectively. Nevertheless, whereas the role for dopamine in positive learning is relatively well accepted, that in learning to avoid negative outcomes is more controversial. Here we further explore D2-receptor-related genetic contributions to probabilistic avoidance in humans, in light of recent data showing that particular DRD2 polymorphisms are associated with functional modulation of receptor expression [Zhang Y, Bertolino A, Fazio L, Blasi G, Rampino A, Romano R, Lee M-LT, Xiao T, Papp A, Wang D, Sadée W (2007) Polymorphisms in human dopamine d2 receptor gene affect gene expression, splicing, and neuronal activity during working memory. Proc Natl Acad Sci U S A 104(51):20552-20557]. We find that a promoter polymorphism rs12364283 associated with transcription and D2 receptor density was strongly and selectively predictive of avoidance-based decisions. Two further polymorphisms (rs2283265 and rs1076560) associated with relatively reduced presynaptic relative to postsynaptic D2 receptor expression were predictive of relative impairments in negative compared to positive decisions. These previously undocumented effects of DRD2 polymorphisms were largely independent of those we reported previously for the C957T polymorphism (rs6277) associated with striatal D2 density. In contrast, effects of the commonly studied Taq1A polymorphism on reinforcement-based decisions were due to indirect association with C957T. Taken together these findings suggest multiple D2-dependent

  3. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda.

    OpenAIRE

    Phadnis, S H; Huang, H V; Berg, D E

    1989-01-01

    We constructed a derivative of transposon Tn5 called Tn5supF for insertion mutagenesis and sequencing DNAs cloned in phage lambda. This element carries a supF amber-suppressor tRNA gene. Its insertion into lambda can be selected by plaque formation by using nonsuppressing (sup0) Escherichia coli for amber mutant lambda phage and sup0 dnaB-amber E. coli for nonamber lambda phage. Tn5supF is just 264 base pairs long. It transposes efficiently and inserts quasi-randomly into DNA targets. The uni...

  4. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    Science.gov (United States)

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  5. Insertion of 3-D-primitives in mesh-based representations: towards compact models preserving the details.

    Science.gov (United States)

    Lafarge, Florent; Keriven, Renaud; Brédif, Mathieu

    2010-07-01

    We propose an original hybrid modeling process of urban scenes that represents 3-D models as a combination of mesh-based surfaces and geometric 3-D-primitives. Meshes describe details such as ornaments and statues, whereas 3-D-primitives code for regular shapes such as walls and columns. Starting from an 3-D-surface obtained by multiview stereo techniques, these primitives are inserted into the surface after being detected. This strategy allows the introduction of semantic knowledge, the simplification of the modeling, and even correction of errors generated by the acquisition process. We design a hierarchical approach exploring different scales of an observed scene. Each level consists first in segmenting the surface using a multilabel energy model optimized by -expansion and then in fitting 3-D-primitives such as planes, cylinders or tori on the obtained partition where relevant. Experiments on real meshes, depth maps and synthetic surfaces show good potential for the proposed approach. PMID:20236893

  6. Crystallinity-based product design: Utilizing the polymorphism of isotactic PP homo- and copolymers

    Science.gov (United States)

    Gahleitner, Markus; Mileva, Daniela; Androsch, René; Gloger, Dietrich; Tranchida, Davide; Sandholzer, Martina; Doshev, Petar

    2015-12-01

    The polymorphism of isotactic polypropylene (iPP) in combination with the strong response of this polymer to nucleation can be utilized for expanding the application range of this versatile polymer. Based on three "case studies" related to β-iPP pressure pipes, ethylene-propylene (EP) random copolymers for thin-wall injection molding and sterilization resistance of cast films we demonstrate ways of combining polymer composition, nucleation and process settings to achieve the desired application performance.

  7. Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity

    OpenAIRE

    Qin, Wei Jie; Yung, Lin Yue Lanry

    2007-01-01

    Sequence-specific DNA detection is important in various biomedical applications such as gene expression profiling, disease diagnosis and treatment, drug discovery and forensic analysis. Here we report a gold nanoparticle-based method that allows DNA detection and quantification and is capable of single nucleotide polymorphism (SNP) discrimination. The precise quantification of single-stranded DNA is due to the formation of defined nanoparticle-DNA conjugate groupings in the presence of target...

  8. Melanin-based colour polymorphism responding to climate change.

    OpenAIRE

    Roulin A.

    2014-01-01

    Climate warming leads to a decrease in biodiversity. Organisms can deal with the new prevailing environmental conditions by one of two main routes, namely evolving new genetic adaptations or through phenotypic plasticity to modify behaviour and physiology. Melanin-based colouration has important functions in animals including a role in camouflage and thermoregulation, protection against UV-radiation and pathogens and, furthermore, genes involved in melanogenesis can pleiotropically regulate b...

  9. Insertion and deletion processes in recent human history.

    Directory of Open Access Journals (Sweden)

    Per Sjödin

    Full Text Available BACKGROUND: Although insertions and deletions (indels account for a sizable portion of genetic changes within and among species, they have received little attention because they are difficult to type, are alignment dependent and their underlying mutational process is poorly understood. A fundamental question in this respect is whether insertions and deletions are governed by similar or different processes and, if so, what these differences are. METHODOLOGY/PRINCIPAL FINDINGS: We use published resequencing data from Seattle SNPs and NIEHS human polymorphism databases to construct a genomewide data set of short polymorphic insertions and deletions in the human genome (n = 6228. We contrast these patterns of polymorphism with insertions and deletions fixed in the same regions since the divergence of human and chimpanzee (n = 10,546. The macaque genome is used to resolve all indels into insertions and deletions. We find that the ratio of deletions to insertions is greater within humans than between human and chimpanzee. Deletions segregate at lower frequency in humans, providing evidence for deletions being under stronger purifying selection than insertions. The insertion and deletion rates correlate with several genomic features and we find evidence that both insertions and deletions are associated with point mutations. Finally, we find no evidence for a direct effect of the local recombination rate on the insertion and deletion rate. CONCLUSIONS/SIGNIFICANCE: Our data strongly suggest that deletions are more deleterious than insertions but that insertions and deletions are otherwise generally governed by the same genomic factors.

  10. Gene-based microsatellites for cassava (Manihot esculenta Crantz: prevalence, polymorphisms, and cross-taxa utility

    Directory of Open Access Journals (Sweden)

    Ugwu Chike D

    2009-09-01

    Full Text Available Abstract Background Cassava (Manihot esculenta Crantz, a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. Results A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula and castor bean (Ricinus communis. Of 168 markers with clean amplification products, 124 (73.8% displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1% amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita whereas 13 (15.3% amplified alleles from castor bean and 9 (10.6% amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. Conclusion A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for

  11. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila

    OpenAIRE

    Häcker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A.

    2003-01-01

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniqu...

  12. Association Study between BDNF Gene Polymorphisms and Autism by Three-Dimensional Gel-Based Microarray

    Directory of Open Access Journals (Sweden)

    Zuhong Lu

    2009-06-01

    Full Text Available Single nucleotide polymorphisms (SNPs are important markers which can be used in association studies searching for susceptible genes of complex diseases. High-throughput methods are needed for SNP genotyping in a large number of samples. In this study, we applied polyacrylamide gel-based microarray combined with dual-color hybridization for association study of four BDNF polymorphisms with autism. All the SNPs in both patients and controls could be analyzed quickly and correctly. Among four SNPs, only C270T polymorphism showed significant differences in the frequency of the allele (χ2 = 7.809, p = 0.005 and genotype (χ2 = 7.800, p = 0.020. In the haplotype association analysis, there was significant difference in global haplotype distribution between the groups (χ2 = 28.19,p = 3.44e-005. We suggest that BDNF has a possible role in the pathogenesis of autism. The study also show that the polyacrylamide gel-based microarray combined with dual-color hybridization is a rapid, simple and high-throughput method for SNPs genotyping, and can be used for association study of susceptible gene with disorders in large samples.

  13. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication.

    OpenAIRE

    Dougherty, J P; Temin, H M

    1988-01-01

    We recently described a protocol for determination of retrovirus mutation rates, that is, the mutation frequency in a single cycle of retrovirus replication (J.P. Dougherty and H.M. Temin, Mol. Cell. Biol. 6:4378-4395, 1987; J.P. Dougherty and H.M. Temin, p. 18-23, in J. H. Miller and M. P. Calos, ed., Gene Transfer Vectors for Mammalian Cells, 1987). We used this protocol to determine the mutation rates for defined mutations in a replicating retrovirus by using a spleen necrosis virus-based ...

  14. Effect of an interface Mg insertion layer on the reliability of a magnetic tunnel junction based on a Co2FeAl full-Heusler alloy

    Science.gov (United States)

    Lee, Jung-Min; Kil, Gyu Hyun; Lee, Gae Hun; Choi, Chul Min; Song, Yun-Heub; Sukegawa, Hiroaki; Mitani, Seiji

    2014-04-01

    The reliability of a magnetic tunnel junction (MTJ) based on a Co2FeAl (CFA) full-Heusler alloy with a MgO tunnel barrier was evaluated. In particular, the effect of a Mg insertion layer under the MgO was investigated in view of resistance drift by using various voltage stress tests. We compared the resistance change during constant voltage stress (CVS) and confirmed a trap/detrap phenomenon during the interval stress test for samples with and without a Mg insertion layer. The MTJ with a Mg insertion layer showed a relatively small resistance change for the CVS test and a reduced trap/detrap phenomenon for the interval stress test compared to the sample without a Mg insertion layer. This is understood to be caused by the improved crystallinity at the bottom of the CFA/MgO interface due to the Mg insertion layer, which provides a smaller number of trap site during the stress test. As a result, the interface condition of the MgO layer is very important for the reliability of a MTJ using a full-Heusler alloy, and the the insert of a Mg layer at the MgO interface is expected to be an effective method for enhancing the reliability of a MTJ.

  15. Methylenetetrahydrofolate reductase gene A1298C polymorphism in pediatric stroke--case-control and family-based study.

    Science.gov (United States)

    Balcerzyk, Anna; Niemiec, Paweł; Kopyta, Ilona; Emich-Widera, Ewa; Pilarska, Ewa; Pienczk-Ręcławowicz, Karolina; Kaciński, Marek; Wendorff, Janusz; Żak, Iwona

    2015-01-01

    Moderate hyperhomocysteinemia is one of the risk factors of pediatric stroke. Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme, which regulates homocysteine metabolism, and some polymorphisms of gene encoding this enzyme are associated with a decreased activity of the enzyme. The aim of the study was to assess an association between the A1298C polymorphism and pediatric stroke. We also evaluated a possible synergistic effect of A1298C and C677T polymorphisms of this gene. The study group consisted of 88 children after ischemic stroke, 142 of their parents and 111 controls. The A1298C polymorphism was genotyped using the restriction fragment length polymorphism method. We used 2 study designs: a case-control model and a family-based association test. The Statistica 7.1 and EpiInfo 6 softwares were used in all analyses. We did not observe any statistically significant differences either in the transmission of the A allele in the family-based test or in the frequency of the A allele in the patients group compared with the controls. We also did not notice any significant additive or synergistic effects between the A1298C and C677T polymorphisms. An analysis of the results obtained in this study and a critical review of previously published studies indicate that the A1298C polymorphism of the MTHFR gene is not related to ischemic stroke in children. PMID:25440348

  16. Ionizing Radiation Detectors Based on Ge-Doped Optical Fibers Inserted in Resonant Cavities

    Directory of Open Access Journals (Sweden)

    Saverio Avino

    2015-02-01

    Full Text Available The measurement of ionizing radiation (IR is a crucial issue in different areas of interest, from environmental safety and industrial monitoring to aerospace and medicine. Optical fiber sensors have recently proven good candidates as radiation dosimeters. Here we investigate the effect of IR on germanosilicate optical fibers. A piece of Ge-doped fiber enclosed between two fiber Bragg gratings (FBGs is irradiated with gamma radiation generated by a 6 MV medical linear accelerator. With respect to other FBG-based IR dosimeters, here the sensor is only the bare fiber without any special internal structure. A near infrared laser is frequency locked to the cavity modes for high resolution measurement of radiation induced effects on the fiber optical parameters. In particular, we observe a variation of the fiber thermo-optic response with the radiation dose delivered, as expected from the interaction with Ge defect centers, and demonstrate a detection limit of 360 mGy. This method can have an impact in those contexts where low radiation doses have to be measured both in small volumes or over large areas, such as radiation therapy and radiation protection, while bare optical fibers are cheap and disposable.

  17. Large enhancement of perpendicular magnetic anisotropy and high annealing stability by Pt insertion layer in (Co/Ni-based multilayers

    Directory of Open Access Journals (Sweden)

    Xi Chen

    2015-09-01

    Full Text Available We have investigated the influence of ultrathin Pt insertion layers on the perpendicular magnetic anisotropy (PMA and annealing stability of Ta/Pt/(Co/Ni×3/Co/Pt/Ta multilayered films. When the Pt layers were inserted at the Co/Ni interfaces, the PMA of the multilayered films decreased monotonically as the thickness of the Pt insertion layer (tPt was increased. However, when the Pt layers were inserted at the Ni/Co interfaces, the PMA increased from 1.39 × 106 to 3.5 × 106 erg/cm3 as tPt increased from 0 to 10 Å. Moreover, the multilayered film containing 6-Å-thick Pt insertion layers that inserted at the Ni/Co interfaces exhibited the highest annealing stability for PMA, which was up to temperature of 480 °C. We hypothesize that the introduced Pt/Co interfaces, due to the Pt insertion layers, are responsible for the enhanced PMA and high annealing stability. This study is particularly important for perpendicularly magnetized spintronic devices that require high PMA and high annealing stability.

  18. Association of Angiotensin-Converting Enzyme Intron 16 Insertion/Deletion and Angiotensin II Type 1 Receptor A1166C Gene Polymorphisms with Preeclampsia in South East of Iran

    Directory of Open Access Journals (Sweden)

    Saeedeh Salimi

    2011-01-01

    Full Text Available Some evidence suggests that a variety of genetic factors contributed in pathogenesis of the preeclampsia. The aim of this study was to assess the association between the angiotensin-converting enzyme (ACE I/D and angiotensin II type1 receptor A1166C polymorphisms with preeclampsia. This study was performed in 125 preeclamptic pregnant women and 132 controls. The I/D Polymorphism of the ACE gene was assessed by polymerase chain reaction and the A1166C Polymorphism of the AT1R gene was determined by restriction fragment length polymorphism. The genotype and allele frequencies of I/D polymorphism differed between two groups. The risk of preeclampsia was 3.2-fold in pregnant women with D allele (OR, 3.2 [95% CI, 1.1 to 3.8]; P=0.01. The distribution of the AT1R gene A1166C polymorphism was similar in affected and control groups. Our results supported that presence of the I/D polymorphism of ACE gene is a marker for the increased risk of preeclampsia.

  19. Genotyping common FSHR polymorphisms based on competitive amplification of differentially melting amplicons (CADMA)

    DEFF Research Database (Denmark)

    Borgbo, Tanni; Sommer Kristensen, Lasse; Lindgren, Ida;

    2014-01-01

    -based genotyping results. Comparing the CADMA-based assays to (AS-PCR) and Sanger sequencing, the CADMA based assays showed an improved analytical sensitivity and a wider applicability. CONCLUSIONS: The new assays provide a reliable, fast and user-friendly genotyping method facilitating a wider implication...... analytical sensitivity. Here, we present a novel version of "competitive amplification of differentially melting amplicons" (CADMA), providing an improved platform for simple, reliable, and cost-effective genotyping. METHODS: Two CADMA based assays were designed for the two common polymorphisms of the FSHR...... gene: rs6165 (c.919A > G, p. Thr307Ala, FSHR 307) and rs6166 (c.2039A > G, p. Asn680Ser, FSHR 680). To evaluate the reliability of the new CADMA-based assays, the genotyping results were compared with two conventional PCR based genotyping methods; allele-specific PCR (AS-PCR) and Sanger sequencing...

  20. Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells

    Science.gov (United States)

    Grabundzija, Ivana; Wang, Jichang; Sebe, Attila; Erdei, Zsuzsanna; Kajdi, Robert; Devaraj, Anantharam; Steinemann, Doris; Szuhai, Károly; Stein, Ulrike; Cantz, Tobias; Schambach, Axel; Baum, Christopher; Izsvák, Zsuzsanna; Sarkadi, Balázs; Ivics, Zoltán

    2013-01-01

    The discovery of direct cell reprogramming and induced pluripotent stem (iPS) cell technology opened up new avenues for the application of non-viral, transposon-based gene delivery systems. The Sleeping Beauty (SB) transposon is highly advanced for versatile genetic manipulations in mammalian cells. We established iPS cell reprogramming of mouse embryonic fibroblasts and human foreskin fibroblasts by transposition of OSKM (Oct4, Sox2, Klf4 and c-Myc) and OSKML (OSKM + Lin28) expression cassettes mobilized by the SB100X hyperactive transposase. The efficiency of iPS cell derivation with SB transposon system was in the range of that obtained with retroviral vectors. Co-expression of the miRNA302/367 cluster together with OSKM significantly improved reprogramming efficiency and accelerated the temporal kinetics of reprogramming. The iPS cells displayed a stable karyotype, and hallmarks of pluripotency including expression of stem cell markers and the ability to differentiate into embryoid bodies in vitro. We demonstrate Cre recombinase-mediated exchange allowing simultaneous removal of the reprogramming cassette and targeted knock-in of an expression cassette of interest into the transposon-tagged locus in mouse iPS cells. This strategy would allow correction of a genetic defect by site-specific insertion of a therapeutic gene construct into ‘safe harbor’ sites in the genomes of autologous, patient-derived iPS cells. PMID:23275558

  1. Prevalence, risk factors and outcomes of velamentous and marginal cord insertions: a population-based study of 634,741 pregnancies.

    Directory of Open Access Journals (Sweden)

    Cathrine Ebbing

    Full Text Available OBJECTIVES: To determine the prevalence of, and risk factors for anomalous insertions of the umbilical cord, and the risk for adverse outcomes of these pregnancies. DESIGN: Population-based registry study. SETTING: Medical Birth Registry of Norway 1999-2009. POPULATION: All births (gestational age >16 weeks to <45 weeks in Norway (623,478 singletons and 11,263 pairs of twins. METHODS: Descriptive statistics and odds ratios (ORs for risk factors and adverse outcomes based on logistic regressions adjusted for confounders. MAIN OUTCOME MEASURES: Velamentous or marginal cord insertion. Abruption of the placenta, placenta praevia, pre-eclampsia, preterm birth, operative delivery, low Apgar score, transferral to neonatal intensive care unit (NICU, malformations, birthweight, and perinatal death. RESULTS: The prevalence of abnormal cord insertion was 7.8% (1.5% velamentous, 6.3% marginal in singleton pregnancies and 16.9% (6% velamentous, 10.9% marginal in twins. The two conditions shared risk factors; twin gestation and pregnancies conceived with the aid of assisted reproductive technology were the most important, while bleeding in pregnancy, advanced maternal age, maternal chronic disease, female foetus and previous pregnancy with anomalous cord insertion were other risk factors. Velamentous and marginal insertion was associated with an increased risk of adverse outcomes such as placenta praevia (OR = 3.7, (95% CI = 3.1-4.6, and placental abruption (OR = 2.6, (95% CI = 2.1-3.2. The risk of pre-eclampsia, preterm birth and delivery by acute caesarean was doubled, as was the risk of low Apgar score, transferral to NICU, low birthweight and malformations. For velamentous insertion the risk of perinatal death at term was tripled, OR = 3.3 (95% CI = 2.5-4.3. CONCLUSION: The prevalence of velamentous and marginal insertions of the umbilical cord was 7.8% in singletons and 16.9% in twin gestations, with marginal insertion being more

  2. Polymorphic amplified typing sequences (PATS) and pulsed-field gel electrophoresis (PFGE) yield comparable results in the strain typing of a diverse set of bovine Escherichia coli O157 isolates

    Science.gov (United States)

    The PCR-based Escherichia coli O157 (O157) strain typing system, Polymorphic Amplified Typing Sequences (PATS), targets insertions-deletions (Indels) and single nucleotide polymorphisms (SNPs) at the XbaI and AvrII(BlnI) restriction enzyme sites, respectively, besides amplifying four known virulenc...

  3. Solid 7Li-NMR and in situ XRD studies of the insertion reaction of lithium with tin oxide and tin-based amorphous composite oxide

    International Nuclear Information System (INIS)

    The lithium insertion reactions with tin (II) oxide (SnO) and tin-based composite oxide (abbreviated as TBCO) are studied by solid 7Li-NMR Knight shift, T1 and T1ρ relaxation rate, TEM and in situ XRD methods. By the insertion reaction for SnO, the lithium oxide and β-tin are produced first at Li/Sn = 2; at Li/Sn = 3 to 6 the products are not simple and a mixture of LiSn2, LiSn, Li5Sn2 and Li7Sn2 alloys is detected during the insertion. For the TBCO, which is revealed as amorphous, mainly constituted by randomly distributed very short-range (order of 10-9 m) regions by TEM observation, it is found that electrochemically inserted lithium forms Li2O and produces metallic tin (Sn) in the first step (Li/Sn 7Sn2 (and Li7Si2), are produced in the second step (Li/Sn >2). During the second step, the Li/Sn ratio of formed lithium-tin alloy is kept at almost 4. By the analyses of 7Li NMR Knight shifts, line shape and in situ XRD, the lithium-inserted TBCOs are characterized as almost amorphous and mixtures of highly ionic components. (author)

  4. The Effects of Clonidine Premedication and Scalp Infiltration of Lidocaine on Hemodynamic Responses to Laryngoscopy and Skull Pin Head-Holder Insertion During Skull Base Procedures

    OpenAIRE

    Jellish, W Scott; Theard, M. Angele; Cheng, Mary Ann; Leonetti, John P.; Crowder, C. Michael; Tempelhoff, Rene

    2001-01-01

    This study was designed to determine if oral clonidine or lidocaine, injected into the scalp before head-holder (H-H) insertion, would attenuate the hemodynamic effects associated with intubation and H-H placement. Thirty-four patients undergoing skull base procedures were randomized to four groups. Group 1 received clonidine 5 mcg/kg po before surgery with 10 to 15 ml of 1% lidocaine infiltrated at pin insertion sites; Group 2 received clonidine with saline infiltration; Group 3 received a p...

  5. Prevalence, Risk Factors and Outcomes of Velamentous and Marginal Cord Insertions: A Population-Based Study of 634,741 Pregnancies

    OpenAIRE

    Ebbing, Cathrine; Kiserud, Torvid; Johnsen, Synnøve Lian; Albrechtsen, Susanne; Rasmussen, Svein

    2013-01-01

    Objectives To determine the prevalence of, and risk factors for anomalous insertions of the umbilical cord, and the risk for adverse outcomes of these pregnancies. Design Population-based registry study. Setting Medical Birth Registry of Norway 1999–2009. Population All births (gestational age >16 weeks to

  6. A Novel Polymorphic Ant Colony -Based Clustering Mechanism for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Min Xiang

    2012-10-01

    Full Text Available In wireless sensor networks, sensor nodes are extremely power constrained, so energy efficient clustering mechanism is mainly considered in the network topology management. A new clustering mechanism based on the polymorphic ant colony (PAC is designed for dynamically controlling the networks clustering structure. According to different functions, the nodes of the networks are respectively defined as the queen ant, the scout ant and worker ant. Based on the calculated cost function and real-time pheromone, the queen ant restructures an optimum clustering structure. Furthermore, the worker ants and the scout ants can send or receive sensing data with optional communication path based on their pheromones. With the mechanism, the energy consumption in inter-cluster and intra-cluster communication for the worker ants and scout ants can be reduced. The simulation results demonstrate that the proposed mechanism can effectively remodel the clustering structure and improve the energy efficiency of the networks.

  7. HLA-G is a component of the chronic lymphocytic leukemia escape repertoire to generate immune suppression: impact of the HLA-G 14 base pair (rs66554220) polymorphism

    Science.gov (United States)

    Rizzo, Roberta; Audrito, Valentina; Vacca, Paola; Rossi, Davide; Brusa, Davide; Stignani, Marina; Bortolotti, Daria; D’Arena, Giovanni; Coscia, Marta; Laurenti, Luca; Forconi, Francesco; Gaidano, Gianluca; Mingari, Maria Cristina; Moretta, Lorenzo; Malavasi, Fabio; Deaglio, Silvia

    2014-01-01

    This work investigates the possibility that HLA-G, a molecule modulating innate and adaptive immunity, is part of an immune escape strategy of chronic lymphocytic leukemia cells. A 14 base pair insertion/deletion polymorphism (rs66554220) in the 3′-untranslated region of HLA-G influences mRNA stability and protein expression. The analysis of a cohort of patients with chronic lymphocytic leukemia confirmed that del/del individuals are characterized by higher levels of surface and soluble HLA-G than subjects with the other two genotypes. In line with its role in immunomodulation, the percentage of regulatory T lymphocytes is higher in del/del patients than in patients with the other genotypes and correlates with the amounts of surface or soluble HLA-G. Furthermore, addition of sHLA-G-rich plasma from patients with chronic lymphocytic leukemia induces natural killer cell apoptosis and impairs natural killer cell lysis, with effects proportional to the amount of soluble HLA-G added. Lastly, the presence of an HLA-G 14 base pair polymorphism is of prognostic value, with del/del patients showing reduced overall survival, as compared to those with other genotypes. These results suggest that: (i) the HLA-G 14 base pair polymorphism influences the levels of surface and soluble HLA-G expression, and (ii) the over-expression of HLA-G molecules contributes to creating tolerogenic conditions. PMID:24362551

  8. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    Science.gov (United States)

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic

  9. Accuracy of Percutaneous Pedicle Screw Insertion Technique with Conventional Dual Fluoroscopy Units and a Retrospective Comparative Study Based on Surgeon Experience.

    Science.gov (United States)

    Nakahara, Masayuki; Yasuhara, Takao; Inoue, Takafumi; Takahashi, Yuichi; Kumamoto, Shinji; Hijikata, Yasukazu; Kusumegi, Akira; Sakamoto, Yushi; Ogawa, Koichi; Nishida, Kenki

    2016-06-01

    Study Design Retrospective comparative study. Objective To evaluate the accuracy of percutaneous pedicle screw (PPS) placement and intraoperative imaging time using dual fluoroscopy units and their differences between surgeons with more versus less experience. Methods One hundred sixty-one patients who underwent lumbar fusion surgery were divided into two groups, A (n = 74) and B (n = 87), based on the performing surgeon's experience. The accuracy of PPS placement and radiation time for PPS insertion were compared. PPSs were inserted with classic technique under the assistance of dual fluoroscopy units placed in two planes. The breach definition of PPS misplacement was based on postoperative computed tomography (grade I: no breach; grade II: fluoroscopy units in the lumbar and sacral spine is fairly accurate and provides good clinical outcomes, even among surgeons lacking experience. PMID:27190733

  10. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    Science.gov (United States)

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species. PMID:27525845

  11. A regenerative electrochemical biosensor for mercury(II) by using the insertion approach and dual-hairpin-based amplification

    International Nuclear Information System (INIS)

    Highlights: • The dual-hairpin structure as a signal amplifier is label-free and handy. • The strategy uses the insertion approach to improve the hybridization efficiency. • This biosensor has a low detection limit (28 pM) for detection of Hg2+. • This biosensor can be easily regenerated by using L-cysteine. - Abstract: A simple and effective biosensor for Hg2+ determination was investigated. The novel biosensor was prepared by the insertion approach that the moiety-labeled DNA inserted into a loosely packed cyclic-dithiothreitol (DTT) monolayer, improving the hybridization efficiency. Electrochemical impedance spectroscopy studies of two biosensors (single-hairpin and dual-hairpin structure DNA modified electrodes) used for Hg2+ detection indicated that the dual-hairpin modified electrode had a larger electron transfer resistance change (ΔRct). Consequently, the dual-hairpin structure was used as a signal amplifier for the preparation of a selective Hg2+ biosensor. This biosensor exhibited an excellent selectivity toward Hg2+ over Cd2+, Pd2+, Co2+ etc. Also, a linear relation was observed between the ΔRct and Hg2+ concentrations in a range from 0.1 nM to 5 μM with a detection limit of 28 pM under optimum conditions. Moreover, the biosensor can be reused by using L-cysteine and successfully applied for detecting Hg2+ in real samples

  12. Manganese Superoxide Dismutase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cencer Patients Treated with Cyclophosphamide Epirubicin and 5-Fluororacil

    DEFF Research Database (Denmark)

    Ording, Anne Gulbech; Cronin Fenton, Deirdre; Christensen, Mariann;

    2012-01-01

    Manganese Superoxide Dismutase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cencer Patients Treated with Cyclophosphamide Epirubicin and 5-Fluororacil......Manganese Superoxide Dismutase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cencer Patients Treated with Cyclophosphamide Epirubicin and 5-Fluororacil...

  13. Manganese Superoxide Dismtase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cancer Patients Treated with Cyclophosphamide Epirubicin and 5-fluorouracil

    DEFF Research Database (Denmark)

    Ording, Anne Gulbech; Cronin Fenton, Deirdre; Christensen, Mariann;

    2013-01-01

    Manganese Superoxide Dismtase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cancer Patients Treated with Cyclophosphamide Epirubicin and 5-fluorouracil......Manganese Superoxide Dismtase Polymorphism and Breast Cancer Recurrence: A Danish Population-Based Case-Control Study of Breast Cancer Patients Treated with Cyclophosphamide Epirubicin and 5-fluorouracil...

  14. Impact of Genetic Polymorphisms on the Smoking-related Risk of Periodontal Disease: the Population-based Study SHIP

    Directory of Open Access Journals (Sweden)

    Schwahn C

    2003-09-01

    Full Text Available Abstract Periodontitis is a bacterial inflammatory disease leading to attachment loss with the consequence of tooth loss. There exists a multifactorial risk pattern including bacterial challenge, smoking, age, sex, diabetes, socio-economic and genetic factors. Smoking has the highest impact on the course of the disease modulated by all the other factors. Here, we report the relationship between smoking and the polymorphisms of genetic polymorphisms inflicted in the pathogenesis. In a randomly selected population-based study, 1083 subjects were typed for the polymorphisms of the IL-1 genotype, Fcγ RIIIb receptor gene, myeloperoxidase and N-acetyltransferase (NAT2 and related to their periodontal state. Smoking behavior was assessed including present and past quality and quantity of smoking. There is a significant dose-effect relationship between the exposure to tobacco smoke and the extent of periodontal disease assessed as attachment loss and tooth loss. Moreover, there are gene-environmental interactions as subjects bearing variant genotypes show an enhanced smoking-associated risk of the disease modulated by these genotypes. In non-smokers, the impact of these genetic polymorphisms is mostly negligible. This study provides support for the hypothesis that subjects bearing genetic variants of polymorphically expressed phenotypes are at an increased risk of periodontitis when smoking. Mostly, this may be accomplished via the influence of smoking-related impairment on defense mechanisms rather than on the pathogenic pathways.

  15. Genetic variability of Amorphophallus muelleri Blume in Java based on Random Amplified Polymorphic DNA

    Directory of Open Access Journals (Sweden)

    DIYAH MARTANTI

    2008-10-01

    Full Text Available Amorphophallus muelleri Blume (Araceae is valued for its glucomanan content for use in food industry (healthy diet food, paper industry, pharmacy and cosmetics. The species is triploid (2n=3x=39 and the seed is developed apomictically. The present research is aimed to identify genetic variability of six population of A. muelleri from Java (consisted of 50 accessions using random amplified polymorphic DNA (RAPD. The six populations of the species are: East Java: (1 Silo-Jember, (2 Saradan-Madiun, (3 IPB (cultivated, from Saradan-Madiun, (4 Panti-Jember, (5 Probolinggo; and Central Java: (6 Cilacap. The results showed that five RAPD primers generated 42 scorable bands of which 29 (69.05% were polymorphic. Size of the bands varied from 300bp to 1.5kbp. The 50 accessions of A. muelleri were divided into two main clusters, some of them were grouped based on their populations, and some others were not. The range of individual genetic dissimilarity was from 0.02 to 0.36. The results showed that among six populations investigated, Saradan population showed the highest levels of genetic variation with mean values of na = 1.500+ 0.5061, ne = 1.3174 + 0.3841, PLP = 50% and He = 0, 0.1832+0.2054, whereas Silo-Jember population showed the lowest levels of genetic variation with mean values na = 1.2619+ 0.4450, ne = 1.1890 + 0.3507, PLP = 26.19% and He = 0.1048+0.1887. Efforts to conserve, domesticate, cultivate and improve genetically should be based on the genetic properties of each population and individual within population, especially Saradan population which has the highest levels of genetic variation, need more attention for its conservation.

  16. Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study.

    Science.gov (United States)

    Lo Presti, Leonardo; Soave, Raffaella; Longhi, Mariangela; Ortoleva, Emanuele

    2010-10-01

    Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.1(11,15).0(2,6).0(16,20))triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C(24)H(30)N(6)) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z', density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z' = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30-40 kJ mol(-1). These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in

  17. HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

    NARCIS (Netherlands)

    Nijveen, H.; Kester, M.G.D.; Hassan, C.; Viars, A.; Ru, A.H.; Jager, de M.; Falkenburg, J.H.F.; Leunissen, J.A.M.; Veelen, van P.A.

    2011-01-01

    T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem

  18. New combination in Veronica (Scrophulariaceae s.l.)based on morphological characters and the seed storage protein polymorphism

    Institute of Scientific and Technical Information of China (English)

    Cem VURAL; Servet (O)ZCAN; Mikail AKBULUT

    2009-01-01

    Veronica erciyasdagi (M. A. Fischer) C. Vural comb. & stat. Nov., previously regarded as a variety, is proposed as a new combination, based on the morphological characters and seed storage protein polymorphism presented in this study. In addition, information about the ecology and conservation status of Veronica erciyas-dagi was reported. This taxon is endemic to central Anatolia, Turkey and is critically endangered.

  19. Polymorphous computing fabric

    Science.gov (United States)

    Wolinski, Christophe Czeslaw; Gokhale, Maya B.; McCabe, Kevin Peter

    2011-01-18

    Fabric-based computing systems and methods are disclosed. A fabric-based computing system can include a polymorphous computing fabric that can be customized on a per application basis and a host processor in communication with said polymorphous computing fabric. The polymorphous computing fabric includes a cellular architecture that can be highly parameterized to enable a customized synthesis of fabric instances for a variety of enhanced application performances thereof. A global memory concept can also be included that provides the host processor random access to all variables and instructions associated with the polymorphous computing fabric.

  20. A single base insertion in the putative transmembrane domain of the tyrosinase gene as a cause for tyrosinase-negative oculocutaneous albinism

    Energy Technology Data Exchange (ETDEWEB)

    Chintamaneni, C.D.; Kobayashi, Y.; Kwon, B.S. (Indiana Univ. School of Medicine, Indianapolis (United States)); Halaban, R. (Yale Univ. School of Medicine, New Haven, CT (United States)); Witkop, C.J. Jr. (Univ. of Minnesota, Minneapolis (United States))

    1991-06-15

    The authors have determined a molecular defect to be the likely basis for inactivity of the tyrosinase from a patient with tyrosinase-negative oculocutaneous albinism. A single base (thymine) was inserted in exon 5 of the tyrosinase gene following codon 471 in the putative transmembrane coding region. This insertion caused a shift in the reading frame of 19 amino acids at the 3{prime} end and introduced a premature termination signal that would be expected to truncate the protein by 21 amino acids at the carboxyl terminus. The albino tyrosinase was not recognized by antibodies directed to the carboxyl terminus of tyrosinase. Furthermore, as shown by gel electrophoresis of the immunoprecipitated protein, the tyrosinase was {approx} 3kDa smaller than normal. Similar immunoprecipitation data were obtained when cloned normal and mutant tyrosinases were expressed in COS-1 cells.

  1. Polymorphism of methylenetetrahydrofolate reductase gene is associated with response to fluorouracil-based chemotherapy in Chinese patients with gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Zhang Xiaoping; Bai Zhibin; Chen Baoan; Feng Jifeng; Yan Feng; Jiang Zhi; Zhong Yuejiao

    2014-01-01

    Background The importance of polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene for the prediction of the response to fluorouracil-based adjuvant chemotherapy in gastric cancer patients remains unclear.The aim of this study is to assess the predictive value of several polymorphisms of the MTHFR gene for clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in Chinese population.Methods Three hundred and sixty-two Chinese patients with gastric cancer were treated with fluorouracil-based adjuvant chemotherapy.DNA samples were isolated from peripheral blood collected before treatment.The three single nucleotide polymorphisms (SNPs) (rs1801131,rs1801133,rs2274976) genotypes of the MTHFR gene were determined by matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).Results The average response rate for chemotherapy was 46.7%.Homozygous genotypes rs2274976G/G (x2=22.7,P <0.01) and rs1801131A/A (x2=14.3,P=0.008) were over-represented in responsive patients.Carriers of the rs2274976A allele genotypes (G/A and A/A) and of the rs1801131C allele genotypes (A/C and C/C) were prevalent in nonresponsive patients.In the haplotype association analysis,there was a significant difference in global haplotype distribution between the groups (x2=20.69,P=0.000 124).Conclusions These results suggest that polymorphisms of the MTHFR gene may be used as predictors of the response to fluorouracil-based chemotherapy for gastric cancer patients in Chinese population.Well-designed,comprehensive,and prospective studies on determining these polymorphisms of MTHFR gene as clinical markers for predicting the response to fluorouracil-based therapy in gastric cancer patients is warranted.

  2. Genetic variations of Lansium domesticum Corr. accessions from Java, Sumatra and Ceram based on Random Amplified Polymorphic DNA fingerprints

    Directory of Open Access Journals (Sweden)

    KUSUMADEWI SRI YULITA

    2011-07-01

    Full Text Available Yulita KS (2011 Genetic variations of Lansium domesticum Corr. accessions from Java, Bengkulu and Ceram based on Random Amplified Polymorphic DNA fingerprints. Biodiversitas 12: 125-130. Duku (Lansium domesticum Corr. is one of popular tropical fruits in SE Asia. The spesies has three varieties, known as duku, langsat and kokosan; and duku is the most popular one for being the sweetiest fruit. Indonesia has several local varieties of duku, such as duku Condet, duku Sumber and duku Palembang. This present study aimed to assess genetic diversity of 47 accessions of duku from Java, Sumatra, and Ceram based on RAPD fingerprints. Ten RAPD’s primers were initially screened and five were selected for the analysis. These five primers (OPA 7, 13, 18, OPB 7, and OPN 12 generated 53 scorable bands with an average of 10.6 polymorphic fragment per primer. Percentage of polymorphism ranged from 16.89% (OPA 7 and OPN 12 to 24.54% (OPB 7 with an average of 20.16% polymorphism. OPB 7 at 450 bp was exclusively possessed by accession 20 (Java, OPA 18 at 500 bp was by accession 6 (Java, 550 bp by 3 clones from Bengkulu. While OPN 12 at 300 bp and OPA 13 at 450 bp were shared among the accessions. Clustering analysis was performed based on RAPD profiles using the UPGMA method. The range of genetic similarity value among accessions was 0.02-0.65 suggesting high variation of gene pool existed among accessions.

  3. A regenerative electrochemical biosensor for mercury(II) by using the insertion approach and dual-hairpin-based amplification

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Jing; Ling, Yu; Gao, Zhong Feng [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Lei, Jing Lei [College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044 (China); Luo, Hong Qun, E-mail: luohq@swu.edu.cn [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Li, Nian Bing, E-mail: linb@swu.edu.cn [Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

    2015-09-15

    Highlights: • The dual-hairpin structure as a signal amplifier is label-free and handy. • The strategy uses the insertion approach to improve the hybridization efficiency. • This biosensor has a low detection limit (28 pM) for detection of Hg{sup 2+}. • This biosensor can be easily regenerated by using L-cysteine. - Abstract: A simple and effective biosensor for Hg{sup 2+} determination was investigated. The novel biosensor was prepared by the insertion approach that the moiety-labeled DNA inserted into a loosely packed cyclic-dithiothreitol (DTT) monolayer, improving the hybridization efficiency. Electrochemical impedance spectroscopy studies of two biosensors (single-hairpin and dual-hairpin structure DNA modified electrodes) used for Hg{sup 2+} detection indicated that the dual-hairpin modified electrode had a larger electron transfer resistance change (ΔR{sub ct}). Consequently, the dual-hairpin structure was used as a signal amplifier for the preparation of a selective Hg{sup 2+} biosensor. This biosensor exhibited an excellent selectivity toward Hg{sup 2+} over Cd{sup 2+}, Pd{sup 2+}, Co{sup 2+} etc. Also, a linear relation was observed between the ΔR{sub ct} and Hg{sup 2+} concentrations in a range from 0.1 nM to 5 μM with a detection limit of 28 pM under optimum conditions. Moreover, the biosensor can be reused by using L-cysteine and successfully applied for detecting Hg{sup 2+} in real samples.

  4. Improved ⅢI-nitrides based light-emitting diodes anti-electrostatic discharge capacity with an AlGaN/GaN stack insert layer

    Institute of Scientific and Technical Information of China (English)

    Li Zhicong; Wang Guohong; Li Jinmin; Li Panpan; Wang Bing; Li Hongjian; Liang Meng; Yao Ran; Li Jing; Deng Yuanming; Yi Xiaoyan

    2011-01-01

    Through insertion of an AlGaN/GaN stack between the u-GaN and n-GaN of GaN-based light-emitting diodes (LEDs),the strain in the epilayer was increased,the dislocation density was reduced.GaN-based LEDs with different Al compositions were compared.6.8% A1 composition in the stacks showed the highest electrostatic discharge (ESD) endurance ability at the human body mode up to 6000 V and the pass yield exceeded 95%.

  5. The effects of clonidine premedication and scalp infiltration of lidocaine on hemodynamic responses to laryngoscopy and skull pin head-holder insertion during skull base procedures.

    Science.gov (United States)

    Jellish, W S; Theard, M A; Cheng, M A; Leonetti, J P; Crowder, C M; Tempelhoff, R

    2001-08-01

    This study was designed to determine if oral clonidine or lidocaine, injected into the scalp before head-holder (H-H) insertion, would attenuate the hemodynamic effects associated with intubation and H-H placement. Thirty-four patients undergoing skull base procedures were randomized to four groups. Group 1 received clonidine 5 mcg/kg po before surgery with 10 to 15 ml of 1% lidocaine infiltrated at pin insertion sites; Group 2 received clonidine with saline infiltration; Group 3 received a placebo preoperatively and had lidocaine infiltrated at pin sites; and Group 4 received a placebo with saline infiltrated. All patients had a standard anesthetic titrated to a 10 to 14 Hz EEG endpoint during laryngoscopy and H-H placement. Mean arterial pressure (MAP) was similar between groups during intubation, but heart rate (HR) increased in patients who did not receive clonidine. H-H application increased HR and MAP in Group 4. HR also increased after H-H placement in patients who received oral clonidine, while patients receiving scalp lidocaine or both clonidine and scalp lidocaine had little change in either value. Clonidine attenuated HR increases after laryngoscopy but not after H-H placement. Lidocaine injected at the pin sites reduced HR, and MAP increased after H-H insertion. The combination of oral clonidine and scalp lidocaine blunted hemodynamic responses to both intubation and H-H placement. PMID:17167618

  6. Allele frequency-based and polymorphism-versus-divergence indices of balancing selection in a new filtered set of polymorphic genes in Plasmodium falciparum.

    Science.gov (United States)

    Ochola, Lynette Isabella; Tetteh, Kevin K A; Stewart, Lindsay B; Riitho, Victor; Marsh, Kevin; Conway, David J

    2010-10-01

    Signatures of balancing selection operating on specific gene loci in endemic pathogens can identify candidate targets of naturally acquired immunity. In malaria parasites, several leading vaccine candidates convincingly show such signatures when subjected to several tests of neutrality, but the discovery of new targets affected by selection to a similar extent has been slow. A small minority of all genes are under such selection, as indicated by a recent study of 26 Plasmodium falciparum merozoite-stage genes that were not previously prioritized as vaccine candidates, of which only one (locus PF10_0348) showed a strong signature. Therefore, to focus discovery efforts on genes that are polymorphic, we scanned all available shotgun genome sequence data from laboratory lines of P. falciparum and chose six loci with more than five single nucleotide polymorphisms per kilobase (including PF10_0348) for in-depth frequency-based analyses in a Kenyan population (allele sample sizes >50 for each locus) and comparison of Hudson-Kreitman-Aguade (HKA) ratios of population diversity (π) to interspecific divergence (K) from the chimpanzee parasite Plasmodium reichenowi. Three of these (the msp3/6-like genes PF10_0348 and PF10_0355 and the surf(4.1) gene PFD1160w) showed exceptionally high positive values of Tajima's D and Fu and Li's F indices and have the highest HKA ratios, indicating that they are under balancing selection and should be prioritized for studies of their protein products as candidate targets of immunity. Combined with earlier results, there is now strong evidence that high HKA ratio (as well as the frequency-independent ratio of Watterson's /K) is predictive of high values of Tajima's D. Thus, the former offers value for use in genome-wide screening when numbers of genome sequences within a species are low or in combination with Tajima's D as a 2D test on large population genomic samples. PMID:20457586

  7. Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism

    OpenAIRE

    Youxiong Que; Yongbao Pan; Yunhai Lu; Cui Yang; Yuting Yang; Ning Huang; Liping Xu

    2014-01-01

    In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information conten...

  8. [Suprapubic catheter insertion].

    Science.gov (United States)

    Neumann, Eva; Schwentner, Christian

    2016-01-01

    The suprapubic catheter enables a percutaneous drainage of urine. The insertion is made superior of the pubic bone through the abdominal wall into the bladder. It allows a permanent drainage of urine bypassing the urethra. The insertion of a suprapubic catheter requires knowledge and expertise. This paper summarizes the basic background and allows to follow the practical application step by step. PMID:26800072

  9. Tie rod insertion test

    CERN Multimedia

    B. LEVESY

    2002-01-01

    The superconducting coil is inserted in the outer vaccum tank and supported by a set of tie rods. These tie rods are made of titanium alloy. This test reproduce the final insertion of the tie rods inside the outer vacuum tank.

  10. Polymorphisms within base and nucleotide excision repair pathways and risk of differentiated thyroid carcinoma.

    Science.gov (United States)

    Cipollini, Monica; Figlioli, Gisella; Maccari, Giuseppe; Garritano, Sonia; De Santi, Chiara; Melaiu, Ombretta; Barone, Elisa; Bambi, Franco; Ermini, Stefano; Pellegrini, Giovanni; Cristaudo, Alfonso; Foddis, Rudy; Bonotti, Alessandra; Romei, Cristina; Vivaldi, Agnese; Agate, Laura; Molinari, Eleonora; Barale, Roberto; Forsti, Asta; Hemminki, Kari; Elisei, Rossella; Gemignani, Federica; Landi, Stefano

    2016-05-01

    The thyrocytes are exposed to high levels of oxidative stress which could induce DNA damages. Base excision repair (BER) is one of the principal mechanisms of defense against oxidative DNA damage, however recent evidences suggest that also nucleotide excision repair (NER) could be involved. The aim of present work was to identify novel differentiated thyroid cancer (DTC) risk variants in BER and NER genes. For this purpose, the most strongly associated SNPs within NER and BER genes found in our previous GWAS on DTC were selected and replicated in an independent series of samples for a new case-control study. Although a positive signal was detected at the nominal level of 0.05 for rs7689099 (encoding for an aminoacid change proline to arginine at codon 117 within NEIL3), none of the considered SNPs (i.e. rs7990340 and rs690860 within RFC3, rs3744767 and rs1131636 within RPA1, rs16962916 and rs3136166 in ERCC4, and rs17739370 and rs7689099 in NEIL3) was associated with the risk of DTC when the correction of multiple testing was applied. In conclusion, a role of NER and BER pathways was evoked in the susceptibility to DTC. However, this seemed to be limited to few polymorphic genes and the overall effect size appeared weak. PMID:27062014

  11. Identification of processed Japanese green tea based on polymorphisms generated by STS-RFLP analysis.

    Science.gov (United States)

    Kaundun, Shiv S; Matsumoto, Satoru

    2003-03-26

    In Japan, tea is generally sold blended, though 90% of the total production is clonal. Due to the increasingly strict consumer need and taste, however, more and more Japanese green teas are being sold under their particular cultivar name. Moreover, tea made from Yabukita, a much appreciated cultivar originally developed in Japan, has recently been produced and imported from a neighboring country. This paper describes a simple and inexpensive methodology capable of identifying fresh and processed Japanese green teas to discourage its fraudulent commercialization. The study was based on 46 main tea cultivars, and polymorphism detected through STS-RFLP analysis of the coding and noncoding DNA regions of three genes, namely phenylalanine ammonia-lyase, chalcone synthase, and dihydroflavonol 4-reductase, for which nucleotide information was available. All 46 tea cultivars analyzed could be easily distinguished using a combination of codominant DNA markers. Yabukita displayed a unique profile when PAL intron was digested with DdeI, thus allowing its rapid authentication at low cost. PMID:12643627

  12. PanoInserts: mobile spatial teleconferencing

    OpenAIRE

    Pece, F.; Steptoe, W.; F. Wanner; Julier, S.; Weyrich, T.; Kautz, J.; Steed, A.

    2013-01-01

    We present PanoInserts: a novel teleconferencing system that uses smartphone cameras to create a surround representation of meeting places. We take a static panoramic image of a location into which we insert live videos from smartphones. We use a combination of marker- and image-based tracking to position the video inserts within the panorama, and transmit this representation to a remote viewer. We conduct a user study comparing our system with fully-panoramic video and conventional webcam vi...

  13. Population-based analysis of the frequency of HFE gene polymorphisms: Correlation with the susceptibility to develop hereditary hemochromatosis.

    Science.gov (United States)

    Katsarou, Martha-Spyridoula; Latsi, Rosana; Papasavva, Maria; Demertzis, Nikolaos; Kalogridis, Thodoris; Tsatsakis, Aristides M; Spandidos, Demetrios A; Drakoulis, Nikolaos

    2016-07-01

    Hereditary hemochromatosis (HH) is an autosomal recessive genetic disease, characterized by increased dietary iron absorption. Due to the absence of an effective excretory mechanism, the excess iron in the body may accumulate resulting in toxic effects. The HFE gene also affects the activity of hepcidin, a hormone which acts as a negative regulator of iron metabolism. In this study, we performed a population-based analysis of the distribution of three hemochromatosis-related polymorphisms in the HFE gene (rs1800562, rs1799945 and rs1800730). DNA from 1,446 non‑related individuals of Greek ethnicity was collected and analyzed, either from whole blood or buccal swabs. The frequency distribution of these HFE gene polymorphisms was then determined. The results revealed that in our Greek population cohort (gr) the frequencies of each polymorphism were as follows: rs1800562: GG (wild‑type)=97.0%, GA=1.5%, AA=1.5%; rs1799945: CC (wild‑type)=74.4%, CG=23.4%, GG=2.2%; rs1800730: AA (wild‑type)=98.1%, AT=1.5% and TT=0.4%. No association between the HFE polymorphisms rs1800562, rs1799945 and rs1800730 and gender could be established. As regards the rs1800562 polymorphism, the A allele (mutant) was ~1.8‑fold more frequent in the European population (eur) than in the Greek population [(gr)=2,3%gl) [rs1800562: (gl)=1%gl)=7%gl)=<1%<(gr)=1.2%]. This suggests that the Greek population may differ genetically from the northern European population, due to influences from neighboring Asian and African populations. These findings also suggest that there is no gender-associated inheritance of these polymorphisms, and gender-specific symptoms appear as a result of independent biological processes. Thus, the early detection of the tendency towards iron accumulation may be achieved by the genotypic analysis of the polymorphisms that may contribute to the development of the hemochromatosis. PMID:27221532

  14. Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti

    Directory of Open Access Journals (Sweden)

    Streit Thomas G

    2009-12-01

    Full Text Available Abstract Background Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti. Results From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51% of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75. Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545. Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed. Conclusion Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient

  15. Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms.

    Science.gov (United States)

    Mo, Shao-Kang; Liu, Ya-Cheng; Wang, Sheng-Qi; Bo, Xiao-Chen; Li, Zhen; Chen, Ying; Ni, Ming

    2016-05-01

    Short tandem repeats (STRs) are conventional genetic markers typically used for paternity and kinship testing. As supplementary markers of STRs, single nucleotide polymorphisms (SNPs) have less discrimination power but broader applicability to degraded samples. The rapid improvement of next-generation sequencing (NGS) and multiplex amplification technologies also make it possible now to simultaneously identify dozens or even hundreds of SNP loci in a single pool. However, few studies have been endeavored to kinship testing based on SNP loci. In this study, we genotyped 90 autosomal human identity SNP loci with NGS, and investigated their testing efficacies based on the likelihood ratio model in eight pedigree scenarios involving paternity, half/full-sibling, uncle/nephew, and first-cousin relationships. We found that these SNPs might be sufficient to discriminate paternity and full-sibling, but impractical for more distant relatives such as uncle and cousin. Furthermore, we conducted an in silico study to obtain the theoretical tendency of how testing efficacy varied with increasing number of SNP loci. For each testing battery in a given pedigree scenario, we obtained distributions of logarithmic likelihood ratio for both simulated relatives and unrelated controls. The proportion of the overlapping area between the two distributions was defined as a false testing level (FTL) to evaluate the testing efficacy. We estimated that 85, 127, 491, and 1,858 putative SNP loci were required to discriminate paternity, full-sibling, half-sibling/uncle-nephew, and first-cousin (FTL, 0.1%), respectively. To test a half-sibling or nephew, an additional uncle relative could be included to decrease the required number of putative SNP loci to ∼320 (FTL, 0.1%). As a systematic computation of paternity and kinship testing based only on SNPs, our results could be informative for further studies and applications on paternity and kinship testing using SNP loci. PMID:26952733

  16. Frequency of anareobic power among brasilians based on dermatoglyphics and R577X polymorphism of the ACTN3 protein

    OpenAIRE

    Carlos Renato Paz; Ramon Cunha Montenegro; Eric de Lucena Barbosa; Asdrúbal Nóbrega Montenegro-Neto; Sérgio Marques de Lucena; Vanduir Soares de Araújo Filho; Paula Roquetti Fernandes; José Fernandes Filho

    2013-01-01

    Dermatoglyphics and analysis of the Alpha-Actinin-3 gene are evaluative instruments frequently used to identify the sportive and general population profile associated with physical performance. This research aimed to determine, based on dermatoglyphic characteristics and the R577X polymorphism of Alpha-Actinin-3, the percentage of people in the State of Paraíba/Brazil, with unfavorable characteristics to excelling in sports that require anaerobic power. A descriptive study of profiles, with e...

  17. Evaluation of 13q14 Status in Patients with Chronic Lymphocytic Leukemia Using Single Nucleotide Polymorphism-Based Techniques

    OpenAIRE

    Hanlon, Katy; Ellard, Sian; Rudin, Claudius E.; Thorne, Susan; Davies, Teresa; Harries, Lorna W.

    2009-01-01

    Deletions of chromosome 13q14 are common in chronic lymphocytic leukemia and other cancers, demonstrating the importance of this region in tumorigenesis. We report the use of two single-nucleotide polymorphism (SNP)-based techniques to determine 13q loss of heterozygosity (LOH) status in 15 patients with CLL: (i) digital SNP (dSNP), where analysis of heterozygous SNPs detects allelic imbalances, and (ii) DNA sequencing, where LOH is identified by comparison of allelic peak heights in normal a...

  18. Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers

    OpenAIRE

    Fernández i Martí, Ángel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

    2012-01-01

    Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the ...

  19. A catalog of neutral and deleterious polymorphism in yeast.

    Directory of Open Access Journals (Sweden)

    Scott W Doniger

    2008-08-01

    Full Text Available The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements, insertion, or deletion polymorphisms (InDels and single-nucleotide polymorphisms (SNPs. While inbreeding depression and heterosis imply that a substantial amount of polymorphism is deleterious, distinguishing deleterious from neutral polymorphism remains a significant challenge. To identify deleterious and neutral DNA sequence variation within Saccharomyces cerevisiae, we sequenced the genome of a vineyard and oak tree strain and compared them to a reference genome. Among these three strains, 6% of the genome is variable, mostly attributable to variation in genome content that results from large InDels. Out of the 88,000 polymorphisms identified, 93% are SNPs and a small but significant fraction can be attributed to recent interspecific introgression and ectopic gene conversion. In comparison to the reference genome, there is substantial evidence for functional variation in gene content and structure that results from large InDels, frame-shifts, and polymorphic start and stop codons. Comparison of polymorphism to divergence reveals scant evidence for positive selection but an abundance of evidence for deleterious SNPs. We estimate that 12% of coding and 7% of noncoding SNPs are deleterious. Based on divergence among 11 yeast species, we identified 1,666 nonsynonymous SNPs that disrupt conserved amino acids and 1,863 noncoding SNPs that disrupt conserved noncoding motifs. The deleterious coding SNPs include those known to affect quantitative traits, and a subset of the deleterious noncoding SNPs occurs in the promoters of genes that show allele-specific expression, implying that some cis-regulatory SNPs are deleterious. Our results show that

  20. Validation-based insertional mutagenesis for identification of Nup214 as a host factor for EV71 replication in RD cells

    International Nuclear Information System (INIS)

    Highlights: •We introduced a new mutagenesis strategy named VBIM to the viral research. •This method can identify either host factors or host restriction factors. •Using VBIM system, we identified Nup214 as a host factor for EV71 replication in RD cells. -- Abstract: Lentiviral validation-based insertional mutagenesis (VBIM) is a sophisticated, forward genetic approach that is used for the investigation of signal transduction in mammalian cells. Using VBIM, we conducted function-based genetic screening for host genes that affect enterovirus 71 (EV71) viral replication. This included host factors that are required for the life cycle of EV71 and host restriction factors that inhibit EV71 replication. Several cell clones, resistant to EV71, were produced using EV71 infection as a selection pressure and the nuclear pore protein 214 (Nup214) was identified as a host factor required for EV71 replication. In SD2-2, the corresponding VBIM lentivirus transformed clone, the expression of endogenous Nup214 was significantly down-regulated by the reverse inserted VBIM promoter. After Cre recombinase-mediated excision of the VBIM promoter, the expression of Nup214 recovered and the clone regained sensitivity to the EV71 infection. Furthermore, over-expression of Nup214 in the cells suggested that Nup214 was promoting EV71 replication. Results of this study indicate that a successful mutagenesis strategy has been established for screening host genes related to viral replication

  1. Validation-based insertional mutagenesis for identification of Nup214 as a host factor for EV71 replication in RD cells

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bei; Zhang, XiaoYu; Zhao, Zhendong, E-mail: timjszzd@163.com

    2013-08-02

    Highlights: •We introduced a new mutagenesis strategy named VBIM to the viral research. •This method can identify either host factors or host restriction factors. •Using VBIM system, we identified Nup214 as a host factor for EV71 replication in RD cells. -- Abstract: Lentiviral validation-based insertional mutagenesis (VBIM) is a sophisticated, forward genetic approach that is used for the investigation of signal transduction in mammalian cells. Using VBIM, we conducted function-based genetic screening for host genes that affect enterovirus 71 (EV71) viral replication. This included host factors that are required for the life cycle of EV71 and host restriction factors that inhibit EV71 replication. Several cell clones, resistant to EV71, were produced using EV71 infection as a selection pressure and the nuclear pore protein 214 (Nup214) was identified as a host factor required for EV71 replication. In SD2-2, the corresponding VBIM lentivirus transformed clone, the expression of endogenous Nup214 was significantly down-regulated by the reverse inserted VBIM promoter. After Cre recombinase-mediated excision of the VBIM promoter, the expression of Nup214 recovered and the clone regained sensitivity to the EV71 infection. Furthermore, over-expression of Nup214 in the cells suggested that Nup214 was promoting EV71 replication. Results of this study indicate that a successful mutagenesis strategy has been established for screening host genes related to viral replication.

  2. MR compatibility aspects of a silicon photomultiplier-based PET/RF insert with integrated digitisation

    International Nuclear Information System (INIS)

    The combination of Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) into a single device is being considered a promising tool for molecular imaging as it combines the high sensitivity of PET with the functional and anatomical images of MRI. For highest performance, a scalable, MR compatible detector architecture with a small form factor is needed, targeting at excellent PET signal-to-noise ratios and time-of-flight information. Therefore it is desirable to use silicon photo multipliers and to digitize their signals directly in the detector modules inside the MRI bore. A preclinical PET/RF insert for clinical MRI scanner was built to demonstrate a new architecture and to study the interactions between the two modalities. The disturbance of the MRI’s static magnetic field stays below 2 ppm peak-to-peak within a diameter of 56 mm (90 mm using standard automatic volume shimming). MRI SNR is decreased by 14%, RF artefacts (dotted lines) are only visible in sequences with very low SNR. Ghosting artefacts are visible to the eye in about 26% of the EPI images, severe ghosting only in 7.6%. Eddy-current related heating effects during long EPI sequences are noticeable but with low influence of 2% on the coincidences count rate. The time resolution of 2.5 ns, the energy resolution of 29.7% and the volumetric spatial resolution of 1.8 mm3 in the PET isocentre stay unaffected during MRI operation. Phantom studies show no signs of other artefacts or distortion in both modalities. A living rat was simultaneously imaged after the injection with 18F-Fluorodeoxyglucose (FDG) proving the in vivo capabilities of the system. (paper)

  3. Evaluation of a 2D fluoroscopy-based navigation system for insertion of the dynamic hip screw (DHS). An experimental study

    International Nuclear Information System (INIS)

    Purpose: Dynamic hip screw (DHS) insertion for the fixation of lateral femoral neck fractures is an accepted surgical treatment method. A computer-assisted planning and navigation system based on 2D fluoroscopy has been developed for guidewire insertion in order to perform screw placement. The image acquisition process was supported by a radiation-saving procedure called 'zero-dose C-arm navigation'. The aim of this study was to evaluate this new system. Materials and Methods: In the context of a sawbone study, we inserted dynamic hip screws. The procedure was performed under navigation control and in the conventional technique in 12 sawbones. Both procedures were performed in an open and closed technique. Results: The computer-assisted technique significantly reduced the number of intraoperative fluoroscopic images (open technique: -8.1 ± 0.5; p < 0.001 - closed technique: -12.3 ± 3.7; p < 0.001) and the number of guidewire passes (open technique: -1.3 ± 1.2; p < 0.05 - closed technique: -1.5 ± 1.2; p < 0,05). There was no difference with respect to precision in both groups. The operation time was significantly longer in the navigation-assisted groups (open technique: + 14.6 ± 5.4 min; p < 0.001 - closed technique: + 13 ± 3 min; p < 0.001). Conclusion: The addition of computer-assisted planning and surgical guidance supported by 'zero-dose C-arm navigation' may be useful for the fixation of lateral femoral neck fractures by the DHS as it reduces the amount of fluoroscopic images and requires fewer drill tracks. Further studies with the goal of reducing the operation time are necessary. (orig.)

  4. MTHFR polymorphisms and 5-FU-based adjuvant chemotherapy in colorectal cancer

    DEFF Research Database (Denmark)

    Afzal, Shoaib; Jensen, S; Vainer, B;

    2009-01-01

    Methylenetetrahydrofolate reductase is a pivotal enzyme in folate metabolism and 5-fluorouracil (5-FU) cytotoxicity. Two common single-nucleotide polymorphisms (SNPs), MTHFR 677C>T (rs1801133) and 1298A>C (rs1801131), reduce enzyme activity. Initially, these SNPs were claimed to predict clinical....../leucovorin chemotherapy after intended curative resection between 1997 and 2003. Clinical data, including relapse rates, overall survival, and tumor stage, were collected. DNA was extracted from formalin-fixed tumor tissue and analyzed for the MTHFR 677C>T and 1298A>C SNPs with real-time PCR. Results: The MTHFR 677C...... colorectal cancer after complete resection; however, the 677C>T polymorphism may be associated with lower toxicity in 5-FU treatment. Implementation of SNP analysis for these polymorphisms for individualized treatment is premature....

  5. Synthesis of a fluorescence resonance energy transfer-based probe containing a tricyclic nucleoside analog for single nucleotide polymorphism typing.

    Science.gov (United States)

    Hayai, Aya; Maeda, Yusuke; Ueno, Yoshihito

    2016-08-01

    Here, we report the synthesis of a fluorescence resonance energy transfer (FRET)-based probe for single nucleotide polymorphism (SNP) typing. The probe contains a fluorescent tricyclic base, 8-amino-3-(2,3-dihydroxypropyl)imidazo[4',5':5,6]pyrido[2,3-d]pyrimidine, as a donor molecule and 7-diethylaminocoumarin-3-carboxylic acid as an acceptor molecule. FRET was observed between the donor and acceptor molecules on the probe. The identity of the target bases on DNA and RNA strands could be determined using the probe. PMID:27329795

  6. HLA polymorphisms in Cabo Verde and Guiné-Bissau inferred from sequence-based typing.

    Science.gov (United States)

    Spínola, Hélder; Bruges-Armas, Jácome; Middleton, Derek; Brehm, António

    2005-10-01

    Human leukocyte antigen (HLA)-A, -B, and -DRB1 polymorphisms were examined in the Cabo Verde and Guiné-Bissau populations. The data were obtained at high-resolution level, using sequence-based typing. The most frequent alleles in each locus was: A*020101 (16.7% in Guiné-Bissau and 13.5% in Cabo Verde), B*350101 (14.4% in Guiné-Bissau and 13.2% in Cabo Verde), DRB1*1304 (19.6% in Guiné-Bissau), and DRB1*1101 (10.1% in Cabo Verde). The predominant three loci haplotype in Guiné-Bissau was A*2301-B*1503-DRB1*1101 (4.6%) and in Cabo Verde was A*3002-B*350101-DRB1*1001 (2.8%), exclusive to northwestern islands (5.6%) and absent in Guiné-Bissau. The present study corroborates historic sources and other genetic studies that say Cabo Verde were populated not only by Africans but also by Europeans. Haplotypes and dendrogram analysis shows a Caucasian genetic influence in today's gene pool of Cabo Verdeans. Haplotypes and allele frequencies present a differential distribution between southeastern and northwestern Cabo Verde islands, which could be the result of different genetic influences, founder effect, or bottlenecks. Dendrograms and principal coordinates analysis show that Guineans are more similar to North Africans than other HLA-studied sub-Saharans, probably from ancient and recent genetic contacts with other peoples, namely East Africans. PMID:16386651

  7. PTEN polymorphisms contribute to clinical outcomes of advanced lung adenocarcinoma patients treated with platinum-based chemotherapy.

    Science.gov (United States)

    Yang, Yang; Xu, Wen; Liu, Di; Ding, Xi; Su, Bo; Sun, Yifeng; Gao, Wen

    2016-06-01

    This study aimed to elucidate the impact of PTEN single nucleotide polymorphism (SNP) on clinical outcomes for advanced lung adenocarcinoma (LAC) patients treated with platinum-based chemotherapy. Three functional SNPs (rs11202607 G>A, rs701848 A>G, and rs11202592 G>C) of PTEN gene were genotyped by using DNA from blood samples of 618 advanced LAC patients, and their relationships with clinical outcomes were analyzed. The carriers of homozygous mutant of rs701848 and rs11202592 polymorphisms revealed significantly worse overall survival (OS) than those with heterozygote or wild-type homozygote (18.83 vs. 21.47 vs. 24.37 months, P = 0.034 and 13.40 vs. 19.03 vs. 21.90 months, P = 0.025, respectively). Subgroup analysis revealed that this association was particularly significant in tumor-lymph-node metastasis (TNM) stage III patients. The objective response rates (ORR) and disease control rates (DCR) of patients with genotype AA, AG, and GG in PTEN rs701848 polymorphism were statistically different (24.1 vs 16.6 vs 12.2 %, P = 0.017 and 82.7 vs 76.0 vs 70.2 %, P = 0.029, respectively). Haplotype analysis revealed a protective effect of the haplotype G-A-A (in the order of rs11202592, rs701848, and rs11202607) on chemotherapy efficacy and survival. Taken together, PTEN polymorphisms may contribute to survival and chemotherapy efficacy of advanced LAC patients treated with platinum-based agents. PMID:26695147

  8. HLA-A Gene Polymorphism Defined by High-Resolution Sequence Based Typing in 161 Northern Chinese Han People

    Institute of Scientific and Technical Information of China (English)

    Chunxia Yan; Haiyan Sun; Xiuqing Zhang; Jian Wang; Huanming Yang; Shengbin Li; Ruilin Wang; Jingxiang Li; Yajun Deng; Dongying Wu; Hongbo Zhang; Hongxing Zhang; Lidong Wang; Chunrong Zhang

    2003-01-01

    Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods--sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590),and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205,A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.

  9. Multipurpose Transposon-Insertion Libraries in Yeast.

    Science.gov (United States)

    Kumar, Anuj

    2016-01-01

    Libraries of transposon-insertion alleles constitute powerful and versatile tools for large-scale analysis of yeast gene function. Transposon-insertion libraries are constructed most simply through mutagenesis of a plasmid-based genomic DNA library; modification of the mutagenizing transposon by incorporation of yeast selectable markers, recombination sites, and an epitope tag enables the application of insertion alleles for phenotypic screening and protein localization. In particular, yeast genomic DNA libraries have been mutagenized with modified bacterial transposons carrying the URA3 marker, lox recombination sites, and sequence encoding multiple copies of the hemagglutinin (HA) epitope. Mutagenesis with these transposons has yielded a large resource of insertion alleles affecting nearly 4000 yeast genes in total. Through well-established protocols, these insertion libraries can be introduced into the desired strain backgrounds and the resulting insertional mutants can be screened or systematically analyzed. Relative to alternative methods of UV irradiation or chemical mutagenesis, transposon-insertion alleles can be easily identified by PCR-based approaches or high-throughput sequencing. Transposon-insertion libraries also provide a cost-effective alternative to targeted deletion approaches, although, in contrast to start-codon to stop-codon deletions, insertion alleles might not represent true null-mutants. For protein-localization studies, transposon-insertion alleles can provide encoded epitope tags in-frame with internal codons; in many cases, these transposon-encoded epitope tags can provide a more accurate localization for proteins in which terminal sequences are crucial for intracellular targeting. Thus, overall, transposon-insertion libraries can be used quickly and economically and have a particular utility in screening for desired phenotypes and localization patterns in nonstandard genetic backgrounds. PMID:27250950

  10. A flow-free droplet-based device for high throughput polymorphic crystallization.

    Science.gov (United States)

    Yang, Shih-Mo; Zhang, Dapeng; Chen, Wang; Chen, Shih-Chi

    2015-06-21

    Crystallization is one of the most crucial steps in the process of pharmaceutical formulation. In recent years, emulsion-based platforms have been developed and broadly adopted to generate high quality products. However, these conventional approaches such as stirring are still limited in several aspects, e.g., unstable crystallization conditions and broad size distribution; besides, only simple crystal forms can be produced. In this paper, we present a new flow-free droplet-based formation process for producing highly controlled crystallization with two examples: (1) NaCl crystallization reveals the ability to package saturated solution into nanoliter droplets, and (2) glycine crystallization demonstrates the ability to produce polymorphic crystallization forms by controlling the droplet size and temperature. In our process, the saturated solution automatically fills the microwell array powered by degassed bulk PDMS. A critical oil covering step is then introduced to isolate the saturated solution and control the water dissolution rate. Utilizing surface tension, the solution is uniformly packaged in the form of thousands of isolating droplets at the bottom of each microwell of 50-300 μm diameter. After water dissolution, individual crystal structures are automatically formed inside the microwell array. This approach facilitates the study of different glycine growth processes: α-form generated inside the droplets and γ-form generated at the edge of the droplets. With precise temperature control over nanoliter-sized droplets, the growth of ellipsoidal crystalline agglomerates of glycine was achieved for the first time. Optical and SEM images illustrate that the ellipsoidal agglomerates consist of 2-5 μm glycine clusters with inner spiral structures of ~35 μm screw pitch. Lastly, the size distribution of spherical crystalline agglomerates (SAs) produced from microwells of different sizes was measured to have a coefficient variation (CV) of less than 5%, showing

  11. A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples

    OpenAIRE

    Kraus, Robert H. S.; vonHoldt, Bridgett; Cocchiararo, Berardino; Harms, Verena; Bayerl, Helmut; Kühn, Ralph; Förster, Daniel W; Fickel, Jörns; Roos, Christian; Nowak, Carsten

    2015-01-01

    Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single-nucleotide polymorphism (SNP)-based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology ...

  12. Family Polymorphism

    DEFF Research Database (Denmark)

    Ernst, Erik

    2001-01-01

    safety and flexibility at the level of multi-object systems. We are granted the flexibility of using different families of kinds of objects, and we are guaranteed the safety of the combination. This paper highlights the inability of traditional polymorphism to handle multiple objects, and presents family...... polymorphism as a way to overcome this problem. Family polymorphism has been implemented in the programming language gbeta, a generalized version of Beta, and the source code of this implementation is available under GPL....

  13. A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding

    OpenAIRE

    Hsieh, Daniel; Davis, Alexander; Nanda, Vikas

    2011-01-01

    Outer membrane β-barrel proteins differ from α-helical inner membrane proteins in lipid environment, secondary structure, and the proposed processes of folding and insertion. It is reasonable to expect that outer membrane proteins may contain primary sequence information specific for their folding and insertion behavior. In previous work, a depth-dependent insertion potential, Ez, was derived for α-helical inner membrane proteins. We have generated an equivalent potential for TM β-barrel prot...

  14. ALS insertion devices

    International Nuclear Information System (INIS)

    The Advanced Light Source (ALS), the first US third generation synchrotron radiation source, is currently under construction at the Lawrence Berkeley Laboratory. The low-emittance, 1.5 GeV electron storage ring and the insertion devices are specifically designed to produce high brightness beams in the UV to soft X-Ray range. The planned initial complement of insertion devices includes four 4.6 m long undulators, with period lengths of 3.9 cm, 5.0 cm (2) and 8.0 cm, and a 2.9 m long wiggler of 16 cm period length. Undulator design is well advanced and fabrication has begun on the 5.0 cm and 8.0 cm period length undulators. This paper discusses ALS insertion device requirements; general design philosophy; and design of the magnetic structure, support structure/drive systems, control system and vacuum system. 18 refs., 9 figs., 5 tabs

  15. Distribution of Insertion- and Deletion-Associated Genetic Polymorphisms among Four Mycobacterium tuberculosis Phospholipase C Genes and Associations with Extrathoracic Tuberculosis: a Population-Based Study

    OpenAIRE

    Kong, Y.; Cave, M D; D. Yang; Zhang, L.; Marrs, C. F.; Foxman, B; Bates, J. H.; Wilson, F.; Mukasa, L. N.; Yang, Z H

    2005-01-01

    The Mycobacterium tuberculosis genome contains four phospholipase C (PLC)-encoding genes, designated plcA, plcB, plcC, and plcD, respectively. Each of the four genes contributes to the overall PLC activity of M. tuberculosis. PLC is hypothesized to contribute to M. tuberculosis virulence. Infection of M. tuberculosis strains carrying a truncated plcD gene is associated with the occurrence of extrathoracic tuberculosis. However, whether the other three plc genes are also associated with extrat...

  16. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers

    OpenAIRE

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-01-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 lan...

  17. Pro-opiomelanocortin gene and melanin-based colour polymorphism in a reptile

    OpenAIRE

    Ducrest A.L.; Ursenbacher S.; Golay P.; Monney J.C.; Mebert K.; Roulin A.; Dubey S

    2014-01-01

    Colour polymorphism is widespread among vertebrates and plays important roles in prey-predator interactions, thermoregulation, social competition, and sexual selection. However, the genetic mechanisms involved in colour variation have been studied mainly in domestic mammals and birds, whereas information on wild animals remains scarce. Interestingly, the pro-opiomelanocortin gene (POMC) gives rise to melanocortin hormones that trigger melanogenesis (by binding the melanocortin-1-receptor; Mc1...

  18. Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism.

    OpenAIRE

    Whittam, T S; Clark, A. G.; Stoneking, M; Cann, R. L.; Wilson, A. C.

    1986-01-01

    Restriction maps of 145 human mtDNAs representing samples from five geographic regions were used to construct multilocus genotypes for 28 genetic loci of the mitochondrial genome. Alleles were defined as distinct combinations of the presence or absence of polymorphic restriction sites within each locus. The 28 loci included 13 genes encoding proteins, 10 genes specifying tRNAs, 2 genes specifying rRNAs, and 3 noncoding regions consisting of the D loop, the light strand origin of replication, ...

  19. Genetic Contributions to Avoidance-Based Decisions: Striatal D2 receptor Polymorphisms

    OpenAIRE

    Frank, Michael J.; Hutchison, Kent

    2009-01-01

    Individuals differ in their tendencies to seek positive decision outcomes or to avoid negative ones. At the neurobiological level, our model suggests that phasic changes in dopamine support learning to reinforce good decisions via striatal D1 receptors, and to avoid maladaptive choices via striatal D2 receptors. Accordingly, in a previous study individual differences in positive and negative learning were strongly modulated by two genetic polymorphisms factors related to striatal D1 and D2 fu...

  20. Population-based investigations to study the association of cardiovascular polymorphisms and adverse pregnancy outcome

    DEFF Research Database (Denmark)

    Lykke, Jacob Alexander; Langhoff-Roos, Jens; Young, Bradford;

    2007-01-01

    Adverse pregnancy outcome refers to placenta-mediated complications that may share a common etiopathogenesis in some cases. Unraveling associations between prothrombotic genetic predispositions and these pregnancy disorders, namely recurrent fetal loss, stillbirth, severe preeclampsia, intrauterine...... study focuses on pro-thrombotic and cardiovascular genetic polymorphisms in a nested-case control study comparing pregnancies with and without an adverse pregnancy outcome in the index pregnancy. This study will be adequately powered to determine the relationship between adverse pregnancy outcome and...

  1. Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism

    Directory of Open Access Journals (Sweden)

    Sukhjiwan Kaur

    2014-01-01

    Full Text Available Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L. genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA, deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain.

  2. Development and evaluation of a LOR-based image reconstruction with 3D system response modeling for a PET insert with dual-layer offset crystal design

    International Nuclear Information System (INIS)

    In this study we present a method of 3D system response calculation for analytical computer simulation and statistical image reconstruction for a magnetic resonance imaging (MRI) compatible positron emission tomography (PET) insert system that uses a dual-layer offset (DLO) crystal design. The general analytical system response functions (SRFs) for detector geometric and inter-crystal penetration of coincident crystal pairs are derived first. We implemented a 3D ray-tracing algorithm with 4π sampling for calculating the SRFs of coincident pairs of individual DLO crystals. The determination of which detector blocks are intersected by a gamma ray is made by calculating the intersection of the ray with virtual cylinders with radii just inside the inner surface and just outside the outer-edge of each crystal layer of the detector ring. For efficient ray-tracing computation, the detector block and ray to be traced are then rotated so that the crystals are aligned along the X-axis, facilitating calculation of ray/crystal boundary intersection points. This algorithm can be applied to any system geometry using either single-layer (SL) or multi-layer array design with or without offset crystals. For effective data organization, a direct lines of response (LOR)-based indexed histogram-mode method is also presented in this work. SRF calculation is performed on-the-fly in both forward and back projection procedures during each iteration of image reconstruction, with acceleration through use of eight-fold geometric symmetry and multi-threaded parallel computation. To validate the proposed methods, we performed a series of analytical and Monte Carlo computer simulations for different system geometry and detector designs. The full-width-at-half-maximum of the numerical SRFs in both radial and tangential directions are calculated and compared for various system designs. By inspecting the sinograms obtained for different detector geometries, it can be seen that the DLO crystal

  3. HLA-G基因14bp插入/缺失多态性与不明原因复发性流产患者相关性的病例对照研究%Association between HLA-G 14-bp Insertion/Deletion Polymorphism and Women with Recurrent Spontaneous Abortions

    Institute of Scientific and Technical Information of China (English)

    张惠湘; 朱永生

    2012-01-01

    目的 探讨HLA-G基因3'非翻译区14bp插入/缺失多态性与不明原因复发性流产患者的相关性.方法 选择343名不明原因复发性流产患者,按照不同流产次数分为流产2次组(n=152),流产3次组(n=132),流产4次及以上组(n=59);268名正常妊娠妇女作为健康对照组.采用聚合酶链反应(PCR)及8%非变性聚丙烯酰胺凝胶电泳分离技术检测HLA-G基因14bp插入/缺失多态性位点在不明原因复发性流产患者及正常妊娠组中的基因型频率分布.结果 HLA-G基因14bp插入/缺失多态性位点的基因型频率分布在流产4次及以上组与正常妊娠组差异有统计学意义(χ2=6.941,P=0.031),流产4次及以上组+14bp等位基因频率分布显著高于正常妊娠组(χ2=4.956,P=0.026,OR=1.573,95%CI:1.054~2.349).结论 H LA-G 14 bp 缺失多态性在维持正常的妊娠中可能有重要作用.%Objective To investigate the association between HLA - G gene 14 - bp insertion/deletion polymorphism in 3 UTR and recurrent spontaneous abortions. Methods In this study, a total of 611 Chinese women were genotyped for the + 14 - bp/14 - bp polymorphism, including 343 who had recurrent spontaneous abortions (two miscarriages; 152, three miscarriages; 132, four or more miscarriages; 59) , 268 women with normal fertility as controls. Results To our knowledge, this is the first report that Significant difference was observed in the distribution of + 14 - bp/ + 14 - bp genotype between controls and the recurrent abortion group with four or more abortions ( X2 = 6. 941, P - 0. 031 ) . The + 14 - bp homozygote sequence was more prominent among those with recurrent spontaneous abortions (four or more recurrent miscarriages) in contrast to fertile control women (X2 = 4.956, P=0.026, OR =1.573, 95%CI: 1.054 ~2. 349). Conclusion A 14 - bp insertion/deletion polymorphism in exon 8 has a possible role in HLA ?G expression in certain cases of recurrent spontaneous abortions. However, additional

  4. Effect of insertion of xanthan-based chlorhexidine gel in the maintenance phase following the treatment of chronic periodontitis

    OpenAIRE

    Verma, Ashish; Sanghi, Swati; Grover, Dimple; Aggarwal, Shweta; Gupta, Rajan; Pandit, Nymphea

    2012-01-01

    Objectives: The aim of this study was to evaluate the efficacy of subgingivally administered xanthan-based chlorhexidine gel when used in the maintenance phase following scaling and root planing (SRP) in the treatment of chronic periodontitis. Materials and Methods: A randomized, controlled, single-center study was conducted involving 92 sites in 46 systemically healthy patients suffering from moderate to advanced chronic periodontitis with isolated pockets. The selected sites were randomized...

  5. The base adaptation of Complete Denture insertion%全口义齿基托的临床检查和调改

    Institute of Scientific and Technical Information of China (English)

    吴国锋

    2012-01-01

    Insertion of Complete Dentures represents the climax of a series of carefully planned and executed clinical procedures for the denture bases. The primary objectives of this appointment are to perfect the adaptation of the dentures to the oral structures and the following steps should be done carefully with great precision. Disclosing wax is used to check the length of the denture borders. The adaptation of the denture bearing surface to the hard and soft tissues of oral structures is tested by the use of pressure indicator paste (P. I. P. ). Phonetic E-valuation should be done with P. I. P. , and confirms that the contour of denture polishing surface works well with the oral soft tissues. This article illustrated and described the above clinical procedures, such as the use of pressure indicating paste and disclosing wax to eliminate potential mucosal irritation immediately following insertion of the denture, and many other important concepts, are beautifully illustrated and described.%全口义齿初戴应该包括一套完整的对义齿基托检查、调改的临床操作步骤,其目的是保证义齿基托与患者口腔组织良好适合.义齿基托检查需要非常仔细并且准确,可以通过以下材料和方法按顺序进行:基托边缘通过边缘指示蜡进行;基托组织面采用压力指示剂检查;基托磨光面也可以通过压力指示剂检查患者发音情况来调改.本文通过临床图片详细介绍了全口义齿基托在临床初戴与调改的整个过程.

  6. Progress in development of coated indexable cemented carbide inserts for machining of iron based work piece materials

    Science.gov (United States)

    Czettl, C.; Pohler, M.

    2016-03-01

    Increasing demands on material properties of iron based work piece materials, e.g. for the turbine industry, complicate the machining process and reduce the lifetime of the cutting tools. Therefore, improved tool solutions, adapted to the requirements of the desired application have to be developed. Especially, the interplay of macro- and micro geometry, substrate material, coating and post treatment processes is crucial for the durability of modern high performance tool solutions. Improved and novel analytical methods allow a detailed understanding of material properties responsible for the wear behaviour of the tools. Those support the knowledge based development of tailored cutting materials for selected applications. One important factor for such a solution is the proper choice of coating material, which can be synthesized by physical or chemical vapor deposition techniques. Within this work an overview of state-of-the-art coated carbide grades is presented and application examples are shown to demonstrate their high efficiency. Machining processes for a material range from cast iron, low carbon steels to high alloyed steels are covered.

  7. Pixel detector insertion

    CERN Multimedia

    CMS

    2015-01-01

    Insertion of the Pixel Tracker, the 66-million-channel device used to pinpoint the vertex of each colliding proton pair, located at the heart of the detector. The geometry of CMS is a cylinder lying on its side (22 meters long and 15 meters high in dia

  8. The Composite Insertion Electrode

    DEFF Research Database (Denmark)

    Atlung, Sven; Zachau-Christiansen, Birgit; West, Keld;

    1984-01-01

    The specific energy obtainable by discharge of porous insertion electrodes is limited by electrolyte depletion in thepores. This can be overcome using a solid ion conductor as electrolyte. The term "composite" is used to distinguishthese electrodes from porous electrodes with liquid electrolyte...

  9. Inserting the CMS solenoid

    CERN Multimedia

    Maximilien Brice

    2005-01-01

    The huge superconducting solenoid for CMS is inserted into the cryostat barrel. CMS uses the world's largest thin solenoid, in terms of energy stored, and is 12 m long, with a diameter of 6 m and weighing 220 tonnes. When turned on the magnet will produce a field strength of 4 T using superconducting niobium-titanium material at 4.5 K.

  10. Performance enhancement of pentacene-based organic field-effect transistor by inserting a WO3 buffer layer

    International Nuclear Information System (INIS)

    The pentacene-based organic field effect transistor (OFET) with a thin transition metal oxide (WO3) layer between pentacene and metal (Al) source/drain electrodes was fabricated. Compared with conventional OFET with only metal Al source/drain electrodes, the introduction of the WO3 buffer layer leads to the device performance enhancement. The effective field-effect mobility and threshold voltage are improved to 1.90 cm2/(V·s) and 13 V, respectively. The performance improvements are attributed to the decrease of the interface energy barrier and the contact resistance. The results indicate that it is an effective approach to improve the OFET performance by using a WO3 buffer layer. (semiconductor devices)

  11. The Insertion and Management of External Ventricular Drains: An Evidence-Based Consensus Statement : A Statement for Healthcare Professionals from the Neurocritical Care Society.

    Science.gov (United States)

    Fried, Herbert I; Nathan, Barnett R; Rowe, A Shaun; Zabramski, Joseph M; Andaluz, Norberto; Bhimraj, Adarsh; Guanci, Mary McKenna; Seder, David B; Singh, Jeffrey M

    2016-02-01

    External ventricular drains (EVDs) are commonly placed to monitor intracranial pressure and manage acute hydrocephalus in patients with a variety of intracranial pathologies. The indications for EVD insertion and their efficacy in the management of these various conditions have been previously addressed in guidelines published by the Brain Trauma Foundation, American Heart Association and combined committees of the American Association of Neurological Surgeons and the Congress of Neurological Surgeons. While it is well recognized that placement of an EVD may be a lifesaving intervention, the benefits can be offset by procedural and catheter-related complications, such as hemorrhage along the catheter tract, catheter malposition, and CSF infection. Despite their widespread use, there are a lack of high-quality data regarding the best methods for placement and management of EVDs to minimize these risks. Existing recommendations are frequently based on observational data from a single center and may be biased to the authors' view. To address the need for a comprehensive set of evidence-based guidelines for EVD management, the Neurocritical Care Society organized a committee of experts in the fields of neurosurgery, neurology, neuroinfectious disease, critical care, pharmacotherapy, and nursing. The Committee generated clinical questions relevant to EVD placement and management. They developed recommendations based on a thorough literature review using the Grading of Recommendations Assessment, Development, and Evaluation system, with emphasis placed not only on the quality of the evidence, but also on the balance of benefits versus risks, patient values and preferences, and resource considerations. PMID:26738503

  12. Population-based investigations to study the association of cardiovascular polymorphisms and adverse pregnancy outcome

    DEFF Research Database (Denmark)

    Lykke, Jacob Alexander; Langhoff-Roos, Jens; Young, Bradford;

    2007-01-01

    Adverse pregnancy outcome refers to placenta-mediated complications that may share a common etiopathogenesis in some cases. Unraveling associations between prothrombotic genetic predispositions and these pregnancy disorders, namely recurrent fetal loss, stillbirth, severe preeclampsia, intrauteri...... pro-thrombotic and cardiovascular genetic polymorphisms. These studies are urgently needed to accurately assess the linkage between family history, presence of adverse pregnancy outcome, and long-term cardiovascular risk....... growth restriction, and placental abruption, requires rigorous epidemiological studies involving large cohorts of patients with sufficient numbers of the adverse pregnancy outcomes in question. Such is the case with the Denmark National Birth Cohort, which was initiated in 1996 and followed pregnant...

  13. Development of a new molecular subtyping tool for Salmonella enterica serovar Enteritidis based on single nucleotide polymorphism genotyping using PCR.

    Science.gov (United States)

    Ogunremi, Dele; Kelly, Hilary; Dupras, Andrée Ann; Belanger, Sebastien; Devenish, John

    2014-12-01

    The lack of a sufficiently discriminatory molecular subtyping tool for Salmonella enterica serovar Enteritidis has hindered source attribution efforts and impeded regulatory actions required to disrupt its food-borne transmission. The underlying biological reason for the ineffectiveness of current molecular subtyping tools such as pulsed-field gel electrophoresis (PFGE) and phage typing appears to be related to the high degree of clonality of S. Enteritidis. By interrogating the organism's genome, we previously identified single nucleotide polymorphisms (SNP) distributed throughout the chromosome and have designed a highly discriminatory PCR-based SNP typing test based on 60 polymorphic loci. The application of the SNP-PCR method to DNA samples from S. Enteritidis strains (n = 55) obtained from a variety of sources has led to the differentiation and clustering of the S. Enteritidis isolates into 12 clades made up of 2 to 9 isolates per clade. Significantly, the SNP-PCR assay was able to further differentiate predominant PFGE types (e.g., XAI.0003) and phage types (e.g., phage type 8) into smaller subsets. The SNP-PCR subtyping test proved to be an accurate, precise, and quantitative tool for evaluating the relationships among the S. Enteritidis isolates tested in this study and should prove useful for clustering related S. Enteritidis isolates involved in outbreaks. PMID:25297333

  14. COMT and MAO-A polymorphisms and obsessive-compulsive disorder: a family-based association study.

    Directory of Open Access Journals (Sweden)

    Aline Santos Sampaio

    Full Text Available Obsessive-compulsive disorder (OCD is a common and debilitating psychiatric illness. Although a genetic component contributes to its etiology, no single gene or mechanism has been identified to the OCD susceptibility. The catechol-O-methyltransferase (COMT and monoamine oxidase A (MAO-A genes have been investigated in previous OCD studies, but the results are still unclear. More recently, Taylor (2013 in a comprehensive meta-analysis of genetic association studies has identified COMT and MAO-A polymorphisms involved with OCD. In an effort to clarify the role of these two genes in OCD vulnerability, a family-based association investigation was performed as an alternative strategy to the classical case-control design.Transmission disequilibrium analyses were performed after genotyping 13 single-nucleotide polymorphisms (eight in COMT and five in MAO-A in 783 OCD trios (probands and their parents. Four different OCD phenotypes (from narrow to broad OCD definitions and a SNP x SNP epistasis were also analyzed.OCD, broad and narrow phenotypes,were not associated with any of the investigated COMT and MAO-A polymorphisms. In addition, the analyses of gene-gene interaction did not show significant epistatic influences on phenotype between COMT and MAO-A.The findings do not support an association between DSM-IV OCD and the variants of COMT or MAO-A. However, results from this study cannot exclude the contribution of these genes in the manifestation of OCD. The evaluation of broader spectrum phenotypes could help to understand the role of these and other genes in the pathophysiology of OCD and its spectrum disorders.

  15. Gender based disruptive selection maintains body size polymorphism in Drosophila melanogaster

    Indian Academy of Sciences (India)

    Jaya Handa; K T Chandrashekara; Khushboo Kashyap; Geetanjali Sageena; Mallikarjun N Shakarad

    2014-09-01

    Darwinian fitness in holometabolous insects like the fruit fly Drosophila melanogaster is reported to be positively correlated with body size. If large individuals in a population have higher fitness, then one would expect directional selection to operate leading to uniformly large individuals. However, size polymorphism persists in nature and needs further probing. We assessed the effect of body size on some of the fitness and fitness-related traits in replicate populations of genotypically large, genotypically small and phenotypically small D. melanogaster flies. In this study, the time taken to attain reproductive maturity and copulation duration were independent of fly size. Fecundity and longevity of large females were significantly higher when they partnered genotypically small males than when they were with genotypically larger or phenotypically small males. The increased female longevity when in association with genotypically small males was not due to selective early death of males that would release the female partner from presumed cost of persistent courtship. On the contrary, the genotypically as well as phenotypically small males had significantly higher longevity than large males. The virility of the genotypically small males was not significantly different from that of genotypically large males. Our results clearly show that selection on body size operates in the opposite direction (disruptive selection) for the two genders, thus explaining the persistence of size polymorphisms in the holometabolous insect, Drosophila melanogaster.

  16. Genetic Variability in Rhizoctonia solani Isolated from Vitis vinifera Based on Amplified Fragment Length Polymorphism

    Directory of Open Access Journals (Sweden)

    Amparo Meza-Moller

    2011-01-01

    Full Text Available Problem statement: Rhizoctonia solani is a potential grapevine pathogen. In order to develop effective methods of control, it is necessary to document its genetic diversity. Approach: The objective of this study was to analyze the genetic variability of R. solani isolated from the rhizosphere of ungrafted V. vinifera var. perlette seedless planted in Sonora, Mexico using Amplified Fragment Length Polymorphism (AFLP. Results: In the selective amplification using eight primer combinations we obtained a total of 446 AFLP markers with a 100% polymorphism. Out of 41 isolates, 36 different AFLP patterns were observed and five were replicates of the same pattern. The dendrogram shows inter- and intrapopulation similarity indexes of 0.26, 0.98 and 0.31, 0.98, respectively. Six groups emerged from the principal components analysis, five of which were clearly defined, while the other one was spread out. Conclusion: We conclude that R. solani growing in Sonoran vineyards shows a high degree of genetic variability, even under similar environmental conditions.

  17. DNA polymorphisms in chickpea accessions as revealed by PCR-based markers.

    Science.gov (United States)

    Yadav, P; Koul, K K; Shrivastava, N; Mendaki, M J; Bhagyawant, S S

    2015-01-01

    Chickpea is a food legume which is alleged to be a preferred source of protein next only to milk. Germplasm of cultivated chickpea available is deficient in desired genetic variation. Genetic manipulations therefore, necessitate the genetic exploitation of its related annual and wild species. 42 RAPD and 41 ISSR markers were employed to ascertain polymorphism across 20 genotypes which were collected from 10 different geographical areas of the world. RAPD marker detected 51% genetic polymorphisms while ISSR marker detected 54 %. With an average of 6.5 each RAPD primer amplified 5—8 bands. Similarly with an average of 7.9 each ISSR primer amplified 4—12 bands. The cluster dendrogram demonstrated a similarity coefficient range from 0.80 to 0.92 due to RAPD markers, whereas with ISSR primers the cluster dendrogram showed similarity coefficient of 0.60 to 1.00. Accessions from same geographical area seem to be genetically similar than those from geographically distant and isolated ones. When however compared, interestingly the ISSR dendrogram showed more correlation with pedigree data than the RAPD dendrogram. The variability index worked out in the present study ranges from 0.79 to 0.96. Since the ultimate reason for such studies is selection of diverse genetic accessions for their recommendation to breeding programmers, the accessions like ICC6263, ICC6306 and ICC17160 can be recommended as parents. Further breeding programmes can therefore be planned to procure additional variation complexes in chickpea genetic stocks. PMID:26516116

  18. Discovery of unfixed endogenous retrovirus insertions in diverse human populations.

    Science.gov (United States)

    Wildschutte, Julia Halo; Williams, Zachary H; Montesion, Meagan; Subramanian, Ravi P; Kidd, Jeffrey M; Coffin, John M

    2016-04-19

    Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that remain nearly intact, a subset of which is present as insertionally polymorphic loci that include approximately full-length (2-LTR) and solo-LTR alleles in addition to the unoccupied site. Several 2-LTR insertions have intact reading frames in some or all genes that are expressed as functional proteins. These properties reflect the activity of HERV-K and suggest the existence of additional unique loci within humans. We sought to determine the extent to which other polymorphic insertions are present in humans, using sequenced genomes from the 1000 Genomes Project and a subset of the Human Genome Diversity Project panel. We report analysis of a total of 36 nonreference polymorphic HERV-K proviruses, including 19 newly reported loci, with insertion frequencies ranging from 0.75 that varied by population. Targeted screening of individual loci identified three new unfixed 2-LTR proviruses within our set, including an intact provirus present at Xq21.33 in some individuals, with the potential for retained infectivity. PMID:27001843

  19. Dependency of tunneling magneto-resistance on Fe insertion-layer thickness in Co2Fe6B2/MgO-based magnetic tunneling junctions

    International Nuclear Information System (INIS)

    For Co2Fe6B2/MgO-based perpendicular magnetic tunneling junctions spin valves with [Co/Pd]n-synthetic-antiferromagnetic (SyAF) layers, the tunneling-magneto-resistance (TMR) ratio strongly depends on the nanoscale Fe insertion-layer thickness (tFe) between the Co2Fe6B2 pinned layer and MgO tunneling barrier. The TMR ratio rapidly increased as tFe increased up to 0.4 nm by improving the crystalline linearity of a MgO tunneling barrier and by suppressing the diffusion of Pd atoms from a [Co/Pd]n-SyAF. However, it abruptly decreased by further increasing tFe in transferring interfacial-perpendicular magnetic anisotropy into the IMA characteristic of the Co2Fe6B2 pinned layer. Thus, the TMR ratio peaked at tFe = 0.4 nm: i.e., 120% at 29 Ωμm2

  20. Performance of the Insertable B-Layer for the ATLAS Pixel Detector during Quality Assurance and a Novel Pixel Detector Readout Concept based on PCIe

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00356268; Pernegger, Heinz

    2016-07-27

    During the first long shutdown of the LHC the Pixel detector has been upgraded with a new 4th innermost layer, the Insertable B-Layer (IBL). The IBL will increase the tracking performance and help with higher than nominal luminosity the LHC will produce. The IBL is made up of 14 staves and in total 20 staves have been produced for the IBL. This thesis presents the results of the final quality tests performed on these staves in an detector-like environment, in order to select the 14 best of the 20 staves for integration onto the detector. The test setup as well as the testing procedure is introduced and typical results of each testing stage are shown and discussed. The overall performance of all staves is presented in regards to: tuning performance, radioactive source measurements, and number of failing pixels. Other measurement, which did not directly impact the selection of staves, but will be important for the operation of the detector or production of a future detector, are included. Based on the experienc...

  1. A Flexible Crypto-system Based upon the REDEFINE Polymorphic ASIC Architecture

    Directory of Open Access Journals (Sweden)

    Ganesh Garga

    2012-01-01

    Full Text Available The highest levels of security can be achieved through the use of more than one type of cryptographic algorithm for each security function. In this paper, the REDEFINE polymorphic architecture is presented as an architecture framework that can optimally support a varied set of crypto algorithms without losing high performance. The presented solution is capable of accelerating the advanced encryption standard (AES and elliptic curve cryptography (ECC cryptographic protocols, while still supporting different flavors of these algorithms as well as different underlying finite field sizes. The compelling feature of this cryptosystem is the ability to provide acceleration support for new field sizes as well as new (possibly proprietary cryptographic algorithms decided upon after the cryptosystem is deployed.Defence Science Journal, 2012, 62(1, pp.25-31, DOI:http://dx.doi.org/10.14429/dsj.62.1438

  2. Genetic diversity analysis of Capsicum spp germplasm bank accessions based on α/β-esterase polymorphism.

    Science.gov (United States)

    Monteiro, E R; Bronzato, A R; Orasmo, G R; Lopes, A C A; Gomes, R L F; Mangolin, C A; Machado, M F P S

    2013-01-01

    Genetic diversity and structure were analyzed in 10 accessions belonging to Banco Ativo de Germoplasma de Capsicum located at Federal University of Piauí in northwestern Brazil that receives pepper samples grown in community gardens in various regions and Brazilian states. Selections were made from seeds of C. chinense (4 accessions), C. annuum (5 accessions), and C. baccatum (1 accession). Samples consisting of leaves were collected from 4-10 plants of each accession (a total of 85 plants). Native polyacrylamide gel electrophoresis was used to identify α- and β-esterase polymorphisms. Polymorphism was clearly detected in 5 loci. Sixteen alleles were found at 5 α/β-esterase loci of the three Capsicum species. In the C. chinense samples, the highest HO and HE values were 0.3625 and 0.4395, respectively, whereas in C. annuum samples, HO and HE values were 0.2980 and 0.3310, respectively; the estimated HO and HE values in C. chinense samples were higher than those detected in C. annuum samples. A deficit of homozygous individuals was found in C. chinense (FIS = -0.6978) and C. annuum (FIS = 0.7750). Genetic differentiation between C. chinense and C. annuum at these loci was high (FST = 0.1867) indicating that C. chinense and C. annuum are genetically structured species for α/β- esterase isozymes. The esterase analysis showed high genetic diversity among the C. chinense and C. annuum samples and very high genetic differentiation (FST = 0.6321) among the C. chinense and C. annuum samples and the C. baccatum accession. PMID:23661440

  3. XPA A23G polymorphism is associated with the elevated response to platinum-based chemotherapy in advanced non-small cell lung cancer

    Institute of Scientific and Technical Information of China (English)

    Jifeng Feng; Xinchen Sun; Ning Sun; Shukui Qin; Fan Li; Hongyan Cheng; Baoan Chen; YuanDong Cao; Jun Ma; Lu Cheng; Zuhong Lu; Jiazhong Ji; Yingfeng Zhou

    2009-01-01

    DNA repair capacity(DRC)is correlated with sensi tivity of cancer cells toward platinum-based chemotherapy.We hypothesize that genetic polymorphisms in DNA repair gene XPA(xeroderma pigmentosum group A)and XPG(xeroderma pigmentosum group G)(ERCC5,excision repair cross-complementation group 5),which result in inter-individual differences in DNA repair efficiency,may predict clinical response to platinum agents in advanced non-small cell lung cancer (NSCLC)patients.In this study,we find that the A→G change of XPA A23G polymorphism significantly increased response to platinum-based chemotherapy.Polymorphism in XPG His46His was associated with a decreased treatment response,but was not statistically significant.

  4. Strength of inserts in titanium alloy machining

    Science.gov (United States)

    Kozlov, V.; Huang, Z.; Zhang, J.

    2016-04-01

    In this paper, a stressed state of a non-worn cutting wedge in a machined titanium alloy (Ti6Al2Mo2Cr) is analyzed. The distribution of contact loads on the face of a cutting tool was obtained experimentally with the use of a ‘split cutting tool’. Calculation of internal stresses in the indexable insert made from cemented carbide (WC8Co) was carried out with the help of ANSYS 14.0 software. Investigations showed that a small thickness of the cutting insert leads to extremely high compressive stresses near the cutting edge, stresses that exceed the ultimate compressive strength of cemented carbide. The face and the base of the insert experience high tensile stresses, which approach the ultimate tensile strength of cemented carbide and increase a probability of cutting insert destruction. If the thickness of the cutting insert is bigger than 5 mm, compressive stresses near the cutting edge decrease, and tensile stresses on the face and base decrease to zero. The dependences of the greatest normal and tangential stresses on thickness of the cutting insert were found. Abbreviation and symbols: m/s - meter per second (cutting speed v); mm/r - millimeter per revolution (feed rate f); MPa - mega Pascal (dimension of specific contact loads and stresses); γ - rake angle of the cutting tool [°] α - clearance angle of the sharp cutting tool [°].

  5. Mechanism of Li insertion into TiO2 polymorphs

    Czech Academy of Sciences Publication Activity Database

    Zukalová, Markéta; Lásková, Barbora; Kavan, Ladislav

    Madrid : Formatex Research Centrum, 2015. s. 248. [The energy and Materials Research Conference - EMR2015. 25.2.2015-27.02.2015, Madrid] R&D Projects: GA ČR GA13-07724S; GA ČR(CZ) GAP108/12/0814; GA MŠk(CZ) LD13060 Grant ostatní: COST(XE) CM1104 Institutional support: RVO:61388955 Keywords : TiO2 * Lithium Subject RIV: CG - Electrochemistry

  6. ANGIOTENSIN I CONVERTING ENZYME GENE POLYMORPHISM AND EXERCISE TRAINABILITY IN ELDERLY WOMEN: AN ELECTROCARDIOLOGICAL APPROACH

    OpenAIRE

    Takuro Tobina; Akira Kiyonaga; Yuko Akagi; Yukari Mori; Kojiro Ishii; Hitoshi Chiba; Munehiro Shindo; Hiroaki Tanaka

    2007-01-01

    Angiotensin I converting enzyme (ACE) gene Insertion / Deletion (I/D) polymorphism is associated with exercise trainability and exercise induced left ventricular hypertrophy. However, it is unclear whether this polymorphism influences exercise trainability in the elderly, and the electrocardiological alterations by exercise training is unknown among the genotypes. We herein investigated the association between ACE gene insertion/deletion (I/D) polymorphism, exercise trainability and the elect...

  7. A gold nanoparticles-based colorimetric test to detect single nucleotide polymorphisms for improvement of personalized therapy of psoriasis

    Science.gov (United States)

    Marsella, Alessandra; Valentini, Paola; Tarantino, Paolo; Congedo, Maurizio; Pompa, Pier Paolo

    2016-04-01

    We report a simple, rapid and low-cost test, based on gold nanoparticles, for the naked-eye colorimetric detection of a signature of single nucleotide polymorphisms (SNPs) relevant for the personalized medicine of psoriasis patients. We validated the colorimetric assay on real-world DNA samples from a cohort of 30 psoriasis patients and we compared the results, in double-blind, with those obtained with two state-of-the-art instrumental techniques, namely reverse dot blotting and direct sequencing, finding 100% agreement. We demonstrated high accuracy, sensitivity and specificity of the colorimetric test that can be easily adapted for the genotypization of different SNPs, important for the pharmacogenomics of various diseases, and in other fields, such as food traceability and population structure analysis.

  8. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Mohamed N. Saad

    2016-01-01

    Full Text Available Genetics of autoimmune diseases represent a growing domain with surpassing biomarker results with rapid progress. The exact cause of Rheumatoid Arthritis (RA is unknown, but it is thought to have both a genetic and an environmental bases. Genetic biomarkers are capable of changing the supervision of RA by allowing not only the detection of susceptible individuals, but also early diagnosis, evaluation of disease severity, selection of therapy, and monitoring of response to therapy. This review is concerned with not only the genetic biomarkers of RA but also the methods of identifying them. Many of the identified genetic biomarkers of RA were identified in populations of European and Asian ancestries. The study of additional human populations may yield novel results. Most of the researchers in the field of identifying RA biomarkers use single nucleotide polymorphism (SNP approaches to express the significance of their results. Although, haplotype block methods are expected to play a complementary role in the future of that field.

  9. XPC Lys939Gln polymorphism is associated with the decreased response to platinum based chemotherapy in advanced non-small-cell lung cancer

    Institute of Scientific and Technical Information of China (English)

    ZHU Xiao-li; CHENG Lu; LU Zu-hong; SUN Xin-chen; CHEN Bao-an; SUN Ning; CHENG Hong-yan; LI Fan; ZHANG Hong-ming; FENG Ji-feng; QIN Shu-kui

    2010-01-01

    Background Platinum-based chemotherapeutics are the most common regimens for advanced non-small-cell lung cancer (NSCLC) patients, and genetic factors are thought to represent important determinants of drug efficacy. We prospectively assessed the status of the XPC Ala499Val and Lys939GIn gene polymorphisms and investigated whether these SNPs can predict the response to cisplatin/carboplatin-based regimens in advanced NSCLC patients in a Chinese population.Methods The treatment outcomes of 96 advanced NSCLC patients who were treated with platinum-based chemotherapy were evaluated. The polymorphic status of xeroderma pigmentosum group C (XPC) gene was genotyped by the 3-D polyacrylamide gel-based DNA microarray method.Results The distributions of XPC Lys939GIn genotypes differed significantly between the response group (complete +partial responses) and the non-response group (stable + progressive disease; P=0.022). The heterozygous A/C genotype carriers had a poorer response rate than the wild A/A genotype carriers in stage Ⅲ (OR, 0.074; 95% CI,0.008-0.704; P=0.023). The XPC Ala499Val polymorphisms were not associated with response to platinum-based chemotherapy.Conclusion Polymorphisms of the XPC gene, Lys939GIn, may be a predictive marker of treatment response for advanced NSCLC patients in stage Ⅲ.

  10. Etude de transistors en couches minces à base de silicium polymorphe pour leur application aux écrans plats à matrice active LCD ou OLED

    OpenAIRE

    Brochet, Julien,

    2011-01-01

    Ce travail a pour objectifs d'apporter des connaissances au niveau des propriétés électriques de transistors en couches minces (TFTs) à base de silicium polymorphe (pm-Si :H), ainsi qu'au niveau de la structure du matériau polymorphe. Nous nous sommes également intéressé à une nouvelle méthode de cristallisation d'une couche de silicium amorphe par interférométrie laser qui présente un fort potentiel pour le développement de matrice active en silicium polycristallin de grandes dimensions. Nou...

  11. Manganese superoxide dismutase Ala-9Val polymorphism and risk of breast cancer in a population-based case–control study of African Americans and whites

    OpenAIRE

    Millikan, Robert C.; Player, Jon; de Cotret, Allan René; Moorman, Patricia; Pittman, Gary; Vannappagari, Vani; Tse, Chiu-Kit J; Keku, Temitope

    2004-01-01

    Introduction A polymorphism in the manganese superoxide dismutase (MnSOD) gene, Ala-9Val, has been examined in association with breast cancer risk in several epidemiologic studies. Results suggest that the Ala allele increases the risk of breast cancer and modifies the effects of environmental exposures that produce oxidative damage to DNA. Methods We examined the role of the MnSOD Ala-9Val polymorphism in a population-based case–control study of invasive and in situ breast cancer in North Ca...

  12. Genetic Diversity of Eurycoma longifolia Jack Based on Random Amplified Polymorphic DNA Marker

    Directory of Open Access Journals (Sweden)

    Rosmaina Rosmaina

    2013-08-01

    Full Text Available Eurycoma longifolia Jack is one of the extensively exploited medicinal plants in Indonesia. The objectives of this study were to obtain information on genetic diversity and population genetic structure of E. longifolia to formulate effective conservation plan. RAPD marker was used to assess the genetic diversity of E. longifolia collected from 5 natural populations in Riau Province. A total of 25 plants were analyzed using 5 RAPD primers, which amplified produced 44 scored DNA bands. The mean observed number of alleles per locus (No, number of effective alleles (Ne, and percentage of polymorphic loci (PPL of E. longifolia were 1.57, 1.34, and 56.80%, respectively. The degree of differentiation among populations of E. longifolia was 0.31 (Ht = 0.29; Hs = 0.20.  The mean value of estimated gene flow among populations of E. longifolia was 1.11 individual per generation. The UPGMA dendogram formed 2 significant clusters. The first cluster consisted of Pelalawan and Kampar populations, while the second cluster was formed from Kuansing, Rohul, and Rohil population. The genetic diversity information in this study is very important to perform efficient conservation and effective future management of its genetic resources.Keywords: Eurycoma longifolia, RAPD marker, genetic variation, conservation DOI: 10.7226/jtfm.19.2.138

  13. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. PMID:26397421

  14. Patterns of sulphation in heparan sulphate: polymorphism based on a common structural theme.

    Science.gov (United States)

    Gallagher, J T; Turnbull, J E; Lyon, M

    1992-04-01

    HS appears to be a well-organised molecule with a domain structure that is apparently unique amongst the GAG family (Gallagher, 1989). Further refinements in sequence analysis are needed to corroborate the simplified model proposed in Fig. 4. It is still not clear why evolution has favoured a structural motif of widely spaced sulphated domains. Presumably, some advantages must accrue to the organism from this design, and one idea, that we have discussed previously, is that the polysaccharide functions as a "template" for the organisation of structural proteins in the ECM and for the binding and presentation of growth factors within the matrix polymer network. The sulphated regions are likely to display considerable conformational versatility as a result of the presence of the iduronate residues, and this property may be very important for the protein-binding properties of the polysaccharides (Casu et al., 1988). Sulphation patterns within these regions could favour oligosaccharide conformations necessary for specific protein interactions. An important question in this context is why different cells express on their surfaces HS with subtle differences in sulphation pattern. Perhaps the polymorphic features of HS are involved in higher-order tissue- and organ-specific mechanisms controlling cellular recognition and morphogenesis. The consistency with which aberrant sulphation of HS is detected in malignant disease (Gallagher and Lyon, 1989) in which cellular recognition and differentiation are impaired, adds some substance to this view. PMID:1516727

  15. Predictive value of XPD polymorphisms on platinum-based chemotherapy in non-small cell lung cancer: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Mantang Qiu

    Full Text Available BACKGROUND: The correlation between xeroderma pigmentosum group D (XPD polymorphisms (Lys751Gln and Asp312Asn and clinical outcomes of non-small cell lung cancer (NSCLC patients, who received platinum-based chemotherapy (Pt-chemotherapy, is still inconclusive. This meta-analysis was aimed to systematically review published evidence and ascertain the exact role of XPD polymorphisms. METHODS: Databases of MEDLINE and EMBASE were searched up to April 2013 to identify eligible studies. A rigorous quality assessment of eligible studies was conducted according the Newcastle-Ottawa Quality Assessment Scales. The relationship between XPD polymorphisms and response to Pt-chemotherapy and survival was analyzed. RESULTS: A total of 22 eligible studies were included and analyzed in this meta-analysis. The overall analysis suggested that the XPD Lys751Gln polymorphism was not associated with response to Pt-chemotherapy or survival. However, the XPD 312Asn allele was significantly associated with poor response to Pt-chemotherapy compared with the Asp312 allele (Asn vs. Asp: OR = 0.435, 95% CI: 0.261-0.726. Additionally, the variant genotype of XPD Asp312Asn polymorphism was associated with favorable survival in Caucasian (AspAsn vs. AspAsp: HR = 0.781, 95% CI: 0.619-0.986 but unfavorable survival in Asian (AspAsn+AsnAsn vs. AspAsp: HR = 1.550, 95% CI: 1.038-2.315. CONCLUSIONS: These results suggest that XPD Asp312Asn polymorphism may function as a predictive biomarker on platinum-based chemotherapy in NSCLC and further studies are warranted.

  16. Protocol of an expertise based randomized trial comparing surgical Venae Sectio versus radiological Puncture of Vena Subclavia for insertion of Totally Implantable Access Port in oncological patients

    Directory of Open Access Journals (Sweden)

    Radeleff Boris

    2008-10-01

    Full Text Available Abstract Background Totally Implantable Access Ports (TIAP are being extensively used world-wide and can be expected to gain further importance with the introduction of new neoadjuvant and adjuvant treatments in oncology. Two different techniques for the implantation can be selected: A direct puncture of a central vein and the utilization of a Seldinger device or the surgical Venae sectio. It is still unclear which technique has the optimal benefit/risk ratio for the patient. Design A single-center, expertise based randomized, controlled superiority trial to compare two different TIAP implantation techniques. 100 patients will be included and randomized pre-operatively. All patients aged 18 years or older scheduled for primary elective implantation of a TIAP under local anesthesia who signed the informed consent will be included. The primary endpoint is the primary success rate of the randomized technique. Control Intervention: Venae Sectio will be employed to insert a TIAP by a surgeon; Experimental intervention: Punction of V. Subclavia will be used to place a TIAP by a radiologist. Duration of study: Approximately 10 months, follow up time: 90 days. Organisation/Responsibility The PORTAS 2 – Trial will be conducted in accordance with the protocol and in compliance with the moral, ethical, and scientific principles governing clinical research as set out in the Declaration of Helsinki (1989 and Good Clinical Practice (GCP. The Center of Clinical Trials at the Department of Surgery, University Hospital Heidelberg is responsible for design and conduct of the trial including randomization and documentation of patients' data. Data management and statistical analysis will be performed by the independent Institute for Medical Biometry and Informatics (IMBI, University of Heidelberg. Trial Registration The trial is registered at ClinicalTrials.gov (NCT00600444.

  17. An aqueous capacitor battery hybrid device based on Na-ion insertion-deinsertion in λ-MnO2 positive electrode

    International Nuclear Information System (INIS)

    Highlights: • λ-MnO2 is synthesized via treating LiMn2O4 with H2SO4. • λ-MnO2 electrode exhibits a high specific capacity of 390.7 mAh g−1 at 13.6 mA g−1. • The capacitor battery AC/λ-MnO2 shows a specific energy of 19.7 Wh Kg−1 at a power density of 3500 W Kg−1. - Abstract: A high-performance capacitor battery AC/λ-MnO2 based on Na-ion insertion-deinsertion into λ-MnO2 in 1 mol dm−3 Na2SO4 solution is successfully demonstrated. A simple acid leaching technique is used to produce λ-MnO2 by treating LiMn2O4 with H2SO4. X-ray power diffraction and inductively coupled plasma analysis provide supporting evidences for the extraction of Li+ from the LiMn2O4, and the particle morphology of λ-MnO2 is studied by scanning and transmission electron microscopy. A high specific capacity of 390.7 mAh g−1 is obtained for the λ-MnO2 electrode at a current density of 13.6 mA g−1 with a nearly 100% efficiency. The capacitor battery AC/λ-MnO2 can operate at a cell voltage as high as 2.2 V, and it exhibits a specific energy of 19.7 Wh Kg−1 at a high power density of 3500 W Kg−1 and a high energy density of 71.7 Wh Kg−1 at a low power density of 403 W Kg−1. It has potentials to be used as an energy storage device for the integration of solar and wind power into the electrical power grid

  18. LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family.

    Science.gov (United States)

    Guffanti, Guia; Gaudi, Simona; Klengel, Torsten; Fallon, James H; Mangalam, Harry; Madduri, Ravi; Rodriguez, Alex; DeCrescenzo, Paula; Glovienka, Emily; Sobell, Janet; Klengel, Claudia; Pato, Michele; Ressler, Kerry J; Pato, Carlos; Macciardi, Fabio

    2016-06-01

    Recent studies show that human-specific LINE1s (L1HS) play a key role in the development of the central nervous system (CNS) and its disorders, and that their transpositions within the human genome are more common than previously thought. Many polymorphic L1HS, that is, present or absent across individuals, are not annotated in the current release of the genome and are customarily termed "non-reference L1s." We developed an analytical workflow to identify L1 polymorphic insertions with next-generation sequencing (NGS) using data from a family in which SZ segregates. Our workflow exploits two independent algorithms to detect non-reference L1 insertions, performs local de novo alignment of the regions harboring predicted L1 insertions and resolves the L1 subfamily designation from the de novo assembled sequence. We found 110 non-reference L1 polymorphic loci exhibiting Mendelian inheritance, the vast majority of which are already reported in dbRIP and/or euL1db, thus, confirming their status as non-reference L1 polymorphic insertions. Four previously undetected L1 polymorphic loci were confirmed by PCR amplification and direct sequencing of the insert. A large fraction of our non-reference L1s is located within the open reading frame of protein-coding genes that belong to pathways already implicated in the pathogenesis of schizophrenia. The finding of these polymorphic variants among SZ offsprings is intriguing and suggestive of putative pathogenic role. Our data show the utility of NGS to uncover L1 polymorphic insertions, a neglected type of genetic variants with the potential to influence the risk to develop schizophrenia like SNVs and CNVs. © 2016 Wiley Periodicals, Inc. PMID:26990047

  19. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  20. Genetic Diversity of Hexaploid Wheat Based on Polymorphism in Quality Characteristics

    Directory of Open Access Journals (Sweden)

    Sarwat Afshan

    2011-07-01

    Full Text Available High Molecular Weight Glutenin Subunits (HMW-GS were used as markers to assess the genetic diversity among 52 local wheat genotypes and their yield producing capacity with the object of exploiting diversity in the commercial varieties and landraces grown in different regions of Pakistan. HMW-GS profiling of wheat genotypes was done through SDS-PAGE; polymorphism was revealed at HMW-GS encoding loci; Glu-A1, Glu-B1 and Glu-D1; alleles 3, 6 and 4 were identified, respectively. The most common composition of HMW-GS in the population was 2*, 17+18, and 2+12. ANOVA revealed significant variation among the varieties for yield parameters and also there is correlation found between these parameters. The average intrapopulation heterozygosity for the three Glu-1 loci was high in Punjab (60.36% compared to the other populations that is Sindh (48.88%, Baluchistan (33.33%, Azad Jammu Kashmir (30.36% and Khyber Pakhtunkhwa (55.98%. Among populations Punjab had maximum genetic similarity of 93.04% with Sindh thus a small genetic distance of 7.21% which showed that the two populations are more identical. Genetic distance was large between the population of Azad Jammu Kashmir and Khyber Pakhtunkhwa. Though the bread-making quality of wheat is good but the heterogeneity is low among the wheat varieties of Pakistan showing a need for improving the genetic pool of the local genotypes for the future breeding programs.

  1. Molecular genetic characterization and urinary excretion pattern of metabolites in two families with MCAD deficiency due to compound heterozygosity with a 13 base pair insertion in one allele

    DEFF Research Database (Denmark)

    Gregersen, N; Winter, V; Lyonnet, S; Saudubray, J M; Wendel, U; Jensen, T G; Andresen, B S; Kølvraa, S; Lehnert, W; Bolund, L

    1994-01-01

    Two families with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency due to compound heterozygosity are described. All patients have a 13 bp insertion in exon 11 of one allele at the MCAD gene locus. In the other allele patients in one of the families harbour the prevalent G985 mutation, and t...

  2. Association between XPD (Lys751G1n Polymorphism and Lung Cancer Risk: A Population-Based Study in Iran

    Directory of Open Access Journals (Sweden)

    Majid Motovali-Bashi

    2014-04-01

    Full Text Available Objective: People are usually susceptible to carcinogenic aromatic amines, present in cigarrette smoke and polluted environment, which can cause DNA damage. Therefore, maintenance of genomic DNA integrity is a direct result of proper function of DNA repair enzymes. Polymorphic diversity could affect the function of repair enzymes and thus augment the risk of different cancers. Xeroderma pigmentosum group D (XPD gene encodes one of the most prominent repair enzymes and the polymorphisms of this gene are thought to be of importance in lung cancer risk. This gene encodes the helicase, which is a component of transcription factor IIH and an important part of the nucleotide excision repair system. Studies reveal that individuals with Lys751Gln polymorphism of XPD gene have a low repairing capacity to delete the damages of ultraviolet light among other XPD polymorphisms. Materials and Methods: In this case-control study, first Lys751Gln polymorphism was genotyped, then its association with lung cancer risk was analyzed. Genomic DNA was extracted from the whole blood sample of 640 individuals from Iran (352 healthy individuals and 288 patients. Allele frequencies and heterozygosity of Lys751Gln polymorphism were determined using polymerase chain reaction-restriction fragment length polymorphism method. Results: According to statistical analyses, lung cancer risk in individuals with Lys751Gln polymorphism (Odd Ratio=1.8, 95% Confidence Interval 0.848-3.819 is approximately twice as high as that of Lys/Lys genotype, however 751Gln/Gln genotype did not relate to lung cancer risk (Odd Ratio=0.7, 95% Confidence Interval 0/307-1/595. Conclusion: This study suggests that heterozygous polymorphism (Lys/Gln increases the sensitivity of lung cancer risk, while homozygous polymorphism (Lys/Lys probably decreases its risk and C allele frequency shows no remarkable increase in the patients.

  3. Association between Alu insertion polymorphisms and HLA class T alleles in Chinese Lisu and Nu ethnic populations%中国傈僳族和怒族群体人类白细胞抗原Ⅰ类基因区Alu插入多态性研究

    Institute of Scientific and Technical Information of China (English)

    董兆梅; 姚宇峰; 史磊; 陶玉芬; 林克勤; 黄小琴; 杨昭庆; 褚嘉祐; 史荔

    2012-01-01

    Objective To investigate the frequencies of HLA-Alu repeat polymorphisms (AluMICB,AluTF,AluHJ,AluHG and AluHF) in Chinese Lisu and Nu ethnic populations.Methods The frequencies of HLA-Alu repeat polymorphisms in above populations were determined with polymerase chain reaction (PCR).The associations between HLA-Alu repeat polymorphisms and HLA-A,HLA-B and HLA-C alleles were also analyzed.Phylogenetic trees were constructed with genetic distance calculated from the frequencies of HLA-Alu repeat polymorphisms.Results Frequencies of AluTF * 2 and AluHF * 2 were different between the two populations (P<0.05),while those of other three insertions were similar.The strength of association between HLA-Alus and HLA alleles were different (P<0.05) in the two populations.Although AluMICB * 2 were associated with HLA-B* 56:01 in both populations,the association was stronger in Lisu population (74.0%) but moderate in Nu population (30.7%).HLA-Alus were associated with particular HLA subtypes,e.g.,AluHG * 2 with certain HLA-A * 02 subtypes.By phylogenetic analysis,Lisu and Nu were clustered together with southern Chinese and Thai populations.Conclusion The distribution of HLA-Alus and the strength of associations between HLA-Alus and HLA class I alleles have varied between the two populations.Study of this association may facilitate identification of origins,evolution,progenitor haplotypes and recombination within the HLA class I region.%目的 研究中国两个隔离群体(傈僳族和怒族)人类白细胞抗原(human leukocyte antigen,HLA)Ⅰ类基因区域内5个HLA-Alu插入多态性(AluMICB、AluTF、AluHJ、AluHG和AluHF)的分布特征.方法 应用聚合酶链反应技术对中国两个隔离群体傈僳族(107人)和怒族(104人)进行HLA-Alu多态性分型.结合HLA基因分型数据,分析这两个群体中HLA-Alu插入与HLA-A、HLA-B和HLA-C基因的关系.根据HLA-Alu频率计算各群体间遗传距离,构建系统进化树.结果 AluTF和AluHF插入

  4. Correction of Multipolar Field Errors in Insertion Regions for the Phase 1 LHC Upgrade and Dynamic Aperture

    CERN Document Server

    Tomás, R; de Maria, R

    2008-01-01

    The Phase 1 upgrade of the LHC interaction regions aims at increasing the machine luminosity by reducing the beam size at the interaction point. This requires an in-depth review of the full insertion region layout and a large set of options have been proposed with conceptually different designs. This paper reports on a general approach for the compensation of the non-linear eld errors of the insertion region magnets by means of dedicated correctors. The goal is to use the same correction approach for all the different layouts. The correction algorithm is based on the computation of the high orders of the polynomial transfer map using MAD-X and Polymorphic Tracking Code, while the actual performance of the method is estimated by computing the dynamic aperture of the layouts under study.

  5. Tribenzoatobismuth(III: a new polymorph

    Directory of Open Access Journals (Sweden)

    Elena V. Boldyreva

    2010-10-01

    Full Text Available A new polymorph (β was obtained for an active pharmaceutical ingredient, bismuth tribenzoate, [Bi(C6H5CO23]. The new β-polymorph is 1.05 times denser than the previously known polymorph [Rae et al. (1998. Acta Cryst. B54, 438–442]. In the β-polymorph, the Bi atom is linked with three benzoate anions, each of them acting as a bidentate ligand, and these assemblies with C3 point symmetry can be considered as `molecules'. The structure of the β-polymorph has no polymeric chains, in contrast to the previously known polymorph. The `molecules' in the β-polymorph are stacked along [001], so that the phenyl rings of the neighbouring molecules are parallel to each other. Based on the pronounced difference in the crystal structures, one can suppose that two polymorphs should differ in the dissolution kinetics and bioavailability.

  6. Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.

    Directory of Open Access Journals (Sweden)

    Jasmine I Daksis

    Full Text Available Human genomic samples are complex and are considered difficult to assay directly without denaturation or PCR amplification. We report the use of a base-specific heteropolymeric triplex, formed by native duplex genomic target and an oligonucleotide third strand probe, to assay for low copy pathogen genomes present in a sample also containing human genomic duplex DNA, or to assay human genomic duplex DNA for Single Nucleotide Polymorphisms (SNP, without PCR amplification. Wild-type and mutant probes are used to identify triplexes containing FVL G1691A, MTHFR C677T and CFTR mutations. The specific triplex structure forms rapidly at room temperature in solution and may be detected without a separation step. YOYO-1, a fluorescent bis-intercalator, promotes and signals the formation of the specific triplex. Genomic duplexes may be assayed homogeneously with single base pair resolution. The specific triple-stranded structures of the assay may approximate homologous recombination intermediates, which various models suggest may form in either the major or minor groove of the duplex. The bases of the stable duplex target are rendered specifically reactive to the bases of the probe because of the activity of intercalated YOYO-1, which is known to decondense duplex locally 1.3 fold. This may approximate the local decondensation effected by recombination proteins such as RecA in vivo. Our assay, while involving triplex formation, is sui generis, as it is not homopurine sequence-dependent, as are "canonical triplexes". Rather, the base pair-specific heteropolymeric triplex of the assay is conformation-dependent. The highly sensitive diagnostic assay we present allows for the direct detection of base sequence in genomic duplex samples, including those containing human genomic duplex DNA, thereby bypassing the inherent problems and cost associated with conventional PCR based diagnostic assays.

  7. Facility target insert shielding assessment

    Energy Technology Data Exchange (ETDEWEB)

    Mocko, Michal [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-06

    Main objective of this report is to assess the basic shielding requirements for the vertical target insert and retrieval port. We used the baseline design for the vertical target insert in our calculations. The insert sits in the 12”-diameter cylindrical shaft extending from the service alley in the top floor of the facility all the way down to the target location. The target retrieval mechanism is a long rod with the target assembly attached and running the entire length of the vertical shaft. The insert also houses the helium cooling supply and return lines each with 2” diameter. In the present study we focused on calculating the neutron and photon dose rate fields on top of the target insert/retrieval mechanism in the service alley. Additionally, we studied a few prototypical configurations of the shielding layers in the vertical insert as well as on the top.

  8. Novel insertion mutation of ABCB1 gene in an ivermectin-sensitive Border Collie.

    Science.gov (United States)

    Han, Jae-Ik; Son, Hyoung-Won; Park, Seung-Cheol; Na, Ki-Jeong

    2010-12-01

    P-glycoprotein (P-gp) is encoded by the ABCB1 gene and acts as an efflux pump for xenobiotics. In the Border Collie, a nonsense mutation caused by a 4-base pair deletion in the ABCB1 gene is associated with a premature stop to P-gp synthesis. In this study, we examined the full-length coding sequence of the ABCB1 gene in an ivermectin-sensitive Border Collie that lacked the aforementioned deletion mutation. The sequence was compared to the corresponding sequences of a wild-type Beagle and seven ivermectin-tolerant family members of the Border Collie. When compared to the wild-type Beagle sequence, that of the ivermectin-sensitive Border Collie was found to have one insertion mutation and eight single nucleotide polymorphisms (SNPs) in the coding sequence of the ABCB1 gene. While the eight SNPs were also found in the family members' sequences, the insertion mutation was found only in the ivermectin-sensitive dog. These results suggest the possibility that the SNPs are species-specific features of the ABCB1 gene in Border Collies, and that the insertion mutation may be related to ivermectin intolerance. PMID:21113104

  9. Endoscopic grommet insertion our experience

    OpenAIRE

    Balasubramanian Thiagarajan; Venkatesan Ulaganathan; Seethalakshmi Narashiman

    2012-01-01

    Grommet insertion the commonest surgical procedure next only to circumcision is usually performed using an operating microscope 1. Authors have been using 4 mm 0 degree nasal endoscopes to perform this procedure during the last 5 years. This is a report of their experience in using endoscope inlieu of microscope in performing this surgery. This study makes a comparative analysis of Endoscopic Grommet insertion viz a viz Microscopic Grommet insertion. For this comparative analysis one year (20...

  10. Subjective Misidentification and Thought Insertion

    OpenAIRE

    Parrott, Matthew Thomas

    2015-01-01

    This essay presents a new account of thought insertion. Prevailing views in both philosophy and cognitive science tend to characterize the experience of thought insertion as missing or lacking some element, such as a ‘sense of agency’, found in ordinary first-person awareness of one’s own thoughts. By contrast, I propose that, rather than lacking something, experiences of thought insertion have an additional feature not present in ordinary conscious experiences of one’s own thoughts. More spe...

  11. Post-CTS Delay Insertion

    OpenAIRE

    Jianchao Lu; Baris Taskin

    2010-01-01

    A post-clock-tree-synthesis (post-CTS) optimization method is proposed that suggests delay insertion at the leaves of the clock tree in order to implement a limited version of clock skew scheduling. Delay insertion is limited on each clock tree branch simultaneous with a global monitoring of the total amount of delay insertion. The delay insertion for nonzero clock skew operation is performed only at the clock sinks in order to preserve the structure and the optimizations implemented in the c...

  12. A fluorescence-based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp

    OpenAIRE

    Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Díez Baños, Pablo; Píriz, Ana; Fickel, Joerns; Sánchez, Antonio

    2011-01-01

    The present study aimed to establish a fluorescence- based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp. Based on the sequences of the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA, we designed a set of genus- specific primers for the amplification of Fasciola ITS-2, with an estimated size of 140 bp. These primers were labelled by fluorescence dyes, and the PCR products were an...

  13. Comparison of the clinical accuracy of cervical (C2-C7) pedicle screw insertion assisted by fluoroscopy, computed tomography-based navigation, and intraoperative three-dimensional C-arm navigation

    Institute of Scientific and Technical Information of China (English)

    LIU Ya-jun; TIAN Wei; LIU Bo; LI Qin; HU Lin; LI Zhi-yu; YUAN Qiang; L(U) Yan-wei; SUN Yu-zhen

    2010-01-01

    Background The complicated anatomy of the cervical spine and the variation among pedicles reduces the accuracy and increases the risk of neurovascular complications associated with screw implantation in this region. In this study, we compared the accuracy of cervical (C2-C7) pedicle screw fixation assisted by X-ray fluoroscopy, computed tomography (CT)-based navigation, or intraoperative three-dimensional (3D) C-arm navigation.Methods This prospective cohort study was performed in 82 consecutive patients who underwent cervical pedicle screw fixation. The accuracy of screw insertion was assessed by postoperative CT scan with 3D reconstruction. The accuracy of screw insertion was assessed as: excellent (screw completely within pedicle); acceptable (≤ 1 mm screw outside pedicle cortex); poor (>1 mm screw outside pedicle cortex).Results A total of 145 screws were inserted in 24 patients who underwent C-arm fluoroscopy. Of these, 96 screws (66.2%) were excellent, 37 (25.5%) were acceptable, and 12 (8.3%) were poor. One hundred and fifty-nine screws were inserted in 29 patients in the CT-based navigation group. Among these, 141 (88.7%) were excellent, 14 (8.8%) were acceptable, and 4 (2.5%) were poor. A total of 140 screws were inserted in 29 patients in the intraoperative 3D C-arm navigation group, of which 127 (90.7%) were excellent, and 13 (9.3%) were acceptable. No severe or permanent neurovascular complications associated with screw insertion were observed in any patient.Conclusione CT-based and intraoperative 3D C-arm navigation were similarly accurate, and were both significantly more accurate than C-arm fluoroscopy for guiding cervical pedicle screw fixation. They were able to accurately guide the angle and depth of screw placement using visual 3D images. These two techniques are therefore preferable for high-risk cervical pedicle screw fixation. The ease and convenience of intraoperative 3D C-arm navigation suggests that it may replace virtual

  14. Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.

    Science.gov (United States)

    Korkuc, Paula; Schippers, Jos H M; Walther, Dirk

    2014-01-01

    Identifying regulatory elements and revealing their role in gene expression regulation remains a central goal of plant genome research. We exploited the detailed genomic sequencing information of a large number of Arabidopsis (Arabidopsis thaliana) accessions to characterize known and to identify novel cis-regulatory elements in gene promoter regions of Arabidopsis by relying on conservation as the hallmark signal of functional relevance. Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. Genes associated with high degrees of variability of their respective upstream regions are preferentially involved in environmental response and signaling processes, while low levels of promoter SNP density are common among housekeeping genes. Known cis-elements were found to exhibit a decreased SNP density than sequence regions not associated with known motifs. For 15 known cis-element motifs, strong positional preferences relative to the transcription start site were detected based on their promoter SNP density profiles. Five novel candidate cis-element motifs were identified as consensus motifs of 17 sequence hexamers exhibiting increased sequence conservation combined with evidence of positional preferences, annotation information, and functional relevance for inducing correlated gene expression. Our study demonstrates that the currently available resolution of SNP data offers novel ways for the identification of functional genomic elements and the characterization of gene promoter sequences. PMID:24204023

  15. Differential diagnosis of Brucella abortus by real-time PCR based on a single-nucleotide polymorphisms.

    Science.gov (United States)

    Kim, Ji-Yeon; Kang, Sung-Il; Lee, Jin Ju; Lee, Kichan; Sung, So-Ra; Erdenebaataar, Janchivdorj; Vanaabaatar, Batbaatar; Jung, Suk Chan; Park, Yong Ho; Yoo, Han-Sang; Her, Moon

    2016-05-01

    To diagnose brucellosis effectively, many genus- and species-specific detection methods based on PCR have been developed. With conventional PCR assays, real-time PCR techniques have been developed as rapid diagnostic tools. Among them, real-time PCR using hybridization probe (hybprobe) has been recommended for bacteria with high DNA homology among species, with which it is possible to make an accurate diagnosis by means of an amplification curve and melting peak analysis. A hybprobe for B. abortus was designed from a specific single-nucleotide polymorphism (SNP) on the fbaA gene. This probe only showed specific amplification of B. abortus from approximately the 14th cycle, given a melting peak at 69°C. The sensitivity of real-time PCR was revealed to be 20 fg/µl by 10-fold DNA dilution, and the detection limit was 4 CFU in clinical samples. This real-time PCR showed greater sensitivity than that of conventional PCR and previous real-time PCR based on Taqman probe. Therefore, this new real-time PCR assay could be helpful for differentiating B. abortus infection with rapidity and accuracy. PMID:26666176

  16. UGT1A1 gene polymorphism: Impact on toxicity and efficacy of irinotecan-based regimens in metastatic colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Christoph Schulz; Volker Heinemann; Andreas Schalhorn; Nikolas Moosmann; Thomas Zwingers; Stefan Boeck; Clemens Giessen; Hans-Joachim Stemmler

    2009-01-01

    AIM: To investigate the correlation between uridine diphosphate glucuronosyl transferase 1A1 ( UGT1A1) gene polymorphisms and irinotecan-associated side effects and parameters of drug efficacy in patients with metastatic colorectal cancer (mCRC) receiving a lowdose weekly irinotecan chemotherapeutic regimen.METHODS: Genotypes were retrospectively evaluated by gene scan analysis on the ABI 310 sequencer of the TATAA box in the promoter region of the UGT1A1 gene in blood samples from 105 patients who had received 1st line irinotecan-based chemotherapy for mCRC.RESULTS: The distribution of the genotypes was as follows: wild type genotype (WT) ( 6/6) 39.0%,heterozygous genotype ( 6/7) 49.5%, and homozygous genotype ( 7/7) 9.5%. The overall response rate (OR) was similar between patients carrying the ( 6/7, 7/7) or the WT genotype ( 6/6) (44.3% vs 43.2%, P = 0.75).Neither time to progression [(TTP) 8.1 vs 8.2 mo, P = 0.97] nor overall survival [(OS) 21.2 vs 18.9 mo, P = 0.73] differed significantly in patients who carried the ( 6/6) when compared to the ( 6/7, 7/7) genotype. No significant differences in toxicity were observed: Grade 3 and 4 delayed diarrhoea [( 6/7, 7/7) vs ( 6/6); 13.0% vs 6.2%, P =0.08], treatment delays [( 6/7, 7/7) vs ( 6/6); 25.1% vs 19.3%, P = 0.24] or dose reductions [( 6/7, 7/7) vs ( 6/6); 21.5% vs 27.2%, P = 0.07].CONCLUSION: This analysis demonstrates the nonsignificant influence of the UGT1A1 gene polymorphism on efficacy and rate of irinotecan-associated toxicity in mCRC patients receiving low-dose irinotecan based chemotherapy.

  17. Modification of ZnS-inserting layer in the TiO2 inverse opal-based photoanode to enhance the efficiency of quantum dot-sensitized solar cells

    Science.gov (United States)

    Deng, Fei; Wan, Xiangyu; Mei, Xingan; Fan, Runzhou; Yan, Xuemin; Wan, Li; Shi, Dean; Xiong, Yan

    2016-07-01

    Modification of ZnS-inserting layer in the titanium dioxide (TiO2) inverse opal-based photoanode was investigated, and it is an effective and easy approach to enhance the efficiency of quantum dot-sensitized solar cells (QDSSCs). The introduction of ZnS between TiO2 and quantum dots (QDs) not only enhanced the light harvesting of QDs on its top, but also lessened the charge-transfer resistances at the TiO2/QD/electrolyte interfaces. The TiO2 inverse opal-based QDSSCs increased the energy conversion efficiency by modifying the ZnS-inserting layer in the photoanode, particularly the CdS/CdSe QD co-sensitized solar cells which attained 79% rate of increase in cell efficiency.

  18. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales

    OpenAIRE

    Nikaido, Masato; Rooney, Alejandro P.; OKADA, Norihiro

    1999-01-01

    Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans, hippopotamuses, and ruminants form a monophyletic group. To further resolve the relationships among these taxa, we now have isolated and characterized 10 additional loci. A phylogenetic analysis of these data was able to resolve relationships among the major cetartiodactyl groups, thereby shedding light...

  19. 血管紧张素转换酶基因多态性与2型糖尿病肾病相关性的Meta分析%Correlation of Angiotensin-Ⅰ Converting Enzyme Gene Insertion (I), Deletion (D) Polymorphism and Type 2 Diabetic Nephropathy: A Meta-Analysis

    Institute of Scientific and Technical Information of China (English)

    左彦方; 龙爱梅; 黄晓青; 沈明静

    2012-01-01

    目的 通过Meta分析评估血管紧张素Ⅰ转换酶(ACE)基因内含子16插入(I)/缺失(D)多态性与2型糖尿病肾病之间的相关性,进而评估小样本研究的偏倚及研究间异质性.方法 计算机检索MEDLINE、EBSCO、EMbase、PubMed、CHKD、CNKI、CBM、VIP和WanFang Data中关于ACE基因插入/缺失多态性与糖尿病肾病(DN)相关性的病例对照研究,同时辅以文献追溯.检索时限均从1994年1月至2011年3月18日.由2位评价者按照纳入和排除标准独立选择文献、提取资料、评价质量,然后采用RevMan 5.0.0软件对纳入研究进行Meta分析.结果 最终纳入61个病例对照研究,共计9 979例2型糖尿病肾病患者,7 252例对照.Meta分析结果显示:与DD+ID基因型相比,Ⅱ基因型2型糖尿病患者发生DN的风险较低[OR=0.65,95%CI (0.57,0.74)].亚组分析结果显示,中国、日本和巴西2型糖尿病患者中,Ⅱ基因型有较低的DN发病风险,而在高加索、中东、印度、墨西哥、韩国、马来西亚2型糖尿病患者中,并未显示出这种相关性.结论 在2型糖尿病患者中,ACE基因插入/缺失多态性与DN相关,Ⅱ基因型个体DN患病率相对其他基因型更低,但不同种族间其相关性存在一定差异.%Objective To perform a meta-analysis and investigate the correlation between angiotensin-I converting enzyme gene insertion (I), deletion (D) polymorphism and type 2 diabetic nephropathy, assessing the bias of small sample size study and heterogeneity between studies. Methods MEDLINE, EBSCO, EMbase, PubMed, CHKD, CNKI, CBM, VIP and WanFang Data were searched (from January 1994 to March 18th 2011) for relevant case-control studies. Two reviewers independently identified the literature according to inclusion and exclusion criteria. Also references of the included literature were retrieved. Then data were extracted and assessed by the Newcastle-Ottawa Scale (NOS). Meta-analysis was performed using RevMan 5.0.0 software

  20. RERTR-12 Insertion 2 Irradiation Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Perez; G. S. Chang; D. M. Wachs; G. A. Roth; N. E. Woolstenhulme

    2012-09-01

    The Reduced Enrichment for Research and Test Reactor (RERTR) experiment RERTR-12 was designed to provide comprehensive information on the performance of uranium-molybdenum (U-Mo) based monolithic fuels for research reactor applications.1 RERTR-12 insertion 2 includes the capsules irradiated during the last three irradiation cycles. These capsules include Z, Y1, Y2 and Y3 type capsules. The following report summarizes the life of the RERTR-12 insertion 2 experiment through end of irradiation, including as-run neutronic analysis results, thermal analysis results and hydraulic testing results.

  1. Insertion device vacuum system designs

    International Nuclear Information System (INIS)

    Synchrotron light source insertion device vacuum systems now in operation and systems proposed for the future are reviewed. An overview of insertion devices is given and four generic vacuum chamber designs, transition section design and pumping considerations are discussed. Examples of vacuum chamber systems are presented

  2. ISR Superconducting High luminosity Insertion

    CERN Multimedia

    1981-01-01

    The picture shows two of the eight superconducting quadrupoles of the low-beta insertion at intersection I8.The increase of luminosity produced by this insertion was above a factor 7. At right one can also see the Open- Axial- Field Magnet. The person is Stephan Pichler. See also 7702690X, 8102123, 8010397, 8008332.

  3. Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens

    Directory of Open Access Journals (Sweden)

    Oulmouden Ahmad

    2006-02-01

    Full Text Available Abstract Background In chickens, three mutant alleles have been reported at the C locus, including the albino mutation, and the recessive white mutation, which is characterized by white plumage and pigmented eyes. The albino mutation was found to be a 6 bp deletion in the tyrosinase (TYR gene. The present work describes an approach to identify the structural rearrangement in the TYR gene associated with the recessive white mutation. Results Molecular analysis of the chicken TYR gene has revealed a major structural difference (Restriction Fragment Length Polymorphism, RFLP in the genomic DNA of the recessive white chicken. A major size difference of 7.7 kb was found in intron 4 of the TYR gene by long-range PCR. Molecular cloning and sequencing results showed the insertion of a complete avian retroviral sequence of the Avian Leukosis Virus (ALV family. Several aberrant transcripts of the tyrosinase gene were found in 10 week old recessive white chickens but not in the homozygous wild type colored chicken. We established a rapid genotyping diagnostic test based on the discovery of this retroviral insertion. It shows that all homozygous carriers of this insertion had a white plumage in various chicken strains. Furthermore, it was possible to distinguish heterozygous carriers from homozygous normal chickens in a segregating line. Conclusion In this study, we conclude that the insertion of a complete avian retroviral sequence in intron 4 of the tyrosinase gene is diagnostic of the recessive white mutation in chickens. This insertion causes aberrant transcripts lacking exon 5, and we propose that this insertion is the causal mutation for the recessive white allele in the chicken.

  4. Frequency of anareobic power among brasilians based on dermatoglyphics and R577X polymorphism of the ACTN3 protein

    Directory of Open Access Journals (Sweden)

    Carlos Renato Paz

    2013-06-01

    Full Text Available Dermatoglyphics and analysis of the Alpha-Actinin-3 gene are evaluative instruments frequently used to identify the sportive and general population profile associated with physical performance. This research aimed to determine, based on dermatoglyphic characteristics and the R577X polymorphism of Alpha-Actinin-3, the percentage of people in the State of Paraíba/Brazil, with unfavorable characteristics to excelling in sports that require anaerobic power. A descriptive study of profiles, with ex post facto typology, was performed. The dermatoglyphic fingerprint characteristics of 309 people (149 males and 160 females were identified, and ACTN3 genotype was analyzed in 96 people (40 males and 56 females. The dermatoglyphic data indicated that 5.8% of the study population fit the classification of anaerobic muscle power predisposition, while 94.2% did not fit on it. The genetic frequency analysis indicated that 19.8% of subjects in the sample had the XX mutant genotype. These results represent a substantial error reduction in the search for and selection of athletes with the potential for high performance, especially in those sports that require AMP.

  5. UTILIZATION OF DNA MARKERS BASED ON MICROSATELLITE POLYMORPHISM FOR IDENTIFICATION OF POTATO VARIETIES CULTIVATED IN THE CZECH REPUBLIC

    Directory of Open Access Journals (Sweden)

    Alena Nováková

    2011-01-01

    Full Text Available In the year 2007, there were one hundred and seventy-eight potato varieties enlisted in the Czech list of registered potato varieties. The classical morphometric approach to characterization is not effective for such a number of varieties especially for identification at the level of tubers. The needfulness of variety identification at the level of tubers is important mainly for trade aspect. The Czech law no.110/1997 Sb. about the food-stuff and tobacco products and the consequential ordinance (MZe č. 332 / 1997 Sb. require guarantee of variety declaration in commercial relation for table potato. In this study we analyzed twenty potato varieties (Solanum tuberosum L. cultivated in the Czech Republic. Every variety was represented by four independent replicates. This set of samples was analyzed by methods of PCR-SSR (Simple Sequence Repeats and PCR-ISSR (Inter Simple Sequence Repeats. We discovered that both of tested methods afford sufficient polymorphism for variety identification, but the method of PCR-ISSR is not utilizable, because we observed the variability within variety. For outright identification of the whole set of potato varieties cultivated in the Czech Republic we recommend to use SSR, AFLP and retrotransposene-based markers as well as morphological markers.

  6. Genetic diversity and relatedness of sweet cherry (Prunus avium L. cultivars based on single nucleotide polymorphic (SNP markers

    Directory of Open Access Journals (Sweden)

    Angel eFernandez i Marti

    2012-06-01

    Full Text Available Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD and SSR markers. This study was carried out to assess the utility of SNP markers generated from 3’UTRs for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars and old cultivars imported from different parts of the world were screened with 7 SSR markers developed from other Prunus species and with 40 SNPs obtained from 3’UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity and polymorphic information content (PIC values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, ‘Stella’ was separated from ‘Compact Stella’. This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3’ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping and study of genetic diversity in sweet cherry.

  7. Association between H-RAS T81C genetic polymorphism and gastrointestinal cancer risk: A population based case-control study in China

    Directory of Open Access Journals (Sweden)

    Li Qilong

    2008-09-01

    Full Text Available Abstract Background Gastrointestinal cancer, such as gastric, colon and rectal cancer, is a major medical and economic burden worldwide. However, the exact mechanism of gastrointestinal cancer development still remains unclear. RAS genes have been elucidated as major participants in the development and progression of a series of human tumours and the single nucleotide polymorphism at H-RAS cDNA position 81 was demonstrated to contribute to the risks of bladder, oral and thyroid carcinoma. Therefore, we hypothesized that this polymorphisms in H-RAS could influence susceptibility to gastrointestinal cancer as well, and we conducted this study to test the hypothesis in Chinese population. Methods A population based case-control study, including 296 cases with gastrointestinal cancer and 448 healthy controls selected from a Chinese population was conducted. H-RAS T81C polymorphism was genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP assay. Results In the healthy controls, the TT, TC and CC genotypes frequencies of H-RAS T81C polymorphism, were 79.24%, 19.87% and 0.89%, respectively, and the C allele frequency was 10.83%. Compared with TT genotype, the TC genotype was significantly associated with an increased risk of gastric cancer (adjusted OR = 3.67, 95%CI = 2.21–6.08, while the CC genotype showed an increased risk as well (adjusted OR = 3.29, 95%CI = 0.54–19.86, but it was not statistically significant. In contrast, the frequency of TC genotype was not significantly increased in colon cancer and rectal cancer patients. Further analysis was performed by combining TC and CC genotypes compared against TT genotype. As a result, a statistically significant risk with adjusted OR of 3.65 (95%CI, 2.22–6.00 was found in gastric cancer, while no significant association of H-RAS T81C polymorphism with colon cancer and rectal cancer was observed. Conclusion These findings indicate, for the first time, that there

  8. Association between H-RAS T81C genetic polymorphism and gastrointestinal cancer risk: A population based case-control study in China

    International Nuclear Information System (INIS)

    Gastrointestinal cancer, such as gastric, colon and rectal cancer, is a major medical and economic burden worldwide. However, the exact mechanism of gastrointestinal cancer development still remains unclear. RAS genes have been elucidated as major participants in the development and progression of a series of human tumours and the single nucleotide polymorphism at H-RAS cDNA position 81 was demonstrated to contribute to the risks of bladder, oral and thyroid carcinoma. Therefore, we hypothesized that this polymorphisms in H-RAS could influence susceptibility to gastrointestinal cancer as well, and we conducted this study to test the hypothesis in Chinese population. A population based case-control study, including 296 cases with gastrointestinal cancer and 448 healthy controls selected from a Chinese population was conducted. H-RAS T81C polymorphism was genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In the healthy controls, the TT, TC and CC genotypes frequencies of H-RAS T81C polymorphism, were 79.24%, 19.87% and 0.89%, respectively, and the C allele frequency was 10.83%. Compared with TT genotype, the TC genotype was significantly associated with an increased risk of gastric cancer (adjusted OR = 3.67, 95%CI = 2.21–6.08), while the CC genotype showed an increased risk as well (adjusted OR = 3.29, 95%CI = 0.54–19.86), but it was not statistically significant. In contrast, the frequency of TC genotype was not significantly increased in colon cancer and rectal cancer patients. Further analysis was performed by combining TC and CC genotypes compared against TT genotype. As a result, a statistically significant risk with adjusted OR of 3.65 (95%CI, 2.22–6.00) was found in gastric cancer, while no significant association of H-RAS T81C polymorphism with colon cancer and rectal cancer was observed. These findings indicate, for the first time, that there is an H-RAS T81C polymorphism existing in Chinese population

  9. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

    Science.gov (United States)

    Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut. PMID:26697032

  10. Association between the insertion/deletion polymorphism of angiotensinⅠ converting enzyme gene and human velocity endurance%人体无氧耐力与血管紧张素Ⅰ转换酶基因插入/缺失多态性的关联

    Institute of Scientific and Technical Information of China (English)

    俞红良; 张瑞萍; 刘涛

    2006-01-01

    异均无显著性意义(P>0.05).结论:人体血管紧张素Ⅰ转换酶基因插入/缺失多态性与速度耐力无关.%BACKGROUND: There are many studies on the association between the insertion/deletion (I/D) polymorphism of angiotensin Ⅰ converting enzyme(ACE) gene and human velocity endurance at home and abroad, but differences in subjects, such as race difference, methods, condition resulted in different findings. 800-meter race is a better test to reflect human velocity endurance. OBJECTIVE: To investigate the association between the I/D polymorphism in the ACE gene and human velocity endurance.DESIGN: Controlled observation.SETTING: Center for Physical Ability, Scientific Research Institute, Chinese PLA Institute of Physical Education. PARTICIPANTS: Forty health male subjects of Han population, aged (21±2) years, were enrolled in the study at the Chinese PLA Institute of Physical Education from June to July 2004. They had similar sports history, and no history of cardiovascular diseases and diabetes mellitus.METHODS: 3 mL blood was extracted from subjects' peripheral veins to detect the I/D polymorphism in ACE gene by using polymerase chain reaction(PCR) technique. The results of 800-meter race were recorded, and the concentration of blood lactic acid was measured before and after 800-meter race with YSI 1 500 SPORT Lactate Analyzer. All the subjects were divided into high-velocity endurance group and low-velocity endurance group according to the results of 800-meter race.MAIN OUTCOME MEASURES: Detection of I/D genotype, result of 800-meter race, and concentration of blood lactic acid.RESULTS: Forty subjects were enrolled and involved in the result analysis. ①There were three I/D genotypes: Ⅱ(490 bp), DD(190 bp), ID(190,490 bp). ②According to the running speed in 800-meter race, 40 subjects were classified into three types: the first 18 subjects were considered astype 1, the last one as type 3, and others as type 2. Analysis of variancede monstrated that the probability of

  11. Targeted chromosomal insertion of large DNA into the human genome by a fiber-modified high-capacity adenovirus-based vector system.

    Directory of Open Access Journals (Sweden)

    Manuel A F V Gonçalves

    Full Text Available A prominent goal in gene therapy research concerns the development of gene transfer vehicles that can integrate exogenous DNA at specific chromosomal loci to prevent insertional oncogenesis and provide for long-term transgene expression. Adenovirus (Ad vectors arguably represent the most efficient delivery systems of episomal DNA into eukaryotic cell nuclei. The most advanced recombinant Ads lack all adenoviral genes. This renders these so-called high-capacity (hc Ad vectors less cytotoxic/immunogenic than those only deleted in early regions and creates space for the insertion of large/multiple transgenes. The versatility of hcAd vectors is been increased by capsid modifications to alter their tropism and by the incorporation into their genomes of sequences promoting chromosomal insertion of exogenous DNA. Adeno-associated virus (AAV can insert its genome into a specific human locus designated AAVS1. Trans- and cis-acting elements needed for this reaction are the AAV Rep78/68 proteins and Rep78/68-binding sequences, respectively. Here, we describe the generation, characterization and testing of fiber-modified dual hcAd/AAV hybrid vectors (dHVs containing both these elements. Due to the inhibitory effects of Rep78/68 on Ad-dependent DNA replication, we deployed a recombinase-inducible gene switch to repress Rep68 synthesis during vector rescue and propagation. Flow cytometric analyses revealed that rep68-positive dHVs can be produced similarly well as rep68-negative control vectors. Western blot experiments and immunofluorescence microscopy analyses demonstrated transfer of recombinase-dependent rep68 genes into target cells. Studies in HeLa cells and in the dystrophin-deficient myoblasts from a Duchenne muscular dystrophy (DMD patient showed that induction of Rep68 synthesis in cells transduced with fiber-modified and rep68-positive dHVs leads to increased stable transduction levels and AAVS1-targeted integration of vector DNA. These results

  12. Rapid Identification and Differentiation of Trichophyton Species, Based on Sequence Polymorphisms of the Ribosomal Internal Transcribed Spacer Regions, by Rolling-Circle Amplification▿

    OpenAIRE

    Kong, Fanrong; Tong, Zhongsheng; Chen, Xiaoyou; Sorrell, Tania; Bin WANG; Wu, Qixuan; Ellis, David; Chen, Sharon

    2008-01-01

    DNA sequencing analyses have demonstrated relatively limited polymorphisms within the fungal internal transcribed spacer (ITS) regions among Trichophyton spp. We sequenced the ITS region (ITS1, 5.8S, and ITS2) for 42 dermatophytes belonging to seven species (Trichophyton rubrum, T. mentagrophytes, T. soudanense, T. tonsurans, Epidermophyton floccosum, Microsporum canis, and M. gypseum) and developed a novel padlock probe and rolling-circle amplification (RCA)-based method for identification o...

  13. The COMTval158met polymorphism is associated with symptom relief during exposure-based cognitive-behavioral treatment in panic disorder

    Directory of Open Access Journals (Sweden)

    Bergström Jan

    2010-11-01

    Full Text Available Abstract Background Cognitive behavioral therapy (CBT represents a learning process leading to symptom relief and resulting in long-term changes in behavior. CBT for panic disorder is based on exposure and exposure-based processes can be studied in the laboratory as extinction of experimentally acquired fear responses. We have recently demonstrated that the ability to extinguish learned fear responses is associated with a functional genetic polymorphism (COMTval158met in the COMT gene and this study was aimed at transferring the experimental results on the COMTval158met polymorphism on extinction into a clinical setting. Methods We tested a possible effect of the COMTval158met polymorphism on the efficacy of CBT, in particular exposure-based treatment modules, in a sample of 69 panic disorder patients. Results We present evidence that panic patients with the COMTval158met met/met genotype may profit less from (exposure-based CBT treatment methods as compared to patients carrying at least one val-allele. No association was found with the 5-HTTLPR/rs25531 genotypes which is presented as additional material. Conclusions We were thus able to transfer findings on the effect of the COMTval158met polymorphism from an experimental extinction study obtained using healthy subjects to a clinical setting. Furthermore patients carrying a COMT val-allele tend to report more anxiety and more depression symptoms as compared to those with the met/met genotype. Limitations of the study as well as possible clinical implications are discussed. Trial registration Clinical Trial Registry name: Internet-Versus Group-Administered Cognitive Behavior Therapy for Panic Disorder (IP2. Registration Identification number: NCT00845260, http://www.clinicaltrials.gov/ct2/show/NCT00845260

  14. Polymorphisms of Genes in the Lipid Metabolism Pathway and the Risk of Biliary Tract Cancers and Stones: A Population-based Case-Control Study in Shanghai, China

    OpenAIRE

    Andreotti, Gabriella; Chen, Jinbo; Gao, Yu-Tang; Rashid, Asif; Chen, Bingshu E.; Rosenberg, Philip; Sakoda, Lori C.; Jie DENG; Shen, Ming-Chang; Wang, Bing-Sheng; Han, Tian-Quan; Zhang, Bai-He; Yeager, Meredith; Welch, Robert; Chanock, Stephen

    2008-01-01

    Biliary tract cancers, encompassing the gallbladder, extrahepatic bile duct, and ampulla of Vater, are uncommon, yet highly fatal malignancies. Gallstones, the primary risk factor for biliary cancers, are linked with hyperlipidemia. We examined the associations of 12 single nucleotide polymorphisms (SNPs) of five genes in the lipid metabolism pathway with the risks of biliary cancers and stones in a population-based case-control study in Shanghai, China. We included 235 gallbladder, 125 extra...

  15. Polymorphisms of dihydropyrimidine dehydrogenase gene and clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in Chinese population

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiao-ping; LU Zu-hong; TONG Na; ZHANG Zheng-dong; XU Pei-pei; PENG Miao-xin; ZHANG Wen-jing; WANG Shuai; BAI Zhi-bin; CHEN Bao-an; FENG Ji-feng; YAN Feng; JIANG Zhi; ZHONG Yue-jiao; WU Jian-zhong; CHEN Lu

    2012-01-01

    Background Dihydropyrimidine dehydrogenase (DPD),a key enzyme involved in the catabolism of 5-fluorouracil (5-FU),is the attractive candidate for pharmacogenetic research on efficacies and toxicities of 5-FU.The aim of this study is to explore the association between polymorphisms of dihydropyrimidine dehydrogenase gene (DPYD) and clinical outcomes of gastric cancer patients treated with fluorouracil-based adjuvant chemotherapy in the Chinese population.Methods Three hundred and sixty-two patients with gastric cancer in the Chinese population were treated with fluorouracil-based adjuvant chemotherapy.The single nucleotide polymorphic genotypes of DPYD were determined by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) using DNA samples isolated from peripheral blood collected before treatment.Results The average response rate for chemotherapy was 46.7%.A significantly different distribution of the rs1801159 (x2=8.76,P=0.012) genotypes was observed.Homozygous genotype rs1801159A/A was over-represented in responsive patients.Conversely,carriers of the rs1801159A/G genotype were prevalent in non-responsive patients.In the haplotype association analysis,there was significant difference in global haplotype distribution between the groups (x2=3.96,P=0.0465).Conclusions These results suggest that polymorphisms of rs1801159 in DPYD may be used as valuable predictors of the response to fluorouracil-based chemotherapy for gastric cancer patients in the Chinese population.Well-designed,comprehensive,and prospective studies on determining these polymorphisms of DPYD as predictive markers for gastric cancer in response to fluorouracil-based therapies are warranted.

  16. Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region

    OpenAIRE

    TAKASU, Masaki; ISHIHARA, Namiko; Tozaki, Teruaki; KAKOI, Hironaga; MAEDA, Masami; MUKOYAMA, Harutaka

    2014-01-01

    ABSTRACT To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences using Basic Local Alignment Search Tool, by mismatch analysis to evaluate the mutation process...

  17. Serotonin gene polymorphisms and bipolar I disorder: focus on the serotonin transporter.

    Science.gov (United States)

    Mansour, Hader A; Talkowski, Michael E; Wood, Joel; Pless, Lora; Bamne, Mikhil; Chowdari, Kodavali V; Allen, Michael; Bowden, Charles L; Calabrese, Joseph; El-Mallakh, Rif S; Fagiolini, Andrea; Faraone, Stephen V; Fossey, Mark D; Friedman, Edward S; Gyulai, Laszlo; Hauser, Peter; Ketter, Terence A; Loftis, Jennifer M; Marangell, Lauren B; Miklowitz, David J; Nierenberg, Andrew A; Patel, Jayendra; Sachs, Gary S; Sklar, Pamela; Smoller, Jordan W; Thase, Michael E; Frank, Ellen; Kupfer, David J; Nimgaonkar, Vishwajit L

    2005-01-01

    The pathogenesis of bipolar disorder may involve, at least in part, aberrations in serotonergic neurotransmission. Hence, serotonergic genes are attractive targets for association studies of bipolar disorder. We have reviewed the literature in this field. It is difficult to synthesize results as only one polymorphism per gene was typically investigated in relatively small samples. Nevertheless, suggestive associations are available for the 5HT2A receptor and the serotonin transporter genes. With the availability of extensive polymorphism data and high throughput genotyping techniques, comprehensive evaluation of these genes using adequately powered samples is warranted. We also report on our investigations of the serotonin transporter, SLC6A4 (17q11.1-q12). An insertion/deletion polymorphism (5HTTLPR) in the promoter region of this gene has been investigated intensively. However, the results have been inconsistent. We reasoned that other polymorphism/s may contribute to the associations and the inconsistencies may be due to variations in linkage disequilibrium (LD) patterns between samples. Therefore, we conducted LD analyses, as well as association and linkage using 12 polymorphisms, including 5HTTLPR. We evaluated two samples. The first sample consisted of 135 US Caucasian nuclear families having a proband with bipolar I disorder (BDI, DSM IV criteria) and available parents. For case-control analyses, the patients from these families were compared with cord blood samples from local Caucasian live births (n = 182). Our second, independent sample was recruited through the Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD, 545 cases, 548 controls). No significant associations were detected at the individual polymorphism or haplotype level using the case-control or family-based analyses. Our analyses do not support association between SLC6A4 and BDI families. Further studies using sub-groups of BDI are worthwhile. PMID:16338761

  18. Rapid identification of Brucella isolates to the species level by real time PCR based single nucleotide polymorphism (SNP analysis

    Directory of Open Access Journals (Sweden)

    Smith Catherine J

    2008-06-01

    Full Text Available Abstract Background Brucellosis, caused by members of the genus Brucella, remains one of the world's major zoonotic diseases. Six species have classically been recognised within the family Brucella largely based on a combination of classical microbiology and host specificity, although more recently additional isolations of novel Brucella have been reported from various marine mammals and voles. Classical identification to species level is based on a biotyping approach that is lengthy, requires extensive and hazardous culturing and can be difficult to interpret. Here we describe a simple and rapid approach to identification of Brucella isolates to the species level based on real-time PCR analysis of species-specific single nucleotide polymorphisms (SNPs that were identified following a robust and extensive phylogenetic analysis of the genus. Results Seven pairs of short sequence Minor Groove Binding (MGB probes were designed corresponding to SNPs shown to possess an allele specific for each of the six classical Brucella spp and the marine mammal Brucella. Assays were optimised to identical reaction parameters in order to give a multiple outcome assay that can differentiate all the classical species and Brucella isolated from marine mammals. The scope of the assay was confirmed by testing of over 300 isolates of Brucella, all of which typed as predicted when compared to other phenotypic and genotypic approaches. The assay is sensitive being capable of detecting and differentiating down to 15 genome equivalents. We further describe the design and testing of assays based on three additional SNPs located within the 16S rRNA gene that ensure positive discrimination of Brucella from close phylogenetic relatives on the same platform. Conclusion The multiple-outcome assay described represents a new tool for the rapid, simple and unambiguous characterisation of Brucella to the species level. Furthermore, being based on a robust phylogenetic framework, the

  19. Evidence for association between Disrupted-in-schizophrenia 1 (DISC1 gene polymorphisms and autism in Chinese Han population: a family-based association study

    Directory of Open Access Journals (Sweden)

    Ruan Yan

    2011-05-01

    Full Text Available Abstract Background Disrupted-in-Schizophrenia 1 (DISC1 gene is one of the most promising candidate genes for major mental disorders. In a previous study, a Finnish group demonstrated that DISC1 polymorphisms were associated with autism and Asperger syndrome. However, the results were not replicated in Korean population. To determine whether DISC1 is associated with autism in Chinese Han population, we performed a family-based association study between DISC1 polymorphisms and autism. Methods We genotyped seven tag single nucleotide polymorphisms (SNPs in DISC1, spanning 338 kb, in 367 autism trios (singleton and their biological parents including 1,101 individuals. Single SNP association and haplotype association analysis were performed using the family-based association test (FBAT and Haploview software. Results We found three SNPs showed significant associations with autism (rs4366301: G > C, Z = 2.872, p = 0.004; rs11585959: T > C, Z = 2.199, p = 0.028; rs6668845: A > G, Z = 2.326, p = 0.02. After the Bonferroni correction, SNP rs4366301, which located in the first intron of DISC1, remained significant. When haplotype were constructed with two-markers, three haplotypes displayed significant association with autism. These results were still significant after using the permutation method to obtain empirical p values. Conclusions Our study provided evidence that the DISC1 may be the susceptibility gene of autism. It suggested DISC1 might play a role in the pathogenesis of autism.

  20. Identification of a novel calcium binding motif based on the detection of sequence insertions in the animal peroxidase domain of bacterial proteins.

    Directory of Open Access Journals (Sweden)

    Saray Santamaría-Hernando

    Full Text Available Proteins of the animal heme peroxidase (ANP superfamily differ greatly in size since they have either one or two catalytic domains that match profile PS50292. The orf PP_2561 of Pseudomonas putida KT2440 that we have called PepA encodes a two-domain ANP. The alignment of these domains with those of PepA homologues revealed a variable number of insertions with the consensus G-x-D-G-x-x-[GN]-[TN]-x-D-D. This motif has also been detected in the structure of pseudopilin (pdb 3G20, where it was found to be involved in Ca(2+ coordination although a sequence analysis did not reveal the presence of any known calcium binding motifs in this protein. Isothermal titration calorimetry revealed that a peptide containing this consensus motif bound specifically calcium ions with affinities ranging between 33-79 µM depending on the pH. Microcalorimetric titrations of the purified N-terminal ANP-like domain of PepA revealed Ca(2+ binding with a K(D of 12 µM and stoichiometry of 1.25 calcium ions per protein monomer. This domain exhibited peroxidase activity after its reconstitution with heme. These data led to the definition of a novel calcium binding motif that we have termed PERCAL and which was abundantly present in animal peroxidase-like domains of bacterial proteins. Bacterial heme peroxidases thus possess two different types of calcium binding motifs, namely PERCAL and the related hemolysin type calcium binding motif, with the latter being located outside the catalytic domains and in their C-terminal end. A phylogenetic tree of ANP-like catalytic domains of bacterial proteins with PERCAL motifs, including single domain peroxidases, was divided into two major clusters, representing domains with and without PERCAL motif containing insertions. We have verified that the recently reported classification of bacterial heme peroxidases in two families (cd09819 and cd09821 is unrelated to these insertions. Sequences matching PERCAL were detected in all kingdoms of

  1. Insertion compounds of uranium oxides

    International Nuclear Information System (INIS)

    Insertion compounds are formed by the intercalation of an electropositive species, such as hydrogen or an alkali metal, with minimal structural rearrangement of the host oxide. In this report a review of the measured structural, thermodynamic and transport properties of the insertion compounds of α-U3O8, α-UO3, γ-UO3, δ-UO3 and related systems is given. (author)

  2. HaploSNPer: a web-based allele and SNP detection tool

    OpenAIRE

    Voorrips Roeland E; Leunissen Jack AM; Tang Jifeng; van der Linden C Gerard; Vosman Ben

    2008-01-01

    Abstract Background Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. ...

  3. Construction of small-insert and large-insert metagenomic libraries.

    Science.gov (United States)

    Simon, Carola; Daniel, Rolf

    2010-01-01

    The vast majority of the Earth's biological diversity is hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is a cultivation-independent molecular approach to assess this unexplored genetic reservoir. In the last few years, a high number of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA. PMID:20830554

  4. Thermal Performance of the XRS Helium Insert

    Science.gov (United States)

    Breon, Susan R.; DiPirro, Michael J.; Tuttle, James G.; Shirron, Peter J.; Warner, Brent A.; Boyle, Robert F.; Canavan, Edgar R.

    1999-01-01

    The X-Ray Spectrometer (XRS) is an instrument on the Japanese Astro-E satellite, scheduled for launch early in the year 2000. The XRS Helium Insert comprises a superfluid helium cryostat, an Adiabatic Demagnetization Refrigerator (ADR), and the XRS calorimeters with their cold electronics. The calorimeters are capable of detecting X-rays over the energy range 0.1 to 10 keV with a resolution of 12 eV. The Helium Insert completed its performance and verification testing at Goddard in January 1999. It was shipped to Japan, where it has been integrated with the neon dewar built by Sumitomo Heavy Industries. The Helium Insert was given a challenging lifetime requirement of 2.0 years with a goal of 2.5 years. Based on the results of the thermal performance tests, the predicted on-orbit lifetime is 2.6 years with a margin of 30%. This is the result of both higher efficiency in the ADR cycle and the low temperature top-off, more than compensating for an increase in the parasitic heat load. This paper presents a summary of the key design features and the results of the thermal testing of the XRS Helium Insert.

  5. A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples.

    Science.gov (United States)

    Kraus, Robert H S; vonHoldt, Bridgett; Cocchiararo, Berardino; Harms, Verena; Bayerl, Helmut; Kühn, Ralph; Förster, Daniel W; Fickel, Jörns; Roos, Christian; Nowak, Carsten

    2015-03-01

    Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single-nucleotide polymorphism (SNP)-based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192 SNP loci selected from the Affymetrix v2 Canine SNP Array. We carefully selected an optimised final set of 96 SNPs (and discarded the worse half), based on assay performance and reliability. We found rates of missing data in this SNP set of <10% and genotyping error of ~1%, which improves genotyping accuracy by nearly an order of magnitude when compared to published data for other marker types. Our approach provides a tool for rapid and cost-effective genotyping of noninvasively collected wildlife samples. The ability to standardise genotype scoring combined with low error rates promises to constitute a major technological advancement and could establish SNPs as a standard marker for future wildlife monitoring. PMID:25042673

  6. An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

    Czech Academy of Sciences Publication Activity Database

    Munoz-Amatriain, M.; Moscou, M. J.; Bhat, P. R.; Bartoš, Jan; Suchánková, Pavla; Šimková, Hana; Endo, T. R.; Fenton, R. D.; Lonardi, S.; Castillo, A. M.; Doležel, Jaroslav; Close, T. J.

    2011-01-01

    Roč. 4, č. 3 (2011), s. 238-249. ISSN 1940-3372 R&D Projects: GA MŠk(CZ) LC06004; GA MŠk ED0007/01/01 Institutional research plan: CEZ:AV0Z50380511 Keywords : Chromosomes sorting * Barley * Nucleotide polymorphism Subject RIV: EB - Genetics ; Molecular Biology

  7. A ferrofluid-based homogeneous assay for highly sensitive and selective detection of single-nucleotide polymorphisms.

    Science.gov (United States)

    Shen, Wei; Lim, Cai Le; Gao, Zhiqiang

    2013-09-21

    A simple and low-cost colorimetric assay utilizing ferrofluidic nanoparticulate probes (FNPs) and a ligase for single-nucleotide polymorphism genotyping is described. Excellent sensitivity and selectivity were accomplished through the engagement of the FNPs and a ligase chain reaction. PMID:23923128

  8. Clinical Significance of Long Non-Coding RNA CASC8 rs10505477 Polymorphism in Lung Cancer Susceptibility, Platinum-Based Chemotherapy Response, and Toxicity

    Directory of Open Access Journals (Sweden)

    Lei Hu

    2016-05-01

    Full Text Available Long non-coding RNA (lncRNA CASC8 rs10505477 polymorphism has been identified to be related to risk of many kinds of cancers, such as colorectal cancer, gastric cancer, and invasive ovarian cancer, and it may be involved in the prognosis of gastric cancer patients who have received platinum-based chemotherapy after surgical treatment. So far, there is no study investigating the clinical significance of lncRNA CASC8 rs10505477 in lung cancer susceptibility and treatment. In this study, we genotyped 498 lung cancer patients and 213 healthy control subjects to explore the correlation between the rs10505477 polymorphism and lung cancer risk in a Chinese population. Among the 498 patients, 467 were selected for the chemotherapy response and toxicity study. We found that the single nucleotide polymorphisms (SNP rs10505477 was greatly related to lung cancer risk in male and adenocarcinoma subgroups in recessive model (adjusted OR = 0.51, 95%CI = 0.29–0.90, p = 0.02; adjusted OR = 0.52, 95%CI = 0.30–0.89, p = 0.02, respectively. It was also closely correlated with platinum-based chemotherapy response in dominant model (adjusted OR = 1.58, 95%CI = 1.05–2.39, p = 0.03. Additionally, we observed that CASC8 rs10505477 polymorphism was significantly relevant to severe hematologic toxicity in non-small-cell lung cancer (NSCLC subgroup in dominant model (adjusted OR = 0.59, 95%CI = 0.35–0.98, p = 0.04 and in additive model (adjusted OR = 0.62, 95%CI = 0.43–0.90, p = 0.01. Furthermore, it was found that rs10505477 polymorphism was greatly associated with gastrointestinal toxicity in SCLC and cisplatin subgroups in dominant model (adjusted OR = 7.82, 95%CI = 1.36–45.07, p = 0.02; adjusted OR = 1.94, 95%CI = 1.07–3.53, p = 0.03, respectively. Thus, lncRNA CASC8 rs10505477 could serve as a possible risk marker for diagnosing lung cancer, and could be used to forecast the response and toxicity of platinum-based treatment in lung cancer patients.

  9. Association between serotonin transporter gene polymorphism and recurrent aphthous stomatitis

    Science.gov (United States)

    Manchanda, Aastha; Iyengar, Asha R.; Patil, Seema

    2016-01-01

    Background: Anxiety-related traits have been attributed to sequence variability in the genes coding for serotonin transmission in  the brain. Two alleles, termed long (L) and short (S) differing by 44 base pairs, are found in a polymorphism identified in the promoter region of serotonin transporter gene. The presence of the short allele  and SS and LS genotypes is found to be associated with the reduced expression of this gene decreasing the uptake of serotonin in the brain leading to various anxiety-related traits. Recurrent aphthous stomatitis (RAS) is an oral mucosal disease with varied etiology including the presence of stress, anxiety, and genetic influences. The present study aimed to determine this serotonin transporter gene polymorphism in patients with RAS and compare it with normal individuals. Materials and Methods: This study included 20 subjects with various forms of RAS and 20 normal healthy age- and gender-matched individuals. Desquamated oral mucosal cells were collected for DNA extraction and subjected to polymerase chain reaction for studying insertion/deletion in the 5-HTT gene-linked polymorphic region. Cross tabulations followed by Chi-square tests were performed to compare the significance of findings, P < 0.05 was considered statistically significant. Results: The LS genotype was the most common genotype found in the subjects with aphthous stomatitis (60%) and controls (40%). The total percentage of LS and SS genotypes and the frequency of S allele were found to be higher in the subjects with aphthous stomatitis as compared to the control group although a statistically significant correlation could not be established, P = 0.144 and 0.371, respectively. Conclusion: Within the limitations of this study, occurrence of RAS was not found to be associated with polymorphic promoter region in serotonin transporter gene.

  10. ACE I/D polymorphism in Indian patients with hypertrophic cardiomyopathy and dilated cardiomyopathy

    DEFF Research Database (Denmark)

    Rai, Taranjit Singh; Dhandapany, Perundurai Subramaniam; Ahluwalia, Tarun Veer Singh;

    2008-01-01

    The study was carried to determine the association of angiotensin converting enzyme (ACE) insertion/deletion (I/D) polymorphism with the risk of hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy (RCM).......The study was carried to determine the association of angiotensin converting enzyme (ACE) insertion/deletion (I/D) polymorphism with the risk of hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy (RCM)....

  11. Aspects and Polymorphism in AspectJ

    DEFF Research Database (Denmark)

    Lorenz, David Harel; Ernst, Erik

    -oriented programming (AOP). In AOP, pieces of crosscutting behavior are extracted from the base code and localized in aspects, losing as a result their polymorphic capabilities while introducing new and unexplored issues. In this paper, we explore what kinds of polymorphism AOP languages should support, using Aspect......J as the basis for the presentation. The results are not exclusive to AspectJ---aspectual polymorphism may make aspects in any comparable AOSD language more expressive and reusable across programs, while preserving safety....

  12. Exciplex elimination in an organic light-emitting diode based on a fluorene derivative by inserting 4,4'-N,N'-dicarbazole-biphenylinto donor/acceptor interface

    International Nuclear Information System (INIS)

    Organic light-emitting diodes (OLEDs) composed of a novel fluorene derivative of 2,3-bis(9,9-dihexyl-9H-fluoren-2-yl)-6,7-difluoroquinoxaline (F2Py) were fabricated, and exciplex emission was observed in the device. To depress the exciplex in an OLED for pure colour light emission, 4, 4'-N,N'-dicarbazole-biphenyl (CBP) was inserted as a separator at the donor/acceptor interface. It was found that the device without the CBP layer emitted a green light peaking at 542 nm from the exciplex and a shoulder peak about 430 nm from F2Py. In contrast, the OLED with CBP layer emitted only a blue light peak at about 432 nm from F2Py. Device efficiencies were calculated by a simulative mode in an injection controlled type mechanism, and the results showed that exciplexes yield much lower quantum efficiency than excitons. The device with CBP has a higher power efficiency as no exciplex was present. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  13. Gene Insertion Patterns and Sites

    Science.gov (United States)

    Vain, Philippe; Thole, Vera

    During the past 25 years, the molecular analysis of transgene insertion patterns and sites in plants has greatly contributed to our understanding of the mechanisms underlying transgene integration, expression, and stability in the nuclear genome. Molecular characterization is also an essential step in the safety assessment of genetically modified crops. This chapter describes the standard experimental procedures used to analyze transgene insertion patterns and loci in cereals and grasses transformed using Agrobacterium tumefaciens or direct transfer of DNA. Methods and protocols enabling the determination of the number and configuration of transgenic loci via a combination of inheritance studies, polymerase chain reaction, and Southern analyses are presented. The complete characterization of transgenic inserts in plants is, however, a holistic process relying on a wide variety of experimental approaches. In this chapter, these additional approaches are not detailed but references to relevant bibliographic records are provided.

  14. Maternal homozygocity for a 14 basepair insertion in exon 8 of the HLA-G gene and carriage of HLA class II alleles restricting HY immunity predispose to unexplained secondary recurrent miscarriage and low birth weight in children born to these patients

    DEFF Research Database (Denmark)

    Christiansen, Ole B; Kolte, Astrid Marie; Dahl, Mette;

    2012-01-01

    Homozygous carriage of a 14 base pair (bp) insertion in exon 8 of the HLA-G gene may be associated with low levels of soluble HLA-G and recurrent miscarriage (RM). We investigated the G14bp insertion(ins)/deletion(del) polymorphism in 339 women with unexplained RM and 125 control women. In all...... patients and patients with secondary RM after a firstborn boy, 19.2% and 23.9%, respectively, were G14bp ins/ins compared with 11.2% of controls (p...

  15. Intermolecular Repulsion through Interfacial Attraction : Toward Engineering of Polymorphs

    NARCIS (Netherlands)

    Kudernac, Tibor; Sändig, Nadja; Fernández Landaluce, Tatiana; Wees, Bart J. van; Rudolf, Petra; Katsonis, Nathalie; Zerbetto, Francesco; Feringa, Ben L.

    2009-01-01

    Understanding the formation of crystalline polymorphs is of importance for various applications of materials science. Polymorphism of Schiff base derivatives has recently attracted considerable attention because of its influence on photochromic and thermochromic properties of their 3D crystals. The

  16. Sequence-Based Polymorphisms in the Mitochondrial D-Loop and Potential SNP Predictors for Chronic Dialysis

    OpenAIRE

    Jin-Bor Chen; Yi-Hsin Yang; Wen-Chin Lee; Chia-Wei Liou; Tsu-Kung Lin; Yueh-Hua Chung; Li-Yeh Chuang; Cheng-Hong Yang; Hsueh-Wei Chang

    2012-01-01

    BACKGROUND: The mitochondrial (mt) displacement loop (D-loop) is known to accumulate structural alterations and mutations. The aim of this study was to investigate the prevalence of single nucleotide polymorphisms (SNPs) within the D-loop among chronic dialysis patients and healthy controls. METHODOLOGY AND PRINCIPAL FINDINGS: We enrolled 193 chronic dialysis patients and 704 healthy controls. SNPs were identified by large scale D-loop sequencing and bioinformatic analysis. Chronic dialysis p...

  17. Genetic variation in Opisthorchis viverrini (Trematoda: Opisthorchiidae) from northeast Thailand and Laos PDR based on random amplified polymorphic DNA analyses

    OpenAIRE

    Sithithaworn, Paiboon; Nuchjungreed, Chadaporn; Srisawangwong, Tuanchai; Ando, Katsuhiko; Petney, Trevor N.; Chilton, Neil B.; Andrews, Ross H.

    2006-01-01

    Genetic variation in Opisthorchis viverrini adults originating from different locations in northeast Thailand and Laos, People’s Democratic Republic (PDR), was examined using random amplified polymorphic DNA (RAPD) analyses. In an initial analysis, the genomic DNA of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among O. viverrini specimens was detected reliably for only four primers. A more detailed RAPD analysis using these...

  18. Polymorphisms in XPD gene could predict clinical outcome of platinum-based chemotherapy for non-small cell lung cancer patients: a meta-analysis of 24 studies.

    Directory of Open Access Journals (Sweden)

    Qin Qin

    Full Text Available OBJECTIVE: Xeroderma pigmentosum group D (XPD is an essential gene involved in the nucleotide excision repair (NER pathway. Two commonly studied single nucleotide polymorphisms (SNPs of XPD (Lys751Gln, A>C, rs13181; Asp312Asn, G>A, rs1799793 are implicated in the modulation of DNA repair capacity, thus related to the responses to platinum-based chemotherapy. Here we performed a meta-analysis to better evaluate the association between the two XPD SNPs and clinical outcome of platinum-based chemotherapy in non-small cell lung cancer (NSCLC patients. METHODS: A comprehensive search of PubMed database was conducted to identify relevant articles. Primary outcomes included objective response (i.e., complete response + partial response vs. stable disease + progressive disease, progression-free survival (PFS and overall survival (OS. The pooled and 95% confidence intervals (CIs of ORs (odds ratios and HRs (hazard ratios were estimated using the fixed or random effect model. RESULTS: Twenty-four studies were eligible according to the inclusion criteria. None of the XPD Lys751Gln/Asp312Asn polymorphisms was associated with objective response, PFS or OS in NSCLC patients treated with platinum drugs. However, in stratified analysis by ethnicity, the XPD Lys751Gln (A>C polymorphism was not significantly associated with increased response in Caucasians (OR=1.35, 95%CI=1.0-1.83, P=0.122 for heterogeneity but was associated with decreased PFS in Asians (HR=1.39, 95%CI=1.07-1.81, P=0.879 for heterogeneity. Furthermore, a statistically significant difference existed in the estimates of effect between the two ethnicities (P=0.014 for TR; PC may have inverse predictive and prognostic role in platinum-based treatment of NSCLC according to different ethnicities. Further studies are needed to validate our findings.

  19. Genetic variability in geographical populations of Culex quinquefasciatus Say (Diptera: Culicidae) from India based on random amplified polymorphic DNA analysis.

    Science.gov (United States)

    Sharma, A K; Mendki, M J; Tikar, S N; Chandel, K; Sukumaran, D; Parashar, B D; Veer, Vijay; Agarwal, O P; Prakash, Shri

    2009-10-01

    Genetic variability and environmental factors may influence the refractiveness, propagation of pathogen and transmission of disease. Random amplified polymorphic DNA (RAPD) is one of the widely used molecular markers for population genetic diversity studies. In present study, RAPD is used to ascertain the genetic variability in Culex quinquefasciatus populations collected from various Indian geographical locations. Out of 50 RAPD primers screened, 14 primers exhibited clear, concrete and distinct banding pattern showing up to 100% polymorphism. Primer OPBD3 was tested with DNA of 14 geographical populations from India (including one laboratory population) showed 21 loci representing 14 populations with 100% polymorphism. The genetic diversity among the populations indicated the Shannon index (I) and gene diversity index (H(ST)), 0.48 and 0.31, respectively among the population, displaying rich genetic variation among the Cx. quinquefasciatus populations. Consensus tree showed two clusters indicating the genetic variation among the various geographical populations. The findings of this study may be useful to understand the population variation under different ecological conditions and development of effective vector management strategies. PMID:19577531

  20. Evaluation of a 2D fluoroscopy-based navigation system for insertion of the dynamic hip screw (DHS). An experimental study; Evaluation eines 2-D-Fluoroskopie-basierten Navigationssystems zur Implantation der dynamischen Hueftschraube (DHS). Eine experimentelle Studie

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, M.C.; Weber, O.; Burger, C.; Wirtz, D.C. [Bonn Univ. (Germany). Dept. of Orthopaedics and Trauma Surgery; Belei, P.; Fuente, M. de la; Strake, M.; Radermacher, K. [Helmholtz-Institute for Biomedical Engineering, Aachen (Germany). Chair of Medical Engineering

    2011-06-15

    Purpose: Dynamic hip screw (DHS) insertion for the fixation of lateral femoral neck fractures is an accepted surgical treatment method. A computer-assisted planning and navigation system based on 2D fluoroscopy has been developed for guidewire insertion in order to perform screw placement. The image acquisition process was supported by a radiation-saving procedure called 'zero-dose C-arm navigation'. The aim of this study was to evaluate this new system. Materials and Methods: In the context of a sawbone study, we inserted dynamic hip screws. The procedure was performed under navigation control and in the conventional technique in 12 sawbones. Both procedures were performed in an open and closed technique. Results: The computer-assisted technique significantly reduced the number of intraoperative fluoroscopic images (open technique: -8.1 {+-} 0.5; p < 0.001 - closed technique: -12.3 {+-} 3.7; p < 0.001) and the number of guidewire passes (open technique: -1.3 {+-} 1.2; p < 0.05 - closed technique: -1.5 {+-} 1.2; p < 0,05). There was no difference with respect to precision in both groups. The operation time was significantly longer in the navigation-assisted groups (open technique: + 14.6 {+-} 5.4 min; p < 0.001 - closed technique: + 13 {+-} 3 min; p < 0.001). Conclusion: The addition of computer-assisted planning and surgical guidance supported by 'zero-dose C-arm navigation' may be useful for the fixation of lateral femoral neck fractures by the DHS as it reduces the amount of fluoroscopic images and requires fewer drill tracks. Further studies with the goal of reducing the operation time are necessary. (orig.)

  1. Beamline Insertions Manager at Jefferson Lab

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Michael C. [Jefferson Lab., Newport News, VA (United States)

    2015-09-01

    The beam viewer system at Jefferson Lab provides operators and beam physicists with qualitative and quantitative information on the transverse electron beam properties. There are over 140 beam viewers installed on the 12 GeV CEBAF accelerator. This paper describes an upgrade consisting of replacing the EPICS-based system tasked with managing all viewers with a mixed system utilizing EPICS and high-level software. Most devices, particularly the beam viewers, cannot be safely inserted into the beam line during high-current beam operations. Software is partly responsible for protecting the machine from untimely insertions. The multiplicity of beam-blocking and beam-vulnerable devices motivates us to try a data-driven approach. The beamline insertions application components are centrally managed and configured through an object-oriented software framework created for this purpose. A rules-based engine tracks the configuration and status of every device, along with the beam status of the machine segment containing the device. The application uses this information to decide on which device actions are allowed at any given time.

  2. Influence of Serotonin Transporter Gene Polymorphisms and Adverse Life Events on Depressive Symptoms in the Elderly: A Population-Based Study

    OpenAIRE

    Davin, Annalisa; Monti, Maria Cristina; Polito, Letizia; Vaccaro, Roberta; Abbondanza, Simona; Gnesi, Marco; Villani, Simona; Guaita, Antonio

    2015-01-01

    Background Depression is common in the elderly. The role of genetic and environmental factors in modulating depressive symptoms is not clear. Methods We evaluated the influence of serotonin transporter gene polymorphisms and recent adverse life events on depressive symptoms in an elderly Italian population. We used data from “InveCe.Ab”, a population-based study of 1321 subjects aged 70–74 years. We used the 15-item Geriatric Depression Scale (GDS) to assess depressive symptoms–a GDS score ≥5...

  3. CYP17 5'-UTR MspA1 polymorphism and the risk of premenopausal breast cancer in a German population-based case–control study

    OpenAIRE

    Verla-Tebit, Emaculate; Wang-Gohrke, Shan; Chang-Claude, Jenny

    2005-01-01

    Introduction Studies on the association between the cytochrome P450c17α gene (CYP17) 5'-untranslated region MspA1 genetic polymorphism and breast cancer risk have yielded inconsistent results. Higher levels of estrogen have been reported among young nulliparous women with the A2 allele. Therefore we assessed the impact of CYP17 genotypes on the risk of premenopausal breast cancer, with emphasis on parity. Methods We used data from a population-based case–control study of women aged below 51 y...

  4. Concepts for stereoselective acrylate insertion

    KAUST Repository

    Neuwald, Boris

    2013-01-23

    Various phosphinesulfonato ligands and the corresponding palladium complexes [{((PaO)PdMeCl)-μ-M}n] ([{( X1-Cl)-μ-M}n], (PaO) = κ2- P,O-Ar2PC6H4SO2O) with symmetric (Ar = 2-MeOC6H4, 2-CF3C6H4, 2,6-(MeO)2C6H3, 2,6-(iPrO)2C 6H3, 2-(2′,6′-(MeO)2C 6H3)C6H4) and asymmetric substituted phosphorus atoms (Ar1 = 2,6-(MeO)2C6H 3, Ar2 = 2′-(2,6-(MeO)2C 6H3)C6H4; Ar1 = 2,6-(MeO)2C6H3, Ar2 = 2-cHexOC 6H4) were synthesized. Analyses of molecular motions and dynamics by variable temperature NMR studies and line shape analysis were performed for the free ligands and the complexes. The highest barriers of ΔGa = 44-64 kJ/mol were assigned to an aryl rotation process, and the flexibility of the ligand framework was found to be a key obstacle to a more effective stereocontrol. An increase of steric bulk at the aryl substituents raises the motional barriers but diminishes insertion rates and regioselectivity. The stereoselectivity of the first and the second methyl acrylate (MA) insertion into the Pd-Me bond of in situ generated complexes X1 was investigated by NMR and DFT methods. The substitution pattern of the ligand clearly affects the first MA insertion, resulting in a stereoselectivity of up to 6:1 for complexes with an asymmetric substituted phosphorus. In the consecutive insertion, the stereoselectivity is diminished in all cases. DFT analysis of the corresponding insertion transition states revealed that a selectivity for the first insertion with asymmetric (P aO) complexes is diminished in the consecutive insertions due to uncooperatively working enantiomorphic and chain end stereocontrol. From these observations, further concepts are developed. © 2012 American Chemical Society.

  5. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    Directory of Open Access Journals (Sweden)

    Theresa A Hill

    Full Text Available The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs. Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP. Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and

  6. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    Science.gov (United States)

    Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  7. Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species.

    Science.gov (United States)

    Blanquer-Maumont, A; Crouau-Roy, B

    1995-10-01

    Dimeric short tandem repeats are a source of highly polymorphic markers in the mammalian genome. Genetic variation at these hypervariable loci is extensively used for linkage analysis, for the identification of individuals, and may be useful for interpopulation and interspecies studies. In this paper, we analyze the variability and the sequences of a segment including three microsatellites, first described in man, in several species of primates (chimpanzee, orangutan, gibbon, and macaque) using the heterologous primers (man primers). This region is located on the human chromosome 6p, near the tumor necrosis factor genes, in the major histocompatibility complex. The fact that these primers work in all species studied indicates that they are conserved throughout the different lineages of the two superfamilies, the Hominoidea and the Cercopithecidea, represented by the macaques. However, the intervening sequence displays intraspecific and interspecific variability. The sites of base substitutions and the insertion/deletion events are not evenly distributed within this region. The data suggest that it is necessary to have a minimal number of repeats to increase the rate of mutation sufficiently to allow the development of polymorphism. In some species, the microsatellites present single base variations which reduce the number of contiguous repeats, thus apparently slowing the rate of additional slippage events. Species with such variations or a low number of repeats are monomorphic. These microsatellite sequences are informative in the comparison of closely related species and reflect the phylogeny of the Old World monkeys, apes, and man. PMID:7563137

  8. Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis.

    Science.gov (United States)

    Poduslo, S E; Dean, M; Kolch, U; O'Brien, S J

    1991-07-01

    A strategy is described that allows the development of polymorphic genetic markers to be characterized in individual genes. Segments of the 3' untranslated regions are amplified, and polymorphisms are detected by digestion with frequently cutting enzymes and with the detection of single-stranded conformation polymorphisms. This allows these genes, or DNA segments, to be placed on the linkage maps of human chromosomes. Polymorphisms in two genes have been identified using this approach. A HaeIII polymorphism was detected in the KIT proto-oncogene, physically assigned to chromosome 4q11-12. This polymorphism is linked to other chromosome 4p markers and is in linkage disequilibrium with a HindIII polymorphism previously described at this locus. We have also identified in the insulin-like growth factor1 receptor gene (IGF1R) a 2-bp deletion that is present at a frequency of .25 in the Caucasian population. Pedigree analysis with this insertion/deletion polymorphism placed the IGF1R gene at the end of the current linkage map of chromosome 15q, consistent with the physical assignment of 15q2526. Thus, polymorphisms in specific genes can be used to related the physical, genetic, and comparative maps of mammalian genomes and to simplify the testing of candidate genes for human diseases. PMID:1676559

  9. Central Solenoid Insert Technical Specification

    Energy Technology Data Exchange (ETDEWEB)

    Martovetsky, Nicolai N [ORNL; Smirnov, Alexandre [ORNL

    2011-09-01

    The US ITER Project Office (USIPO) is responsible for the ITER central solenoid (CS) contribution to the ITER project. The Central Solenoid Insert (CSI) project will allow ITER validation the appropriate lengths of the conductors to be used in the full-scale CS coils under relevant conditions. The ITER Program plans to build and test a CSI to verify the performance of the CS conductor. The CSI is a one-layer solenoid with an inner diameter of 1.48 m and a height of 4.45 m between electric terminal ends. The coil weight with the terminals is approximately 820 kg without insulation. The major goal of the CSI is to measure the temperature margin of the CS under the ITER direct current (DC) operating conditions, including determining sensitivity to load cycles. Performance of the joints, ramp rate sensitivity, and stability against thermal or electromagnetic disturbances, electrical insulation, losses, and instrumentation are addressed separately and therefore are not major goals in this project. However, losses and joint performance will be tested during the CSI testing campaign. The USIPO will build the CSI that will be tested at the Central Solenoid Model Coil (CSMC) Test Facility at the Japan Atomic Energy Agency (JAEA), Naka, Japan. The industrial vendors (the Suppliers) will report to the USIPO (the Company). All approvals to proceed will be issued by the Company, which in some cases, as specified in this document, will also require the approval of the ITER Organization. Responsibilities and obligations will be covered by respective contracts between the USIPO, called Company interchangeably, and the industrial Prime Contractors, called Suppliers. Different stages of work may be performed by more than one Prime Contractor, as described in this specification. Technical requirements of the contract between the Company and the Prime Contractor will be covered by the Fabrication Specifications developed by the Prime Contractor based on this document and approved by

  10. The first LHC insertion quadrupole

    CERN Multimedia

    2004-01-01

    An important milestone was reached in December 2003 at the CERN Magnet Assembly Facility. The team from the Accelerator Technology - Magnet and Electrical Systems group, AT-MEL, completed the first special superconducting quadrupole for the LHC insertions which house the experiments and major collider systems. The magnet is 8 metres long and contains two matching quadrupole magnets and an orbit corrector, a dipole magnet, used to correct errors in quadrupole alignment. All were tested in liquid helium and reached the ultimate performance criteria required for the LHC. After insertion in the cryostat, the superconducting magnet will be installed as the Q9 quadrupole in sector 7-8, the first sector of the LHC to be put in place in 2004. Members of the quadrupole team, from the AT-MEL group, gathered around the Q9 quadrupole at its inauguration on 12 December 2003 in building 181.

  11. Insertion device calculations with mathematica

    Energy Technology Data Exchange (ETDEWEB)

    Carr, R. [Stanford Synchrotron Radiation Lab., CA (United States); Lidia, S. [Univ. of California, Davis, CA (United States)

    1995-02-01

    The design of accelerator insertion devices such as wigglers and undulators has usually been aided by numerical modeling on digital computers, using code in high level languages like Fortran. In the present era, there are higher level programming environments like IDL{reg_sign}, MatLab{reg_sign}, and Mathematica{reg_sign} in which these calculations may be performed by writing much less code, and in which standard mathematical techniques are very easily used. The authors present a suite of standard insertion device modeling routines in Mathematica to illustrate the new techniques. These routines include a simple way to generate magnetic fields using blocks of CSEM materials, trajectory solutions from the Lorentz force equations for given magnetic fields, Bessel function calculations of radiation for wigglers and undulators and general radiation calculations for undulators.

  12. ATLAS insertable B-layer

    Czech Academy of Sciences Publication Activity Database

    Marčišovský, Michal

    2011-01-01

    Roč. 633, č. 1 (2011), "S224"-"S225". ISSN 0168-9002. [International workshop on radiation imaging detector s /11./. Praha, 26.06.2009-02.07.2009] R&D Projects: GA MŠk LA08015; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : ATLAS * pixel detector * insertable B-layer Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.207, year: 2011

  13. Vacuum guidelines for ISA insertions

    International Nuclear Information System (INIS)

    Vacuum requirements place design restrictions on the ISA insertions. The vacuum tube diameter, given a distance L between pumps, is determined by the desorption of molecules from the wall under the impact of ions created by the beam, whereas the thickness of the tube must be sufficient to prevent collapse. In addition, the entire vacuum chamber must be able to be baked out at approximately 2000C

  14. Brazilian Plasmodium falciparum isolates: investigation of candidate polymorphisms for artemisinin resistance before introduction of artemisinin-based combination therapy

    Directory of Open Access Journals (Sweden)

    Rosenthal Philip J

    2010-12-01

    Full Text Available Abstract Background This study was performed to better understand the genetic diversity of known polymorphisms in pfatpase6 and pfmdr1 genes before the introduction of ACT in Brazil, in order to get a genotypic snapshot of Plasmodium falciparum parasites that may be used as baseline reference for future studies. Methods Parasites from P. falciparum samples collected in 2002, 2004 and 2006-2007 were genotyped using PCR and DNA sequencing at codons 86, 130, 184, 1034, 1042, 1109 and 1246 for pfmdr1 gene, and 243, 263, 402, 431, 623, 630, 639, 683, 716, 776, 769 and 771 for pfatpase6 gene. Results A pfmdr1 haplotype NEF/CDVY was found in 97% of the samples. In the case of pfatpase6, four haplotypes, wild-type (37%, 630 S (35%, 402 V (5% and double-mutant 630 S + 402 V (23%, were detected. Conclusion Although some polymorphism in pfmdr1 and pfatpase6 were verified, no reported haplotypes in both genes that may mediate altered response to ACT was detected before the introduction of this therapy in Brazil. Thus, the haplotypes herein described can be very useful as a baseline reference of P. falciparum populations without ACT drug pressure.

  15. HTS Insert Magnet Design Study

    CERN Document Server

    Devaux, M; Fleiter, J; Fazilleau, P; Lécrevisse, T; Pes, C; Rey, J-M; Rifflet, J-M; Sorbi, M; Stenvall, A; Tixador, P; Volpini, G

    2011-01-01

    Future accelerator magnets will need to reach higher field in the range of 20 T. This field level is very difficult to reach using only Low Temperature Superconductor materials whereas High Temperature Superconductors (HTS) provide interesting opportunities. High current densities and stress levels are needed to design such magnets. YBCO superconductor indeed carries large current densities under high magnetic field and provides good mechanical properties especially when produced using the IBAD approach. The HFM EUCARD program studies the design and the realization of an HTS insert of 6 T inside a Nb3Sn dipole of 13T at 4.2 K. In the2HTS insert, engineering current densities higher than 250 MA/m under 19 T are required to fulfill the specifications. The stress level is also very severe. YBCO IBAD tapes theoretically meet these challenges from presented measurements. The insert protection is also a critical because HTS materials show low quench propagation velocities and the coupling with the Nb3Sn magnet make...

  16. Immediate post-placental IUD insertion: the expulsion problem.

    Science.gov (United States)

    Thiery, M; Van Kets, H; Van der Pas, H

    1985-04-01

    This paper reports an evaluation of immediate post-placental insertion of a non-copper (Lippes Loop D) and several copper-bearing IUD models (TCu200, TCu220C, MLCu375, MLCu250, Nova T-PP, DimélysR). Based on the analysis of a total of 2,646 insertions and 55,794 woman-months of experience, we conclude that placement of an IUD within ten minutes of delivery of the placenta is a valuable alternative to interval insertion, because this method is safe and effective. Effectiveness was significantly lower for the Lippes Loop D than for the T- and ML-IUD models tested, the latter showing roughly comparable pertinent event rates. Pertinent event rates for copper IUDs were influenced by the skill of the operator; age of the recipient only had a significant effect on effectiveness, whereas parity had no significant effect on pertinent event rates. The single and still unsolved problem associated with immediate postpartum insertion is the greater likelihood of expulsion compared with interval insertion, and this hazard is significantly much greater for the Loop than for the copper-bearing devices assessed. The evolution of the expulsion rates shows a constant time-relationship. This pattern makes it obvious why follow-up of recipients, at least during the first trimester following insertion, is mandatory if immediate post-placental IUD insertion is to be optimally effective. PMID:4006467

  17. Generating Novel Allelic Variation Through Activator Insertional Mutagenesis in Maize

    OpenAIRE

    Bai, Ling; Singh, Manjit; Pitt, Lauren; Sweeney, Meredith; Brutnell, Thomas P.

    2007-01-01

    The maize transposable element Activator (Ac) has been exploited as an insertional mutagen to disrupt, clone, and characterize genes in a number of plant species. To develop an Ac-based mutagenesis platform for maize, a large-scale mutagenesis was conducted targeting the pink scutellum1 locus. We selected 1092 Ac transposition events from a closely linked donor Ac, resulting in the recovery of 17 novel ps1 alleles. Multiple phenotypic classes were identified corresponding to Ac insertions in ...

  18. Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus

    Directory of Open Access Journals (Sweden)

    Wei Lu

    2012-06-01

    Full Text Available Single nucleotide polymorphisms (SNPs are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for the aquaculture industry in East Asian countries. HRM analysis revealed that all the loci showed polymorphisms when evaluated using 40 A. japonicus individuals collected from a natural population. The minor allele frequency ranged from 0.035 to 0.489. The observed and expected heterozygosities ranged from 0.050 to 0.833 and 0.073 to 0.907, respectively. Thirteen loci were found to depart significantly from Hardy–Weinberg equilibrium (HWE after Bonferroni corrections. Significant linkage disequilibrium (LD was detected in one pair of markers. These SNP markers are expected to be useful for future quantitative trait loci (QTL analysis, and to facilitate marker-assisted selection (MAS in A. japonicus.

  19. Manganese superoxide dismutase Ala-9Val polymorphism and risk of breast cancer in a population-based case–control study of African Americans and whites

    International Nuclear Information System (INIS)

    A polymorphism in the manganese superoxide dismutase (MnSOD) gene, Ala-9Val, has been examined in association with breast cancer risk in several epidemiologic studies. Results suggest that the Ala allele increases the risk of breast cancer and modifies the effects of environmental exposures that produce oxidative damage to DNA. We examined the role of the MnSOD Ala-9Val polymorphism in a population-based case–control study of invasive and in situ breast cancer in North Carolina. Genotypes were evaluated for 2025 cases (760 African Americans and 1265 whites) and for 1812 controls (677 African Americans and 1135 whites). The odds ratio for MnSOD Ala/Ala versus any MnSOD Val genotypes was not elevated in African Americans (odds ratio = 0.9, 95% confidence interval = 0.7–1.2) or in whites (odds ratio = 1.0, 95% confidence interval = 0.8–1.2). Greater than additive joint effects were observed for the Ala/Ala genotype and smoking, radiation to the chest, and occupational exposure to ionizing radiation. Antagonism was observed between the Ala/Ala genotype and the use of nonsteroidal anti-inflammatory drugs. The MnSOD genotype may contribute to an increased risk of breast cancer in the presence of specific environmental exposures. These results provide further evidence for the importance of reactive oxygen species and of oxidative DNA damage in the etiology of breast cancer

  20. Moderating Effects of Genetic Polymorphisms on Improvements in Cognitive Impairment in Breast Cancer Survivors Participating in a 6-Week Mindfulness-Based Stress Reduction Program.

    Science.gov (United States)

    Lengacher, Cecile A; Reich, Richard R; Kip, Kevin E; Paterson, Carly L; Park, Hyun Y; Ramesar, Sophia; Jim, Heather S L; Alinat, Carissa B; Park, Jong Y

    2015-07-01

    Breast cancer (BC) survivors often report cognitive impairment, which may be influenced by single-nucleotide polymorphisms (SNPs). The purpose of this study was to test whether particular SNPs were associated with changes in cognitive function in BC survivors and whether these polymorphisms moderated cognitive improvement resulting from the Mindfulness-Based Stress Reduction for Breast Cancer (MBSR[BC]) program. BC survivors recruited from Moffitt Cancer Center and the University of South Florida's Breast Health Program, who had completed adjuvant radiation and/or chemotherapy treatment, were randomized to either the 6-week MBSR(BC) program (n = 37) or usual care (UC; n = 35) group. Measures of cognitive function and demographic and clinical history data were attained at baseline and at 6 and 12 weeks. A total of 10 SNPs from eight genes known to be related to cognitive function were analyzed using blood samples. Results showed that SNPs in four genes (ankyrin repeat and kinase domain containing 1 [ANKK1], apolipoprotein E [APOE], methylenetetrahydrofolate reductase [MTHFR], and solute carrier family 6 member 4 [SLC6A4]) were associated with cognitive impairment. Further, rs1800497 in ANKK1 was significantly associated with improvements in cognitive impairment in response to MBSR(BC). These results may help to identify individuals who would be better served by MBSR(BC) or other interventions. PMID:25882604

  1. Association between microRNA polymorphisms and cancer risk based on the findings of 66 case-control studies.

    Directory of Open Access Journals (Sweden)

    Xiao Pin Ma

    Full Text Available MicroRNAs (miRNAs are small non-coding RNA molecules, which participate in diverse biological processes and may regulate tumor suppressor genes or oncogenes. Single nucleotide polymorphisms (SNPs in miRNA may contribute to diverse functional consequences, including cancer development, by altering miRNA expression. Numerous studies have shown the association between miRNA SNPs and cancer risk; however, the results are generally debatable and inconclusive, mainly due to limited statistical power. To assess the relationship between the five most common SNPs (miR-146a rs2910164, miR-196a2 rs11614913, miR-499 rs3746444, miR-149 rs2292832, and miR-27a rs895919 and the risk cancer development, we performed a meta-analysis of 66 published case-control studies. Crude odds ratios at 95% confidence intervals were used to investigate the strength of the association. No association was observed between rs2910164 and cancer risk in the overall group. However, in stratified analysis, we found that either the rs2910164 C allele or the CC genotype was protective against bladder cancer, prostate cancer, cervical cancer, and colorectal cancer, whereas it was a risk factor for papillary thyroid carcinoma and squamous cell carcinoma of the head and neck (SCCHN. Further, rs11614913 was found to be significantly associated with decreased cancer risk, in particular, for bladder cancer, gastric cancer, and SCCHN. For miR-499, a significant association was found between the rs3746444 polymorphism and cancer risk in pooled analysis. In subgroup analysis, similar results were mainly observed for breast cancer. Finally, no association was found between rs2292832 and rs895919 polymorphisms and cancer risk in the overall group and in stratified analysis. In summary, miR-196a2 rs11614913, miR-146a rs2910164, and miR-499 rs3746444 are risk factors for cancer development, whereas mir-149 rs2292832 and miR-27a rs895919 are not associated with cancer risk.

  2. An insert-based enzymatic cell culture system to rapidly and reversibly induce hypoxia: investigations of hypoxia-induced cell damage, protein expression and phosphorylation in neuronal IMR-32 cells

    Directory of Open Access Journals (Sweden)

    Ying Huang

    2013-11-01

    Ischemia-reperfusion injury and tissue hypoxia are of high clinical relevance because they are associated with various pathophysiological conditions such as myocardial infarction and stroke. Nevertheless, the underlying mechanisms causing cell damage are still not fully understood, which is at least partially due to the lack of cell culture systems for the induction of rapid and transient hypoxic conditions. The aim of the study was to establish a model that is suitable for the investigation of cellular and molecular effects associated with transient and long-term hypoxia and to gain insights into hypoxia-mediated mechanisms employing a neuronal culture system. A semipermeable membrane insert system in combination with the hypoxia-inducing enzymes glucose oxidase and catalase was employed to rapidly and reversibly generate hypoxic conditions in the culture medium. Hydrogen peroxide assays, glucose measurements and western blotting were performed to validate the system and to evaluate the effects of the generated hypoxia on neuronal IMR-32 cells. Using the insert-based two-enzyme model, hypoxic conditions were rapidly induced in the culture medium. Glucose concentrations gradually decreased, whereas levels of hydrogen peroxide were not altered. Moreover, a rapid and reversible (onoff generation of hypoxia could be performed by the addition and subsequent removal of the enzyme-containing inserts. Employing neuronal IMR-32 cells, we showed that 3 hours of hypoxia led to morphological signs of cellular damage and significantly increased levels of lactate dehydrogenase (a biochemical marker of cell damage. Hypoxic conditions also increased the amounts of cellular procaspase-3 and catalase as well as phosphorylation of the pro-survival kinase Akt, but not Erk1/2 or STAT5. In summary, we present a novel framework for investigating hypoxia-mediated mechanisms at the cellular level. We claim that the model, the first of its kind, enables researchers to rapidly and

  3. Intra-specific relationships among Tibetan Eared-pheasants based on randomly amplified polymorphic DNA(RAPD) analysis

    Institute of Scientific and Technical Information of China (English)

    DING Wei; ZHANG Zhengwang; CHANG Jiang; ZHANG Er; WU Xiushan; ZHANG Jinguo

    2006-01-01

    The Tibetan Eared-pheasant Crossoptilon harmani is a rare species native to China.A captive population has been established in the Beijing Zoo since 1999.In order to determine the kinship of the offsprings in 2001,randomly amplified polymorphic DNA (RAPD) was used to examine the parenthood of seven Tibetan Eared-pheasants in the Beijing Zoo.To amplify the genomic DNA of each individual,53 arbitrary primers were selected.The results of amplifica tions showed that 14 primers had clear and distinct RAPD patterns.Totally,226 amplified fragments were generated by RAPD in this study.Cluster analysis of the seven Tibetan Eared-pheasants indicated that all the four young birds had the same father (No.5 male).This study provides a practical method to determine the relationship of offsprings whose parents are unknown in birds.

  4. Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms.

    Directory of Open Access Journals (Sweden)

    John E Bowers

    Full Text Available The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences targeting 86,023 unigenes from sunflower (Helianthus annuus L. and related species to test for single-feature polymorphisms (SFPs in a recombinant inbred line (RIL mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801. We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.

  5. An Insertable Passive LC Pressure Sensor Based on an Alumina Ceramic for In Situ Pressure Sensing in High-Temperature Environments

    OpenAIRE

    Jijun Xiong; Chen Li; Pinggang Jia; Xiaoyong Chen; Wendong Zhang; Jun Liu; Chenyang Xue; Qiulin Tan

    2015-01-01

    Pressure measurements in high-temperature applications, including compressors, turbines, and others, have become increasingly critical. This paper proposes an implantable passive LC pressure sensor based on an alumina ceramic material for in situ pressure sensing in high-temperature environments. The inductance and capacitance elements of the sensor were designed independently and separated by a thermally insulating material, which is conducive to reducing the influence of the temperature on ...

  6. Analysis of DNA methylation variation in wheat genetic background after alien chromatin introduction based on methylation-sensitive amplification polymorphism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    During the process of alien germplasm introduced into wheat genome by chromosome engineering,extensive genetic variations of genome structure and gene expression in recipient could be induced.In this study,we performed GISH(genome in situ hybridization)and AFLP(amplified fragment length polymorphism) on wheat-rye chromosome transIocation lines and their parents to detect the identity in genomic structure of different translocation lines.The results showed that the genome primary structure variations were not obviously detected in different translocation lines except the same 1RS chromosome translocation.Methylation sensitive amplification polymorphism(MSAP)analyses on genomic DNA showed that the ratios of fully-methylated sites were significantly increased in translocation lines(CN12,20.15%;CN17,20.91%;CN18,22.42%),but the ratios of hemimethylated sites were significantly lowered(CN12,21.41%;CN17,23.43%;CN18,22.42%),whereas 16.37%were fully-methylated and 25.44%were hemimethylated in case of their wheat parent.Twenty-nine classes of methylation patterns were identified in a comparative assay of cytosine methylation patterns between wheat-rye translocation lines and their wheat parent,including 13 hypermethylation patterns(33.74%),9 demethylation patterns(22.76%)and 7 uncertain patterns(4.07%).In further sequence analysis,the alterations of methylation pattern affected both repetitive DNA sequences,such as retrotransposons and tandem repetitive sequences,and low-copy DNA.

  7. Field Errors in Hybrid Insertion Devices

    OpenAIRE

    Schlueter, R.D.

    1995-01-01

    Hybrid magnet theory as applied to the error analyses used in the design of Advanced Light Source (ALS) insertion devices is reviewed. Sources of field errors in hybrid insertion devices are discussed.

  8. Field errors in hybrid insertion devices

    Energy Technology Data Exchange (ETDEWEB)

    Schlueter, R.D. [Lawrence Berkeley Lab., CA (United States)

    1995-02-01

    Hybrid magnet theory as applied to the error analyses used in the design of Advanced Light Source (ALS) insertion devices is reviewed. Sources of field errors in hybrid insertion devices are discussed.

  9. A new insertion sequence for incremental Delaunay triangulation

    Institute of Scientific and Technical Information of China (English)

    Jian-Fei Liu; Jin-Hui Yan; S.H.Lo

    2013-01-01

    Incremental algorithm is one of the most popular procedures for constructing Delaunay triangulations (DTs).However,the point insertion sequence has a great impact on the amount of work needed for the construction of DTs.It affects the time for both point location and structure update,and hence the overall computational time of the triangulation algorithm.In this paper,a simple deterministic insertion sequence is proposed based on the breadth-first-search on a Kd-tree with some minor modifications for better performance.Using parent nodes as search-hints,the proposed insertion sequence proves to be faster and more stable than the Hilbert curve order and biased randomized insertion order (BRIO),especially for non-uniform point distributions over a wide range of benchmark examples.

  10. Human-specific HERV-K insertion causes genomic variations in the human genome.

    Directory of Open Access Journals (Sweden)

    Wonseok Shin

    Full Text Available Human endogenous retroviruses (HERV sequences account for about 8% of the human genome. Through comparative genomics and literature mining, we identified a total of 29 human-specific HERV-K insertions. We characterized them focusing on their structure and flanking sequence. The results showed that four of the human-specific HERV-K insertions deleted human genomic sequences via non-classical insertion mechanisms. Interestingly, two of the human-specific HERV-K insertion loci contained two HERV-K internals and three LTR elements, a pattern which could be explained by LTR-LTR ectopic recombination or template switching. In addition, we conducted a polymorphic test and observed that twelve out of the 29 elements are polymorphic in the human population. In conclusion, human-specific HERV-K elements have inserted into human genome since the divergence of human and chimpanzee, causing human genomic changes. Thus, we believe that human-specific HERV-K activity has contributed to the genomic divergence between humans and chimpanzees, as well as within the human population.

  11. Delayed bowel perforation following suprapubic catheter insertion

    OpenAIRE

    Mehta Ajay; Ahmed Shwan J; Rimington Peter

    2004-01-01

    Abstract Background Complications of suprapubic catheter insertion are rare but can be significant. We describe an unusual complication of a delayed bowel perforation following suprapubic catheter insertion. Case presentation A gentleman presented with features of peritonitis and feculent discharge along a suprapubic catheter two months after insertion of the catheter. Conclusion Bowel perforation is the most feared complication of suprapubic catheter insertion especially in patients with low...

  12. Does 'insertion' work? France's minimum income"

    OpenAIRE

    Whitton, Timothy

    1993-01-01

    International audience France's Revenu Minimum d Insertion (RMI) received the approval of the French Parliament on 1st December1988, and came into effect shortly afterwardsi. In addition to a means test, the RMI is conditional upon signature of a contract (le contrat d'insertion) by which its recipients pledge themselves to take whatever action the RMI authorities recommend in order to re-insert themselves in main-stream society. Insertion is a difficult concept to translate into English. ...

  13. RNA-Editing with Combined Insertion and Deletion Preserves Regularity

    Directory of Open Access Journals (Sweden)

    E.P. de Vink

    2013-01-01

    Full Text Available We consider two elementary forms of string rewriting called guided insertion/deletion and guided rewriting. The original strings are modified depending on the match with a given set of auxiliary strings, called guides. Guided insertion/deletion considers matching of a string and a guide with respect to a specific correspondence of strings. Guided rewriting considers matching of a string and a guide with respect to an equivalence relation on the alphabet. Guided insertion/deletion is inspired by {RNA}-editing, a biological process by which the original genetic information stored in DNA is modified before its final expression. The formalism here allows for simultaneous insertion and deletion of string elements. Guided rewriting, based on a letter-to-letter relation, is technically more appealing than guided insertion/deletion. We prove that guided rewriting preserves regularity: for every regular language its closure under guided rewriting is regular too. In the proof we will rely on the auxiliary notion of a slice sequence. We establish a correspondence of slice sequences and guide rewrite sequences. Because of their left-to-right nature, slice sequences are more convenient to deal with than guided rewrite sequences in the construction of the finite automata that we encounter in the proofs of regularity. Based on the result for guided rewriting we establish that guided insertion/deletion preserves regularity as well.

  14. Regional insertion: an emergent approach

    International Nuclear Information System (INIS)

    The Brazilian Electrical Sector incorporates new variables that expressing the extensive spectrum of environmental impacts in the take of decisions, referring to the viability of realizing a electrical undertaking, attends the several restrictions that are important by the sector and by the society in the environment area and promotes the adequate generation of liquid benefits, consequential of the electrical undertaking. Due to these factors, the Electrical Sector is improving the concept of regional insertion, with the sectorial expansion in long-dated and the created demand in the environmental and social area, focalizing the solution for these questions. (C.G.C.). 1 fig, 2 tabs

  15. Tetrahedral mesh for needle insertion

    OpenAIRE

    Syvertsen, Rolf Anders

    2007-01-01

    This is a Master’s thesis in how to make a tetrahedral mesh for use in a needle insertion simulator. It also describes how it is possible to make the simulator, and how to improve it to make it as realistic as possible. The medical simulator uses a haptic device, a haptic scene graph and a FEM for realistic soft tissue deformation and interaction. In this project a tetrahedral mesh is created from a polygon model, and then the mesh has been loaded into the HaptX haptic scene graph. The object...

  16. A functional HOTAIR rs12826786 C>T polymorphism is associated with breast cancer susceptibility and poor clinicopathological characteristics in a Turkish population: a hospital-based case-control study.

    Science.gov (United States)

    Bayram, Süleyman; Sümbül, Ahmet Taner; Dadaş, Erdoğan

    2016-04-01

    Hox transcript antisense intergenic RNA (HOTAIR), a long non-coding RNA (lncRNA), is pervasively overexpressed and correlated with tumor invasion, progression, metastasis, and poor prognosis in various human cancers including breast cancer (BC) that plays a role as an oncogenic molecule. A common functional single-nucleotide polymorphism (SNP) (rs12826786 C>T) at the HOTAIR promoter has been reported to influence HOTAIR expression and gastric adenocarcinoma susceptibility, but relation of HOTAIR rs12826786 C>T polymorphism with BC susceptibility and clinicopathological characteristics has yet to be reported. To explore the association of the HOTAIR rs12826786 C>T polymorphism with the risk of BC in a Turkish population, a hospital-based case-control study was carried out consisting of 123 BC patients and 122 age-matched healthy controls. HOTAIR rs12826786 C>T polymorphism was determined by real-time polymerase chain reaction (PCR) using TaqMan assay. We found that women carrying TT genotype of HOTAIR rs12826786 C>T polymorphism had an increased risk of developing BC in both codominant (odds ratio (OR) = 2.24, 95 % confidence interval (CI) 1.05-4.81, P = 0.02) and recessive (OR = 2.49, 95 % CI 1.25-4.97, P = 0.008) inheritance models. Moreover, TT genotype of HOTAIR rs12826786 C>T polymorphism was significantly related with multiple clinicopathological characteristics concerned with worse BC progression such as advanced TNM stage (III and IV), larger tumor size (T3 and T4), and distant metastasis (M1), as well as poor histological grade (III) (P T polymorphism might play crucial roles in genetic susceptibility and poor prognosis for BC in Turkish population, further independent studies are needed to confirm our results in a larger series, as well as in patients of distinct populations. PMID:26577852

  17. Genetic polymorphism of GSTP1 and ERCC1 correlated with response to platinum-based chemotherapy in non-small cell lung cancer.

    Science.gov (United States)

    Lv, Hongying; Han, Ting; Shi, Xiaoli; Yao, Yasai; Yao, Yongru; Qiu, Wensheng; Yue, Lu; Liang, Jun

    2014-08-01

    The study aims to investigate whether the glutathione S transferase P1 (GSTP1) and excision repair cross-complementing group 1 (ERCC1) polymorphism influence the response to treatment with platinum-based chemotherapy in Chinese patients with non-small cell lung cancer. Ninety-one patients with metastatic non-small lung cancer were evaluated. Blood samples were obtained from each patient before chemotherapy. They are all administered modified TP, GP, NP regimens. Curative effects in patients were evaluated after at least two cycles of treatment. TTP was calculated. The response rate of GSTP1 with G/G + G/A group and A/A group is 54.55 % (24/44) and 21.28 % (10/47) (P = 0.001), respectively. The response rate of ERCC1 with C/C group and C/T + T/T group is 51.11 % (23/45) and 23.91 % (11/46) (P = 0.007), respectively. Patients with both G/G + G/A and C/C has the response rate of 64.52 % (20/31) (P = 0.000). Logistic regression analysis shows a significant increased chance of treatment response in patients with G/G + G/A genotype versus A/A genotype (P = 0.008) and with T/T + C/T genotype versus C/C genotype (P = 0.001). The median TTP of all patients is 7.32 months. The TTP of individuals with G/G + G/A genotype is 9.56 months, and those with A/A genotype had an TTP of 5.23 months. The TTP of individuals with C/C genotype is 9.16 months, and those with T/T + C/T genotype is 5.53 months. Kaplan-Meier analysis shows that ERCC1 and GSTP1 polymorphisms are correlated with TTP. The log-rank test is was marginally significant (P < 0.01). GSTP1 and ERCC1 polymorphism are correlated with response to platinum-based chemotherapy and have prognostic value for TTP. PMID:24958519

  18. Morphotropy, isomorphism, and polymorphism of Ln2M2O7-based (Ln = La-Lu, Y, Sc; M = Ti, Zr, Hf, Sn) oxides

    International Nuclear Information System (INIS)

    Structural studies of compounds of variable composition and measurements of their conductivity have made it possible to identify new oxygen-ion-conducting rare-earth pyrochlores, Ln2Ti2O7 (Ln = Dy-Lu) and Ln2Hf2O7 (Ln = Eu, Gd), with intrinsic high-temperature oxygen ion conductivity (up to 1.4 × 10−2 S/cm at 800°C). Twenty six systems have been studied, and more than 50 phases based on the Ln2M2O7 (Ln= La-Lu; M = Ti, Zr, Hf) oxides have been synthesized and shown to be potential oxygen ion conductors. The morphotropy and polymorphism of the Ln2M2O7 (Ln = La-Lu; M = Ti, Zr, Hf) rare-earth pyrochlores have been analyzed in detail for the first time. Thermodynamic and kinetic (growth-related) phase transitions have been classified with application to the pyrochlore family

  19. Polychlorinated biphenyls, cytochrome P450 1A1 (CYP1A1) polymorphisms, and breast cancer risk among African American women and white women in North Carolina: a population-based case-control study

    OpenAIRE

    Li, Yu; Millikan, Robert C.; Douglas A Bell; Cui, Lisa; Tse, Chiu-Kit J; Newman, Beth; Conway, Kathleen

    2004-01-01

    Introduction Epidemiologic studies have not shown a strong relationship between blood levels of polychlorinated biphenyls (PCBs) and breast cancer risk. However, two recent studies showed a stronger association among postmenopausal white women with the inducible M2 polymorphism in the cytochrome P450 1A1 (CYP1A1) gene. Methods In a population-based case-control study, we evaluated breast cancer risk in relation to PCBs and the CYP1A1 polymorphisms M1 (also known as CYP1A1*2A), M2 (CYP1A1*2C),...

  20. Evaluation of single nucleotide polymorphisms of Pro12Ala in peroxisome proliferator-activated receptor-γ and Gly308Ala in tumor necrosis factor-α genes in obese Asian Indians: a population-based study

    Directory of Open Access Journals (Sweden)

    Namita Bhagat

    2010-10-01

    Full Text Available Namita Bhagat1,2, Mukta Agrawal1, Kalpana Luthra3, Naval K Vikram4, Anoop Misra4, Rajeev Gupta21Department of Home Science, University of Rajasthan, Jaipur, Rajasthan, India; 2Department of Medicine, Fortis Escorts Hospital, Jaipur, Rajasthan, India; 3Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India; 4Department of Medicine, All India Institute of Medical Sciences, New Delhi, IndiaBackground: A population-based case control study was performed to determine the associations of Pro12Ala polymorphism in peroxisome proliferator-activated receptor-γ (PPARG and Gly308Ala polymorphism in tumor necrosis factor-α (TNFA genes in obese subjects.Patients and methods: Of 1,400 eligible subjects, ≥20 years, we recruited only 1,127. For extreme phenotype case-control design, we evaluated 201 subjects with body mass index (BMI ≥30 kg/m2 (Group 1 and 143 with BMI <20 kg/m2 (Group 2. Clinical, anthropometric, biochemical, and nutritional details and polymorphisms were estimated.Results: In Group 1, the dietary intake of calories and fats was higher, physical activity was lower, and prevalence of truncal obesity, hypertension, high total cholesterol, low high-density lipoprotein cholesterol, and diabetes was greater than in Group 2. There were no homozygous polymorphisms of either gene. Heterozygous Pro12Ala polymorphism in PPARG was found in 15 (7.5% subjects in Group 1 and 3 (2.1% subjects in Group 2 (P = 0.028, and heterozygous Gly308Ala polymorphism in TNFA was found in 19 (9.5% in Group 1 and 7 (4.9% in Group 2 (P = 0.115. Presence of heterozygous polymorphism in PPARG and TNFA-predicted obesity with univariate odds ratio ([OR], 95% confidence intervals of 2.25 (1.32–3.84, P = 0.003 and 1.48 (1.10–1.99, P = 0.009 and with multivariate OR 1.74 (1.03–2.93, P = 0.038 and 1.46 (1.05–2.03, P = 0.024, respectively. The addition of dietary and physical activity variables did not result in significant change

  1. Identification of Thiobacillus ferrooxidans strains based on restriction fragment length polymorphism analysis of 16S rDNA.

    Science.gov (United States)

    Kamimura, K; Wakai, S; Sugio, T

    2001-01-01

    The 16S rDNA sequences from ten strains of Thiobacillus ferrooxidans were amplified by PCR. The products were compared by performing restriction fragment length polymorphism (RFLP) analysis with restriction endonucleases Alu I, Hap II, Hha I, and Hae III. The RFLP patterns revealed that T. ferrooxidans could be distinguished from other iron- or sulphur-oxidizing bacteria such as T. thiooxidans NB1-3, T. caldus GO-1, Leptospirillum ferrooxidans and the marine iron-oxidizing bacterium strain KU2-11. The RFLP patterns obtained with Alu I, Hap II, and Hae III were the same for nine strains of T. ferrooxidans except for strain ATCC 13661. The RFLP patterns for strains NASF-1 and ATCC 13661 with Hha I were distinct from those for other T. ferrooxidans strains. The 16S rDNA sequence of T. ferrooxidans NASF-1 possessed an additional restriction site for Hha I. These results show that iron-oxidizing bacteria isolated from natural environments were rapidly identified as T. ferrooxidans by the method combining RFLP analysis with physiological analysis. PMID:11414499

  2. Genetic Polymorphism of Nine Non-CODIS STR Loci in Hu-nan Province-based Chinese Han Population

    Institute of Scientific and Technical Information of China (English)

    GUO Juan-juan; LIU Ying; GUO Ya-dong; YAN Jie; CHANG Yun-feng; CAI Ji-feng; LU Ting; ZHA Lagabaiyila

    2014-01-01

    Objective To determine the allelic frequency distribution and genetic parameters of nine non-CODIS DNA index systems of the short tandemrepeat (STR ) loci (D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05). Methods A total of 353 blood samples were collected, extracted, amplified, and analyzed fromunrelated healthy individuals of Han na-tionality in Hunan Province, China. Results O ne hundred and fourteen alleles were observed in the pop-ulation with corresponding allelic frequencies ranged from0.001 0 to 0.323 0. For all the nine non-CODIS STR loci, the observed genotypic data showed no significant deviations fromthe Hardy-W einberg equi-librium. The Ho, He, PIC, D P, and PE of the studied non-CODIS STR loci ranged from0.108 0 to 0.195 0, 0.805 0 to 0.892 0, 0.770 0 to 0.860 0, 0.925 0 to 0.966 0 and 0.607 0 to 0.780 0, respectively. Conclusion N ine non-CODIS STR loci have high degrees of polymorphisms, which may be useful in in-dividual forensic identification and parentage testing in forensic practice.

  3. Influence of Serotonin Transporter Gene Polymorphisms and Adverse Life Events on Depressive Symptoms in the Elderly: A Population-Based Study.

    Directory of Open Access Journals (Sweden)

    Annalisa Davin

    Full Text Available Depression is common in the elderly. The role of genetic and environmental factors in modulating depressive symptoms is not clear.We evaluated the influence of serotonin transporter gene polymorphisms and recent adverse life events on depressive symptoms in an elderly Italian population. We used data from "InveCe.Ab", a population-based study of 1321 subjects aged 70-74 years. We used the 15-item Geriatric Depression Scale (GDS to assess depressive symptoms-a GDS score ≥5 points (GDS≥5 indicated the presence of clinically relevant symptoms-and performed 5-HTTLPR and rs25531 genotyping to obtain the triallelic polymorphism of the serotonin transporter. We used the Geriatric Adverse Life Events Scale to measure adverse life events, and logistic regression models to evaluate the role of genotype and recent adverse life events in depressive symptoms, controlling for potential confounders and independent predictors.Two hundred subjects (15.76% had a GDS≥5. The 5-HTTLPR triallelic polymorphism was significantly associated with GDS≥5. Only S'S' carriers showed an increased risk of depressive symptoms (ORadj = 1.81, p = .022; one extra adverse life event increased this risk by 14% (p = .061 independently of genotype. Other factors significantly related to GDS≥5 were: female gender (ORadj = 2.49, p < .001, age (ORadj = 1.19, p = .007, a history of depression (ORadj = 4.73, p < .001, and comorbidity (ORadj = 1.23, p = .001. One extra adverse life event increased the risk of depressive symptoms by 57% (p = .005 only in the L'L' carriers, while antidepressant intake was directly related to GDS≥5 in the L'S' carriers (ORadj = 2.46, p = .036 and borderline significant in the S'S' carriers (ORadj = 2.41, p = .081.The S'S' genotype and recent exposure to adverse life events were independently associated with depressive symptoms. The S'S' genotype, compared with the environment, exerted a predominant effect on depressive symptoms, suggesting that it

  4. Association Between 5-HTTLPR Polymorphism and Tics after Treatment with Methylphenidate in Korean Children with Attention-Deficit/Hyperactivity Disorder

    OpenAIRE

    Park, Seo Yeon; Kim, Eun Joo; Cheon, Keun-Ah

    2015-01-01

    Abstract Objectives: The purpose of this study is to examine the relationship between 5-HTTLPR polymorphism (44-bp insertion/deletion polymorphism of serotonin transporter gene) and methylphenidate (MPH) treatment response, as well as the association between the adverse events of MPH treatment and 5-HTTLPR polymorphism in children with attention-deficit/hyperactivity disorder (ADHD). Methods: A total of 114 children with ADHD (mean age 9.08 ± 1.94 years) were recruited from the child psychiat...

  5. Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.

    OpenAIRE

    Clark, TG; Andrew, T.; Cooper, GM; Margulies, EH; Mullikin, JC; Balding, DJ

    2007-01-01

    BACKGROUND: We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and measures of evolutionary constraint. RESULTS: Indel rates are observed to be reduced approximately 20-fold to 60-fold in exonic regions, 5-fold to 10-fold in sequence that exhib...

  6. Genetically regulated epigenetic transcriptional activation of retrotransposon insertion confers mouse dactylaplasia phenotype

    OpenAIRE

    Kano, Hiroki; Kurahashi, Hiroki; Toda, Tatsushi

    2007-01-01

    Dactylaplasia, characterized by missing central digital rays, is an inherited mouse limb malformation that depends on two genetic loci. The first locus, Dac, is an insertional mutation around the dactylin gene that is inherited as a semidominant trait. The second locus is an unlinked modifier, mdac/Mdac, that is polymorphic among inbred strains. Mdac dominantly suppresses the dactylaplasia phenotype in mice carrying Dac. However, little is known about either locus or the nature of their inter...

  7. Intensional Effect Polymorphism

    OpenAIRE

    Long, Yuheng; Liu, Yu David; Rajan, Hridesh

    2015-01-01

    Type-and-effect systems are a powerful tool for program construction and verification. We describe intensional effect polymorphism, a new foundation for effect systems that integrates static and dynamic effect checking. Our system allows the effect of polymorphic code to be intensionally inspected through a lightweight notion of dynamic typing. When coupled with parametric polymorphism, the powerful system utilizes runtime information to enable precise effect reasoning, while at the same time...

  8. 基于G-四链体结构多态性的核酸纳米技术%DNA Nanotechnology Based on Polymorphic G-Quadruplex

    Institute of Scientific and Technical Information of China (English)

    郑琳; 王宪; 张金利; 李韡

    2011-01-01

    Guanine (G)-rich oligonucleotides can self-assemble into polymorphic G-quadruplexes via stacking of G-quartets which are a biologically relevant alternative of the classical Watson-Crick double helix.Unique molecular recognition properties of G-quadruplex can be utilized to induce orderly organizing of nanoparticles and design nanodevices with stimulu-response functions, which have promising applications in DNA nanotechnology.This article introduced the polymorphism of G-quadruplexes and reviewed the DNA nanotechnology based on structural transition of G-quadruplex, especially focusing on nanomaterials self-organization and nanodevices design, and then illustrated the prospects of its development trend.%G-四链体是由富G核酸形成的独特四链螺旋结构,区别于遵循A-T、G-C碱基互补配对原则形成的传统Watson-Crick双链结构.基于G-四链体的特异分子识别特性,能够引导纳米粒子的有序组装、赋予纳米器件以刺激一响应功能,使得核酸纳米技术领域的内容更丰富多样.本文介绍了G-四链体的结构多态性,从纳米材料组装和纳米器件设计两个方面综述了基于G-四链体结构转变的核酸纳米技术,并对其研究前景进行了展望.

  9. The Renalase Asp37Glu polymorphism is not associated with hypertension and cardiovascular events in an urban-based prospective cohort: the Malmö Diet and cancer study

    Directory of Open Access Journals (Sweden)

    Fava Cristiano

    2012-07-01

    Full Text Available Abstract Background Renalase (gene name RNLS, a recently discovered enzyme with monoamine oxidase activity, is implicated in the degradation of catecholamines. Recent studies delineate a possible role of this enzyme in blood pressure (BP maintenance and cardiac protection and two single nucleotide polymorphisms, RNLS rs2576178 A > G and rs2296545 C > G have been associated with hypertension. The latter SNP leads to a non synonymous Asp to Glu substitution deleting a flavin adenine dinucleotide (FAD binding site with possible impaired functionality. We tested the hypothesis that these polymorphisms could affect BP levels, hypertension prevalence, and risk of incident cardiovascular events in middle-aged Swedes. Methods The polymorphisms were genotyped in 5696 participants of the population-based Cardiovascular Cohort of the "Malmö Diet and Cancer" (MDC-CC. The incidence of cardiovascular events (coronary events [n = 408], strokes [n = 330], heart failure [n = 190] and atrial fibrillation/flutter [n = 406] was monitored for an average of approximately 15 years of follow-up. Results Both before and after adjustment for sex, age and BMI the polymorphisms did not show any effect on BP level and hypertension prevalence. Before and after adjustment for major cardiovascular risk factors, the hazard ratio for cardiac and cerebrovascular events was not significantly different in carriers of different genotypes. A significant interaction was found between the rs2296545 C > G and age with respect to BP/hypertension. Conclusions Our data do not support a major role for these RNLS polymorphisms in determining BP level and incident events at population level. The positive interaction with age suggest that the effect of the rs2296545 C > G polymorphism, if any, could vary between different ages.

  10. Dependency of tunneling magneto-resistance on Fe insertion-layer thickness in Co{sub 2}Fe{sub 6}B{sub 2}/MgO-based magnetic tunneling junctions

    Energy Technology Data Exchange (ETDEWEB)

    Chae, Kyo-Suk [MRAM Center, Department of Electronics and Computer Engineering, Hanyang University, Seoul 133-791 (Korea, Republic of); Samsung Electronics Co., Ltd., San #16 Banwol-dong, Hwasung-City, Gyeonggi-Do 445-701 (Korea, Republic of); Park, Jea-Gun, E-mail: parkjgL@hanyang.ac.kr [MRAM Center, Department of Electronics and Computer Engineering, Hanyang University, Seoul 133-791 (Korea, Republic of)

    2015-04-21

    For Co{sub 2}Fe{sub 6}B{sub 2}/MgO-based perpendicular magnetic tunneling junctions spin valves with [Co/Pd]{sub n}-synthetic-antiferromagnetic (SyAF) layers, the tunneling-magneto-resistance (TMR) ratio strongly depends on the nanoscale Fe insertion-layer thickness (t{sub Fe}) between the Co{sub 2}Fe{sub 6}B{sub 2} pinned layer and MgO tunneling barrier. The TMR ratio rapidly increased as t{sub Fe} increased up to 0.4 nm by improving the crystalline linearity of a MgO tunneling barrier and by suppressing the diffusion of Pd atoms from a [Co/Pd]{sub n}-SyAF. However, it abruptly decreased by further increasing t{sub Fe} in transferring interfacial-perpendicular magnetic anisotropy into the IMA characteristic of the Co{sub 2}Fe{sub 6}B{sub 2} pinned layer. Thus, the TMR ratio peaked at t{sub Fe} = 0.4 nm: i.e., 120% at 29 Ωμm{sup 2}.

  11. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.

    Science.gov (United States)

    Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R; Wang, Xiaolu

    2016-03-01

    Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon. PMID:27162496

  12. Sequence-based polymorphisms in the mitochondrial D-loop and potential SNP predictors for chronic dialysis.

    Directory of Open Access Journals (Sweden)

    Jin-Bor Chen

    Full Text Available BACKGROUND: The mitochondrial (mt displacement loop (D-loop is known to accumulate structural alterations and mutations. The aim of this study was to investigate the prevalence of single nucleotide polymorphisms (SNPs within the D-loop among chronic dialysis patients and healthy controls. METHODOLOGY AND PRINCIPAL FINDINGS: We enrolled 193 chronic dialysis patients and 704 healthy controls. SNPs were identified by large scale D-loop sequencing and bioinformatic analysis. Chronic dialysis patients had lower body mass index, blood thiols, and cholesterol levels than controls. A total of 77 SNPs matched with the positions in reference of the Revised Cambridge Reference Sequence (CRS were found in the study population. Chronic dialysis patients had a significantly higher incidence of 9 SNPs compared to controls. These include SNP5 (16108Y, SNP17 (16172Y, SNP21 (16223Y, SNP34 (16274R, SNP35 (16278Y, SNP55 (16463R, SNP56 (16519Y, SNP64 (185R, and SNP65 (189R in D-loop of CRS. Among these SNPs with genotypes, SNP55-G, SNP56-C, and SNP64-A were 4.78, 1.47, and 5.15 times more frequent in dialysis patients compared to controls (P<0.05, respectively. When adjusting the covariates of demographics and comorbidities, SNP64-A was 5.13 times more frequent in dialysis patients compared to controls (P<0.01. Furthermore, SNP64-A was found to be 35.80, 3.48, 4.69, 5,55, and 4.67 times higher in female patients and in patients without diabetes, coronary artery disease, smoking, and hypertension in an independent significance manner (P<0.05, respectively. In patients older than 50 years or with hypertension, SNP34-A and SNP17-C were found to be 7.97 and 3.71 times more frequent (P<0.05 compared to patients younger than 50 years or those without hypertension, respectively. CONCLUSIONS AND SIGNIFICANCE: The results of large-scale sequencing suggest that specific SNPs in the mtDNA D-loop are significantly associated with chronic dialysis. These SNPs can be considered

  13. Delayed bowel perforation following suprapubic catheter insertion

    Directory of Open Access Journals (Sweden)

    Mehta Ajay

    2004-12-01

    Full Text Available Abstract Background Complications of suprapubic catheter insertion are rare but can be significant. We describe an unusual complication of a delayed bowel perforation following suprapubic catheter insertion. Case presentation A gentleman presented with features of peritonitis and feculent discharge along a suprapubic catheter two months after insertion of the catheter. Conclusion Bowel perforation is the most feared complication of suprapubic catheter insertion especially in patients with lower abdominal scar. The risk may be reduced with the use of ultrasound scan guidance.

  14. Nozzle insert for mixed mode fuel injector

    Science.gov (United States)

    Lawrence, Keith E.

    2006-11-21

    A fuel injector includes a homogenous charge nozzle outlet set and a conventional nozzle outlet set controlled respectively, by first and second needle valve members. The homogeneous charged nozzle outlet set is defined by a nozzle insert that is attached to an injector body, which defines the conventional nozzle outlet set. The nozzle insert is a one piece metallic component with a large diameter segment separated from a small diameter segment by an annular engagement surface. One of the needle valve members is guided on an outer surface of the nozzle insert, and the nozzle insert has an interference fit attachment to the injector body.

  15. A HTS dipole insert coil constructed

    CERN Document Server

    Ballarino, A; Rey, J M; Stenvall, A; Sorbi, M; Tixador, P

    2013-01-01

    This report is the deliverable report 7.4.1 “A HTS dipole insert coil constructed“. The report has three parts: “Design report for the HTS dipole insert”, “One insert pancake prototype coil constructed with the setup for a high field test”, and “All insert components ordered”. The three report parts show that, although the insert construction will be only completed by end 2013, all elements are present for a successful completion and that, given the important investments done by the participants, there is a full commitment of all of them to finish the project

  16. Influence of Methylenetetrahydrofolate Reductase C677T Polymorphism on the Risk of Lung Cancer and the Clinical Response to Platinum-Based Chemotherapy for Advanced Non-Small Cell Lung Cancer: An Updated Meta-Analysis

    OpenAIRE

    Zhu, Ning; Gong, Yi; He, Jian; Xia, Jingwen; Chen, Xiaodong

    2013-01-01

    Purpose Methylenetetrahydrofolate reductase (MTHFR) has been implicated in lung cancer risk and response to platinum-based chemotherapy in advanced non-small cell lung cancer (NSCLC). However, the results are controversial. We performed meta-analysis to investigate the effect of MTHFR C677T polymorphism on lung cancer risk and response to platinum-based chemotherapy in advanced NSCLC. Materials and Methods The databases of PubMed, Ovid, Wanfang and Chinese Biomedicine were searched for eligib...

  17. Genotyping of a tri-allelic polymorphism by a novel melting curve assay in MTHFD1L: an association study of nonsyndromic Cleft in Ireland

    LENUS (Irish Health Repository)

    Minguzzi, Stefano

    2012-04-20

    AbstractBackgroundPolymorphisms within the MTHFD1L gene were previously associated with risk of neural tube defects in Ireland. We sought to test the most significant MTHFD1L polymorphisms for an association with risk of cleft in an Irish cohort. This required the development of a new melting curve assay to genotype the technically challenging MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406).MethodsMelting curve analysis was used to genotype the MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406) and a Single Nucleotide Polymorphism rs17080476 in an Irish cohort consisting of 981 Irish case-parent trios and 1,008 controls. Tests for association with nonsyndromic cleft lip with or without cleft palate and cleft palate included case\\/control analysis, mother\\/control analysis and Transmission Disequilibrium Tests of case-parent trios.ResultsA successful melting curve genotyping assay was developed for the deletion\\/insertion polymorphism (rs3832406). The TDT analysis initially showed that the rs3832406 polymorphism was associated with isolated cleft lip with or without cleft palate. However, corrected p-values indicated that this association was not significant.ConclusionsMelting Curve Analysis can be employed to successfully genotype challenging polymorphisms such as the MTHFD1L triallelic deletion\\/insertion polymorphism (DIP) reported here (rs3832406) and is a viable alternative to capillary electrophoresis. Corrected p-values indicate no association between MTHFD1L and risk of cleft in an Irish cohort.

  18. Polymorphisms in base excision DNA repair genes and association with melanoma risk in a pilot study on Central-South Italian population.

    Science.gov (United States)

    Santonocito, Concetta; Scapaticci, Margherita; Penitente, Romina; Paradisi, Andrea; Capizzi, Rodolfo; Lanza-Silveri, Sara; Ficarra, Silvana; Landi, Francesco; Zuppi, Cecilia; Capoluongo, Ettore

    2012-10-01

    Base excision repair plays a key role in the removing of DNA damage from exposure to endogenous and exogenous carcinogens. The BER pathway removes alterations of a single oxidized, reduced or methylated base. Recently some studies have explored the association between risk for cutaneous melanoma and non-synonymous single-nucleotide polymorphisms (nsSNPs) in DNA-repair genes, although with contradictory results. We hypothesized that common nsSNPs of BER genes, specifically ADPRT rs1136410, XRCC1 rs25487, rs25489, rs1799782, APEX1 rs1130409, OGG1 rs1052133, LIG3 rs3136025 and MUTYH rs3219466, may contribute to risk of melanoma. The aim of this study is to investigate whether or not a correlation between these nsSNPs and melanoma risk and/or aggressiveness is present. 167 melanoma patients and 186 healthy control subjects were analysed. By multivariate statistical analysis no association was found between nsSNP and melanoma aggressiveness, while only the two XRCC1 (rs25487 and rs25489) nsSNPs showed a strong correlation (p<0.001) with melanoma risk. To our knowledge this is the first study reporting an association between BER nsSNPs and melanoma risk in Central-South Italian individuals. Our findings, if confirmed in larger population studies, will allow the inclusion of these XRCC1 nsSNPs in a screening panel for those individuals at higher risk for melanoma. PMID:22687647

  19. Genetic Variations of Kinase Inserts Domain Receptor (KDR) Gene Are Associated with the Risk of Astrocytomas.

    Science.gov (United States)

    Gao, Yufei; Ma, Piyong; He, Yichun; Liu, Yan; Jiang, Yang

    2016-05-01

    Astrocytomas is one of the most common central nervous system (CNS) tumors with high mortality rate. Kinase insert domain receptor (KDR) is involved in the regulation of tumor angiogenesis, migration, and vascular permeability. The aim of the study was to explore the relationship between KDR polymorphisms and risk of astrocytomas. Blood samples were collected from 157 astrocytomas patients and 160 healthy controls. Three tag-SNPs (rs2071559C/T, rs2305948T/C, and rs1870377A/T) were identified from the International HapMap Project Databases and genotyped using the method of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). We evaluated the astrocytomas risk caused by individual SNPs and haplotype using odds ratios (ORs) and their 95 % confidence intervals (CIs). In the overall individual SNP analysis, the C allele of rs2071559 was correlated with an increased risk of astrocytomas. However, individuals with mutant allele A and genotype TA + AA of rs1870377 showed a protective effect against astrocytomas. Subgroup analysis based on WHO tumor grade revealed that the C allele of rs2071559 had more influence with the risk of astrocytomas in the grade III-IV (OR = 1.91) subgroup than the grade I-II (OR = 1.47) group. Genotype TT of rs2305948 was found to be significantly associated with susceptibility of astrocytomas only in the grade III-IV subgroup. The protective effect of rs1870377 did not reveal significant difference between the grade III-IV and grade I-II subgroups. Meanwhile, stratified analysis demonstrated that mutation of rs2071559 and rs2305948 could elevate the risk of astrocytomas more significantly in the subgroup of smokers than the nonsmokers. Interestingly, the protective effect of rs1870377 was more obvious in the nonsmokers than the smokers. Additionally, haplotype-specific analysis showed that haplotype CCT and CTT were related with an increased risk of astrocytomas. We found that individual with variants of rs

  20. Characterization and performance of alumina inserts reinforced with zirconia

    International Nuclear Information System (INIS)

    Alumina-based ceramics reinforced with zirconia were produced as inserts to be used as cutting tools. The objective of this work was to characterize and to evaluate the inserts as well as their performance in service. Additions of zirconia varying from 0.05 up to 0.20 wt% were done in alumina in order to select that composition presenting the best mechanical behavior. To do this, four-point bending mechanical strength, hardness and fracture toughness measurements were carried out. The best performance was found for alumina processing 0.010 wt.% of zirconia addition. The addition of zirconia was made with the objective of giving higher toughness to the insert throughout the microcracking reinforcing mechanism. The alumina reinforced inserts were compared with inserts of alumina without zirconia. It was accomplished by performing machining tests onto a SAE 1045 steel. The obtained results indicated that the zirconia reinforcement was able to improve the performance of the alumina cutting tools considerably. (author)

  1. Insertion of nanoparticles into polymer brush under variable solvent conditions

    Science.gov (United States)

    Egorov, S. A.

    2012-10-01

    In this work, two-dimensional lattice-based self-consistent field theory is used to study the free energy cost associated with the insertion of a nanoparticle into a polymer brush. The nanoparticle is modeled as a cylinder and the self-consistent field equations are formulated on a cylindrical lattice. The use of two-dimensional formalism makes it possible to take into account the distortion of the brush density profile due to the embedded nanoinclusion. The insertion free energy penalty is analyzed as a function of the particle size, the brush grafting density, and the solvent quality. In agreement with the earlier simulation work, we find that the insertion free energy cost increases both with the particle size and the brush grafting density and decreases with deteriorating solvent quality. For nanoparticles located deep inside the brush, the insertion free energy is shown to scale with either squared (good solvent) or cubed (poor solvent) monomer volume fraction profile, in agreement with the earlier theoretical results. For shallow nanoinclusions located close to the brush surface, the insertion free energy is shown to scale linearly with the monomer volume fraction profile under both good and theta solvent conditions, again in agreement with the earlier work.

  2. Overview of insertion device controls at the Advanced Photon Source

    Science.gov (United States)

    Ramanathan, Mohan; Smith, Martin; Grimmer, John; Merritt, Michael

    2002-03-01

    The Advanced Photon Source (APS) is a third-generation synchrotron with major emphasis on insertion device (ID) sources. Currently, there are 25 sectors instrumented out of a possible 35 ID sources. Most of the insertion devices are undulators. Beamlines have been using the ID radiation at the APS for more than five years. The control system of choice at the APS is the experimental physics and industrial control system (EPICS) (http://www.aps.anl.gov/epics). Based on operational experience, the ID control system has been completely revamped. During user operations, the beamline user has complete control of the insertion device. Various interfaces, from RS-232 to EPICS channel access, have been provided for the users to control the IDs. The control system software has been designed to accommodate scanning of the insertion device synchronized to each user's beamline monochromator. The users have the option of operating the device in a tapered mode. The control software allows the users to control the undulators in energy space from the fundamental to the seventh harmonic. The design philosophy of the insertion device control system will be discussed. The implementation and operational experience will be presented in detail.

  3. Assessment of plutonium and minor actinides insertions in HTR

    International Nuclear Information System (INIS)

    Based in the specifications of the high temperature reactor - HTR developed by H. J. Ruetten and K. Haas (Nucl. Eng. and Design: 195, 353-360, 2000), it was studied the possibility of insertion of minor actinides in this type of reactor. In this first study, carried out with the WIMSD5 code, the effective multiplication factor and the temperature reactivity coefficient had been evaluated. The behavior of the multiplication factor with fuel burnup for the standard fuel composition (with PuO2) as well as for the case with the insertion of minor actinides originated from a PWR spent fuel, was as expected. The results suggest the possibility of insertion of joint plutonium and minor actinides in the fuel composition. (author)

  4. Can GSTM1 and GSTT1 polymorphisms predict clinical outcomes of chemotherapy in gastric and colorectal cancers? A result based on the previous reports

    Directory of Open Access Journals (Sweden)

    Liu H

    2016-06-01

    Full Text Available Haixia Liu,1,* Wei Shi,2,* Lianli Zhao,3 Dianlu Dai,4 Jinghua Gao,5 Xiangjun Kong6 1Department of Ultrasound, 2Office of Medical Statistics, 3Human Resource Department, 4Department of Surgical Oncology, 5Department of Medical Oncology, 6Central Laboratory, Cangzhou Central Hospital, Yunhe District, Cangzhou, People’s Republic of China *These authors contributed equally to this study and should be considered cofirst authors Background: Gastric and colorectal cancers remain the major causes of cancer-related death. Although chemotherapy improves the prognosis of the patients with gastrointestinal cancers, some patients do not benefit from therapy and are exposed to the adverse effects. The polymorphisms in genes including GSTM1 and GSTT1 have been explored to predict therapeutic efficacy; however, the results were inconsistent and inconclusive. Materials and methods: A systematic review and meta-analysis was performed by searching relevant studies about the association between the GSTM1 and GSTT1 polymorphisms and chemotherapy efficacy in gastrointestinal cancers in databases such as PubMed, EMBASE, Web of Science, Chinese National Knowledge Infrastructure, and Wanfang database up to January 10, 2016. Subgroup analyses were also performed according to ethnicity, cancer type, evaluation criteria, study type, chemotherapy type, and age. Results: A total of 19 articles containing 3,217 cases were finally included. Overall analysis suggested that no significance was found between overall toxicity, neurotoxicity, neutropenia, gastrointestinal toxicity, tumor response, and progression-free survival, and the polymorphisms in GSTM1 and GSTT1, while GSTM1 polymorphism associated with overall survival (OS; hazard ratio =1.213, 95% confidence interval =1.060–1.388, P=0.005. Subgroup analyses suggested that neurotoxicity was associated with GSTM1 polymorphism in the Asian population, neutropenia was associated with GSTM1 polymorphism in palliative

  5. A Flip Turn for Membrane Protein Insertion

    OpenAIRE

    Shao, Sichen; Hegde, Ramanujan S.

    2011-01-01

    The transmembrane domains in a membrane protein must be recognized and correctly oriented before their insertion into the lipid bilayer. Devaraneni et al. (2011) generate snapshots at different stages of membrane protein biogenesis, revealing a dynamic set of steps that imply an unexpectedly flexible membrane insertion machinery.

  6. HLA-G Polymorphism (rs16375) and Acute Rejection in Liver Transplant Recipients

    OpenAIRE

    2014-01-01

    Background. HLA-G molecules exhibit immunomodulatory properties that can delay graft rejection. The 14 bp insertion/deletion polymorphism (INDEL) (rs16375) influences the stability of final HLA-G mRNA and its soluble isoforms. Objective. The present study aimed to investigate the possible association between this polymorphism and the incidence of acute rejection in Iranian liver transplant recipients. Methods. Different genotypes were evaluated by PCR. The patients who had acute rejection wit...

  7. ErbB polymorphisms: insights and implications for response to targeted cancer therapeutics

    OpenAIRE

    Alaoui-Jamali, Moulay A.; Morand, Grégoire B.; da Silva, Sabrina Daniela

    2015-01-01

    Advances in high-throughput genomic-scanning have expanded the repertory of genetic variations in DNA sequences encoding ErbB tyrosine kinase receptors in humans, including single nucleotide polymorphisms (SNPs), polymorphic repetitive elements, microsatellite variations, small-scale insertions and deletions. The ErbB family members: EGFR, ErbB2, ErbB3, and ErbB4 receptors are established as drivers of many aspects of tumor initiation and progression to metastasis. This knowledge has provided...

  8. ErbB polymorphisms: Insights and implications for response to targeted cancer therapeutics

    OpenAIRE

    Alaoui-Jamali, Moulay A.; Gregoire Bernard Rene Morand; Sabrina Daniela Silva

    2015-01-01

    Advances in high-throughput genomic-scanning have expanded the repertory of genetic variations in DNA sequences encoding ErbB tyrosine kinase receptors in humans, including single nucleotide polymorphisms (SNPs), polymorphic repetitive elements, microsatellite variations, small-scale insertions and deletions. The ErbB family members: EGFR, ErbB2, ErbB3 and ErbB4 receptors are established as drivers of many aspects of tumor initiation and progression to metastasis. This knowledge has provided ...

  9. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing

    Directory of Open Access Journals (Sweden)

    Richard S. Fletcher

    2016-04-01

    Full Text Available Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.

  10. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.

    Science.gov (United States)

    Fletcher, Richard S; Herrmann, David; Mullen, Jack L; Li, Qinfei; Schrider, Daniel R; Price, Nicholas; Lin, Junjiang; Grogan, Kelsi; Kern, Andrew; McKay, John K

    2016-01-01

    Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes. PMID:26801646

  11. Genetic diversity of maternal lineage in the endangered Kiso horse based on polymorphism of the mitochondrial DNA D-loop region.

    Science.gov (United States)

    Takasu, Masaki; Ishihara, Namiko; Tozaki, Teruaki; Kakoi, Hironaga; Maeda, Masami; Mukoyama, Harutaka

    2014-11-01

    To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences using Basic Local Alignment Search Tool, by mismatch analysis to evaluate the mutation processes using Arlequin, and by building a phylogenetic tree showing the relationship of the mtDNA haplotypes for 24 horse breeds around the world using Molecular Evolutionary Genetics Analysis softwear. The results suggested that various horses that came to Japan stayed at Kiso region and became ancestors of Kiso horse and also genetically supported the theory that the Kiso horse was historically improved by other Japanese native horse breeds. Next, we analyzed the diversity of current maternal lineage by classifying the resulting sequences, and by calculating the haplotype diversity and nucleotide diversity using Arlequin. Then, we visualized the relationship among haplotypes by a median-joining network using NETWORK 4.6.0.0. The results suggested the diversity of maternal lineage in the Kiso horse was reasonably maintained. Lastly, we predicted future change of the diversity of maternal lineage in Kiso horse by assessing the regional distribution of the acquired haplotypes. The distribution suggested that diversity of maternal lineage would possibly be reducing. PMID:25056676

  12. Impact of HIV-1 reverse transcriptase polymorphism F214L on virological response to thymidine analogue based regimens in ART-naïve and experienced patients

    DEFF Research Database (Denmark)

    Silberstein, F; Cozzi-Lepri, A; Ruiz, L;

    2007-01-01

    BACKGROUND: A negative association between the polymorphism F214L and type 1 thymidine analogue (TA) mutations (TAMs) has been observed. However, the virological response to TAs according to the detection of F214L has not been evaluated. METHODS: We studied 590 patients from EuroSIDA who started TA...... therapy for the first time as part of potent combination antiretroviral therapy (cART) and who were tested for genotypic resistance within the past 6 months. End points were median reduction in the week 24 viral load and time to virological failure (2 consecutive VL measurements >400 copies/mL after at...... least 6 months of the TA-containing cART). RESULTS: In ART-naive patients, the prevalence of F214L was 17%. By 48 months after starting TA-based cART, the proportion of patients who experienced virological failure was 16% in patients with 214L and 36% in those with 214F (P=.03). In a multivariable Cox...

  13. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms

    Science.gov (United States)

    Hui, Wenli; Zhang, Sinong; Zhang, Chao; Wan, Yinsheng; Zhu, Juanli; Zhao, Gang; Wu, Songdi; Xi, Dujuan; Zhang, Qinlu; Li, Ningning; Cui, Yali

    2016-02-01

    Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.

  14. Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection.

    Science.gov (United States)

    Taylor, Angela J; Lappi, Victoria; Wolfgang, William J; Lapierre, Pascal; Palumbo, Michael J; Medus, Carlota; Boxrud, David

    2015-10-01

    Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis of S. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmental S. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of the S. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method for S. Enteritidis. PMID:26269623

  15. Using Yeast Transposon-Insertion Libraries for Phenotypic Screening and Protein Localization.

    Science.gov (United States)

    Kumar, Anuj

    2016-01-01

    This protocol details how to use a transposon-insertion library for phenotypic screening and protein localization. The insertion library was generated by mutagenesis of a plasmid-based yeast genomic DNA library by using a multipurpose transposon; the transposon produces gene disruptions, and, by Cre-mediated recombination at lox sites incorporated within the transposon, alleles with an in-frame insertion can be truncated to a residual transposon encoding multiple copies of the hemagglutinin epitope. Insertions are generated in yeast by shuttle mutagenesis. Yeast genomic DNA containing a transposon insertion is released from the library, and the mutagenized DNA sequences are introduced into a desired strain of yeast, where the insertion alleles replace native loci by homologous recombination. The insertion mutants can be screened for phenotypes, and the site of transposon insertion can subsequently be identified in selected mutants by inverse polymerase chain reaction (PCR). In-frame insertions within genes of interest can be truncated to an epitope-tagged allele by Cre-lox recombination, and the subcellular localization of the encoded protein product can be identified by standard methods of indirect immunofluorescence. In summary, the transposon-insertion libraries represent an informative resource for large-scale mutagenesis, presenting a straightforward alternative to labor-intensive targeted approaches for the construction of deletion alleles and fluorescent protein fusions. PMID:27250939

  16. The case-only independence assumption: associations between genetic polymorphisms and smoking among controls in two population-based studies

    OpenAIRE

    Hodgson, M Elizabeth; Olshan, Andrew F.; North, Kari E; Poole, Charles L; Zeng, Donglin; Tse, Chiu-Kit; Keku, Tope O; Galanko, Joseph; Sandler, Robert; Millikan, Robert C.

    2012-01-01

    The independence assumption for a case-only analysis of statistical interaction, i. e. that genetic (G) and environmental exposures (E) are not associated in the source population, is often checked in surrogate populations. Few studies have examined G-E association in empirical data, particularly in controls from population-based studies, the type of controls expected to provide the most valid surrogate estimates of G-E association. We used controls from two population-based case-control stud...

  17. Development and comparison of projection and image space 3D nodule insertion techniques

    Science.gov (United States)

    Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Samei, Ehsan

    2016-04-01

    This study aimed to develop and compare two methods of inserting computerized virtual lesions into CT datasets. 24 physical (synthetic) nodules of three sizes and four morphologies were inserted into an anthropomorphic chest phantom (LUNGMAN, KYOTO KAGAKU). The phantom was scanned (Somatom Definition Flash, Siemens Healthcare) with and without nodules present, and images were reconstructed with filtered back projection and iterative reconstruction (SAFIRE) at 0.6 mm slice thickness using a standard thoracic CT protocol at multiple dose settings. Virtual 3D CAD models based on the physical nodules were virtually inserted (accounting for the system MTF) into the nodule-free CT data using two techniques. These techniques include projection-based and image-based insertion. Nodule volumes were estimated using a commercial segmentation tool (iNtuition, TeraRecon, Inc.). Differences were tested using paired t-tests and R2 goodness of fit between the virtually and physically inserted nodules. Both insertion techniques resulted in nodule volumes very similar to the real nodules (<3% difference) and in most cases the differences were not statistically significant. Also, R2 values were all <0.97 for both insertion techniques. These data imply that these techniques can confidently be used as a means of inserting virtual nodules in CT datasets. These techniques can be instrumental in building hybrid CT datasets composed of patient images with virtually inserted nodules.

  18. Site-selected insertional mutagenesis of tomato with maize Ac and Ds elements.

    Science.gov (United States)

    Cooley, M B; Goldsbrough, A P; Still, D W; Yoder, J I

    1996-08-27

    Site-selected insertion (SSI) is a PCR-based technique which uses primers located within the transposon and a target gene for detection of transposon insertions into cloned genes. We screened tomato plants bearing single or multiple copies of maize Ac or Ds transposable elements for somatic insertions at one close-range target and two long-range targets. Eight close-range Ds insertions near the right border of the T-DNA were recovered. Sequence analysis showed a precise junction between the transposon and the target for all insertions. Two insertions in separate plants occurred at the same site, but others appeared dispersed in the region of the right T-DNA border with no target specificity. However, insertions showed a preference for one orientation of the transposon. Use of plants with multiple Ac (HiAc) or Ds (HiDs) elements allowed detection of somatic insertions at two single-copy genes, PG (polygalacturonase) and DFR (dihydroflavonol 4-reductase). Certain HiDs plants showed much higher rates of insertion into PG than others. Insertions in PG and DFR were found throughout the gene regions monitored and, with the exception of one insertion in PG, the junctions between transposon and target were exact. SSI analysis of progeny from the HiDs parents revealed that in some cases the tendency to incur high levels of somatic insertions in PG was inherited. Inheritance of this character is an indication that SSI could be used to direct a search for germinal PG insertions in tomato. PMID:8804392

  19. Skin Blood Perfusion and Cellular Response to Insertion of Insulin Pen Needles With Different Diameters

    DEFF Research Database (Denmark)

    Præstmark, Kezia Ann; Stallknecht, Bente Merete; Bo Jensen, Casper;

    2014-01-01

    there was a trend of an increased response with increasing needle diameter. Skin blood perfusion response to pen needle insertions rank according to needle diameter, and the tissue response caused by hooked 32G needles corresponds to that of 28G needles. The relation between needle diameter and trauma...... skin blood perfusion response around needle insertion sites. Three common sized pen needles of 28G, 30G, and 32G as well as hooked 32G needles, were inserted into the neck skin of pigs and then removed. Laser Speckle Contrast Analysis was used to measure skin blood perfusion for 20 minutes after the...... insertions. Seven pigs were included in the study and a total of 118 randomized needle insertions were conducted. Histology was made of tissue samples inserted with 18G, 28G, and 32G needles, and stained to quantify red and white blood cell response. Based on area under curve, calculated for each individual...

  20. A fuel insert shuffle planner expert system

    International Nuclear Information System (INIS)

    During the refueling outage of a pressurized water reactor, the fuel assembly inserts must be moved from their current fuel assemblies to the proper fuel assemblies for the next cycle core design. The crane movement pattern, or shuffle plan, to perform this operation should be as efficient as possible because a less efficient plan could cause the power plant to be shut down for a longer period of time. The current method to develop this plan requires three to four man-weeks of a reactor engineer's time. This plan is developed by the reactor engineer who uses his expertise from previous insert shuffles. Further modifications to this plan are sometimes required due to either changes in the desired core load pattern or damaged fuel or inserts. These changes generally require two to four man-days during the plant outage time. A full-scale prototype of an insert shuffle advisor expert system has been developed to create the insert shuffle plan. This system substantially reduces the manpower requirements needed to develop this plan. It is also a vehicle for preserving the expertise needed to develop this plan. Since the plan can be developed more quickly with the insert shuffle advisor, several strategies can be tried. This gives the potential for a more efficient insert shuffle plan than could be found by the reactor engineer. A more efficient plan means that the power plant could be shut down for a shorter period of time. This would have considerable financial advantages

  1. Lithium Insertion in LixMn2O4, 0

    DEFF Research Database (Denmark)

    West, Keld; Zachau-Christiansen, Birgit; Skaarup, Steen

    lithium insertion/extraction reactions is better at the higher voltages (versus Li/Li+), and particularly at the 4 V plateau. The lithium insertion/extraction reaction at the 1 V plateau although essentially reversible is associated with a significant voltage hysteresis.......The electrochemical lithium insertion properties of highly crystalline LixMn2O4 are investigated in the approximate lithium insertion range 0 < x < 4. Using liquid and PEO based polymer electrolytes at room and elevated temperatures, it is shown that for this material, the reversibility of the...

  2. Lithium Insertion in LixMn2O4, 0

    DEFF Research Database (Denmark)

    West, Keld; Zachau-Christiansen, Birgit; Skaarup, Steen

    The electrochemical lithium insertion properties of highly crystalline LixMn2O4 are investigated in the approximate lithium insertion range 0 < x < 4. Using liquid and PEO based polymer electrolytes at room and elevated temperatures, it is shown that for this material, the reversibility of the...... lithium insertion/extraction reactions is better at the higher voltages (versus Li/Li+), and particularly at the 4 V plateau. The lithium insertion/extraction reaction at the 1 V plateau although essentially reversible is associated with a significant voltage hysteresis....

  3. Meta-analysis of the association between COX-2 polymorphisms and risk of colorectal cancer based on case-control studies.

    Directory of Open Access Journals (Sweden)

    Qiliu Peng

    Full Text Available OBJECTIVE: Cyclooxygenase-2 (COX-2 is an inducible enzyme converting arachidonic acid to prostaglandins and playing important roles in inflammatory diseases as well as tumor development. Previous studies investigating the association between COX-2 polymorphisms and colorectal cancer (CRC risk reported conflicting results. We performed a meta-analysis of all available studies to explore this association. METHODS: All studies published up to October 2013 on the association between COX-2 polymorphisms and CRC risk were identified by searching electronic databases PubMed, EMBASE, and Cochrane library. The association between COX-2 polymorphisms and CRC risk was assessed by odds ratios (ORs together with their 95% confidence intervals (CIs. RESULTS: Ten studies with 6,774 cases and 9,772 controls were included for -1195A>G polymorphism, 13 studies including 6,807 cases and 10,052 controls were available for -765G>C polymorphism, and 8 studies containing 5,121 cases and 7,487 controls were included for 8473T>C polymorphism. With respect to -765G>C polymorphism, we did not find a significant association with CRC risk when all eligible studies were pooled into the meta-analysis. However, in subgroup analyses by ethnicity and cancer location, with a Bonferroni corrected alpha of 0.05/2, statistical significant increased CRC risk was found in the Asian populations (dominant model CC+CG vs. GG: OR = 1.399, 95%CI: 1.113-1.760, P = 0.004 and rectum cancer patients (CC vs. GG: OR = 2.270, 95%CI: 1.295-3.980, P = 0.004; Recessive model CC vs. CG+GG: OR = 2.269, 95%CI: 1.297-3.970, P = 0.004. In subgroup analysis according to source of control, no significant association was detected. With respect to -1195A>G and 8473T>C polymorphisms, no significant association with CRC risk was demonstrated in the overall and subgroup analyses. CONCLUSIONS: The present meta-analysis suggests that the COX-2 -765G>C polymorphism may be a risk factor for

  4. Differential diagnosis of Brucella abortus by real-time PCR based on a single-nucleotide polymorphisms

    OpenAIRE

    Kim, Ji-Yeon; Kang, Sung-Il; Lee, Jin Ju; Lee, Kichan; SUNG, So-Ra; ERDENEBAATAAR, Janchivdorj; VANAABAATAR, Batbaatar; Jung, Suk Chan; Park, Yong Ho; Yoo, Han-Sang; Her, Moon

    2015-01-01

    To diagnose brucellosis effectively, many genus- and species-specific detection methods based on PCR have been developed. With conventional PCR assays, real-time PCR techniques have been developed as rapid diagnostic tools. Among them, real-time PCR using hybridization probe (hybprobe) has been recommended for bacteria with high DNA homology among species, with which it is possible to make an accurate diagnosis by means of an amplification curve and melting peak analysis. A hybprobe for B. ab...

  5. Ampelomyces mycoparasites from apple powdery mildew identified as a distinct group based on single-stranded conformation polymorphism analysis of the rDNA ITS region.

    Science.gov (United States)

    Szentiványi, Orsolya; Kiss, Levente; Russell, John C; Kovács, Gábor M; Varga, Krisztina; Jankovics, Tünde; Lesemann, Silke; Xu, Xiang-Ming; Jeffries, Peter

    2005-04-01

    Pycnidial fungi belonging to the genus Ampelomyces are the most common natural antagonists of powdery mildews worldwide. During a study of the interactions between apple powdery mildew (Podosphaera leucotricha) and Ampelomyces mycoparasites, 52 new Ampelomyces isolates were obtained from P. leucotricha and, in addition, 13 new isolates from other species of the Erysiphaceae in four European countries. Their genetic diversity was screened using single-stranded conformation polymorphism (SSCP) analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA). For comparison, 24 isolates obtained from genetic resource collections or other sources were included in this study. Based on the ITS-SSCP patterns, the isolates were placed in eight groups. The isolates belonged to two types based on their growth in culture. The faster-growing and the slower-growing isolates were included in different SSCP groups. A phylogenetic analysis of the ITS sequences of representatives of these groups confirmed the results obtained with the SSCP method, and showed that the faster-growing isolates do not belong to Ampelomyces as suggested by earlier studies. All the isolates from P. leucotricha fell into a distinct SSCP group of genetically homogeneous isolates. This suggests that Ampelomyces mycoparasites which occur in apple powdery mildew are slightly different from the other Ampelomyces groups which contain mycoparasites from various powdery mildew species. This may be because the main growth period of Ampelomyces mycoparasites in apple powdery mildew is isolated in time from that of Ampelomyces isolates that occur in other species of the Erysiphaceae. P. leucotricha starts its life-cycle early in the season, usually in March-April, while most powdery mildews are active in the same environments only late in the year. PMID:15912930

  6. Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman

    Directory of Open Access Journals (Sweden)

    Egarter-Vigl Eduard

    2009-06-01

    Full Text Available Abstract Background Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman. Results The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups. Conclusion The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.

  7. Accurate Insertion Loss Measurements of the Juno Patch Array Antennas

    Science.gov (United States)

    Chamberlain, Neil; Chen, Jacqueline; Hodges, Richard; Demas, John

    2010-01-01

    This paper describes two independent methods for estimating the insertion loss of patch array antennas that were developed for the Juno Microwave Radiometer instrument. One method is based principally on pattern measurements while the other method is based solely on network analyzer measurements. The methods are accurate to within 0.1 dB for the measured antennas and show good agreement (to within 0.1dB) of separate radiometric measurements.

  8. Phase transition and vapochromism in molecular assemblies of a polymorphic zinc(II) Schiff-base complex.

    Science.gov (United States)

    Oliveri, Ivan Pietro; Malandrino, Graziella; Di Bella, Santo

    2014-09-15

    This paper reports for the first time the irreversible thermally induced phase transition, accompanied by color change, and the vapochromic behavior of an amphiphilic, Lewis acidic Zn(II) Schiff-base complex, through detailed X-ray diffraction, thermogravimetric analysis and differential scanning calorimetry, and optical absorption studies. The unprecedented irreversible phase transition for such kind of complexes is associated with a thermal, lamellar-to-hexagonal columnar structural transition, which involves a different arrangement of each molecular unit within the assembled structure, H- and J-type aggregates, respectively, responsible for the thermochromic behavior. The vapochromism, investigated either in powder samples or in thermally annealed cast films, is related to the formation of 1:1 adducts upon exposure to vapors of strong Lewis bases and implies dramatic optical absorption variations and naked-eye observation of the change in color from red-brown to red. The chemisorption process is fast, completely reversible, reproducible, and selective for amines. The reversible switching of the chemisorption-desorption process in cast films is demonstrated by successive cycles, amine exposure and subsequent heating, by monitoring the substantial optical absorption changes in the visible region. Vapochromism of this material can potentially be used to detect vapors of volatile amines. PMID:25148651

  9. HB+ inserted into the CMS Solenoid

    CERN Multimedia

    Tejinder S. Virdee, CERN

    2006-01-01

    The first half of the barrel hadron calorimeter (HB+) has been inserted into the superconducting solenoid of CMS, in preparation for the magnet test and cosmic challenge. The operation went smoothly, lasting a couple of days.

  10. Effect of GSTP1 and ABCC4 gene polymorphisms on response and toxicity of cyclophosphamide-epirubicin-5-fluorouracil-based chemotherapy in Bangladeshi breast cancer patients.

    Science.gov (United States)

    Islam, Md Siddiqul; Islam, Mohammad Safiqul; Parvin, Salma; Ahmed, Maizbah Uddin; Bin Sayeed, Muhammad Shahdaat; Uddin, Mir Muhammad Nasir; Hussain, Syed Md Akram; Hasnat, Abul

    2015-07-01

    The most important cytotoxic drug namely, cyclophosphamide used in breast cancer along with epirubicin and 5-fluorouracil, is transported by ABCC transporters and detoxified by glutathione S-transferases (GSTs). The activities of these enzymes and transporters may vary in different population due to the presence of genetic polymorphisms. This study was aimed to evaluate the effects of GSTP1rs1695 and ABCC4rs9561778 polymorphisms on the response and toxicities produced by chemotherapy used in the treatment of Bangladeshi breast cancer patients. A total of 200 and 56 patients with invasive breast cancers were recruited from different public and private hospitals of Bangladesh of which 117 patients received neoadjuvant chemotherapy to examine the response as well as the toxicity, and another 139 patients received adjuvant chemotherapy to evaluate only the toxicity. Genetic polymorphisms of the mentioned genes were detected by using Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR RFLP). Patients carrying AG and AG plus GG genotype of GSTP1rs1695 were more likely to have a good response, whereas no association of ABCC4rs9561778 was found with the chemotherapy response. Patients carrying GT and GT plus TT genotypes of ABCC4rs9561778 were found to be associated with anemia, neutropenia, leukopenia, and gastrointestinal toxicities when compared with GG genotype whereas no association was found with thrombocytopenia. GSTP1rs1695 was not associated with any type of toxicities investigated. Our result indicates that GSTP1rs1695 polymorphism was strongly associated with the response of chemotherapy, whereas ABCC4rs9561778 polymorphism was significantly related with chemotherapy-induced toxicities. PMID:25677905

  11. A Preliminary Genetic Investigation of Rastrelliger Kanagurta Based on Random Amplified Polymorphic DNA and Mitochondrial ND2 Gene

    Institute of Scientific and Technical Information of China (English)

    Siti Azizah Mohd Nor; Abu Talib A; Mohd Ghows M A; Samsudin B

    2008-01-01

    In a preliminary investigation, Random Amplified Polymorphie DNA (RAPD) analysis and partial mitochon-drial ND2 gene sequencing were conducted to study the genetic variation of the Indian mackerel, Rastrelliger kanagurta along a 450 km stretch of its distribution on the west coast of Peninsular Malaysia. A total of 53 individuals from 6 popu-lations were analyzed using 4 RAPD primers and a sub-sample of 15 individuals was chosen for sequencing of partial ND2 gene. Comparison between the 2 markers revealed genetic structuring in the RAPD results but genetic homogeneity for ND2 gene. Based on the former there may be at least 2 genetically differentiated groups of Rastrelliger kanagurta a-long this stretch.

  12. Polymorphisms in MTHFR, MS and CBS genes and homocysteine levels in a Pakistani population.

    Directory of Open Access Journals (Sweden)

    Mohsin Yakub

    Full Text Available BACKGROUND: Hyperhomocysteinemia (>15 µmol/L is highly prevalent in South Asian populations including Pakistan. In order to investigate the genetic determinants of this condition, we studied 6 polymorphisms in genes of 3 enzymes--methylenetetrahydrofolate reductase (MTHFR; C677T; A1298C, methionine synthase (MS; A2756G, cystathionine-β-synthase (CBS; T833C/844ins68, G919A involved in homocysteine metabolism and investigated their interactions with nutritional and environmental factors in a Pakistani population. METHODOLOGY/PRINCIPAL FINDINGS: In a cross-sectional survey, 872 healthy adults (355 males and 517 females; age 18-60 years were recruited from a low-income urban population in Karachi. Fasting venous blood was obtained and assessed for plasma/serum homocysteine; folate, vitamin B12, pyridoxal phosphate and blood lead. DNA was isolated and genotyping was performed by PCR-RFLP (restriction-fragment-length-polymorphism based assays. The average changes in homocysteine levels for MTHFR 677CT and TT genotypes were positive [β(SE β, 2.01(0.63 and 16.19(1.8 µmol/L, respectively]. Contrary to MTHFR C677T polymorphism, the average changes in plasma homocysteine levels for MS 2756AG and GG variants were negative [β(SE β, -0.56(0.58 and -0.83(0.99 µmol/L, respectively]. The average change occurring for CBS 844ins68 heterozygous genotype (ancestral/insertion was -1.88(0.81 µmol/L. The combined effect of MTHFR C677T, MS A2756G and CBS 844ins68 genotypes for plasma homocysteine levels was additive (p value <0.001. Odds of having hyperhomocysteinemia with MTHFR 677TT genotype was 10-fold compared to MTHFR 677CC genotype [OR (95%CI; 10.17(3.6-28.67]. Protective effect towards hyperhomocysteinemia was observed with heterozygous (ancestral/insertion genotype of CBS 844ins68 compared to homozygous ancestral type [OR (95% CI; 0.58 (0.34-0.99]. Individuals with MTHFR 677CT or TT genotypes were at a greater risk of hyperhomocysteinemia in folate and

  13. An Unusual Complication of Suprapubic Catheter Insertion

    Directory of Open Access Journals (Sweden)

    Krishnan Ananthakrishnan

    2006-01-01

    Full Text Available A patient who had a small bowel mesentery perforation following insertion of a suprapubic catheter (SPC is described. He had no bowel complaints immediately following the procedure, but presented 10 weeks later with insidious onset bowel obstruction due to the kink caused by the catheter. This complication occurred despite cystoscopy control and adequate bladder distension prior to the procedure. This isolated case illustrates the fact that regardless of the ease and frequency of SPC insertion, complications do occur.

  14. Association of GSTs gene polymorphisms with treatment outcome of advanced non-small cell lung cancer patients with cisplatin-based chemotherapy

    OpenAIRE

    Wu, Gun; Jiang, Bin; Liu, Xiaoqin; Shen, Yi; Yang, Shujuan

    2015-01-01

    We evaluated the association of GSTM1 null/present, GSTT1 null/present, and GSTP1 IIe105Val polymorphisms with the clinical response to chemotherapy and treatment outcome of NSCLC. Between October 2009 and October 2012, a total of 282 patients with advanced NSCLC were enrolled into our study, and they were followed up until October 2014. The genotypes of GSTM1, GSTT1, and GSTP1 IIe105Val were performed by polymerase chain reaction (PCR) coupled with restriction fragment length polymorphism (R...

  15. Z-2 Threaded Insert Design and Testing

    Science.gov (United States)

    Ross, Amy; Rhodes, Richard; Jones, Robert J.; Graziosi, David; Ferl, Jinny; Sweeny, Mitch; Scarborough, Stephen

    2016-01-01

    NASA's Z-2 prototype space suit contains several components fabricated from an advanced hybrid composite laminate consisting of IM10 carbon fiber and fiber glass. One requirement was to have removable, replaceable helicoil inserts to which other suit components would be fastened. An approach utilizing bonded in inserts with helicoils inside of them was implemented. During initial assembly, cracking sounds were heard followed by the lifting of one of the blind inserts out of its hole when the screws were torqued. A failure investigation was initiated to understand the mechanism of the failure. Ultimately, it was determined that the pre-tension caused by torqueing the fasteners is a much larger force than induced from the pressure loads of the suit which was not considered in the insert design. Bolt tension is determined by dividing the torque on the screw by a k value multiplied by the thread diameter of the bolt. The k value is a factor that accounts for friction in the system. A common value used for k for a non-lubricated screw is 0.2. The k value can go down by as much as 0.1 if the screw is lubricated which means for the same torque, a much larger tension could be placed on the bolt and insert. This paper summarizes the failure investigation that was performed to identify the root cause of the suit failure and details how the insert design was modified to resist a higher pull out tension.

  16. Association of Common Polymorphisms in the Nicotinic Acetylcholine Receptor Alpha4 Subunit Gene with an Electrophysiological Endophenotype in a Large Population-Based Sample

    Science.gov (United States)

    Mobascher, A.; Diaz-Lacava, A.; Wagner, M.; Gallinat, J.; Wienker, T. F.; Drichel, D.; Becker, T.; Steffens, M.; Dahmen, N.; Gründer, G.; Thürauf, N.; Kiefer, F.; Kornhuber, J.; Toliat, M. R.; Thiele, H.; Nürnberg, P.; Steinlein, O.; Winterer, G.

    2016-01-01

    Variation in genes coding for nicotinic acetylcholine receptor (nAChR) subunits affect cognitive processes and may contribute to the genetic architecture of neuropsychiatric disorders. Single nucleotide polymorphisms (SNPs) in the CHRNA4 gene that codes for the alpha4 subunit of alpha4/beta2-containing receptors have previously been implicated in aspects of (mostly visual) attention and smoking-related behavioral measures. Here we investigated the effects of six synonymous but functional CHRNA4 exon 5 SNPs on the N100 event-related potential (ERP), an electrophysiological endophenotype elicited by a standard auditory oddball. A total of N = 1,705 subjects randomly selected from the general population were studied with electroencephalography (EEG) as part of the German Multicenter Study on nicotine addiction. Two of the six variants, rs1044396 and neighboring rs1044397, were significantly associated with N100 amplitude. This effect was pronounced in females where we also observed an effect on reaction time. Sequencing of the complete exon 5 region in the population sample excluded the existence of additional/functional variants that may be responsible for the observed effects. This is the first large-scale population-based study investigation the effects of CHRNA4 SNPs on brain activity measures related to stimulus processing and attention. Our results provide further evidence that common synonymous CHRNA4 exon 5 SNPs affect cognitive processes and suggest that they also play a role in the auditory system. As N100 amplitude reduction is considered a schizophrenia-related endophenotype the SNPs studied here may also be associated with schizophrenia outcome measures. PMID:27054571

  17. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

    Directory of Open Access Journals (Sweden)

    Francesca Bertolini

    Full Text Available Few studies investigated the donkey (Equus asinus at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca. The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing and Ion Torrent (RRL runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

  18. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

    Science.gov (United States)

    Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca

    2015-01-01

    Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450

  19. The role of WWOX polymorphisms on COPD susceptibility and pulmonary function traits in Chinese: a case-control study and family-based analysis

    Science.gov (United States)

    Xie, Chenli; Chen, Xiaoliang; Qiu, Fuman; Zhang, Lisha; Wu, Di; Chen, Jiansong; Yang, Lei; Lu, Jiachun

    2016-01-01

    Single nucleotide polymorphisms (SNPs) in the WW domain containing oxidoreductase (WWOX) gene were recently identified to be quantitative trait loci for lung function and thus likely to be susceptible biomarkers for COPD. However, the associations between WWOX SNPs and COPD risk are still unclear. Here, by conducting a two-center case-control study including 1511 COPD cases and 1677 controls and a family-based analysis comprising 95 nuclear pedigrees, we tested the associations between five SNPs that are rs10220974C >T, rs3764340C >G, rs12918952G >A, rs383362G >T, rs12828G >A of WWOX and COPD risk as well as the hereditary inclination of these loci among COPD families. We found that the SNP rs383362G >T was significantly associated with an increased risk of COPD in a T allele-number dependent-manner (OR = 1.30, 95%CI = 1.11 - 1.52). The T allele was more prone to over transmit to sick children and sibs than the G allele (Z = 2.900, P = 0.004). Moreover, the forced expiratory volume in one second/forced vital capacity (FEV1/FVC), FEV1/predicted-FEV1 and annual FEV1 also significantly decreased in the rs383362T carriers compared to the rs383362GG carriers. For other SNPs, no significant association was observed for COPD and pulmonary function. Taken together, our data demonstrated that the SNP rs383362G >T of WWOX plays a role in COPD inheritance. PMID:26902998

  20. The polymorphism of YWHAE, a gene encoding 14-3-3epsilon, and brain morphology in schizophrenia: a voxel-based morphometric study.

    Directory of Open Access Journals (Sweden)

    Mikio Kido

    Full Text Available BACKGROUND: YWHAE is a possible susceptibility gene for schizophrenia that encodes 14-3-3epsilon, a Disrupted-in-Schizophrenia 1 (DISC1-interacting molecule, but the effect of variation in its genotype on brain morphology remains largely unknown. METHODS: In this voxel-based morphometric magnetic resonance imaging study, we conducted whole-brain analyses regarding the effects of YWHAE single-nucleotide polymorphisms (SNPs (rs28365859, rs11655548, and rs9393 and DISC1 SNP (rs821616 on gray matter volume in a Japanese sample of 72 schizophrenia patients and 86 healthy controls. On the basis of a previous animal study, we also examined the effect of rs28365859 genotype specifically on hippocampal volume. RESULTS: Whole-brain analyses showed no significant genotype effect of these SNPs on gray matter volume in all subjects, but we found significant genotype-by-diagnosis interaction for rs28365859 in the left insula and right putamen. The protective C allele carriers of rs28365859 had a significantly larger left insula than the G homozygotes only for schizophrenia patients, while the controls with G allele homozygosity had a significantly larger right putamen than the C allele carriers. The C allele carriers had a larger right hippocampus than the G allele homozygotes in schizophrenia patients, but not in healthy controls. No significant interaction was found between rs28365859 and DISC1 SNP on gray matter volume. CONCLUSIONS: These different effects of the YWHAE (rs28365859 genotype on brain morphology in schizophrenia and healthy controls suggest that variation in its genotype might be, at least partly, related to the abnormal neurodevelopment, including in the limbic regions, reported in schizophrenia. Our results also suggest its specific role among YWHAE SNPs in the pathophysiology of schizophrenia.

  1. Formation of nanofilms on cell surfaces to improve the insertion efficiency of a nanoneedle into cells

    Energy Technology Data Exchange (ETDEWEB)

    Amemiya, Yosuke [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562 (Japan); Kawano, Keiko [Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-26 Naka-cho, Koganei, Tokyo 184-8588 (Japan); Matsusaki, Michiya; Akashi, Mitsuru [Department of Applied Chemistry, Graduate School of Engineering Science, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871 (Japan); Nakamura, Noriyuki [Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-26 Naka-cho, Koganei, Tokyo 184-8588 (Japan); Nakamura, Chikashi, E-mail: chikashi-nakamura@aist.go.jp [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562 (Japan); Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-26 Naka-cho, Koganei, Tokyo 184-8588 (Japan)

    2012-04-13

    Highlights: Black-Right-Pointing-Pointer We examined the insertion efficiency of nanoneedles into fibroblast and neural cells. Black-Right-Pointing-Pointer Nanofilms formed on cell surfaces improved the insertion efficiency of nanoneedles. Black-Right-Pointing-Pointer Nanofilms improved the insertion efficiency even in Y27632-treated cells. -- Abstract: A nanoneedle, an atomic force microscope (AFM) tip etched to 200 nm in diameter and 10 {mu}m in length, can be inserted into cells with the aid of an AFM and has been used to introduce functional molecules into cells and to analyze intracellular information with minimal cell damage. However, some cell lines have shown low insertion efficiency of the nanoneedle. Improvement in the insertion efficiency of a nanoneedle into such cells is a significant issue for nanoneedle-based cell manipulation and analysis. Here, we have formed nanofilms composed of extracellular matrix molecules on cell surfaces and found that the formation of the nanofilms improved insertion efficiency of a nanoneedle into fibroblast and neural cells. The nanofilms were shown to improve insertion efficiency even in cells in which the formation of actin stress fibers was inhibited by the ROCK inhibitor Y27632, suggesting that the nanofilms with the mesh structure directly contributed to the improved insertion efficiency of a nanoneedle.

  2. Root cause of incomplete control rod insertions at Westinghouse reactors

    Energy Technology Data Exchange (ETDEWEB)

    Ray, S. [Westinghouse, Monroeville, PA (United States)

    1997-01-01

    Within the past year, incomplete RCCA insertions have been observed on high burnup fuel assemblies at two Westinghouse PWRs. Initial tests at the Wolf Creek site indicated that the direct cause of the incomplete insertions observed at Wolf Creek was excessive fuel assembly thimble tube distortion. Westinghouse committed to the NRC to perform a root cause analysis by the end of August, 1996. The root cause analysis process used by Westinghouse included testing at ten sites to obtain drag, growth and other characteristics of high burnup fuel assemblies. It also included testing at the Westinghouse hot cell of two of the Wolf Creek incomplete insertion assemblies. A mechanical model was developed to calculate the response of fuel assemblies when subjected to compressive loads. Detailed manufacturing reviews were conducted to determine if this was a manufacturing related issue. In addition, a review of available worldwide experience was performed. Based on the above, it was concluded that the thimble tube distortion observed on the Wolf Creek incomplete insertion assemblies was caused by unusual fuel assembly growth over and above what would typically be expected as a result of irradiation exposure. It was determined that the unusual growth component is a combination of growth due to oxide accumulation and accelerated growth, and would only be expected in high temperature plants on fuel assemblies that see long residence times and high power duties.

  3. Root cause of incomplete control rod insertions at Westinghouse reactors

    International Nuclear Information System (INIS)

    Within the past year, incomplete RCCA insertions have been observed on high burnup fuel assemblies at two Westinghouse PWRs. Initial tests at the Wolf Creek site indicated that the direct cause of the incomplete insertions observed at Wolf Creek was excessive fuel assembly thimble tube distortion. Westinghouse committed to the NRC to perform a root cause analysis by the end of August, 1996. The root cause analysis process used by Westinghouse included testing at ten sites to obtain drag, growth and other characteristics of high burnup fuel assemblies. It also included testing at the Westinghouse hot cell of two of the Wolf Creek incomplete insertion assemblies. A mechanical model was developed to calculate the response of fuel assemblies when subjected to compressive loads. Detailed manufacturing reviews were conducted to determine if this was a manufacturing related issue. In addition, a review of available worldwide experience was performed. Based on the above, it was concluded that the thimble tube distortion observed on the Wolf Creek incomplete insertion assemblies was caused by unusual fuel assembly growth over and above what would typically be expected as a result of irradiation exposure. It was determined that the unusual growth component is a combination of growth due to oxide accumulation and accelerated growth, and would only be expected in high temperature plants on fuel assemblies that see long residence times and high power duties

  4. Preliminary Analysis on Reactivity Insertion Transient of Natural Circulation Reactor

    International Nuclear Information System (INIS)

    When a malfunction of the reactor control system occurs, there's a chance that the positive reactivity is inserted into the core, resulting in the increase of the core power. With the combination of the failure of the related safety features, this may raise the temperature of the core material beyond the design limit to break its integrity. For the fast nuclear reactors like FFTF and CRBRP, the overpower trip is initiated when the power reaches 115% of rated value to keep the fuel from melting. In this study, the system response to the reactivity insertion transient on a liquid metal cooled natural circulation reactor is analyzed utilizing an in-house code based on a momentum integral model. Utilizing an in-house system analysis code, a set of numerical simulation is carried out on the reactivity ramp insertion transients which showed that the role of reactivity feedback is significant in mitigating the time to failure, and the evolution of the natural circulation mass flow is rather slow to generate meaningful feedback effect. It is also observed that in terms of the peak cladding temperature, smaller reactivity insertion transient generated more severe outcome owing to increased accumulation of the thermal energy within fuel pins. Thus, it may require an extra attention to carefully monitor and capture the mild transients to avoid potential drastic results

  5. The ATLAS Insertable B-Layer Project

    CERN Document Server

    Miucci, A; The ATLAS collaboration

    2014-01-01

    The ATLAS experiment will upgrade its Pixel Detector with the installation of a new pixel layer in 2013-14. The new sub-detector, named Insertable B-layer (IBL), will be installed between the existing Pixel Detector and a new smaller radius beam-pipe at a radius of 3.3 cm. To cope with the high radiation and pixel occupancy due to the proximity to the interaction point, a new read-out chip and two different silicon sensor technologies (planar and 3D) have been de- veloped. Furthermore, the physics performance should be improved through the reduction of pixel size while a low material budget should be imposed. A new mechanical support using lightweight staves and a CO2 based cooling system is used. An overview of the IBL project and the status of the production of staves and the qualification of the assembly procedure, the loaded module electrical integrity and the read-out chain will be presented.

  6. X-ray repair cross-complementing gene 1 Arg399GIn polymorphism and glioma risk among Asians A meta-analysis based on 2326 cases and 3610 controls

    Institute of Scientific and Technical Information of China (English)

    Liang Zhang; Zhiqun Qiu; Jiaohua Luo; Weiqun Shu

    2012-01-01

    OBJECTIVE:Previous reports have demonstrated that X-ray repair cross-complementing gene 1 (XRCC1) Arg399GIn polymorphism is a possible risk factor for several cancers.Published data on the association of XRCC1Arg399GIn polymorphism with glioma susceptibility have generated conflicting results.This study is designed to precisely estimate the relationship.DATA RETRIEVAL:A computer-based online retrieval of Medline,EMBASE,OVID,Sciencedirect,and Chinese National Knowledge Infrastructure was performed to search papers regarding association of XRCC1 Arg399GIn polymorphisms with glioma published up to April 2012.SELECTION CRITERIA:Two investigators selected data independently.Meta analysis was then performed for the selected studies using STATA 11.0 software after strict selection.Heterogeneity test,sensitivity analysis and publication bias assessments were then conducted.MAIN OUTCOME MEASURES:Association of XRCC1 Arg399GIn polymorphism with glioma risk.RESULTS:A total of nine case-controlled studies comprising 2 326 cases and 3 610 controls were selected for final analysis.The overall data failed to indicate a significant association of XRCC1 Arg399GIn polymorphism with glioma risk (GIn/GIn vs.Arg/Arg:odds ratio (OR) =1.11; 95% confidence interval (Cl) =0.94-1.31; dominant model:OR =1.06; 95%Cl=0.95-1.18; recessive model:OR =1.04; 95%Cl=0.81-1.34).However,subgroup analysis regarding ethnicity showed an increased risk among Asians (GIn/GIn vs.Arg/Arg:OR =1.70; 95%Cl=1.17-2.46; dominant model:OR =1.40; 95%Cl=1.10-1.78; recessive model:OR =1.46; 95%Cl =1.04-2.05) but not Caucasians or mixed ethnicities.CONCLUSION:XRCC1 Arg399GIn polymorphism might modify the susceptibility to glioma among Asians but not Caucasians.Further large and well-designed studies are needed to confirm this conclusion.

  7. Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping.

    Science.gov (United States)

    Vasiliou, V; Bairoch, A; Tipton, K F; Nebert, D W

    1999-08-01

    As currently being performed with an increasing number of superfamilies, a standardized gene nomenclature system is proposed here, based on divergent evolution, using multiple alignment analysis of all 86 eukaryotic aldehyde dehydrogenase (ALDH) amino-acid sequences known at this time. The ALDHs represent a superfamily of NAD(P)(+)-dependent enzymes having similar primary structures that oxidize a wide spectrum of endogenous and exogenous aliphatic and aromatic aldehydes. To date, a total of 54 animal, 15 plant, 14 yeast, and three fungal ALDH genes or cDNAs have been sequenced. These ALDHs can be divided into a total of 18 families (comprising 37 subfamilies), and all nonhuman ALDH genes are named here after the established human ALDH genes, when possible. An ALDH protein from one gene family is defined as having approximately or = 60% amino-acid identity and are expected to be located at the same subchromosomal site. For naming each gene, it is proposed that the root symbol 'ALDH' denoting 'aldehyde dehydrogenase' be followed by an Arabic number representing the family and, when needed, a letter designating the subfamily and an Arabic number denoting the individual gene within the subfamily; all letters are capitalized in all mammals except mouse and fruit fly, e.g. 'human ALDH3A1 (mouse, Drosophila Aldh3a1).' It is suggested that the Human Gene Nomenclature Guidelines (http://++www.gene.ucl.ac.uk/nomenclature/guidelines.h tml) be used for all species other than mouse and Drosophila. Following these guidelines, the gene is italicized, whereas the corresponding cDNA, mRNA, protein or enzyme activity is written with upper-case letters and without italics, e.g. 'human, mouse or Drosophila ALDH3A1 cDNA, mRNA, or activity'. If an orthologous gene between species cannot be identified with certainty, sequential naming of these genes will be carried out in chronological order as they are reported to us. In addition, 20 human ALDH variant alleles that have been reported

  8. Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions.

    Science.gov (United States)

    Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Edge, Thomas; Topp, Edward; Neumann, Norman F

    2015-11-01

    Host specificity in E. coli is widely debated. Herein, we used supervised learning logic-regression-based analysis of intergenic DNA sequence variability in E. coli in an attempt to identify single nucleotide polymorphism (SNP) biomarkers of E. coli that are associated with natural selection and evolution toward host specificity. Seven-hundred and eighty strains of E. coli were isolated from 15 different animal hosts. We utilized logic regression for analyzing DNA sequence data of three intergenic regions (flanked by the genes uspC-flhDC, csgBAC-csgDEFG, and asnS-ompF) to identify genetic biomarkers that could potentially discriminate E. coli based on host sources. Across 15 different animal hosts, logic regression successfully discriminated E. coli based on animal host source with relatively high specificity (i.e., among the samples of the non-target animal host, the proportion that correctly did not have the host-specific marker pattern) and sensitivity (i.e., among the samples from a given animal host, the proportion that correctly had the host-specific marker pattern), even after fivefold cross validation. Permutation tests confirmed that for most animals, host specific intergenic biomarkers identified by logic regression in E. coli were significantly associated with animal host source. The highest level of biomarker sensitivity was observed in deer isolates, with 82% of all deer E. coli isolates displaying a unique SNP pattern that was 98% specific to deer. Fifty-three percent of human isolates displayed a unique biomarker pattern that was 98% specific to humans. Twenty-nine percent of cattle isolates displayed a unique biomarker that was 97% specific to cattle. Interestingly, even within a related host group (i.e., Family: Canidae [domestic dogs and coyotes]), highly specific SNP biomarkers (98% and 99% specificity for dog and coyotes, respectively) were observed, with 21% of dog E. coli isolates displaying a unique dog biomarker and 61% of coyote isolates

  9. Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

    DEFF Research Database (Denmark)

    Mengel-From, Jonas; Sanchez Sanchez, Juan Jose; Børsting, Claus;

    2005-01-01

    /ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000-5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package...

  10. Photoinduced Four-State Three-Step Ordering Transformation of Photochromic Terthiophene at a Liquid/Solid Interface Based on Two Principles: Photochromism and Polymorphism.

    Science.gov (United States)

    Yokoyama, Soichi; Hirose, Takashi; Matsuda, Kenji

    2015-06-16

    We have investigated photoinduced ordering transformation of a photochromic terthiophene derivative by scanning tunneling microscopy (STM) at the trichlorobenzene (TCB)/highly oriented pyrolytic graphite (HOPG) interface. The open-ring and annulated isomers of the terthiophene formed two-dimensional molecular orderings with different patterns while the closed-ring isomer did not form any ordering. The ordering of the open-ring isomer exhibited polymorphism depending on the concentration of supernatant solution. Upon UV light irradiation to a solution of the open-ring isomer or the closed-ring isomer, ordering composed of the annulated isomer was irreversibly formed. Upon visible light irradiation or thermal stimulus to the closed-ring isomer, the two kinds of polymorph composed of the open-ring isomer were formed due to the polymorphism. By controlling photochromism and polymorphism among four states made of three photochemical isomers, four-state three-step transformation was achieved by in situ photoirradiation from a solution of the closed-ring isomer (no ordering) into the ordering composed of the open-ring isomer (ordering α and β) followed by the orderings composed of the annulated isomer (ordering γ). PMID:26005903

  11. No association between cytochrome P450 2D6 gene polymorphism and risk of acute leukemia: evidence based on a meta-analysis

    Institute of Scientific and Technical Information of China (English)

    RUAN Xiao-lan; LI Sheng; ZENG Xian-tao; XIA Ling-hui; HU Yu

    2013-01-01

    Background Many studies indicated the human cytochrome P450 2D6 (CYP2D6) gene polymorphism was associated with acute leukemia (AL) susceptibility,however,the results were inconsistent.So we performed this meta-analysis to evaluate the relationship between CYP2D6*3 or CYP2D6*4 polymorphism and AL susceptibility.Methods We searched PubMed database up to February 20,2013,and finally yielded 9 case-control studies including 1343 cases and 1843 controls which tested the association between CYP2D6*3 or *4 polymorphism and AL.After data extraction,we conducted a meta-analysis using the Comprehensive Meta Analysis software.Results Overall,no significant association between CYP2D6*3 or *4 polymorphism and AL risk was found in this metaanalysis (+ vs.-:OR=1.13,95% CI=0.79-1.63; +/+ vs.-/-:OR=1.73,95% C/=0.99-3.02;-/+ vs.-/-:OR=1.03,95% C/=0.68-1.56; (-/+ and +/+) vs.-/-:OR=1.08,95% C/=0.72-1.63; +/+ vs.(-/+ and-/-):OR=1.76,95% C/=0.98-3.17).Similar results were also been found in stratified subgroup analysis.There was no publication bias.Conclusion CYP2D6*3 or *4 polymorphism might not be associated with AL susceptibility.However,the results need to be further confirmed by well-designed and high quality randomized controlled trials with larger sample sizes.

  12. Polymorphic ecthymatoid dermosporidiosis

    Directory of Open Access Journals (Sweden)

    Ghorpade A

    2008-01-01

    Full Text Available We report the case of a young Chhattisgarhi male with polymorphic dermosporidiosis (cutaneous rhinosporidiosis. He had multiple subcutaneous nodules and an ecthymatoid skin lesion along with nasal rhinosporidiosis. The diagnosis was confirmed by demonstration of sporangia with endospores in fine-needle aspiration cytology (FNAC, histopathology, and imprint smear from the skin lesions. Treatment was by surgical excision, electrocoagulation, and dapsone. There was no recurrence. Dermatologists should be aware of the diverse cutaneous manifestations of this primarily nasal disease. This is the second published report of polymorphic dermosporidiosis, and the first one reporting an ecthymatoid lesion.

  13. Polymorphs of Pridopidine Hydrochloride

    DEFF Research Database (Denmark)

    Zimmermann, A.; Frostrup, B.; Bond, A. D.

    2012-01-01

    Pridopidine hydrochloride (Huntexil, Neuro-Search A/S, Ballerup, Denmark) is a dopaminergic stabilizer, currently in development for the treatment of motor symptoms associated with Huntington's disease. In this study, two polymorphic forms are characterized, forms I and II. The crystal structures...... crystallization to form II is observed. The polymorphs are enantiotropically related, form I being stable at ambient conditions and form II being stable above 127 degrees C. At around 180 degrees C, the differential scanning calorimetry thermogram of a mixture of forms land II shows a solid-state transition from...

  14. Computer Simulation of the Phase Stabilities of Lithiated TiO2 Polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Rosso, Kevin M.; Yang, Zhenguo; Liu, Jun

    2010-11-01

    The structure and phase stability of a series of lithiated titania polymorphs were determined using spin unrestricted density functional theory and the B3LYP exchange-correlation potential. These calculations were performed following the linear combination of atomic orbital approach. The lithium content, x, of the titania phases was varied from 0 to 1. Rutile and anatase were found to be the most stable polymorphs in the absence of lithium. Anatase and ramsdellite were calculated to become energetically favored over rutile upon lithium insertion. The hexagonal, spinel, and rocksalt polymorphs were predicted to have stabilities approaching that of rutile with increasing lithium content. At x=1, the hexagonal, spinel, rocksalt and rutile polymorphs showed essentially equivalent total energies. This prediction is consistent with the experimental observation that rutile electrodes, in particular those that consist of nanomaterials, undergo a phase transformation to the hexagonal, spinel, or rocksalt structure upon lithium insertion. In addition, a set of potential parameters was developed to model lithium insertion with a potential shell model. The potential model was found to give good agreement with the structure and energetics of the lithiated titania polymorphs, as determined with the ab initio calculations, at all lithium contents.

  15. AC loss performance of CS insert coil

    International Nuclear Information System (INIS)

    The ITER Central Solenoid (CS) model coil and the CS insert coil were fabricated, and the test was carried out. The AC loss measurement of the coil is one of the most important tests to determine coil performance. The AC loss of a short sample conductor for the CS insert coil was measured by using the calorimetric method, and the coupling time constants of the conductor were estimated to be 30 ms and 20 ms for pulse and discharge tests, respectively. The AC loss of the CS insert coil was measured by using the calorimetric method for pulse and discharge tests. The coupling time constant estimated from the result of the pulse tests was 34 ms and almost equal to that of the short sample. The coupling time constant for the discharge test was estimated to be 140 ms and about 4 times that of the pulse test. (author)

  16. Teaching polymorphism early

    DEFF Research Database (Denmark)

    2005-01-01

    Is it possible to teach dynamic polymorphism early? What techniques could facilitate teaching it in Java. This panel will bring together people who have considered this question and attempted to implement it in various ways, some more completely than others. It will also give participants an...

  17. Enzyme polymorphisms in Canarium

    Science.gov (United States)

    Fifty-two accessions of Canarium involving seven species, C. ovatum, C. album, C. megalanthum, C. harveyi, C. indicum, C. mehenbethene, and C. odontophyllum were studied for isozyme polymorphisms. Starch gel electrophoresis with a histidine-citrate buffer system (pH 6.5) was employed to assay six en...

  18. Investigation of Uranium Polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Sweet, Lucas E.; Henager, Charles H.; Hu, Shenyang Y.; Johnson, Timothy J.; Meier, David E.; Peper, Shane M.; Schwantes, Jon M.

    2011-08-01

    The UO3-water system is complex and has not been fully characterized, even though these species are common throughout the nuclear fuel cycle. As an example, most production schemes for UO3 result in a mixture of up to six or more different polymorphic phases, and small differences in these conditions will affect phase genesis that ultimately result in measureable changes to the end product. As a result, this feature of the UO3-water system may be useful as a means for determining process history. This research effort attempts to better characterize the UO3-water system with a variety of optical techniques for the purpose of developing some predictive capability for estimating process history in polymorphic phases of unknown origin. Three commercially relevant preparation methods for the production of UO3 were explored. Previously unreported low temperature routes to β- and γ-UO3 were discovered. Raman and fluorescence spectroscopic libraries were established for pure and mixed polymorphic forms of UO3 in addition to the common hydrolysis products of UO3. An advantage of the sensitivity of optical fluorescence microscopy over XRD has been demonstrated. Preliminary aging studies of the α and γ forms of UO3 have been conducted. In addition, development of a 3-D phase field model used to predict phase genesis of the system was initiated. Thermodynamic and structural constants that will feed the model have been gathered from the literature for most of the UO3 polymorphic phases.

  19. Active interlock for storage ring insertion devices

    International Nuclear Information System (INIS)

    The insertion devices in the NSLS x-ray ring produce such intense photon beams that passive measures alone are not adequate to protect the vacuum chamber. An active interlock is used to prevent thermal damage from improperly steered electron beams. The interlock system measures the position of the electron beam on both sides of the insertion devices using pick-up electrodes and interrupts the rf if the beam moves outside a safe window. The interlock features redundant circuitry as well as an automatic testing procedure. 1 ref., 4 figs

  20. Installation of the LHC experimental insertions

    CERN Document Server

    Bartolome-Jimenez, S

    2004-01-01

    The installation of the LHC experimental insertions, and particularly the installation of the low-beta quadrupoles, raises many technical challenges due to the stringent alignment specifications and to the difficulty of access in very confined areas. The compact layout with many lattice elements, vacuum components, beam control instrumentation and the presence of shielding does not allow for any improvisation in the installation procedure. This paper reviews all the constraints that need to be taken into account when installing the experimental insertions. It describes the chronological sequence of installation and discusses the technical solutions that have been adopted.

  1. INSTALLATION OF THE LHC EXPERIMENTAL INSERTIONS

    CERN Document Server

    Bartolome-Jimenez, S

    2004-01-01

    The installation of the LHC experimental insertions, and particularly the installation of the Low-Beta quadrupoles, raises many technical challenges due to the stringent alignment specifications and to the difficulty of access in very confined areas. The compact layout with many lattice elements, vacuum components, beam control instrumentation and the presence of shielding does not allow for any improvisation in the installation procedure. This paper reviews all the constraints that need to be taken into account when installing the experimental insertions. It describes the chronological sequence of installation and discusses the technical solutions that have been adopted.

  2. Correlation between base-excision repair gene polymorphisms and levels of in-vitro BPDE-induced DNA adducts in cultured peripheral blood lymphocytes.

    Directory of Open Access Journals (Sweden)

    Hongping Yu

    Full Text Available In vitro benzo[a]pyrene diol epoxide (BPDE-induced DNA adducts in cultured peripheral lymphocytes have been shown to be a phenotypic biomarker of individual's DNA repair phenotype that is associated with cancer risk. In this study, we explored associations between genotypes of base-excision repair genes (PARP1 Val762Ala, APEX1 Asp148Glu, and XRCC1 Arg399Gln and in vitro BPDE-induced DNA adducts in cultured peripheral blood lymphocytes in 706 cancer-free non-Hispanic white subjects. We found that levels of BPDE-induced DNA adducts were significantly higher in ever smokers than in never smokers and that individuals with the Glu variant genotypes (i.e., Asp/Glu and Glu/Glu exhibited lower levels of BPDE-induced DNA adducts than did individuals with the common Asp/Asp homozygous genotype (median RAL levels: 32.0 for Asp/Asp, 27.0 for Asp/Glu, and 17.0 for Glu/Glu, respectively; P(trend = 0.030. Further stratified analysis showed that compared with individuals with the common APEX1-148 homozygous Asp/Asp genotype, individuals with the APEX1-148Asp/Glu genotype or the Glu/Glu genotype had a lower risk of having higher-level adducts (adjusted OR = 0.60, 95% CI: 0.36-0.98 and adjusted OR = 0.47, 95% CI: 0.26-0.86, respectively; P(trend = 0.012 among smokers. Such an effect was not observed in non-smokers. However, there was no significant interaction between the APEX1 Asp148Glu polymorphism and smoking exposure in this study population (P = 0.512. Additional genotype-phenotype analysis found that the APEX1-148Glu allele had significantly increased expression of APEX1 mRNA in 270 Epstein-Barr virus-transformed lymphoblastoid cell lines, which is likely associated with more active repair activity. Our findings suggest that the functional APEX1-148Glu allele is associated with reduced risk of having high levels of BPDE-induced DNA adducts mediated with high levels of mRNA expression.

  3. Family-based association study of interleukin 10 (IL10) and interleukin 10 receptor alpha (IL10RA) functional polymorphisms in schizophrenia in Polish population.

    Science.gov (United States)

    Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Pawlak, Joanna; Zaremba, Dorota; Twarowska-Hauser, Joanna

    2016-08-15

    Schizophrenia is a heterogeneous disorder and its etiology remains incompletely elucidated. Among possible causes, immunological factors have been implicated in its pathogenesis and course. Interleukin-10 (IL10) and it's receptor IL10RA may play an important role for immunological aspects in etiologies of major psychiatric disorders including schizophrenia. The aim of this study was to perform a transmission disequilibrium test (TDT) on a group of 146 schizophrenia trios from the Polish population. Functional polymorphisms from IL10 (rs1800872, rs1800871, rs1800896, rs1800890, and rs6676671) and IL10RA (rs3135932 and rs2229113) genes were analyzed. A lack of association with schizophrenia was detected for IL10 and IL10RA single polymorphisms and haplotypes. PMID:27397081

  4. Vector insert-targeted integrative antisense expression system for plasmid stabilization.

    Science.gov (United States)

    Luke, Jeremy M; Carnes, Aaron E; Hodgson, Clague P; Williams, James A

    2011-01-01

    Some DNA vaccine and gene therapy vector-encoded transgenes are toxic to the E. coli plasmid production host resulting in poor production yields. For plasmid products undergoing clinical evaluation, sequence modification to eliminate toxicity is undesirable because an altered vector is a new chemical entity. We hypothesized that: (1) insert-encoded toxicity is mediated by unintended expression of a toxic insert-encoded protein from spurious bacterial promoters; and (2) that toxicity could be eliminated with antisense RNA-mediated translation inhibition. We developed the pINT PR PL vector, a chromosomally integrable RNA expression vector, and utilized it to express insert-complementary (anti-insert) RNA from a single defined site in the bacterial chromosome. Anti-insert RNA eliminated leaky fluorescent protein expression from a target plasmid. A toxic retroviral gag pol helper plasmid produced in a gag pol anti-insert strain had fourfold improved plasmid fermentation yields. Plasmid fermentation yields were also fourfold improved when a DNA vaccine plasmid containing a toxic Influenza serotype H1 hemagglutinin transgene was grown in an H1 sense strand anti-insert production strain, suggesting that in this case toxicity was mediated by an antisense alternative reading frame-encoded peptide. This anti-insert chromosomal RNA expression technology is a general approach to improve production yields with plasmid-based vectors that encode toxic transgenes, or toxic alternative frame peptides. PMID:20607625

  5. False-Negative-Rate Based Approach for Selecting Top Single-Nucleotide Polymorphisms in the First Stage of a Two-Stage Genome-Wide Association Study

    OpenAIRE

    Huang, Zhuying; Wang, Jian; Wu, Chih-Chieh; Richard S Houlston; Bondy, Melissa L.; Shete, Sanjay

    2011-01-01

    Genome-wide association (GWA) studies, where hundreds of thousands of single-nucleotide polymorphisms (SNPs) are tested simultaneously, are becoming popular for identifying disease loci for common diseases. Most commonly, a GWA study involves two stages: the first stage includes testing the association between all SNPs and the disease and the second stage includes replication of SNPs selected from the first stage to validate associations in an independent sample. The first stage is considered...

  6. Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages

    DEFF Research Database (Denmark)

    Brión, María; Sanchez, Juan J; Balogh, Kinga;

    2005-01-01

    . From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A "Major Y-chromosome haplogroup typing kit" has...... worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage....

  7. Effects of GSTM1/GSTT1 Gene Polymorphism and Fruit & Vegetable Consumption on Antioxidant Biomarkers and Cognitive Function in the Elderly: A Community Based Cross-Sectional Study

    OpenAIRE

    Yuan, Linhong; Ma, Weiwei; Liu, Jinmeng; Meng, Liping; Liu, Jixia; Li, Shuang; Han, Jing; Liu, Quanri; Feng, Lingli; Wang, Chao; Xiao, Rong

    2014-01-01

    Background It was reported that Glutathione S-transferase (GST) gene polymorphism and fruit and vegetable (FV) intake were associated with body antioxidant capacity. The oxidative/anti-oxidative imbalance played an important role in the pathogenesis of AD. However, the association of GST genotype, dietary FV consumption with body antioxidant biomarkers and cognitive function in the elderly is not clear. Objective The aim of the present study was to determine the association of GST genotype, a...

  8. FADS Gene Polymorphisms Confer the Risk of Coronary Artery Disease in a Chinese Han Population through the Altered Desaturase Activities: Based on High-Resolution Melting Analysis

    OpenAIRE

    Li, Si-Wei; Lin, Kun; Ma, Pei; Zhang, Zhen-Lu; Zhou, Yi-Dan; Lu, Shuang-Yan; Zhou, Xin; Liu, Song-Mei

    2013-01-01

    Objective We explored the desaturase activities and the correlation of fatty acid desaturases (FADS) gene single nucleotide polymorphisms (SNPs) with plasma fatty acid in coronary artery disease (CAD) patients in a Chinese Han population. Methods Plasma fatty acids were measured by gas chromatography in CAD patients (n = 505) and a control group (n = 510). Five SNPs in the FADS gene were genotyped with high-resolution melting (HRM) methods. Results After adjustment, D6D activity, assessed as ...

  9. Calculation of magnetic error fields in hybrid insertion devices

    International Nuclear Information System (INIS)

    The Advanced Light Source (ALS) at the Lawrence Berkeley Laboratory requires insertion devices with fields sufficiently accurate to take advantage of the small emittance of the ALS electron beam. To maintain the spectral performance of the synchrotron radiation and to limit steering effects on the electron beam these errors must be smaller than 0.25%. This paper develops a procedure for calculating the steering error due to misalignment of the easy axis of the permanent magnet material. The procedure is based on a three dimensional theory of the design of hybrid insertion devices developed by one of us. The acceptable tolerance for easy axis misalignment is found for a 5 cm period undulator proposed for the ALS. 11 refs., 5 figs

  10. Construction of targeted insertion mutations in Francisella tularensis subsp. novicida.

    Science.gov (United States)

    Liu, Jirong; Zogaj, Xhavit; Barker, Jeffrey R; Klose, Karl E

    2007-10-01

    Francisella tularensis is one of the most deadly bacterial agents, yet most of the genetic determinants of pathogenesis are still unknown. We have developed an efficient targeted mutagenesis strategy in the model organism F. tularensis subsp. novicida by utilizing universal priming of optimized antibiotic resistance cassettes and splicing by overlap extension (SOE). This process enables fast and efficient construction of targeted insertion mutations in F. tularensis subsp. novicida that have characteristics of nonpolar mutations; optimized targeted mutagenesis strategies will promote the study of this mysterious bacterium and facilitate vaccine development against tularemia. Moreover the general strategy of gene disruption by PCR-based antibiotic resistance cassette insertion is broadly applicable to many bacterial species. PMID:18019340

  11. Research of Insertion Mechanism of Flexible Search and Rescue Robot

    Directory of Open Access Journals (Sweden)

    Shen Linyong

    2015-01-01

    Full Text Available Due to various factors, the global scope disaster events occur inevitably every year. Terrorism, natural disasters or destructive earthquakes tend to cause a large number of people buried in the ruins of buildings. The research of search and rescue instruments research is mainly focused on snake-like robot and life detector both at home and abroad. The endoscopic search and rescue robot in this paper combines the characteristics of these two kinds of search and rescue equipment. This thesis mainly studies the insertion mechanism of endoscopic flexible search and rescue robot. Based on the mechanics characteristics of the flexible robot body, this paper analyzes several common failure modes during the insertion into the ruins. This article puts forward the scheme of segmented gradual pulling-pushing, which plays an important role in promoting search and rescue work.

  12. Flexibility in targeting and insertion during bacterial membrane protein biogenesis

    International Nuclear Information System (INIS)

    The biogenesis of Escherichia coli inner membrane proteins (IMPs) is assisted by targeting and insertion factors such as the signal recognition particle (SRP), the Sec-translocon and YidC with translocation of (large) periplasmic domains energized by SecA and the proton motive force (pmf). The use of these factors and forces is probably primarily determined by specific structural features of an IMP. To analyze these features we have engineered a set of model IMPs based on endogenous E. coli IMPs known to follow distinct targeting and insertion pathways. The modified model IMPs were analyzed for altered routing using an in vivo protease mapping approach. The data suggest a facultative use of different combinations of factors

  13. Plasminogen activator inhibitor-1 4G/5G polymorphism and retinopathy risk in type 2 diabetes: a meta-analysis

    OpenAIRE

    Zhang Tengyue; Pang Chong; Li Ningdong; Zhou Elaine; Zhao Kanxing

    2013-01-01

    Abstract Background Mounting evidence has suggested that plasminogen activator inhibitor-1 (PAI-1) is a candidate for increased risk of diabetic retinopathy. Studies have reported that insertion/deletion polymorphism in the PAI-1 gene may influence the risk of this disease. To comprehensively address this issue, we performed a meta-analysis to evaluate the association of PAI-1 4G/5G polymorphism with diabetic retinopathy in type 2 diabetes. Methods Data were retrieved in a systematic manner a...

  14. ErbB polymorphisms: insights and implications for response to targeted cancer therapeutics.

    Science.gov (United States)

    Alaoui-Jamali, Moulay A; Morand, Grégoire B; da Silva, Sabrina Daniela

    2015-01-01

    Advances in high-throughput genomic-scanning have expanded the repertory of genetic variations in DNA sequences encoding ErbB tyrosine kinase receptors in humans, including single nucleotide polymorphisms (SNPs), polymorphic repetitive elements, microsatellite variations, small-scale insertions and deletions. The ErbB family members: EGFR, ErbB2, ErbB3, and ErbB4 receptors are established as drivers of many aspects of tumor initiation and progression to metastasis. This knowledge has provided rationales for the development of an arsenal of anti-ErbB therapeutics, ranging from small molecule kinase inhibitors to monoclonal antibodies. Anti-ErbB agents are becoming the cornerstone therapeutics for the management of cancers that overexpress hyperactive variants of ErbB receptors, in particular ErbB2-positive breast cancer and non-small cell lung carcinomas. However, their clinical benefit has been limited to a subset of patients due to a wide heterogeneity in drug response despite the expression of the ErbB targets, attributed to intrinsic (primary) and to acquired (secondary) resistance. Somatic mutations in ErbB tyrosine kinase domains have been extensively investigated in preclinical and clinical setting as determinants for either high sensitivity or resistance to anti-ErbB therapeutics. In contrast, only scant information is available on the impact of SNPs, which are widespread in genes encoding ErbB receptors, on receptor structure and activity, and their predictive values for drug susceptibility. This review aims to briefly update polymorphic variations in genes encoding ErbB receptors based on recent advances in deep sequencing technologies, and to address challenging issues for a better understanding of the functional impact of single versus combined SNPs in ErbB genes to receptor topology, receptor-drug interaction, and drug susceptibility. The potential of exploiting SNPs in the era of stratified targeted therapeutics is discussed. PMID:25699077

  15. ErbB polymorphisms: Insights and implications for response to targeted cancer therapeutics

    Directory of Open Access Journals (Sweden)

    Moulay A Alaoui-Jamali

    2015-02-01

    Full Text Available Advances in high-throughput genomic-scanning have expanded the repertory of genetic variations in DNA sequences encoding ErbB tyrosine kinase receptors in humans, including single nucleotide polymorphisms (SNPs, polymorphic repetitive elements, microsatellite variations, small-scale insertions and deletions. The ErbB family members: EGFR, ErbB2, ErbB3 and ErbB4 receptors are established as drivers of many aspects of tumor initiation and progression to metastasis. This knowledge has provided rationales for the development of an arsenal of anti-ErbB therapeutics, ranging from small molecule kinase inhibitors to monoclonal antibodies. Anti-ErbB agents are becoming the cornerstone therapeutics for the management of cancers that overexpress hyperactive variants of ErbB receptors, in particular ErbB2-positive breast cancer and non-small cell lung carcinomas. However, their clinical benefit has been limited to a subset of patients due to a wide heterogeneity in drug response despite the expression of the ErbB targets, attributed to intrinsic (primary and to acquired (secondary resistance. Somatic mutations in ErbB tyrosine kinase domains have been extensively investigated in preclinical and clinical setting as determinants for either high sensitivity or resistance to anti-ErbB therapeutics. In contrast, only scant information is available on the impact of SNPs, which are widespread in genes encoding ErbB receptors, on receptor structure and activity, and their predictive values for drug susceptibility. This review aims to briefly update polymorphic variations in genes encoding ErbB receptors based on recent advances in deep sequencing technologies, and to address challenging issues for a better understanding of the functional impact of single versus combined SNPs in ErbB genes to receptor topology, receptor-drug interaction, and drug susceptibility. The potential of exploiting SNPs in the era of stratified targeted therapeutics is discussed.

  16. BDNF Val66Met polymorphism and bipolar disorder in European populations: A risk association in case-control, family-based and GWAS studies.

    Science.gov (United States)

    Li, Ming; Chang, Hong; Xiao, Xiao

    2016-09-01

    Brain-derived neurotrophic factor (BDNF) is a nerve growth factor that has antidepressant-like effects in animal models and may be implicated in the etiology of mood-related phenotypes. A functional polymorphism (Val66Met) in the BDNF gene was demonstrated to influence BDNF's secretion and function, as well as mood and cognitive related phenotypes. However, previous genetic association studies of Val66Met polymorphism in the clinical risk of mood disorders have been complicated, possibly due to phenotypic diversity, underpowered statistical association or ancestry-specific effects. Here, we collected mood phenotypic and genetic data in over 90,000 individuals from diverse ethnic groups and conducted a systematic meta-analysis. The results showed that the Val66Met polymorphism was significantly associated with BPD in Europeans (Pmeta=0.0029, OR=1.136), but not in Asians (Pmeta=0.443). Also, it appears that the risk for MDD conferred by BDNF is waning, as the Val66Met variant was not associated with MDD in either European or Asian samples (Pmeta>0.5). PMID:27236043

  17. FAS and FASL Gene Polymorphisms Are Not Associated with Hepatitis B Virus Infection Based on a Case-Control Study in a Brazilian Population

    Directory of Open Access Journals (Sweden)

    Bárbara B. Santana

    2013-01-01

    Full Text Available Objective. This study investigated the association of the single nucleotide polymorphisms (SNPs in the FAS and FASL genes with the outcome of hepatitis B virus (HBV infection. Methods. Blood samples were collected from 116 HBV-infected patients at the Hospital of the Santa Casa de Misericordia Foundation (Belém, PA, Brazil. Seronegative individuals were used as controls. DNA samples were extracted from the leukocytes and assayed using the polymerase chain reaction (PCR followed by RFLP analysis with restriction endonucleases. Results. The frequencies of the mutant genotypes for -670FAS (GG, Ivs2nt-124FASL (GG, Ivs3nt-169FASL (ΔT/ΔT, and -844FASL (TT were higher in the HBV patients, and the FAS-1377AA genotype was more frequent in the control group; however, the differences between the allele and genotype frequencies were not statistically significant. When the HBV patient population was divided into two groups (inactive carriers and active chronic hepatitis patients, the mutant genotypes were found to be more prevalent in the active chronic hepatitis group with respect to the FAS gene polymorphisms; however, this difference was not statistically significant. Conclusions. The results suggest that the polymorphisms in FAS and FASL genes are not associated with HBV infection or even with the natural history of the infection in the Brazilian Amazon region.

  18. Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers.

    Science.gov (United States)

    Wang, T; Zou, Q D; Qi, S Y; Wang, X F; Wu, Y Y; Liu, N; Zhang, Y M; Zhang, Z J; Li, H T

    2016-01-01

    Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process. PMID:27525883

  19. SARS-CoV Genome Polymorphism: A Bioinformatics Study

    Institute of Scientific and Technical Information of China (English)

    Gordana M. Pavlovi(c)-Lazeti(c); Nenad S. Miti(c); Andrija M. Tomovi(c); Mirjana D. Pavlovi(c); Milo(s) V.Beljanski

    2005-01-01

    A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification.The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position).Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes:TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes.Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.

  20. Insertion/Insertion Genotype of Angiotensin I-Converting-Enzyme Gene Predicts Risk of Myocardial Infarction in North East India.

    Science.gov (United States)

    Baruah, Sukanya; Chaliha, Mriganka S; Borah, Prasanta K; Rajkakati, Rashmi; Borua, Prodeep K; Mahanta, Jagadish

    2016-04-01

    Myocardial infarction (MI) is common in India and the disease occurs at a relatively younger age. We wanted to look for association of Angiotensin I-converting enzyme (ACE) gene with MI in North East India. We also wanted to examine possible environmental interaction of ACE gene with established cardiovascular risk factors in causation of MI. In the study carried out in Assam Medical College, 200 consecutive confirmed cases of MI were recruited. Equal numbers of age- and sex-matched control subjects from hospital workers and patients attending the hospital for diseases unrelated to cardiovascular disease were enrolled. Structured questionnaires were used to note demographic and clinical factors. Cardiovascular risk factors were determined from history, physical examination and biochemical investigations. ACE insertion/deletion (I/D) polymorphism was determined by PCR method. Interaction of ACE gene with other risk factors was noted. The study identified ACE II genotype (odds ratio = 3.02; 95% CI 1.40-6.51), smoking, hypertension, diabetes and serum triglyceride > 150 mg/dl as independent risk factors for MI. ACE II genotype showed greater risk in non-smokers, non-hypertensives, non-diabetics and in subjects with LDL-C < 130 mg/dl. Low HDL cholesterol enhanced the genetic risk. Subjects with ACE II genotype have an independent risk of developing MI, specially in low cardiovascular risk subjects. PMID:26687160

  1. Description and characterization of IS994, a putative IS3 family insertion sequence from the salmon pathogen, Renibacterium salmoninarum.

    Science.gov (United States)

    Rhodes, L D; Grayson, T H; Alexander, S M; Strom, M S

    2000-02-22

    Renibacterium salmoninarum, a slowly growing, Gram-positive bacterium, is responsible for bacterial kidney disease in salmonid fishes world-wide. To date, no mobile genetic elements have been reported for this pathogen. Here, we describe the first insertion sequence (IS) identified from R. salmoninarum. This element, IS994, has a significant predicted amino acid sequence homology (64.8 and 71.9%) to the two open reading frames encoding the transposase of IS6110 of Mycobacterium tuberculosis. Protein parsimony and protein distance matrix analyses show that IS994 is a member of group IS51 of the IS3 family. From a conservative estimate, there are at least 17 chromosomal insertions of IS994 or closely related elements. Sequence analysis of seven of these loci reveals single nucleotide polymorphisms throughout the element (including the terminal inverted repeats), a 15bp insertion in three of the seven loci, and an absence of flanking direct repeats or conserved insertion site. Restriction fragment length polymorphism analysis of XbaI-digested chromosomal DNA shows variations among European and North American isolates, indicating that IS994 may be a useful molecular marker for epizootiological studies. PMID:10689192

  2. Lesion insertion in the projection domain: Methods and initial results

    International Nuclear Information System (INIS)

    Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

  3. Lesion insertion in the projection domain: Methods and initial results

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia, E-mail: mccollough.cynthia@mayo.edu [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States)

    2015-12-15

    Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

  4. A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type▿†

    OpenAIRE

    den Bakker, Henk C.; Moreno Switt, Andrea I; Cummings, Craig A.; Hoelzer, Karin; Degoricija, Lovorka; Rodriguez-Rivera, Lorraine D; Wright, Emily M.; Fang, Rixun; Davis, Margaret; Root, Tim; Schoonmaker-Bopp, Dianna; Musser, Kimberlee A.; Villamil, Elizabeth; Waechter, HaeNa; Kornstein, Laura

    2011-01-01

    In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak of Salmonella enterica subsp. enterica serovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIX...

  5. The Science and Issues of Human DNA Polymorphisms: A Training Workshop for High School Biology Teachers

    Energy Technology Data Exchange (ETDEWEB)

    Micklos, David A.

    2006-10-30

    This project achieved its goal of implementing a nationwide training program to introduce high school biology teachers to the key uses and societal implications of human DNA polymorphisms. The 2.5-day workshop introduced high school biology faculty to a laboratory-based unit on human DNA polymorphisms â which provides a uniquely personal perspective on the science and Ethical, Legal and Social Implications (ELSI) of the Human Genome Project. As proposed, 12 workshops were conducted at venues across the United States. The workshops were attended by 256 high school faculty, exceeding proposed attendance of 240 by 7%. Each workshop mixed theoretical, laboratory, and computer work with practical and ethical implications. Program participants learned simplified lab techniques for amplifying three types of chromosomal polymorphisms: an Alu insertion (PV92), a VNTR (pMCT118/D1S80), and single nucleotide polymorphisms (SNPs) in the mitochondrial control region. These polymorphisms illustrate the use of DNA variations in disease diagnosis, forensic biology, and identity testing - and provide a starting point for discussing the uses and potential abuses of genetic technology. Participants also learned how to use their Alu and mitochondrial data as an entrée to human population genetics and evolution. Our work to simplify lab techniques for amplifying human DNA polymorphisms in educational settings culminated with the release in 1998 of three Advanced Technology (AT) PCR kits by Carolina Biological Supply Company, the nationâÂÂs oldest educational science supplier. The kits use a simple 30-minute method to isolate template DNA from hair sheaths or buccal cells and streamlined PCR chemistry based on Pharmacia Ready-To-Go Beads, which incorporate Taq polymerase, deoxynucleotide triphosphates, and buffer in a freeze-dried pellet. These kits have greatly simplified teacher implementation of human PCR labs, and their use is growing at a rapid pace. Sales of human

  6. Chicken models of retroviral insertional mutagenesis

    Czech Academy of Sciences Publication Activity Database

    Pečenka, Vladimír; Karafiát, Vít; Dvořák, Michal

    New York: Springer, 2011 - (Dupuy, A.; Largaespada, D.), s. 77-112 ISBN 978-1-4419-7655-0 R&D Projects: GA ČR GA301/09/1727 Institutional research plan: CEZ:AV0Z50520514 Keywords : insertional mutagenesis * chicken model * MAV retroviruses Subject RIV: EB - Genetics ; Molecular Biology

  7. Chicken models of retroviral insertional mutagenesis

    Czech Academy of Sciences Publication Activity Database

    Pečenka, Vladimír; Karafiát, Vít; Dvořák, Michal

    New York : Springer, 2011 - (Dupuy, A.; Largaespada, D.), s. 77-112 ISBN 978-1-4419-7655-0 R&D Projects: GA ČR GA301/09/1727 Institutional research plan: CEZ:AV0Z50520514 Keywords : insertional mutagenesis * chicken model * MAV retroviruses Subject RIV: EB - Genetics ; Molecular Biology

  8. A design for vertical crossing insertions

    Energy Technology Data Exchange (ETDEWEB)

    Garren, A.

    1985-10-01

    A crossing insertion designed for an SSC with vertically separated 1-in-1 beam lines is presented in this note. The author supposes that the beam lines consist of separate magnets in separate cryostats separated by about 70 cm. He then describes the design, where vertical separation is done with four vertical dipoles producing a steplike beam line.

  9. Polymorphism of cholinesterase: Possible insertion of the various molecular forms in cellular structures

    International Nuclear Information System (INIS)

    In T28 cell cultures, the author has analyzed the metabolism of acetylcholinesterase G1 and G4 forms by the method of heavy isotope labeling. It is shown that the enzyme is synthesized as an inactive precursor, and the G1 is renewed much faster than G4. Half-replacement of pre-existing light molecules by newly synthesized heavy molecules were observed after 3.5 hours and 40 hours, respectively. Most of the synthesized enzyme is rapidly degraded and both G1 and G4 consist of several metabolic pools. For example, the author considers at least three pools of G1: a fast pool which is mostly degraded, but also partially polymerized into G2 and G4, a medium pool which is at least partially secreted, and a slow pool which is degraded, with half-lives ranging from 1 hour to 10 hours

  10. Genetic diversity of 38 insertion-deletion polymorphisms in Jewish populations.

    Science.gov (United States)

    Ferragut, J F; Pereira, R; Castro, J A; Ramon, C; Nogueiro, I; Amorim, A; Picornell, A

    2016-03-01

    Population genetic data of 38 non-coding biallelic autosomal indels are reported for 466 individuals, representing six populations with Jewish ancestry (Ashkenazim, Mizrahim, Sephardim, North African, Chuetas and Bragança crypto-Jews). Intra-population diversity and forensic parameters values showed that this set of indels was highly informative for forensic applications in the Jewish populations studied. Genetic distance analysis demonstrated that this set of markers efficiently separates populations from different continents, but does not seem effective for molecular anthropology studies in Mediterranean region. Finally, it is important to highlight that although the genetic distances between Jewish populations were small, significant differences were observed for Chuetas and Bragança Jews, and therefore, specific databases must be used for these populations. PMID:26610303

  11. Polymorphisms in human telomerase reverse transcriptase (hTERT) gene and susceptibility to gastric cancer in a Turkish population: Hospital-based case-control study.

    Science.gov (United States)

    Bayram, Süleyman; Ülger, Yakup; Sümbül, Ahmet Taner; Kaya, Berrin Yalinbaş; Genç, Ahmet; Rencüzoğullari, Eyyüp; Dadaş, Erdoğan

    2016-07-01

    Erosion of telomeres, tandem nucleotide repeats (TTAGGG)n that cap the end of eukaryotic chromosomes, has been related with carcinogenesis. The human telomerase reverse transcriptase (hTERT) gene is encoded the rate-limiting catalytic subunit of the telomerase complexes, which is essential for the protection of telomeric DNA length and chromosomal stability. The purpose of this study was to examine the effect of four functional single nucleotide polymorphisms (SNPs) of hTERT (rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G) on susceptibility to gastric cancer (GC) in Turkish population. The genotype frequency of hTERT rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G polymorphisms were determined by using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan methods in 104 subjects with GC and 209 healthy control subjects. We found that hTERT rs2736109 G>A (AA+AG vs. GG OR=1.68 95% CI=1.01-2.81, P=0.04), rs2735940 T>C (CC vs. CT+TT: OR=2.53 95% CI=1.01-6.13, P=0.03), and rs2736100 T>G (TT vs. TG+GG: OR=2.27 95% CI=1.23-4.17, P=0.006) polymorphisms were associated with risk of GC. In the haplotype analysis, hTERT Grs2736109/Trs2735940/Ars2853669/Grs2736100 haplotype was also related with an increased risk of GC (OR=1.75; 95% CI: 1.05-2.93, P=0.03). Because this is the first study regarding the hTERT rs2736109 G>A, rs2735940 T>C, rs2853669 A>G and rs2736100 T>G polymorphisms and the risk of GC susceptibility in the literature, further independent studies are needed to verify our results in a larger sample sizes, as well as in patients of different populations. PMID:27016301

  12. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    International Nuclear Information System (INIS)

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses

  13. Association analyses of DNA polymorphisms in bovine SREBP-1, LXRα,FADS1 genes with fatty acid composition in Canadian commercial crossbred beef steers

    OpenAIRE

    Han, C.; Vinsky, M.; Aldai Elkoro-Iribe, Noelia; Dugan, M. E. R.; McAllister, T. A.; Li, C.

    2013-01-01

    Two previously reported DNA polymorphisms of sterol regulatory element binding transcription factor 1 (SREBP1) and liver X receptor alpha (LXRα) and two DNA polymorphisms of fatty acid desaturase 1 (FADS1) were evaluated for associations with fatty acids in brisket adipose tissue of Canadian cross-bred beef steers. The polymorphism of 84 bp insert/deletion in intron 5 of SREBP1 was significantly associated with the concentration of 9c C17:1 (P=0.013). The G>A single nucleotide polymorph...

  14. Screw-Thread Inserts As Temporary Flow Restrictors

    Science.gov (United States)

    Trimarchi, Paul

    1992-01-01

    Coil-spring screw-thread inserts found useful as temporary flow restrictors. Inserts placed in holes through which flow restricted, effectively reducing cross sections available for flow. Friction alone holds inserts against moderate upstream pressures. Use of coil-spring thread inserts as flow restrictors conceived as inexpensive solution to problem of adjusting flow of oxygen through orifices in faceplate into hydrogen/oxygen combustion chamber. Installation and removal of threaded inserts gentle enough not to deform orifice tubes.

  15. Comparison of conventional Injection Mould Inserts to Additively Manufactured Inserts using Life Cycle Assessment

    DEFF Research Database (Denmark)

    Hofstätter, Thomas; Bey, Niki; Mischkot, Michael;

    2016-01-01

    Polymer Additive Manufacturing can be used to produce soft tooling inserts for injection moulding. Compared to conventional tooling, the energy and time consumption during production are significantly lower. As the life time of such inserts is significantly shorter than the life time of traditional...... potential environmental impact and yield throughout the development and pilot phase. Insert geometry is particularly advantageous for pilot production and small production sizes. In this research, Life Cycle Assessment is used to compare the environmental impact of soft tooling by Additive Manufacturing...

  16. «Brazil power and multinational corporation»: brazilian multinational corporations, foreign policy and the international insertion of Brazil. An analysis based on the contributions of Robert Gilpin

    Directory of Open Access Journals (Sweden)

    Esteban Actis

    2013-05-01

    Full Text Available The first decade of the XXI century evidenced transformations in the international order’s financial dimension due to the growth in the so-called emerging powers. An indicator of such phenomenon is the emergence of multinational corporations from the developing world -MNC Latecomers-, turning certain countries, as is the case of Brazil, into net issuers of Foreign Direct Investment flows. In this sense, this paper analyzes the impact that the emergence and consolidation of Brazilian multinational corporations has had since 2003 until now on the foreign policy and the international insertion of Brazil (and vice versa, taking into consideration Robert Gilpin’s classical work, “U.S. power and multinational corporation: the political economy of foreign direct investment.” Gilpin’s framework shall be useful for empirical contrast of this study case.

  17. Insertion losses in micromachined free-space optical cross-connects due to fiber misalignments

    Science.gov (United States)

    Martinez, Sergio O.; Courtois, Bernard

    2001-04-01

    One of the most promising applications of MOEMS in Optical Networks is represented by free-space electro-mechanical Optical Cross-Connects (OXCs); these components show lower attenuation and lower insertion losses than concurrent components based on waveguides. Although some commercial micromachined electro-mechanical OXCs have been recently announced in the market, further deployment of these devices will certainly require decreasing insertion losses by proper design techniques of both, the electromechanical devices and the system packaging. In this document, we study insertion losses in micromachined free-space OXCs and the related packaging challenges; we assume in our discussions Single Mode Fiber (SMF) Cross-Connects using mirrors as beam steering devices. We start with an introduction to micromachined OXCs architectures, actuation mechanisms and collimators. In section 2, we present a study of insertion losses in SMFs links; the coupled effect of lateral and angular fiber misalignments is discussed. In section 3, we discuss insertion losses in OXCs when quarter-pitch GRIN lenses are used as fiber collimators; both sections 2 and 3 are based on Gaussian beam optics. In section 4, we explore the application of Scalar Diffraction Theory to OXC design, this is for calculating insertion losses including diffraction at the mirror plane. Finally, conclusions on insertion losses and the required fiber positioning accuracy are given.

  18. Soft Tissue Phantoms for Realistic Needle Insertion: A Comparative Study.

    Science.gov (United States)

    Leibinger, Alexander; Forte, Antonio E; Tan, Zhengchu; Oldfield, Matthew J; Beyrau, Frank; Dini, Daniele; Rodriguez Y Baena, Ferdinando

    2016-08-01

    Phantoms are common substitutes for soft tissues in biomechanical research and are usually tuned to match tissue properties using standard testing protocols at small strains. However, the response due to complex tool-tissue interactions can differ depending on the phantom and no comprehensive comparative study has been published to date, which could aid researchers to select suitable materials. In this work, gelatin, a common phantom in literature, and a composite hydrogel developed at Imperial College, were matched for mechanical stiffness to porcine brain, and the interactions during needle insertions within them were analyzed. Specifically, we examined insertion forces for brain and the phantoms; we also measured displacements and strains within the phantoms via a laser-based image correlation technique in combination with fluorescent beads. It is shown that the insertion forces for gelatin and brain agree closely, but that the composite hydrogel better mimics the viscous nature of soft tissue. Both materials match different characteristics of brain, but neither of them is a perfect substitute. Thus, when selecting a phantom material, both the soft tissue properties and the complex tool-tissue interactions arising during tissue manipulation should be taken into consideration. These conclusions are presented in tabular form to aid future selection. PMID:26666228

  19. Modeling and characterization of partially inserted electrical connector faults

    Science.gov (United States)

    Tokgöz, ćaǧatay; Dardona, Sameh; Soldner, Nicholas C.; Wheeler, Kevin R.

    2016-03-01

    Faults within electrical connectors are prominent in avionics systems due to improper installation, corrosion, aging, and strained harnesses. These faults usually start off as undetectable with existing inspection techniques and increase in magnitude during the component lifetime. Detection and modeling of these faults are significantly more challenging than hard failures such as open and short circuits. Hence, enabling the capability to locate and characterize the precursors of these faults is critical for timely preventive maintenance and mitigation well before hard failures occur. In this paper, an electrical connector model based on a two-level nonlinear least squares approach is proposed. The connector is first characterized as a transmission line, broken into key components such as the pin, socket, and connector halves. Then, the fact that the resonance frequencies of the connector shift as insertion depth changes from a fully inserted to a barely touching contact is exploited. The model precisely captures these shifts by varying only two length parameters. It is demonstrated that the model accurately characterizes a partially inserted connector.

  20. Polymorphisms in thymidylate synthase gene and susceptibility to breast cancer in a Chinese population: a case-control analysis

    Directory of Open Access Journals (Sweden)

    Liu Jiyong

    2006-05-01

    Full Text Available Abstract Background Accumulative evidence suggests that low folate intake is associated with increased risk of breast cancer. Polymorphisms in genes involved in folate metabolism may influence DNA methylation, nucleotide synthesis, and thus individual susceptibility to cancer. Thymidylate synthase (TYMS is a key enzyme that participates in folate metabolism and catalyzes the conversion of dUMP to dTMP in the process of DNA synthesis. Two potentially functional polymorphisms [a 28-bp tandem repeat in the TYMS 5'-untranslated enhanced region (TSER and a 6-bp deletion/insertion in the TYMS 3'-untranslated region (TS 3'-UTR] were suggested to be correlated with alteration of thymidylate synthase expression and associated with cancer risk. Methods To test the hypothesis that polymorphisms of the TYMS gene are associated with risk of breast cancer, we genotyped these two polymorphisms in a case-control study of 432 incident cases with invasive breast cancer and 473 cancer-free controls in a Chinese population. Results We found that the distribution of TS3'-UTR (1494del6 genotype frequencies were significantly different between the cases and controls (P = 0.026. Compared with the TS3'-UTR del6/del6 wild-type genotype, a significantly reduced risk was associated with the ins6/ins6 homozygous variant genotype (adjusted OR = 0.58, 95% CI = 0.35–0.97 but not the del6/ins6 genotype (OR = 1.09, 95% CI = 0.82–1.46. Furthermore, breast cancer risks associated with the TS3'-UTR del6/del6 genotype were more evident in older women, postmenopausal subjects, individuals with a younger age at first-live birth and individuals with an older age at menarche. However, there was no evidence for an association between the TSER polymorphism and breast cancer risks. Conclusion These findings suggest that the TS3'-UTR del6 polymorphism may play a role in the etiology of breast cancer. Further larger population-based studies as well as functional evaluation of the

  1. Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms

    OpenAIRE

    Sammeth Michael; Rothgänger Jörg; Berssenbrügge Christoph; Weniger Thomas; Mellmann Alexander; Stoye Jens; Harmsen Dag

    2007-01-01

    Abstract Background For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP) implementation that is a heuristic variant of the newly described EDSI algo...

  2. Does the ACE I/D polymorphism, alone or in combination with the ACTN3 R577X polymorphism, influence muscle power phenotypes in young, non-athletic adults?

    OpenAIRE

    Rodríguez Romo, Gabriel; Ruiz, Jonatan R.; Santiago, Catalina; Fiuza Luces, Carmen; Gonzalez Freire, Marta; Gomez Gallego, Felix; Moran, Maria; Lucía Mulas, Alejandro

    2010-01-01

    We investigated the association of the angiotensin converting enzyme gene (ACE) insertion/deletion (I/D) polymorphism, alone or in combination with the α-actinin-3 gene (ACTN3) R577X polymorphism, with jumping (vertical squat and counter-movement jump tests) and sprint ability (30 m dash) in non-athletic, healthy young adults [N = 281 (214 male), mean (SD) age 21 (2) years]. We did not observe any effect of the ACE I/D polymorphism on study phenotypes. We repeated the analyses separately in m...

  3. Tiled Polymorphic Temporal Media

    OpenAIRE

    Hudak, Paul; Janin, David

    2014-01-01

    International audience Tiled Polymorphic Temporal Media (Tiled PTM) is an algebraic approach to specifying the composition of multimedia values having an inherent temporal quality --- for example sound clips, musical scores, computer animations, and video clips. Mathematically, one can think of a tiled PTM as a tiling in the one dimension of time. A tiled PTM value has two synchronization marks that specify, via an effective notion of tiled product, how the tiled PTMs are positioned in tim...

  4. Polymorphism of Atorvastatin

    Czech Academy of Sciences Publication Activity Database

    Urbanová, Martina; Brus, Jiří; Šeděnková, Ivana; Kobera, Libor; Kratochvíl, B.; Maixner, J.

    Zagreb : Ruder Boškovic Institute, 2008 - (Smreč, V.). s. 20 ISBN 978-953-6690-77-0. [Central European NMR Symposium and Bruker NMR Users Meeting CEUM 2008 /10./. 29.09.2008-30.09.2008, Zagreb] R&D Projects: GA MŠk 2B08021 Institutional research plan: CEZ:AV0Z40500505 Keywords : polymorphism * atorvastatin Subject RIV: CE - Biochemistry

  5. The Association of Sport Performance with ACE and ACTN3 Genetic Polymorphisms: A Systematic Review and Meta-Analysis

    OpenAIRE

    Ma, Fang; Yang, Yu; Li, XiangWei; Zhou, Feng; Gao, Cong; Li, Mufei; Gao, Lei

    2013-01-01

    Background Genetic polymorphism is suggested to be associated with human physical performance. The angiotensin I-converting enzyme insertion/deletion (ACE I/D) polymorphism and the α-actinin-3 gene (ACTN3) R577X polymorphism have been most widely studied for such association analysis. However, the findings are frequently heterogeneous. We aim to summarize the associations of ACE I/D and ACTN3 R577X with sport performance by means of meta-analysis. Methods We systematically reviewed and quanti...

  6. Association of MHTFR Ala222Val (rs1801133 polymorphism and breast cancer susceptibility: An update meta-analysis based on 51 research studies

    Directory of Open Access Journals (Sweden)

    Yu Liwa

    2012-12-01

    Full Text Available Abstract Background The association between MHTFR Ala222Val polymorphism and breast cancer (BC risk are inconclusive. To derive a more precise estimation of the relationship, a systematic review and meta-analysis was performed. Methods A comprehensive search was conducted through researching MEDLINE, EMBASE, PubMed, Web of Science, Chinese Biomedical Literature database (CBM and China National Knowledge Infrastructure (CNKI databases before August 2012. Crude odds ratios (ORs with 95% confidence intervals (CIs were calculated to estimate the strength of the association. Results A total of 51 studies including 20,907 cases and 23,905 controls were involved in this meta-analysis. Overall, significant associations were found between MTHFR Ala222Val polymorphism and BC risk when all studies pooled into the meta-analysis (Ala/Ala vs Val/Val: OR=0.870, 95%CI=0.789–0.958,P=0.005; Ala/Val vs Val/Val: OR=0.895, 95%CI=0.821–0.976, P=0.012; dominant model: OR=0.882, 95%CI=0.808–0.963, P=0.005; and recessive model: OR = 0.944, 95%CI=0.898–0.993, P=0.026; Ala allele vs Val allele: OR = 0.935, 95%CI=0.887–0.986, P=0.013. In the subgroup analysis by ethnicity, the same results were found in Asian populations, while no significant associations were found for all comparison models in other Ethnicity populations. Conclusion In conclusion, our meta-analysis provides the evidence that MTHFR Ala222Val gene polymorphisms contributed to the breast cancer development. Virtual slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1966146911851976

  7. The association between the ring finger protein 213 (RNF213) polymorphisms and moyamoya disease susceptibility: a meta-analysis based on case-control studies.

    Science.gov (United States)

    Sun, Xun-Sha; Wen, Jun; Li, Jiao-Xing; Lai, Rong; Wang, Yu-Fang; Liu, Hui-Jiao; Sheng, Wen-Li

    2016-06-01

    A number of studies assessed the association of ring finger protein 213 (RNF213) gene polymorphisms with moyamoya disease (MMD), but the results were not entirely consistent. This meta-analysis was performed to explore the relationship between RNF213 polymorphisms and moyamoya disease in Asian population. A systematic search from the PubMed, MEDLINE, EMBASE, ISI web of science, CNKI, China CBM and WANFANG DATA databases was conducted to retrieve published studies until March 2015. Statistical analyses were performed using the STATA12.0 software. Fixed or random effects model, subgroup analysis, sensitivity analysis, and publication bias were used to improve the comprehensive analysis. Eight papers including 904 MMD patients and 2258 controls were recruited in the meta-analysis. rs112735431 was closely associated with the risk of MMD among Asian population in all genetic models (dominant model: OR 103.39, 95 % CI 52.25-204.55, P = 1.69e-40; recessive model: OR 16.45, 95 % CI 6.00-45.10, P = 5.33e-08; additive model: OR 61.49, 95 % CI 22.07-171.33, P = 3.32e-15), especially in the Japanese population. Subgroup analysis revealed highly statistically significant higher risk in the patients with family histories. Although another polymorphism rs148731719 showed no significant association with the MMD, rs138130613 was found to be related to the higher risk in Chinese population (dominant model: OR 8.34, 95 % CI 1.72-40.47, P = 0.008). Our meta-analysis strengthens RNF213 rs112735431 is closely associated with the increased risk of MMD in Japanese, and the screening combined with rs112735431 and rs138130613may improve the detection rate for MMD in China. PMID:26847828

  8. Coupling Neurogenetics (GARS™ and a Nutrigenomic Based Dopaminergic Agonist to Treat Reward Deficiency Syndrome (RDS: Targeting Polymorphic Reward Genes for Carbohydrate Addiction Algorithms

    Directory of Open Access Journals (Sweden)

    Kenneth Blum

    2015-06-01

    Full Text Available Earlier work from our laboratory, showing anti-addiction activity of a nutraceutical consisting of amino-acid precursors and enkephalinase inhibition properties and our discovery of the first polymorphic gene (Dopamine D2 Receptor Gene [DRD2] to associate with severe alcoholism serves as a blue-print for the development of "Personalized Medicine" in addiction. Prior to the later genetic finding, we developed the concept of Brain Reward Cascade, which continues to act as an important component for stratification of addiction risk through neurogenetics. In 1996 our laboratory also coined the term "Reward Deficiency Syndrome (RDS" to define a common genetic rubric for both substance and non-substance related addictive behaviors. Following many reiterations we utilized polymorphic targets of a number of reward genes (serotonergic, Opioidergic, GABAergic and Dopaminergic to customize KB220 [Neuroadaptogen- amino-acid therapy (NAAT] by specific algorithms. Identifying 1,000 obese subjects in the Netherlands a subsequent small subset was administered various KB220Z formulae customized according to respective DNA polymorphisms individualized that translated to significant decreases in both Body Mass Index (BMI and weight in pounds. Following these experiments, we have been successfully developing a panel of genes known as "Genetic Addiction Risk Score" (GARSpDX™. Selection of 10 genes with appropriate variants, a statistically significant association between the ASIMedia Version-alcohol and drug severity scores and GARSpDx was found A variant of KB220Z in abstinent heroin addicts increased resting state functional connectivity in a putative network including: dorsal anterior cingulate, medial frontal gyrus, nucleus accumbens, posterior cingulate, occipital cortical areas, and cerebellum. In addition, we show that KB220Z significantly activates, above placebo, seed regions of interest including the left nucleus accumbens, cingulate gyrus, anterior

  9. Coupling Neurogenetics (GARS™) and a Nutrigenomic Based Dopaminergic Agonist to Treat Reward Deficiency Syndrome (RDS): Targeting Polymorphic Reward Genes for Carbohydrate Addiction Algorithms

    Science.gov (United States)

    Blum, Kenneth; Simpatico, Thomas; Badgaiyan, Rajendra D.; Demetrovics, Zsolt; Fratantonio, James; Agan, Gozde; Febo, Marcelo; Gold, Mark S.

    2016-01-01

    Earlier work from our laboratory, showing anti-addiction activity of a nutraceutical consisting of amino-acid precursors and enkephalinase inhibition properties and our discovery of the first polymorphic gene (Dopamine D2 Receptor Gene [DRD2]) to associate with severe alcoholism serves as a blue-print for the development of “Personalized Medicine” in addiction. Prior to the later genetic finding, we developed the concept of Brain Reward Cascade, which continues to act as an important component for stratification of addiction risk through neurogenetics. In 1996 our laboratory also coined the term “Reward Deficiency Syndrome (RDS)” to define a common genetic rubric for both substance and non-substance related addictive behaviors. Following many reiterations we utilized polymorphic targets of a number of reward genes (serotonergic, Opioidergic, GABAergic and Dopaminergic) to customize KB220 [Neuroadaptogen- amino-acid therapy (NAAT)] by specific algorithms. Identifying 1,000 obese subjects in the Netherlands a subsequent small subset was administered various KB220Z formulae customized according to respective DNA polymorphisms individualized that translated to significant decreases in both Body Mass Index (BMI) and weight in pounds. Following these experiments, we have been successfully developing a panel of genes known as “Genetic Addiction Risk Score” (GARSpDX)™. Selection of 10 genes with appropriate variants, a statistically significant association between the ASI-Media Version-alcohol and drug severity scores and GARSpDx was found A variant of KB220Z in abstinent heroin addicts increased resting state functional connectivity in a putative network including: dorsal anterior cingulate, medial frontal gyrus, nucleus accumbens, posterior cingulate, occipital cortical areas, and cerebellum. In addition, we show that KB220Z significantly activates, above placebo, seed regions of interest including the left nucleus accumbens, cingulate gyrus, anterior

  10. Association between 17q25.3-rs6465657 polymorphism and prostate cancer susceptibility: a meta-analysis based on 19 studies

    Directory of Open Access Journals (Sweden)

    Jiang X

    2016-07-01

    Full Text Available Xiao Jiang,1,2 Mei Zhang,3 Xiao-Yan Bai,1 Shujing Li,1 Huijian Wu1 1Laboratory of Molecular Medicine & Pharmacy, School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People’s Republic of China; 2Department of Gastroenterology, Dalian Municipal Central Hospital Affiliated of Dalian Medical University, Dalian, People’s Republic of China; 3Department of Biochemistry and Molecular Biology, Heilongjiang University of Chinese Medicine, Haerbin, People’s Republic of China Background: Genome-wide association studies have identified rs6465657 polymorphism at chromosome 17q25.3 as a new prostate cancer (PCa susceptibility locus in people of European descent. However, subsequent replication studies have yielded inconsistent results among different ethnicities. In this study, a comprehensive meta-analysis was conducted to systematically evaluate the relationship between rs6465657 polymorphism and PCa risk.Methods: All the articles involved were identified from PubMed, EMBASE, Web of Science, EBSCO databases, and Google Scholar before December 2015. The odds ratios (ORs with corresponding 95% confidence internals (95% CIs were pooled under the allele model. Fourteen eligible articles with 19 studies were finally included.Results: In the overall population, the 17q25.3-rs6465657C allele was found to be significantly associated with increased risk of PCa compared to the T allele (OR =1.097; 95% CI: 1.061–1.134; P<0.001. In the subgroup analysis stratified by ethnicity, significantly increased risk was found in the Caucasian population (OR =1.120; 95% CI: 1.078–1.162; P<0.001, while the difference of OR did not reach the statistical significance in the Asian or African-American population. The analyses of sensitivity indicated the robust stability of the results, and the Begg’s and Egger’s test indicated that no publication bias existed.Conclusion: The current meta-analysis suggested that the 17q25.3-rs6465657

  11. Molecular identification of bacteria by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene.

    OpenAIRE

    Widjojoatmodjo, M N; Fluit, A.C.; Verhoef, J

    1995-01-01

    PCR-single-strand conformation polymorphism (PCR-SSCP) analysis is a rapid and convenient technique for the detection of mutations and allelic variants. We have adapted this technique for the identification of bacteria by PCR with fluorescein-labeled primers chosen from the conserved regions of the 16S rRNA gene flanking a variable region. The PCR product was denatured, separated on a nondenaturing gel, and detected by an automated DNA sequencer. The mobility of the single-stranded DNA is seq...

  12. Quantitative assessment of the influence of TP63 gene polymorphisms and lung cancer risk: evidence based on 93,751 subjects.

    Directory of Open Access Journals (Sweden)

    Liang Zhang

    Full Text Available BACKGROUND: Several genome-wide association studies on lung cancer (LC have reported similar findings of a new susceptibility locus, 3q28. After that, a number of studies reported that the rs10937405, and rs4488809 polymorphism in chromosome 3q28 has been implicated in LC risk. However, the studies have yielded contradictory results. METHODS: PubMed, ISI web of science, EMBASE and the Chinese National Knowledge Infrastructure databases were systematically searched to identify relevant studies. Data were abstracted independently by two reviewers. A meta-analysis was performed to examine the association between rs10937405, rs4488809 polymorphism at 3q28 and susceptibility to LC. Odds ratios (ORs and 95% confidence intervals (95% CIs were calculated. Heterogeneity and publication bias were also tested. RESULTS: A total of 9 studies including 35,961 LC cases and 57,790 controls were involved in this meta-analysis. An overall random-effects per-allele OR of1.19 (95% CI: 1.14-1.25; P<10(-5 and 1.19 (95% CI: 1.13-1.25; P<10(-5 was found for the rs10937405 and rs4488809 polymorphism respectively. Similar results were also observed using dominant or recessive genetic model. After stratified by ethnicity, significant associations were found among East Asians (per-allele OR = 1.22, 95% CI: 1.17-1.27; P<10(-5; whereas no significant associations were found among Caucasians for rs10937405. In the sub-group analysis by sample size, significantly increased risks were found for these polymorphisms in all genetic models. When analyzed according to histological type, the effects of rs10937405, and rs4488809 at 3q28 on the risk of lung cancer were significant mostly for lung adenocarcinoma. CONCLUSIONS: Our findings demonstrated that rs10937405-G allele and rs4488809-G allele might be risk-conferring factors for the development of lung cancer, especially for East Asian populations.

  13. Polymorphisms of mitochondrially encoded proteins.

    OpenAIRE

    Spinner, N B; King, M. C.

    1986-01-01

    Polymorphisms of mitochondrially encoded proteins can be detected in human lymphocytes by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Using an SDS-polyacrylamide 8 M urea system, 17 mitochondrially encoded proteins are distinguishable. Three of these (ME-6, ME-8, and ME-17) were polymorphic among 92 individuals screened, and these polymorphisms are reported here for the first time. With SDS-polyacrylamide electrophoresis without urea, 18 mitochondrial proteins are de...

  14. MORPH INSERTION AND ALLOMORPHY IN OPTIMALITY THEORY

    OpenAIRE

    Eulalia Bonet

    2004-01-01

    The goal of this paper is to compare two different hypotheses about the insertion of morphs and allomorphy in Optimality Theory. One of them, the Morphs through Constraifits Hypothesis (MCH) claims that the phonological realization of morphemes (morphs) is introduced through language-particular constraints. The other hypothesis, the Morphs in the Input Hypothesis (MIH) claims that the inputs to GEN contain al1 the relevant phonological information. It is shown that the MIH is clearly superior...

  15. Roles for retrotransposon insertions in human disease.

    Science.gov (United States)

    Hancks, Dustin C; Kazazian, Haig H

    2016-01-01

    Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans. PMID:27158268

  16. Thermal performance of tubular heat exchanger with multiple twisted-tape inserts

    Institute of Scientific and Technical Information of China (English)

    Suriya Chokphoemphun; Monsak Pimsarn; Chinaruk Thianpong; Pongjet Promvonge

    2015-01-01

    The paper presents an experimental investigation on enhanced heat transfer and pressure loss characteristics by using single, double, triple, and quadruple twisted-tape inserts in a round tube having a uniform heat-fluxed wal . The investigation has been conducted in the heat exchanger tube inserted with various twisted-tape numbers for co-and counter-twist arrangements for the turbulent air flow, Reynolds number (Re) from 5300 to 24000. The typical single twisted-tape inserts at two twist ratios, y/w=4 and 5, are used as the base case, while the other multiple twisted-tape inserts are at y/w=4 only. The experimental results of heat transfer and pressure drop in terms of Nusselt number (Nu) and friction factor (f), respectively, reveal that Nu increases with the increment of Re and of twisted-tape number. The values of Nu for the inserted tube are in a range of 1.15–2.12 times that for the plain tube while f is 1.9–4.1 times. The thermal enhancement factor of the inserted tube under similar pumping power is evaluated and found to be above unity except for the single and the double co-twisted tapes. The quadruple counter-twisted tape insert provides the maximum thermal performance.

  17. Cochlear Dummy Electrodes for Insertion Training and Research Purposes: Fabrication, Mechanical Characterization, and Experimental Validation

    Directory of Open Access Journals (Sweden)

    Jan-Philipp Kobler

    2015-01-01

    Full Text Available To develop skills sufficient for hearing preservation cochlear implant surgery, surgeons need to perform several electrode insertion trials in ex vivo temporal bones, thereby consuming relatively expensive electrode carriers. The objectives of this study were to evaluate the insertion characteristics of cochlear electrodes in a plastic scala tympani model and to fabricate radio opaque polymer filament dummy electrodes of equivalent mechanical properties. In addition, this study should aid the design and development of new cochlear electrodes. Automated insertion force measurement is a new technique to reproducibly analyze and evaluate the insertion dynamics and mechanical characteristics of an electrode. Mechanical properties of MED-EL’s FLEX28, FLEX24, and FLEX20 electrodes were assessed with the help of an automated insertion tool. Statistical analysis of the overall mechanical behavior of the electrodes and factors influencing the insertion force are discussed. Radio opaque dummy electrodes of comparable characteristics were fabricated based on insertion force measurements. The platinum-iridium wires were replaced by polymer filament to provide sufficient stiffness to the electrodes and to eradicate the metallic artifacts in X-ray and computed tomography (CT images. These low-cost dummy electrodes are cheap alternatives for surgical training and for in vitro, ex vivo, and in vivo research purposes.

  18. Heads or tails: L1 insertion-associated 5' homopolymeric sequences

    Directory of Open Access Journals (Sweden)

    Meyer Thomas J

    2010-02-01

    Full Text Available Abstract Background L1s are one of the most successful autonomous mobile elements in primate genomes. These elements comprise as much as 17% of primate genomes with the majority of insertions occurring via target primed reverse transcription (TPRT. Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications. Results We report on loci with sequence architecture consistent with variants of the twin priming mechanism and introduce dual priming, a mechanism that could generate similar sequence characteristics. These insertions take the form of truncated L1s with hallmarks of classical TPRT insertions but having a poly(T simple repeat at the 5' end of the insertion. We identified loci using computational analyses of the human, chimpanzee, orangutan, rhesus macaque and marmoset genomes. Insertion site characteristics for all putative loci were experimentally verified. Conclusions The 39 loci that passed our computational and experimental screens probably represent inversion-deletion events which resulted in a 5' inverted poly(A tail. Based on our observations of these loci and their local sequence properties, we conclude that they most probably represent twin priming events with unusually short non-inverted portions. We postulate that dual priming could, theoretically, produce the same patterns. The resulting homopolymeric stretches associated with these insertion events may promote genomic instability and create potential target sites for future retrotransposition events.

  19. Cochlear Dummy Electrodes for Insertion Training and Research Purposes: Fabrication, Mechanical Characterization, and Experimental Validation

    Science.gov (United States)

    Kobler, Jan-Philipp; Dhanasingh, Anandhan; Kiran, Raphael; Jolly, Claude; Ortmaier, Tobias

    2015-01-01

    To develop skills sufficient for hearing preservation cochlear implant surgery, surgeons need to perform several electrode insertion trials in ex vivo temporal bones, thereby consuming relatively expensive electrode carriers. The objectives of this study were to evaluate the insertion characteristics of cochlear electrodes in a plastic scala tympani model and to fabricate radio opaque polymer filament dummy electrodes of equivalent mechanical properties. In addition, this study should aid the design and development of new cochlear electrodes. Automated insertion force measurement is a new technique to reproducibly analyze and evaluate the insertion dynamics and mechanical characteristics of an electrode. Mechanical properties of MED-EL's FLEX28, FLEX24, and FLEX20 electrodes were assessed with the help of an automated insertion tool. Statistical analysis of the overall mechanical behavior of the electrodes and factors influencing the insertion force are discussed. Radio opaque dummy electrodes of comparable characteristics were fabricated based on insertion force measurements. The platinum-iridium wires were replaced by polymer filament to provide sufficient stiffness to the electrodes and to eradicate the metallic artifacts in X-ray and computed tomography (CT) images. These low-cost dummy electrodes are cheap alternatives for surgical training and for in vitro, ex vivo, and in vivo research purposes. PMID:26247024

  20. Strong association of the polymorphisms in PBEF1 and knee OA risk: a two-stage population-based study in China.

    Science.gov (United States)

    Chu, Minjie; Rong, Jiesheng; Wang, Yidan; Zhu, Lin; Xing, Baifen; Tao, Yuchun; Zhuang, Xun; Zhao, Yashuang; Jiang, Liying

    2016-01-01

    The association of Pre-B cell colony enhancing factor 1 (PBEF1) with obesity, together with its pro-inflammatory properties suggests that PBEF1 might be another crucial mediator that links inflammation with obesity and primary osteoarthritis (OA). We hypothesized that polymorphisms in PBEF1 may modify the risk of developing OA. Thus we systematically screened 4 tagging polymorphisms (rs4730153, rs2058540, rs3801267 and rs16872158) in PBEF1 and evaluated the association between the genetic variants and OA risk in a two-stage case-control study including 196 cases and 442 controls in the first stage and 143 cases and 238 controls in the second stage. In the first stage, two SNPs (rs4730153 and rs16872158) were found to be potentially associated with OA risk (P < 0.05), which were further confirmed in the second stage with similar effects. After combining the two stages, we found that rs4730153 was significantly associated with decreased risk of OA in an additive genetic model (P < 0.05), while rs16872158 showed increased risk of developing OA (P < 0.05). Combined analysis of these 2 SNPs showed a significant allele-dosage association between the number of risk alleles and OA risk (Ptrend = 5.25 × 10(-5)). These findings indicate that genetic variants in PBEF1 gene may modify individual susceptibility to OA in the Chinese population. PMID:26752339

  1. FADS gene polymorphisms confer the risk of coronary artery disease in a Chinese Han population through the altered desaturase activities: based on high-resolution melting analysis.

    Directory of Open Access Journals (Sweden)

    Si-Wei Li

    Full Text Available OBJECTIVE: We explored the desaturase activities and the correlation of fatty acid desaturases (FADS gene single nucleotide polymorphisms (SNPs with plasma fatty acid in coronary artery disease (CAD patients in a Chinese Han population. METHODS: Plasma fatty acids were measured by gas chromatography in CAD patients (n = 505 and a control group (n = 510. Five SNPs in the FADS gene were genotyped with high-resolution melting (HRM methods. RESULTS: After adjustment, D6D activity, assessed as arachidonic acid (AA, C20:4n-6/linoleic acid (LA, C18:2n-6, was higher in CAD patients (pT and rs174460 C>T were different between the two groups. The rs174537 T allele was associated with a lower risk of CAD [OR 0.743, 95% CI (0.624, 0.884, p = 0.001]. Carriers of the rs174460 C allele were associated with a higher risk of CAD [OR 1.357, 95% CI (1.106, 1.665, p = 0.003]. CONCLUSIONS: We firstly report that the rs174460 C allele is associated with a higher risk of CAD, and confirm that the rs174537 T allele is associated with a lower risk of CAD. Our results indicate that FADS gene polymorphisms are likely to influence plasma fatty acid concentrations and desaturase activities.

  2. Insertional Mutagenesis by a Hybrid PiggyBac and Sleeping Beauty Transposon in the Rat

    OpenAIRE

    Furushima, Kenryo; Jang, Chuan-Wei; Chen, Diane W.; Xiao, Ningna; Overbeek, Paul A.; Behringer, Richard R.

    2012-01-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac trans...

  3. Nitric Oxide Concentration and Other Salivary Changes after Insertion of New Complete Dentures in Edentulous Subjects

    OpenAIRE

    Maria de Lourdes Breseghelo; Lídia Andreu Guillo; Túlio Eduardo Nogueira; Cláudio Rodrigues Leles

    2016-01-01

    Objective. To assess changes in levels of salivary nitric oxide (NO) after insertion of new complete dentures and its association with clinical and salivary parameters. Methods. Nineteen fully edentulous subjects were included, mean age 64.4. Unstimulated whole saliva was collected before and after insertion of the dentures, at follow-up visits, and after 12 months. The concentration of the final stable NO product (nitrite) was measured by a colorimetric assay based on the Griess reaction. Cl...

  4. Identification of new IS711 insertion sites in Brucella abortus field isolates

    Directory of Open Access Journals (Sweden)

    Moriyón Ignacio

    2011-08-01

    Full Text Available Abstract Background Brucellosis is a zoonosis caused by Brucella spp., a group of highly homogeneous bacteria. The insertion sequence IS711 is characteristic of these bacteria, and occurs in variable numbers and positions, but always constant within a given species. This species-associated polymorphism is used in molecular typing and identification. Field isolates of B. abortus, the most common species infecting cattle, typically carry seven IS711 copies (one truncated. Thus far, IS711 transposition has only been shown in vitro and only for B. ovis and B. pinnipedialis, two species carrying a high number of IS711 copies, but never in other Brucella species, neither in vitro nor in field strains. Results We found several B. abortus strains isolated from milk and aborted fetuses that carried additional IS711 copies in two hitherto undescribed insertion sites: one in an intergenic region near to the 3' end of a putative lactate permease gene and the other interrupting the sequence of a marR transcriptional regulator gene. Interestingly, the second type of insertion was identified in isolates obtained repeatedly from the same herd after successive brucellosis outbreaks, an observation that proves the stability and virulence of the new genotype under natural conditions. Sequence analyses revealed that the new copies probably resulted from the transposition of a single IS711 copy common to all Brucella species sequenced so far. Conclusions Our results show that the replicative transposition of IS711 can occur under field conditions. Therefore, it represents an active mechanism for the emergence of genetic diversity in B. abortus thus contributing to intra-species genetic polymorphism.

  5. High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

    Directory of Open Access Journals (Sweden)

    Bus Anja

    2012-06-01

    Full Text Available Abstract Background The complex genome of rapeseed (Brassica napus is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD fragments for polymorphism detection and genotyping. Results More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the Brassica rapa reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the B. rapa chromosomes, which suggests that there might be an equal distribution over the Brassica oleracea chromosomes, too. The representation of Gene Ontology (GO terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category. Conclusions Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as B. napus.

  6. Gene polymorphisms of renin-angiotensin-aldosterone system components and the progression of chronic kidney diseases

    Directory of Open Access Journals (Sweden)

    Agata Kujawa-Szewieczek

    2010-08-01

    Full Text Available The renin-angiotensin-aldosterone system (RAAS plays an important role in the pathogenesis of hypertension as well as cardiovascular diseases and chronic kidney diseases. Among the most frequently studied RAAS gene polymorphisms are the angiotensin-converting enzyme insertion/deletion (I/D, angiotensinogen M235T and angiotensin II receptor type 1 A1166C polymorphisms.A significant correlation was found between the I/D polymorphism and cardiovascular morbidity and mortality rates. However, there was no significant correlation between I/D, M235T, A1166C polymorphism and arterial hypertension. The role of I/D polymorphism in the development and progression of chronic kidney disease is also non-conclusive. However, DD genotype has been identified as relevant for loss of renal function both in patients with IgA nephropathy and in patients of Asian origin with diabetic nephropathy.The relationship between RAAS gene polymorphism and transplanted kidney function has not been confirmed in large prospective and retrospective studies. Conclusion: there is no clear opinion concerning the influence of RAAS genotypes on the prevalence of post-transplant hypertension or erythrocytosis.Although a role of RAAS gene polymorphism in kidney function deterioration could not be ruled out, it is more likely that a variety of genetic and environmental factors influence the progression of chronic kidney diseases.

  7. PRNP promoter polymorphisms are associated with BSE susceptibility in Swiss and German cattle

    Directory of Open Access Journals (Sweden)

    Ziegler Ute

    2007-04-01

    Full Text Available Abstract Background Non-synonymous polymorphisms within the prion protein gene (PRNP influence the susceptibility and incubation time for transmissible spongiform encephalopathies (TSE in some species such as sheep and humans. In cattle, none of the known polymorphisms within the PRNP coding region has a major influence on susceptibility to bovine spongiform encephalopathy (BSE. Recently, however, we demonstrated an association between susceptibility to BSE and a 23 bp insertion/deletion (indel polymorphism and a 12 bp indel polymorphism within the putative PRNP promoter region using 43 German BSE cases and 48 German control cattle. The objective of this study was to extend this work by including a larger number of BSE cases and control cattle of German and Swiss origin. Results Allele, genotype and haplotype frequencies of the two indel polymorphisms were determined in 449 BSE cattle and 431 unaffected cattle from Switzerland and Germany including all 43 German BSE and 16 German control animals from the original study. When breeds with similar allele and genotype distributions were compared, the 23 bp indel polymorphism again showed a significant association with susceptibility to BSE. However, some additional breed-specific allele and genotype distributions were identified, mainly related to the Brown breeds. Conclusion Our study corroborated earlier findings that polymorphisms in the PRNP promoter region have an influence on susceptibility to BSE. However, breed-specific differences exist that need to be accounted for when analyzing such data.

  8. Based Upon Repeat Pattern (BURP: an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms

    Directory of Open Access Journals (Sweden)

    Sammeth Michael

    2007-10-01

    Full Text Available Abstract Background For typing of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that this region also reflects long-term epidemiology. However, no automated and objective algorithm existed to cluster different repeat regions. In this study, the Based Upon Repeat Pattern (BURP implementation that is a heuristic variant of the newly described EDSI algorithm was investigated to infer the clonal relatedness of different spa types. For calibration of BURP parameters, 400 representative S. aureus strains with different spa types were characterized by MLST and clustered using eBURST as "gold standard" for their phylogeny. Typing concordance analysis between eBURST and BURP clustering (spa-CC were performed using all possible BURP parameters to determine their optimal combination. BURP was subsequently evaluated with a strain collection reflecting the breadth of diversity of S. aureus (JCM 2002; 40:4544. Results In total, the 400 strains exhibited 122 different MLST types. eBURST grouped them into 23 clonal complexes (CC; 354 isolates and 33 singletons (46 isolates. BURP clustering of spa types using all possible parameter combinations and subsequent comparison with eBURST CCs resulted in concordances ranging from 8.2 to 96.2%. However, 96.2% concordance was reached only if spa types shorter than 8 repeats were excluded, which resulted in 37% excluded spa types. Therefore, the optimal combination of the BURP parameters was "exclude spa types shorter than 5 repeats" and "cluster spa types into spa-CC if cost distances are less than 4" exhibiting 95.3% concordance to eBURST. This algorithm identified 24 spa-CCs, 40 singletons, and excluded only 7.8% spa types. Analyzing the natural population with these parameters, the comparison of whole-genome micro-array groupings (at the level of 0.31 Pearson correlation index

  9. Reverse genetics in Chlamydomonas: a platform for isolating insertional mutants

    Directory of Open Access Journals (Sweden)

    de Montaigu Amaury

    2011-07-01

    Full Text Available Abstract A method was developed to identify insertional mutants of Chlamydomonas reinhardtii disrupted for selected target genes. The approach relies on the generation of thousands of transformants followed by PCR-based screenings that allow for identification of strains harboring the introduced marker gene within specific genes of interest. Our results highlight the strengths and limitations of two independent screens that differed in the nature of the marker DNA used (PCR-amplified fragment containing the plasmid-free marker versus entire linearized plasmid with the marker and in the strategies used to maintain and store transformants.

  10. Calibration aspects of binaural sound reproduction over insert earphones

    DEFF Research Database (Denmark)

    Hoffmann, Pablo F.; Markovic, Milos; Olesen, Søren Krarup; Madsen, Esben; Hammershøi, Dorte

    Earphones are nowadays widely adopted for the reproduction of audio material in mobile multimedia and communication platforms, e.g. smartphones. Reproduction of high-quality spatial sound on such platforms can dramatically improve their applicability, and since two channels are always available in...... earphone-based reproduction, binaural reproduction can be applied directly. This paper is concerned with the theoretical and practical aspects relevant to the correct reproduction of binaural signals over insert earphones. To this purpose, a theoretical model originally developed to explain the acoustic...

  11. Frequency of HLA-G exon 8 polymorphisms and kidney allograft outcome in Iranian population.

    Science.gov (United States)

    Aghdaie, Mahdokht H; Azarpira, Negar; Kazemi, Kurosh; Geramizadeh, Bita; Darai, Masumeh; Malekhoseini, Seid Ali

    2011-06-01

    The 14-bp polymorphism in exon 8 of the HLA-G gene is associated with HLA-G mRNA stability and the patterns of alternative isoform splicing and may influence the functionality of the HLA-G molecule. HLA-G expression was related to allograft acceptance and fewer episodes of acute rejection during heart, kidney and liver-kidney transplantation. In order to determine a possible correlation between the 14-bp insertion/deletion polymorphism and kidney allograft outcome in our population, genomic DNA was isolated from 144 patients who had received isolated kidney allografts. The recipients was divided into two groups, grafts presenting features of rejection group and a non-rejection group, and compared them with a control group of 100 healthy subjects. There was no significant difference in allelic frequencies of 14-bp insertion/deletion polymorphism between normal controls and kidney transplant patients. No significant difference was found between the RG and the NRG regarding the 14-bp genotypes and alleles. Therefore, additional studies with more sample size from other populations with analysis of other HLA-G polymorphisms are necessary to define this polymorphism as a valuable clinical marker. PMID:21107725

  12. Role of ACE and PAI-1 Polymorphisms in the Development and Progression of Diabetic Retinopathy.

    Directory of Open Access Journals (Sweden)

    Saba Saleem

    Full Text Available In the present study we determined the association of angiotensin converting enzyme (ACE and plasminogen activator inhibitor-1 (PAI-1 gene polymorphisms with diabetic retinopathy (DR and its sub-clinical classes in Pakistani type 2 diabetic patients. A total of 353 diabetic subjects including 160 DR and 193 diabetic non retinopathy (DNR as well as 198 healthy controls were genotyped by allele specific polymerase chain reaction (PCR for ACE Insertion/Deletion (ID polymorphism, rs4646994 in intron 16 and PAI-1 4G/5G (deletion/insertion polymorphism, rs1799768 in promoter region of the gene. To statistically assess the genotype-phenotype association, multivariate logistic regression analysis was applied to the genotype data of DR, DNR and control individuals as well as the subtypes of DR. The ACE genotype ID was found to be significantly associated with DR (p = 0.009, odds ratio (OR 1.870 [95% confidence interval (CI = 1.04-3.36] and its sub-clinical class non-proliferative DR (NPDR (p = 0.006, OR 2.250 [95% CI = 1.098-4.620], while PAI polymorphism did not show any association with DR in the current cohort. In conclusion in Pakistani population the ACE ID polymorphism was observed to be significantly associated with DR and NPDR, but not with the severe form of the disease i.e. proliferative DR (PDR.

  13. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg;

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification and...... briefly describe the methods that are preferred for SNP typing in forensic genetics. In addition, we will illustrate how SNPs can be used as investigative leads in the police investigation by discussing the use of ancestry informative markers and forensic DNA phenotyping. Modern DNA sequencing...

  14. Evaluation of a projection-domain lung nodule insertion technique in thoracic CT

    Science.gov (United States)

    Ma, Chi; Chen, Baiyu; Koo, Chi Wan; Takahashi, Edwin A.; Fletcher, Joel G.; McCollough, Cynthia H.; Levin, David L.; Kuzo, Ronald S.; Viers, Lyndsay D.; Vincent Sheldon, Stephanie A.; Leng, Shuai; Yu, Lifeng

    2016-04-01

    Task-based assessment of computed tomography (CT) image quality requires a large number of cases with ground truth. Inserting lesions into existing cases to simulate positive cases is a promising alternative approach. The aim of this study was to evaluate a recently-developed raw-data based lesion insertion technique in thoracic CT. Lung lesions were segmented from patient CT images, forward projected, and reinserted into the same patient CT projection data. In total, 32 nodules of various attenuations were segmented from 21 CT cases. Two experienced radiologists and 2 residents blinded to the process independently evaluated these inserted nodules in two sub-studies. First, the 32 inserted and the 32 original nodules were presented in a randomized order and each received a rating score from 1 to 10 (1=absolutely artificial to 10=absolutely realistic). Second, the inserted and the corresponding original lesions were presented side-by-side to each reader, who identified the inserted lesion and provided a confidence score (1=no confidence to 5=completely certain). For the randomized evaluation, discrimination of real versus artificial nodules was poor with areas under the receiver operative characteristic curves being 0.69 (95% CI: 0.58-0.78), 0.57 (95% CI: 0.46-0.68), and 0.62 (95% CI: 0.54-0.69) for the 2 radiologists, 2 residents, and all 4 readers, respectively. For the side-by-side evaluation, although all 4 readers correctly identified inserted lesions in 103/128 pairs, the confidence score was moderate (2.6). Our projection-domain based lung nodule insertion technique provides a robust method to artificially generate clinical cases that prove to be difficult to differentiate from real cases.

  15. PARP-1 Val762Ala polymorphism and risk of cancer: a meta-analysis based on 39 case-control studies.

    Directory of Open Access Journals (Sweden)

    Qin Qin

    Full Text Available BACKGROUND: Poly(ADP-ribose polymerase-1 (PARP-1 is a nuclear chromatin-associated enzyme involved in several important cellular processes, particularly in the DNA repair system. PARP-1 rs1136410: C>T is among the most studied polymorphisms and likely involved in human carcinogenesis. However, results from previous studies are inconclusive. Thus, a meta-analysis was conducted to derive a more precise estimation of the effects of this enzyme. METHODOLOGY AND PRINCIPAL FINDINGS: A comprehensive search was conducted in the PubMed and EMBASE databases until December 9, 2013. A total of 39 studies with 16,783 cancer cases and 23,063 control subjects were included in the meta-analysis on the basis of the inclusion and exclusion criteria. No significant association between the PARP-1 Val762Ala polymorphism and cancer risk was found when all of the studies were pooled into the analysis (VA + AA vs. VV: OR = 1.03, 95% CI = 0.95-1.11. The subgroup analysis of cancer types revealed that the -762Ala allele was associated with increased risk of gastric, cervical, and lung cancers and a decreased risk of glioma. In addition, a significantly increased risk of cancer associated with the polymorphism was observed in Asian descendents (VA + AA vs. VV: OR = 1.17, 95% CI = 1.09-1.25; AA vs. VV: OR = 1.28, 95% CI = 1.08-1.51; VA vs. VV: OR = 1.12, 95% CI = 1.04-1.20; AA vs. VA + VV: OR = 1.09, 95% CI = 1.03-1.39. These results also indicated that a joint effect between PARP-1 Val762Ala and XRCC1 Arg399Gln could be involved in the risk of cancer development (OR = 3.53, 95% CI = 1.30-9.59. CONCLUSION: The present meta-analysis provides evidence that the PARP-1 Val762Ala may be involved in cancer development at least in some ethnic groups (Asian or some specific cancer types (gastric, cervical, and lung cancers, and glioma.

  16. Analysis of Single Nucleotide Polymorphism Panels for Bovine DNA Identification

    OpenAIRE

    Blanchard, Kimberly A.

    2013-01-01

    Single nucleotide polymorphisms (SNPs) are single base-pair variations that exist between individuals. There are approximately a million or more SNPs located throughout the genome of each individual animal. Therefore, by taking advantage of these unique polymorphisms, SNPs can be used to resolve questions of unknown parentage in the livestock industry. Currently a panel of 88 SNPs, obtained from a panel of 121 SNPs originally created by USDA-MARC, is commercially available from Fluidigm®. The...

  17. Fatores estratégicos explorados pelas empresas processadoras de lácteos para inserir-se no mercado de bebidas à base de soja Strategic factors explored by dairy processing companies for their insertion in the soy-based beverage market

    Directory of Open Access Journals (Sweden)

    Nadir Paula da Rosa

    2011-06-01

    Full Text Available Esta pesquisa pretende caracterizar e compreender a inter-relação entre fatores de natureza mercadológica e competitiva, considerados pelos gestores de empresas brasileiras processadoras de lácteos para se inserir no mercado de bebidas à base de soja. O método utilizado foi o de estudo multi-caso, aplicando como técnicas de pesquisa: i coleta de dados secundários; ii entrevistas com tomadores de decisão em duas empresas brasileiras, que atuam no setor lácteo e que estão se inserindo no mercado de bebidas à base de soja; iii entrevistas com especialistas do setor lácteo; iv grupos focais com consumidores representantes de segmentos-alvo do mercado de bebidas à base de soja. Os resultados revelam que as empresas estudadas perceberam o mercado de bebidas à base de soja como uma oportunidade em função de seu forte crescimento decorrente de mudanças nos hábitos de consumo. Essas organizações exploram a possibilidade de ampliar e diversificar suas linhas de produtos, aproveitando-se de fatores competitivos favoráveis como a flexibilidade organizacional e o compartilhamento de suas estruturas de produção e de comercialização. Porém, existe a percepção de restrições relacionadas ao acesso a recursos financeiros e ao desenvolvimento das capacitações necessárias para empreender a consolidação da marca e diferenciar seus produtos nesse novo mercado.The present paper aims to characterize and understand the interrelationship among market and competitive factors that are considered by Brazilian managers for the insertion of dairy processing companies in the soy-based beverage market. The method used was the multi-case study, applied through the following research techniques: i collection of secondary data; ii interviews with the decision makers of two Brazilian companies that act in the dairy sector and that are being inserted in the soy-based beverage market; iii interviews with experts in the dairy sector; iv focus groups

  18. A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs

    Directory of Open Access Journals (Sweden)

    Qi Weihong

    2009-12-01

    Full Text Available Abstract Background In order to provide a cost-effective tool to analyse pharmacogenetic markers in malaria treatment, DNA microarray technology was compared with sequencing of polymerase chain reaction (PCR fragments to detect single nucleotide polymorphisms (SNPs in a larger number of samples. Methods The microarray was developed to affordably generate SNP data of genes encoding the human cytochrome P450 enzyme family (CYP and N-acetyltransferase-2 (NAT2 involved in anti-malarial drug metabolisms and with known polymorphisms, i.e. CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, and NAT2. Results For some SNPs, i.e. CYP2A6*2, CYP2B6*5, CYP2C8*3, CYP2C9*3/*5, CYP2C19*3, CYP2D6*4 and NAT2*6/*7/*14, agreement between both techniques ranged from substantial to almost perfect (kappa index between 0.61 and 1.00, whilst for other SNPs a large variability from slight to substantial agreement (kappa index between 0.39 and 1.00 was found, e.g. CYP2D6*17 (2850C>T, CYP3A4*1B and CYP3A5*3. Conclusion The major limit of the microarray technology for this purpose was lack of robustness and with a large number of missing data or with incorrect specificity.

  19. Simultaneous Analysis of SEPT9 Promoter Methylation Status, Micronuclei Frequency, and Folate-Related Gene Polymorphisms: The Potential for a Novel Blood-Based Colorectal Cancer Biomarker

    Directory of Open Access Journals (Sweden)

    Gloria Ravegnini

    2015-12-01

    Full Text Available One challenge in colorectal cancer (CRC is identifying novel biomarkers to be introduced in screening programs. The present study investigated the promoter methylation status of the SEPT9 gene in peripheral blood samples of subjects’ positive fecal occult blood test (FOBT. In order to add new insights, we investigated the association between SEPT9 promoter methylation and micronuclei frequency, and polymorphisms in the folate-related pathway genes. SEPT9 promoter methylation, micronuclei frequency, and genotypes were evaluated on 74 individuals’ FOBT positive. Individuals were subjected to a colonoscopy that provided written informed consent for study participation. SEPT9 promoter methylation status was significantly lower in the CRC group than controls (p = 0.0006. In contrast, the CaCo2 cell-line, analyzed as a tissue specific model of colon adenocarcinoma, showed a significantly higher percentage of SEPT9 promoter methylation compared to the CRC group (p < 0.0001. Linear regression analysis showed an inverse correlation between micronuclei frequency and the decrease in the methylation levels of SEPT9 promoter region among CRC patients (β = −0.926, p = 0.0001. With regard to genotype analysis, we showed the involvement of the DHFR polymorphism (rs70991108 in SEPT9 promoter methylation level in CRC patients only. In particular, the presence of at least one 19 bp del allele significantly correlates with decreased SEPT9 promoter methylation, compared to the 19 bp ins/ins genotype (p = 0.007. While remaining aware of the strengths and limitations of the study, this represents the first evidence of a novel approach for the early detection of CRC, using SEPT9 promoter methylation, micronuclei frequency and genotypes, with the potential to improve CRC risk assessment.

  20. Effects of GSTM1/GSTT1 gene polymorphism and fruit & vegetable consumption on antioxidant biomarkers and cognitive function in the elderly: a community based cross-sectional study.

    Directory of Open Access Journals (Sweden)

    Linhong Yuan

    Full Text Available It was reported that Glutathione S-transferase (GST gene polymorphism and fruit and vegetable (FV intake were associated with body antioxidant capacity. The oxidative/anti-oxidative imbalance played an important role in the pathogenesis of AD. However, the association of GST genotype, dietary FV consumption with body antioxidant biomarkers and cognitive function in the elderly is not clear.The aim of the present study was to determine the association of GST genotype, and dietary FV intake, with antioxidant biomarkers and cognitive function in the elderly.Food frequency questionnaire was used to collect data of dietary FV intakes in 504 community dwelling elderly aged from 55 to 75 years old. GSTM1 and GSTT1 genotypes were determined by using multiple-PCR method. Plasma and erythrocyte antioxidant biomarkers were measured. Cognitive function was measured by using Montreal Cognitive Assessment. Statistical analysis was applied for exploring the association of GST genotype and FV intake with antioxidant biomarkers level and cognitive function in the elderly.Individual GSTM1 or GSTT1 gene deletion affects body antioxidant biomarkers levels, including erythrocyte GST activity, plasma total antioxidant capacity, and glutathione levels. GSTM1and/or GSTT1 gene deletion have no effects on cognitive function in the surveyed participants. The effect of GST genotype on antioxidant biomarkers are FV intake dependent. There is interaction of FV intake and GST genotype on cognitive function in the elderly.GST genotype or daily FV consumption impact body antioxidant biomarkers, but not cognitive function in the elderly. There were combined effects of GST genotype and FV consumption on cognitive function in the elderly population. Large scale perspective population study is required to explore the association of GST genetic polymorphism, FV consumption and antioxidant biomarkers and cognitive function in the elderly.

  1. Patterns of Genetic Diversity and Structure at Fine Scale of an Endangered Moroccan Endemic Tree (Argania spinosa L. Skeels Based on ISSR Polymorphism

    Directory of Open Access Journals (Sweden)

    Jamila MOUHADDAB

    2015-12-01

    Full Text Available The preservation of the diversity of endangered populations of argan trees, in their natural habitat, is a crucial step toward their conservation. The aim of the present study was to evaluate the genetic diversity of the argan trees in the wild, and to establish a phylogenetic map using DNA fingerprints. The ultimate goal was to develop a core set that would represent the existing diversity in the whole germplasm. In regard to this, 200 samples of Argania spinosa individual trees were collected from 10 different provenances in the region of Essaouira (Morocco. The genetic variation between and within these argan trees was investigated using previously described Inter-Simple Sequence Repeat markers. These markers generated a total of 149 fragments, in which 148 (99.33% were polymorphic. The samples collected in the ‘Ouled Lhaj’ provenance showed the lowest diversity (% of polymorphic locus P=48.32%; genetic diversity Nei h=0.153; allelic richness A=1.483, compared to those collected in the ‘Mramer’ provenance (%P=68.46%; h=0.233; A=1.685. Also, the results showed a high level of genetic differentiation among provenances (AMOVA=44%, Gst=0.40, and a limited gene flow (Nm=0.73 between the provenances. In addition, these data suggested a low correlation between the genetic diversity of the tree and their respective geographical location in relation to the proximity to the littoral. Finally, a core collection of 13 genotypes that represent the essential of the detected diversity was established. The distribution pattern of this genetic diversity provides an important baseline data for the conservation strategies of argan tree species in the wild.

  2. Association of Lactobacillus crispatus with fructo-oligosaccharides and ascorbic acid in hydroxypropyl methylcellulose vaginal insert.

    Science.gov (United States)

    Vitali, Beatrice; Abruzzo, Angela; Parolin, Carola; Palomino, Rogers Alberto Ñahui; Dalena, Francesco; Bigucci, Federica; Cerchiara, Teresa; Luppi, Barbara

    2016-01-20

    The aim of this work was to develop a synbiotic vaginal insert containing the probiotic strain Lactobacillus crispatus BC5, the prebiotic substrate fructo-oligosaccharide and the antioxidant agent ascorbic acid, for the prophylaxis and therapy of vaginal infections. Mucoadhesive in situ gelling vaginal inserts based on hydroxypropyl methylcellulose were prepared by freeze-drying, stored at +2-8 °C for 90 days and characterized in terms of technological and functional properties. Complete survival of L. crispatus BC5 was found immediately after insert preparation (96.08%) as well as after 90 days of storage (95.82%) in the vaginal inserts containing fructo-oligosaccharide, ascorbic acid and skimmed milk. Synbiotic inserts showed improved mucoadhesion ability (from three- to five-fold) with respect to a standard formulation based on hydroxypropyl methylcellulose alone. Moreover, inserts allowed to modulate lactobacilli release in virtue of the different amounts of fructo-oligosaccharide. Finally, antimicrobial activity was exerted by L. crispatus BC5 released from the vaginal formulation. PMID:26572459

  3. Roles for retrotransposon insertions in human disease

    OpenAIRE

    Dustin C Hancks; Kazazian, Haig H.

    2016-01-01

    Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a “copy-and-paste” mechanism, LINE-1 is able...

  4. Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) Furnace Development

    Science.gov (United States)

    Crouch, Myscha R.; Carswell, William E.; Farmer, Jeff; Rose, Fred; Tidwell, Paul H., II

    2000-01-01

    The Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) are microgravity furnaces under development at Marshall Space Flight Center. The furnaces are being developed for the first Materials Science Research Rack (MSRR-1) of the Materials Science Research Facility (MSRF), one of the first International Space Station (ISS) scientific payloads. QMI is a Bridgman furnace with quench capability for studying interface behavior during directional solidification of metallic and alloy materials. DMI will be a Bridgman-Stockbarger furnace to study diffusion processes in semiconductors. The design for each insert, both QMI and DMI, is driven by specific science, operations and safety requirements, as well as by constraints arising from resource limitations, such as volume, mass and power. Preliminary QMI analysis and testing indicates that the design meets these requirements.

  5. Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) furnace development

    International Nuclear Information System (INIS)

    The Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) are microgravity furnaces under development at Marshall Space Flight Center. The furnaces are being developed for the first Materials Science Research Rack (MSRR-1) of the Materials Science Research Facility (MSRF), one of the first International Space Station (ISS) scientific payloads. QMI is a Bridgman furnace with quench capability for studying interface behavior during directional solidification of metallic and alloy materials. DMI will be a Bridgman-Stockbarger furnace to study diffusion processes in semiconductors. The design for each insert, both QMI and DMI, is driven by specific science, operations and safety requirements, as well as by constraints arising from resource limitations, such as volume, mass and power. Preliminary QMI analysis and testing indicates that the design meets these requirements

  6. Polymorphisms in NFkB, PXR, LXR and risk of colorectal cancer in a prospective study of Danes

    DEFF Research Database (Denmark)

    Andersen, Vibeke; Christensen, Jane; Overvad, Kim; Tjønneland, Anne; Vogel, Ulla Birgitte

    2010-01-01

    red and processed meat in relation to CRC risk. Carriers of NFkB -94deletion were at 3% increased risk pr 25 gram meat per day (95% CI: 0.98-1.09) whereas homozygous carriers of the insertion were not at increased risk (p for interaction = 0.03). PXR and LXR polymorphisms were not associated with CRC......Background Transcription factors and nuclear receptors constitute a link between exposure to heterocyclic amines and polycyclic aromatic hydrocarbons from meat and tobacco smoke and colorectal cancer (CRC) risk. The aim of this study was to investigate if polymorphisms in nuclear factor kappa......-B, pregnane X receptor, and liver X receptor were associated with risk of CRC, and to investigate possible interactions with lifestyle factors such as smoking, meat consumption, and NSAID use. Methods The polymorphisms nuclear factor kappa-B (NFkB, NFKB1) -94 insertion/deletion ATTG (rs28362491), pregnane X...

  7. A minimalist technique for insertion of intrauterine devices

    Directory of Open Access Journals (Sweden)

    Norman David Goldstuck

    2015-05-01

    Full Text Available The world’s population is approaching 7 billion. As a general rule, the countries with the highest population have the least available healthcare resources, the most notable exception being the United States of America (USA. Most of these countries have an urgent need to reduce their populations. The intrauterine device (IUD is used by the largest number of contraceptives world-wide and it has a proven record in reducing unwanted pregnancies. Its efficacy rate as a long-acting reversible contraceptive is matched only by subdermal implants which are not as cost effective. Although the rates of pelvic infection are elevated in many countries with low-resource health care systems, we now know that pelvic infection rates are independent of IUD usage. This is therefore no longer a contraindication for using IUDs on a large scale in family planning programs. The technique of IUD insertion as described in most textbooks and journals is unnecessarily complex and based on ritual rather than good clinical evidence. This is particularly interesting in that at a time where we prefer evidence based medicine there are still so many clinical practice sacred cows. This article advocates a simplification of the technique for inserting IUDs. The scientific rationale for simplifying the technique is presented, as well as evidence that it is as safe if not safer than the currently suggested methods, if used for the correct type of IUD acceptors.

  8. Polymeric Biodegradable Stent Insertion in the Esophagus

    Directory of Open Access Journals (Sweden)

    Kai Yang

    2016-04-01

    Full Text Available Esophageal stent insertion has been used as a well-accepted and effective alternative to manage and improve the quality of life for patients diagnosed with esophageal diseases and disorders. Current stents are either permanent or temporary and are fabricated from either metal or plastic. The partially covered self-expanding metal stent (SEMS has a firm anchoring effect and prevent stent migration, however, the hyperplastic tissue reaction cause stent restenosis and make it difficult to remove. A fully covered SEMS and self-expanding plastic stent (SEPS reduced reactive hyperplasia but has a high migration rate. The main advantage that polymeric biodegradable stents (BDSs have over metal or plastic stents is that removal is not require and reduce the need for repeated stent insertion. But the slightly lower radial force of BDS may be its main shortcoming and a post-implant problem. Thus, strengthening support of BDS is a content of the research in the future. BDSs are often temporarily effective in esophageal stricture to relieve dysphagia. In the future, it can be expect that biodegradable drug-eluting stents (DES will be available to treat benign esophageal stricture, perforations or leaks with additional use as palliative modalities for treating malignant esophageal stricture, as the bridge to surgery or to maintain luminal patency during neoadjuvant chemoradiation.

  9. Horizontally separated 1-in-1 crossing insertions

    Energy Technology Data Exchange (ETDEWEB)

    Syphers, M.J. [Fermi National Accelerator Lab., Batavia, IL (United States)

    1985-10-01

    Previous to this workshop, realistic lattices have been developed for vertically separated l-in-l (e.g., D.E. Johnson, A.A. Garren) and 2-in-1 (e.g., S. Heifets) magnets as well as for horizontally separated 2-in-l magnets (e.g., SSC RDS). Bringing together the widely separated ({approximately}60-70 cm) beams in a reasonable length of tunnel and keeping the dispersion zero at the interaction point has been difficult in the vertical l-in-l case. Most designs have required spacial 2-in-1 quadrupoles near the interaction point where the beams are separated by 15 cm or less. It is not clear that such magnets, as dictated by some of these lattice designs, can easily be built. The purpose of this exercise is to provide a crossing insertion for a realistic lattice which involves horizontally separated l-in-l magnets. The following horizontal crossing insertions, which incorporate the dispersion suppressors and phase trombones into the major arcs, need no special 2-in-1 magnets near the interaction point. The dispersion at the IP created by the horizontal crossing can be cancelled by the dispersion suppressor and one set of triplets.

  10. External ear canal cholesteatoma after ventilation tube insertion and mastoidectomy

    Directory of Open Access Journals (Sweden)

    Đerić Dragoslava

    2012-01-01

    Full Text Available Introduction. Etiopathogenetically, there are two types of chollesteatomas: congenital, and acquired. Numerous theories in the literature try to explain the nature of the disease, however, the question about cholesteatomas remain still unanswered. The aim of the study was to present a case of external ear canal cholesteatoma (EEC developed following microsurgery (ventilation tube insertion and mastoidectomy, as well as to point ant possible mechanisms if its development. Case report. A 16-yearold boy presented a 4-month sense of fullness in the ear and otalgia on the left side. A year before, mastoidectomy and posterior atticotomy were performed with ventilation tube placement due to acute purulent mastoiditis. Diagnosis was based on otoscopy examination, audiology and computed tomography (CT findings. CT showed an obliterative soft-tissue mass completely filled the external ear canal with associated erosion of subjacent the bone. There were squamous epithelial links between the canal cholesteatoma and lateral tympanic membrane surface. They originated from the margins of tympanic membrane incision made for a ventilation tube (VT insertion. The position of VT was good as well as the aeration of the middle ear cavity. The tympanic membrane was intact and of normal appearance without middle ear extension or mastoid involvement of cholesteatoma. Cholesteatoma and ventilation tube were both removed. The patient recovered without complications and shortly audiology revealed hearing improving. Follow-up 2 years later, however, showed no signs of the disease. Conclusion. There could be more than one potential delicate mechanism of developing EEC in the ear with VT insertion and mastoidectomy. It is necessary to perform routine otologic surveillance in all patients with tubes. Affected ear CT scan is very helpful in showing the extent of cholesteatoma and bony defects, which could not be assessed by otoscopic examination alone.

  11. Correlation between the Insertion/Deletion Mutations of Prion Protein Gene and BSE Susceptibility and Milk Performance in Dairy Cows

    Institute of Scientific and Technical Information of China (English)

    Shen-rong Hu; Yong-tao Huai; Chuan-ying Pan; Chu-zhao Lei; Hong Chen; Xian-yong Lan

    2013-01-01

    Objective To investigate the 23 bp and 12 bp insertion/deletion (indel) mutations within the bovine prion protein (PRNP) gene in Chinese dairy cows, and to detect the associations of two indel mutations with BSE susceptibility and milk performance. Methods Based on bovine PRNP gene sequence, two pairs of primers for testing the 23 bp and 12 bp indel mutations were designed. The PCR ampliifcation and agarose electrophoresis were carried out to distinguish the different genotypes within the mutations. Moreover, based on previous data from other cattle breeds and present genotypic and allelic frequencies of two indels mutations in this study, the corrections between the two indel mutations and BSE susceptibility were tested, as well as the relationships between the mutations and milk performance traits were analyzed in this study based on the statistical analyses. Results In the analyzed Chinese Holstein population, the frequencies of two“del”alleles in 23 bp and 12 bp indel muations were more frequent. The frequency of haplotype of 23del-12del was higher than those of 23del-12ins and 23ins-12del. From the estimated r2 and D’ values, two indel polymorphisms were linked strongly in the Holstein population (D’=57.5%, r2=0.257). Compared with the BSE-affected cattle populations from the reported data, the signiifcant differences of genotypic and allelic frequencies were found among present Holstein and some BSE-affected populations (P0.05). Conclusions These observations revealed that the inlfuence of two indel mutations within the bovine PRNP gene on BSE depended on the breed and they did not affect the milk production traits, which layed the foundation for future selection of resistant animals, and for improving health conditions for dairy breeding against BSE in China.

  12. Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

    KAUST Repository

    Allam, Amin

    2015-07-14

    Motivation: Next-generation sequencing generates large amounts of data affected by errors in the form of substitutions, insertions or deletions of bases. Error correction based on the high-coverage information, typically improves de novo assembly. Most existing tools can correct substitution errors only; some support insertions and deletions, but accuracy in many cases is low. Results: We present Karect, a novel error correction technique based on multiple alignment. Our approach supports substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the sequenced genome. Experiments with data from Illumina, 454 FLX and Ion Torrent sequencing machines demonstrate that Karect is more accurate than previous methods, both in terms of correcting individual-bases errors (up to 10% increase in accuracy gain) and post de novo assembly quality (up to 10% increase in NGA50). We also introduce an improved framework for evaluating the quality of error correction.

  13. Polymorphism of exon 3 of the HLA-G gene

    DEFF Research Database (Denmark)

    Hviid, T V; Meldgaard, Michael; Sørensen, S;

    1997-01-01

    HLA-G is a non-classical MHC class I gene with a limited tissue distribution. The most pronounced expression is detected in the cytotrophoblast of first trimester placenta. It is possible to detect mRNA for HLA-G in preimplantation blastocysts where expression is correlated with a high cleavage...... rate of embryos. HLA-G seems to play an important role in the feto-maternal relationship. The polymorphism of the HLA-G locus is not fully clarified. One study has shown extensive nucleotide sequence variation in the exon 3 (alpha-2 domain) in healthy African Americans. A few studies in other...... populations have only revealed a limited polymorphism. We investigated the polymorphism of the exon 3 of HLA-G by means of Polymerase Chain Reaction (PCR)-Single Strand Conformation Polymorphism (SSCP)- and DNA sequencing analysis in a Danish population. We detected four single-base substitutions in exon 3...

  14. Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype

    Directory of Open Access Journals (Sweden)

    Kim Tae-Ho

    2007-11-01

    Full Text Available Abstract Background Osteoporosis is defined as the loss of bone mineral density that leads to bone fragility with aging. Population-based case-control studies have identified polymorphisms in many candidate genes that have been associated with bone mass maintenance or osteoporotic fracture. To investigate single nucleotide polymorphisms (SNPs that are associated with osteoporosis, we examined the genetic variation among Koreans by analyzing 81 genes according to their function in bone formation and resorption during bone remodeling. Methods We resequenced all the exons, splice junctions and promoter regions of candidate osteoporosis genes using 24 unrelated Korean individuals. Using the common SNPs from our study and the HapMap database, a statistical analysis of deviation in heterozygosity depicted. Results We identified 942 variants, including 888 SNPs, 43 insertion/deletion polymorphisms, and 11 microsatellite markers. Of the SNPs, 557 (63% had been previously identified and 331 (37% were newly discovered in the Korean population. When compared SNPs in the Korean population with those in HapMap database, 1% (or less of SNPs in the Japanese and Chinese subpopulations and 20% of those in Caucasian and African subpopulations were significantly differentiated from the Hardy-Weinberg expectations. In addition, an analysis of the genetic diversity showed that there were no significant differences among Korean, Han Chinese and Japanese populations, but African and Caucasian populations were significantly differentiated in selected genes. Nevertheless, in the detailed analysis of genetic properties, the LD and Haplotype block patterns among the five sub-populations were substantially different from one another. Conclusion Through the resequencing of 81 osteoporosis candidate genes, 118 unknown SNPs with a minor allele frequency (MAF > 0.05 were discovered in the Korean population. In addition, using the common SNPs between our study and HapMap, an

  15. Contributions by the CAG-repeat Polymorphism of the Androgen Receptor Gene and Circulating Androgens to Muscle Size. Odense Androgen Study - A Population-based Study of 20-29 Year-old Danish Men

    DEFF Research Database (Denmark)

    Nielsen, Torben Leo; Hagen, Claus; Wraae, Kristian;

    2007-01-01

    Context: The number of CAG-repeats within the CAG-repeat polymorphism of the androgen receptor gene is inversely correlated with the transcriptional activity of the androgen receptor. Objective: To study the effect of the CAG-repeat number and circulating androgens on muscle size, to examine the...... CAG-repeat number in relation to body fat mass and circulating androgens, and to identify the best hormonal marker of low muscle size amongst total testosterone, bioavailable testosterone, and dihydrotestosterone. Design, Setting, and Participants: Population-based study of 783 Danish men aged 20......-repeat number correlated inversely with thigh and axial muscle area and with lower and upper extremity lean body mass. Except for upper extremity lean body mass, these findings remained significant in multivariate analyses controlling for circulating androgens, physical activity, smoking, alcohol intake...

  16. Observations of the origin and insertion of the plantar aponeurosis based on anatomic and sonographic analysis%跖腱膜起点的解剖及超声影像学研究

    Institute of Scientific and Technical Information of China (English)

    程迅生; 章仁品; 罗福成; 张勇

    2009-01-01

    Objective To identify the exact origin and insertion of plantar aponeurosis and the anatomic relationship of calcaneal spur to plantar aponeurosis. Methods Fourteen specimen of feet were dissected and radiographed. Three fetus feet were observed histologically. Sonographic evaluation was carried out on 20 normal adults and 52 patients with plantar fasciitis. Results (1) Anatomic observation found that plantar aponeurosis was located under the medial process of caleaneus but not attached to it, and proximally attached to the plantar aspect of calcaneal tuborosity. The insertion (origin) of plantar aponeurosis was not a point but a face. Posteriorly the plantar aponeurosis and fascia of Archlles heel were fused or transmigrated together,entirely covered and attached very coherently to the plantar and posterior aspect of calcaneal tuborosity. (2) Histological observation of heel of fetuses found plantar aponeurosis and fascia of Arehlles heel were eosinophil band-like structure. Both continued at the plantar and posterior aspect of calcaneus and attached closely to bone at this area. There were no significant demarcation between them. (3) Sonographic evaluation:normal plantar aponeurosis showed a thin band-like echo, its orgin attached to entire plantar aspect of calcaneal tuberosity and continued with fascia coming posteriorly from Archlles heel. No distinct boundary existed between these two fascias. When plantar fasciitis occurred, the orgin of plantar aponeurosis thickened significantly,this phenomenon could be detected in wholly plantar aspect of calcaneal tuberrosity. The heel spur didn't located within plantar aponeurosis. Conclusions Plantar aponeurosis orginates from entire plantar aspect of cancaneal tuberosity. Heel spur oeeures in the orgin of the intrinsic musculature, such as flexor digitorum brevis,and doesn't locate within plantar aponeurosis.%目的 研究跖腱膜起点的确切部位及其与跟骨骨刺的关系.方法 对14只足标

  17. Development of Magnesium-Insertion Positive Electrode for Rechargeable Magnesium Batteries

    Institute of Scientific and Technical Information of China (English)

    Huatang YUAN; Lifang JIAO; Jiansheng CAO; Xiusheng LIU; Ming ZHAO; Yongmei WANG

    2004-01-01

    Magnesium-based rechargeable batteries might be an interesting future alternative to lithium-based batteries. It is so far well known that Mg2+ ion insertion into ion-transfer hosts proceeds slowly compared with Li+, so it is necessary to realize fast Mg2+ transport in the host in addition to other requirements as practical cathode materials for magnesium batteries. Positive electrode materials based on inorganic transition-metal oxides, sulfides, and borides are the only ones used up to now to insert magnesium ions. In this paper, the available results of research on materials suitable as possible, for secondary magnesium batteries, are reviewed.

  18. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-01

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. PMID:27016340

  19. TiO2 polymorphs in ‘rocking-chair’ Li-ion batteries

    Directory of Open Access Journals (Sweden)

    Vanchiappan Aravindan

    2015-07-01

    Full Text Available This review describes the overall research activities focused on developing high-performance Li-ion batteries (LIBs fabricated with various TiO2 polymorphs as insertion anodes. Although several polymorphs of TiO2 have been reported, only the anatase, rutile, bronze, and brookite phases have proven promising. The bronze phase's lower insertion potential, high reversibility and high current performance makes it an attractive candidate for constructing high power and high energy density Li-ion power packs. In addition, the bronze phase exhibits superior performance over the conventional, commercialized spinel Li4Ti5O12 anodes when coupled with the olivine phase LiFePO4. This exceptional behavior of the bronze phase opens new avenues for the development of high power LIBs capable of powering zero emission transportation and grid storage.

  20. Correlation Between CASC8, SMAD7 Polymorphisms and the Susceptibility to Colorectal Cancer: An Updated Meta-Analysis Based on GWAS Results.

    Science.gov (United States)

    Yao, Kunhou; Hua, Long; Wei, Lunshou; Meng, Jiming; Hu, Junhong

    2015-11-01

    Genome-wide association studies (GWASs) and a number of case-control studies have suggested that several single nucleotide polymorphisms (SNPs), rs7837328, rs7014346, rs6983267, rs10505477 on CASC8 gene and rs4939827, rs4464148, rs12953717 on SMAD7 gene are significantly correlated with the susceptibility to colorectal cancer (CRC). For the sake of clarifying the association, a meta-analysis was conducted and population heterogeneity was considered in the study.A total of 34 articles including 90 studies (168,471 cases and 163,223 controls) that evaluated the relationship between the CASC8, SMAD7 genes and the risk of CRC under the allelic model were reviewed. Also subgroup analysis was performed by ethnicity (Caucasian, Asian, and African) and all of the analyses were implemented in R 3.2.1 software.Pooled data from the meta-analysis revealed that the A allele of rs7837328, the A allele of rs7014346, the G allele of rs6983267, the A allele of rs10505477, the T allele of rs4939827, the T of rs4464148, and the T of rs12953717 were significantly associated with an increased risk of CRC under the allelic model. Additionally, subgroup analyses of 6 SNPs by ethnicity (rs4464148 excepted) witnessed that the A allele of rs7837328, the G allele of rs6983267, and the T of rs12953717 were notably associated with an increased risk of CRC among Caucasian and Asian. Furthermore, the A allele of rs7014346, the A allele of rs10505477, and the T allele of rs4939827 were significantly related with an elevated risk of CRC only among Caucasian.Our study suggested that for CASC8 gene, SNP of rs7837328 and rs6983267 are risk factors for CRC among both Caucasian and Asian whereas rs7014346 and rs10505477 are risky gene polymorphisms only among Caucasian. For SMAD7 gene, rs4939827 and rs4464148 are risk factors for CRC among Caucasian whereas rs12953717 could elevate the susceptibility to CRC in both Caucasian and Asian. PMID:26579801