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Sample records for based insertion polymorphism

  1. Simultaneous detection of the exon 10 polymorphism and a novel intronic single base insertion polymorphism in the XPD gene using single strand conformation polymorphism.

    Science.gov (United States)

    Kumar, Rajiv; Angelini, Sabrina; Hemminki, Kari

    2003-03-01

    We developed a new method based on the single strand conformation polymorphism (SSCP) technique for the detection of a G23591A (Asp312Asn) polymorphism in exon 10 of the XPD gene. In the process we also identified a novel polymorphism 23623C-ins (IVS10+17C-ins) in intron 10 of the same gene. With this newly developed SSCP-based method of genotyping we could detect both polymorphisms in the same assay and thus consequently determine the haplotype. In order to determine the population frequency of the novel polymorphism and the haplotype frequency, 302 healthy individuals were genotyped. The allelic frequency of the 23623C-ins intronic polymorphism was 0.16, whereas the frequency of the variant allele for the G23591A polymorphism was 0.39. Forty-three individuals (14%) were heterozygous for both polymorphisms but none carried polymorphic variants for both G23591A and 23623C-ins on the same allele. The effect of the novel intronic insertion polymorphism, which is located 16 nt downstream of the 3'-end of exon 10 of the XPD gene and involves a mononucleotide C repeat sequence, on expression remains to be determined.

  2. Polymorphic Alu insertions among Mayan populations.

    Science.gov (United States)

    Herrera, R J; Rojas, D P; Terreros, M C

    2007-01-01

    The Mayan homeland within Mesoamerica spans five countries: Belize, El Salvador, Guatemala, Honduras and Mexico. There are indications that the people we call the Maya migrated from the north to the highlands of Guatemala as early as 4000 B.C. Their existence was village-based and agricultural. The culture of these Preclassic Mayans owes much to the earlier Olmec civilization, which flourished in the southern portion of North America. In this study, four different Mayan groups were examined to assess their genetic variability. Ten polymorphic Alu insertion (PAI) loci were employed to ascertain the genetic affinities among these Mayan groups. North American, African, European and Asian populations were also examined as reference populations. Our results suggest that the Mayan groups examined in this study are not genetically homogeneous.

  3. 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

    2015-07-01

    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.

  4. Templated sequence insertion polymorphisms in the human genome

    Science.gov (United States)

    Onozawa, Masahiro; Aplan, Peter

    2016-11-01

    Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

  5. Voltage-programming-based capillary gel electrophoresis for the fast detection of angiotensin-converting enzyme insertion/deletion polymorphism with high sensitivity.

    Science.gov (United States)

    Woo, Nain; Kim, Su-Kang; Kang, Seong Ho

    2016-08-01

    A voltage-programming-based capillary gel electrophoresis method with a laser-induced fluorescence detector was developed for the fast and highly sensitive detection of DNA molecules related to angiotensin-converting enzyme insertion/deletion polymorphism, which has been reported to influence predisposition to various diseases such as cardiovascular disease, high blood pressure, myocardial infarction, and Alzheimer's disease. Various voltage programs were investigated for fast detection of specific DNA molecules of angiotensin-converting enzyme insertion/deletion polymorphism as a function of migration time and separation efficiency to establish the effect of voltage strength to resolution. Finally, the amplified products of the angiotensin-converting enzyme insertion/deletion polymorphism (190 and 490 bp DNA) were analyzed in 3.2 min without losing resolution under optimum voltage programming conditions, which were at least 75 times faster than conventional slab gel electrophoresis. In addition, the capillary gel electrophoresis method also successfully applied to the analysis of real human blood samples, although no polymorphism genes were detected by slab gel electrophoresis. Consequently, the developed voltage-programming capillary gel electrophoresis method with laser-induced fluorescence detection is an effective, rapid analysis technique for highly sensitive detection of disease-related specific DNA molecules.

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

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    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

  7. New approaches for genotyping of Helicobacter pylori based on amplification of polymorphisms in intergenic DNA regions and at the insertion site of the cag pathogenicity island.

    Science.gov (United States)

    Bereswill, S; Schönenberger, R; Thies, C; Stähler, F; Strobel, S; Pfefferle, P; Wille, L; Kist, M

    2000-11-01

    The population of the gastric pathogen Helicobacter pylori shows a high degree of genetic diversity. It is well established that heterogeneity at the isolate level is caused by nucleotide transitions within genes, differences in the gene order, and by genetic instability of single genes as well as of a large virulence-associated genomic DNA region, the cag pathogenicity island (PAI). Analysis of intergenic regions with specific PCR-assays developed in this study, revealed that DNA polymorphisms in the noncoding DNA localized in front of the genes ribA and vacA and at the insertion site of the cag PAI contribute to the genetic diversity of H. pylori and are useful for differentiation of individual isolates. Thirteen individual genotypes were identified by PCR analysis of these polymorphic loci in 487, 241, and 182 clinical H. pylori isolates. Sequence analysis revealed that genetic variability in front of genes ribA and vacA, and in the intergenic region at the PAI insertion site is caused by insertion and deletions of so-far-unknown DNA sequences as well as by parts of the H. pylori IS elements IS605 and IS606, respectively. The new genotypes identified could be used to differentiate antrum and corpus isolates from the same patients. Their combination with vacA allele subtypes and with the cagA status allowed to differentiate 140 isolates in 51 subtypes. In 36 cases the corresponding genotype patterns were isolate specific. In summary, the results confirm that DNA polymorphisms in intergenic regions contribute to the genetic diversity of H. pylori. Although individual H. pylori genotypes were not associated with peptic ulcer disease, the PCR-based approaches for their detection developed here should be of use for further investigation of genetic diversity in H. pylori and for epidemiological purposes.

  8. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  9. 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...

  10. Insertion polymorphisms of mobile genetic elements in sexual and asexual populations of Daphnia pulex.

    Science.gov (United States)

    Jiang, Xiaoqian; Tang, Haixu; Ye, Zhiqiang; Lynch, Michael

    2017-01-04

    Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified 9 asexual-specific fixed TE insertions, 8 LTR retrotransposons and 1 DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except 1 TE insertion located on a contig from chromosome 7, the other 8 asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all 9 asexual-specific fixed TE insertions can also be detected in some D. pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.

  11. Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex

    Science.gov (United States)

    Ye, Zhiqiang; Lynch, Michael

    2017-01-01

    Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals. PMID:28057730

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

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    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.

  13. 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.

  14. Insertion/deletion polymorphisms in the ΔNp63 promoter are a risk factor for bladder exstrophy epispadias complex.

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    Simon Wilkins

    Full Text Available Bladder exstrophy epispadias complex (BEEC is a severe congenital anomaly; however, the genetic and molecular mechanisms underlying the formation of BEEC remain unclear. TP63, a member of TP53 tumor suppressor gene family, is expressed in bladder urothelium and skin over the external genitalia during mammalian development. It plays a role in bladder development. We have previously shown that p63(-/- mouse embryos developed a bladder exstrophy phenotype identical to human BEEC. We hypothesised that TP63 is involved in human BEEC pathogenesis. RNA was extracted from BEEC foreskin specimens and, as in mice, ΔNp63 was the predominant p63 isoform. ΔNp63 expression in the foreskin and bladder epithelium of BEEC patients was reduced. DNA was sequenced from 163 BEEC patients and 285 ethnicity-matched controls. No exon mutations were detected. Sequencing of the ΔNp63 promoter showed 7 single nucleotide polymorphisms and 4 insertion/deletion (indel polymorphisms. Indel polymorphisms were associated with an increased risk of BEEC. Significantly the sites of indel polymorphisms differed between Caucasian and non-Caucasian populations. A 12-base-pair deletion was associated with an increased risk with only Caucasian patients (p = 0.0052 Odds Ratio (OR = 18.33, whereas a 4-base-pair insertion was only associated with non-Caucasian patients (p = 0.0259 OR = 4.583. We found a consistent and statistically significant reduction in transcriptional efficiencies of the promoter sequences containing indel polymorphisms in luciferase assays. These findings suggest that indel polymorphisms of the ΔNp63 promoter lead to a reduction in p63 expression, which could lead to BEEC.

  15. The PML gene is linked to a megabase-scale insertion/deletion restriction fragment length polymorphism

    Energy Technology Data Exchange (ETDEWEB)

    Goy, A.; Xiao, Y.H.; Passalaris, T. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others

    1995-03-20

    The PML gene located on chromosome band 15q22 is involved with the RAR{alpha} locus (17q21) in a balanced reciprocal translocation uniquely observed in acute promyelocytic leukemia. Physical mapping studies by pulsed-field gel electrophoresis revealed that the PML gene is flanked by two CpG islands that are separated by a variable distance in normal individuals. Several lines of evidence demonstrate that this is the consequence of a large insertion/deletion polymorphism linked to the PML locus: (1) overlapping fragments obtained with a variety of rare-cutting restriction enzymes demonstrated the same variability in distance between the flanking CpG islands; (2) mapping with restriction enzymes insensitive to CpG methylation confirmed that the findings were not a consequence of variable methylation of CpG dinucleotides; (3) the polymorphism followed a Mendelian inheritance pattern. This polymorphism is localized 3{prime} to the PML locus. There are five common alleles, described on the basis of BssHII fragments, ranging from 220 to 350 kb with increments of approximately 30 kb between alleles. Both heterozygous (61%) and homozygous (391%) patterns were observed in normal individuals. Mega-base-scale insertion/deletion restriction fragment length polymorphisms are very rare and have been described initially in the context of multigene families. Such structures have been also reported as likely regions of genetic instability. High-resolution restriction mapping of this particular structure linked to the PML locus is underway. 47 refs., 4 figs., 1 tab.

  16. 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.

  17. Angiotensin Converting Enzyme Gene Insertion/Deletion Polymorphism and Vesicoureteral Reflux in Children

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    Ai, Jin-Wei; Liu, Yu; Zeng, Xian-Tao; Lei, Qing; Zou, Li; Pei, Bin

    2015-01-01

    Abstract Vesicoureteral reflux (VUR) is a common and serious urinary disease in children. It usually causes renal scar, urinary tract infection, and chronic renal failure. Previous studies showed the angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism might be associated with VUR; however, the conclusions were inconsistent. Therefore we used the meta-analytic approach to clarify the effect of ACE I/D polymorphism on VUR risk. We systematically searched the PubMed, CNKI, and EMBASE databases to identify all the potentially related studies published up to February 4, 2015. Two reviewers independently selected studies and extracted data. The strength of the association was assessed using odd ratio (OR) with its 95% confidence interval (CI) based on fixed or random effects model. The STATA 12.0 software was used for data analysis. A total of 14 case–control studies involving 1197 VUR patients and 1320 healthy controls met the eligibility criteria. Results of meta-analysis showed significant association between ACE I/D polymorphism and VUR risk (D vs. I: OR = 1.28, 95% CI = 1.06–1.54, P = 0.01; DD vs. II: OR = 1.44, 95% CI = 1.12–1.85, P = 0.01; DD vs. DI + II: OR = 1.49, 95% CI = 1.23–1.79, P < 0.01; DD + DI vs. II: OR = 1.20, 95% CI = 0.84–1.72, P = 0.31). Subgroup analyses revealed varied results. In Turkish people, results of all the genetic models other than DI vs. II showed statistical significance; in Caucasians, DD vs. DI + II showed statistical significance; and in Asians, DI versus II showed statistical significance. Our meta-analysis indicated that the ACE I/D polymorphism might be associated with increased risk of VUR in children. However, due to the limitations, we suggest conducting additional studies with larger sample size and adjustment for various risk factors, in the future for further clarification. PMID:26717402

  18. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease.

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    Moyes, David; Griffiths, David J; Venables, Patrick J

    2007-07-01

    Human endogenous retroviruses (HERVs) result from ancestral infection by infectious viruses over millions of years of primate evolution. Some are transcriptionally active, express proteins and therefore have the potential to cause disease. Here we review the controversial attempts to link them with cancer and autoimmunity. The main difficulty is that most HERVs investigated to date are present at the same locus in 100% of the population. However, a new class of insertionally polymorphic HERV-K family members, present in a minority of individuals, has recently been described. We propose that insertionally polymorphic HERVs could be novel genetic risk factors and hence provide a new lease of life for research into HERVs and disease.

  19. Dopamine D2 receptor gene -141C Insertion/Deletion polymorphism in Turkish schizophrenic patients.

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    Kurt, Hulyam; Dikmen, Miris; Basaran, Ayşe; Yenilmez, Cinar; Ozdemir, Figen; Degirmenci, Irfan; Gunes, Hasan Veysi; Kucuk, Meral Urhan; Mutlu, Fezan

    2011-02-01

    Schizophrenia is a chronic and neuropsychiatric disease that affects about 0.5-1% of the world's population. An increase in dopamine and dopamine D2 receptor (DRD2) gene products has been well described in schizophrenic patients. Several groups have studied the relationship between dopaminergic hyperactivity and cellular communications have obtained discordant results. Studies searching for the relationship between the schizophrenia and DRD2 gene have gained more interest. Our objective was to determine the relationships among schizophrenic symptoms in schizophrenia subtypes and severity of symptoms in terms of DRD2 gene -141C Insertion/Deletion [Ins/Del; I/D] polymorphism by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) assay method. Genomic DNA was prepared from peripheral blood by using salt extraction method. After amplification of genomic DNA, PCR products were digested with BstNI restriction enzyme for the detection of DRD2 gene -141C Ins/Del polymorphism in 73 schizophrenic patients and 60 healthy control subjects. The allelic frequencies of the DRD2 gene -141C Ins/Del polymorphism in case and control groups were 79.5 and 77.5% for I allele; 20.5 and 22.5% for D allele respectively. There was no significant difference in frequencies of genotypes and alleles between the two groups. In schizophrenic and control subjects, there were no significant relationship in severity of the disease and schizophrenia types among the -141C Ins/Del genotypes and alleles.

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

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    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.

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

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    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

  2. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

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    Christine Dubreuil-Tranchant

    2011-01-01

    Full Text Available Miniature Inverted-repeat Transposable Elements (MITEs are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

  3. 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...

  4. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

    Science.gov (United States)

    Watkins, W Scott; Rogers, Alan R; Ostler, Christopher T; Wooding, Steve; Bamshad, Michael J; Brassington, Anna-Marie E; Carroll, Marion L; Nguyen, Son V; Walker, Jerilyn A; Prasad, B V Ravi; Reddy, P Govinda; Das, Pradipta K; Batzer, Mark A; Jorde, Lynn B

    2003-07-01

    We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

  5. Genetic change in the polynesian population of Easter Island: evidence from Alu insertion polymorphisms.

    Science.gov (United States)

    González-Pérez, E; Esteban, E; Via, M; García-Moro, C; Hernández, M; Moral, P

    2006-11-01

    The origin of Pacific islanders is still an open issue in human population genetics. To address this topic we analyzed a set of 18 Alu insertion polymorphisms in a total of 176 chromosomes from native Easter Island inhabitants (Rapanui). Available genealogical records allowed us to subdivide the total island sample into two groups, representative of the native population living in the island around 1900, and another formed by individuals with some ancestors of non-Rapanui origin. Significant genetic differentiation was found between these groups, allowing us to make some biodemographic and historical inferences about the origin and evolution of this geographically isolated island population. Our data are consistent with equivalent and recent contributions from Amerindian and European migrants to the 1900s Rapanui population, with an accelerated increase in the European gene flow during the 20(th) century, especially since the 1960s. Comparative analysis of our results with other available Alu variation data on neighbouring populations supports the "Voyaging Corridor" model of Polynesian human settlement, which indicates that pre-Polynesians are mainly derived from Southeast Asian and Wallacean populations rather than from Taiwan or the Philippines. This study underlines the importance of sampling and taking into account historical information in genetic studies to unravel the recent evolution of human populations.

  6. Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms.

    Science.gov (United States)

    Pimenta, J R; Pena, S D J

    2010-03-30

    We developed a panel of 40 multiplexed short insertion-deletion (indel) polymorphic loci with widespread chromosomal locations and allele frequencies close to 0.50 in the European population. We genotyped these markers in 360 unrelated self-classified White Brazilians and 50 mother-child-probable father trios with proven paternity. The average heterozygosity (gene diversity) per locus was 0.48, and the combined probability of identity (matching probability) for the 40-locus set was 3.48 x 10(-17). The combined power of exclusion of the indel panel was 0.9997. The efficiency of the 40 indel set in the exclusion of falsely accused individuals in paternity casework was equivalent to the CODIS set of 13 microsatellites. The geometric mean of the paternity indices of the 50 mother-child-probable father trios was 17,607. This panel of 40 short indels was found to have excellent performance. Thus, especially because of its simplicity and low cost, and the fact that it is composed of genomic markers that have very low mutation rates, it represents a useful new tool for human paternity testing.

  7. Alu insertion polymorphisms in the Balkans and the origins of the Aromuns.

    Science.gov (United States)

    Comas, D; Schmid, H; Braeuer, S; Flaiz, C; Busquets, A; Calafell, F; Bertranpetit, J; Scheil, H-G; Huckenbeck, W; Efremovska, L; Schmidt, H

    2004-03-01

    We have analysed 11 human-specific Alu insertion polymorphisms in the Balkans to elucidate the origins of the Aromuns, a linguistic isolate inhabiting scattered areas in the Balkan Peninsula. Four Aromun samples (two from the Republic of Macedonia, one from Albania, and one from Romania) and five neighbouring populations (Macedonians, Albanians, Romanians, Greeks, and Turks) were analysed by means of genetic distances, principal components and analyses of the molecular variance (AMOVA). Three hypotheses were tested: Aromuns are Romanophonic Greeks; the result of a Romanian southward migration; or local descendants of the Thracians. The analyses show that the Aromuns do not constitute a homogeneous group separated from the rest of the Balkan populations. Grouping by language or geography does not explain the genetic differences observed in the region, suggesting a lack of genetic structure in the area. Aromuns do not seem to be particularly related to Greeks, Romanians, or to other Romance speakers. The Aromuns might have their origin to the south of the Danube river, with extensive gene flow with the neighbouring populations. The present results suggest a common ancestry of all Balkan populations, including Aromuns, with a lack of correlation between genetic differentiation and language or ethnicity, stressing that no major migration barriers have existed in the making of the complex Balkan human puzzle.

  8. Insertion/deletion polymorphisms in the promoter region of BRM contribute to risk of hepatocellular carcinoma in Chinese populations.

    Directory of Open Access Journals (Sweden)

    Xueren Gao

    Full Text Available BACKGROUND: BRM (Brahma homologue is well known for its critical role in tumor suppression and cancer development. Genetic variations in the promoter region of BRM have been suggested to be associated with loss of BRM expression and lung cancer risk. To the authors' knowledge, no study on the role of BRM genetic polymorphisms in hepatocellular carcinoma (HCC risk has been performed. METHODOLOGY/PRINCIPAL FINDINGS: In two independent case-control studies containing 796 HCC cases and 806 cancer-free individuals, we genotyped two putative functional insertion/deletion (indel polymorphisms [BRM-1321 (rs3832613 and BRM-741 (rs34480940] within promoter region of BRM in Chinese populations using a PCR-based method. Real-time RT-PCR analysis was used to explore the genotype-phenotype correlation between these polymorphisms and BRM expression in both tissue samples and HCC cell lines. Logistic regression analysis showed that compared to BRM-1321del/del genotype, the ins/del and ins/ins variant genotypes had an increased HCC risk [adjusted odds ratio (OR = 1.47, 95% confidence interval (CI = 1.19-1.82; adjusted OR = 2.55, 95% CI = 1.75-3.72, respectively]. No significant association between BRM-741 and HCC incidence was observed. However, stratification analysis revealed a significant association between ins/ins genotype of BRM-741 and increased HCC susceptibility in smokers (adjusted OR = 2.07, 95% CI = 1.33-3.22. Quantitative PCR analyses demonstrated that the genotypes of BRM-1321 and the corresponding haplotypes were significantly correlated with BRM expression in vivo. Compared with ins/ins genotype, subjects carrying ins/del and del/del genotype had 2.30 and 4.99 fold higher BRM expression in HCC tissue samples, respectively. Similar trends were observed in western blot analysis at protein level. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that BRM promoter polymorphism (BRM-1321 could regulate BRM expression and may serve as a potential marker

  9. Association of the Alu insertion polymorphism in the progesterone receptor gene with breast cancer in a Mexican population

    Science.gov (United States)

    Figuera, Luis E.; Flores-Ramos, Liliana Gómez; Puebla-Pérez, Ana María; Zúñiga-González, Guillermo Moisés

    2015-01-01

    Introduction The progesterone receptor (PR) gene plays an important role in reproduction-related events. Data on polymorphisms in the PR gene have revealed associations with cancer, particularly for the Alu insertion polymorphism, which has been suggested to affect progesterone receptor function and contribute to tumor promotion in the mammary gland. Material and methods We examined the role of the Alu insertion polymorphism in the PR gene by comparing the genotypes of 209 healthy Mexican women with those of 481 Mexican women with breast cancer (BC). Results The genotype frequencies observed in the controls and BC patients were 0% and 4% for T2/T2 (Alu insertion), 16% and 21% for T1/T2, and 84% and 75% for T1/T1 (Alu deletion), respectively. The obtained odds ratio (OR) was 1.7, with a 95% confidence interval (95% CI) of 1.1–2.6, p = 0.009, for the T1/T2–T2/T2 genotypes. The association was also evident when the distributions of the T1/T2–T2/T2 genotypes in patients in the following categories were compared: obesity grade II (OR = 1.81, 95% CI: 1.03–3.18, p = 0.039) and the chemotherapy response (OR = 1.91, 95% CI: 1.27–3.067, p = 0.002). Conclusions The T1/T2–T2/T2 genotypes of the Alu insertion polymorphism in the PR gene are associated with BC susceptibility in the analyzed Mexican population. PMID:26170848

  10. 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.

  11. Typing and clustering of Yersinia pseudotuberculosis isolates by restriction fragment length polymorphism analysis using insertion sequences.

    Science.gov (United States)

    Voskresenskaya, E; Savin, C; Leclercq, A; Tseneva, G; Carniel, E

    2014-06-01

    Yersinia pseudotuberculosis is an enteropathogen that has an animal reservoir and causes human infections, mostly in temperate and cold countries. Most of the methods previously used to subdivide Y. pseudotuberculosis were performed on small numbers of isolates from a specific geographical area. One aim of this study was to evaluate the typing efficiency of restriction fragment length polymorphism of insertion sequence hybridization patterns (IS-RFLP) compared to other typing methods, such as serotyping, ribotyping, and multilocus sequence typing (MLST), on the same set of 80 strains of Y. pseudotuberculosis of global origin. We found that IS100 was not adequate for IS-RFLP but that both IS285 and IS1541 efficiently subtyped Y. pseudotuberculosis. The discriminatory index (DI) of IS1541-RFLP (0.980) was superior to those of IS285-RFLP (0.939), ribotyping (0.944), MLST (0.861), and serotyping (0.857). The combination of the two IS (2IS-RFLP) further increased the DI to 0.998. Thus, IS-RFLP is a powerful tool for the molecular typing of Y. pseudotuberculosis and has the advantage of exhibiting well-resolved banding patterns that allow for a reliable comparison of strains of worldwide origin. The other aim of this study was to assess the clustering power of IS-RFLP. We found that 2IS-RFLP had a remarkable capacity to group strains with similar genotypic and phenotypic markers, thus identifying robust populations within Y. pseudotuberculosis. Our study thus demonstrates that 2IS- and even IS1541-RFLP alone might be valuable tools for the molecular typing of global isolates of Y. pseudotuberculosis and for the analysis of the population structure of this species.

  12. Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits.

    Science.gov (United States)

    Comas, D; Calafell, F; Benchemsi, N; Helal, A; Lefranc, G; Stoneking, M; Batzer, M A; Bertranpetit, J; Sajantila, A

    2000-10-01

    An analysis of 11 I Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans, Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting a strong genetic barrier matching the geographical Mediterranean Sea barrier. The restriction to gene flow may be attributed to the navigational hazards across the Straits, but cultural factors must also have played a role. Some degree of gene flow from sub-Saharan Africa can be detected in the southern part of North Africa and in Saharawi and Southeastern Moroccans, as a result of a continuous gene flow across the Sahara desert that has created a south-north cline of sub-Saharan Africa influence in North Africa. Iberian samples show a substantial degree of homogeneity and fall within the cluster of European-based genetic diversity.

  13. Association between DBH 19 bp insertion/deletion polymorphism and cognition in first-episode schizophrenic patients.

    Science.gov (United States)

    Hui, Li; Zhang, Xuan; Yu, Ya Qin; Han, Mei; Huang, Xu Feng; Chen, Da Chun; Wang, Zhi Ren; Du, Wei Li; Kou, Chang Gui; Yu, Qiong; Kosten, Thomas R; Zhang, Xiang Yang

    2013-07-01

    Many genes associated with dopamine (DA) and norepinephrine (NE) systems influence cognitive deficits of schizophrenia patients, but one key enzyme is dopamine beta-hydroxylase (DBH), which converts DA to NE and whose activity and levels are under strong genetic control. This study examines the association of the 19 bp insertion/deletion (Ins/Del) polymorphism in the 5' flank of the DBH gene with cognitive deficits in first-episode schizophrenic patients (FEP). We assessed the cognitive function in 195 FEP and 304 healthy controls using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). The 19 bp Ins/Del polymorphism of DBH gene was genotyped. Our results showed that the allelic and genotypic frequencies of the 19 bp Ins/Del polymorphism significantly differed between FEP and healthy controls (both p 0.05). Immediate memory abilities significantly differed by genotype (p<0.05) but not genotype×diagnosis. Immediate memory score was lower in FEP with DBH5'-Del/Del genotype (61.3 ± 17.2) than those with DBH5'-Ins/Ins genotype (68.6 ± 16.2; p < 0.05). The 19 bp Del allele was associated with poorer immediate memory performance than the Ins allele in FEP (p < 0.05). However, healthy controls did not show any differences in cognitive function indices between the Ins and Del for either the allele or genotype of the 19 bp Ins/Del polymorphism. Our findings suggest that the DBH5'-Ins/Del polymorphism may play a role in susceptibility to FEP. The DBH5'-Ins/Del polymorphism may also influence immediate memory in FEP. Moreover, FEP had poorer cognitive function than healthy controls in all examined cognitive domains except for the visuospatial/constructional index.

  14. ACE Insertion/Deletion Polymorphism and Diabetic Nephropathy: Clinical Implications of Genetic Information

    Directory of Open Access Journals (Sweden)

    Sung-Kyu Ha

    2014-01-01

    Full Text Available Approximately 20–40% of diabetic patients develop nephropathy which is the leading cause of ESRD in developed countries. The ACE I/D polymorphism is thought to be a marker for functional polymorphism which regulates circulating and tissue ACE activity. While the initial study found a protective effect of the II genotype on the development of nephropathy in IDDM patients, subsequent studies have addressed the role of ACE I/D polymorphism in the development and progression of diabetic nephropathy. RAAS blockers are the first line drugs for the treatment hypertension associated with diabetes and have been widely used in everyday clinical practice for the purpose of reducing proteinuria in patients with various renal diseases. However, the antiproteinuric effect of RAAS blockers is variable and the percentage of reducing proteinuria is in the range of 20–80%. The antiproteinuric effect of RAAS blockers may be related to a number of factors: the type or the dose of RAAS blockers, the duration of therapy, the level of sodium intake, and the type of patient’s ACE I/D genotype. Besides the nongenetic factors, drug responses, can be influenced by ACE gene polymorphism. In this review, we discuss the relationship between ACE I/D polymorphism and diabetic nephropathy and therapeutic response of RAAS blockers.

  15. Association of AluYb8 insertion/deletion polymorphism in the MUTYH gene with mtDNA maintain in the type 2 diabetes mellitus patients.

    Science.gov (United States)

    Guo, Wenwen; Zheng, Bixia; Guo, Dong; Cai, Zhenming; Wang, Yaping

    2015-07-05

    A common AluYb8-element insertion/deletion polymorphism of the MUTYH gene (AluYb8MUTYH) is a novel genetic risk factor for type 2 diabetes mellitus (T2DM). In the present study, mtDNA sequencing analysis indicated that the mtDNA sequence heteroplasmy was not associated with AluYb8MUTYH polymorphism. To better understand the genetic risk for T2DM, we investigated the association of this polymorphism with mtDNA content, mtDNA breakage and mtDNA transcription in the leukocytes of T2DM patients. The mtDNA content and unbroken mtDNA were significantly increased in the mutant patients than in the wild-type patients (P <0.05, respectively). However, no association between mtDNA transcription and AluYb8MUTYH variant was observed. The results suggested that the AluYb8MUTYH variant was associated with an altered mtDNA maintain in T2DM patients. The high level of mtDNA content observed in the mutant patients may have resulted from inefficient base excision repair of mitochondrial MUTYH and a compensatory mechanism that is triggered by elevated oxidative stress.

  16. Angiotensin-Converting Enzyme Gene Insertion/Deletion Polymorphism and Small Vessel Cerebral Stroke in Indian Population

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    Puttachandra Prabhakar

    2014-01-01

    Full Text Available Background. Hypertension is an established risk factor for small-vessel cerebral stroke and the renin-angiotensin system plays an important role in the maintenance of blood pressure. We aimed at evaluating the contribution of the angiotensin-converting enzyme (ACE gene insertion/deletion (I/D polymorphism to the risk of small-vessel stroke in south Indian population. Materials and Methods. We investigated 128 patients diagnosed with small-vessel stroke and 236 age, and gender-matched healthy controls. ACE I/D polymorphism was detected by polymerase chain reaction. Results. Hypertension was significantly more prevalent in the patient group and was associated with 6-fold increase in risk for stroke. ACE genotypes were in Hardy-Weinberg equilibrium in both patients and controls. Prevalence of DD, ID, and II genotypes in cases (34.4%, 43.7%, and 28% did not differ significantly from controls (31.8%, 43.2%, and 25%. The polymorphism was not associated with small-vessel stroke (OR: 1.34; 95% CI: 0.52–1.55. However, diastolic blood pressure was associated with the ACE I/D genotypes in the patients. (DD; 90.2±14.2> ID; 86.2±11.9> II; 82.3±7.8 mm Hg,  P=0.047. Conclusion. Our study showed that hypertension, but not ACE I/D polymorphism, increased the risk of small-vessel stroke.

  17. Association of Angiotensin Converting Enzyme Insertion-Deletion Polymorphism with Hypertension in Emiratis with Type 2 Diabetes Mellitus and Its Interaction with Obesity Status

    Directory of Open Access Journals (Sweden)

    Habiba Alsafar

    2015-01-01

    Full Text Available The association of Angiotensin Converting Enzyme (ACE insertion-deletion (I/D polymorphism with Type 2 Diabetes Mellitus (T2DM and hypertension has been extensively studied throughout various ethnic populations but largely with inconsistent findings. We investigated these associations in Emirati population and their interaction with obesity status. Saliva samples were collected from a total of 564 Emiratis (277 T2DM and 297 healthy. DNA was extracted and the samples were genotyped for ACE I/D polymorphism by a PCR based method followed by gel electrophoresis. Upon evaluation of the ACE I/D polymorphism amongst all T2DM, hypertensive patients, and respective controls regardless of obesity status, ACE DD genotype was not found to be associated with either T2DM [odds ratio (OR = 1.34, p=0.086] or hypertension [odd ratio (OR = 1.02, p=0.93]. When the genetic variants amongst the nonobese and obese population were analyzed separately, the risk genotype ACE DD conferred significantly increased risk of hypertension in nonobese population [odds ratio (OR = 1.80, p=0.02] but was found to be protective against the hypertension in the obese group ((OR = 0.54, p=0.01. However, there was no effect of obesity status on the association of ACE genotypes with T2DM. The risk of hypertension associated with ACE DD is modulated by obesity status and hence future genetic association studies should take obesity into account for the interpretation of data. We also confirmed that ACE I/D polymorphism is not associated with T2DM risk in Emirati population.

  18. Association of Angiotensin Converting Enzyme Insertion-Deletion Polymorphism with Hypertension in Emiratis with Type 2 Diabetes Mellitus and Its Interaction with Obesity Status.

    Science.gov (United States)

    Alsafar, Habiba; Hassoun, Ahmed; Almazrouei, Shaikha; Kamal, Wala; Almaini, Mustafa; Odama, Unini; Rais, Naushad

    2015-01-01

    The association of Angiotensin Converting Enzyme (ACE) insertion-deletion (I/D) polymorphism with Type 2 Diabetes Mellitus (T2DM) and hypertension has been extensively studied throughout various ethnic populations but largely with inconsistent findings. We investigated these associations in Emirati population and their interaction with obesity status. Saliva samples were collected from a total of 564 Emiratis (277 T2DM and 297 healthy). DNA was extracted and the samples were genotyped for ACE I/D polymorphism by a PCR based method followed by gel electrophoresis. Upon evaluation of the ACE I/D polymorphism amongst all T2DM, hypertensive patients, and respective controls regardless of obesity status, ACE DD genotype was not found to be associated with either T2DM [odds ratio (OR) = 1.34, p = 0.086] or hypertension [odd ratio (OR) = 1.02, p = 0.93]. When the genetic variants amongst the nonobese and obese population were analyzed separately, the risk genotype ACE DD conferred significantly increased risk of hypertension in nonobese population [odds ratio (OR) = 1.80, p = 0.02] but was found to be protective against the hypertension in the obese group ((OR) = 0.54, p = 0.01). However, there was no effect of obesity status on the association of ACE genotypes with T2DM. The risk of hypertension associated with ACE DD is modulated by obesity status and hence future genetic association studies should take obesity into account for the interpretation of data. We also confirmed that ACE I/D polymorphism is not associated with T2DM risk in Emirati population.

  19. 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

    , given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X......-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...

  20. Association between an insertion/deletion polymorphism in IL-1A gene and cancer risk: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Ma L

    2015-12-01

    Full Text Available Ling Ma,1 Ning Zhou21Department of Stomatology, 2Department of Anesthesiology, No 454 Hospital, PLA, Nanjing, Jiangsu, People’s Republic of ChinaPurpose: Previous studies have reported the association of an insertion/deletion (Ins/Del polymorphism (rs3783553 in the 3' untranslated region of interleukin-1A (IL-1A with the risk of cancer, such as oral squamous cell carcinoma, nasopharyngeal carcinoma, and cervical carcinoma. However, the results are still inconsistent. The present meta-analysis aimed to clarify the association of IL-1A rs3783553 polymorphism with cancer risk.Methods: All eligible studies were selected from PubMed, Web of Science, and Chinese National Knowledge Infrastructure up to September 2, 2015. Summary odds ratios (ORs and 95% confidence intervals (CIs were used to evaluate cancer risk.Results: A total of ten case–control studies with 4,514 cases and 6,689 controls were included this meta-analysis. We found that IL-1A rs3783553 polymorphism was significantly associated with cancer risk (Ins/Ins + Ins/Del vs Del/Del: OR =0.79, 95% CI =0.67–0.92; Ins/Ins vs Del/Del: OR =0.61, 95% CI =0.47–0.79; Ins/Ins vs Ins/Del + Del/Del: OR =0.67, 95% CI =0.55–0.83; Ins vs Del: OR =0.81, 95% CI =0.72–0.92. In the stratified analyses, significant effects were found among Asian populations (Ins/Ins + Ins/Del vs Del/Del: OR =0.81, 95% CI =0.69–0.95 and cervical carcinoma (Ins/Ins vs Del/Del: OR =0.51, 95% CI =0.34–0.76; Ins/Ins vs Ins/Del + Del/Del: OR =0.52, 95% CI =0.35–0.78.Conclusion: Our meta-analysis suggests that the IL-1A rs3783553 polymorphism contributes to susceptibility to cancer. However, well-designed studies with larger sample sizes are required to verify the results.Keywords: IL-1A, polymorphism, cancer, meta-analysis

  1. Cost-effectiveness of ACE inhibitor therapy to prevent dialysis in nondiabetic nephropathy : Influence of the ACE insertion/deletion polymorphism

    NARCIS (Netherlands)

    Vegter, Stefan; Perna, A.; Hiddema, W.; Ruggenenti, P.; Remuzzi, G.; Navis, Ger Jan; Postma, Maarten

    2009-01-01

    Introduction End-stage renal disease is associated with high health-care costs and low quality of life compared with chronic kidney disease. The renoprotective effectiveness of angiotensin-converting enzyme inhibitors (ACEi) is largely determined by the ACE insertion/deletion (I/D) polymorphism. We

  2. 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-

  3. A fast and easy real-time PCR genotyping method for the HLA-G 14-bp insertion/deletion polymorphism in the 3' untranslated region

    DEFF Research Database (Denmark)

    Djurisic, S; Sørensen, A E; Hviid, T V F

    2012-01-01

    and reliable method to screen for the HLA-G 14-bp insertion/deletion polymorphism using an optimized real-time polymerase chain reaction protocol. The genotyping assay has been validated by comparison with conventional methods. As results can be obtained within a few hours, the assay will have a potential...

  4. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.

    Science.gov (United States)

    Naville, Magali; Chalopin, Domitille; Volff, Jean-Nicolas

    2014-01-01

    Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

  5. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.

    Directory of Open Access Journals (Sweden)

    Magali Naville

    Full Text Available Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2% of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

  6. Bovine spongiform encephalopathy associated insertion/deletion polymorphisms of the prion protein gene in the four beef cattle breeds from North China.

    Science.gov (United States)

    Zhu, Xiang-Yuan; Feng, Fu-Ying; Xue, Su-Yuan; Hou, Ting; Liu, Hui-Rong

    2011-10-01

    Two insertion/deletion (indel) polymorphisms of the prion protein gene (PRNP), a 23-bp indel in the putative promoter region and a 12-bp indel within intron I, are associated with the susceptibility to bovine spongiform encephalopathy (BSE) in cattle. In the present study, the polymorphism frequencies of the two indels in four main beef cattle breeds (Hereford, Simmental, Black Angus, and Mongolian) from North China were studied. The results showed that the frequencies of deletion genotypes and alleles of 23- and 12-bp indels were lower, whereas the frequencies of insertion genotypes and alleles of the two indels were higher in Mongolian cattle than in the other three cattle breeds. In Mongolian cattle, the 23-bp insertion / 12-bp insertion was the major haplotype, whereas in Hereford, Simmental, and Black Angus cattle, the 23-bp deletion / 12-bp deletion was the major haplotype. These results demonstrated that Mongolian cattle could be more resistant to BSE, compared with the other three cattle breeds, because of its relatively low frequencies of deletion genotypes and alleles of 23- and 12-bp indel polymorphisms. Thus, this race could be important for selective breeding to improve resistance against BSE in this area.

  7. CTG repeats distribution and Alu insertion polymorphism at myotonic dystrophy (DM) gene in Amhara and Oromo populations of Ethiopia.

    Science.gov (United States)

    Gennarelli, M; Pavoni, M; Cruciani, F; De Stefano, G; Dallapiccola, B; Novelli, G

    1999-01-01

    Myotonic dystrophy (DM) is a dominantly inherited neuromuscular disease, highly variable and multisystemic, which is caused by the expansion of a CTG repeat located in the 3' untranslated region of the DMPK gene. Normal alleles show a copy number of 5-37 repeats on normal chromosomes, amplified to 50-3000 copies on DM chromosomes. The trinucleotide repeat shows a trimodal allele distribution in the majority of the examined population. The first class includes alleles carrying (CTG)5, the second class, alleles in the range 7-18 repeats, and the third class, alleles (CTG) > or =19. The frequency of this third class is directly related to the prevalence of DM in different populations, suggesting that normal large-sized alleles predispose toward DM. We studied CTG repeat allele distribution and Alu insertion and/or deletion polymorphism at the myotonic dystrophy locus in two major Ethiopian populations, the Amhara and Oromo. CTG allele distribution and haplotype analysis on a total of 224 normal chromosomes showed significant differences between the two ethnic groups. These differences have a bearing on the out-of-Africa hypothesis for the origin of the DM mutation. In addition, (CTG) > or =19 were exclusively detected in the Amhara population, confirming the predisposing role of these alleles compared with the DM expansion-mutation.

  8. Forensic evaluation and population genetic study of 30 insertion/deletion polymorphisms in a Chinese Yi group.

    Science.gov (United States)

    Zhang, Yu-Dang; Shen, Chun-Mei; Jin, Rui; Li, Ya-Ni; Wang, Bo; Ma, Li-Xia; Meng, Hao-Tian; Yan, Jiang-Wei; Dan Wang, Hong-; Yang, Ze-Long; Zhu, Bo-Feng

    2015-05-01

    Insertion/deletion polymorphisms have become a research hot spot in forensic science due to their tremendous potential in recent years. In the present study, we investigated 30 indel loci in a Chinese Yi ethnic group. The allele frequencies of the short allele of the 30 indel loci were in the range of 0.1025-0.9221. The power of discrimination values were observed ranging from to 0.2630 (HLD111 locus) to 0.6607 (HLD70 locus) and probability of exclusion values ranged from 0.0189 (HLD111 locus) to 0.2343 (HLD56 locus). The combined power of discrimination and power of exclusion for 30 loci in the studied Yi group were 0.99999999995713 and 0.97746, respectively, which showed tremendous potential for forensic personal identification in the Yi group. Moreover, the DA distances, phylogenetic tree, principal component analysis, and cluster analysis showed the Yi group had close genetic relationships with the Tibetan, South Korean, Chinese Han, and She groups.

  9. Genotyping of PCR-based polymorphisms and linkage-disequilibrium analysis at the NF1 locus

    Energy Technology Data Exchange (ETDEWEB)

    Purandare, S.M.; Viskochil, D.H.; Cawthon, R. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

    1996-07-01

    Six polymorphism across the NF1 gene have been adapted for genotyping through application of PCR-based assays. Three exon-based polymorphisms - at positions 702, 2034, and 10647 in the NF1 cDNA - were genotyped by mutagenically separated PCR (MS-PCR). A fourth polymorphism, DV1.9, is an L1 insertion element in intron 30, and the other two polymorphisms, GXAlu and EVI-20, are short tandem repeats in intron 27b. All the polymorphisms were evaluated in a cohort of 110 CEPH individuals who previously had been analyzed by use of eight RFLPs at the NF1 locus. Pairwise linkage-disequilibrium analyses with the six PCR-based polymorphisms and their flanking markers demonstrated disequilibrium between all tested loci. Genotypes of the four diallelic polymorphisms (702, 2034, 10647, and DV1.9) were also evaluated in cohorts from the CEPH, African, and Japanese populations. The CEPH and Japanese cohorts showed similar heterozygosities and linkage-disequilibrium coefficients. The African cohort showed a higher degree of heterozygosity and lower linkage-disequilibrium values, compared with the CEPH and Japanese cohorts. 36 refs., 2 figs., 3 tabs.

  10. Identification of Alternative Variants and Insertion of the Novel Polymorphic AluYl17 in TSEN54 Gene during Primate Evolution

    Directory of Open Access Journals (Sweden)

    Ja-Rang Lee

    2016-01-01

    Full Text Available TSEN54 encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified an AluSx-derived alternative transcript in TSEN54 of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR amplification and TSEN54 sequence analysis of primate and human samples identified five novel alternative transcripts, including the AluSx exonized transcript. Additionally, we performed comparative expression analysis via RT-qPCR in various cynomolgus, rhesus monkey, and human tissues. RT-qPCR amplification revealed differential expression patterns. Furthermore, genomic PCR amplification and sequencing of primate and human DNA samples revealed that AluSx elements were integrated in human and all of the primate samples tested. Intriguingly, in langur genomic DNA, an additional AluY element was inserted into AluSx of intron eight of TSEN54. The new AluY element showed polymorphic insertion. Using standardized nomenclature for Alu repeats, the polymorphic AluY of the langur TSEN54 was designated as being of the AluYl17 subfamily. Our results suggest that integration of the AluSx element in TSEN54 contributed to diversity in transcripts and induced lineage- or species-specific evolutionary events such as alternative splicing and polymorphic insertion during primate evolution.

  11. 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.

  12. Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa.

    Science.gov (United States)

    Vandelannoote, Koen; Jordaens, Kurt; Bomans, Pieter; Leirs, Herwig; Durnez, Lies; Affolabi, Dissou; Sopoh, Ghislain; Aguiar, Julia; Phanzu, Delphin Mavinga; Kibadi, Kapay; Eyangoh, Sara; Manou, Louis Bayonne; Phillips, Richard Odame; Adjei, Ohene; Ablordey, Anthony; Rigouts, Leen; Portaels, Françoise; Eddyani, Miriam; de Jong, Bouke C

    2014-02-01

    Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types.

  13. The Angiotensin Converting Enzyme Insertion/Deletion polymorphism is not associated with an increased risk of death or bronchopulmonary dysplasia in ventilated very low birth weight infants

    Directory of Open Access Journals (Sweden)

    Baier R John

    2004-12-01

    Full Text Available Abstract Background The ACE gene contains a polymorphism consisting of either the presence (insertion, I or absence (deletion, D of a 287 bp alu repeat in intron 16. The D allele is associated with increased ACE activity in both tissue and plasma. The DD genotype is associated with risk of developing ARDS and mortality. The frequency of the D allele is higher in patients with pulmonary fibrosis, sarcoidosis and berylliosis. The role of this polymorphism has not been studied in the development of BPD in the premature newborn. Methods ACE I/D genotype was determined in 245 (194 African-American, 47 Caucasian and 4 Hispanic mechanically ventilated infants weighing less than 1250 grams at birth and compared to outcome (death and/or development of BPD. Results The incidence of the D allele in the study population was 0.58. Eighty-eight (35.9% infants were homozygous DD, 107 (43.7% were heterozygous ID and 50 (20.4% were homozygous II. There were no significant differences between genotype groups with respect to ethnic origin, birth weight, gestation, or gender. There was no effect of the ACE I/D polymorphism on mortality or development of BPD (O2 on 28 days or 36 weeks PCA. Secondary outcomes (intraventricular hemorrhage and periventricular leukomalacia similarly were not influenced by the ACE ID polymorphism. Conclusions The ACE I/D polymorphism does not significantly influence the development of BPD in ventilated infants less than 1250 grams.

  14. The association between functional HLA-G 14bp insertion/deletion and +3142 C>G polymorphisms and susceptibility to multiple sclerosis.

    Science.gov (United States)

    Ben Fredj, Nadia; Sakly, Kaouthar; Bortolotti, Daria; Aissi, Mouna; Frih-Ayed, Mahbouba; Rotola, Antonella; Caselli, Elisabetta; Cura, Franscesca; Sakly, Nabil; Aouni, Mahjoub; Di Luca, Dario; Rizzo, Roberta

    2016-12-01

    We aimed to investigate two main polymorphisms in the 3' untranslated region (3'UTR) of the HLA-G gene [14bp insertion/deletion (INS/DEL) and +3142 C>G] and to assess their impact on the soluble HLA-G (sHLA-G) production in patients with multiple sclerosis (MS). This study included 60 patients with relasping-remitting (RR) MS and 112 healthy donors (HD). Mutations were identified by PCR and PCR-RFLP, and serum sHLA-G quantification was performed by ELISA. For the 14bp INS/DEL polymorphism, variants frequencies were similar in patients and controls, whereas a significant increased frequency of the +3142 G allele was found in MS patients compared to HD (63.4% vs 52.3%, p=0.04; OR=1.58, 95%CI=1.003-2.48). In addition, an association was found between MS susceptibility and the haplotypes regrouping both studied polymorphisms. Indeed, the 14bp DEL/+3142 G haplotype frequency was significantly increased in MS patients compared to HD (20.8% vs 12.5%, p=0.04, OR=1.84). On the other hand, no associations were detected between both polymorphisms and clinical parameters, except the lower age of disease onset (ADO) in patients with the +3142 C/C genotype. Moreover, our study doesn't show any significant variation of sHLA-G serum levels between patients and controls. Our findings showed that the +3142 C>G, but not the 14bp INS/DEL, polymorphism may constitute a genetic susceptibility factor to MS in the Tunisian population. However, no association was found between the two polymorphisms and sHLA-G serum levels.

  15. Vascular Endothelial Growth Factor Gene Polymorphism (rs2010963 and Its Receptor, Kinase Insert Domain-Containing Receptor Gene Polymorphism (rs2071559, and Markers of Carotid Atherosclerosis in Patients with Type 2 Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Sebastjan Merlo

    2016-01-01

    Full Text Available Background. The current study was designed to reveal possible associations between the polymorphisms of the vascular endothelial growth factor (VEGF gene (rs2010963 and its receptor, kinase insert domain-containing receptor (KDR gene polymorphism (rs2071559, and markers of carotid atherosclerosis in patients with type 2 diabetes mellitus (T2DM. Patients and Methods. 595 T2DM subjects and 200 control subjects were enrolled. The carotid intima-media thickness (CIMT and plaque characteristics (presence and structure were assessed ultrasonographically. Biochemical analyses were performed using standard biochemical methods. Genotyping of VEGF/KDR polymorphisms (rs2010963, rs2071559 was performed using KASPar assays. Results. Genotype distributions and allele frequencies of the VEGF/KDR polymorphisms (rs2010963, rs2071559 were not statistically significantly different between diabetic patients and controls. In our study, we demonstrated an association between the rs2071559 of KDR and either CIMT or the sum of plaque thickness in subjects with T2DM. We did not, however, demonstrate any association between the tested polymorphism of VEGF (rs2010963 and either CIMT, the sum of plaque thickness, the number of involved segments, hsCRP, the presence of carotid plaques, or the presence of unstable carotid plaques. Conclusions. In the present study, we demonstrated minor effect of the rs2071559 of KDR on markers of carotid atherosclerosis in subjects with T2DM.

  16. 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

    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 components stroke...... susceptibility genes did not affect blood pressure reduction, heart rate reduction, or cardiovascular events in patients with hypertension and LVH, or treatment differences between losartan and atenolol on these endpoints. These results suggest that the observed effects of losartan versus atenolol...... whether the insertion/deletion (I/D) polymorphism of the angiotensin-converting enzyme (ACE) gene and 12 other previously well-characterized polymorphisms of hypertension susceptibility genes affected blood pressure reduction, heart rate reduction, cardiovascular events, and/or response to treatment...

  17. Decreased peak bone mass is associated with a 3-bp deletion/insertion of the CYP19 intron 4 polymorphism: preliminary data from the GOOS study.

    Science.gov (United States)

    Kastelan, D; Grubic, Z; Kraljevic, I; Duric, K; Kardum, I; Dusek, T; Stingl, K; Giljevic, Z; Kerhin-Brkljacic, V; Suchanek, E; Korsic, M

    2007-06-01

    Finding that estrogen plays an important role in bone homeostasis in men prompted research on relationship of polymorphism at the CYP19 gene and the bone mass. Therefore, influence of 3-bp deletion/insertion polymorphism of CYP19 (TTTA)7 allele on the peak bone mass attainment in males was studied. Fifty-eight unrelated male participants, aged 21-35, were selected depending on the presence of (TTTA)7 (no.=19) or (TTTA)7-3 (no.=39) alleles from the initial cohort of 92 young males. Heterozygotes (TTTA)7/(TTTA)7-3 (no.=13) were not included in the analysis. Serum levels of estradiol, free testosterone, 25-hydroxyvitamin D, bone alkaline phosphatase, osteocalcin, and beta-crosslaps were measured. Bone mass was measured by DXA at the hip and at the spine. (TTTA)7-3 allele was associated with significantly lower femoral neck bone mineral density (BMD) (p=0.02). Logistic regression model indicated strong association of (TTTA)7-3 allele with low BMD in the range of osteopenia/osteoporosis (p=0.014, odds ratio 12.36, confidence intervals 1.65-92.46). In the present study association of 3-bp deletion polymorphism of the (TTTA)7 allele with decreased peak bone mass in males is reported for the first time. However, further studies are necessary to elucidate the functional relevance of this polymorphism.

  18. 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

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

    DEFF Research Database (Denmark)

    Nordestgaard, Børge G; Kontula, Kimmo; Benn, Marianne;

    2010-01-01

    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 components stroke......, myocardial infarction, and cardiovascular death, or treatment differences between losartan and atenolol on these endpoints, as assessed by Cox proportional hazards models including baseline Framingham risk score and LVH. CONCLUSION: ACE insertion/deletion and 12 other polymorphisms of hypertension...

  20. A retroelement modifies pre-mRNA splicing: the murine Glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion.

    Science.gov (United States)

    Becker, Kristina; Braune, Marlen; Benderska, Natalya; Buratti, Emanuele; Baralle, Francisco; Villmann, Carmen; Stamm, Stefan; Eulenburg, Volker; Becker, Cord-Michael

    2012-09-01

    The glycine receptor-deficient mutant mouse spastic carries a full-length long interspersed nuclear element (LINE1) retrotransposon in intron 6 of the glycine receptor β subunit gene, Glrb(spa). The mutation arose in the C57BL/6J strain and is associated with skipping of exon 6 or a combination of the exons 5 and 6, thus resulting in a translational frameshift within the coding regions of the GlyR β subunit. The effect of the Glrb(spa) LINE1 insertion on pre-mRNA splicing was studied using a minigene approach. Sequence comparison as well as motif prediction and mutational analysis revealed that in addition to the LINE1 insertion the inactivation of an exonic splicing enhancer (ESE) within exon 6 is required for skipping of exon 6. Reconstitution of the ESE by substitution of a single residue was sufficient to prevent exon skipping. In addition to the ESE, two regions within the 5' and 3' UTR of the LINE1 were shown to be critical determinants for exon skipping, indicating that LINE1 acts as efficient modifier of subtle endogenous splicing phenotypes. Thus, the spastic allele of the murine glycine receptor β subunit gene is a two-hit mutation, where the hypomorphic alteration in an ESE is amplified by the insertion of a LINE1 element in the adjacent intron. Conversely, the LINE1 effect on splicing may be modulated by individual polymorphisms, depending on the insertional environment within the host genome.

  1. Prevalence of the angiotensin I converting enzyme insertion/deletion polymorphism, plasma angiotensin converting enzyme activity, and left ventricular mass in a normotensive Chilean population.

    Science.gov (United States)

    Jalil, J E; Piddo, A M; Cordova, S; Chamorro, G; Braun, S; Jalil, R; Vega, J; Jadue'P, L; Lavandero, S; Lastra, P

    1999-07-01

    The aim of this study was to estimate the prevalence of the different alleles of the angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism and associated plasma ACE activity, as well as cardiac echocardiographic structure, in a healthy Chilean population. We selected 117 healthy normotensive subjects (aged 45 to 60 years, middle socioeconomic status, nonobese, and nondiabetic) from a population-based study concerning the prevalence of risk factors for chronic diseases (Conjunto de Acciones Para la Reducción Multifactorial de las Enfermedades no Transmisibles [CARMEN]). The frequencies of the I and D alleles were 0.57 and 0.43, respectively. Mean plasma ACE activity was 15.3 +/- 3.9 U/mL. Compared with subjects with the II genotype, plasma ACE activity was significantly higher in subjects with the ID and DD genotypes with no difference between them. No correlation was observed between blood pressure and plasma ACE activity. Among the three different genotypes there was no difference in left ventricular (LV) dimensions or in LV mass. No correlation between plasma ACE activity and LV mass was observed for either gender or different genotypes. Multivariate linear regression analysis using LV mass and LV mass index as dependent variables showed independent effects (P < .05) for gender (higher LV mass in men) and diastolic blood pressure, but not for the DD genotype. In conclusion, in this population, the presence of the D allele on the ACE gene determined higher circulating ACE activity. However, in this normotensive healthy population, male gender and diastolic blood pressure, but not the presence of the D allele, were associated with increased LV mass.

  2. 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

    2016-08-10

    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 increase the risk of renal scar in children with VUR.

  3. Prevalence of genetic polymorphisms of methylenetetrahydrofolate reductase C677T and angiotensin I-converting enzyme (insertion/deletion in Sétif population, Algeria

    Directory of Open Access Journals (Sweden)

    Bakhouche Houcher

    2013-03-01

    Full Text Available The aim of the present study was to assess the frequencies of angiotensin I-converting enzyme (ACE; OMIM: 106180 and methylenetetrahydrofolate reductase (MTHFR; OMIM: 607093 polymorphisms in the Algerian population to further facilitate investigations on possible associations with various pathologies. The study was carried out on 146 apparently healthy individuals (65 males, 81 females who were randomly selected from an Algerian population of the Setif region (north-eastern Algeria. Their age ranged from 24 to 48 years. Using polymerase chain reaction based methods, genotypic frequencies of MTHFR C677T (rs. 1801133 and ACE I/D (rs. 1799752 polymorphisms were determined. No significant difference was found between genders regarding the distribution of ACE I/D and MTHFR C677T polymorphisms. In general, the prevalence of the D allele of the ACE polymorphism was 70.5%. The study population was in the Hardy-Weinberg equilibrium (Chi-Square=0.55, df=1, P=0.758. The allelic frequency of the 677T allele (for MTHFR C677T polymorphism was 35.3%. The study population was in the Hardy-Weinberg equilibrium (Chi-Square=1.05, df=1, P=0.304. The surprisingly high incidence of minor alleles of the polymorphisms among our population requires further studies in vascular and other diseases.

  4. Effect of insertion speed on tissue response and insertion mechanics of a chronically implanted silicon-based neural probe.

    Science.gov (United States)

    Welkenhuysen, M; Andrei, A; Ameye, L; Eberle, W; Nuttin, B

    2011-11-01

    In this study, the effect of insertion speed on long-term tissue response and insertion mechanics was investigated. A dummy silicon parylene-coated probe was used in this context and implanted in the rat brain at 10 μm/s (n = 6) or 100 μm/s (n = 6) to a depth of 9 mm. The insertion mechanics were assessed by the dimpling distance, and the force at the point of penetration, at the end of the insertion phase, and after a 3-min rest period in the brain. After 6 weeks, the tissue response was evaluated by estimating the amount of gliosis, inflammation, and neuronal cell loss with immunohistochemistry. No difference in dimpling, penetration force, or the force after a 3-min rest period in the brain was observed. However, the force at the end of the insertion phase was significantly higher when inserting the probes at 100 μm/s compared to 10 μm/s. Furthermore, an expected tissue response was seen with an increase of glial and microglial reactivity around the probe. This reaction was similar along the entire length of the probe. However, evidence for a neuronal kill zone was observed only in the most superficial part of the implant. In this region, the lesion size was also greatest. Comparison of the tissue response between insertion speeds showed no differences.

  5. 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

    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...

  6. Space Acquisitions: Space Based Infrared System Could Benefit from Technology Insertion Planning

    Science.gov (United States)

    2015-04-01

    Space Based Infrared System (SBIRS) Constellation with Defense Support Program (DSP) Augmentation (Nominal) 5 Figure 3: Key Space Based Infrared...5 GAO-15-366 Space Acquisitions Figure 2: Space Based Infrared System (SBIRS) Constellation with Defense Support Program (DSP) Augmentation...SPACE ACQUISITIONS Space Based Infrared System Could Benefit from Technology Insertion Planning Report to the

  7. Association Between Plasminogen Activator Inhibitor-1-675 4G/5G Insertion/Deletion Polymorphism and Chronic Obstructive Pulmonary Disease.

    Science.gov (United States)

    Essa, Enas S; El Wahsh, Rabab A

    2016-12-01

    Molecular pathology of chronic obstructive pulmonary disease (COPD) is still being investigated to discover relationships with disease pathogenesis. Evidence of plasminogen activator inhibitor-1 (PAI-1) overexpression in the sputum and the blood of COPD patients is growing. We aimed to investigate the potential relation between PAI-1 promoter 4G/5G insertion/deletion polymorphism and COPD development. In a case-control study, we genotyped 117 COPD patients and 160 control subjects for PAI-1 promoter 4G/5G polymorphism by an allele-specific polymerase chain reaction analysis. All subjects were male smokers. In the co-dominant model, there was a significant difference in the distribution of 5G/5G, 4G/5G and 4G/4G genotypes between COPD patients and controls (p = 0.002). In the recessive model, carriers of 4G/4G genotype were significantly higher in COPD patients than controls (p = 0.01). Carriers of 4G/4G genotype were at higher risk to develop COPD than those carrying 5G/5G or 4G/5G genotypes (crude odds ratio (OR) = 2.10, 95% confidence interval (CI) = 1.19-3.73, adjusted OR = 2.5, 95% CI = 1.22-3.99). In conclusion, PAI-1 4G/5G genetic variations are associated with COPD development in males.

  8. Association of DD Genotype of Insertion/Deletion Polymorphism of Angiotensin-Converting Enzyme Gene with Systemic Lupus Erythematosus and Lupus Nephropathy

    Directory of Open Access Journals (Sweden)

    Saeedeh Salimi

    2013-10-01

    Full Text Available Background: Systemic lupus erythematosus (SLE is a multisystem disease with unknown etiology. We hypothesized that insertion/deletion (I/D polymorphism of angiotensin-converting enzyme (ACE gene may influence the development and/or progression of SLE and lupus nephritis. Materials and Methods: In a crass sectional case-control study, genomic DNA from 106 SLE patients and 103 healthy controls matched for sex, age, and ethnicity, were genotyped for the (I/D polymorphism of ACE gene by polymerase chain reaction (PCR. Comparison of quantitative variants between two groups was assessed by student t-test and association between qualitative variables was analyzed by the chi-square or Fisher exact tests. Results: The frequency of DD genotype in SLE patients was significantly higher than control group (25.5 % vs. 14 %, and the risk of SLE was 2.2 times greater in subjects with DD genotype than the individual by DI and II genotypes (OR, 2.2 [95% CI, 1.1 to 4.4]; p=0.023. The distribution of D allele in SLE patients was significantly higher (p=0.021 compare to controls (47 and 36.4, respectively. The Risk of nephropathy in SLE patients with DD genotype was three times more than other genotypes (OR, 3 [95% CI, 1.1 to 8]; p=0.027].Conclusion: This study demonstrated that ACE DD genotype acts as a risk factor on SLE and Lupus nephropathy in an Iranian population.

  9. Modulation of the renal response to ACE inhibition by ACE insertion/deletion polymorphism during hyperglycemia in normotensive, normoalbuminuric type 1 diabetic patients.

    Science.gov (United States)

    Weekers, Laurent; Bouhanick, Béatrice; Hadjadj, Samy; Gallois, Yves; Roussel, Ronen; Pean, Franck; Ankotche, Amos; Chatellier, Gilles; Alhenc-Gelas, François; Lefebvre, Pierre J; Marre, Michel

    2005-10-01

    ACE inhibition protects kidney function, but ACE insertion/deletion (I/D) polymorphism affects renal prognosis in type 1 diabetic patients. ACE genotype may influence the renal benefits of ACE inhibition. We studied the impact of ACE I/D polymorphism on the renal hemodynamic changes induced by ACE inhibition in type 1 diabetes. We studied renal hemodynamics (glomerular filtration rate [GFR], effective renal plasma flow [ERPF], filtration fraction [GFR/ERPF], mean arterial pressure [MAP], and total renal resistances [MAP/ERPF]) repeatedly during normoglycemia and then hyperglycemia in 12 normotensive, normoalbuminuric type 1 diabetes and the II genotype (associated with nephroprotection) versus 22 age- and sex-matched subjects with the ACE D allele after three randomly allocated 2- to 6-week periods on placebo, 1.25 mg/day ramipril, and 5 mg/day ramipril in a double-blind, cross-over study. During normoglycemia, the hemodynamic changes induced by ramipril were similar in both genotypes. During hyperglycemia, the changes induced by ramipril were accentuated in the II genotype group and attenuated dose dependently in the D allele group (treatment-genotype interaction P values for ERPF, 0.018; MAP, 0.018; and total renal resistances, 0.055). These results provide a basis to different renal responses to ACE inhibition according to ACE genotype in type 1 diabetes.

  10. Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms

    Directory of Open Access Journals (Sweden)

    Wifak El Moncer

    2011-01-01

    Full Text Available The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma group at a relatively high frequency. This frequency was similar to that found in sub-Saharans from Nigeria, but significantly different from those found in the Gabes sample and in other North African populations. Our molecular results, consistent with the skin color status, suggest a sub-Saharan origin of this particular Tunisian group.

  11. PEA: Polymorphic Encryption Algorithm based on quantum computation

    OpenAIRE

    Komninos, N.; Mantas, G.

    2011-01-01

    In this paper, a polymorphic encryption algorithm (PEA), based on basic quantum computations, is proposed for the encryption of binary bits. PEA is a symmetric key encryption algorithm that applies different combinations of quantum gates to encrypt binary bits. PEA is also polymorphic since the states of the shared secret key control the different combinations of the ciphertext. It is shown that PEA achieves perfect secrecy and is resilient to eavesdropping and Trojan horse attacks. A securit...

  12. Improvement of the insertion axis for cochlear implantation with a robot-based system.

    Science.gov (United States)

    Torres, Renato; Kazmitcheff, Guillaume; De Seta, Daniele; Ferrary, Evelyne; Sterkers, Olivier; Nguyen, Yann

    2017-02-01

    It has previously reported that alignment of the insertion axis along the basal turn of the cochlea was depending on surgeon' experience. In this experimental study, we assessed technological assistances, such as navigation or a robot-based system, to improve the insertion axis during cochlear implantation. A preoperative cone beam CT and a mastoidectomy with a posterior tympanotomy were performed on four temporal bones. The optimal insertion axis was defined as the closest axis to the scala tympani centerline avoiding the facial nerve. A neuronavigation system, a robot assistance prototype, and software allowing a semi-automated alignment of the robot were used to align an insertion tool with an optimal insertion axis. Four procedures were performed and repeated three times in each temporal bone: manual, manual navigation-assisted, robot-based navigation-assisted, and robot-based semi-automated. The angle between the optimal and the insertion tool axis was measured in the four procedures. The error was 8.3° ± 2.82° for the manual procedure (n = 24), 8.6° ± 2.83° for the manual navigation-assisted procedure (n = 24), 5.4° ± 3.91° for the robot-based navigation-assisted procedure (n = 24), and 3.4° ± 1.56° for the robot-based semi-automated procedure (n = 12). A higher accuracy was observed with the semi-automated robot-based technique than manual and manual navigation-assisted (p robot-based system reduces both the error and the variability of the alignment with a defined optimal axis.

  13. Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans.

    Science.gov (United States)

    Berkman, Ceren Caner; Dinc, Havva; Sekeryapan, Ceran; Togan, Inci

    2008-05-01

    In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. In the present study, insertion frequencies of 10 Alu loci (A25 = 0.07, APO = 0.96, TPA25 = 0.44, ACE = 0.37, B65 = 0.57, PV92 = 0.18, FXIIIB = 0.52, D1 = 0.40, HS4.32 = 0.66, and HS4.69 = 0.30) have been determined in the Anatolian population. Together with the data compiled from other databases, the similarity of the Anatolian population to that of the Balkans and Central Asia has been visualized by multidimensional scaling method. Analysis suggested that, genetically, Anatolia is more closely related with the Balkan populations than to the Central Asian populations. Central Asian contribution to Anatolia with respect to the Balkans was quantified with an admixture analysis. Furthermore, the association between the Central Asian contribution and the language replacement episode was examined by comparative analysis of the Central Asian contribution to Anatolia, Azerbaijan (another Turkic speaking country) and their neighbors. In the present study, the Central Asian contribution to Anatolia was estimated as 13%. This was the lowest value among the populations analyzed. This observation may be explained by Anatolia having the lowest migrant/resident ratio at the time of migrations.

  14. Associations of ACE gene insertion/deletion polymorphism, ACE activity, and ACE mRNA expression with hypertension in a Chinese population.

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    Qingfang He

    Full Text Available The present study was designed to explore the association of angiotensin converting enzyme (ACE gene insertion/deletion (I/D, rs4646994 polymorphism, plasma ACE activity, and circulating ACE mRNA expression with essential hypertension (EH in a Chinese population. In addition, a new detection method for circulating ACE mRNA expression was explored.The research was approved by the ethics committee of Zhejiang Provincial Center for Disease Prevention and Control. Written informed consent was obtained prior to the investigation. 221 hypertensives (cases and 221 normotensives (controls were interviewed, subjected to a physical examination, and provided blood for biochemical and genetic tests. The ACE mRNA expression was analyzed by real time fluorescent quantitative Reverse Transcription PCR (FQ-RT-PCR. We performed logistic regression to assess associations of ACE I/D genotypes, ACE activity, and ACE mRNA expression levels with hypertension.The results of the multivariate logistic regression analysis showed that the additive model (ID, DD versus II of the ACE genotype revealed an association with hypertension with adjusted OR of 1.43(95% CI: 1.04-1.97, and ACE ID genotype with adjusted OR of 1.72(95% CI: 1.01-2.92, DD genotype with adjusted OR of 1.94(95% CI: 1.01-3.73, respectively. In addition, our data also indicate that plasma ACE activity (adjusted OR was 1.13(95% CI: 1.08-1.18 was significantly related to hypertension. However, the plasma ACE mRNA expressions were not different between the cases and controls.ACE I/D polymorphism and ACE activity revealed significant influence on hypertension, while circulating ACE mRNA expression was not important factors associated with hypertension in this Chinese population. The detection of circulating ACE mRNA expression by FQ-RT-PCR might be a useful method for early screening and monitoring of EH.

  15. 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.

  16. A Dummy Scan Flip-Flop Insertion Algorithm based on Driving Vertex

    Science.gov (United States)

    Liu, H. L.; Li, L.; Zhang, Z. X.; Zhou, W. T.

    2017-03-01

    Commonly termed as Hardware Trojans, is an emerging issue for global hardware security. The research on Hardware Trojan detection is urgent and significant. Dummy Scan Flip-Flop(DSFF) structure could be used to improve the probability of hardware Trojan activation, which is significant to hardware Trojan detection, especially during the design phase. In this express, an algorithm for inserting the DSFF structure based on driving vertex is proposed. According to the experimental results, under the same transition probability threshold(Pth), compared to the state-of-art, the proposed algorithm can reduce both the inserting complexity and the induced area overhead of the DSFF insertion. The maximum area optimization rate can reach 44.8%. The simulation results on S386 and S38584 benchmark circuits indicate that the proposed algorithm can significantly reduce Trojan authentication time by increasing activation probability of hardware Trojan circuits.

  17. 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.

  18. Internet-Based Optimization and Choice of Insert Grooves for Face-Milling

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Manufacture is facing more furiously competition in the new century. It tends to be globalized. Rapid response and technology innovation have become the key factor to the success of manufacture enterprise. At present, internet-based manufacturing develops rapidly. With the development of engineering material and machining techniques, better cutting properties of metal cutting tools are required. The world is paying more attention to the study of indexable carbide inserts with three-dimensional complex groov...

  19. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

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    Katarzyna A. Wojcik

    2014-10-01

    Full Text Available Keratoconus (KC is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER. Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1 were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1 nor the c.2285T>C polymorphism of the poly(ADP-ribose polymerase-1 (PARP-1 was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease.

  20. 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…

  1. Flow cytometry-based DNA hybridization and polymorphism analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cai, H.; Kommander, K.; White, P.S.; Nolan, J.P.

    1998-07-01

    Functional analysis of the humane genome, including the quantification of differential gene expression and the identification of polymorphic sites and disease genes, is an important element of the Human Genome Project. Current methods of analysis are mainly gel-based assays that are not well-suited to rapid genome-scale analyses. To analyze DNA sequence on a large scale, robust and high throughput assays are needed. The authors are developing a suite of microsphere-based approaches employing fluorescence detection to screen and analyze genomic sequence. The approaches include competitive DNA hybridization to measure DNA or RNA targets in unknown samples, and oligo ligation or extension assays to analyze single-nucleotide polymorphisms. Apart from the advances of sensitivity, simplicity, and low sample consumption, these flow cytometric approaches have the potential for high throughput multiplexed analysis using multicolored microspheres and automated sample handling.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sonje, Ashish G.; Mahajan, Hitendra S., E-mail: hsmahajan@rediffmail.com

    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. - Highlights: • Chitosan–gellan gum polyelectrolyte complex based inserts have been prepared. • The synthesized polymer complex demonstrated important insert properties. • No toxicity was observed toward nasal mucosa. • In vivo study demonstrates the enhancement of bioavailability.

  3. Identification and examination of a novel 9-bp insert/deletion polymorphism on porcine SFTPA1 exon 2 associated with acute lung injury using an oleic acid-acute lung injury model.

    Science.gov (United States)

    Zhang, Yuebo; Zhang, Longchao; Wang, Ligang; Qiao, Lijuan; Liang, Jing; Yan, Hua; Zhao, Kebin; Liu, Xin; Wang, Lixian

    2015-06-01

    The pulmonary surfactant-associated protein (SFTPA1, SP-A) gene has been studied as a candidate gene for lung disease resistance in humans and livestock. The objective of the present study was to identify polymorphisms of the porcine SFTPA1 gene coding region and its association with acute lung injury (ALI). Through DNA sequencing and the PCR-single-strand conformation polymorphism method, a novel 9-bp nucleotide insertion (+) or deletion (-) was detected on exon 2 of SFTPA1, which causes a change in three amino acids, namely, alanine (Ala), glycine (Gly) and proline (Pro). Individuals of three genotypes (-/-, +/- and +/+) were divided into equal groups from 60 Rongchang pigs that were genotyped. These pigs were selected for participation in the oleic acid (OA)-ALI model by 1-h and 3-h injections of OA, and there were equal numbers of pigs in the control and injection groups. The lung water content, a marker for acute lung injury, was measured in this study; there is a significant correlation between high lung water content and the presence of the 9-bp indel polymorphism (P polymorphism causing altered expression of the gene. The individuals with the -/- genotype showed lower lung water content than the +/+ genotype pigs, which suggests that polymorphism could be a potential marker for lung disease-resistant pig breeding and that pig can be a potential animal model for human lung disease resistance in future studies.

  4. The protective effect of adenoidectomy on pediatric tympanostomy tube re-insertions: a population-based birth cohort study.

    Directory of Open Access Journals (Sweden)

    Mao-Che Wang

    Full Text Available Adenoidectomy in conjunction with tympanostomy tube insertion for treating pediatric otitis media with effusion and recurrent acute otitis media has been debated for decades. Practice differed surgeon from surgeon. This study used population-based data to determine the protective effect of adenoidectomy in preventing tympanostomy tube re-insertion and tried to provide more evidence based information for surgeons when they do decision making.Retrospective birth cohort study.This study used the National Health Insurance Research Database for the period 2000-2009 in Taiwan. The tube reinsertion rate and time to tube re-insertion among children who received tympanostomy tubes with or without adenoidectomy were compared. Age stratification analysis was also done to explore the effects of age.Adenoidectomy showed protective effects on preventing tube re-insertion compared to tympanostomy tubes alone in children who needed tubes for the first time (tube re-insertion rate 9% versus 5.1%, p = 0.002 and longer time to re-insertions, p = 0.01, especially those aged over 4 years when they had their first tube surgery. After controlling the effect of age, adenoidectomy reduced the rate of re-insertion by 40% compared to tympanostomy tubes alone (aHR: 0.60; 95% CI: 0.41-0.89. However, the protective effect of conjunction adenoidectomy was not obvious among children with a second tympanostomy tube insertion. Children who needed their first tube surgery at the age 2-4 years were most prone to have tube re-insertions, followed by the age group of 4-6 years.Adenoidectomy has protective effect in preventing tympanostomy tube re-insertions compared to tympanostomy tubes alone, especially for children older than 4 years old and who needed tubes for the first time. Nonetheless, clinicians should still weigh the pros and cons of the procedure for their pediatric patients.

  5. 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.

  6. Identification of a short interspersed repetitive element insertion polymorphism in the porcine MX1 promoter associated with resistance to porcine reproductive and respiratory syndrome virus infection.

    Science.gov (United States)

    Li, Yanping; Liang, Sen; Liu, Hao; Sun, Yi; Kang, Li; Jiang, Yunliang

    2015-08-01

    The myxovirus resistance (Mx) proteins belong to the dynamin superfamily and are important for innate host defence against RNA viruses. In this study, we demonstrate that positive elements are present in the two promoter regions of -2713 to -2565 and -688 to -431 in the porcine MX1 gene. Sequencing and alignment of the amplified porcine MX1 gene promoter region identified a short interspersed repetitive element (SINE) insertion of 275 bp at site -547. At this site, allele B (an insertion of 275 bp) is dominant in Chinese indigenous pig breeds but has a workable minor allele frequency in western lean-type pig breeds. Luciferase activity was compared between promoters with and without the insertion of the 275-bp fragment in transiently transfected MARC-145 cells. The insertion of the 275-bp fragment increased the luciferase activity significantly (P MX1 gene promoter region is a potential DNA marker for PRRS resistance in pigs.

  7. 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.

  8. 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.

  9. PERMUTATION-BASED POLYMORPHIC STEGO-WATERMARKS FOR PROGRAM CODES

    Directory of Open Access Journals (Sweden)

    Denys Samoilenko

    2016-06-01

    Full Text Available Purpose: One of the most actual trends in program code protection is code marking. The problem consists in creation of some digital “watermarks” which allow distinguishing different copies of the same program codes. Such marks could be useful for authority protection, for code copies numbering, for program propagation monitoring, for information security proposes in client-server communication processes. Methods: We used the methods of digital steganography adopted for program codes as text objects. The same-shape symbols method was transformed to same-semantic element method due to codes features which makes them different from ordinary texts. We use dynamic principle of marks forming making codes similar to be polymorphic. Results: We examined the combinatorial capacity of permutations possible in program codes. As a result it was shown that the set of 5-7 polymorphic variables is suitable for the most modern network applications. Marks creation and restoration algorithms where proposed and discussed. The main algorithm is based on full and partial permutations in variables names and its declaration order. Algorithm for partial permutation enumeration was optimized for calculation complexity. PHP code fragments which realize the algorithms were listed. Discussion: Methodic proposed in the work allows distinguishing of each client-server connection. In a case if a clone of some network resource was found the methodic could give information about included marks and thereby data on IP, date and time, authentication information of client copied the resource. Usage of polymorphic stego-watermarks should improve information security indexes in network communications.

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

    NARCIS (Netherlands)

    Tang, J.; Vosman, B.; Voorrips, R.E.; Linden, van der C.G.; Leunissen, J.A.M.

    2006-01-01

    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

  11. Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data

    Science.gov (United States)

    Whole genome sequencing studies can directly identify causative mutations for subsequent use in genomic evaluations, but sequence variant identification is a lengthy and sometimes inaccurate process. The speed and accuracy of identifying small insertions and deletions of sequence, collectively terme...

  12. FRET-Based Localization of Fluorescent Protein Insertions Within the Ryanodine Receptor Type 1

    OpenAIRE

    Raina, Shweta A.; Jeffrey Tsai; Montserrat Samsó; Fessenden, James D.

    2012-01-01

    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) inse...

  13. Basic study for ultrasound-based navigation for pedicle screw insertion using transmission and backscattered methods.

    Directory of Open Access Journals (Sweden)

    Ziqiang Chen

    Full Text Available 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.

  14. Fabrication of a glucose biosensor based on inserted barrel plating gold electrodes.

    Science.gov (United States)

    Hsu, Cheng-Teng; Chung, Hsieh-Hsun; Tsai, Dong-Mung; Fang, Mei-Yen; Hsiao, Hung-Chan; Zen, Jyh-Myng

    2009-01-01

    We demonstrate here the application of barrel plating gold electrodes for fabricating a new type of disposable amperometric glucose biosensor. It is prepared by inserting two barrel plating gold electrodes onto an injection molding plastic base followed by immobilizing with a bioreagent layer and membrane on the electrode surface. The primary function of barrel plating is to provide an economical way to electroplate manufactured parts. The manufacture procedure is simple and can increase the fabrication precision for automation in mass production. At the two-electrode system, the detection of glucose is linear up to 800 mg/dL (i.e., 44.5 mM, r(2) > 0.99) in pH 7.4 PBS with a sensitivity of 0.71 microA/mM. Excellent sensor-to-sensor reproducibility shows coefficients of variation of only 0.8-1.4% for the detection of 56.5-561.0 mg/dL glucose. In laboratory trials 176 capillary blood samples with a range of 30-572 mg/dL glucose are used to evaluate the clinical application of the biosensor. A good linear correlation is observed between the measured values of the proposed biosensor and laboratory reference. Error grid analysis verifies that the proposed technique is promising in fabricating biosensor strips on a mass scale. As successfully demonstrated by using whole blood glucose as a model analyte, the fabrication technique can extend into other barrel plating noble metal electrodes for various applications.

  15. Superior long-term stability of a glucose biosensor based on inserted barrel plating gold electrodes.

    Science.gov (United States)

    Hsu, Cheng-Teng; Hsiao, Hung-Chan; Fang, Mei-Yen; Zen, Jyh-Myng

    2009-10-15

    Disposable one shot usage blood glucose strips are routinely used in the diagnosis and management of diabetes mellitus and their performance can vary greatly. In this paper we critically evaluated the long-term stability of glucose strips made of barrel plating gold electrodes. Compared to other glucose biosensing platforms of vapor deposited palladium and screen printed carbon electrodes, the proposed glucose biosensor was found to show the best stability among the three biosensing platforms in thermal acceleration experiments at 40 degrees C for 6 months with an average bias of 3.4% at glucose concentrations of 5-20 mM. The precision test of this barrel plating gold glucose biosensor also showed the best performance (coefficients of variation in the range of 1.4-2.4%) in thermal acceleration experiments at 40 degrees C, 50 degrees C and 70 degrees C for 27 days. Error grid analysis revealed that all measurements fell in zone A and zone B. Regression analysis showed no significant difference between the proposed biosensor and the reference method at 99% confidence level. The amperometric glucose biosensor fabricated by inserting two barrel plating gold electrodes onto an injection-molding plastic base followed by immobilizing with a bio-reagent layer and membrane was very impressive with a long-term stability up to 2.5 years at 25 degrees C. Overall, these results indicated that the glucose oxidase/barrel plating gold biosensing platform is ideal for long-term accurate glycemic control.

  16. 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

  17. Physics-based RF/microwave characterization of wave interactions within electrical connectors with partial insertion faults

    Science.gov (United States)

    Tokgöz, Çaǧatay; Dardona, Sameh

    2016-09-01

    Electrical failures in avionics systems may result from connector faults. If fault precursors are not detected in advance, they may lead to hard failures such as open and short circuits that could ultimately result in fire or loss of flight critical systems. Therefore, It is crucial to detect, locate, and characterize fault precursors for timely preventive maintenance and mitigation before hard failures occur. In this paper, a physics-based connector model consisting of multiple coaxial line sections with different characteristic impedances and lengths is proposed. Method of Moments (MoM) analyses were performed using commercial electromagnetic simulation software, FEKO, for transverse electric and magnetic (TEM) wave propagation through a connector. The physical parameters of the connector were optimized to match the measured S parameters for multiple insertion depths. The proposed models represent the connector for multiple insertion depths by varying only two length parameters at a time while other parameters are fixed. Insertion depth-dependent resonant frequency shifts observed during measurement are also captured by the model over the full range of fully inserted to barely touching contacts. Hence, the models provide accurate representations of the connector and properly detect precursors to partial insertion faults.

  18. Angiotensin-converting enzyme insertion/deletion polymorphism and susceptibility to allergic rhinitis in Chinese populations: a systematic review and meta-analysis.

    Science.gov (United States)

    Huang, Ruo-Fei; Dong, Pin; Zhang, Tian-Zhen; Ying, Xin-Jiang; Hu, Hua

    2016-02-01

    In view of the controversies surrounding the angiotensin-converting enzyme (ACE)-allergic rhinitis (AR) association, a systematic review and meta-analysis of the ACE genetic association studies of AR was performed in Chinese populations. PubMed, Springer Link, OvidSP, Chinese biomedical database, Chinese national knowledge infrastructure, Chinese VIP and Wanfang databases were searched for related studies. A total of 4 studies including 415 AR patients and 309 controls were involved in this meta-analysis. Overall, significant association was found between ACE I/D polymorphism and AR risk when all studies in Chinese populations pooled into the meta-analysis (allele, OR 1.50, 95 % CI 1.19-1.90; homozygous, OR 2.59, 95 % CI 1.52-4.41, recessive, OR 2.05, 95 % CI 1.27-3.32). In the subgroup analysis by ethnicity, ACE I/D polymorphism was associated with significant elevated risks of AR in Chinese Han under homozygous and recessive models (homozygous, OR 4.36, 95 % CI 1.76-10.82, recessive, OR 2.51, 95 % CI 1.18-5.34). In conclusion, this meta-analysis provides the evidence that ACE I/D polymorphism may contribute to the AR development in Chinese populations and studies with large sample size and wider spectrum of population are warranted to verify this finding.

  19. 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.

  20. Formulation and Evaluation of Chitosan-Chondroitin Sulphate Based Nasal Inserts for Zolmitriptan

    Directory of Open Access Journals (Sweden)

    Kirandeep Kaur

    2013-01-01

    Full Text Available Bioadhesive nasal dosage forms are an attractive method for overcoming rapid mucociliary clearance transport in the nose and for delivering the drug directly to brain. The present study was designed to formulate chondroitin sulphate (CS and chitosan (CH nasal inserts employing zolmitriptan, an antimigraine drug. The interpolymer complexes (IPC formed between –COO− and – groups of CS and group of CH were characterized by infrared spectroscopy (IR, differential scanning analysis (DSC, and zeta potential studies. The unloaded and loaded nasal inserts were evaluated for water uptake studies, and bioadhesive strength studies, scanning electron microscopic studies (SEM. The in vitro drug release and in situ permeation studies were carried out on loaded nasal inserts. The DSC and IR studies confirmed the formation of a complex between the two polymers. The results indicated that the formulation F1 (CH : CS; 30 : 70 was demonstrating the highest bioadhesive strength and zeta potential. The presence of porous structure in the nasal inserts was confirmed by the SEM analysis. Further, in vitro and in situ release studies demonstrated that formulations F9 and F11 (drug : polymer; 1 : 10 were releasing 90% and 98% zolmitriptan over a period of 8 h. It can be concluded that nasal inserts formulated from chitosan-chondroitin sulphate (CH-CS interpolymer complex (IPC can be used for delivery of antimigraine drug to brain.

  1. Formulation and Evaluation of Chitosan-Chondroitin Sulphate Based Nasal Inserts for Zolmitriptan

    Science.gov (United States)

    Kaur, Kirandeep; Kaur, Gurpreet

    2013-01-01

    Bioadhesive nasal dosage forms are an attractive method for overcoming rapid mucociliary clearance transport in the nose and for delivering the drug directly to brain. The present study was designed to formulate chondroitin sulphate (CS) and chitosan (CH) nasal inserts employing zolmitriptan, an antimigraine drug. The interpolymer complexes (IPC) formed between –COO− and –OSO3− groups of CS and –NH3+ group of CH were characterized by infrared spectroscopy (IR), differential scanning analysis (DSC), and zeta potential studies. The unloaded and loaded nasal inserts were evaluated for water uptake studies, and bioadhesive strength studies, scanning electron microscopic studies (SEM). The in vitro drug release and in situ permeation studies were carried out on loaded nasal inserts. The DSC and IR studies confirmed the formation of a complex between the two polymers. The results indicated that the formulation F1 (CH : CS; 30 : 70) was demonstrating the highest bioadhesive strength and zeta potential. The presence of porous structure in the nasal inserts was confirmed by the SEM analysis. Further, in vitro and in situ release studies demonstrated that formulations F9 and F11 (drug : polymer; 1 : 10) were releasing 90% and 98% zolmitriptan over a period of 8 h. It can be concluded that nasal inserts formulated from chitosan-chondroitin sulphate (CH-CS) interpolymer complex (IPC) can be used for delivery of antimigraine drug to brain. PMID:24175310

  2. 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.

  3. 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.

  4. Association between the SERPINE1 (PAI-1) 4G/5G insertion/deletion promoter polymorphism (rs1799889) and pre-eclampsia: a systematic review and meta-analysis.

    Science.gov (United States)

    Zhao, Linlu; Bracken, Michael B; Dewan, Andrew T; Chen, Suzan

    2013-03-01

    The SERPINE1 -675 4G/5G promoter region insertion/deletion polymorphism (rs1799889) has been implicated in the pathogenesis of pre-eclampsia (PE), but the genetic association has been inconsistently replicated. To derive a more precise estimate of the association, a systematic review and meta-analysis was conducted. This study conformed to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. PubMed (MEDLINE), Scopus and HuGE Literature Finder literature databases were systematically searched for relevant studies. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for the allelic comparison (4G versus 5G) and genotypic comparisons following the co-dominant (4G/4G versus 5G/5G and 4G/5G versus 5G/5G), dominant (4G/4G+4G/5G versus 5G/5G) and recessive (4G/4G versus 4G/5G+5G/5G) genetic models. Between-study heterogeneity was quantified by I(2) statistics and publication bias was appraised with funnel plots. Sensitivity analysis was conducted to evaluate the robustness of meta-analysis findings. Meta-analysis of 11 studies involving 1297 PE cases and 1791 controls found a significant association between the SERPINE1 -675 4G/5G polymorphism and PE for the recessive genetic model (OR = 1.36, 95% CI: 1.13-1.64, P = 0.001), a robust finding according to sensitivity analysis. A low level of between-study heterogeneity was detected (I(2) = 20%) in this comparison, which may be explained by ethnic differences. Funnel plot inspection did not reveal evidence of publication bias. In conclusion, this study provides a comprehensive examination of the available literature on the association between SERPINE1 -675 4G/5G and PE. Meta-analysis results support this polymorphism as a likely susceptibility variant for PE.

  5. Design and evaluation of guar gum-based ofloxacin sustained release ocular insert

    Directory of Open Access Journals (Sweden)

    Sunil Kumar

    2012-01-01

    Full Text Available To prepare ocular inserts of ofloxacin using guar gum as a polymer for sustained delivery over a period of 24 h. Ofloxacin ocular inserts were prepared by the solvent casting method using guar gum in different proportions (0.5% w/v, 0.75% w/v and 1.0% w/v. The prepared formulations were evaluated for thickness, weight variation, percentage drug content, surface pH, folding endurance, percentage moisture absorption and loss, percentage swelling, mechanical strength and in vitro transcorneal permeation. In vitro transcorneal permeation study was performed on goat cornea using a modified Franz diffusion cell. The inserts were found to be of uniform thickness (ranging from 51.230 ± 0.385 μm to 109.275 ± 0.522 μm and weight (1.720 ± 0.079 mg to 3.402 ± 0.105 mg. The % drug content in the inserts was found to vary between 95.450 ± 0.427% and 98.471 ± 0.225. The cumulative % drug releases from the formulation ranged from 38.19 to 75.21 over a period of 24 h. All the formulations followed a zero order release pattern. The in vitro transcorneal study revealed that an increase in concentration of the polymer slowed down the release of ofloxacin from the formulation. Ocular inserts using guar gum as a polymer were successfully prepared and can be effectively used for sustained ocular delivery over a period of 24 h.

  6. Single nucleotide polymorphism-based validation of exonic splicing enhancers.

    Directory of Open Access Journals (Sweden)

    William G Fairbrother

    2004-09-01

    Full Text Available Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality, which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE-ESE method. Aligning the single nucleotide polymorphisms (SNPs from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 +/- 0.05. This selection is strongest for the predicted ESEs that are located near splice sites. Our results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and also suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.

  7. 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.

  8. Insertion devices

    CERN Document Server

    Bahrdt, J

    2006-01-01

    The interaction of an insertion device with the electron beam in a storage ring is discussed. The radiation property including brightness, ux and polarization of an ideal and real planar and helical / elliptical device is described. The magnet design of planar, helical, quasiperiodic devices and of devices with a reduced on axis power density are resumed.

  9. Vaginal inserts based on chitosan and carboxymethylcellulose complexes for local delivery of chlorhexidine: preparation, characterization and antimicrobial activity.

    Science.gov (United States)

    Bigucci, Federica; Abruzzo, Angela; Vitali, Beatrice; Saladini, Bruno; Cerchiara, Teresa; Gallucci, Maria Caterina; Luppi, Barbara

    2015-01-30

    The aim of this work was to prepare vaginal inserts based on chitosan/carboxymethylcellulose polyelectrolyte complexes for local delivery of chlorhexidine digluconate. Complexes were prepared with different chitosan/carboxymethylcellulose molar ratios at a pH value close to pKa interval of the polymers and were characterized in terms of physico-chemical properties, complexation yield and drug loading. Then complexes were used to prepare inserts as vaginal dosage forms and their physical handling, morphology, water-uptake ability and drug release properties as well as antimicrobial activity toward Candida albicans and Escherichia coli were evaluated. Results confirmed the ionic interaction between chitosan and carboxymethylcellulose and the influence of the charge amount on the complexation yield. Complexes were characterized by high values of drug loading and showed increasing water-uptake ability with the increase of carboxymethylcellulose amount. The selection of appropriate chitosan/carboxymethylcellulose molar ratios allowed to obtain cone-like shaped solid inserts, easy to handle and able to hydrate releasing the drug over time. Finally, the formulated inserts showed antimicrobial activity against common pathogens responsible for vaginal infections.

  10. New polymorphic variants of human blood clotting factor IX

    Energy Technology Data Exchange (ETDEWEB)

    Surin, V.L.; Luk`yanenko, A.V.; Tagiev, A.F.; Smirnova, O.V. [Hematological Research Center, Moscow (Russian Federation); Plutalov, O.V.; Berlin, Yu.A. [Shemyakin Institute of Bioorganic Chemistry, Moscow (Russian Federation)

    1995-04-01

    The polymorphism of Alu-repeats, which are located in the introns of the human factor IX gene (copies 1-3), was studied. To identify polymorphic variants, direct sequencing of PCR products that contained appropriate repeats was used. In each case, 20 unrelated X chromosomes were studied. A polymorphic Dra I site was found near the 3{prime}-end of Alu copy 3 within the region of the polyA tract. A PCR-based testing system with internal control of restriction hydrolysis was suggested. Testing 81 unrelated X chromosomes revealed that the frequency of the polymorphic Dra I site is 0.23. Taq I polymorphism, which was revealed in Alu copy 4 of factor IX gene in our previous work, was found to be closely linked to Dra I polymorphism. Studies in linkage between different types of polymorphisms of the factor IX gene revealed the presence of a rare polymorphism in intron a that was located within the same minisatellite region as the known polymorphic insertion 50 bp/Dde I. However, the size of the insertion in our case was 26 bp. Only one polymorphic variant was found among over 150 unrelated X chromosomes derived from humans from Moscow and its vicinity. 10 refs., 4 figs., 1 tab.

  11. Structural and electronic modifications induced by lithium insertion in Sn-based oxide glasses

    Science.gov (United States)

    Robert, Florent; Morato, Françoise; Chouvin, Jérôme; Aldon, Laurent; Lippens, Pierre Emmanuel; Fourcade, Josette Olivier; Jumas, Jean-Claude; Simon, Bernard; Biensan, Philippe

    The irreversible mechanisms of lithium insertion in amorphous tin composite oxides SnB 0.6P 0.4O 2.9 have been studied by X-ray diffraction (XRD) and 119Sn Mössbauer spectroscopy. The determination of the Lamb-Mössbauer factor has allowed us to evaluate the relative numbers of different tin atoms (Sn II, Sn 0). We show that insertion of lithium reduces the Sn II into Sn 0 atoms, which form nanoparticles of active species. The lithium ions act as glass modifiers, breaking the bonds within MOM' (M, M'=B, P, Sn) bridges and forming non-bridging MO δ- bonds.

  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. 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.

  14. 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

  15. FPGA-based fused smart-sensor for tool-wear area quantitative estimation in CNC machine inserts.

    Science.gov (United States)

    Trejo-Hernandez, Miguel; Osornio-Rios, Roque Alfredo; de Jesus Romero-Troncoso, Rene; Rodriguez-Donate, Carlos; Dominguez-Gonzalez, Aurelio; Herrera-Ruiz, Gilberto

    2010-01-01

    Manufacturing processes are of great relevance nowadays, when there is a constant claim for better productivity with high quality at low cost. The contribution of this work is the development of a fused smart-sensor, based on FPGA to improve the online quantitative estimation of flank-wear area in CNC machine inserts from the information provided by two primary sensors: the monitoring current output of a servoamplifier, and a 3-axis accelerometer. Results from experimentation show that the fusion of both parameters makes it possible to obtain three times better accuracy when compared with the accuracy obtained from current and vibration signals, individually used.

  16. A Silicon-on-Insulator-Based Thermo-Optic Waveguide Switch with Low Insertion Loss and Fast Response

    Institute of Scientific and Technical Information of China (English)

    LI Yan-Ping; YU Jin-Zhong; CHEN Shao-Wu

    2005-01-01

    @@ A silicon-on-insulator-based thermo-optic waveguide switch integrated with spot size converters is designed and fabricated by inductively coupled plasma reactive ion etching. The device shows good characteristics, including low insertion loss of 8 ± 1 dB for wavelength 1530-1580nm and fast response times of 4.6 μs for rising edge and 1.9μs for falling edge. The extinction ratios of the two channels are 19.1 and 18 dB, respectively.

  17. General Approach for Introduction of Various Chemical Labels in Specific RNA Locations Based on Insertion of Amino Linkers

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer

    2013-11-01

    Full Text Available Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine functions (amino linkers with their subsequent selective derivatization by appropriate chemicals. This article is a brief review on methods for site-specific introduction of amino linkers in different RNAs. These methods comprise: (i incorporation of a nucleoside carrying an amino-linker or a function that can be substituted with it into oligoribonucleotides in the course of their chemical synthesis; (ii assembly of amino linker-containing RNAs from short synthetic fragments via their ligation; (iii synthesis of amino linker-modified RNAs using T7 RNA polymerase; (iv insertion of amino linkers into unmodified RNAs at functional groups of a certain type such as the 5'-phosphates and N7 of guanosine residues and (v introduction of an amino linker into long highly structured RNAs exploiting an approach based on sequence-specific modification of nucleic acids. Particular reporter groups used for derivatization of amino linker-containing RNAs together with types of RNA derivatives obtained and fields of their application are presented.

  18. Improving Nurses' Peripheral Intravenous Catheter Insertion Knowledge, Confidence, and Skills Using a Simulation-Based Blended Learning Program

    Science.gov (United States)

    Keleekai, Nowai L.; Schuster, Catherine A.; Murray, Connie L.; King, Mary Anne; Stahl, Brian R.; Labrozzi, Laura J.; Gallucci, Susan; LeClair, Matthew W.; Glover, Kevin R.

    2016-01-01

    Introduction Peripheral intravenous catheter (PIVC) insertion is one of the most common invasive procedures performed in a hospital, but most nurses receive little formal training in this area. Blended PIVC insertion training programs that incorporate deliberate simulated practice have the potential to improve clinical practice and patient care. Methods The study was a randomized, wait-list control group with crossover using nurses on three medical/surgical units. Baseline PIVC knowledge, confidence, and skills assessments were completed for both groups. The intervention group then received a 2-hour PIVC online course, followed by an 8-hour live training course using a synergistic mix of three simulation tools. Both groups were then reassessed. After crossover, the wait-list group received the same intervention and both groups were reassessed. Results At baseline, both groups were similar for knowledge, confidence, and skills. Compared with the wait-list group, the intervention group had significantly higher scores for knowledge, confidence, and skills upon completing the training program. After crossover, the wait-list group had similarly higher scores for knowledge, confidence, and skills than the intervention group. Between the immediate preintervention and postintervention periods, the intervention group improved scores for knowledge by 31%, skills by 24%, and decreased confidence by 0.5%, whereas the wait-list group improved scores for knowledge by 28%, confidence by 16%, and skills by 15%. Conclusions Results demonstrate significant improvements in nurses' knowledge, confidence, and skills with the use of a simulation-based blended learning program for PIVC insertion. Transferability of these findings from a simulated environment into clinical practice should be further explored. PMID:27504890

  19. 汉族人群血管紧张素转换酶基因插入/缺失(I/D)的遗传多态性%Genetic polymorphism of angiotensin-converting enzyme gene insertion/deletion in Chinese Han population

    Institute of Scientific and Technical Information of China (English)

    高纯; 顾国浩; 夏正

    2006-01-01

    BACKGROUND: The angiotensin-converting enzyme (ACE) is the important component of the renin-angiotensin-aldosterone system (RAS). The ACE gene has, in fact,insertion/deletion polymorphism in intron 16, consisting of a 287-base pair Alu repeat sequence. ACE gene heterozygotes insertion/deletion (I/D) polymorphism is correlated with cardiovascular disease and IgA nephropathy and other diseases. OBJECTIVE: To investigate the distribution of ACE gene I/D polymor-phism in Chinese Han population in comparison with other known ethnic populations. DESIGN: Observation study on healthy individuals of Han nationality. SETTING: Key Laboratory of Clinical Immunology of Jiangsu Province; Department of Laboratory Medicine, First Hospital Affiliated to Soochow University; Department of aboratory Medicine, College of Medical Technology of Jiangsu University PARTICIPANTS: Totally 241 healthy individuals who received the healthy examination in the First Hospital of Soochow University between December 2005 and January 2006 were recruited in the experiment. They were 152 male and 89 female , with mean age of (27±8)years. All the participants without blood relationship were Han nationality from Suzhou region in China, free from disorder of hepatic, renal, endocrine and cardio- cerebrovascular diseases which were confirmed by clinical and experimen- tal examination. METHODS: Genotype of ACE gene I/D polymorphism allele of 241 healthy individuals of Han nationality was detected with polymerase chain reaction (PCR). PCR purified products with genotype of deletion/deletion (DD) and insertion/insertion (Ⅱ) polymorphism were performed DNA sequencing with fluorescence-labeled end termination method. MAIN OUTCOME MEASURES: Genotype and allele frequency of ACE gene I/D, as well as the comparison between them and those of other ethnic population. RESULTS: All the 241 subjects participated in final result analysis. ① The genotypes of ACE were DD, Ⅱ and ID. Compared with allele Ⅰ, allele D

  20. 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.

  1. 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.

  2. 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...

  3. The binding and insertion of imidazolium-based ionic surfactants into lipid bilayers: the effects of the surfactant size and salt concentration.

    Science.gov (United States)

    Lee, Hwankyu; Jeon, Tae-Joon

    2015-02-28

    Imidazolium-based ionic surfactants with hydrocarbon tails of different sizes were simulated with lipid bilayers at different salt concentrations. Starting with the random position of ionic surfactants outside the bilayer, surfactants with long tails mostly insert into the bilayer, while those with short tails show the insertion of fewer surfactant molecules, indicating the effect of the tail length. In particular, surfactants with a tail of two or four hydrocarbons insert and reversibly detach from the bilayer, while the inserted longer surfactants cannot be reversibly detached because of the strong hydrophobic interaction with lipid tails, in quantitative agreement with experiments. Longer surfactants insert more deeply and irreversibly into the bilayer and thus increase lateral diffusivities of the bilayer, indicating that longer surfactants more significantly disorder lipid bilayers, which also agrees with experiments regarding the effect of the tail length of ionic surfactants on membrane permeability and toxicity. Addition of NaCl ions weakens the electrostatic interactions between headgroups of surfactants and lipids, leading to the binding of fewer surfactants into the bilayer. In particular, our simulation findings indicate that insertion of ionic surfactants can be initiated by either the hydrophobic interaction between tails of surfactants and lipids or the electrostatic binding between imidazolium heads and lipid heads, and the strength of hydrophobic and electrostatic interactions depends on the tail length of surfactants.

  4. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    Science.gov (United States)

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-07-22

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

  5. 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.

  6. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals.

    Science.gov (United States)

    Vukosavljev, M; Esselink, G D; van 't Westende, W P C; Cox, P; Visser, R G F; Arens, P; Smulders, M J M

    2015-01-01

    The first hurdle in developing microsatellite markers, cloning, has been overcome by next-generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still performed manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Of 48 tested two markers failed to amplify, but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multilocus markers largely overlapped. Of the remainder, half were replicate markers (i.e. multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6-20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy therefore represents a major step forward in the development of highly polymorphic microsatellite markers.

  7. 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.

  8. Outcomes of upper airway reconstructive surgery for obstructive sleep apnea syndrome based on polysomnography after nasopharyngeal tube insertion

    Institute of Scientific and Technical Information of China (English)

    LI Shu-hua; WU Da-hai; BAO Ji-min; SHI Hong-jin

    2013-01-01

    Background The most common obstruction sites for obstructive sleep apnea hypopnea syndrome (OSAHS) are the oropharynx and the glossopharyx.The diagnosis of glossopharyngeal airway obstruction is difficult.The study aimed to assess the effect of upper airway reconstructive surgery for OSAHS based on polysomnography (PSG) after nasopharyngeal tube insertion (NPT-PSG),and to evaluate the clinical value of NPT-PSG in localizing the obstructive sites.Methods Seventy-nine OSAHS patients diagnosed with PSG were included in the study.PSG was repeated with a nasopharyngeal tube in place (NPT-PSG).Results of the two PSGs were compared.A NPT-PSG apnea hypopnea index (AHI) greater than 15 times per hour was used as a threshold for glossopharyngeal surgery.The cause of glossopharyngeal airway obstruction was taken into consideration in planning glossopharyngeal surgery.Assessment of efficacy was followed-up.Results After NPT-PSG,patients' AHI significantly decreased and lowest oxygen saturation (LaSO2) significantly increased.Of the 79 patients,47 were treated with uvulopalatopharyngoplasty (UPPP) alone and 32 with UPPP + glossopharyngeal surgery.Thirty-two patients were considered cured,33 markedly improved,and 14 failed.The overall surgery success rate was 82.3%.Conclusions NPT-PSG can be used as a diagnosis tool for localizing airway obstruction in OSAHS patients.Surgical treatment based on NPT-PSG results in good treatment efficacy.

  9. Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model.

    Science.gov (United States)

    Lu, Wei; Tamura, Takeyuki; Song, Jiangning; Akutsu, Tatsuya

    2014-01-01

    In this paper, we consider the Minimum Reaction Insertion (MRI) problem for finding the minimum number of additional reactions from a reference metabolic network to a host metabolic network so that a target compound becomes producible in the revised host metabolic network in a Boolean model. Although a similar problem for larger networks is solvable in a flux balance analysis (FBA)-based model, the solution of the FBA-based model tends to include more reactions than that of the Boolean model. However, solving MRI using the Boolean model is computationally more expensive than using the FBA-based model since the Boolean model needs more integer variables. Therefore, in this study, to solve MRI for larger networks in the Boolean model, we have developed an efficient Integer Programming formalization method in which the number of integer variables is reduced by the notion of feedback vertex set and minimal valid assignment. As a result of computer experiments conducted using the data of metabolic networks of E. coli and reference networks downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we have found that the developed method can appropriately solve MRI in the Boolean model and is applicable to large scale-networks for which an exhaustive search does not work. We have also compared the developed method with the existing connectivity-based methods and FBA-based methods, and show the difference between the solutions of our method and the existing methods. A theoretical analysis of MRI is also conducted, and the NP-completeness of MRI is proved in the Boolean model. Our developed software is available at "http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/minRect/minRect.html."

  10. Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model.

    Directory of Open Access Journals (Sweden)

    Wei Lu

    Full Text Available In this paper, we consider the Minimum Reaction Insertion (MRI problem for finding the minimum number of additional reactions from a reference metabolic network to a host metabolic network so that a target compound becomes producible in the revised host metabolic network in a Boolean model. Although a similar problem for larger networks is solvable in a flux balance analysis (FBA-based model, the solution of the FBA-based model tends to include more reactions than that of the Boolean model. However, solving MRI using the Boolean model is computationally more expensive than using the FBA-based model since the Boolean model needs more integer variables. Therefore, in this study, to solve MRI for larger networks in the Boolean model, we have developed an efficient Integer Programming formalization method in which the number of integer variables is reduced by the notion of feedback vertex set and minimal valid assignment. As a result of computer experiments conducted using the data of metabolic networks of E. coli and reference networks downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG database, we have found that the developed method can appropriately solve MRI in the Boolean model and is applicable to large scale-networks for which an exhaustive search does not work. We have also compared the developed method with the existing connectivity-based methods and FBA-based methods, and show the difference between the solutions of our method and the existing methods. A theoretical analysis of MRI is also conducted, and the NP-completeness of MRI is proved in the Boolean model. Our developed software is available at "http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/minRect/minRect.html."

  11. Integer Programming-Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model

    Science.gov (United States)

    Song, Jiangning; Akutsu, Tatsuya

    2014-01-01

    In this paper, we consider the Minimum Reaction Insertion (MRI) problem for finding the minimum number of additional reactions from a reference metabolic network to a host metabolic network so that a target compound becomes producible in the revised host metabolic network in a Boolean model. Although a similar problem for larger networks is solvable in a flux balance analysis (FBA)-based model, the solution of the FBA-based model tends to include more reactions than that of the Boolean model. However, solving MRI using the Boolean model is computationally more expensive than using the FBA-based model since the Boolean model needs more integer variables. Therefore, in this study, to solve MRI for larger networks in the Boolean model, we have developed an efficient Integer Programming formalization method in which the number of integer variables is reduced by the notion of feedback vertex set and minimal valid assignment. As a result of computer experiments conducted using the data of metabolic networks of E. coli and reference networks downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we have found that the developed method can appropriately solve MRI in the Boolean model and is applicable to large scale-networks for which an exhaustive search does not work. We have also compared the developed method with the existing connectivity-based methods and FBA-based methods, and show the difference between the solutions of our method and the existing methods. A theoretical analysis of MRI is also conducted, and the NP-completeness of MRI is proved in the Boolean model. Our developed software is available at “http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/minRect/minRect.html.” PMID:24651476

  12. 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

  13. Direct determination of MUC5B promoter haplotypes based on the method of single-strand conformation polymorphism and their statistical estimation.

    Science.gov (United States)

    Kamio, Koichiro; Matsushita, Ikumi; Tanaka, Goh; Ohashi, Jun; Hijikata, Minako; Nakata, Koh; Tokunaga, Katsushi; Azuma, Arata; Kudoh, Shoji; Keicho, Naoto

    2004-09-01

    Haplotype-based human genome research is important in identifying disease susceptibility genes efficiently. Although haplotype reconstruction by statistical methods is widely used, direct haplotype determination by molecular techniques has also been developed as a complementary method for statistical estimation. In this study, we demonstrate a molecular haplotyping method making use of single-strand conformation polymorphism (SSCP) gels. We identified 10 common SNPs and a dinucleotide insertion/deletion polymorphism within 2-kb region upstream of the transcription initiation site of MUC5B and determined haplotype structure, dividing the region into two DNA fragments. Real haplotypes were determined unambiguously by our SSCP-based analysis with fragments longer than 1 kb. Haplotypes reconstructed from diploid genotypes in the same region by the statistical methods including EM algorithm were also evaluated. Direct comparison between statistical estimation and direct determination of haplotypes revealed that major haplotypes containing multiple marker sites showing strong LD are estimated in great accuracy but that a variety of haplotypes reflecting weak LD are not reconstructed precisely enough. Our data can be helpful in implementing molecular haplotyping or statistical estimation, since usage of these methods may be determined depending on the haplotype structures.

  14. A detector insert based on continuous scintillators for hybrid MR-PET imaging of the human brain

    Science.gov (United States)

    Rato Mendes, P.; Cuerdo, R.; Sarasola, I.; García de Acilu, P.; Navarrete, J.; Vela, O.; Oller, J. C.; Cela, J. M.; Núñez, L.; Pastrana, M.; Romero, L.; Willmott, C.

    2013-02-01

    We are developing a positron emission tomography (PET) insert for existing magnetic resonance (MR) equipment, aiming at hybrid MR-PET imaging. Our detector block design is based on trapezoid-shaped LYSO:Ce monolithic scintillators coupled to magnetically compatible Hamamatsu S8550-02 silicon avalanche photodiode (APD) matrices with a dedicated ASIC front-end readout from GammaMedica-Ideas (Fornebu, Norway). The detectors are position sensitive, capable of determining the incidence point of 511 keV gammas with an intrinsic spatial resolution on the order of 2 mm by means of supervised learning neural-network (NN) algorithms. These algorithms, apart from providing continuous coordinates, are also intrinsically corrected for depth of interaction effects and thus parallax-free. Recently we have implemented an advanced prototype featuring two heads with four detector blocks each and final front-end and readout electronics, improving the spatial resolution of reconstructed point source images down to 1.7 mm full width at half maximum (FWHM). Presently we are carrying out operational tests of components and systems under magnetic fields using a 3 T MR scanner. In this paper we present a description of our project, a summary of the results obtained with laboratory prototypes, and the strategy to build and install the complete system at the nuclear medicine department of a collaborating hospital.

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

    Science.gov (United States)

    Ying, Lin; Yumei, Zhou

    2010-12-01

    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 translated from Chinese into English was established. Lexical errors in the corpus and the error causes were analyzed qualitatively and quantitatively. Some examples were used to analyze the lexical errors and their causes, and some strategies for translating vocabulary in DPIs were proposed according to Eugene Nida's translation theory. This study will not only help translators and medical workers reduce errors in C-E translation of vocabulary in DPIs and other types of medical texts but also shed light on the learning and teaching of C-E translation of medical texts.

  16. A detector insert based on continuous scintillators for hybrid MR–PET imaging of the human brain

    Energy Technology Data Exchange (ETDEWEB)

    Rato Mendes, P., E-mail: pedro.rato@ciemat.es [CIEMAT, Avenida Complutense 40, 28040 Madrid (Spain); Cuerdo, R.; Sarasola, I.; García de Acilu, P.; Navarrete, J.; Vela, O.; Oller, J.C.; Cela, J.M. [CIEMAT, Avenida Complutense 40, 28040 Madrid (Spain); Núñez, L.; Pastrana, M. [Hospital Universitario Puerta de Hierro Majadahonda, Manuel de Falla 1, 28222 Majadahonda (Spain); Romero, L.; Willmott, C. [CIEMAT, Avenida Complutense 40, 28040 Madrid (Spain)

    2013-02-21

    We are developing a positron emission tomography (PET) insert for existing magnetic resonance (MR) equipment, aiming at hybrid MR–PET imaging. Our detector block design is based on trapezoid-shaped LYSO:Ce monolithic scintillators coupled to magnetically compatible Hamamatsu S8550-02 silicon avalanche photodiode (APD) matrices with a dedicated ASIC front-end readout from GammaMedica-Ideas (Fornebu, Norway). The detectors are position sensitive, capable of determining the incidence point of 511 keV gammas with an intrinsic spatial resolution on the order of 2 mm by means of supervised learning neural-network (NN) algorithms. These algorithms, apart from providing continuous coordinates, are also intrinsically corrected for depth of interaction effects and thus parallax-free. Recently we have implemented an advanced prototype featuring two heads with four detector blocks each and final front-end and readout electronics, improving the spatial resolution of reconstructed point source images down to 1.7 mm full width at half maximum (FWHM). Presently we are carrying out operational tests of components and systems under magnetic fields using a 3 T MR scanner. In this paper we present a description of our project, a summary of the results obtained with laboratory prototypes, and the strategy to build and install the complete system at the nuclear medicine department of a collaborating hospital.

  17. 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...

  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. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Gómez Marcela

    2009-12-01

    Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

  20. Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae

    Directory of Open Access Journals (Sweden)

    Kambiranda Devaiah

    2011-01-01

    Full Text Available Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae, Pueraria tuberosa (Roxb. ex Willd. DC (Fabaceae, Adenia hondala (Gaertn. de Wilde (Passifloraceae and pith of Cycas circinalis L. (Cycadaceae are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD technique. Furthermore, sequence characterized amplified region (SCAR primers (IM1F and IM1R were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species.

  1. 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.

  2. High-performance single crystal organic field-effect transistors based on two dithiophene-tetrathiafulvalene (DT-TTF) polymorphs.

    Science.gov (United States)

    Pfattner, Raphael; Mas-Torrent, Marta; Bilotti, Ivano; Brillante, Aldo; Milita, Silvia; Liscio, Fabiola; Biscarini, Fabio; Marszalek, Tomasz; Ulanski, Jacek; Nosal, Andrzej; Gazicki-Lipman, Maciej; Leufgen, Michael; Schmidt, Georg; Molenkamp, Laurens W; Laukhin, Vladimir; Veciana, Jaume; Rovira, Concepció

    2010-10-01

    Solution prepared single crystal organic field-effect transistors (OFETs) combine low-cost with high performance due to structural ordering of molecules. However, in organic crystals polymorphism is a known phenomenon, which can have a crucial influence on charge transport. Here, the performance of solution-prepared single crystal OFETs based on two different polymorphs of dithiophene-tetrathiafulvalene, which were investigated by confocal Raman spectroscopy and X-ray diffraction, are reported. OFET devices prepared using different configurations show that both polymorphs exhibited excellent device performance, although the -phase revealed charge carrier mobility between two and ten times higher in accordance to the closer stacking of the molecules.

  3. 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...

  4. Feeding tube insertion - gastrostomy

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/002937.htm Feeding tube insertion - gastrostomy To use the sharing features on this page, please enable JavaScript. A gastrostomy feeding tube insertion is the placement of a feeding ...

  5. Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism.

    Science.gov (United States)

    Rozemuller, E H; Bouwens, A G; van Oort, E; Versluis, L F; Marsh, S G; Bodmer, J G; Tilanus, M G

    1995-01-01

    An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. 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: experience.

  7. Compatibility of selected plant-based shortening as lard substitute: microstructure, polymorphic forms and textural properties

    Directory of Open Access Journals (Sweden)

    N. A.M. Yanty

    2017-03-01

    Full Text Available A study was carried out to determine the compatibility of three plant-based shortening mixtures to lard shortening (LD in terms of microstructure, polymorphic forms, and textural properties. The shortenings of binary, ternary, and quaternary fat mixtures were prepared according to a standard procedure by blending mee fat (MF with palm stearin (PS in a 99:1 (w/w ratio; avocado fat (Avo with PS and cocoa butter (CB in a 84:7:9 (w/w ratio; palm oil (PO with PS, soybean oil (SBO and CB in a 38:5:52:5 (w/w ratio, respectively. The triacylglycerol composition, polymorphic forms, crystal morphology, and textural properties of the shortening were evaluated. This study found that all three plant-based shortenings and LD shortening were similar with respect to their consistency, hardness and compression and adhesiveness values. However, all plant-based shortening was found to be dissimilar to LD shortening with respect to microstructure.

  8. Polymorphous Low-Grade Adenocarcinoma of the Tongue Base Treated by Transoral Robotic Surgery

    Directory of Open Access Journals (Sweden)

    Jeong Hong Kim

    2015-01-01

    Full Text Available Polymorphous low-grade adenocarcinoma is a rare malignancy arising from the minor salivary glands in the aerodigestive system, most frequently the hard palate. The treatment of choice is wide surgical resection, and the efficacy of radiotherapy has not been confirmed. A 54-year-old male presenting with a mass at the base of the tongue performed transoral laser microsurgery. The pathologic diagnosis was polymorphous low-grade adenocarcinoma. Complete surgical excision was performed via transoral robotic surgery without a flap reconstruction of the surgical defect. Without complications of bleeding or injury to the hypoglossal nerve, proper surgical margins were obtained, and no recurrence was found after 6 months after surgery. The patient did not complain of dysphagia or aspiration. We conclude that, in surgery for tongue base tumors with unknown malignant potential, transoral robotic surgery can be considered for achieving a definite resection avoiding a mandibulotomy without complications of dysphagia or aspiration after confirmation of malignancy with a frozen biopsy.

  9. 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.

  10. Sequence and single-base polymorphisms of the bovine alpha-lactalbumin 5'-flanking region.

    Science.gov (United States)

    Bleck, G T; Bremel, R D

    1993-04-30

    The alpha-lactalbumin (alpha LA)-encoding gene is a potential quantitative trait locus in dairy animals. In cattle, the production of alpha LA is tightly coupled to the onset of lactation and it serves as a regulatory subunit of the enzyme responsible for lactose synthesis. Lactose is the major osmole controlling water movement in the mammary gland. To better understand the control of bovine alpha LA expression, the 5'-flanking region of a Holstein alpha LA gene was cloned and sequenced. The sequenced clone contains 1952 bp of 5'-flanking region and 66-bp of the protein-coding region. Three single-bp polymorphisms were identified within this region. These polymorphisms occur at positions +15, +21 and +54 relative to the mRNA transcription start point (tsp). The +15 and +21 variations occur in the region encoding the 5'-untranslated region of the mRNA-coding sequence. The +54 polymorphism is a silent mutation in the SP-coding region of the gene. A polymerase chain reaction (PCR, Cetus)-based screening method has been employed to analyze the genotype of cattle at the +15 position. A total of 501 randomly selected cattle from seven breeds were screened for this allele. Of these animals, only the Holstein breed of cattle was found to contain the +15 variation and it occurs at a gene frequency of 32%. Sequence comparisons were conducted between the 5'-flanking regions of the bovine-milk-protein encoding genes, alpha LA, beta-casein and alpha S1-casein, which are coordinately expressed. Regions of similarity extending to 350 bp in length were observed between these sequences.

  11. 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.

  12. 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.

  13. Gel-based nonradioactive single-strand conformational polymorphism and mutation detection: limitations and solutions.

    Science.gov (United States)

    Gupta, Vibhuti; Arora, Reetakshi; Gochhait, Sailesh; Bairwa, Narendra K; Bamezai, Rameshwar N K

    2014-01-01

    Single-strand conformation polymorphism (SSCP) for screening mutations/single-nucleotide polymorphisms (SNPs) is a simple, cost-effective technique, saving an expensive exercise of sequencing each and every polymerase chain reaction product and assisting in choosing only the amplicons of interest with expected mutations. The principle of detection of small changes in DNA sequences is based on changes in single-strand DNA conformations. The changes in electrophoretic mobility that SSCP detects are sequence dependent. The limitations faced in SSCP range from routine polyacrylamide gel electrophoresis (PAGE) problems to the problems of resolving mutant DNA bands. Both these problems can be solved by controlling PAGE conditions and by varying physical and environmental conditions such as pH, temperature, voltage, gel type and percentage, addition of additives or denaturants, and others. Despite much upgrading of the technology for mutation detection, SSCP remains the method of choice to analyze mutations and SNPs in order to understand genomic variations, both spontaneous and induced, and the genetic basis of diseases.

  14. 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%.

  15. Estimating population size using single-nucleotide polymorphism-based pedigree data.

    Science.gov (United States)

    Spitzer, Robert; Norman, Anita J; Schneider, Michael; Spong, Göran

    2016-05-01

    Reliable population estimates are an important aspect of sustainable wildlife management and conservation but can be difficult to obtain for rare and elusive species. Here, we test a new census method based on pedigree reconstruction recently developed by Creel and Rosenblatt (2013). Using a panel of 96 single-nucleotide polymorphisms (SNPs), we genotyped fecal samples from two Swedish brown bear populations for pedigree reconstruction. Based on 433 genotypes from central Sweden (CS) and 265 from northern Sweden (NS), the population estimates (N = 630 for CS, N = 408 for NS) fell within the 95% CI of the official estimates. The precision and accuracy improved with increasing sampling intensity. Like genetic capture-mark-recapture methods, this method can be applied to data from a single sampling session. Pedigree reconstruction combined with noninvasive genetic sampling may thus augment population estimates, particularly for rare and elusive species for which sampling may be challenging.

  16. An insertion algorithm for catabolizability

    CERN Document Server

    Blasiak, Jonah

    2009-01-01

    Motivated by our recent work relating canonical bases to combinatorics of Garsia-Procesi modules \\cite{B}, we give an insertion algorithm that computes the catabolizability of the insertion tableau of a standard word. This allows us to characterize catabolizability as the statistic on words invariant under Knuth transformations, certain (co)rotations, and a new operation called a catabolism transformation. We also prove a Greene's Theorem-like characterization of catabolizability, and a result about how cocyclage changes catabolizability, strengthening a similar result in \\cite{SW}.

  17. 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.

  18. 血管紧张素转换酶基因插入/缺失多态性与飞行员加速度耐力的相关性研究%Research on Relationship Between Insertion/Delation Polymorphism of Angiotensin Converting Enzyme Gene and Acceleration Tolerance of Pilots

    Institute of Scientific and Technical Information of China (English)

    蔡庆; 刘红巾; 邹志康; 陈涛; 马中立

    2013-01-01

    Objective To investigate the association of insertion/deletion (I/D) polymorphism of the angioten-sin-converting enzyme (ACE) gene with acceleration ( +Gz) tolerance of pilots. Methods Polymerase chain reaction (PCR) was used to determine the genotypes for an insertion/delation (I/D) polymorphism of the ACE gene in 50 pilots with high + Gz tolerance and 32 pilots with low + Gz tolerance. Results The genotype II and I allele frequency were significantly higher in the pilots with high + Gz tolerance (58. 00% and 0. 76) than that in the pilots with low + Gz tolerance (18. 75% and 0. 47, P <0. 01). Conclusion It is suggested that I gene of ACE may play a role in + Gz tolerance of pilots.%目的 探讨飞行员血管紧张素转换酶(ACE)基因插入或缺失(I/D)多态性与飞行员加速度耐力的相关性.方法 用聚合酶链反应(PCR)扩增技术检测50例高+Gz耐力飞行员和32例低+Gz耐力飞行员的ACE基因I/D多态性.结果 高+Gz耐力飞行员组Ⅱ基因型(58.00%)和I等位基因频率(0.76)显著高于低+ Gz耐力飞行员组(分别为18.75%和0.47,P<0.01).结论 ACE I基因有可能在飞行员的+ Gz耐力中起重要作用.

  19. Clinical effect of peripherally inserted central catheters based on modified seldinger technique under guidance of vascular ultrasound

    Science.gov (United States)

    Wang, Qingguo; Wang, Ni; Sun, Yuzhen

    2016-01-01

    Objective: To observe and analyze the application effect of ultrasound-guided modified Seldinger technique (MST) in Peripherally Inserted Central Catheter (PICC) catheterization. Methods: Two hundred patients treated with PICC catheterization from January 2013 to December 2015 were selected and randomly divided into two groups, namely, observation group and control group. The observation group adopted ultrasound-guided MST for catheterization while the control group applied traditional puncture technique for catheterization. Then efficacy of catheterization, success rate of catheterization and incidence rates of complications were compared between two groups. Results: Various indicators of catheterization effects of the observation group were better than those of the control group, and the differences were statistically significant (Psatisfaction and comfort level of patients. PMID:27882017

  20. Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

    Science.gov (United States)

    Zhao, Junfei; Sheng, Jinsong; Rubin, Donald H.

    2016-01-01

    Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap) host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins. We herein reported 712 candidate cellular genes, characterizing distinct topological network and evolutionary signatures, and occupying central hubs in the human interactome. Cell cycle phase-specific network analysis showed that host cell cycle programs played critical roles during viral replication (e.g. MYC and TAF4 regulating G0/1 phase). Moreover, the viral perturbation of host cellular networks reflected disease etiology in that host genes (e.g. CTCF, RHOA, and CDKN1B) identified were frequently essential and significantly associated with Mendelian and orphan diseases, or somatic mutations in cancer. Computational drug repositioning framework via incorporating drug-gene signatures from the Connectivity Map into the virus-host interactome identified 110 putative druggable antiviral targets and prioritized several existing drugs (e.g. ajmaline) that may be potential for antiviral indication (e.g. anti-Ebola). In summary, this work provides a powerful methodology with a tight integration of gene-trap insertional mutagenesis testing and systems biology to identify new antiviral targets and drugs for the development of broadly acting and targeted clinical antiviral therapeutics. PMID:27632082

  1. Genome relationship among nine species of Millettieae (Leguminosae: Papilionoideae) based on random amplified polymorphic DNA (RAPD).

    Science.gov (United States)

    Acharya, Laxmikanta; Mukherjee, Arup Kumar; Panda, Pratap Chandra

    2004-01-01

    Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.

  2. 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...

  3. 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...

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Meisel P

    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.

  6. CXCR1 and SLC11A1 polymorphisms affect susceptibility to cutaneous leishmaniasis in Brazil: a case-control and family-based study

    Directory of Open Access Journals (Sweden)

    Oliveira Joyce

    2010-01-01

    Full Text Available Abstract Background L. braziliensis causes cutaneous (CL and mucosal (ML leishmaniasis. Wound healing neutrophil (PMN and macrophage responses made following the bite of the vector sand fly contribute to disease progression in mice. To look at the interplay between PMN and macrophages in disease progression in humans we asked whether polymorphisms at genes that regulate their infiltration or function are associated with different clinical phenotypes. Specifically, CXCR1 (IL8RA and CXCR2 (IL8RB are receptors for chemokines that attract PMN to inflammatory sites. They lie 30-260 kb upstream of SLC11A1, a gene known primarily for its role in regulating macrophage activation, resistance to leishmaniasis, and wound healing responses in mice, but also known to be expressed in PMN, macrophages and dendritic cells. Methods Polymorphic variants at CXCR1, CXCR2 and SLC11A1 were analysed using Taqman or ABI fragment separation technologies in cases (60 CL; 60 ML, unrelated controls (n = 120, and multicase families (104 nuclear families; 88 ML, 250 CL cases from Brazil. Logistic regression analysis, family-based association testing (FBAT and haplotype analysis (TRANSMIT were performed. Results Case-control analysis showed association between the common C allele (OR 2.38; 95% CI 1.23-4.57; P = 0.009 of CXCR1_rs2854386 and CL, supported by family-based (FBAT; Z score 2.002; P = 0.045 analysis (104 nuclear families; 88 ML, 250 CL cases. ML associated with the rarer G allele (Z score 1.999; P = 0.046. CL associated with a 3' insertion/deletion polymorphism at SLC11A1 (Z score 2.549; P = 0.011. Conclusions The study supports roles for CXCR1 and SLC11A1 in the outcome of L. braziliensis infection in humans. Slc11a1 does not influence cutaneous lesion development following needle injection of Leishmania in mice, suggesting that its role here might relate to the action of PMN, macrophage and/or dendritic cells in the wound healing response to the sand fly bite

  7. Family-based association analysis of beta(2)-adrenergic receptor polymorphisms in the Childhood Asthma Management Program

    NARCIS (Netherlands)

    Silverman, EK; Kwiatkowski, DJ; Sylvia, JS; Lazarus, R; Drazen, JM; Lange, C; Laird, NM; Weiss, ST

    2003-01-01

    Background: beta(2)-Adrenergic receptor (B2AR) polymorphisms have been associated with a variety of asthma-related phenotypes, but association results have been inconsistent across different studies. Objective: We sought to apply family-based association methods to individual single nucleotide polym

  8. Association of "ADAM10" and "CAMK2A" Polymorphisms with Conduct Disorder: Evidence from Family-Based Studies

    Science.gov (United States)

    Jian, Xue-Qiu; Wang, Ke-Sheng; Wu, Tie-Jian; Hillhouse, Joel J.; Mullersman, Jerald E.

    2011-01-01

    Twin and family studies have shown that genetic factors play a role in the development of conduct disorder (CD). The purpose of this study was to identify genetic variants associated with CD using a family-based association study. We used 4,720 single nucleotide polymorphisms (SNPs) from the Illumina Panel and 11,120 SNPs from the Affymetrix 10K…

  9. Pyrosequencing with di-base addition for single nucleotide polymorphism genotyping.

    Science.gov (United States)

    Pu, Dan; Mao, Chengguang; Cui, Lunbiao; Shi, Zhiyang; Xiao, Pengfeng

    2016-05-01

    We develop color code-based pyrosequencing with di-base addition for analysis of single nucleotide polymorphisms (SNPs). When a di-base is added into the polymerization, one or several two-color code(s) containing the type and the number of incorporated nucleotides will be produced. The code information obtained in a single run is useful to genotype SNPs as each allelic variant will give a specific pattern compared to the two other variants. Special care has to be taken while designing the di-base dispensation order. Here, we present a detailed protocol for establishing sequence-specific di-base addition to avoid nonsynchronous extension at the SNP sites. By using this technology, as few as 50 copies of DNA templates were accurately sequenced. Higher signals were produced and thus a relatively lower sample amount was required. Furthermore, the read length of per flow was increased, making simultaneous identification of multiple SNPs in a single sequencing run possible. Validation of the method was performed by using templates with two SNPs covering 37 bp and with three SNPs covering 58 bp as well as 82 bp. These SNPs were successfully genotyped by using only a sequencing primer in a single PCR/sequencing run. Our results demonstrated that this technology could be potentially developed into a powerful methodology to accurately determine SNPs so as to diagnose clinical settings.

  10. 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.

  11. Association between the DRD2-141C Insertion/Deletion polymorphism and schizophrenia Associação entre o polimorfismo -141C Ins/Del do gene do DRD2 e esquizofrenia

    Directory of Open Access Journals (Sweden)

    Quirino Cordeiro

    2009-06-01

    Full Text Available Epidemiological studies have demonstrated that the genetic component is an important risk factor for the development of schizophrenia. The genes that codify the different compounds of the dopaminergic system have created interest for molecular investigations in patients with schizophrenia because the antipsychotic drugs, especially those of first generation, act on this cerebral system. Thus the aim of the present study was to investigate the possible association between the -141 Ins/Del (rs1799732 polymorphism of the dopamine receptor type 2 (DRD2 and schizophrenia. The distribution of the alleles and genotypes of the studied polymorphism was investigated in a sample of 229 patients and 733 controls. There were statistical differences in the allelic (χ2=9.78; p=0.001 and genotypic genotypic (χ2=12.74; p=0.001 distributions between patients and controls. Thus the -141C Ins/Del polymorphism of the DRD2 gene (allele Ins was associated to the SCZ phenotype in the investigated sample.Estudos epidemiológicos têm demonstrado que o componente genético é um importante fator de risco para o desenvolvimento de esquizofrenia. Os genes que codificam os diferentes componentes do sistema dopaminérgico passaram a despertar interesse para os estudos moleculares em pacientes com esquizofrenia, devido ao fato dos antipsicóticos, em especial os de primeira geração, exercerem sua ação nesse sistema. Assim, o objetivo do presente estudo foi investigar a possível associação entre polimorfismo -141C Ins/Del (rs1799732 do gene do receptor dopaminérgico tipo 2 (DRD2 e esquizofrenia. Um total de 229 pacientes e 733 controles pareados para sexo e idade foi selecionado com o objetivo de investigar a distribuição dos alelos e genótipos do polimorfismo investigado entre os grupos de pacientes e controles. Houve diferença estatisticamente significante nas distribuições alélica (χ2=9,78; p=0,001 e genotípica (χ2=12,74; p=0,001 entre pacientes e

  12. MICA polymorphism in a population from north Morocco, Metalsa Berbers, using sequence-based typing.

    Science.gov (United States)

    Piancatelli, Daniela; Del Beato, Tiziana; Oumhani, Khadija; El Aouad, Rajae; Adorno, Domenico

    2005-08-01

    The MICA gene encodes a family of nonclassical major histocompatibility complex class I molecules. Data on MICA polymorphism in different populations are still limited. In the present study, MICA allele frequencies (af) were assessed in 82 unrelated healthy individuals from a Moroccan Berber population named Metalsa (ME) by means of sequence-based typing of exons 2, 3, 4, and 5. In consideration of the linkage disequilibrium existing between MICA and human leukocyte antigen (HLA) class I alleles, MICA/HLA-B, MICA/HLA-Cw, and MICA/HLA-A haplotype frequencies (hf) were estimated. A wide allelic distribution including 16 different MICA alleles was found in ME. The most common MICA alleles were MICA*00801 (af = 0.268), *004 (0.232), *00902 (0.140), *00901 (0.085), and *00901 (0.073). The most common MICA/HLA-B haplotypes were MICA*004-B*4403 and MICA*009-B*50 (hf = 0.113 for both these haplotypes). Some known MICA and HLA-B associations were confirmed in this population. Noteworthy was the high frequency of MICA*009 (af = 0.226); the high frequency of B*50 found in ME (af = 0.114) permitted us to evidence the associations of MICA*00902 with B*5001 (hf = 0.068) or *5002 (hf = 0.045), whereas MICA*00901 was mainly associated with B*5101 (hf = 0.038), which corresponds to the previously described association MICA*009/A6-HLA-B*51. This study extends the previous knowledge on MICA polymorphism to a North African white population and may have implications for disease associations and transplantation.

  13. Prediction formulas for individual opioid analgesic requirements based on genetic polymorphism analyses.

    Directory of Open Access Journals (Sweden)

    Kaori Yoshida

    Full Text Available The analgesic efficacy of opioids is well known to vary widely among individuals, and various factors related to individual differences in opioid sensitivity have been identified. However, a prediction model to calculate appropriate opioid analgesic requirements has not yet been established. The present study sought to construct prediction formulas for individual opioid analgesic requirements based on genetic polymorphisms and clinical data from patients who underwent cosmetic orthognathic surgery and validate the utility of the prediction formulas in patients who underwent major open abdominal surgery.To construct the prediction formulas, we performed multiple linear regression analyses using data from subjects who underwent cosmetic orthognathic surgery. The dependent variable was 24-h postoperative or perioperative fentanyl use, and the independent variables were age, gender, height, weight, pain perception latencies (PPL, and genotype data of five single-nucleotide polymorphisms (SNPs. To examine the utility of the prediction formulas, we performed simple linear regression analyses using subjects who underwent major open abdominal surgery. Actual 24-h postoperative or perioperative analgesic use and the predicted values that were calculated using the multiple regression equations were incorporated as dependent and independent variables, respectively.Multiple linear regression analyses showed that the four SNPs, PPL, and weight were retained as independent predictors of 24-h postoperative fentanyl use (R² = 0.145, P = 5.66 × 10⁻¹⁰ and the two SNPs and weight were retained as independent predictors of perioperative fentanyl use (R² = 0.185, P = 1.99 × 10⁻¹⁵. Simple linear regression analyses showed that the predicted values were retained as an independent predictor of actual 24-h postoperative analgesic use (R² = 0.033, P = 0.030 and perioperative analgesic use (R² = 0.100, P = 1.09 × 10⁻⁴, respectively.We constructed

  14. An Elementary Account of Needle Insertion

    Institute of Scientific and Technical Information of China (English)

    张文兵; 霍则军

    2004-01-01

    @@ Based on the authors' clinical and personal experiences, several pain-inducing factors easily to be ignored by the operators when quick needle insertion is applied, and the authors' first invented slow painless needle insertion method are introduced in the article.

  15. 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.

  16. 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.

  17. Chest tube insertion - slideshow

    Science.gov (United States)

    ... presentations/100008.htm Chest tube insertion - series—Normal anatomy To use the sharing features ... pleural space is the space between the inner and outer lining of the lung. It is normally very thin, and lined only ...

  18. 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.

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

    Science.gov (United States)

    Wang, Bei; Zhang, Xiaoyu; Zhao, Zhendong

    2013-08-01

    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.

  20. Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

    Science.gov (United States)

    de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

    2009-01-01

    Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs.

  1. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  2. Multipurpose Transposon-Insertion Libraries in Yeast.

    Science.gov (United States)

    Kumar, Anuj

    2016-06-01

    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.

  3. Comparing Leaf and Root Insertion

    Directory of Open Access Journals (Sweden)

    Jaco Geldenhuys

    2010-07-01

    Full Text Available We consider two ways of inserting a key into a binary search tree: leaf insertion which is the standard method, and root insertion which involves additional rotations. Although the respective cost of constructing leaf and root insertion binary search trees trees, in terms of comparisons, are the same in the average case, we show that in the worst case the construction of a root insertion binary search tree needs approximately 50% of the number of comparisons required by leaf insertion.

  4. CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA.

    Science.gov (United States)

    Miura, Hiromi; Gurumurthy, Channabasavaiah B; Sato, Takehito; Sato, Masahiro; Ohtsuka, Masato

    2015-08-05

    Knockdown mouse models, where gene dosages can be modulated, provide valuable insights into gene function. Typically, such models are generated by embryonic stem (ES) cell-based targeted insertion, or pronuclear injection, of the knockdown expression cassette. However, these methods are associated with laborious and time-consuming steps, such as the generation of large constructs with elements needed for expression of a functional RNAi-cassette, ES-cell handling, or screening for mice with the desired knockdown effect. Here, we demonstrate that reliable knockdown models can be generated by targeted insertion of artificial microRNA (amiRNA) sequences into a specific locus in the genome [such as intronic regions of endogenous eukaryotic translation elongation factor 2 (eEF-2) gene] using the Clustered Regularly Interspaced Short Palindromic Repeats/Crispr associated 9 (CRISPR/Cas9) system. We used in vitro synthesized single-stranded DNAs (about 0.5-kb long) that code for amiRNA sequences as repair templates in CRISPR/Cas9 mutagenesis. Using this approach we demonstrate that amiRNA cassettes against exogenous (eGFP) or endogenous [orthodenticle homeobox 2 (Otx2)] genes can be efficiently targeted to a predetermined locus in the genome and result in knockdown of gene expression. We also provide a strategy to establish conditional knockdown models with this method.

  5. Keyboard and Mouse Insertion Authorization System Based on Filter Drive%基于过滤驱动的键盘鼠标插入授权系统

    Institute of Scientific and Technical Information of China (English)

    姜富强; 郑扣根

    2011-01-01

    In order to assure the information security of financial ATM, this paper studies and analyzes the keyboard and mouse drivers in Windows operating system, and based on filter driver, designs and implements keyboard and mouse insertion authorization system.The authorization system can detect the insertion of USB or PS/2 interfaced keyboard and mouse into the computer, and keeps the new device disabled before authorized.The final tests demonstrate that the system can be deployed and run on Windows XP and Windows 7 stably and efficiently.%为保证ATM的信息安全,分析Windows上键盘和鼠标设备驱动的工作原理,设计并实现基于过滤驱动的键盘鼠标插入事件授权系统.该授权系统能准确捕捉USB和PS/2接口的键盘鼠标设备的插拔事件,保证新插入的设备在系统授权前处于禁用状态.测试结果表明,系统能在Windows XP和Windows 7操作系统上高效稳定地运行.

  6. The Composite Insertion Electrode

    DEFF Research Database (Denmark)

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

    1984-01-01

    . The theoretical basis for such electrodes is discussedand, using a simplified model, equations are derived to describe the distribution of potential and current duringdischarge/charge operation. Under the assumption that the insertion compound particles are small enough to ensureequilibrium, and that the local...... electrode potential depends linearly on the degree of insertion, these equations are solvedto obtain analytical expressions for the discharge curve. It is shown that the parameters which determine the dischargebehavior for a given discharge current are simply related to the effective ionic and electronic...

  7. 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.

  8. Digital camera and smartphone as detectors in paper-based chemiluminometric genotyping of single nucleotide polymorphisms.

    Science.gov (United States)

    Spyrou, Elena M; Kalogianni, Despina P; Tragoulias, Sotirios S; Ioannou, Penelope C; Christopoulos, Theodore K

    2016-10-01

    Chemi(bio)luminometric assays have contributed greatly to various areas of nucleic acid analysis due to their simplicity and detectability. In this work, we present the development of chemiluminometric genotyping methods in which (a) detection is performed by using either a conventional digital camera (at ambient temperature) or a smartphone and (b) a lateral flow assay configuration is employed for even higher simplicity and suitability for point of care or field testing. The genotyping of the C677T single nucleotide polymorphism (SNP) of methylenetetrahydropholate reductase (MTHFR) gene is chosen as a model. The interrogated DNA sequence is amplified by polymerase chain reaction (PCR) followed by a primer extension reaction. The reaction products are captured through hybridization on the sensing areas (spots) of the strip. Streptavidin-horseradish peroxidase conjugate is used as a reporter along with a chemiluminogenic substrate. Detection of the emerging chemiluminescence from the sensing areas of the strip is achieved by digital camera or smartphone. For this purpose, we constructed a 3D-printed smartphone attachment that houses inexpensive lenses and converts the smartphone into a portable chemiluminescence imager. The device enables spatial discrimination of the two alleles of a SNP in a single shot by imaging of the strip, thus avoiding the need of dual labeling. The method was applied successfully to genotyping of real clinical samples. Graphical abstract Paper-based genotyping assays using digital camera and smartphone as detectors.

  9. Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors.

    Science.gov (United States)

    Schindler, Daniel; Milbredt, Sarah; Sperlea, Theodor; Waldminghaus, Torsten

    2016-12-16

    Efficient assembly of large DNA constructs is a key technology in synthetic biology. One of the most popular assembly systems is the MoClo standard in which restriction and ligation of multiple fragments occurs in a one-pot reaction. The system is based on a smart vector design and type IIs restriction enzymes, which cut outside their recognition site. While the initial MoClo vectors had been developed for the assembly of multiple transcription units of plants, some derivatives of the vectors have been developed over the last years. Here we present a new set of MoClo vectors for the assembly of fragment libraries and insertion of constructs into bacterial chromosomes. The vectors are accompanied by a computer program that generates a degenerate synthetic DNA sequence that excludes "forbidden" DNA motifs. We demonstrate the usability of the new approach by construction of a stable fluorescence repressor operator system (FROS).

  10. 血管紧张素转换酶基因插入或缺失多态性与飞行员原发性高血压的相关性%Relationship between insertion/deletion polymorphism of the angiotensin-convetting enzyme gene and essential hypertension in pilots

    Institute of Scientific and Technical Information of China (English)

    蔡庆; 刘红巾; 陈涛; 朱美财

    2011-01-01

    目的 探讨血管紧张素转换酶(ACE)基因插入或缺失(L/D)多态性和飞行员原发性高血压的相关性,为飞行员原发性高血压的预防提供依据.方法 用聚合酶链反应(PCR)扩增检测48例飞行员原发性高血压患者和50例飞行员健康对照者的ACE基因I/D多态性.结果 飞行员高血压组ACE DD基因型(25%)和D等位基因频率(0.47)显著高于健康对照组(分别为8%和0.30).结论 ACE DD基因型和D等位基因与飞行员原发性高血压病相关.%Objective To investigate the relationship between insertion/delation (I/D) polymorphism of the angiotensin-converting enzyme (ACE) gene and essential hypertension of pilots and provide an important reference for essential hypertension of pilots. Methods 48 pilots with essential hypertension and SO healthy control pilots were genotyped for the I/D polymorphism of the ACE gene by the polymerase chain reaction (PCR). Results It was showed that the genotype DD and D allele frequency of ACE were significantly higher in pilots with essential hypertension (25% and 0.47) than that in healthy control subjects (8% and 0.30). Conclusion The genotype DD and D allele of ACE were correlated with essential hypertension in pilots.

  11. 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.

  12. 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

  13. Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

    OpenAIRE

    Kabadjova, Petia; Dousset, Xavier; Le Cam, Virginie; Prevost, Hervé

    2002-01-01

    A novel strategy for identification of Carnobacterium food isolates based on restriction fragment length polymorphism (RFLP) of PCR-amplified 16S-23S ribosomal intergenic spacer regions (ISRs) was developed. PCR amplification from all Carnobacterium strains studied always yielded three ISR amplicons, which were designated the small ISR (S-ISR), the medium ISR (M-ISR), and the large ISR (L-ISR). The lengths of these ISRs varied from one species to another. Carnobacterium divergens NCDO 2763T a...

  14. 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.

  15. 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

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

    Science.gov (United States)

    Zhang, Xuezhu; Stortz, Greg; Sossi, Vesna; Thompson, Christopher J.; Retière, Fabrice; Kozlowski, Piotr; Thiessen, Jonathan D.; Goertzen, Andrew L.

    2013-12-01

    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

  17. 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

  18. Effect of an interface Mg insertion layer on the reliability of a magnetic tunnel junction based on a Co{sub 2}FeAl full-Heusler alloy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jungmin; Kil, Gyuhyun; Lee, Gaehun; Choi, Chulmin; Song, Yunheub [Hanyang University, Seoul (Korea, Republic of); Sukegawa, Hiroaki; Mitani, Seiji [National Institute for Materials Science, Ibaraki (Japan)

    2014-04-15

    The reliability of a magnetic tunnel junction (MTJ) based on a Co{sub 2}FeAl (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.

  19. A time-temperature integrator based on fluorescent and polymorphic compounds.

    Science.gov (United States)

    Gentili, Denis; Durso, Margherita; Bettini, Cristian; Manet, Ilse; Gazzano, Massimo; Capelli, Raffaella; Muccini, Michele; Melucci, Manuela; Cavallini, Massimiliano

    2013-01-01

    Despite the variety of functional properties of molecular materials, which make them of interest for a number of technologies, their tendency to form inhomogeneous aggregates in thin films and to self-organize in polymorphs are considered drawbacks for practical applications. Here, we report on the use of polymorphic molecular fluorescent thin films as time temperature integrators, a class of devices that monitor the thermal history of a product. The device is fabricated by patterning the fluorescent model compound thieno(bis)imide-oligothiophene. The fluorescence colour of the pattern changes as a consequence of an irreversible phase variation driven by temperature, and reveals the temperature at which the pattern was exposed. The experimental results are quantitatively analysed in the range 20-200°C and interpreted considering a polymorph recrystallization in the thin film. Noteworthy, the reported method is of general validity and can be extended to every compound featuring irreversible temperature-dependent change of fluorescence.

  20. 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.

  1. Toward the authentication of wines of Nemea denomination of origin through cleaved amplified polymorphic sequence (CAPS)-based assay.

    Science.gov (United States)

    Spaniolas, Stelios; Tsachaki, Maroussa; Bennett, Malcolm J; Tucker, Gregory A

    2008-09-10

    In the present study, we developed a cleaved amplified polymorphic sequence (CAPS)-based assay as a first attempt to detect fraud in grapevine musts with a long-term objective to establish an analytical methodology to authenticate wines of Nemea denomination of origin (Agiorgitiko). The analytical assay makes use of a single nucleotide polymorphism that discriminates Agiorgitiko and Cabernet Sauvignon varieties. The latter grape variety is one of the major adulterants for Nemea wines. Agiorgitiko grapevine must was spiked with Cabernet Sauvignon in several ratios (v/v) from 50 down to 10%, and the subsequent mixes were subjected to alcoholic microfermentation. DNA was extracted from all mixture samples up to the end of the fermentation process and was subjected to the CAPS assay. Both standard agarose gel and lab-on-a-chip capillary electrophoresis illustrated the ability of the method to detect the presence of Cabernet Sauvignon down to 10% throughout the whole fermentation process.

  2. Morphological and sequence-related amplified polymorphism-based molecular diversity of local and exotic wheat genotypes.

    Science.gov (United States)

    Abdelkhalik, S M; Salem, A K M; Abdelaziz, A R; Ammar, M H

    2016-04-28

    Assessing genetic diversity is a prerequisite for the genetic improvement of wheat. Molecular markers offer accurate and reproducible means for assessing genetic diversity. Field performance and sequence-related amplified polymorphism (SRAP)-based assessment of molecular diversity was carried out on a set of 10 local and introduced bread wheat (Triticum sativum L.) genotypes grown in the middle arid region of Saudi Arabia. The results revealed highly significant differences among the studied phenological traits and revealed a significant amount of genetic diversity across the tested genotypes. The overall performance revealed the superiority of KSU 102 in terms of yield and its components, with a yield potential of 8.7 tons/ha. Highly significant and positive correlations were observed among grain yield and biological yield, and also, spike length and spike weight. Thirteen SRAP primer combinations successfully amplified 954 fragments. The total number of genetic loci analyzed was 312. The overall polymorphism ratio was 99.67%, ranging from 98 to 100%. The polymorphic information content values ranged from 0.67 for ME11 x EM5 to 0.97 for ME9 x EM4 and ME11 x EM6, respectively. The wheat genotypes were clustered based on their genetic constitution and origin. The results demonstrate the power of SRAP primers for detecting molecular diversity and for varietal discrimination. The results show that high levels of genetic diversity exist, and suggest the potential of the tested materials for wheat crop improvement in the arid central region of Saudi Arabia.

  3. Molecular typing of nosocomial Staphylococcus aureus strains associated to biofilm based on the coagulase and protein A gene polymorphisms

    Science.gov (United States)

    Salehzadeh, Ali; Zamani, Hojjatolah; Langeroudi, Maedeh Keshtkar; Mirzaie, Amir

    2016-01-01

    Objective(s): Staphylococcus aureus is an important bacterial pathogen responsible for a variety numbers of nosocomial and community acquired infections. Biofilm formation is regarded as an important factor in the establishment of S. aureus infection. The contribution of the genetic background of S. aureus to biofilm formation is poorly understood. The aim of the present work was to genotype S. aureus strains associated to biofilm based on the coagulase and protein A genes and to evaluate the association between the genetic background and the biofilm forming ability of clinical S. aureus isolates. Materials and Methods: A total number of 100 S. aureus were isolated from nosocomial infections and biofilm formation capability was investigated using phenotypic assay and molecular detection of biofilm associated genes. The strains were genotyped based on coagulase (coa) and protein A (spa) gene polymorphisms using restriction fragments length polymorphism-polymerase chain reaction (RFLP-PCR). Results: RFLP-PCR of coa gene generated two types and three subtypes. Amplification of spa gene resulted in two banding patterns and their restriction digestion generated three subtypes. The combined coa and spa RFLP patterns generated nine genotypes (G1-G9). The genotypes G4 and G1 were the most prevalent (32.1% and 24.3%, respectively). Conclusion: High clonal diversity of S. aureus strains able to produce biofilm was observed. Biofilm formation correlates with the spa and coa clonal lineage in our population and testing for multiple gene polymorphisms could be employed for local epidemiologic purposes. PMID:28096965

  4. Molecular typing of nosocomial Staphylococcus aureus strains associated to biofilm based on the coagulase and protein A gene polymorphisms

    Directory of Open Access Journals (Sweden)

    Ali Salehzadeh

    2016-12-01

    Full Text Available Objective(s: Staphylococcus aureus is an important bacterial pathogen responsible for a variety numbers of nosocomial and community acquired infections. Biofilm formation is regarded as an important factor in the establishment of S. aureus infection. The contribution of the genetic background of S. aureus to biofilm formation is poorly understood. The aim of the present work was to genotype S. aureus strains associated to biofilm based on the coagulase and protein A genes and to evaluate the association between the genetic background and the biofilm forming ability of clinical S. aureus isolates. Materials and Methods: A total number of 100 S. aureus were isolated from nosocomial infections and biofilm formation capability was investigated using phenotypic assay and molecular detection of biofilm associated genes. The strains were genotyped based on coagulase (coa and protein A (spa gene polymorphisms using restriction fragments length polymorphism-polymerase chain reaction (RFLP-PCR. Results: RFLP-PCR of coa gene generated two types and three subtypes. Amplification of spa gene resulted in two banding patterns and their restriction digestion generated three subtypes. The combined coa and spa RFLP patterns generated nine genotypes (G1-G9. The genotypes G4 and G1 were the most prevalent (32.1% and 24.3%, respectively. Conclusion: High clonal diversity of S. aureus strains able to produce biofilm was observed. Biofilm formation correlates with the spa and coa clonal lineage in our population and testing for multiple gene polymorphisms could be employed for local epidemiologic purposes.

  5. Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping

    Science.gov (United States)

    Expressed sequence tags (ESTs) were analyzed in silico in order to identify single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) in cotton. A total of 1349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, m...

  6. A study of insertion/delation polymorphism of the angiotensin-converting enzyme gene and serum ACE concentration in pilots%飞行员血管紧张素转换酶基因插入/缺失 多态性及其血清水平的研究

    Institute of Scientific and Technical Information of China (English)

    刘红巾; 蔡庆; 纪桂英; 朱美财; 占志; 王荫静

    2001-01-01

    Objective To understand insertion/delation (I/D ) polymorphism of the angiotensin-converting enzyme (ACE) gene and serum ACE co ncentration in pilots, and to explore the relationship between ACE gene I/D poly morphism and the perfomance of the pilots. Methods The study p opulation consisted of 118 pilots and 96 healthy subjects as controls. The genot ypes for an I/D polymorphism in intron 16 of the ACE gene were determined by the polymerase chain reaction (PCR). The serum ACE concentration was measured by hi gh-performance liquid chromatography with the use of an artificial substrate.[ WTHZ  Results The I/D polymorphism in intron 16 of the ACE gene was c ategorized into three genotypes: two deletion alleles (genotype DD), heterozygou s alleles (genotype ID), and two insertion alleles (genotype II). The genotype I I and I allele frequency were significantly higher in pilots (44.07% and 0.65) than that in healthy subjects (31.25% and 0.52). The ACE gene I/D polymorphis m is strongly associated with serum ACE levels(DD>ID, DD>II). Conclusio n It is suggested that I gene of ACE may play a role in perfomance of t he pilots.%目的了解飞行员血管紧张素转换酶(ACE)基因插入/缺失( I/D)多态性及其血清水平,探讨ACE基因多态性与飞行员耐力可能的关系。方法飞行员118例,健康对照者96例,用聚合酶链反应(PCR)扩增技术检测ACE基因I /D多态性,用比色法测定血清ACE水平。结果位于ACE基因第16内含子的I/D多态性经PCR扩增后呈三种基因型:纯合子插入型(II)、纯合子缺失型(DD)和杂合子插入/缺失型(I/D)。飞行员组II基因型(44.07%)和Ⅰ等位基因频率(0.65)显著高于健康对照组(分别为31.25%和0.52)。 ACE基因多态性与血清ACE水平明显相关(DD>ID, D D>II)。结论 ACE Ⅰ基因有可能在飞行员的飞行耐力中起重要作用。

  7. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y.; Zhang, X.; Dantas Machado, A. C.; Ding, Y.; Chen, Z.; Qin, P. Z.; Rohs, R.; Chen, L.

    2013-07-08

    The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.

  8. Numerical modeling of first experiments on PbLi MHD flows in a rectangular duct with foam-based SiC flow channel insert

    Energy Technology Data Exchange (ETDEWEB)

    Smolentsev, S., E-mail: sergey@fusion.ucla.edu [University of California, Los Angeles (United States); Courtessole, C.; Abdou, M.; Sharafat, S. [University of California, Los Angeles (United States); Sahu, S. [Institute of Plasma Research (India); Sketchley, T. [University of California, Los Angeles (United States)

    2016-10-15

    Highlights: • Numerical studies were performed as a pre-experimental analysis to the experiment on MHD PbLi flows in a rectangular duct with a flow channel insert (FCI). • Dynamic testing of foam-based SiC foam-based CVD coated FCI has been performed using MaPLE facility at UCLA. • Two physical models were proposed to explain the experimental results and 3D and 2D computations performed using COMSOL, HIMAG and UCLA codes. • The obtained results suggest that more work on FCI development, fabrication and testing has to be done to assure good hermetic properties before the implementation in a fusion device. - Abstract: A flow channel insert (FCI) is the key element of the DCLL blanket concept. The FCI serves as electrical and thermal insulator to reduce the MHD pressure drop and to decouple the temperature-limited ferritic structure from the flowing hot lead-lithium (PbLi) alloy. The main focus of the paper is on numerical computations to simulate MHD flows in the first experiments on PbLi flows in a stainless steel rectangular duct with a foam-based silicon carbide (SiC) FCI. A single uninterrupted long-term (∼6500 h) test has recently been performed on a CVD coated FCI sample in the flowing PbLi in a magnetic field up to 1.5 T at the PbLi temperature of 300 °C using the MaPLE loop at UCLA. An unexpectedly high MHD pressure drop measured in this experiment suggests that a PbLi ingress into the FCI occurred in the course of the experiment, resulting in degradation of electroinsulating FCI properties. The ingress through the protective CVD layer was further confirmed by the post-experimental microscopic analysis of the FCI. The numerical modeling included 2D and 3D computations using HIMAG, COMSOL and a UCLA research code to address important flow features associated with the FCI finite length, fringing magnetic field, rounded FCI corners and also to predict changes in the MHD pressure drop in the unwanted event of a PbLi ingress. Two physical

  9. No association of genetic polymorphisms in CYP1B1 with primary open-angle glaucoma: a meta- and gene-based analysis

    OpenAIRE

    Dong, Shuqian; Yang, Jingyun; Yu, Weihong; Kota, Pravina; Xia, Xiaobo; Xu, Huizhuo

    2012-01-01

    Purpose To examine the effects of genetic polymorphisms in cytochrome P450, subfamily 1, polypeptide 1 (C1P1B1) on primary open-angle glaucoma (POAG). Methods A systematic literature search was performed, and random-effects meta-analyses were used to evaluate genetic polymorphisms in CYP1B1 with POAG. A gene-based analysis was conducted to investigate the cumulative effects of genetic polymorphisms in CYP1B1. Results A total of six studies from published papers were included in our analysis. ...

  10. VEGFA polymorphisms and cardiovascular anomalies in 22q11 microdeletion syndrome: a case-control and family-based study.

    Science.gov (United States)

    Calderón, Juan Francisco; Puga, Alonso R; Guzmán, M Luisa; Astete, Carmen Paz; Arriaza, Marta; Aracena, Mariana; Aravena, Teresa; Sanz, Patricia; Repetto, Gabriela M

    2009-01-01

    Microdeletion 22q11 in humans causes velocardiofacial and DiGeorge syndromes. Most patients share a common 3Mb deletion, but the clinical manifestations are very heterogeneous. Congenital heart disease is present in 50-80% of patients and is a significant cause of morbidity and mortality. The phenotypic variability suggests the presence of modifiers. Polymorphisms in the VEGFA gene, coding for the vascular endothelial growth factor A, have been associated with non-syndromic congenital heart disease, as well as with the presence of cardiovascular anomalies in patients with microdeletion 22q11. We evaluated the association of VEGFA polymorphisms c.-2578C>A (rs699947), c.-1154G>A (rs1570360) and c.-634C>G (rs2010963) with congenital heart disease in Chilean patients with microdeletion 22q11. The study was performed using case-control and family-based association designs. We evaluated 122 patients with microdeletion 22q11 and known anatomy of the heart and great vessels, and their parents. Half the patients had congenital heart disease. We obtained no evidence of association by either method of analysis. Our results provide further evidence of the incomplete penetrance of the cardiovascular phenotype of microdeletion 22ql 1, but do not support association between VEGFA promoter polymorphisms and the presence of congenital heart disease in Chilean patients with this syndrome.

  11. Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica.

    Science.gov (United States)

    Matsumoto, A; Tsumura, Y

    2004-12-01

    We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (approximately 30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (Pobtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.

  12. 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.

  13. 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....

  14. CYP1A1 genetic polymorphism and polycyclic aromatic hydrocarbons on pulmonary function in the elderly: haplotype-based approach for gene-environment interaction.

    Science.gov (United States)

    Choi, Yoon-Hyeong; Kim, Jin Hee; Hong, Yun-Chul

    2013-08-29

    Lung function may be impaired by environmental pollutants not only acting alone, but working with genetic factors as well. Few epidemiologic studies have been conducted to explore the interplay of polycyclic aromatic hydrocarbons (PAHs) exposure and genetic polymorphism on lung function in the elderly. For genetic polymorphism, haplotype is considered a more informative unit than single nucleotide polymorphism markers. Therefore, we examined the role of haplotype based-CYP1A1 polymorphism in the effect of PAHs exposure on lung function in 422 participants from a community-based panel of elderly adults in Seoul, Korea. Linear mixed effect models were fit to evaluate the association of PAH exposure markers (urinary 1-hydroxypyrene and 2-naphthol) with FVC, FEV₁, FEV₁/FVC, and FEF₂₅₋₇₅, and then the interaction with CYP1A1 haplotype constructed from three single nucleotide polymorphisms of the gene (rs4646421/rs4646422/rs1048943). Urinary 1-hydroxypyrene levels were inversely associated with FEV₁/FVC (ppolymorphisms on lung functions. Our findings suggest that PAH exposure producing 1-hydroxypyrene as a metabolite compromises lung function in the elderly, and that haplotype-based CYP1A1 polymorphism modifies the risk.

  15. 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...

  16. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2004-01-01

    Full Text Available Abstract Background Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison. Results In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors. Conclusions We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at http://minisatellites.u-psud.fr now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial

  17. Population-based case-control study of DRD2 gene polymorphisms and alcoholism.

    Science.gov (United States)

    Bhaskar, L V K S; Thangaraj, K; Non, A L; Singh, Lalji; Rao, V R

    2010-10-01

    Several independent lines of evidence for genetic contributions to vulnerability to alcoholism exist. Dopamine is thought to play a major role in the mechanism of reward and reinforcement in response to alcohol. D2 dopamine receptor (DRD2) gene has been among the stronger candidate genes implicated in alcoholism. In this study, alcohol use was assessed in 196 randomly selected Kota individuals of Nilgiri Hills, South India. Six DRD2 SNPs were assessed in 81 individuals with alcoholism and 151 controls to evaluate the association between single nucleotide polymorphisms (SNPs) and alcoholism. Of the three models (dominant, recessive, and additive) tested for association between alcoholism and DRD2 SNPs, only the additive model shows association for three loci (rs1116313, TaqID, and rs2734835). Of six studied polymorphisms, five are in strong linkage disequilibrium forming onesingle haplotype block. Though the global haplotype analysis with these five SNPs was not significant, haplotype analysis using all six SNPs yielded a global P value of .033, even after adjusting for age. These findings support the importance of dopamine receptor gene polymorphisms in alcoholism. Further studies to replicate these findings in different populations are needed to confirm these results.

  18. 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.

  19. Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.

    Indian Academy of Sciences (India)

    Anukool Srivastava; Samir V. Sawant; Satya Narayan Jena

    2015-12-01

    Microarrays offer an opportunity to explore the functional sequence polymorphism among different cultivars of many crop plants. The Affymetrix microarray expression data of five genotypes of Gossypium hirsutum L. at six different fibre developmental stages was used to identify single feature polymorphisms (SFPs). The background corrected and quantile-normalized log2 intensity values of all probes of triplicate data of each cotton variety were subjected to SFPs call by using SAM procedure in R language software. We detected a total of 37,473 SFPs among six pair genotype combinations of two superior (JKC777 and JKC725) and three inferior (JKC703, JKC737 and JKC783) using the expression data. The 224 SFPs covering 51 genes were randomly selected from the dataset of all six fibre developmental stages of JKC777 and JKC703 for validation by sequencing on a capillary sequencer. Of these 224 SFPs, 132 were found to be polymorphic and 92 monomorphic which indicate that the SFP prediction from the expression data in the present study confirmed a ∼ 58.92% of true SFPs. We further identified that most of the SFPs are associated with genes involved in fatty acid, flavonoid, auxin biosynthesis etc. indicating that these pathways significantly involved in fibre development.

  20. A buffer insertion and simultaneous sizing timing optimization algorithm

    Institute of Scientific and Technical Information of China (English)

    Yin Guoli; Lin Zhenghui

    2006-01-01

    A path-based timing optimization algorithm for buffer insertion and simultaneous sizing is proposed.Firstly, candidate buffer insertion location and buffer size for each branch in a given routing path were obtained via localized timing optimization. Then, through evaluating each potential insertion against design objectives, potential optimal buffer insertion locations and sizes for the whole routing tree were determined. At last, by removing redundant buffer insertion operations which do not maximize S ( so ), given timing requirements are finally fulfilled through minimum number of buffers.

  1. Combination of DNA-based and conventional methods to detect human leukocyte antigen polymorphism and its use for paternity testing.

    Science.gov (United States)

    Kereszturya, László; Rajczya, Katalin; Lászikb, András; Gyódia, Eva; Pénzes, Mária; Falus, András; Petrányia, Gyõzõ G

    2002-03-01

    In cases of disputed paternity, the scientific goal is to promote either the exclusion of a falsely accused man or the affiliation of the alleged father. Until now, in addition to anthropologic characteristics, the determination of genetic markers included human leukocyte antigen gene variants; erythrocyte antigens and serum proteins were used for that reason. Recombinant DNA techniques provided a new set of highly variable genetic markers based on DNA nucleotide sequence polymorphism. From the practical standpoint, the application of these techniques to paternity testing provides greater versatility than do conventional genetic marker systems. The use of methods to detect the polymorphism of human leukocyte antigen loci significantly increases the chance of validation of ambiguous results in paternity testing. The outcome of 2384 paternity cases investigated by serologic and/or DNA-based human leukocyte antigen typing was statistically analyzed. Different cases solved by DNA typing are presented involving cases with one or two accused men, exclusions and nonexclusions, and tests of the paternity of a deceased man. The results provide evidence for the advantage of the combined application of various techniques in forensic diagnostics and emphasizes the outstanding possibilities of DNA-based assays. Representative examples demonstrate the strength of combined techniques in paternity testing.

  2. Hydrogen insertion in titanium carbide based thin films (nc-TiC{sub x}/a-C:H) - comparison with bulk TiC{sub x}

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Julien; Jaoul, Cédric, E-mail: jaoul@ensil.unilim.fr; Glandut, Nicolas; Lefort, Pierre

    2016-08-01

    Nanocomposites composed of titanium carbide nanosized grains embedded in an amorphous hydrogenated carbon matrix (nc-TiC{sub x}/a-C:H) are prepared by hybrid Magnetron Sputtering - PECVD process using a titanium metal target and gaseous C{sub 6}H{sub 6}. By controlling the benzene flow rate, thin films with different carbon content are obtained. The structures of nc-TiC{sub x}/a-C:H materials are analyzed by X-ray diffraction, X-ray photoelectron and Raman spectroscopic methods. The electrochemical hydrogen insertion, as studied by cyclic voltammetry, strongly depends on the carbon content in the thin films. The correlation between the hydrogen insertion ability and the structure of materials are discussed. Furthermore, we show that the hydrogen insertion in these thin films reaches values much more significant than in bulk substoichiometric titanium carbide obtained by reactive sintering. - Highlights: • nc-TiC{sub x}/a-C:H thin films are prepared hybrid Magnetron Sputtering - PECVD process. • Different carbon contents are obtained by changing the hydrocarbon flowrate. • Expanded lattice parameter of the TiC{sub x} phase and a-C:H phase are observed. • Electrochemical hydrogen insertion strongly depends on the carbon content. • The maximum insertion is 22 times more important than bulk TiC{sub x}.

  3. Association between the p53 codon 72 polymorphism and primary open-angle glaucoma risk: Meta-analysis based on 11 case–control studies

    Directory of Open Access Journals (Sweden)

    Mohsen Gohari

    2016-01-01

    Full Text Available The TP53 is important in functions of cell cycle control, apoptosis, and maintenance of DNA integrity. Studies on the association between p53 codon 72 polymorphism and primary open-angle glaucoma (POAG risk have yielded conflicting results. Published literature from PubMed and Web of Science databases was retrieved. All studies evaluating the association between p53 codon 72 polymorphisms and POAG were included. Pooled odds ratio (OR and 95% confidence interval (CI were calculated. Eleven separate studies including 2541 cases and 1844 controls were pooled in the meta-analysis. We did not detect a significant association between POAG risk and p53 codon 72 polymorphism overall population except allele genetic model (C vs. G: OR = 0.961, 95% CI = 0.961–0.820, P = 0.622. In the stratified analysis for Asians and Caucasians, there was an association between p53 codon 72 polymorphism and POAG. In the dominant model in the overall population and by ethnicity subgroups, the highest elevated POAG risk was presented. In summary, these results indicate that p53 codon 72 polymorphism is likely an important genetic factor contributing to susceptibility of POAG. However, more case–controls studies based on larger sample size and stratified by ethnicity are suggested to further clarify the relationship between p53 codon 72 polymorphism and POAG.

  4. Freezing capture of polymorphic aggregates of bolaamphiphilic (L)-valine-based molecular hydrogelators.

    Science.gov (United States)

    Nebot, Vicent J; Díaz-Oltra, Santiago; Smets, Johan; Fernández Prieto, Susana; Miravet, Juan F; Escuder, Beatriu

    2014-05-01

    Nanostructured xerogels have been prepared by the freeze-drying of hydrogels and aggregates formed by bolaamphiphilic L-valine derivatives after aging under different environmental conditions. A wide variety of shapes and sizes has been achieved by a simple methodology. These nanostructures have been studied by SEM and WAXD and a dramatic influence of structural flexibility on the kinetics of aggregation has been observed. Such flexibility and a modulation of the hydrophobic effect have shown a profound influence in the packing of these compounds and revealed a high degree of polymorphism.

  5. 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.

  6. Implementation of a Permeable Membrane Insert-based Infection System to Study the Effects of Secreted Bacterial Toxins on Mammalian Host Cells.

    Science.gov (United States)

    Flaherty, Rebecca A; Lee, Shaun W

    2016-08-19

    Many bacterial pathogens secrete potent toxins to aid in the destruction of host tissue, to initiate signaling changes in host cells or to manipulate immune system responses during the course of infection. Though methods have been developed to successfully purify and produce many of these important virulence factors, there are still many bacterial toxins whose unique structure or extensive post-translational modifications make them difficult to purify and study in in vitro systems. Furthermore, even when pure toxin can be obtained, there are many challenges associated with studying the specific effects of a toxin under relevant physiological conditions. Most in vitro cell culture models designed to assess the effects of secreted bacterial toxins on host cells involve incubating host cells with a one-time dose of toxin. Such methods poorly approximate what host cells actually experience during an infection, where toxin is continually produced by bacterial cells and allowed to accumulate gradually during the course of infection. This protocol describes the design of a permeable membrane insert-based bacterial infection system to study the effects of Streptolysin S, a potent toxin produced by Group A Streptococcus, on human epithelial keratinocytes. This system more closely mimics the natural physiological environment during an infection than methods where pure toxin or bacterial supernatants are directly applied to host cells. Importantly, this method also eliminates the bias of host responses that are due to direct contact between the bacteria and host cells. This system has been utilized to effectively assess the effects of Streptolysin S (SLS) on host membrane integrity, cellular viability, and cellular signaling responses. This technique can be readily applied to the study of other secreted virulence factors on a variety of mammalian host cell types to investigate the specific role of a secreted bacterial factor during the course of infection.

  7. 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.

  8. Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- and informatics-based approach.

    Directory of Open Access Journals (Sweden)

    Megan P Hall

    Full Text Available PURPOSE: To determine how a single nucleotide polymorphism (SNP- and informatics-based non-invasive prenatal aneuploidy test performs in detecting trisomy 13. METHODS: Seventeen trisomy 13 and 51 age-matched euploid samples, randomly selected from a larger cohort, were analyzed. Cell-free DNA was isolated from maternal plasma, amplified in a single multiplex polymerase chain reaction assay that interrogated 19,488 SNPs covering chromosomes 13, 18, 21, X, and Y, and sequenced. Analysis and copy number identification involved a Bayesian-based maximum likelihood statistical method that generated chromosome- and sample-specific calculated accuracies. RESULTS: Of the samples that passed a stringent DNA quality threshold (94.1%, the algorithm correctly identified 15/15 trisomy 13 and 49/49 euploid samples, for 320/320 correct copy number calls. CONCLUSIONS: This informatics- and SNP-based method accurately detects trisomy 13-affected fetuses non-invasively and with high calculated accuracy.

  9. 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.

  10. Genome relationships among Lotus species based on random amplified polymorphic DNA (RAPD).

    Science.gov (United States)

    Campos, L P; Raelson, J V; Grant, W F

    1994-06-01

    The ability of random amplified polymorphic DNA (RAPD) to distinguish among different taxa of Lotus was evaluated for several geographically dispersed accessions of four diploid Lotus species, L. tennis Waldst. et Kit, L. alpinus Schleich., L. japonicus (Regel) Larsen, and L. uliginosus Schkuhr and for the tetraploid L. corniculatus L., in order to ascertain whether RAPD data could offer additional evidence concerning the origin of the tetraploid L. corniculatus. Clear bands and several polymorphisms were obtained for 20 primers used for each species/accession. The evolutionary pathways among the species/accessions presented in a cladogram were expressed in terms of treelengths giving the most parsimonious reconstructions. Accessions within the same species grouped closely together. It is considered that L. uliginosus which is most distantly related to L. corniculatus, may be excluded as a direct progenitor of L. corniculatus, confirming previous results from isoenzyme studies. Lotus alpinus is grouped with accessions of L. corniculatus, which differs from previous studies. With this exception, these findings are in agreement with previous experimental studies in the L. corniculatus group. The value of the RAPD data to theories on the origin of L. corniculatus is discussed.

  11. 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.

  12. Genotyping of FCN and MBL2 Polymorphisms Using Pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans Ole; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...

  13. 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

    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...

  14. Impedance calculation for ferrite inserts

    Energy Technology Data Exchange (ETDEWEB)

    Breitzmann, S.C.; Lee, S.Y.; /Indiana U.; Ng, K.Y.; /Fermilab

    2005-01-01

    Passive ferrite inserts were used to compensate the space charge impedance in high intensity space charge dominated accelerators. They study the narrowband longitudinal impedance of these ferrite inserts. they find that the shunt impedance and the quality factor for ferrite inserts are inversely proportional to the imaginary part of the permeability of ferrite materials. They also provide a recipe for attaining a truly passive space charge impedance compensation and avoiding narrowband microwave instabilities.

  15. Targeted oligonucleotide-mediated microsatellite identification (TOMMI from large-insert library clones

    Directory of Open Access Journals (Sweden)

    Ren Jun

    2005-11-01

    Full Text Available Abstract Background In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD than does a di-allelic marker system 1. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced. Results Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI, an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC, average heterozygosity (HT, and effective allele number (NE for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds. Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles in this heterogeneous sampling. Most of the publicly available (porcine microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be

  16. Facts and fictions about polymorphism.

    Science.gov (United States)

    Cruz-Cabeza, Aurora J; Reutzel-Edens, Susan M; Bernstein, Joel

    2015-12-01

    We present new facts about polymorphism based on (i) crystallographic data from the Cambridge Structural Database (CSD, a database built over 50 years of community effort), (ii) 229 solid form screens conducted at Hoffmann-La Roche and Eli Lilly and Company over the course of 8+ and 15+ years respectively and (iii) a dataset of 446 polymorphic crystals with energies and properties computed with modern DFT-d methods. We found that molecular flexibility or size has no correlation with the ability of a compound to be polymorphic. Chiral molecules, however, were found to be less prone to polymorphism than their achiral counterparts and compounds able to hydrogen bond exhibit only a slightly higher propensity to polymorphism than those which do not. Whilst the energy difference between polymorphs is usually less than 1 kcal mol(-1), conformational polymorphs are capable of differing by larger values (up to 2.5 kcal mol(-1) in our dataset). As overall statistics, we found that one in three compounds in the CSD are polymorphic whilst at least one in two compounds from the Roche and Lilly set display polymorphism with a higher estimate of up to three in four when compounds are screened intensively. Whilst the statistics provide some guidance of expectations, each compound constitutes a new challenge and prediction and realization of targeted polymorphism still remains a holy grail of materials sciences.

  17. Single-strand conformation polymorphism-based analysis reveals genetic variation within Spirometra erinacei (Cestoda: Pseudophyllidea) from Australia.

    Science.gov (United States)

    Zhu, X Q; Beveridge, I; Berger, L; Barton, D; Gasser, R B

    2002-04-01

    This study examined genetic variability within Spirometra erinacei (Cestoda: Pseudophyllidea) from different host species and geographical origins in Australia using a polymerase chain reaction (PCR)-based mutation detection approach, followed by DNA sequencing. Part of the cytochrome c oxidase subunit 1 gene (p cox 1) was amplified by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and representative samples from different host species were selected for DNA sequencing. While no variation in SSCP profiles was detected among S. erinacei samples from dog, fox, cat, tiger snake and python, they differed in profile from 5 specimens from the green tree frog (Litoria caerulea). This was supported by sequence data which demonstrated that p cox 1 sequences of samples from the latter host species differed at 8 of 393 (2%) nucleotide positions from those from the non-amphibian host. Using a nucleotide difference in the p cox 1 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to unequivocally delineate between samples from non-amphibian and amphibian hosts. These findings demonstrate the existence of at least two genotypes within S. erinacei, which may have important implications for studying the epidemiology, ecology and systematics of this cestode.

  18. Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.

    Science.gov (United States)

    Fernandez I Marti, Angel; 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 world were screened with seven 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 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.

  19. 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.

  20. Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome

    Directory of Open Access Journals (Sweden)

    Byun Hyang-Min

    2012-02-01

    Full Text Available Abstract Background Retrotransposons have been extensively studied in plants and animals and have been shown to have an impact on human genome dynamics and evolution. Their ability to move within genomes gives retrotransposons to affect genome instability. Methods we examined the polymorphic inserted AluYa5, evolutionary young Alu, in the progesterone receptor gene to determine the effects of Alu insertion on molecular environment. We used mono-allelic inserted cell lines which carry both Alu-present and Alu-absent alleles. To determine the epigenetic change and gene expression, we performed restriction enzyme digestion, Pyrosequencing, and Chromatin Immunoprecipitation. Results We observed that the polymorphic insertion of evolutionally young Alu causes increasing levels of DNA methylation in the surrounding genomic area and generates inactive histone tail modifications. Consequently the Alu insertion deleteriously inactivates the neighboring gene expression. Conclusion The mono-allelic Alu insertion cell line clearly showed that polymorphic inserted repetitive elements cause the inactivation of neighboring gene expression, bringing aberrant epigenetic changes.

  1. 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

  2. Polymorphic Alu insertions and their associations with HLA Ⅰ alleles in Yugu and Zhuang ethnic populations%中国壮族和裕固族群体HLAⅠ类区域Alu插入多态性及其与HLA-A位点的相关性

    Institute of Scientific and Technical Information of China (English)

    史磊; 杨昭庆; 褚嘉祐; 姚宇峰; 史荔; 陶玉芬; 于亮; 黄小琴; 林克勤; 易文; 孙浩

    2011-01-01

    Many studies have show that the structurally polymorphic Alu insertion within HLA class I region are useful tools for investigating the origin, evolmion and recombination of HLA class Ⅰ progenitor haplotypes and gene diversity in different ethnic populations.In the present study, we determined the frequencies of HLA-Alus (i.e., AluMICB, AluTF,AluHJ, AluHG, and AluHF) in Zhuang and Yugu ethnic populations at first.Then combined with HLA genotyping data.we studied associations between HLA-Alus and HLA-A alleles in Zhuang, Yugu Bulang, Dai, and Hani ethnic populations.Our results showed that (l) the frequencies of five HLA-Alus were 1.5%~ 35.8% and 9.2%~34.8% in Zhuang and Yugu, respectively: and (2) the results of association between HLA-A alleles and HLA-Alu showed strong association between AluHG insalion and HLA-A *02 subtypes in all populations, association between AluHJ insertion and HLA-A *2402 in all populations, and association between AluHJ inseflion and HLA-A V/O/, -A *2407 in Bulang.The present study suggested that the distribution of HLA-Alus as well as the associations between HLA-Alus and HLA class I alleles are variable in different ethnic populations.HLA Alus alone or together with the HLA classⅠ alieles are informative genetic markers for the identification of HLA class I allele and variation of haplotype lineages in different populations.%近年来研究发现:位于HLAⅠ类基因区域的Alu插入是研究不同群体HLAⅠ类基因区域祖先单倍型和HLAⅠ类基因多样性产生、进化和重组的理想工具.文章对中国壮族和裕固族群体HLAⅠ类基因区域5个Alu插入多态性(AluMICB、AluTF、AluHJ、AluHG和AluHF)进行研究,结合HLA基因分型数据,分析壮族、裕固族、哈尼族、布朗族和傣族5个民族群体中Alu插入与HLA-A等位基因的关系.研究结果显示:(1)壮族和裕固族人群中5个Alu插入频率范围分别为1.5%~35.8%和9.2~34.8%,AluMICB、AluTF和Alu,HF插入

  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. 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.

  5. A comparative study of landmark-based topographic method versus the formula method for estimating depth of insertion of right subclavian central venous catheters

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    Tejesh C Anandaswamy

    2016-01-01

    Full Text Available Background and Aims: Subclavian central venous catheterisation (CVC is employed in critically ill patients requiring long-term central venous access. There is no gold standard for estimating their depth of insertion. In this study, we compared the landmark topographic method with the formula technique for estimating depth of insertion of right subclavian CVCs. Methods: Two hundred and sixty patients admitted to Intensive Care Unit requiring subclavian CVC were randomly assigned to either topographic method or formula method (130 in each group. Catheter tip position in relation to the carina was measured on a post-procedure chest X-ray. The primary endpoint was the need for catheter repositioning. Mann–Whitney test and Chi-square test was performed for statistical analysis using SPSS for windows version 18.0 (Armonk, NY: IBM Corp. Results: Nearly, half the catheters positioned by both the methods were situated >1 cm below the carina and required repositioning. Conclusion: Both the techniques were not effective in estimating the approximate depth of insertion of right subclavian CVCs.

  6. Multiplex and quantitative pathogen detection with high-resolution capillary electrophoresis-based single-strand conformation polymorphism.

    Science.gov (United States)

    Hwang, Hee Sung; Shin, Gi Won; Chung, Boram; Na, Jeongkyeong; Jung, Gyoo Yeol

    2013-01-01

    Among the molecular diagnostic methods for bacteria-induced diseases, capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) combined with 16S rRNA gene-specific PCR has enormous potential because it can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S rRNA gene-specific markers into separate peaks. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this report, a protocol for the detection of 12 pathogenic bacteria is provided. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing the easy identification of the pathogens.

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

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    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.

  8. 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.

  9. Plasmodium falciparum Polymorphisms associated with ex vivo drug susceptibility and clinical effectiveness of artemisinin-based combination therapies in Benin.

    Science.gov (United States)

    Dahlström, Sabina; Aubouy, Agnès; Maïga-Ascofaré, Oumou; Faucher, Jean-François; Wakpo, Abel; Ezinmègnon, Sèm; Massougbodji, Achille; Houzé, Pascal; Kendjo, Eric; Deloron, Philippe; Le Bras, Jacques; Houzé, Sandrine

    2014-01-01

    Artemisinin-based combination therapies (ACTs) are the main option to treat malaria, and their efficacy and susceptibility must be closely monitored to avoid resistance. We assessed the association of Plasmodium falciparum polymorphisms and ex vivo drug susceptibility with clinical effectiveness. Patients enrolled in an effectiveness trial comparing artemether-lumefantrine (n = 96), fixed-dose artesunate-amodiaquine (n = 96), and sulfadoxine-pyrimethamine (n = 48) for the treatment of uncomplicated malaria 2007 in Benin were assessed. pfcrt, pfmdr1, pfmrp1, pfdhfr, and pfdhps polymorphisms were analyzed pretreatment and in recurrent infections. Drug susceptibility was determined in fresh baseline isolates by Plasmodium lactate dehydrogenase enzyme-linked immunosorbent assay (ELISA). A majority had 50% inhibitory concentration (IC50) estimates (the concentration required for 50% growth inhibition) lower than those of the 3D7 reference clone for desethylamodiaquine, lumefantrine, mefloquine, and quinine and was considered to be susceptible, while dihydroartemisinin and pyrimethamine IC50s were higher. No association was found between susceptibility to the ACT compounds and treatment outcome. Selection was observed for the pfmdr1 N86 allele in artemether-lumefantrine recrudescences (recurring infections) (4/7 [57.1%] versus 36/195 [18.5%]), and of the opposite allele, 86Y, in artesunate-amodiaquine reinfections (new infections) (20/22 [90.9%] versus 137/195 [70.3%]) compared to baseline infections. The importance of pfmdr1 N86 in lumefantrine tolerance was emphasized by its association with elevated lumefantrine IC50s. Genetic linkage between N86 and Y184 was observed, which together with the low frequency of 1246Y may explain regional differences in selection of pfmdr1 loci. Selection of opposite alleles in artemether-lumefantrine and artesunate-amodiaquine recurrent infections supports the strategy of multiple first-line treatment. Surveillance based on clinical, ex

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

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    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.

  11. 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.

  12. The modulator driven polymorphism of Zr(IV) based metal-organic frameworks

    Science.gov (United States)

    Drache, Franziska; Bon, Volodymyr; Senkovska, Irena; Getzschmann, Jürgen; Kaskel, Stefan

    2017-01-01

    The reaction of ZrCl4 and 2,5-thiophenedicarboxylic acid (H2tdc) in the presence of trifluoroacetic acid (Htfa) as modulator results in the formation of the new metal-organic framework (MOF) named DUT-126 (DUT = Dresden University of Technology). The nature and concentration of modulators are found to be decisive synthetic parameters affecting the topology of the formed product. DUT-126 (hbr) extends the series of polymorphs differing in topology, namely DUT-67 (reo), DUT-68 (bon) and DUT-69 (bct) to four, where DUT-67 and DUT-68 show the same eight-connected secondary building units as in DUT-126. In DUT-126, linker molecules have a peculiar orientation, resulting in hbr topology, which is described for the first time in this work for MOFs. DUT-126 contains three pore types, including two micropores surrounding mesoporous channels. DUT-126 is stable against hydrolysis and features permanent porosity with a specific surface area of 1297 m2 g-1 and a total pore volume of 0.48 cm3 g-1, calculated from the nitrogen physisorption isotherm measured at 77 K. This article is part of the themed issue 'Coordination polymers and metal-organic frameworks: materials by design'.

  13. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

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    Mark McMullan

    Full Text Available The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC of guppies (Poecilia reticulata to study the turnover rate of alleles (temporal genetic differentiation, G'(ST. Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1 overdominant selection, (2 fluctuating population size within a metapopulation, and (3 the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST outlier analysis may obscure the signal of selection.

  14. 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

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

    Science.gov (United States)

    Fernandez i Marti, Angel; 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 world were screened with seven 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 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. PMID:22737155

  16. Association and treatment response to capecitabine-based chemoradiotherapy with CYP2C9 polymorphism in head and neck cancer

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    S Paul

    2011-01-01

    Full Text Available Aims : The aim of the present study is to investigate the association of polymorphism in cytochrome P450 2C9 (CYP2C9 with head and neck squamous cell carcinoma (HNSCC and response in patients receiving chemoradiotherapy. Materials and Methods : One hundred ten males suffering from locally advanced head and neck squamous cell carcinoma and an equal number of healthy controls were genotyped for CYP2C9FNx012 and CYP2C9FNx013, leading to poor metabolizers (PMs by PCR-based RFLP. Each case was assessed thoroughly for treatment response following WHO criteria. Results : The frequency of heterozygous genotypes of both CYP2C9FNx012 (27.3% and CYP2C9FNx013 (20.1% were found to be significantly higher in the HNSCC cases as compared to the healthy controls. Tobacco intake in the form of chewing or smoking and alcohol intake resulted in several fold increase in the risk to HNSCC in the cases carrying variant genotypes of CYP2C9FNx012 or CYP2C9FNx013. Further, majority of the cases assessed for response (134 carrying variant alleles of both CYP2C9FNx012 (65.3% or CYP2C9FNx013 (70.58% were found to respond poorly to the radio-chemotherapy. Conclusions : The data suggests a significant association of the CYP2C9 polymorphism with HNSCC and treatment outcome underlining the importance of pretherapeutic genotyping in determining the treatment schedule.

  17. Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S-23S rDNA spacer polymorphism analysis.

    Science.gov (United States)

    Bergamo, Rogério F; Novo, Maria Teresa M; Veríssimo, Ricardo V; Paulino, Luciana C; Stoppe, Nancy C; Sato, Maria Inês Z; Manfio, Gilson P; Prado, Paulo Inácio; Garcia, Oswaldo; Ottoboni, Laura M M

    2004-09-01

    Restriction fragment length polymorphism (RFLP) and sequence analyses of the PCR-amplified 16S-23S rDNA intergenic spacer (ITS) were used for differentiating Acidithiobacillus thiooxidans strains from other related acidithiobacilli, including A. ferrooxidans and A. caldus. RFLP fingerprints obtained with AluI, DdeI, HaeIII, HinfI and MspI enabled the differentiation of all Acidithiobacillus reference strains into species groups. The A. thiooxidans strains investigated (metal mine isolates) yielded identical RFLP patterns to the A. thiooxidans type strain (ATCC 19377(T)), except for strain DAMS, which had a distinct pattern for all enzymes tested. Fourteen A. ferrooxidans mine strains were assigned to 3 RFLP groups, the majority of which were grouped with A. ferrooxidans ATCC 23270(T). The spacer region of one representative strain from each of the RFLP groups obtained was subjected to sequence analysis, in addition to eleven additional A. thiooxidans strains isolated from sediment and water samples, and A. caldus DSM 8584(T). The tRNA(IIe) and tRNA(Ala) genes, present in all strains analyzed, showed high sequence similarity. Phylogenetic analysis of the ITS sequences differentiated all three Acidithiobacillus species. Inter- and infraspecific genetic variations detected were mainly due to the size and sequence polymorphism of the ITS3 region. Mantel tests showed no significant correlation between ITS sequence similarity and the geographical origin of strains. The results showed that the 16S-23S rDNA spacer region is a useful target for the development of molecular-based methods aimed at the detection, rapid differentiation and identification of acidithiobacilli.

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

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    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

  19. The Simulation of Insertion and Extraction Force between Clip and Clip Seat Based on MARC%基于MARC的卡扣插拔力仿真分析

    Institute of Scientific and Technical Information of China (English)

    岳石锋; 陶志军; 卢孝贵; 邱春晓; 魏佳斌

    2014-01-01

    There are insertion force and extraction force between clip and clip seat(dog house) combination which is caused by interference between them. In order to make the assembly suitable,the consideration of reasonable interference should be taken. But the interference is not the only element which will affect the value of insertion and extraction force. The height of clip seat(dog house),one of the factors which has some relationship with the insertion and extraction force, should be taken into account. Now take one of car front door inner covers (ABS) compared with mudguards for example, there will be CAE analysis and experiment which can evaluate the exact factors affecting the insertion and extraction force. So the appropriate interference value can be set.%卡扣与卡扣座配合,在将卡扣插入、拔出卡扣座时由于存在过盈配合,故存在插入力、拔出力。而考虑到产品的装配性,插入力、拔出力需控制在一定的范围内才能保证其装配性,因此需要考虑合适过盈量以满足合适的插入、拔出力。但是过盈量并不是唯一影响插入、拔出力的因素,卡扣座的高度也是影响插入、拔出力的因素之一,也需要进行验证。今以某型ABS前三角内盖板与某型挡泥板为例,通过CAE解析,确定过盈量、卡扣座高度对插入力、拔出力的影响关系,以确定合适的过盈量,为后续同类产品设计提供参考依据。

  20. Effect of the XRCC1 and XRCC3 Genetic Polymorphisms on the Efficacy of Platinum-based Chemotherapy in Patients with Advanced Non-small Cell Lung Cancer

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    Chong’an XU

    2011-12-01

    Full Text Available Background and objective DNA repair gene polymorphisms can be used to predict the sensitivity of platinum-based chemotherapy. Thus, such polymorphisms are important for the individual treatment of non-small cell lung cancer (NSCLC. The aim of this study is to investigate the relationship between X-ray repair cross complementing protein 1 (XRCC1 and X-ray repair cross complementing protein 3 (XRCC3 gene polymorphisms and the chemosensitivity of platinum-based chemotherapy in patients with advanced NSCLC. Methods Genomic DNA were extracted from the sera of a total of 130 patients with advanced NSCLC who received platinum-based chemotherapy. XRCC1 Arg194 Trp, Arg399 Gln, and XRCC3 Thr241 Met were genotyped using the polymerase chain reaction-restriction fragment length polymorphism method, and the relationship between XRCC1 and XRCC3 polymorphisms and chemotherapy sensitivity was analyzed. Results A total of 130 patients with advanced NSCLC received platinum-based chemotherapy, with an overall response rate of 33.8% after two chemotherapy cycles. The XRCC1 194 and 399 genetic polymorphisms, but not XRCC3 241, were found to be related to the chemosensitivity. The objective response rate of the patients with at least one XRCC1 194 Trp allele was 2.5 times higher than that of Arg/Arg genotype carriers (42.1% vs 22.2%, OR=2.545, 95%CI: 1.159-5.590, P=0.020. The objective response rate of the XRCC1 399 Arg/Arg genotype carriers was significantly higher than that of the patients with at least one Gln allele (45.5% vs 21.9%, OR=0.336, 95%CI: 0.156-0.722, P=0.005. Combined effects between XRCC1 194 and XRCC1 399 were observed. The objective response rate of the patients with at least one XRCC1 194 Trp allele and a 399 Arg/Arg genotype was significantly higher than that of patients with 194 Arg/Arg and 399 Arg/Gln genotypes (44.4% vs 18.8%, OR=3.467, 95%CI: 1.223-9.782, P=0.019. Moreover, XRCC1 and XRCC3 have a combined effect in predicting chemosensitivity

  1. A CRITICAL APPRAISAL OF PACKAGE INSERTS IN INDIA

    Directory of Open Access Journals (Sweden)

    Makbool Ali M.

    2016-06-01

    Full Text Available formation is a Package Insert. It is a printed leaflet that contains information based on regulatory guidelines for the safe and effective use of a drug. Incomplete and incorrect product information may have serious consequences including disability or death. In India, the concept of package insert is governed by the Drugs and Cosmetics Act (1940 and Rules (1945. Keeping this in mind, this study was designed to assess the presentation and completeness of drug information provided in the currently available package inserts for allopathic drugs in India. AIM To evaluate the presentation and completeness of drug information provided in the currently available package inserts for allopathic drugs in India. OBJECTIVES To evaluate drug information in package inserts according to headings mentioned in Section 6.2 and 6.3 of Schedule D, Drugs and Cosmetics Rules, 1945. MATERIAL AND METHODS Package inserts accompanying allopathic medicines were obtained from a drug store and three pharmacies around a tertiary care centre in Western India on request over a 1-month period. The package inserts were included in the study and analysed for the presentation and completeness of information according to the headings mentioned in Section 6.2 and Section 6.3 of Schedule D, The Drugs and Cosmetics Rules, 1945. RESULTS 110 package inserts were analysed in the study. None of the reviewed package insert contained all the sections as required by the Drugs and Cosmetic Rules. CONCLUSION To avoid medication errors due to deficits in drug information in package inserts, tighter monitoring of package inserts by regulatory authorities is recommended. Steps should be taken to ensure that the information in the package inserts follows a standard layout for easy and convenient comprehension.

  2. 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

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

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    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.

  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. Gas turbine vane cooling air insert

    Energy Technology Data Exchange (ETDEWEB)

    North, W.E.; Hultgren, K.G.; Dishman, C.D.; Van Heusden, G.S.

    1992-09-08

    This patent describes a gas turbine. It comprises turbine vanes, each of the vanes supplied with cooling air and having: an airfoil portion forming a first cavity having an insert disposed therein for directing the flow of the cooling air, the insert having first and second insert ends; a shroud portion from which the airfoil portion extends, the insert attached to the shroud portion at the first insert end; an insert extension extending through a portion of the insert and extending beyond the first insert end, the insert extension and the insert forming an annular gap therebetween separating the insert from the insert extension; a plate covering at least a portion of the shroud, the plate having a first hole formed therein through which the insert extension extends; and at least a first seal extending between the insert extension and the insert, and sealing the annular gap therebetween. This patent also describes a method of making a gas turbine. It comprises welding a first tubular insert adjacent its first end to a vane outer shroud; partially inserting a second tubular insert into the first tubular member and attaching the second tubular insert thereto; placing a plate having a hole formed therein on the outer shroud so that the hole surrounds the second tubular insert; and attaching the second tubular insert to the plate by placing a first seal between the first and second tubular inserts and attaching the first seal to each of the first and second tubular inserts, and placing a second seal between the second tubular insert and the plate and welding the second seal to the second tubular insert and the plate.

  6. Influence of angiotensin converting enzyme gene insertion/deletion polymorphism and β3-adrenergic receptor gene Trp64Arg polymorphism on fetal growth and neonatal insulin sensitivity%血管紧张素转化酶基因插入/缺失多态性及β3肾上腺素能受体基因Trp64Arg多态性对胎儿宫内发育及新生儿胰岛素敏感性的影响

    Institute of Scientific and Technical Information of China (English)

    崔蕴璞; 韩彤妍; 王新利; 叶鸿瑁

    2008-01-01

    Objective To understand the influence of angiotensin converting enzyme(ACE)gene insertion/deletion(I/D)polymorphism and β3-adrenergic receptor(β3-AR)gene Trp64Arg polymorphism on fetal growth and neonatal insulin sensitivity.Methods Totally 296 newborn infants were selected into our study and divided into 2 groups according to gestational age and birth weight:adequate-for-gestationalage(AGA)group(222 cases)and small-for-gestational-age(SGA)group(74 case).Serum glucose and insulin were examined in the morning of the 3rd day before milk.Insulin sensitivity was evaluated by homeostasis model assessment(HOMA)equation.β3-AR gene Trp64Arg polymorphism and ACE gene I/D polymorphism(202 cases)were analysed using polymerase chain reaction-restricted fragment length polymorphism(PCR-RFLP)technique.Gestational age,birth weight,birth weight percentage,serum glucose,insulin and HOMA-IR were compared among different genotype groups.Statistical analysis was performed with the SPSS 10.0 software.Results No significant difference was found between the sernm glucose level of SGA group(4.03±1.05 mmol/L)and AGA group(4.05±1.14 mmol/L),P=0.008. The serum insulin level(converted into Ln)of SGA group(2.262±0.746)was significantly higher than that of AGA group(1.757±0.805),P<0.001.The HOMA-IR(also convened into Ln)level of SGA group(0.217±0.367)was also significantly higher than that of AGA group(0.001±0.378),P<0.001. In the SGA group β3-AR gene Arg64 allele carriers had higher serum insulin and HOMA-IR level(botll changed to Ln,2.654±0.701,0.371±0.338)compared with noncarriers(2.074±0.698,0.143± O.360),P<0.05.The ACE gene DD genotype carriers had higher serum insulin and HOMA-IR level(both were converted into Ln,2.19 4-0.91,0.5l 4-1.01)compared with II(1.77 ±0.85,0.02 ±0.93) and ID genotype group(1.77 ±0.83,0.05 ±0.91),P<0.05.The ACE gene DD carriers had lower birth weight percentage compared with II and ID genotype group.P<0.05.When both genes'polymorphisms were taken

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

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    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

  8. Gold supported on zirconia polymorphs for hydrogen generation from formic acid in base-free aqueous medium

    Science.gov (United States)

    Bi, Qing-Yuan; Lin, Jian-Dong; Liu, Yong-Mei; He, He-Yong; Huang, Fu-Qiang; Cao, Yong

    2016-10-01

    Formic acid (FA) has attracted considerable attention as a safe and convenient hydrogen storage material for renewable energy transformation. However, development of an efficient heterogeneous catalyst for selective FA decomposition for ultraclean H2 gas in the absence of any alkalis or additives under mild conditions remains a major challenge. Based on our previous work on Au/ZrO2 as a robust and efficient catalyst for FA dehydrogenation in amine system, we report here ZrO2 with different nanocrystal polymorphs supported Au nanoparticles can achieve near completion of FA dehydrogenation in base-free aqueous medium. Of significant importance is that an excellent rate of up to 81.8 L H2 gAu-1 h-1 in open system and highly pressurized gas of 5.9 MPa in closed one can be readily attained at 80 °C for Au/m-ZrO2. In situ diffuse reflectance infrared Fourier transform (DRIFT) and CO2-temperature programmed desorption (TPD) techniques revealed that Au/m-ZrO2 exhibits a higher density of surface basic sites than Au/t-ZrO2 and Au/a-ZrO2. Basic sites in surface can substantially facilitate crucial FA deprotonation process which appears to be a key factor for achieving high dehydrogenation activity. The H/D exchange between solvent of H2O and substrate of FA was observed by the kinetic isotope effect experiments.

  9. Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes.

    Science.gov (United States)

    Gao, Jiaxue; Ma, Lan; Lei, Zhen; Wang, Zhenxin

    2016-03-01

    The mapping of specific single nucleotide polymorphisms (SNPs) in patients' genome is a critical process for the development of personalized therapy. In this work, a DNA microarray-based resonance light scattering (RLS) assay has been developed for multiplexed detection of breast cancer related SNPs with high sensitivity and selectivity. After hybridization of the desired target single-stranded DNAs (ssDNAs) with the ssDNA probes on a microarray, the polyvalent ssDNA modified 13 nm gold nanoparticles (GNPs) are employed to label the hybridization reaction through the formation of a three-stranded DNA system. The H2O2-mediated enlargement of GNPs is then used to enhance the RLS signal. The microarray-based RLS assay provides a detection limit of 10 pM (S/N = 3) for the target ssDNA and determines an allele frequency as low as 1.0% in the target ssDNA cocktail. Combined with an asymmetric PCR technique, the proposed assay shows good accuracy and sensitivity in profiling 4 SNPs related to breast cancer of three selected cell lines.

  10. SITDEM: A simulation tool for disease/endpoint models of association studies based on single nucleotide polymorphism genotypes

    Science.gov (United States)

    Oh, Jung Hun; Deasy, Joseph O.

    2016-01-01

    The association analysis between single nucleotide polymorphisms (SNPs) and disease or endpoint in genome-wide association studies (GWAS) has been considered as a powerful strategy for investigating genetic susceptibility and for identifying significant biomarkers. The statistical analysis approaches with simulated data have been widely used to review experimental designs and performance measurements. In recent years, a number of authors have proposed methods for the simulation of biological data in the genomic field. However, these methods use large-scale genomic data as a reference to simulate experiments, which may limit the use of the methods in the case where the data in specific studies are not available. Few methods use experimental results or observed parameters for simulation. The goal of this study is to develop a Web application called SITDEM to simulate disease/endpoint models in three different approaches based on only parameters observed in GWAS. In our simulation, a key task is to compute the probability of genotypes. Based on that, we randomly sample simulation data. Simulation results are shown as a function of p-value against odds ratio or relative risk of a SNP in dominant and recessive models. Our simulation results show the potential of SITDEM for simulating genotype data. SITDEM could be particularly useful for investigating the relationship among observed parameters for target SNPs and for estimating the number of variables (SNPs) required to result in significant p-values in multiple comparisons. The proposed simulation tool is freely available at http://www.snpmodel.com. PMID:24480173

  11. A critical appraisal of medication package inserts

    Directory of Open Access Journals (Sweden)

    Pranjit Narzaree

    2015-10-01

    Full Text Available Introduction: Package Inserts (PIs refers to officially specified document that accompanies a drug for relevant, updated and unbiased information for rational drug use based on regulatory guidelines as per section 6.2 and 6.3 of schedule D of Indian Drug and cosmetic Act 1945. But some studies had shown non-uniformity with suboptimal level of informations which frequently can lead to medication errors. Hence this study was conducted to evaluate the completeness of PIs.Aim: To critically evaluate package inserts of allopathic medicines.Material and Methods: 100 allopathic drug PIs were collected from pharmacies in Rohtak and were checked for the presence of each heading as per schedule D criteria, followed by scrutiny of the information included under the heading. Indian guidelines were also compared with US FDA guidelines for PIs.Scoring of package inserts: The informations were evaluated for completeness and scored as 1 if present otherwise scored as zero for no information or partial information. Scores for each heading were calculated by totaling the scores of all the package inserts. The total scores were expressed as absolute numbers and percentages.Results:  On an average PIs analyzed for the completeness of the criteria scored 10 (Mean± SD = 9.73±2.48 out of 16. Absence of common layout and headings caused inconvenience. In comparison to US FDA guidelines it lacked, disclaimer statement, boxed warning, revision date, approval date, toll-free number etc.Conclusion: PIs don’t seem to be serving effectively because of multiple deficiencies like completeness, uniformity, absence of headings.Keywords: Critical appraisal, package inserts.

  12. 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.

  13. XPC Ala499Val and XPG Asp1104His polymorphisms and digestive system cancer risk: a meta-analysis based on model-free approach.

    Science.gov (United States)

    Yu, Guangsheng; Wang, Jianlu; Dong, Jiahong; Liu, Jun

    2015-01-01

    Many studies have reported the association between XPC Ala499Val and XPG Asp1104His polymorphisms and digestive system cancer susceptibility, but the results were inconclusive. We performed a meta-analysis, using a comprehensive strategy based on the allele model and a model-free approach, to derive a more precise estimation of the relationship between XPC Ala499Val and XPG Asp1104His polymorphisms with digestive system cancer risk. For XPC Ala499Val, no significant cancer risk was found in the allele model (OR = 0.98, 95% CI: 0.86-1.11) and with model-free approach (ORG = 0.97, 95% CI: 0.83-1.13). For XPG Asp1104His, there was also no association between this polymorphism and cancer risk in the allele model (OR = 1.03, 95% CI: 0.96-1.11) and with the model-free approach (ORG = 1.04, 95% CI: 0.95-1.14). Therefore, this meta-analysis suggests that the XPC Ala499Val and XPG Asp1104His polymorphisms were not associated with digestive system cancer risk. Further large and well-designed studies are needed to confirm these findings.

  14. Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

    Science.gov (United States)

    Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

    1998-01-01

    All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

  15. 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.

  16. 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.

  17. Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley

    Science.gov (United States)

    Takahagi, Kotaro; Uehara-Yamaguchi, Yukiko; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo; Mochida, Keiichi; Saisho, Daisuke

    2016-01-01

    Barley is one of the founder crops of Old world agriculture and has become the fourth most important cereal worldwide. Information on genome-scale DNA polymorphisms allows elucidating the evolutionary history behind domestication, as well as discovering and isolating useful genes for molecular breeding. Deep transcriptome sequencing enables the exploration of sequence variations in transcribed sequences; such analysis is particularly useful for species with large and complex genomes, such as barley. In this study, we performed RNA sequencing of 20 barley accessions, comprising representatives of several biogeographic regions and a wild ancestor. We identified 38,729 to 79,949 SNPs in the 19 domesticated accessions and 55,403 SNPs in the wild barley and revealed their genome-wide distribution using a reference genome. Genome-scale comparisons among accessions showed a clear differentiation between oriental and occidental barley populations. The results based on population structure analyses provide genome-scale properties of sub-populations grouped to oriental, occidental and marginal groups in barley. Our findings suggest that the oriental population of domesticated barley has genomic variations distinct from those in occidental groups, which might have contributed to barley’s domestication. PMID:27616653

  18. Are "functionally related polymorphisms" of renin-angiotensin-aldosterone system gene polymorphisms associated with hypertension?

    NARCIS (Netherlands)

    Hahntow, I.N.; Mairuhu, G.; Valkengoed, I.G.M.; Koopmans, R.P.; Michel, M.C.

    2010-01-01

    ABSTRACT: BACKGROUND: Genotype-phenotype association studies are typically based upon polymorphisms or haplotypes comprised of multiple polymorphisms within a single gene. It has been proposed that combinations of polymorphisms in distinct genes, which functionally impact the same phenotype, may hav

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

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    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

  20. Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-Based typing of Candida albicans.

    Science.gov (United States)

    Garcia-Hermoso, Dea; Cabaret, Odile; Lecellier, Gael; Desnos-Ollivier, Marie; Hoinard, Damien; Raoux, Dorothée; Costa, Jean-Marc; Dromer, Françoise; Bretagne, Stéphane

    2007-12-01

    For genotyping Candida albicans isolates, two PCR-based methods have recently emerged: multilocus sequence typing (MLST), based on the sequence of selected genes, and microsatellite length polymorphism (MLP), based on the length of PCR products containing variable numbers of short DNA repeats. To compare the two methods in their abilities to differentiate and group C. albicans isolates, we selected 50 independent isolates collected at the National Reference Center for Mycoses and Antifungals. MLST typing was performed using sequencing of seven loci as described at (http://test1.mlst.net). The MLP method consisted of a single multiplex PCR testing three different loci. Dendrograms were constructed by the unweighted pair group cluster method with Euclidean metric for both methods. The correlation between the distance matrices was performed with a Mantel test tested with 1,000 random permutations. The sensitivity and specificity of the MLP typing system were determined after allocating MLST groups for the greater number of isolates of each distinct MLP group. The discriminatory power index was >0.99, and the distances between the isolates were highly correlated with both systems. The Mantel coefficient and the Pearson product-moment correlation coefficient were 35,699 and 0.32, respectively (P < or = 1.2 x 10(-6)). Using MLP, the average specificity and sensitivity of clustering compared to MLST were 83% and 73%, respectively, when the singletons were excluded. The two methods are similarly discriminatory and can be interchangeable depending on the objectives. MLP is less expensive and faster than MLST. However, MLST is currently more accurate and additional standardization is needed for MLP.

  1. Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.

    Science.gov (United States)

    Said, Halima M; Krishnamani, Keshav; Omar, Shaheed V; Dreyer, Andries W; Sansom, Bianca; Fallows, Dorothy; Ismail, Nazir A

    2016-10-01

    The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.

  2. Insertion of a single-molecule magnet inside a ferromagnetic lattice based on a 3D bimetallic oxalate network: towards molecular analogues of permanent magnets.

    Science.gov (United States)

    Clemente-León, Miguel; Coronado, Eugenio; Gómez-García, Carlos J; López-Jordà, Maurici; Camón, Agustín; Repollés, Ana; Luis, Fernando

    2014-02-03

    The insertion of the single-molecule magnet (SMM) [Mn(III)(salen)(H2O)]2(2+) (salen(2-) = N,N'-ethylenebis-(salicylideneiminate)) into a ferromagnetic bimetallic oxalate network affords the hybrid compound [Mn(III)(salen)(H2O)]2[Mn(II)Cr(III)(ox)3]2⋅(CH3OH)⋅(CH3CN)2 (1). This cationic Mn2 cluster templates the growth of crystals formed by an unusual achiral 3D oxalate network. The magnetic properties of this hybrid magnet are compared with those of the analogous compounds [Mn(III)(salen)(H2O)]2[Zn(II)Cr(III)(ox)3]2⋅(CH3OH)⋅(CH3CN)2 (2) and [In(III)(sal2-trien)][Mn(II)Cr(III)(ox)3]⋅(H2O)0.25⋅(CH3OH)0.25⋅(CH3CN)0.25 (3), which are used as reference compounds. In 2 it has been shown that the magnetic isolation of the Mn2 clusters provided by their insertion into a paramagnetic oxalate network of Cr(III) affords a SMM behavior, albeit with blocking temperatures well below 500 mK even for frequencies as high as 160 kHz. In 3 the onset of ferromagnetism in the bimetallic Mn(II) Cr(III) network is observed at Tc = 5 K. Finally, in the hybrid compound 1 the interaction between the two magnetic networks leads to the antiparallel arrangement of their respective magnetizations, that is, to a ferrimagnetic phase. This coupling induces also important changes on the magnetic properties of 1 with respect to those of the reference compounds 2 and 3. In particular, compound 1 shows a large magnetization hysteresis below 1 K, which is in sharp contrast with the near-reversible magnetizations that the SMMs and the oxalate ferromagnetic lattice show under the same conditions.

  3. Development of ocular inserts for cattle.

    Science.gov (United States)

    Greer, R T; Ryoo, J P

    1987-06-01

    Ring shaped ocular inserts have been developed to administer a therapeutic level of tylosin tartrate throughout a five day period to treat pinkeye in cattle. The inserts are based on polyvinyl chloride rings which are dip coated with a copolymer containing the antibiotic (tylosin tartrate). Scanning electron microscope (SEM) characterization of surfaces has been of value to evaluate the presence and extent of surface flaws in the hydrogel coating, and to contribute to improvement in fabrication of the rings to insure the establishment of satisfactory seals at joints, uniformity of microporosity and cross sections, and the absence of significant cracking or flaking. In vitro release rates were determined using thin layer chromatography techniques, and rates were seen to be above a few micrograms of antibiotic per hour for experiments as long as nine days at simulated tear rates as high as 2 milliliters per hour.

  4. Perception and Action in Teleoperated Needle Insertion.

    Science.gov (United States)

    Nisky, I; Pressman, A; Pugh, C M; Mussa-Ivaldi, F A; Karniel, A

    2011-01-01

    We studied the effect of delay on perception and action in contact with a force field that emulates elastic soft tissue with a rigid nonlinear boundary. Such a field is similar to forces exerted on a needle during teleoperated needle insertion. We found that delay causes motor underestimation of the stiffness of this nonlinear soft tissue, without perceptual change. These experimental results are supported by simulation of a simplified mechanical model of the arm and neural controller, and a model for perception of stiffness, which is based on regression in the force-position space. In addition, we show that changing the gain of the teleoperation channel cancels the motor effect of delay without adding perceptual distortion. We conclude that it is possible to achieve perceptual and motor transparency in virtual one-dimensional remote needle insertion task.

  5. App-assisted external ventricular drain insertion.

    Science.gov (United States)

    Eftekhar, Behzad

    2016-09-01

    The freehand technique for insertion of an external ventricular drain (EVD) is based on fixed anatomical landmarks and does not take individual variations into consideration. A patient-tailored approach based on augmented-reality techniques using devices such as smartphones can address this shortcoming. The Sina neurosurgical assist (Sina) is an Android mobile device application (app) that was designed and developed to be used as a simple intraoperative neurosurgical planning aid. It overlaps the patient's images from previously performed CT or MRI studies on the image seen through the device camera. The device is held by an assistant who aligns the images and provides information about the relative position of the target and EVD to the surgeon who is performing EVD insertion. This app can be used to provide guidance and continuous monitoring during EVD placement. The author describes the technique of Sina-assisted EVD insertion into the frontal horn of the lateral ventricle and reports on its clinical application in 5 cases as well as the results of ex vivo studies of ease of use and precision. The technique has potential for further development and use with other augmented-reality devices.

  6. 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.

  7. XRCC3 Thr241Met polymorphism and clinical outcomes of NSCLC patients receiving platinum-based chemotherapy: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Xiao-yong Shen

    Full Text Available INTRODUCTION: X-ray repair cross-complementing protein 3 (XRCC3 is an essential gene involved in the double-strand break repair pathway. Published evidence has shown controversial results about the relationship between XRCC3 Thr241Met polymorphism and clinical outcomes of non-small cell lung cancer (NSCLC patients receiving platinum-based chemotherapy. METHODS: A systematic review and meta-analysis was performed to evaluate the predictive value of XRCC3 Thr241Met polymorphism on clinical outcomes of advanced NSCLC receiving platinum-based chemotherapy. Response to chemotherapy, overall survival (OS and progression-free survival (PFS were analyzed. RESULTS: A number of 11 eligible studies were identified according to the inclusion criteria. Carriers of the variant XRCC3 241Met allele were significantly associated with good response to platinum-based chemotherapy (ThrMet/MetMet vs. ThrThr: OR  = 1.509, 95% CI: 1.099-2.072, Pheterogeneity  = 0.618. The XRCC3 Thr241Met polymorphism was not associated with OS (MetMet vs. ThrThr, HR  = 0.939, 95% CI:0.651-1.356, Pheterogeneity  = 0.112 or PFS (MetMet vs. ThrThr, HR  = 0.960, 95% CI: 0.539-1.710, Pheterogeneity  = 0.198. Additionally, no evidence of publication bias was observed. CONCLUSIONS: This systematic review and meta-analysis shows that carriers of the XRCC3 241Met allele are associated with good response to platinum-based chemotherapy in advanced NSCLC, while the XRCC3 Thr241Met polymorphism is not associated with OS or PFS.

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

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    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

  9. Effect of inserting of thin Rubrene layer on performance of Organic Light-Emitting Diodes based on Zn(BTz){sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Tomova, R L; Petrova, P K; Stoycheva-Topalova, R T, E-mail: reni@clf.bas.b [Institute of optical materials and technologies ' Acad. J. Malinowski' , Bulgarian Academy of Sciences, ' Acad. G. Bonchev' str. bl. 109, 1113 Sofia (Bulgaria)

    2010-11-01

    Organic light-emitting diodes (OLEDs) with improved performances are fabricated using a thin (1 nm) yellow-emitting layer of 5,6,11,12-tetraphenylnaphthacene (Rubrene) inserted at different position in green emitting electroluminescent (EL) layer of bis-(2-(2-hydroxyphenyl) benzothiazole)zinc (Zn(BTz){sub 2}) in configuration: ITO/PVK:TPD/ Zn(BTz){sub 2} (x nm)/ Rubrene (1 nm)/ Zn(BTz){sub 2} (75-x nm)/Al, where PVK:TPD is a hole transporting layer of N, N'-bis(3-methylphenyl)-N, N'-diphenylbenzidine (TPD) incorporated in poly(N-vinylcarbazole) (PVK) matrix and Al is a cathode. EL spectra predominantly influenced by Rubrene emission when the doping layer is close to (PVK:TPD)/ Zn(BTz){sub 2} (x{yields} 0-15 nm) and to Zn(BTz){sub 2}/Al (x{yields} 70-75 nm) interfaces and shift toward emission of Zn(BTz){sub 2} increasing the distance of Rubrene from both interfaces (x{yields}35 nm). The same dependence of the EL efficiency on the position of the doping Rubrene layer in the OLED structure was found.

  10. Clinical Significance of POU5F1P1 rs10505477 Polymorphism in Chinese Gastric Cancer Patients Receving Cisplatin-Based Chemotherapy after Surgical Resection

    Directory of Open Access Journals (Sweden)

    Lili Shen

    2014-07-01

    Full Text Available This study aimed to investigate the association between POU class5 homeobox 1 pseudogene 1 gene (POU5F1P1 rs10505477 polymorphism and the prognosis of Chinese gastric cancer patients, who received cisplatin-based chemotherapy after surgical resection. POU5F1P1 rs10505477 was genotyped using the SNaPshot method in 944 gastric cancer patients who received gastrectomy. The association of rs10505477 G > A polymorphism with the progression and prognosis in gastric cancer patients was statistically analyzed using the SPSS version 18.0 for Windows. The results reveal that rs10505477 polymorphism has a negatively effect on the overall survival of gastric cancer patients in cisplatin-based chemotherapy subgroup (HR = 1.764, 95% CI = 1.069–2.911, p = 0.023. Our preliminary study indicates for the first time that POU5F1P1 rs10505477 is correlated with survival of gastric cancer patients who receving cisplatin-based chemotherapy after gastrectomy. Further studies are warranted to investigate the mechanism and to verify our results in different populations.

  11. A PCR-based assay for discriminating Cervus and Rangifer (Cervidae) antlers with mitochondrial DNA polymorphisms.

    Science.gov (United States)

    Kim, Young Hwa; Kim, Eung Soo; Ko, Byong Seob; Oh, Seung-Eun; Ryuk, Jin-Ah; Chae, Seong Wook; Lee, Hye Won; Choi, Go Ya; Seo, Doo Won; Lee, Mi Young

    2012-07-01

    This study describes a method for discriminating Rangifer antlers from true Cervus antlers using agarose gel electrophoresis, capillary electrophoresis, quantitative real-time PCR, and allelic discrimination. Specific primers labeled with fluorescent tags were designed to amplify fragments from the mitochondrial D-loop genes for various Cervus subspecies and Rangifer tarandus differentially. A 466-bp fragment that was observed for both Cervus and Rangifer antlers served as a positive control, while a 270-bp fragment was specifically amplified only from Rangifer antlers. Allelic discrimination was used to differentiate between Cervus and Rangifer antlers, based on the amplification of specific alleles for both types of antlers. These PCR-based assays can be used for forensic and quantitative analyses of Cervus and Rangifer antlers in a single step, without having to obtain any sequence information. In addition, multiple PCR-based assays are more accurate and reproducible than a single assay for species-specific analysis and are especially useful in this study for the identification of original Cervus deer products from fraudulent Rangifer antlers.

  12. 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.

  13. Growth condition optimization and mobility enhancement through inserting AlAs monolayer in the InP-based InxGa1-xAs/In0.52Al0.48As HEMT structures

    Science.gov (United States)

    Zhou, Shu-Xing; Qi, Ming; Ai, Li-Kun; Xu, An-Huai

    2016-09-01

    The structure of InP-based InxGa1-xAs/In0.52Al0.48As pseudomorphic high electron mobility transistor (PHEMT) was optimized in detail. Effects of growth temperature, growth interruption time, Si δ-doping condition, channel thickness and In content, and inserted AlAs monolayer (ML) on the two-dimensional electron gas (2DEG) performance were investigated carefully. It was found that the use of the inserted AlAs monolayer has an enhancement effect on the mobility due to the reduction of interface roughness and the suppression of Si movement. With optimization of the growth parameters, the structures composed of a 10 nm thick In0.75Ga0.25As channel layer and a 3 nm thick AlAs/In0.52Al0.48As superlattices spacer layer exhibited electron mobilities as high as 12500 cm2·V-1·s-1 (300 K) and 53500 cm2·V-1·s-1 (77 K) and the corresponding sheet carrier concentrations (Ns) of 2.8 × 1012 cm-2 and 2.9 × 1012 cm-2, respectively. To the best of the authors’ knowledge, this is the highest reported room temperature mobility for InP-based HEMTs with a spacer of 3 nm to date. Project supported by the National Natural Science Foundation of China (Grant No. 61434006).

  14. Genetic diversity in somatic mutants of grape (Vitis vinifera) cultivar Italia based on random amplified polymorphic DNA.

    Science.gov (United States)

    Maia, S H Z; Mangolin, C A; Collet, S A O; Machado, M F P S

    2009-01-13

    Random amplified polymorphic DNA (RAPD) markers were used to detect polymorphism and to examine relationships among four table grape clones from northwestern Paraná, in southern Brazil. The 10 primers used for RAPD fingerprints generated 126 reproducible fragments, of which 63, 68, 76, and 72 were polymorphic in cultivars Italia, Rubi, Benitaka, and Brasil, respectively. Among the primers, OPP-08 generated the highest number of fragments, whereas OPE-15 was the most efficient for discriminating polymorphic fragments. The distribution of the clones by cluster analysis indicated that there were no differences in RAPD markers between the colored mutant and the original clone (cultivar Italia), supporting the hypothesis that the non-colored and the colored mutant are the same cultivar. However, we found high levels of polymorphism within and between the cultivars Italia, Rubi, Benitaka, and Brasil (65.1%), contrary to a previous hypothesis that the four clones are genetically uniform. This confirmed our expectation of genetic variation among the clones and within each clone. We conclude that the primers are useful for analyzing the development of the genetic diversity within each of these clones.

  15. Identification of three major Bemisia tabaci biotypes in China based on morphological and DNA polymorphisms

    Institute of Scientific and Technical Information of China (English)

    Baoli Qiu; Yanping Chen; Li Liu; Weilu Peng; Xiaoxi Li; Yuzhou Du; Shunxiang Ren

    2009-01-01

    The sweet potato whitefly, Bemisia tabaci, is a complex species, and many of its biotypes are important agricultural pests. The B and Q biotypes are invasive and coexist with the native Cv biotype on vegetable and ornamental crops in China. In this study, these three bio-types were identified based on their morphological characteristics, RAPD-PCR analysis, and DNA sequences of the COl gene. The ante-rior and posterior wax fringes of the B, Q, and Cv biotypes significantly differed from each other. Based on this morphological characteristic, the three biotypes can easily be distinguished in greenhouses and fields. Genomic DNA RAPD-PCR band patterns also revealed differences between these biotypes using the H16 primer. The B biotype has three bright DNA bands between 250 and 600 bp, the Q biotype only has one bright band at ~300 bp, while the Cv biotype has no band between 250 and 500 bp. Both the Cv and Q biotypes have two bright bands at ~750 and 1000 bp while the B biotype has only one band at ~1000 bp. Based on the COI gene, the genetic identity between B and Cv, B and Q, and Q and CV was 85.8%, 94.7%, and 86.0%, respectively. The MP tree indicated that the phylogenetic relationship between the B and Q biotypes is much closer than that between the B and Cv or the Q and Cv biotypes. The uses of the morphological, RAPD-PCR, and DNA sequencing methods in biotype identification of B. tabaci are discussed.

  16. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen.

    Science.gov (United States)

    Croll, Daniel; Zala, Marcello; McDonald, Bruce A

    2013-06-01

    Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen Zymoseptoria tritici. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB) cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of Z. tritici originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for adaptive evolution in

  17. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen.

    Directory of Open Access Journals (Sweden)

    Daniel Croll

    2013-06-01

    Full Text Available Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen Zymoseptoria tritici. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of Z. tritici originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for

  18. Apolipoprotein E gene polymorphism and dyslipidaemia in adult Asian Indians: A population based study from calcutta, India

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    Das Mithun

    2008-01-01

    Full Text Available Aim : The study was aimed to determine the association of Apolipoprotein E (apo E gene polymorphisms on lipid levels in Asian Indian population. Methods : A total of 350 (184 males and 166 females adult (30 years and above Asian Indians of Calcutta and suburb participated in the study. Anthropometric measures, lipids profiles, and blood glucose measures were collected. Out of 350 subjects, a sample of 70 individuals was selected randomly for genotyping after adjusting for age and sex. The apo E gene polymorphisms were determined by agarose gel electrophoresis. Results : The apo E polymorphism showed significant association with dyslipidaemia (P=0.0135 with e3/4 combination has had the highest occurrence of dyslipidaemia and metabolic syndrome (MS followed by ε4/4 Conclusions : The ε4 allele of apo E gene independent of other risk factors is associated with dyslipidaemia in particular with low HDLc and high TC: HDLc ratio.

  19. Development of Expressed Sequence Tag (EST)-based Cleaved Amplified Polymorphic Sequence (CAPS) markers of tea plant and their application to cultivar identification.

    Science.gov (United States)

    Ujihara, Tomomi; Taniguchi, Fumiya; Tanaka, Jun-Ichi; Hayashi, Nobuyuki

    2011-03-09

    To develop cleaved amplified polymorphic sequence (CAPS) markers for cultivar identification of the tea leaf, 5 primer pairs designed on the basis of genes that encode proteins related to nitrogen assimilation and 26 primer pairs based on expressed sequence tag (EST) sequences of the root of tea plant were screened. From combinations of primer pair and restriction enzyme that showed polymorphism among tea plants, 16 markers were selected and applied to DNA fingerprinting of Japanese tea cultivars. Sixty-three cultivars, except for a bud sport (Kiraka) and its original cultivar (Yabukita) and a pair that was the progeny of the same crossing parent (Harumoegi and Sakimidori), were distinguished from one another. By combining the 16 markers with previously developed CAPS markers and observing the physical appearance, 67 cultivars were distinguishable. The cultivars involve approximately 95% of total tea cultivating area in Japan; therefore, about 95% of tea leaves produced in Japan can be authenticated by labeling their cultivars.

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

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    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.

  1. Association between IL-10 gene polymorphisms and susceptibility of tuberculosis: evidence based on a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Bin Liang

    Full Text Available BACKGROUND: A number of observational studies have been conducted to investigate the association of IL-10 gene polymorphisms with tuberculosis (TB susceptibility. However, the results of different studies were inconsistent. The aim of this study was to investigate the relationship between IL-10 -1082G/A, -819T/C, and -592A/C polymorphisms and TB risk by meta-analysis. METHODS: A literature search was conducted among six English databases (PubMed, Embase, Web of Science, Science Direct, SpringerLink and EBSCO and two Chinese databases (Wanfang and Chinese National Knowledge Infrastructure databases to identify studies involving association between IL-10 -1082G/A, -819T/C, and -592A/C polymorphisms and TB susceptibility before May. 2013. Statistical analysis was performed using Revman 5.0 and Stata 12.0. RESULTS: A total of 31 studies with 6,559 cases and 7,768 controls were included in this meta-analysis. The results showed that three polymorphisms (-1082G/A, -819T/C, and -592A/C in the IL-10 gene were not associated with the risk of TB in general population. In the subgroup analysis by ethnicity, IL-10 -1082G/A polymorphism was associated with TB risk in Europeans (AA+AG vs. GG: OR =  0.57, 95% CI = 0. 0.37-0.89, P = 0.01 and Americans (AA+AG vs. GG: OR =  0.39, 95% CI = 0.27-0.57, P<0.01, and IL-10 -819T/C (C allele vs. T allele: OR = 0.83, 95% CI = 0.72-0.96, P = 0.01 and -592A/C (CC+AC vs. AA: OR =  0.65, 95% CI = 0.49-0.85, P = 0.002 polymorphisms were significantly associated with TB risk in Asians. CONCLUSION: This meta-analysis provides strong evidence that IL-10-1082G/A polymorphism was associated with TB risk in Europeans and Americans, and IL-10 -819T/C and -592A/C polymorphisms could be risk factors for TB in Asians. Additional well designed large studies were required for the validation of our results.

  2. Identification of lung cancer oncogenes based on the mRNA expression and single nucleotide polymorphism profile data.

    Science.gov (United States)

    Wang, Y; Mei, Q; Ai, Y Q; Li, R Q; Chang, L; Li, Y F; Xia, Y X; Li, W H; Chen, Y

    2015-01-01

    This study aimed to identify the oncogenes associated with lung cancer based on the mRNA and single nucleotide polymorphism (SNP) profile data. The mRNA expression profile data of GSE43458 (80 cancer and 30 normal samples) and SNP profile data of GSE33355 (61 pairs of lung cancer samples and control samples) were downloaded from Gene Expression Omnibus database. Common genes between the mRNA profile and SNP profile were identified as the lung cancer oncogenes. Risk subpathways of the selected oncogenes with the SNP locus were analyzed using the iSubpathwayMiner package in R. Moreover, protein-protein interaction (PPI) network of the oncogenes was constructed using the HPRD database and then visualized using the Cytoscape. Totally, 3004 DEGs (1105 up-regulated and 1899 down-regulated) and 125 significant SNPs closely related to 174 genes in the lung cancer samples were identified. Also, 39 common genes, like PFKP (phosphofructokinase, platelet) and DGKH-rs11616202 (diacylglycerol kinase, eta) that enriched in sub-pathways such as galactose metabolism, fructose and mannose metabolism, and pentose phosphate pathway, were identified as the lung cancer oncogenes. Besides, PIK3R1 (phosphoinositide-3-kinase, regulatory subunit 1), RORA (RAR-related orphan receptor A), MAGI3 (membrane associated guanylate kinase, WW and PDZ domain containing 3), PTPRM (protein tyrosine phosphatase, receptor type, M), and BMP6 (bone morphogenetic protein 6) were the hub genes in PPI network. Our study suggested that PFKP and DGKH that enriched in galactose metabolism, fructose and mannose metabolism pathway, as well as PIK3R1, RORA, and MAGI3, may be the lung cancer oncogenes.

  3. Desmotropy, polymorphism, and solid-state proton transfer: four solid forms of an aromatic o-hydroxy Schiff base.

    Science.gov (United States)

    Rubčić, Mirta; Užarević, Krunoslav; Halasz, Ivan; Bregović, Nikola; Mališ, Momir; Dilović, Ivica; Kokan, Zoran; Stein, Robin S; Dinnebier, Robert E; Tomišić, Vladislav

    2012-04-27

    The Schiff base derived from salicylaldehyde and 2-amino-3-hydroxypyridine affords a diversity of solid forms, two polymorphic pairs of the enol-imino (D1 a and D1 b) and keto-amino (D2 a and D2 b) desmotropes. The isolated phases, identified by IR spectroscopy, X-ray crystallography, and (13)C cross-polarization/magnetic angle spinning (CP/MAS) NMR spectroscopy, display essentially planar molecular conformations characterized by strong intramolecular hydrogen bonds of the O-H⋅⋅⋅N (D1) or N-H⋅⋅⋅O (D2) type. A change in the position of the proton within this O⋅⋅⋅H⋅⋅⋅N system is accompanied by substantially different molecular conformations and, subsequently, by divergent supramolecular architectures. The appearance and interconversion conditions for each of the four phases have been established on the basis of a number of solution and solvent-free experiments, and evaluated against the results of computational studies. Solid phases readily convert into the most stable form (D1 a) upon exposure to methanol vapor, heating, or by mechanical treatment, and these transformations are accompanied by a change in the color of the sample. The course of thermally induced transformations has been monitored in detail by means of temperature-resolved powder X-ray diffraction and infrared spectroscopy. Upon dissolution, all forms equilibrate immediately, as confirmed by NMR and UV/Vis spectroscopy in several solvents, with the equilibrium shifted far towards the enol tautomer. This study reveals the significance of peripheral groups in the stabilization of metastable tautomers in the solid state.

  4. 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. PMID:27274339

  5. 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

  6. The use of dimorphic Alu insertions in human DNA fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Novick, G.E.; Gonzalez, T.; Garrison, J.; Novick, C.C.; Herrera, R.J. [Florida International Univ., Miami, FL (United States). Dept. of Biological Sciences; Batzer, M.A. [Lawrence Livermore National Lab., CA (United States); Deininger, P.L. [Louisiana State Univ., New Orleans, LA (United States). Medical Center

    1992-12-04

    We have characterized certain Human Specific Alu Insertions as either dimorphic (TPA25, PV92, APO), sightly dimorphic (C2N4 and C4N4) or monomorphic (C3N1, C4N6, C4N2, C4N5, C4N8), based on studies of Caucasian, Asian, American Black and African Black populations. Our approach is based upon: (1) PCR amplification using primers directed to the sequences that flank the site of insertion of the different Alu elements studied; (2) gel electrophoresis and scoring according to the presence or absence of an Alu insertion in one or both homologous chromosomes; (3) allelic frequencies calculated and compared according to Hardy-Weinberg equilibrium. Our DNA fingerprinting procedure using PCR amplification of dimorphic Human Specific Alu insertions, is stable enough to be used not only as a tool for genetic mapping but also to characterize populations, study migrational patterns and track the inheritance of human genetic disorders.

  7. 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.

  8. 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.

  9. Inserting Agility in System Development

    Science.gov (United States)

    2012-07-01

    Agile IT Acquisition, IT Box, Scrum Inserting Agility in System Development Matthew R. Kennedy and Lt Col Dan Ward, USAF With the fast-paced nature...1,700 individuals and 71 countries, found Scrum and eXtreme Programming to be the most widely followed method- ologies (VersionOne, 2007). Other...University http://www.dau.mil 259 Defense ARJ, July 2012, Vol. 19 No. 3 : 249–264 Scrum Scrum is a framework used for project management, which is

  10. 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...

  11. A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis

    DEFF Research Database (Denmark)

    Thierry, Simon; Hamidjaja, Raditijo A.; Girault, Guillaume

    2013-01-01

    Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and represent informative DNA markers extensively used to analyze phylogenetic relationships between strains. Medium to high throughput, open methodologies able to test many SNPs in a minimum time are therefore in great...

  12. A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis

    NARCIS (Netherlands)

    Thierry, S.; Hamidjaja, R.A.; Girault, G.; Lofstrom, C.; Ruuls-van Stalle, E.M.F.; Sylviane, D.

    2013-01-01

    Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and represent informative DNA markers extensively used to analyze phylogenetic relationships between strains. Medium to high throughput, open methodologies able to test many SNPs in a minimum time are therefore in great ne

  13. 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.

  14. Leptin Receptor Gene Gln223Arg Polymorphism Is Not Associated with Hypertension: A Preliminary Population-Based Cross-Sectional Study

    Directory of Open Access Journals (Sweden)

    Geórgia das Graças Pena

    2014-01-01

    Full Text Available Hypertension is responsible for high morbidity and mortality as one of the most important cardiometabolic risk factors. The aim of the study was to investigate whether the Gln223Arg in the leptin receptor (LEPR influences the prevalence of hypertension. A cross-sectional study was carried out in individuals aged ≥ 18 years. Polymorphism identification was performed using PCR-RFLP analysis. Participants with blood pressure ≥ 140/90 mmHg or medication use were considered hypertensive. Frequencies, means, cross-tabulations, and multivariate models were produced to study differences in hypertension prevalence by genotypes. The study includes 470 participants. The frequency of GG polymorphism variant was 10.43%, 46.81% AG, and 42.77% AA. The distribution of hypertension frequency by LEPR genotypes was the following: AA 43.8%, AG 40.4%, and GG 40.8%; there were no significant differences between groups. Comparative analysis which used multivariate Poisson regression adjusted by many potential confounders (age, sex, schooling, smoking, alcohol intake, obesity, and family history of parental obesity did not modify this result. In this large sample of population-based study, the association of the LEPR Gln223Arg gene polymorphism with hypertension was not observed.

  15. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci.

    Science.gov (United States)

    Liu, Z H; Anderson, J A; Hu, J; Friesen, T L; Rasmussen, J B; Faris, J D

    2005-08-01

    Efficient user-friendly methods for mapping plant genomes are highly desirable for the identification of quantitative trait loci (QTLs), genotypic profiling, genomic studies, and marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. Target region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects a large number of loci from a single reaction without extensive pre-PCR processing of samples. In the investigation reported here, we used both SSRs and TRAPs to generate over 700 markers for the construction of a genetic linkage map in a hard red spring wheat intervarietal recombinant inbred population. A framework map consisting of 352 markers accounted for 3,045 cM with an average density of one marker per 8.7 cM. On average, SSRs detected 1.9 polymorphic loci per reaction, while TRAPs detected 24. Both marker systems were suitable for assigning linkage groups to chromosomes using wheat aneuploid stocks. We demonstrated the utility of the maps by identifying major QTLs for days to heading and reduced plant height on chromosomes 5A and 4B, respectively. Our results indicate that TRAPs are highly efficient for genetic mapping in wheat. The maps developed will be useful for the identification of quality and disease resistance QTLs that segregate in this population.

  16. The association between the TP53 Arg72Pro polymorphism and colorectal cancer: An updated meta-analysis based on 32 studies

    Science.gov (United States)

    Tian, Xin; Dai, Shundong; Sun, Jing; Jiang, Shenyi; Jiang, Youhong

    2017-01-01

    Several previous studies evaluated the association between the Arg72Pro (rs1042522) polymorphism in the TP53 tumor suppressor gene and colorectal cancer (CRC). However, the results are conflicting. This meta-analysis aimed to shed new light on the precise association between TP53 variants and CRC. We analyzed 32 published case-control studies involving 8,586 cases and 10,275 controls using crude odd ratios (ORs) with 95% confidence intervals (CIs). The meta-analysis was performed using a fixed-effect or random-effects model, as appropriate. We found that the TP53 Arg72Pro polymorphism was not significantly associated with CRC risk in the overall population. However, subgroup analysis based on ethnicity revealed an increased risk of CRC among Asians (CC vs. GC+GG: OR=1.22, 95% CI: 1.02-1.45), and similar results were found for rectal cancer (CC vs. GC+GG: OR=1.34, 95% CI: 1.120-1.62). These results suggest that the TP53 Arg72Pro polymorphism CC genotype may contribute to an increased risk of CRC, especially for rectal cancer and among Asians. PMID:27901479

  17. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories.

    Science.gov (United States)

    DaCosta, Jeffrey M; Sorenson, Michael D

    2016-01-01

    Genotype-by-sequencing (GBS) methods have revolutionized the field of molecular ecology, but their application in molecular phylogenetics remains somewhat limited. In addition, most phylogenetic studies based on large GBS data sets have relied on analyses of concatenated data rather than species tree methods that explicitly account for genealogical stochasticity among loci. We explored the utility of "double-digest" restriction site-associated DNA sequencing (ddRAD-seq) for phylogenetic analyses of the Lagonosticta firefinches (family Estrildidae) and the Vidua brood parasitic finches (family Viduidae). As expected, the number of homologous loci shared among samples was negatively correlated with genetic distance due to the accumulation of restriction site polymorphisms. Nonetheless, for each genus, we obtained data sets of ∼3000 loci shared in common among all samples, including a more distantly related outgroup taxon. For all samples combined, we obtained >1000 homologous loci despite ∼20my divergence between estrildid and parasitic finches. In addition to nucleotide polymorphisms, the ddRAD-seq data yielded large sets of indel and locus presence-absence polymorphisms, all of which had higher consistency indices than mtDNA sequence data in the context of concatenated parsimony analyses. Species tree methods, using individual gene trees or single nucleotide polymorphisms as input, generated results broadly consistent with analyses of concatenated data, particularly for Lagonosticta, which appears to have a well resolved, bifurcating history. Results for Vidua were also generally consistent across methods and data sets, although nodal support and results from different species tree methods were more variable. Lower gene tree congruence in Vidua is likely the result of its unique evolutionary history, which includes rapid speciation by host shift and occasional hybridization and introgression due to incomplete reproductive isolation. We conclude that dd

  18. Aspects and Polymorphism in AspectJ

    DEFF Research Database (Denmark)

    Lorenz, David Harel; Ernst, Erik

    2003-01-01

    -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 AspectJ...... 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....

  19. Angiotensin-converting enzyme gene I/D polymorphism and renal disease

    NARCIS (Netherlands)

    Navis, G; van der Kleij, FGH; de Zeeuw, D; de Jong, PE

    1999-01-01

    In recent years a vast amount of data has been published on the association between the insertion/deletion (VD) polymorphism of the gene coding for angiotensin-converting enzyme and renal disease. It has be come clear that the polymorphism does not affect the prevalence of renal disease. However, da

  20. Angiotensinogen and ACE gene polymorphisms and risk of atrial fibrillation in the general population

    DEFF Research Database (Denmark)

    Ravn, Lasse S; Benn, Marianne; Nordestgaard, Børge G

    2008-01-01

    proteins in this system predict risk of atrial fibrillation. METHODS AND RESULTS: We genotyped 9235 individuals from the Danish general population, The Copenhagen City Heart Study, for the a-20c, g-6a, T174M, and M235T polymorphisms in the angiotensinogen gene and the insertion/deletion (I/D) polymorphism...

  1. Mitochondrial DNA polymorphisms in Phytophthora infestans: new haplotypes are identified and re-defined by PCR.

    Science.gov (United States)

    Yang, Zhi-Hui; Qi, Ming-Xing; Qin, Yu-Xuan; Zhu, Jie-Hua; Gui, Xiu-Mei; Tao, Bu; Xu, Xiao-Hu; Zhang, Fu-Guang

    2013-11-01

    Polymorphisms of mitochondrial DNA (mt-DNA) are particularly useful for monitoring specific pathogen populations like Phytophthora infestans. Basically type I and II of P. infestans mt-DNA were categorized by means of polymorphism lengths caused by an ~2 kb insertion, which can be detected via restriction enzyme digestion. In addition genome sequencing of haplotype Ib has been used as a simple Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method to indirectly identify type I and II alterations through EcoR I restriction enzyme DNA fragment patterns of the genomic P4 area. However, with the common method, wrong mt-DNA typing occurs due to an EcoR I recognition site mutation in the P4 genomic area. Genome sequencing of the four haplotypes (Ia, Ib, IIa, and IIb) allowed us to thoroughly examine mt-DNA polymorphisms and we indentified two hypervariable regions (HVRs) named HVRi and HVRii. The HVRi length polymorphism caused by a 2 kb insertion/deletion was utilized to identify mt-DNA types I and II, while another length polymorphism in the HVRii region is caused by a variable number of tandem repeats (n = 1, 2, or 3) of a 36 bp sized DNA stretch and was further used to determine mt-DNA sub-types, which were described as R(n = 1, 2, or 3). Finally, the P. infestans mt-DNA haplotypes were re-defined as IR(1) or IIR(2) according to PCR derived HVRi and HVRii length polymorphisms. Twenty-three isolates were chosen to verify the feasibility of our new approach for identifying mt-DNA haplotypes and a total of five haplotypes (IR(1), IR(2), IR(3), IIR(2) and IIR(3)) were identified. Additionally, we found that six isolates determined as type I by our method were mistakenly identified as type II by the PCR-RFLP technique. In conclusion, we propose a simple and rapid PCR method for identification of mt-DNA haplotypes based on sequence analyses of the mitochondrial P. infestans genome.

  2. 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.

  3. 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.

  4. SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.

    Science.gov (United States)

    Ruiz-Rojas, J J; Sargent, D J; Shulaev, V; Dickerman, A W; Pattison, J; Holt, S H; Ciordia, A; Veilleux, Richard E

    2010-08-01

    As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA. Bioinformatics analysis of flanking sequences revealed little preference for insertion site with regard to G/C content; left borders tended to retain more of the plasmid backbone than right borders. Primers were developed from F. vesca flanking sequences to attempt to amplify products from both parents of the reference F. vesca 815 x F. bucharica 601 mapping population. Polymorphism occurred as: presence/absence of an amplification product for 16 primer pairs and different size products for 12 primer pairs, For 46 mutants, where polymorphism was not found by PCR, the amplification products were sequenced to reveal SNP polymorphism. A cleaved amplified polymorphic sequence/derived cleaved amplified polymorphism sequence (CAPS/dCAPS) strategy was then applied to find restriction endonuclease recognition sites in one of the parental lines to map the SNP position of 74 of the T-DNA insertion lines. BLAST search of flanking regions against GenBank revealed that 46 of 108 flanking sequences were close to presumed strawberry genes related to annotated genes from other plants.

  5. 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

  6. JT/LJT connector insert material evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Baca, J.R.F.

    1991-10-01

    Different insert (insulator) materials are undergoing evaluation to replace the Fiberite E-3938 BE96 material currently used. Also being evaluated is the reconfiguration of the insert and metal shell-edge geometries for the purpose of reducing the alleged interference principally responsible for insert damage.

  7. The effect of type of vaginal insert and dose of pLH on embryo production, following fixed-time AI in a progestin-based superstimulatory protocol in Nelore cattle.

    Science.gov (United States)

    Nogueira, Marcelo F Gouveia; Fragnito, Paulo S; Trinca, Luzia A; Barros, Ciro M

    2007-02-01

    The objective was to analyze and report field data focusing on the effect of type of progesterone-releasing vaginal insert and dose of pLH on embryo production, following a superstimulatory protocol involving fixed-time artificial insemination (FTAI) in Nelore cattle (Bos taurus indicus). Donor heifers and cows (n = 68; 136 superstimulations over 2 years) received an intravaginal, progesterone-releasing insert (CIDR or DIB, with 1.9 or 1.0 g progesterone, respectively) and 3-4 mg of estradiol benzoate (EB) i.m. at random stages of the estrous cycle. Five days later (designated Day 0), cattle were superstimulated with a total of 120-200 mg of pFSH (Folltropin-V), given twice daily in decreasing doses from Days 0 to 3. All cattle received two luteolytic doses of PGF2alpha at 08:00 and 20:00 h on Day 2 and progesterone inserts were removed at 20:00 h on Day 3 (36 h after the first PGF2alpha injection). Ovulation was induced with pLH (Lutropin-V, 12.5 or 25 mg, i.m.) at 08:00 h on Day 4 with FTAI 12, 24 and in several cases, 36 h later. Embryos were recovered on Days 11 or 12, graded and transferred to synchronous recipients. Overall, the mean (+/-S.E.M.) number of total ova/embryos (13.3 +/- 0.8) and viable embryos (9.4 +/- 0.6) and pregnancy rate (43.5%; 528/1213) did not differ among groups, but embryo viability rate (overall, 70.8%) was higher in donors with a DIB (72.3%) than a CIDR (68.3%, P = 0.007). In conclusion, the administration of pLH 12 h after progesterone removal in a progestin-based superstimulatory protocol facilitated fixed-time AI in Nelore donors, with embryo production, embryo viability and pregnancy rates after embryo transfer, comparable to published results where estrus detection and AI was done. Results suggested a possible alternative, which would eliminate the need for estrus detection in donors.

  8. 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

  9. Deep ultraviolet photodetectors based on p-Si/ i-SiC/ n-Ga2O3 heterojunction by inserting thin SiC barrier layer

    Science.gov (United States)

    An, Yuehua; Zhi, Yusong; Wu, Zhenping; Cui, Wei; Zhao, Xiaolong; Guo, Daoyou; Li, Peigang; Tang, Weihua

    2016-12-01

    Deep ultraviolet photodetectors based on p-Si/ n-Ga2O3 and p-Si/ i-SiC/ n-Ga2O3 heterojunctions were fabricated by laser molecular beam epitaxial (L-MBE), respectively. In compare with p-Si/ n-Ga2O3 heterostructure-based photodetector, the dark current of p-Si/ i-SiC/ n-Ga2O3-based photodetector decreased by three orders of magnitude, and the rectifying behavior was tuned from reverse to forward. In order to improve the quality of the photodetector, we reduced the oxygen vacancies of p-Si/ i-SiC/ n-Ga2O3 heterostructures by changing the oxygen pressure during annealing. As a result, the rectification ratio ( I F/ I R) of the fabricated photodetectors was 36 at 4.5 V and the photosensitivity was 5.4 × 105% under the 254 nm light illumination at -4.5 V. The energy band structure of p-Si/ n-Ga2O3 and p-Si/ i-SiC/ n-Ga2O3 heterostructures was schematic drawn to explain the physic mechanism of enhancement of the performance of p-Si/ i-SiC/ n-Ga2O3 heterostructure-based deep UV photodetector by introduction of SiC layer.

  10. Reversible Li-insertion in nanoscaffolds: A promising strategy to alter the hydrogen sorption properties of Li-based complex hydrides

    NARCIS (Netherlands)

    Ngene, Peter; Verkuijlen, Margriet H. W.; Barre, Charlotte; Kentgens, Arno P. M.; de Jongh, Petra E.

    2016-01-01

    Intercalation and de-intercalation of lithium into graphene layers is a well-established phenomenon in Li-ion battery technology. Here we show how this phenomenon can be exploited to destabilize, and alter the hydrogen sorption behaviour of Li-based metal hydrides (LiBH4 and LiAlH4), thereby achievi

  11. Identification of weakly beta-hemolytic porcine spirochetes by biochemical reactions, PCR-based restriction fragment length polymorphism analysis and species-specific PCR.

    Science.gov (United States)

    Ohya, Tatsuo; Araki, Hiroshi; Sueyoshi, Masuo

    2008-08-01

    We examined the usefulness of PCR-based restriction fragment length polymorphism (PCR-RFLP) and species-specific PCR combined with a newly devised rapid biochemical test using microplates for identifying weakly beta-hemolytic intestinal spirochetes (WBHIS) isolated from pigs. WBHIS strains showing atypical biochemical characteristics were decisively identified at the species level by PCR-RFLP and species-specific PCR. Identification of WBHIS at the species level in routine diagnostic work will certainly contribute to clarifying the pathogenicity of WBHIS.

  12. No association between MspI allele of the ADRA2A polymorphism and ADHD: meta-analysis of family-based studies.

    Science.gov (United States)

    Shiffrin, Nina D; Gruber, June; Glatt, Stephen J; Faraone, Stephen V

    2013-08-01

    There is evidence for a genetic contribution to attention-deficit hyperactivity disorder (ADHD), although no candidate genes have attained genome-wide significance to date. Given that the noradrenergic system has been implicated in ADHD, the gene for the α2-adrenergic receptor (ADRA2A) has been hypothesized to contribute to the pathogenesis of ADHD. The present investigation reports results from a meta-analysis of family-based studies that did not find a significant association between the MspI polymorphism of the ADRA2A gene and ADHD.

  13. 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.

  14. 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

  15. 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

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

    Science.gov (United States)

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

    2015-08-31

    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 the inductance element and improving the quality factor of the sensor. In addition, the sensor was fabricated using thick film integrated technology from high-temperature materials that ensure stable operation of the sensor in high-temperature environments. Experimental results showed that the sensor accurately monitored pressures from 0 bar to 2 bar at temperatures up to 800 °C. The sensitivity, linearity, repeatability error, and hysteretic error of the sensor were 0.225 MHz/bar, 95.3%, 5.5%, and 6.2%, respectively.

  17. Polymorph and isomer conversion of complexes based on CuI and PPh3 easily observed via luminescence.

    Science.gov (United States)

    Maini, Lucia; Braga, Dario; Mazzeo, Paolo P; Ventura, Barbara

    2012-01-14

    Reactions between copper(I) iodide and triphenylphosphine have been explored in solution and in the solid state and six luminescent coordination complexes have been obtained and characterized by X-ray diffraction and UV-vis spectroscopy and photophysics. Solid-state reactions of CuI with PPh(3) in different conditions (kneading, vapour digestion) and stoichiometries resulted in the formation of high ratio ligand:metal compounds while tetrameric structures could be obtained only by solution reactions. Crystal structures were determined by single crystal X-ray diffraction while purity of the bulk product was checked by powder diffraction (XRPD). Three different tetrameric structures with 1:1 stoichiometry have been synthesized: two closed cubane-type polymorphs [CuI(PPh(3))](4) (form 1a) and [CuI(PPh(3))](4) (form 1b) and an open step-like isomer [CuI(PPh(3))](4) (form 2). The conversions between the polymorphs and isomers have been studied and characterized by XRPD. The most stable form [CuI(PPh(3))](4) (form 1b) can convert into the open step-like isomer [CuI(PPh(3))](4) (form 2) in a slurry experiment with EtOH or CH(2)Cl(2) or AcCN and converts back into [CuI(PPh(3))](4)1b when exposed to vapors of toluene. At room temperature all the tetrameric compounds exhibit luminescence in the solid state and, notably, the two polymorphs show a dissimilar dual emission at low temperature. The luminescence features in the solid state seem to be peculiarly related to the presence of the aromatic phosphine ligand and depend on the Cu-Cu distance in the cluster.

  18. Brain-derived neurotrophic factor (BDNF) Val66Met polymorphism and post-stroke dementia: a hospital-based study from northern Iran.

    Science.gov (United States)

    Rezaei, Sajjad; Asgari Mobarake, Karim; Saberi, Alia; Keshavarz, Parvaneh; Leili, Ehsan Kazemnejad

    2016-06-01

    Brain-derived neurotrophic factor (BDNF) Val66Met polymorphism is associated with functional and cognitive outcomes of stroke and plays a key role in preventing neuronal death. This study aimed to answer the following question: does BDNF Val66Met polymorphism prognosticate survival status and risk of post-stroke dementia (PSD)? In a retrospective cohort study, 206 patients with ischemic stroke (IS) entered the study. They were consecutively being admitted to the neurology clinic in Poursina Hospital (northern Iran) from 2012 to 2014. The diagnosis of PSD was based on DSM-5 criteria. The current and the premorbid cognitive statuses of the patients were respectively assessed through the third edition of Addenbrooke's Cognitive Examination and the Informant Questionnaire on Cognitive Decline in the Elderly. BDNF Val66Met gene polymorphism was determined by PCR-RFLP. On average, 48 patients (23.3 %) developed PSD 6 months after IS. Log-rank test showed that the survival rate of at least one Val-allele carriers was significantly lower than that of Met/Met homozygotes (P = 0.0005), and the former developed PSD sooner than the latter (375, 492 days, respectively). Cox model showed that heterozygous carriers of Val/Met were at greater risk of PSD over time (HR 2.280, 95 % CI 1.566-4.106, P = 0.006). However, the risk ratio of patients with PSD among different BDNF genotypes decreased after adjusting demographic, clinical, and vascular risk factors, and was no longer statistically significant (AHR 2.434, 95 % CI 0.597-9.926, P = 0.215). Val-allele carriers or Val/Met genotypes were more quickly diagnosed as having dementia after IS. However, this genetic vulnerability became more destructive when it was added to demographic, clinical, and vascular risk factors.

  19. 元任务插入的多星成像侦察任务聚类启发式算法%Heuristic Clustering Algorithm of Multiple Satellite Imaging Reconnaissance Tasks Based on Atomic Task Insertion

    Institute of Scientific and Technical Information of China (English)

    徐培德; 王建江; 许语拉

    2012-01-01

    At the time of multiple satellites execute reconnaissance tasks in cooperation, Clustering of multiple satellite imaging reconnaissance tasks is able to improve integrated Reconnaissance efficiency of multiple satellites. Based on satellite imaging reconnaissance atomic tasks clustering relations and restriction conditions,this paper establishes mathematics programming model of multiple satellite imaging reconnaissance tasks clustering, then it presents heuristic clustering algorithm based on atomic task insertion to solve the model. Finally the algorithm is validated by an example.%在多颗卫星协同执行侦察任务时,多星成像侦察任务聚类能够提高多颗卫星的整体侦察效率.根据卫星成像侦察元任务之间的聚类关系及约束条件,建立了数学规划模型,并提出了模型求解的基于元任务插入的启发式聚类算法,最后结合实例验证了算法的有效性.

  20. Association Between Interleukin 4 Gene Seventy-Base-Pair Variable Number of Tandem Repeats Polymorphism and Uterine Leiomyoma

    Directory of Open Access Journals (Sweden)

    Salimi

    2014-06-01

    Full Text Available Background Uterine Leiomyoma (UL is the most common gynecological tumor and a public health problem. Higher serum interleukin 4 (IL-4 level, as an anti-inflammatory cytokine that regulates TH1/TH2 cells balance, has been observed in the uterine cavity. Objectives The aim of this study was to investigate the association between IL4 gene variable number of tandem repeats (VNTR polymorphism and the risk of UL in southeast of Iran. Patients and Methods We compared of 99 patients with UL with that of 102 healthy controls. The IL4 VNTR polymorphism was genotyped by gel electrophoresis after PCR amplification. Results There was no significant association between RP*1/RP*2 and RP*2/RP*2 genotypes and UL; however, a significant association between RP*2/RP*2 genotype and UL was found after adjustment for age (OR, 4; 95% CI, 1.3-12.4; and P = 0.015. The frequency of RP*2 allele was significantly higher in women with UL (OR, 1.9; 95% CI, 1.1-3.5; and P = 0.03. Conclusions The IL4 VNTR RP*2/RP*2 genotype could be an age-related risk factor for UL. Moreover, the frequency of RP*2 allele was significantly higher in women with UL.

  1. Genetic analysis and ecological association of Hina genes based on single nucleotide polymorphisms (SNPs) in wild barley, Hordeum spontaneum.

    Science.gov (United States)

    Li, Wei-Tao; Huang, Xia; Wang, Ji-Rui; Chen, Guo-Yue; Nevo, Eviatar; Zheng, You-Liang; Wei, Yu-Ming

    2010-02-01

    Specific primers were designed to amplify the sequences of Hina genes from 121 wild barley (Hordeum spontaneum) accessions belonging to 18 populations from Iran, Israel and Turkey. Forty-nine single nucleotide polymorphisms (SNPs), nine indels, and 26 haplotypes were determined by sequence analysis. The genetic polymorphism (P), genetic diversity (He), and Shannon's information index (I) in the 18 populations were 0.486, 0.181 and 0.269, respectively. Approximately 2/3 genetic variations of Hina genes were presented within populations, while approximately 1/3 genetic variations were observed between populations. Broad gene flow (Nm= 3.31) and low genetic variation (Gst= 0.0702) were detected. However, the genetic differentiation between populations was independent of geographical distances according to the Mantel test (p = 0.478). The result of Spearman rank correlations (r(s)) showed that the genetic indices (P, He and I) of Hina were not significantly correlated with ecological factors. Only eight SNP positions correlated significantly with ecological factors. Of the eight SNP positions that positively correlated with ecological factors, only one SNP (769, T-C) was located in the coding region; however, it was not responsible for the amino acid change.

  2. 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.

  3. Polymorphism of the prion protein gene (PRNP) in Polish cattle affected by classical bovine spongiform encephalopathy.

    Science.gov (United States)

    Gurgul, Artur; Czarnik, Urszula; Urszula, Czarnik; Larska, Magdalena; Polak, Mirosław P; Strychalski, Janusz; Słota, Ewa

    2012-05-01

    Recent attempts to discover genetic factors affecting cattle resistance/susceptibility to bovine spongiform encephalopathy (BSE) have led to the identification of two insertion/deletion (indel) polymorphisms, located within the promoter and intron 1 of the prion protein gene PRNP, showing a significant association with the occurrence of classical form of the disease. Because the effect of the polymorphisms was studied only in few populations, in this study we investigated whether previously described association of PRNP indel polymorphisms with BSE susceptibility in cattle is also present in Polish cattle population. We found a significant relation between the investigated PRNP indel polymorphisms (23 and 12 bp indels), and susceptibility of Polish Holstein-Friesian cattle to classical BSE (P < 0.05). The deletion variants of both polymorphisms were related to increased susceptibility, whereas insertion variants were protective against BSE.

  4. Sequential cooling insert for turbine stator vane

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Russel B

    2017-04-04

    A sequential flow cooling insert for a turbine stator vane of a small gas turbine engine, where the impingement cooling insert is formed as a single piece from a metal additive manufacturing process such as 3D metal printing, and where the insert includes a plurality of rows of radial extending impingement cooling air holes alternating with rows of radial extending return air holes on a pressure side wall, and where the insert includes a plurality of rows of chordwise extending second impingement cooling air holes on a suction side wall. The insert includes alternating rows of radial extending cooling air supply channels and return air channels that form a series of impingement cooling on the pressure side followed by the suction side of the insert.

  5. Autism and serotonin transporter gene polymorphisms: a systematic review and meta-analysis.

    Science.gov (United States)

    Huang, Christine H; Santangelo, Susan L

    2008-09-05

    The serotonin transporter gene (5-HTT) plays a crucial role in serotonergic neurotransmission and has been found to be associated, with varying degrees of significance, with many diseases, including autism. Prior association studies of autism have yielded conflicting results regarding the association between two common 5-HTT polymorphisms, the promoter insertion/deletion (5-HTTLPR) and the intron 2 VNTR (STin2 VNTR). We conducted a systematic review and meta-analysis to test the following hypotheses: (i) there is an association between autism and either or both of the 5-HTTLPR and STin2 VNTR polymorphisms, and (ii) the S allele of 5-HTTLPR and/or the STin2.12 allele of the VNTR are the specific risk alleles for autism. All published family-based and population based studies were examined to determine the overall strength of association between 5-HTT polymorphisms and autism. After exclusion of studies with overlapping samples and studies whose data did not allow for calculation of an odds ratio, 16 studies were included for final analyses, all but two of which used a family-based design. The meta-analysis failed to find a significant overall association between either of the 5-HTT polymorphisms examined and autism. Further, no allelic transmission distortion was found when studies of simplex (11 studies) and multiplex (3 studies) family samples were analyzed separately. However, there was significant heterogeneity by ethnicity; family based studies of US mixed population samples showed preferential transmission of the S allele of 5-HTTLPR (S allele:L allele = 247:183), while there was no allelic distortion among the family-based studies of European and Asian samples.

  6. dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.

    Science.gov (United States)

    Tahira, Tomoko; Baba, Shingo; Higasa, Koichiro; Kukita, Yoji; Suzuki, Yutaka; Sugano, Sumio; Hayashi, Kenshi

    2005-08-01

    We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

  7. Association of polymorphisms of the CHI3L1 gene with asthma and atopy: a populations-based study of 6514 Danish adults

    DEFF Research Database (Denmark)

    Rathcke, Camilla Noelle; Holmkvist, Johan; Husmoen, Lise Lotte N;

    2009-01-01

    and lung function in a large population-based sample of adults. METHODS/PRINCIPAL FINDINGS: Eleven single nucleotide polymorphisms (SNPs) of CHI3L1 including rs4950928 were genotyped in 6514 individuals. Asthma was defined as self-reported history of physician-diagnosed asthma. Total IgE and specific Ig......BACKGROUND: YKL-40 is a chitinase-like glycoprotein encoded by the chitinase 3-like 1 gene, CHI3L1, localized at chromosome 1q32.1. Increased levels of serum YKL-40 have been reported to be a biomarker for asthma and a reduced lung function. Interestingly, the C-allele of the -131 C-->G (rs4950928......) polymorphism of CHI3L1 has been shown to associate with bronchial hyperresponsiveness and reduced lung function suggesting that variations in CHI3L1 may influence risk of asthma. The objective of the present study was to investigate the association of common variation in the CHI3L1 locus with asthma, atopy...

  8. Genetically based polymorphisms in morphology and life history associated with putative host races of the water lily leaf beetle, Galerucella nymphaeae.

    Science.gov (United States)

    Pappers, Stephanie M; van der Velde, Gerard; Ouborg, N Joop; van Groenendael, Jan M

    2002-08-01

    A host race is a population that is partially reproductively isolated from other conspecific populations as a direct consequence of adaptation to a specific host. The initial step in host race formation is the establishment of genetically based polymorphisms in, for example, morphology, preference, or performance. In this study we investigated whether polymorphisms observed in Galerucella nymphaeae have a genetic component. Galerucella nymphaeae, the water lily leaf beetle, is a herbivore which feeds and oviposits on the plant hosts Nuphar lutea and Nymphaea alba (both Nymphaeaceae) and Rumex hydrolapathum and Polygonum amphibium (both Polygonaceae). A full reciprocal crossing scheme (16 crosses, each replicated 10 times) and subsequent transplantation of 1,001 egg clutches revealed a genetic basis for differences in body length and mandibular width. The heritability value of these traits, based on midparent-offspring regression, ranged between 0.53 and 0.83 for the different diets. Offspring from Nymphaeaceae parents were on average 12% larger and had on average 18% larger mandibles than offspring from Polygonaceae parents. Furthermore, highly significant correlations were found between feeding preference of the offspring and the feeding preference of their parents. Finally, two fitness components were measured: development time and survival. Development time was influenced by diet, survival both by cross type and diet, the latter of which suggest adaptation of the beetles. This suggestion is strengthened by a highly significant cross x diet interaction effect for development time as well as for survival, which is generally believed to indicate local adaptation. Although no absolute genetic incompatibility among putative host races was observed, survival of the between-host family offspring, on each diet separately, was lower than the survival of the within-host family offspring on that particular host. Survival of offspring of two Nymphaeaceae parents was about

  9. 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

  10. Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis

    DEFF Research Database (Denmark)

    Hansen, Mette H H; Young, Sewall; Jørgensen, Hanne Birgitte Hede;

    2011-01-01

    We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154...... previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics...... and quantitative genetics...

  11. 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.

  12. 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}.

  13. Treatment based on syndrome differentiation of irregular menstruation after intrauterine device insertion%放置宫内节育器后月经不调辨证论治

    Institute of Scientific and Technical Information of China (English)

    吕应慧

    2014-01-01

    Intrauterine device (IUD) is the most convenient, safety, long lasting and economic method of contraception for women at childbearing age[1]. Abnormal menstruation is the main adverse reaction after intrauterine device (IUD) insertion, also the main reason of the discontinuation of IUD, mainly for menorrhagia, namely menstruation too much and prolonged menstruation, drip or irregular. This article only states cases given treatment based on syndrome differentiation of Traditional Chinese Medicine in recent years which has reached great curative effects.%宫内节育器是目前育龄妇女最方便、安全、长效且经济的避孕方法[1]。月经异常是宫内节育器的主要不良反应,也是宫内节育器停用的主要原因,主要表现为月经过多,即月经量增多或流血时间和经期延长、点滴或不规则。本文仅对近几年在临床中遇到的病例运用中医中药进行分型辨证论治取得了较好疗效。

  14. 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.

  15. 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.

  16. 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.

  17. The M129V polymorphism of codon 129 in the prion gene (PRNP) in the Danish population

    DEFF Research Database (Denmark)

    Dyrbye, Henrik; Broholm, Helle; Dziegiel, Morten Hanefeld

    2008-01-01

    the distribution of the codon 129 polymorphism. The occurrence of three other relevant polymorphisms were investigated: An alanine (Ala) silent mutation on codon 117, an aspargine-serine (Asn-Ser) mutation on codon 171 and deletions or insertions in the moeity known as the octapeptide region of PRNP. DNA...

  18. Characterization of swine leukocyte antigen (SLA) polymorphism by sequence-based and PCR-SSP methods in Chinese Bama miniature pigs.

    Science.gov (United States)

    Gao, Caixia; Jiang, Qian; Guo, Dongchun; Liu, Jiasen; Han, Lingxia; Qu, Liandong

    2014-07-01

    The highly polymorphic swine leukocyte antigen (SLA) genes have been repeatedly shown to influence swine immune traits, disease resistance, vaccine responsiveness and tumour penetrance. Analysis of the SLA diversity in as many pig breeds as possible is important to clarify the relationships between SLA genes and diseases or traits, and develop these pigs as valuable animal models for biomedical research. The Chinese Bama miniature pig breed is an economically significant breed that is available at several research institutions in China. In this study, we identified a total of 32 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing nine class I and seven class II haplotypes using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. The possible functional sites of the SLA genes were predicted and analyzed by comparison with those of the human and mouse. Based on the sequence information, we subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the progeny. In the studied cohort (2n = 562), the most prevalent Haplotype Hp-35.6 (SLA-1(∗)1201, SLA-1(∗)1301-SLA-3(∗)0502-SLA-2(∗)1001-DRB1(∗)0501-DQB1(∗)0801) was identified in 182 Bama pigs with a frequency of 32.38%. The presence of the duplicated SLA-1 locus was confirmed in five of the class I haplotypes. Moreover, we identified two crossovers within the class I region and one between the class I and class II regions, which corresponded to recombination frequencies of 0.36% and 0.18%, respectively. The information of this study is essential for an understanding of the SLA allelic architecture and diversity, and it will be helpful for studying the adaptive immune response and further developing the more effective vaccines in the context of SLA specificities.

  19. Isolation of sequences flanking Ac insertion sites by Ac casting.

    Science.gov (United States)

    Wang, Dafang; Peterson, Thomas

    2013-01-01

    Localizing Ac insertions is a fundamental task in studying Ac-induced mutation and chromosomal rearrangements involving Ac elements. Researchers may sometimes be faced with the situation in which the sequence flanking one side of an Ac/Ds element is known, but the other flank is unknown. Or, a researcher may have a small sequence surrounding the Ac/Ds insertion site and needs to obtain additional flanking genomic sequences. One way to rapidly clone unknown Ac/Ds flanking sequences is via a PCR-based method termed Ac casting. This approach utilizes the somatic transposition activity of Ac during plant development, and provides an efficient means for short-range genome walking. Here we describe the principle of Ac casting, and show how it can be applied to isolate Ac macrotransposon insertion sites.

  20. Genetic aspects of targeted insertion mutagenesis in yeasts.

    Science.gov (United States)

    Klinner, U; Schäfer, B

    2004-05-01

    Targeted insertion mutagenesis is a main molecular tool of yeast science initially applied in Saccharomyces cerevisiae. The method was extended to fission yeast Schizosaccharomyces pombe and to "non-conventional" yeast species, which show specific properties of special interest to both basic and applied research. Consequently, the behaviour of such non-Saccharomyces yeasts is reviewed against the background of the knowledge of targeted insertion mutagenesis in S. cerevisiae. Data of homologous integration efficiencies obtained with circular, ends-in or ends-out vectors in several yeasts are compared. We follow details of targeted insertion mutagenesis in order to recognize possible rate-limiting steps. The route of the vector to the target and possible mechanisms of its integration into chromosomal genes are considered. Specific features of some yeast species are discussed. In addition, similar approaches based on homologous recombination that have been established for the mitochondrial genome of S. cerevisiae are described.

  1. High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

    NARCIS (Netherlands)

    Koudijs, M.J.; Klijn, C.; van der Weyden, L.; Kool, J.; ten Hoeve, J.; Sie, D.; Prasetyanti, P.R.; Schut, E.; Kas, S.; Whipp, T.; Cuppen, E.; Wessels, L.; Adams, D.J.; Jonkers, J.

    2011-01-01

    Retroviral and transposon-based insertional mutagenesis (IM) screens are widely used for cancer gene discovery in mice. Exploiting the full potential of IM screens requires methods for high-throughput sequencing and mapping of transposon and retroviral insertion sites. Current protocols are based on

  2. INSULATING CERAMIC INSERTS FOR CASTING PRODUCTS FROM ALUMINUM ALLOYS

    OpenAIRE

    2015-01-01

    The paper analyses production of reusable ceramic insulating inserts applied in permanent mold casting of aluminum alloys. It presents results of manufacturing of ceramic products from synthesized materials based on wollastonite, secondary grog, aluminum slag, etc. The paper demonstrates prospects of their applying.

  3. INSULATING CERAMIC INSERTS FOR CASTING PRODUCTS FROM ALUMINUM ALLOYS

    Directory of Open Access Journals (Sweden)

    A. T. Volochko

    2015-01-01

    Full Text Available The paper analyses production of reusable ceramic insulating inserts applied in permanent mold casting of aluminum alloys. It presents results of manufacturing of ceramic products from synthesized materials based on wollastonite, secondary grog, aluminum slag, etc. The paper demonstrates prospects of their applying.

  4. Marginal adaptation of ceramic inserts after cementation

    NARCIS (Netherlands)

    Ozcan, M; Pfeiffer, P; Nergiz, [No Value

    2002-01-01

    The advantage of using ceramic inserts is to prevent major drawbacks of composite resins such as polymerization shrinkage, wear and microleakage. This in vitro study evaluated the marginal adaptation of two approximal ceramic insert systems after cementation to the cavities opened with ultrasonic ti

  5. HOW TO REDUCE NEEDLE INSERTION INDUCED PAIN

    Institute of Scientific and Technical Information of China (English)

    王斌; 董莉

    2001-01-01

    Acupuncture needle insertion always results in pain in the local area due to stimulating the free nerve endings—algesireceptors of the skin. In spite of mildness, this pain may induce many patients' fright, and thus, hinders more extensive application of acupuncture. In the present paper, the author introduces some methods for reducing needle insertion induced pain.

  6. Insertion/Deletion Polymorphism in the Angiotensin Ⅰ-Converting Enzyme Gene and Risk of Progression of Diabetic Nephropathy in Noninsulin-dependant Diabetes Mellitus among the Han Chinese Population:A Meta-analysis%血管紧张素Ⅰ转换酶基因插入/缺失多态性与中国汉族2型糖尿病人群肾病发病风险相关性的Meta分析

    Institute of Scientific and Technical Information of China (English)

    彭少华; 陈婷; 李彩蓉; 陈勇

    2012-01-01

    目的 评价血管紧张素Ⅰ转换酶(ACE)基因插入/缺失(I/D)多态性与中国汉族2型糖尿病人群发生肾病风险的相关性.方法 由两名评价者独立采用计算机检索中国生物医学文献数据库、中国期刊全文数据库、中文科技期刊全文数据库和万方数据库中的ACE基因I/D多态性与糖尿病肾病(DN)的病例对照研究,检索时间范围均为1994-01-01-2011-03-10.对符合纳入标准的研究进行纳入研究质量及数据提取后,采用RevMan5.1.6软件进行Meta分析.结果 共纳入24项病例对照研究,共3 206例患者.Meta分析结果显示,中国汉族人群携带至少1个I等位基因可以降低38%的DN发生风险[OR=0.62,95%CI(0.52,0.75),P<0.00001];携带含有I等位基因的基因型能够使发生DN的风险降低45%[OR=0.55,95%CI(0.44,0.69),P<0.00001];携带含有D等位基因的基因型能够使发生DN的风险增加1.74倍[OR=1.74,95%CI(1.30,2.31),P=0.0002].敏感性分析表明结果稳健性均较好.结论 ACE基因I/D多态性与中国汉族2型糖尿病人群肾病易感性密切相关,D等位基因可能是易感基因,I等位基因可能是保护基因,但仍需进一步论证.%Objective To evaluate the relationship between the insertion/deletion ( I/D ) polymorphism in the angiotensin I - converting enzyme ( ACE ) gene and risk of the progression of diabetic nephropathy ( DN ) in noninsulin dependant diabetes mellitus ( NIDDM ) among the Han Chinese population. Methods Case - control studies of ACE gene I/D polymorphism and DN among the Han Chinese population that were published from January, 1994 to March, 2011 were indepently searched by two reviewers in databases including CNKI, CBM, VIP, and Wanfang. After having assessed the quality of these studies, we performed a meta - analysis using RevMan 5. 1. 6 software. Results A total of 24 case - control studies involving 3 206 patients met the inclusion criteria. Meta - analysis showed that, in the NIDDM subjects

  7. Differentiation of Candida glabrata, C. nivariensis and C. bracarensis based on fragment length polymorphism of ITS1 and ITS2 and restriction fragment length polymorphism of ITS and D1/D2 regions in rDNA

    DEFF Research Database (Denmark)

    Mirhendi, H; Bruun, B; Schønheyder, H C

    2011-01-01

    Different molecular methods for the discrimination of Candida glabrata, C. bracarensis and C. nivariensis were evaluated and the prevalence of these species among Danish blood isolates investigated. Control strains were used to determine fragment length polymorphism in the ITS1, ITS2, ITS1-5.8S...

  8. Family-based association study of dopaminergic genes polymorphisms and EAS temperamental traits [Polimorfizmy w genach systemu dopaminergicznego a cechy temperamentu EAS – rodzinne badanie asocjacyjne

    Directory of Open Access Journals (Sweden)

    Dragan, Wojciech Ł.

    2013-04-01

    Full Text Available Aim. The aim of the present study was to identify relations between several polymorphisms in dopamine genes (DRD2,DRD3, DRD4, SNAP-25, ANKK1and DAT1 and temperamental traits distinguished in the EAS theory. In this study the family-based method was used.Method. The study was run on 149 biological families with one or two children aged 3-12. Temperamental data were obtained using Buss and Plomin EAS-C Temperament Questionnaire.Results. Significant associations between two SNPs in the SNAP-25 gene (rs363039 and rs363050 and shyness was found. Significant relationships of this trait with haplotypes in DAT1 and SNAP-25 genes was also identified. Conclusion. The data collected suggest that variability in dopamine genes may have impact on the development of temperamental shyness, which is recognized as a fear of strangers.

  9. Long-distance effects of insertional mutagenesis.

    Directory of Open Access Journals (Sweden)

    Ruchi Singhal

    Full Text Available BACKGROUND: Most common systems of genetic engineering of mammalian cells are associated with insertional mutagenesis of the modified cells. Insertional mutagenesis is also a popular approach to generate random alterations for gene discovery projects. A better understanding of the interaction of the structural elements within an insertional mutagen and the ability of such elements to influence host genes at various distances away from the insertion site is a matter of considerable practical importance. METHODOLOGY/PRINCIPAL FINDINGS: We observed that, in the context of a lentiviral construct, a transcript, which is initiated at an internal CMV promoter/enhancer region and incorporates a splice donor site, is able to extend past a collinear viral LTR and trap exons of host genes, while the polyadenylation signal, which is naturally present in the LTR, is spliced out. Unexpectedly, when a vector, which utilizes this phenomenon, was used to produce mutants with elevated activity of NF-κB, we found mutants, which owed their phenotype to the effect of the insert on a gene located tens or even hundreds of kilobases away from the insertion site. This effect did not result from a CMV-driven transcript, but was sensitive to functional suppression of the insert. Interestingly, despite the long-distance effect, expression of loci most closely positioned to the insert appeared unaffected. CONCLUSIONS/SIGNIFICANCE: We concluded that a polyadenylation signal in a retroviral LTR, when occurring within an intron, is an inefficient barrier against the formation of a hybrid transcript, and that a vector containing a strong enhancer may selectively affect the function of genes far away from its insertion site. These phenomena have to be considered when experimental or therapeutic transduction is performed. In particular, the long-distance effects of insertional mutagenesis bring into question the relevance of the lists of disease-associated retroviral integration

  10. Association of Angiotensin Converting Enzyme Gene I/D Polymorphism With Type 2 Diabetes Mellitus

    Institute of Scientific and Technical Information of China (English)

    MIN YANG; CHANG-CHUN QIU; QUN XU; HONG-DING XIANG

    2006-01-01

    To investigate the association of angiotensin converting enzyme (ACE) gene insertion/deletion (I/D)polymorphism with type 2 diabetes mellitus (T2DM). Methods Two hundred and nine patients with T2DM diagnosed based on the criteria for diabetes mellitus in 1999 by WHO and 221 controls were recruited from general population of Dongcheng District in Beijing. All subjects were genotyped for the I/D polymorphism of ACE gene by PCR-fragment length polymorphism (FLP) assay. Blood pressure, levels of plasma glucose, lipids and serum insulin were determined. Body mass index (BMI),waist-hip ratio (WHR) and homeostasis model assessment-insulin resistance index (HOMA-IR) were calculated. Results The genotype frequencies for ACE genes DD, ID, and Ⅱ were 19.1%, 42.1%, and 38.8% in patients, respectively, and 9.6%,49.4%, and 41.0% in controls, respectively. The ACE DD genotype frequency was significantly higher in patients than in controls (χ2=7.61, P=0.022). Multivariate logistic regression analysis showed that the ACE DD genotype was a risk factor for T2DM, with the OR of 2.35 (95% CI 1.17-4.71) adjusted for age, sex, BMI, WHR, blood pressure, and serum cholesterol levels.Conclusion The ACE DD genotype is associated with the increased susceptibility to type 2 diabetes mellitus.

  11. NIG_MoG: a mouse genome navigator for exploring intersubspecific genetic polymorphisms.

    Science.gov (United States)

    Takada, Toyoyuki; Yoshiki, Atsushi; Obata, Yuichi; Yamazaki, Yukiko; Shiroishi, Toshihiko

    2015-08-01

    The National Institute of Genetics Mouse Genome database (NIG_MoG; http://molossinus.lab.nig.ac.jp/msmdb/) primarily comprises the whole-genome sequence data of two inbred mouse strains, MSM/Ms and JF1/Ms. These strains were established at NIG and originated from the Japanese subspecies Mus musculus molossinus. NIG_MoG provides visualized genome polymorphism information, browsing single-nucleotide polymorphisms and short insertions and deletions in the genomes of MSM/Ms and JF1/Ms with respect to C57BL/6J (whose genome is predominantly derived from the West European subspecies M. m. domesticus). This allows users, especially wet-lab biologists, to intuitively recognize intersubspecific genome divergence in these mouse strains using visual data. The database also supports the in silico screening of bacterial artificial chromosome (BAC) clones that contain genomic DNA from MSM/Ms and the standard classical laboratory strain C57BL/6N. NIG_MoG is thus a valuable navigator for exploring mouse genome polymorphisms and BAC clones that are useful for studies of gene function and regulation based on intersubspecific genome divergence.

  12. Molecular cloning and polymorphism of major histocompatibility complex class I genes from grass carp (Ctenophayngodon idellus)

    Institute of Scientific and Technical Information of China (English)

    XIA Chun; XU Guangxian; LIN Changyou; HU Tuanjun; YAN Ruoqian; George F GAO

    2004-01-01

    In order to clarify the molecular sequences,allelic polymorphism and the tertiary structure of grass carp (Ctenophayngodon idellus) MHC class I,and to further study their relationship with disease resistances,grass carp MHC class I gene (Ctid-MHC I) was cloned from a cDNA library and the allelic polymorphism in the population was investigated.The results showed that most of the variations exist in the peptide-binding domain (PBD) and high polymorphism was identified in the Ctid-MHC I allelic genes from 12 individuals.Based on the genetic distance,Ctid-MHC class I can be classified into 6 types (from Ctid-MHC I-UA to Ctid-MHC I-UF) which were subdivided into 9 lineages (from A to I).Comparison of the Ctid-MHC I among animals and humans showed that the key amino acids of the peptide binding sites are conserved.Analysis of the tertiary structure of the PBD between Grass carp and human crystallographic data of HLA-A2,the variation with insertion or deletion was found in eight regions (A~H).The phylogenetic tree of MHC class I indicates the evolution of MHC class I among grass carp,fish,amphibian,birds,higher vertebrates and humans.

  13. 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.

  14. 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.

  15. Molecular basis of hereditary fructose intolerance: mutations and polymorphisms in the human aldolase B gene.

    Science.gov (United States)

    Tolan, D R

    1995-01-01

    Mutations in the human aldolase B gene that result in hereditary fructose intolerance have been characterized extensively. Although the majority of subjects have been from northern Europe, subjects from other geographical regions and ethnic groups have been identified. At present 21 mutations have been reported; 15 of these are single base substitutions, resulting in nine amino acid replacements, four nonsense codons, and two putative splicing defects. Two large deletions, two four-base deletions, a single-base deletion, and a seven-base deletion/one-base insertion have been found. This last mutation leads to a defect in splicing and it is likely that one of the small deletions does as well. Regions of the enzyme where mutations have been observed recurrently are encoded by exons 5 and 9. Indeed, the three most common mutations are found in these exons. Two of these prevalent HFI mutations arose from a common ancestor and spread throughout the population by genetic drift. This finding was based on linkage to two sequence polymorphisms, which are among very few informative polymorphic markers that have been identified within the aldolase B gene. Because of the prevalence of a few HFI alleles, and the recent advances in molecular methods for identifying and screening for mutation, the diagnosis of HFI by molecular screening methods should become routine. These molecular diagnostic methods will be extremely beneficial for this often difficult to diagnose and sometimes fatal disease.

  16. Design of weft-insertion system of three-dimensional loom based on servo-cylinder%基于伺服电动缸的立体织机引纬系统的设计

    Institute of Scientific and Technical Information of China (English)

    陈革; 张景慧; 周其洪

    2013-01-01

    In order to insert the weft into the multi-shed while 3-D weaving, according to the special requirements on rapier loom's weft-insertion system for weaving three-dimensional fabric, a new rapier weft-insertion system is presented. The paper introduced the design of three-dimensional loom's weft-insertion system, including the driving system' s hardware configure and its software' s controlling principle. The weft insertion system is computer-controlled and servo-cylinder driven so as to control the rapier's movement on the three-dimensional loom. This method greatly simplifies the weft-insertion system, achieves weft-insertion with variable travel, and improves the flexibility and reliability. The weft-insertion system designed has been applied to a three-dimensional loom prototype successfully.%为实现立体织物中多层经纱形成的多个梭口引纬,分析了剑杆引纬的运动规律以及剑杆织机引纬机构的特点.根据织造三维机织物对立体织机引纬机构的特殊要求,设计了一种新型的剑杆引纬系统.介绍了立体织机引纬系统的总体设计,驱动系统的硬件配置以及控制软件的基本原理.该引纬系统采用计算机控制、伺服电动缸驱动的方法来控制立体织机的剑杆运动,不但简化了引纬机构,还可实现变动程引纬,提高了立体织机引纬的灵活性和可靠性.所设计的引纬系统已应用于立体织机的样机开发.

  17. The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

    Science.gov (United States)

    Chong, Zechen; Zhai, Weiwei; Li, Chunyan; Gao, Min; Gong, Qiang; Ruan, Jue; Li, Juan; Jiang, Lan; Lv, Xuemei; Hungate, Eric; Wu, Chung-I

    2013-12-01

    Studies of protein evolution have focused on amino acid substitutions with much less systematic analysis on insertion and deletions (indels) in protein coding genes. We hence surveyed 7,500 genes between Drosophila melanogaster and D. simulans, using D. yakuba as an outgroup for this purpose. The evolutionary rate of coding indels is indeed low, at only 3% of that of nonsynonymous substitutions. As coding indels follow a geometric distribution in size and tend to fall in low-complexity regions of proteins, it is unclear whether selection or mutation underlies this low rate. To resolve the issue, we collected genomic sequences from an isogenic African line of D. melanogaster (ZS30) at a high coverage of 70× and analyzed indel polymorphism between ZS30 and the reference genome. In comparing polymorphism and divergence, we found that the divergence to polymorphism ratio (i.e., fixation index) for smaller indels (size ≤ 10 bp) is very similar to that for synonymous changes, suggesting that most of the within-species polymorphism and between-species divergence for indels are selectively neutral. Interestingly, deletions of larger sizes (size ≥ 11 bp and ≤ 30 bp) have a much higher fixation index than synonymous mutations and 44.4% of fixed middle-sized deletions are estimated to be adaptive. To our surprise, this pattern is not found for insertions. Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.

  18. Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference

    Directory of Open Access Journals (Sweden)

    Quinn Thomas W

    2008-11-01

    Full Text Available Abstract Background Chicken repeat 1 (CR1 is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Results Elucidation of the exact octomer repeat sequence (TTCTGTGA allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%. Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed. Conclusion This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.

  19. Genomic diversity of Mycobacterium tuberculosis Beijing strains isolated in Tuscany, Italy, based on large sequence deletions, SNPs in putative DNA repair genes and MIRU-VNTR polymorphisms.

    Science.gov (United States)

    Garzelli, Carlo; Lari, Nicoletta; Rindi, Laura

    2016-03-01

    The Beijing genotype of Mycobacterium tuberculosis is cause of global concern as it is rapidly spreading worldwide, is considered hypervirulent, and is most often associated to massive spread of MDR/XDR TB, although these epidemiological or pathological properties have not been confirmed for all strains and in all geographic settings. In this paper, to gain new insights into the biogeographical heterogeneity of the Beijing family, we investigated a global sample of Beijing strains (22% from Italian-born, 78% from foreign-born patients) by determining large sequence polymorphism of regions RD105, RD181, RD150 and RD142, single nucleotide polymorphism of putative DNA repair genes mutT4 and mutT2 and MIRU-VNTR profiles based on 11 discriminative loci. We found that, although our sample of Beijing strains showed a considerable genomic heterogeneity, yielding both ancient and recent phylogenetic strains, the prevalent successful Beijing subsets were characterized by deletions of RD105 and RD181 and by one nucleotide substitution in one or both mutT genes. MIRU-VNTR analysis revealed 47 unique patterns and 9 clusters including a total of 33 isolates (41% of total isolates); the relatively high proportion of Italian-born Beijing TB patients, often occurring in mixed clusters, supports the possibility of an ongoing cross-transmission of the Beijing genotype to autochthonous population. High rates of extra-pulmonary localization and drug-resistance, particularly MDR, frequently reported for Beijing strains in other settings, were not observed in our survey.

  20. 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

    The European Consortium "High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons--SNPforID", has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sampl...

  1. Sequential cooling insert for turbine stator vane

    Science.gov (United States)

    Jones, Russell B; Krueger, Judson J; Plank, William L

    2014-04-01

    A sequential impingement cooling insert for a turbine stator vane that forms a double impingement for the pressure and suction sides of the vane or a triple impingement. The insert is formed from a sheet metal formed in a zigzag shape that forms a series of alternating impingement cooling channels with return air channels, where pressure side and suction side impingement cooling plates are secured over the zigzag shaped main piece. Another embodiment includes the insert formed from one or two blocks of material in which the impingement channels and return air channels are machined into each block.

  2. Tapasin gene polymorphism in systemic onset juvenile rheumatoid arthritis: a family-based case-control study.

    Science.gov (United States)

    Bukulmez, Hulya; Fife, Mark; Tsoras, Monica; Thompson, Susan D; Twine, Natalie A; Woo, Patricia; Olson, Jane M; Elston, Robert C; Glass, David N; Colbert, Robert A

    2005-01-01

    Juvenile rheumatoid arthritis (JRA) comprises a group of chronic systemic inflammatory disorders that primarily affect joints and can cause long-term disability. JRA is likely to be a complex genetic trait, or a series of such traits, with both genetic and environmental factors contributing to the risk for developing the disease and to its progression. The HLA region on the short arm of chromosome 6 has been intensively evaluated for genetic contributors to JRA, and multiple associations, and more recently linkage, has been detected. Other genes involved in innate and acquired immunity also map to near the HLA cluster on 6p, and it is possible that variation within these genes also confers risk for developing JRA. We examined the TPSN gene, which encodes tapasin, an endoplasmic reticulum chaperone that is involved in antigen processing, to elucidate its involvement, if any, in JRA. We employed both a case-control approach and the transmission disequilibrium test, and found linkage and association between the TPSN allele (Arg260) and the systemic onset subtype of JRA. Two independent JRA cohorts were used, one recruited from the Rheumatology Clinic at Cincinnati Children's Hospital Medical Center (82 simplex families) and one collected by the British Paediatric Rheumatology Group in London, England (74 simplex families). The transmission disequilibrium test for these cohorts combined was statistically significant (chi2 = 4.2, one degree of freedom; P = 0.04). Linkage disequilibrium testing between the HLA alleles that are known to be associated with systemic onset JRA did not reveal linkage disequilibrium with the Arg260 allele, either in the Cincinnati systemic onset JRA cohort or in 113 Caucasian healthy individuals. These results suggest that there is a weak association between systemic onset JRA and the TPSN polymorphism, possibly due to linkage disequilibrium with an as yet unknown susceptibility allele in the centromeric part of chromosome 6.

  3. New Lesions Detected by Single Nucleotide Polymorphism Array–Based Chromosomal Analysis Have Important Clinical Impact in Acute Myeloid Leukemia

    Science.gov (United States)

    Tiu, Ramon V.; Gondek, Lukasz P.; O'Keefe, Christine L.; Huh, Jungwon; Sekeres, Mikkael A.; Elson, Paul; McDevitt, Michael A.; Wang, Xiao Fei; Levis, Mark J.; Karp, Judith E.; Advani, Anjali S.; Maciejewski, Jaroslaw P.

    2009-01-01

    Purpose Cytogenetics is the primary outcome predictor in acute myeloid leukemia (AML). Metaphase cytogenetics (MC) detects an abnormal karyotype in only half of patients with AML, however. Single nucleotide polymorphism arrays (SNP-A) can detect acquired somatic uniparental disomy (UPD) and other cryptic defects, even in samples deemed normal by MC. We hypothesized that SNP-A will improve detection of chromosomal defects in AML and that this would enhance the prognostic value of MC. Patients and Methods We performed 250K and 6.0 SNP-A analyses on 140 patients with primary (p) and secondary (s) AML and correlated the results with clinical outcomes and Flt-3/nucleophosmin (NPM-1) status. Results SNP-A is more sensitive than MC in detecting unbalanced lesions (pAML, 65% v 39%, P = .002; and sAML, 78% v 51%, P = .003). Acquired somatic UPD, not detectable by MC, was common in our AML cohort (29% in pAML and 35% in sAML). Patients with SNP-A lesions including acquired somatic UPD exhibited worse overall survival (OS) and event-free survival (EFS) in pAML with normal MC and in pAML/sAML with abnormal MC. SNP-A improved the predictive value of Flt-3 internal tandem duplication/NPM-1 status, with inferior survival seen in patients with additional SNP-A defects. Multivariate analyses confirmed the independent predictive value of SNP-A defects for OS (hazard ratio [HR] = 2.52; 95% CI, 1.29 to 5.22; P = .006) and EFS (HR = 1.72; 95% CI, 1.12 to 3.48; P = .04). Conclusion SNP-A analysis allows enhanced detection of chromosomal abnormalities and provides important prognostic impact in AML. PMID:19770377

  4. 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.

  5. 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.

  6. 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.

  7. Development and application of single-tube multiplex real-time PCR for lineage classification of Mycobacterium tuberculosis based on large sequence polymorphism in Northeast Thailand.

    Science.gov (United States)

    Faksri, Kiatichai; Hanchaina, Rattanavinan; Sangka, Arunnee; Namwat, Wises; Lulitanond, Viraphong

    2015-07-01

    An appreciation of the genetic diversity of Mycobacterium tuberculosis (Mtb) is needed for effective planning of strategies in tuberculosis (TB) control. Large sequence polymorphisms (LSPs) are the molecular epidemiological and evolutionary markers for classification of Mtb into East Asian (EA) or Beijing, Indo-Oceanic (IO), Euro-American (EuA) and East African-Indian (EAI) lineages. We aimed to develop a single-tube multiplex real-time PCR assay using melting curve analysis for lineage classification of Mtb based on LSPs. The technique was optimized and tested with well-characterized strains (n = 89). The developed technique was then applied to classify Mtb isolates from TB patients (n = 256) randomly recruited from 19 provinces covering Northeast Thailand in 2013-2014. The technique demonstrated 100% sensitivity and specificity based on well-characterized strains compared to conventional techniques. The detection limit of the technique is 0.05 ng of genomic DNA of Mtb. The 256 Mtb isolates represented IO (n = 178, 70%), Beijing (n = 60, 23%) and EuA (n = 18, 7%) lineages. Significant associations of the Beijing lineage with drug resistance (p < 0.001) and younger average age of TB patients (p < 0.001) compared to other lineages were shown. The single-tube multiplex real-time PCR technique provides a simple, rapid and high performance tool for characterizing Mtb based on LSPs.

  8. Multilocus Family-Based Association Analysis of Seven Candidate Polymorphisms with Essential Hypertension in an African-Derived Semi-Isolated Brazilian Population

    Science.gov (United States)

    Kimura, L.; Angeli, C. B.; Auricchio, M. T. B. M.; Fernandes, G. R.; Pereira, A. C.; Vicente, J. P.; Pereira, T. V.; Mingroni-Netto, R. C.

    2012-01-01

    Background. It has been widely suggested that analyses considering multilocus effects would be crucial to characterize the relationship between gene variability and essential hypertension (EH). Objective. To test for the presence of multilocus effects between/among seven polymorphisms (six genes) on blood pressure-related traits in African-derived semi-isolated Brazilian populations (quilombos). Methods. Analyses were carried out using a family-based design in a sample of 652 participants (97 families). Seven variants were investigated: ACE (rs1799752), AGT (rs669), ADD2 (rs3755351), NOS3 (rs1799983), GNB3 (rs5441 and rs5443), and GRK4 (rs1801058). Sensitivity analyses were further performed under a case-control design with unrelated participants only. Results. None of the investigated variants were associated individually with both systolic and diastolic BP levels (SBP and DBP, respectively) or EH (as a binary outcome). Multifactor dimensionality reduction-based techniques revealed a marginal association of the combined effect of both GNB3 variants on DBP levels in a family-based design (P = 0.040), whereas a putative NOS3-GRK4 interaction also in relation to DBP levels was observed in the case-control design only (P = 0.004). Conclusion. Our results provide limited support for the hypothesis of multilocus effects between/among the studied variants on blood pressure in quilombos. Further larger studies are needed to validate our findings. PMID:23056922

  9. Shrink-Fit Solderable Inserts Seal Hermetically

    Science.gov (United States)

    Croucher, William C.

    1992-01-01

    Shrink-fit stainless-steel insert in aluminum equipment housing allows electrical connectors to be replaced by soldering, without degrading hermeticity of housing or connector. Welding could destroy electrostatic-sensitive components and harm housing and internal cables. Steel insert avoids problems because connector soldered directly to it rather than welded to housing. Seals between flange and housing, and between connector and flange resistant to leaks, even after mechanical overloading and thermal shocking.

  10. Insertion and deletion mutagenesis of the human cytomegalovirus genome

    Energy Technology Data Exchange (ETDEWEB)

    Spaete, R.R.; Mocarski, E.S.

    1987-10-01

    Studies on human cytomegalovirus (CMV) have been limited by a paucity of molecular genetic techniques available for manipulating the viral genome. The authors have developed methods for site-specific insertion and deletion mutagenesis of CMV utilizing a modified Escherichia coli lacZ gene as a genetic marker. The lacZ gene was placed under the control of the major ..beta.. gene regulatory signals and inserted into the viral genome by homologous recombination, disrupting one of two copies of this ..beta.. gene within the L-component repeats of CMV DNA. They observed high-level expression of ..beta..-galactosidase by the recombinant in a temporally authentic manner, with levels of this enzyme approaching 1% of total protein in infected cells. Thus, CMV is an efficient vector for high-level expression of foreign gene products in human cells. Using back selection of lacZ-deficient virus in the presence of the chromogenic substrate 5-bromo-4-chloro-3-indolyl ..beta..-D-galactoside, they generated random endpoint deletion mutants. Analysis of these mutant revealed that CMV DNA sequences flanking the insert had been removed, thereby establishing this approach as a means of determining whether sequences flanking a lacZ insertion are dispensable for viral growth. In an initial test of the methods, they have shown that 7800 base pairs of one copy of L-component repeat sequences can be deleted without affecting viral growth in human fibroblasts.

  11. 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.

  12. Proper Angle of Sono-guided Central Venous Line Insertion

    Science.gov (United States)

    Barzegari, Hassan; Forouzan, Arash; Fahimi, Mohammad Ali; Zohrevandi, Behzad; Ghanavati, Mandana

    2016-01-01

    Introduction: Determining the proper angle for inserting central venous catheter (CV line) is of great importance for decreasing the complications and increasing success rate. The present study was designed to determine the proper angle of needle insertion for internal jugular vein catheterization. Methods: In the present case series study, candidate patients for catheterization of the right internal jugular vein under guidance of ultrasonography were studied. At the time of proper placing of the catheter, photograph was taken and Auto Cad 2014 software was used to measure the angles of the needle in the sagittal and axial planes, as well as patient’s head rotation. Result: 114 patients with the mean age of 56.96 ± 14.71 years were evaluated (68.4% male). The most common indications of catheterization were hemodialysis (55.3%) and shock state (24.6%). The mean angles of needle insertion were 102.15 ± 6.80 for axial plane, 36.21 ± 3.12 for sagittal plane and the mean head rotation angle was 40.49 ± 5.09. Conclusion: Based on the results of the present study it seems that CV line insertion under the angles 102.15 ± 6.80 degrees in the axial plane, 36.21 ± 3.12 in the sagittal plane and 40.49 ± 5.09 head rotation yield satisfactory results. PMID:27299146

  13. Photonics Research and Technology Insertion

    Science.gov (United States)

    2015-06-05

    2010 B. Additional Pipeline Projects B.1 Spectral Reflectance Imaging Biosensor (SRIB) Task Managers: Professor Selim Unlu/Dr. Helen...enhanced resonance effects, namely small mode volume and high Q, dramatically reduces the detection limit of optical resonance based biosensors

  14. Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

    Science.gov (United States)

    Sanseverino, Walter; Hénaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastián E; Garcia-Mas, Jordi; Casacuberta, Josep Maria

    2015-10-01

    The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.

  15. Angiotensin converting enzyme gene polymorphism in type II diabetics with nephropathy

    OpenAIRE

    Naresh, V. V. S.; Reddy, A. L. K.; Sivaramakrishna, G.; Sharma, P. V. G. K.; Vardhan, R. V.; Kumar, V. Siva

    2009-01-01

    Nephropathy is an important and a frequent complication of long-term type II diabetic nephropathy. Strong evidence exists that genetic predisposition plays a major role in the development of diabetic nephropathy. Recent studies have implicated association between angiotensin converting enzyme (ACE) insertion/deletion (I/D) gene polymorphism and nephropathy. The deletion gene polymorphism of ACE gene has been shown to be associated with increased activity of this enzyme. This study examines th...

  16. 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.

  17. Design and Implementation of Simultaneous Shield And Repeater Insertion for On-chip Interconnects

    Directory of Open Access Journals (Sweden)

    M. Surendra Goud Mr. Y. Sreenivas Goud

    2012-02-01

    Full Text Available A Resource based optimization is a new approach for high performance integrated circuits. The method is applied to simultaneous shield and repeater insertion, resulting in minimum coupling noise under power, delay, and area constraints Repeater insertion is a well known design technique to reduce the delay required to propagate a signal along a line. Shielding inserts an additional line between a victim line and an aggressor line. Finally placing a shield beside and inserting repeaters along a victim line and are chosen to exemplify the resource based optimization process. In the active shielding architecture shield driving circuits as 4:1 multiplexer, full adder, multipliers are inserted. The power consumption of active shielding architecture is observed to be approximately 20% less compare to passive shielding architecture. The main aim of this is minimize the coupling noise under power, delay, and area constraints

  18. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene.

    Science.gov (United States)

    Yadegar, Abbas; Alebouyeh, Masoud; Lawson, Andy J; Mirzaei, Tabassom; Nazemalhosseini Mojarad, Ehsan; Zali, Mohammad Reza

    2014-06-01

    Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.

  19. A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex

    Science.gov (United States)

    Zhang, Hao; Brankovics, Balázs; van der Lee, Theo A.J.; Waalwijk, Cees; van Diepeningen, Anne A.D.; Xu, Jin; Xu, Jingsheng

    2016-01-01

    The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type. PMID:27812414

  20. 基于苹果基因组开发梨的多态性SSR引物%Development of Polymorphic SSR Primers for Pear Based on Apple Genome

    Institute of Scientific and Technical Information of China (English)

    关玲; 黄金凤; 刘金义; 高志红; 章镇; 乔玉山

    2012-01-01

    从NCBI网站获取‘金冠,苹果基因组数据,在每条染色体上随机设计4对共68对引物.利用梨品种‘黄冠,和‘莱阳茌梨'及其F1代杂交群体(共94个单株)对这些引物的应用性进行验证,同时分析了该群体遗传多样性.(1)引物扩增结果显示,有40对引物可以扩增出预期目的条带,占设计引物数量的58.82%,其中16对引物能够扩增出多态性条带.(2)群体遗传多样性分析结果显示,有16对多态性引物扩增产物的等位基因数平均为2.312 5,有效等位基因数平均为2.001 4,平均杂合度观测值、期望杂合度和香农指数分别为0.548 3、0.490 5和0.746 2,表明可以在梨上运用.研究证明,SSR位点在苹果与梨之间可以转移应用.%The genome data of Malus×domestica Borkh. 'Golden Delicious' were downloaded from NCBI website,and 68 SSR primers I. E. Four pairs from every chromosome were designed according to the SSR loci of genome and these primers were detected using 94 F1 progenies of Pyrus 'Huangguan' (from Pyrus bretschneideri ' Xuehuali'×X Pyrus pyri folia 'Shinseiki') × Pyrus bretschneideri ' Laiyang Chili', and the genetic diversity of this progeny was analyzed. The results were shown that; (l)the amounts of primer which could produce the expected product is 40 (58. 82% of total primers), and 16 primers were shown polymorphic by PCR reaction. (2)Based on the results of amplification using the 16 polymorphic primers in the above progeny, the average number of alleles (Na) and the effective number of alleles (Ne) were 2.312 5 and 2.001 4, respectively. The mean observed heterozygosity (Ho), the mean expected heterozy-gosity (He) and the mean Shannon's information index (I) were 0. 548 3,0. 490 5 and 0. 746 2 respectively. 16 polymorphic primers used for Pyrus L. Were developed based on apple genome. The transferability of the SSR locus from genus Malus to Pyrus was also demonstrated in this paper.

  1. Association of 677 C>T (rs1801133 and 1298 A>C (rs1801131 polymorphisms in the MTHFR gene and breast cancer susceptibility: a meta-analysis based on 57 individual studies.

    Directory of Open Access Journals (Sweden)

    Kai Li

    Full Text Available OBJECTIVE: The 677 C>T and 1298 A>C polymorphisms of methylenetetrahydrofolate reductase (MTHFR gene have been widely reported and considered to have a significant effect on breast cancer risk, but the results are inconsistent. A meta-analysis based on 57 eligible studies was carried out to clarify the role of MTHFR gene polymorphisms in breast cancer. METHODS AND RESULTS: Eligible articles were identified by searching databases including PubMed, Web of Science, EMBASE, CNKI and CBM for the period up to August 2012. Finally, a total of 57 studies were included in this meta-analysis. Crude ORs with 95% CIs were used to assess the association between the MTHFR polymorphisms and breast cancer risk. The pooled ORs were performed with additive model, dominant model and recessive model, respectively. Subgroup analysis was also performed by ethnicity. The statistical heterogeneity across studies was examined with χ2-based Q-test. A meta-analysis was performed using the Stata 12.0 software. Overall, the 677 C allele was significantly associated with breast cancer risk (OR = 0.942, 95%CI = 0.898 to 0.988 when compared with the 677 T allele in the additive model, and the same results were also revealed under other genetic models. Simultaneously, the 1298 A allele was not associated with the breast cancer susceptibility when compared with the 1298 C allele (OR = 0.993, 95%CI = 0.978 to 1.009. Furthermore, analyses under the dominant, recessive and the allele contrast model yielded similar results. CONCLUSIONS: The results of this meta-analysis suggest that 677 C>T polymorphism in the MTHFR gene may contribute to breast cancer development. However, the 1298 A>C polymorphism is not significantly associated with increased risks of breast cancer.

  2. Genetic polymorphisms of ADH1B, ADH1C and ALDH2, alcohol consumption, and the risk of gastric cancer: the Japan Public Health Center-based prospective study.

    Science.gov (United States)

    Hidaka, Akihisa; Sasazuki, Shizuka; Matsuo, Keitaro; Ito, Hidemi; Sawada, Norie; Shimazu, Taichi; Yamaji, Taiki; Iwasaki, Motoki; Inoue, Manami; Tsugane, Shoichiro

    2015-02-01

    The association between alcohol consumption, genetic polymorphisms of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) and gastric cancer risk is not completely understood. We investigated the association between ADH1B (rs1229984), ADH1C (rs698) and ALDH2 (rs671) polymorphisms, alcohol consumption and the risk of gastric cancer among Japanese subjects in a population-based, nested, case-control study (1990-2004). Among 36 745 subjects who answered the baseline questionnaire and provided blood samples, 457 new gastric cancer cases matched to 457 controls were used in the analysis. The odds ratios (OR) and corresponding 95% confidence intervals (CI) were calculated using logistic regression models. No association was observed between alcohol consumption, ADH1B (rs1229984), ADH1C (rs698) and ALDH2 (rs671) polymorphisms and gastric cancer risk. However, considering gene-environmental interaction, ADH1C G allele carriers who drink ≥150 g/week of ethanol had a 2.5-fold increased risk of gastric cancer (OR = 2.54, 95% CI = 1.05-6.17) relative to AA genotype carriers who drink 0 to alcohol consumption and gastric cancer risk, it is important to consider both alcohol consumption level and ADH1C and ALDH2 polymorphisms.

  3. 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

  4. The insertion loss of screens under the influence of wind

    DEFF Research Database (Denmark)

    Rasmussen, Karsten Bo; Arranz, Marta Galindo

    1998-01-01

    in the vertical wind speed profile when the wind field passes the screen. Theinfluence of turbulence is also implemented. The experimental part of the investigation relieson a scale model technique based upon a 1:25 scaling ratio and a triggered spark source. Themain results relate to the size of the insertion...... loss of a screen under windy conditions and tothe acoustic importance of the redirection of the flow before and after the screen....

  5. Reverse genetics in Chlamydomonas: a platform for isolating insertional mutants

    OpenAIRE

    de Montaigu Amaury; Magneschi Leonardo; Catalanotti Claudia; Yang Wenqiang; Mus Florence; Pootakham Wirulda; Gonzalez-Ballester David; Higuera Jose J; Prior Matthew; Galván Aurora; Fernandez Emilio; Grossman Arthur R

    2011-01-01

    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...

  6. A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens

    Science.gov (United States)

    Tchesnokova, Veronika; Avagyan, Hovhannes; Billig, Mariya; Chattopadhyay, Sujay; Aprikian, Pavel; Chan, Diana; Pseunova, Julietta; Rechkina, Elena; Riddell, Kim; Scholes, Delia; Fang, Ferric C.; Johnson, James R.; Sokurenko, Evgeni V.

    2016-01-01

    Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations (“septatypes”) were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy. PMID:26925427

  7. Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers.

    Science.gov (United States)

    Batley, Jacqueline; Jewell, Erica; Edwards, David

    2007-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

  8. Hamstring tendons insertion - an anatomical study

    Directory of Open Access Journals (Sweden)

    Cristiano Antonio Grassi

    2013-09-01

    Full Text Available OBJECTIVE: To study the anatomy of the hamstring tendons insertion and anatomical rela-tionships. METHODS: Ten cadaver knees with medial and anterior intact structures were selected. The dissection was performed from anteromedial access to exposure of the insertion of the flexor tendons (FT, tibial plateau (TP and tibial tuberosity (TT. A needle of 40 × 12 and a caliper were used to measure the distance of the tibial plateau of the knee flexor tendons insertion at 15 mm from the medial border of the patellar tendon and tibial tuberosity to the insertion of the flexor tendons of the knee. The angle between tibial plateau and the insertion of the flexor tendons of the knee (A-TP-FT was calculated using Image Pro Plus software. RESULTS: The mean distance TP-FT was 41 ± 4.6 mm. The distance between the TT-FT was 6.88 ± 1 mm. The (A-TP-FT was 20.3 ± 4.9°. CONCLUSION: In the anterior tibial flexor tendons are about 40 mm from the plateau with an average of 20°.

  9. 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...

  10. 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.

  11. Study of the Interface between Steel Insert and Aluminum Casting in EPC

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The effective surface treatment method for steel insert composited with Al base metal by expendable pattern casting (EPC) process and the bonding interface between steel insert and Al base metal were investigated. It was found that Zn plating on steel insert was effective on improving the bonding property between steel insert and Al base metal in EPC process. Zn is thought to promote the formation of diffusion layer. But almost none content of Zn was observed in the boundary which had been plated on the steel insert. A diffusion layer consisting of Al, Si and Fe was formed at the insert/alloy interface and its hardness was higher than the steel insert as matter of course Al base metal. This layer turned out to be intermetallic compounds of Al-Si-Fe system. Higher pouring temperature promoted the diffusion of Fe into Al alloy, so Fe content in intermetallic layers increased at higher pouring temperature. The layer nearest to steel disappeared due to applied pressure.

  12. Predictability of IL-28B-polymorphism on protease-inhibitor-based triple-therapy in chronic HCV-genotype-1 patients: A meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Nicolae-Catalin; Mechie; Christian; Rver; Silke; Cameron; Ahmad; Amanzada

    2014-01-01

    AIM: To investigate the predictability of interleukin-28 B single nucleotide polymorphism rs12979860 with respect to sustained virological response(SVR) in chronically hepatitis C virus(HCV) genotype-1 patients treated with a protease-inhibitor and pegylated interferon-α(Peg-INF-α) based triple-therapy. METHODS: We searched PubMed, the Cochrane Library and Web of Knowledge for studies regarding the interleukin 28B(IL-28B)-genotype and protease-inhibitor based triple-therapy. Ten studies with 2707 patients were included into this meta-analysis. We used regression methods in order to investigate determinants of SVR.RESULTS: IL-28B-CC-genotype patients achieved higher SVR rates(odds 5.34, 95%CI: 3.81-7.49) than IL-28B-non-CC-genotype patients(1.88, 95%CI: 1.43-2.48) receiving triple-therapy. The line of therapy(treatment-nave or-experienced for Peg-INF-α) did not affect the predictive value of IL-28B(P = 0.1). IL-28BCC-genotype patients treated with protease inhibitorbased triple-therapy consisting of Boceprevir, Simeprevir, Telaprevir or Vaniprevir showed odds of 3.38, 14.66, 7.84 and 2.91, respectively. The odds for CC genotype patients treated with Faldaprevir cannot be quantified, as only a single study with a 100% SVR rate was available.CONCLUSION: IL-28B-SNP predicts the outcome for chronic HCV genotype-1 patients receiving protease inhibitor-based triple-therapy. The predictive value varies between the different protease inhibitors.

  13. 14-bp ins/del polymorphism and +3142C>G SNP of the HLA-G gene have a significant impact on acute rejection after liver transplantation.

    Science.gov (United States)

    Thude, Hansjörg; Janssen, Maike; Sterneck, Martina; Nashan, Björn; Koch, Martina

    2016-12-01

    Expression of human leukocyte antigen G (HLA-G) has been associated with increased graft survival and decreased rejection episodes. It has been described that the HLA-G 14-base pair (bp) insertion/deletion (ins/del) (rs66554220) and +3142C>G (rs1063320) gene polymorphisms modify the expression level of HLA-G. The aim of the study was to investigate whether these HLA-G polymorphisms have an impact on acute rejection after liver transplantation. In total, 146 liver transplant recipients (57 with acute rejection and 89 without acute rejection) and 99 corresponding liver donors were genotyped for both polymorphisms. In liver transplantation the 14-bp ins/ins and the +3142GG genotypes are more frequent in recipients without rejection compared to recipients with rejection (3.5% vs. 31.5%, p=In contrast, in liver donors we could not reveal an association. We conclude that 14-bp ins/ins and +3142GG genotypes of HLA-G in liver transplant recipients are of importance for prediction of acute rejection after liver transplantation. Thus genotyping of liver recipients for both polymorphisms might be useful to stratify liver transplant recipients according to the risk of acute liver transplant rejection.

  14. Angiotensinogen and ACE gene polymorphisms and risk of atrial fibrillation in the general population

    DEFF Research Database (Denmark)

    Ravn, Lasse Steen; Benn, Marianne; Nordestgaard, Børge

    2008-01-01

    Objectives The renin-angiotensin system may play a role in the pathogenesis of atrial fibrillation, and renin-angiotensin system blockers reduce the risk of atrial fibrillation. We hypothesized that polymorphisms in the angiotensinogen and angiotensin-converting enzyme (ACE) genes encoding proteins...... in this system predict risk of atrial fibrillation. Methods and results We genotyped 9235 individuals from the Danish general population, The Copenhagen City Heart Study, for the a-20c, g-6a, T174M, and M235T polymorphisms in the angiotensinogen gene and the insertion/deletion (I/D) polymorphism in the ACE gene...

  15. On the Insertion Time of Cuckoo Hashing

    CERN Document Server

    Fountoulakis, Nikolaos; Steger, Angelika

    2010-01-01

    Cuckoo hashing is an efficient technique for creating large hash tables with high space utilization and guaranteed constant access times. There, each item can be placed in a location given by any one out of k different hash functions. In this paper we investigate further the random walk heuristic for inserting in an online fashion new items into the hash table. Provided that k > 2 and that the number of items in the table is below (but arbitrarily close) to the theoretically achievable load threshold, we show a polylogarithmic bound for the maximum insertion time that holds with high probability.

  16. 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

  17. Electroforming of Tool Inserts for Injection Molding of Optical or Microfluidic Components

    DEFF Research Database (Denmark)

    Tang, Peter Torben; Christensen, Thomas R.; Jensen, Martin F.

    2004-01-01

    monitoring) and environmental (waste water monitoring) applications. Optical components in polymer materials can be used for consumer electronics and for sensor systems. The presentation will include the complete fabrication scheme for tool inserts based on machining and electroforming. Electroforming...

  18. Detection of Ribosomal DNA Sequence Polymorphisms in the Protist Plasmodiophora brassicae for the Identification of Geographical Isolates

    Directory of Open Access Journals (Sweden)

    Rawnak Laila

    2017-01-01

    Full Text Available Clubroot is a soil-borne disease caused by the protist Plasmodiophora brassicae (P. brassicae. It is one of the most economically important diseases of Brassica rapa and other cruciferous crops as it can cause remarkable yield reductions. Understanding P. brassicae genetics, and developing efficient molecular markers, is essential for effective detection of harmful races of this pathogen. Samples from 11 Korean field populations of P. brassicae (geographic isolates, collected from nine different locations in South Korea, were used in this study. Genomic DNA was extracted from the clubroot-infected samples to sequence the ribosomal DNA. Primers and probes for P. brassicae were designed using a ribosomal DNA gene sequence from a Japanese strain available in GenBank (accession number AB526843; isolate NGY. The nuclear ribosomal DNA (rDNA sequence of P. brassicae, comprising 6932 base pairs (bp, was cloned and sequenced and found to include the small subunits (SSUs and a large subunit (LSU, internal transcribed spacers (ITS1 and ITS2, and a 5.8s. Sequence variation was observed in both the SSU and LSU. Four markers showed useful differences in high-resolution melting analysis to identify nucleotide polymorphisms including single- nucleotide polymorphisms (SNPs, oligonucleotide polymorphisms, and insertions/deletions (InDels. A combination of three markers was able to distinguish the geographical isolates into two groups.

  19. Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus hospital clone EMRSA-15.

    Science.gov (United States)

    Holmes, A; McAllister, G; McAdam, P R; Hsien Choi, S; Girvan, K; Robb, A; Edwards, G; Templeton, K; Fitzgerald, J R

    2014-02-01

    The EMRSA-15 clone is a major cause of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections in the UK and elsewhere but existing typing methodologies have limited capacity to discriminate closely related strains, and are often poorly reproducible between laboratories. Here, we report the design, development and validation of a genome-wide single nucleotide polymorphism (SNP) typing method and compare it to established methods for typing of EMRSA-15. In order to identify discriminatory SNPs, the genomes of 17 EMRSA-15 strains, selected to represent the breadth of genotypic and phenotypic diversity of EMRSA-15 isolates in Scotland, were determined and phylogenetic reconstruction was carried out. In addition to 17 phylogenetically informative SNPs, five binary markers were included to form the basis of an EMRSA-15 genotyping assay. The SNP-based typing assay was as discriminatory as pulsed-field gel electrophoresis, and significantly more discriminatory than staphylococcal protein A (spa) typing for typing of a representative panel of diverse EMRSA-15 strains, isolates from two EMRSA-15 hospital outbreak investigations, and a panel of bacteraemia isolates obtained in healthcare facilities in the east of Scotland during a 12-month period. The assay is a rapid, and reproducible approach for epidemiological analysis of EMRSA-15 clinical isolates in Scotland. Unlike established methods the DNA sequence-based method is ideally suited for inter-laboratory comparison of identified genotypes, and its flexibility lends itself to supplementation with additional SNPs or markers for the identification of novel S. aureus strains in other regions of the world.

  20. Single nucleotide polymorphism array-based karyotyping in acute myeloid leukemia or myelodysplastic syndrome with trisomy 8 as the sole chromosomal abnormality.

    Science.gov (United States)

    Hahm, Chorong; Mun, Yeung Chul; Seong, Chu Myong; Han, Sung-Hee; Chung, Wha Soon; Huh, Jungwon

    2013-01-01

    The clinical heterogeneity of patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) with trisomy 8 as the sole abnormality may result from cytogenetically undetectable genetic changes. The purpose of this study was to identify hidden genomic aberrations not detected by metaphase cytogenetics (MC) using high-resolution single nucleotide polymorphism array (SNP-A)-based karyotyping in AML/MDS patients with a sole trisomy 8. The study group included 8 patients (3 AML and 5 MDS) and array-based karyotyping was done using whole-genome SNP-A (SNP 6.0 and SNP 2.7M). By SNP-A, additional genomic aberrations not detected by MC were identified in 2 patients: 1 AML patient exhibited a copy-neutral loss of heterozygosity (CN-LOH) of 3q21.1-q29 and 11q13.1-q25 and the other patient with MDS (refractory cytopenia with unilineage dysplasia) had CN-LOH of 2p25.3-p15. In particular, the latter patient progressed to AML 18 months after the diagnosis. In 3 patients, aberrations in addition to trisomy 8 were not identified by SNP-A. In the remaining 3 patients, SNP-A could not detect trisomy 8, while trisomy 8 was found in 25-67% of metaphase cells by MC. This study suggests that additional genomic aberrations may in fact be present even in cases of trisomy 8 as sole abnormality by MC, and SNP-A could be a useful karyotyping tool to identify hidden aberrations such as CN-LOH.

  1. 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

  2. CCL5-403, CCR5-59029, and Delta32 polymorphisms and cancer risk: a meta-analysis based on 20,625 subjects.

    Science.gov (United States)

    Ying, Houqun; Wang, Jie; Gao, Xueren

    2014-06-01

    Associations between CCL5-403, CCR5-59029, and Delta32 polymorphisms and cancer risk are inconclusive. To derive a more precise estimation of the association, we performed a meta-analysis by searching PubMed, EMBASE, Google scholar, and WanFang databases. A total of 20 eligible articles with 39 studies were included. Of those studies, there were 21 studies for CCR5-Delta32 polymorphism, 9 studies for CCR5-59029 polymorphism, and 9 studies for CCL5-403 polymorphism. Combined analysis revealed no associations between these polymorphisms and cancer risk. However, subgroup analysis by ethnicity suggested that CCR5-59029 polymorphism was associated with the risk of cancer among Asian populations (A vs. G: odds ratio (OR)=1.36, 95 % confidence interval (CI) 1.13-1.65, P H=0.27; AA vs. GG: OR=2.07, 95 % CI 1.37-3.12, P H=0.17; GA+AA vs. GG: OR=1.35, 95 % CI 1.03-1.77, P H=0.92; AA vs. GA+GG: OR=1.98, 95 % CI 1.01-3.88, P H=0.08), but not among Caucasian populations. CCL5-403 polymorphism was associated with the risk of cancer among African populations (A vs. G: OR=0.68, 95 % CI 0.55-0.83, P H=0.14; AA vs. GG: OR=0.51, 95 % CI 0.33-0.77, P H=0.52; AG vs. GG: OR=0.58, 95 % CI 0.42-0.80, P H=0.14; AG+AA vs. GG: OR=0.56, 95 % CI 0.41-0.75, P H=0.13), but not among Caucasian populations and Asian populations. Overall, this meta-analysis indicated that CCR5-Delta32 was not associated with the risk of cancer. CCR5-59029 polymorphism contributed to cancer risk among Asian populations, and CCL5-403 polymorphism was associated with the decreased risk of cancer among African populations.

  3. Meta-analysis of the association between COX-2 polymorphisms and risk of colorectal cancer based on case-control studies.

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    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. A novel insertion mutation in the cartilage-derived morphogenetic protein-1 (CDMP1 gene underlies Grebe-type chondrodysplasia in a consanguineous Pakistani family

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    Ansar Muhammad

    2008-11-01

    Full Text Available Abstract Background Grebe-type chondrodysplasia (GCD is a rare autosomal recessive syndrome characterized by severe acromesomelic limb shortness with non-functional knob like fingers resembling toes. Mutations in the cartilage-derived morphogenetic protein 1 (CDMP1 gene cause Grebe-type chondrodysplasia. Methods Genotyping of six members of a Pakistani family with Grebe-type chondrodysplasia, including two affected and four unaffected individuals, was carried out by using polymorphic microsatellite markers, which are closely linked to CDMP1 locus on chromosome 20q11.22. To screen for a mutation in CDMP1 gene, all of its coding exons and splice junction sites were PCR amplified from genomic DNA of affected and unaffected individuals of the family and sequenced directly in an ABI Prism 310 automated DNA sequencer. Results Genotyping results showed linkage of the family to CDMP1 locus. Sequence analysis of the CDMP1 gene identified a novel four bases insertion mutation (1114insGAGT in exon 2 of the gene causing frameshift and premature termination of the polypeptide. Conclusion We describe a 4 bp novel insertion mutation in CDMP1 gene in a Pakistani family with Grebe-type chondrodysplasia. Our findings extend the body of evidence that supports the importance of CDMP1 in the development of limbs.

  5. COMPARATIVE STUDY OF EARLY POSTPARTUM IUCD INSERTION TO INTERVAL IUCD INSERTION

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    Shibani Devi

    2016-07-01

    Full Text Available INTRODUCTION According to National Family Health Survey-3, Indian women have 13% unmet need for contraception and according to District Level Household & Facility Survey-3, it is 21.3% in the postpartum period. Postpartum intrauterine contraceptive device insertion - both immediately post-placental delivery and somewhat later, but within 48 hours after delivery are options which merit consideration as the woman is likely to have a high motivation for accepting contraception and the healthcare centre provides a convenient setting for insertion of IUCD. AIM Comparison of efficacy and complications of IUCD insertions in post-placental with interval period: 6-month followup. METHOD This perspective study was conducted among 100 women: - 50 women had IUCD inserted within 10 minutes of placental delivery and 50 had insertion more than 6 weeks after delivery. They were followed till 6 months post insertion and were compared regarding early and late complications, continuation rates and expulsion rates. RESULT At the end of six months, we found higher occurrence of lower abdominal pain, heavy menstrual bleeding in case of interval insertion as compared to post-placental insertion which was statistically significant (p value-0.04 & 0.007 respectively. However, the expulsion rates of post-placental IUCD were somewhat elevated (14% compared to interval insertions (2%. Continuation rates at the end of 6 months in both the groups were 82% and 86% respectively which is comparable. CONCLUSION Post-placental IUCD is thus found to be an ideal method to meet the unmet need of postpartum women as it is easily accessible and convenient for both women and their health care providers, is associated with less discomfort and fewer side effects and allow women to obtain safe, long acting, highly effective contraception while still in the health care system.

  6. A predictive model of intein insertion site for use in the engineering of molecular switches.

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    James Apgar

    Full Text Available Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54. In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch.

  7. 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.

  8. A species-specific primer pair for distinguishing between Paramisgurnus dabryanus and Misgurnus anguillicaudatus based on mitochondrial DNA polymorphisms.

    Science.gov (United States)

    Liu, Yongfu; Hou, Jilun; Wang, Guixing; Zhang, Xiaoyan; Liu, Haijin

    2016-07-01

    Paramisgurnus dabryanus and Misgurnus anguillicaudatus (family Cobitidae) are loaches with high morphological similarity. In this study, we designed primers to distinguish between Paramisgurnus dabryanus and Misgurnus anguillicaudatus based on the length differences in the mitochondrial COXII to tRNA(Lys) gene region. Samples of P. dabryanus and M. anguillicaudatus from different geographical locations were collected and amplified to verify primer specificity. The results of electrophoresis revealed the successful amplification of all P. dabryanus and M. anguillicaudatus DNA samples, which had distinct, specific-specific sizes (214 bp for P. dabryanus and 285 bp for M. anguillicaudatus). In conclusion, the new primers provide fast, reliable, and accurate identification between P. dabryanus and M. anguillicaudatus.

  9. Population genetic variation of the Southern Ocean krill, Euphausia superba, in the Western Antarctic Peninsula region based on mitochondrial single nucleotide polymorphisms (SNPs)

    Science.gov (United States)

    Batta-Lona, Paola G.; Bucklin, Ann; Wiebe, Peter H.; Patarnello, Tomaso; Copley, Nancy J.

    2011-07-01

    The Southern Ocean krill, Euphausia superba, is one of the best-studied marine zooplankton species in terms of population genetic diversity and structure; with few exceptions, previous studies have shown the species to be genetically homogeneous at larger spatial scales. The goals of this study are to examine sub-regional scale population genetic diversity and structure of E. superba using molecular characters selected with this goal in mind, and to thereby examine hypotheses of the source(s) of recruitment for krill populations of the Western Antarctic Peninsula (WAP). Collections were made throughout the WAP region during US GLOBEC cruises in austral fall, 2001 and 2002. A total of 585 E. superba (including all 6 furcilia larval stages, juveniles, and adults) was analyzed after confirmation of species identification using a competitive multiplexed species-specific PCR (SS-PCR) reaction based on mitochondrial cytochrome oxidase I (mtCOI) sequences. The molecular markers used were allele frequencies at single nucleotide polymorphism (SNP) sites in the gene encoding mitochondrial Cytochrome b (cyt b). Four SNP sites that showed desirable patterns of allelic variation were selected; alleles were detected using a multiplexed single-base extension PCR protocol. A total of 22 SNP haplotypes (i.e., strings of polymorphisms at the four SNP sites) was observed; haplotype diversity (Hd)=0.811 (s.d.=0.008). Analysis of molecular variation within and among samples, areas (i.e., Marguerite Bay, Crystal Sound, shelf, and offshore) and collection years revealed no difference between 2001 and 2002 collections overall, although differences between 2001 and 2002 collections from Marguerite Bay explained 7.4% of the variance ( FST=0.072; p=0.002±0.001). Most of the variation (96.3%) occurred within samples each year, with no significant differentiation among areas. There was small, but significant differentiation among samples within areas in 2001 (4.6%; FST=0.045; p=0.015±0

  10. 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.

  11. Detection of low-abundance KRAS mutations in colorectal cancer using microfluidic capillary electrophoresis-based restriction fragment length polymorphism method with optimized assay conditions.

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    Huidan Zhang

    Full Text Available Constitutively active KRAS mutations have been found to be involved in various processes of cancer development, and render tumor cells resistant to EGFR-targeted therapies. Mutation detection methods with higher sensitivity will increase the possibility of choosing the correct individual therapy. Here, we established a highly sensitive and efficient microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP platform for low-abundance KRAS genotyping with the combination of µCE and RFLP techniques. By using our self-built sensitive laser induced fluorescence (LIF detector and a new DNA intercalating dye YOYO-1, the separation conditions of µCE for ΦX174 HaeIII DNA marker were first optimized. Then, a Mav I digested 107-bp KRAS gene fragment was directly introduced into the microfluidic device and analyzed by µCE, in which field amplified sample stacking (FASS technique was employed to obtain the enrichment of the RFLP digestion products and extremely improved the sensitivity. The accurate analysis of KRAS statuses in HT29, LS174T, CCL187, SW480, Clone A, and CX-1 colorectal cancer (CRC cell lines by µCE-based RFLP were achieved in 5 min with picoliter-scale sample consumption, and as low as 0.01% of mutant KRAS could be identified from a large excess of wild-type genomic DNA (gDNA. In 98 paraffin-embedded CRC tissues, KRAS codon 12 mutations were discovered in 28 (28.6%, significantly higher than that obtained by direct sequencing (13, 13.3%. Clone sequencing confirmed these results and showed this system could detect at least 0.4% of the mutant KRAS in CRC tissue slides. Compared with direct sequencing, the new finding of the µCE-based RFLP platform was that KRAS mutations in codon 12 were correlated with the patient's age. In conclusion, we established a sensitive, fast, and cost-effective screening method for KRAS mutations, and successfully detected low-abundance KRAS mutations in clinical

  12. Association of POLK polymorphisms with platinum-based chemotherapy response and severe toxicity in non-small cell lung cancer patients.

    Science.gov (United States)

    Shao, Minhua; Jin, Bo; Niu, Yanjie; Ye, Junyi; Lu, Daru; Han, Baohui

    2014-11-01

    Lung cancer is the leading cause of tumor-derived death. Although target therapy is proven very efficient, traditionally platinum-based chemotherapies are still primary treatment for most patients. Platinum can suppress the tumor growth and impair normal cells together. The primary aim of the present study was to study the potential role of translesion synthesis (TLS) that might play in platinum-chemotherapy tolerance and side-effect. In present study, a total of 663 patients who were newly histologically diagnosed with advanced NSCLC (aNSCLC) were enrolled. Treatment response was classified into four categories: complete response, partial response, stable disease, and progressive disease. Incidence of gastrointestinal and hematological toxicities was assessed twice a week during the whole first-line treatment. Eleven SNPs of POLK were genotyped. The associations between SNPs and treatment response or toxicity were analyzed with logistic regression model. Cox regression was used for survival analysis between SNPs and progression-free survival or overall survival. We identified that rs3213801 and rs5744533 showed complete linkage in the present study, and they were significantly associated with treatment response (adjusted P = 0.044), together with rs5744655 (adjusted P = 0.039). rs1018119 was correlated with gastrointestinal toxicity in smokers specially (adjusted P = 0.041). Besides, rs3756558 was associated with hematological toxicity and overall toxicity in smokers and combined cohort with additive model. We also identified the significant association between two SNPs, rs10077427 and rs5744545, and PFS. The polymorphism of POLK, an important gene in TLS, participates in platinum-chemotherapy tolerance and side-effect.

  13. 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.

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    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.

  14. The polymorphism of YWHAE, a gene encoding 14-3-3epsilon, and brain morphology in schizophrenia: a voxel-based morphometric study.

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    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.

  15. Association of Common Polymorphisms in the Nicotinic Acetylcholine Receptor Alpha4 Subunit Gene with an Electrophysiological Endophenotype in a Large Population-Based Sample.

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    A Mobascher

    Full Text Available 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.

  16. Analysis of p53 gene mutations in human gliomas by polymerase chain reaction-based single-strand conformation polymorphism and DNA sequencing.

    Science.gov (United States)

    Sarkar, F H; Kupsky, W J; Li, Y W; Sreepathi, P

    1994-03-01

    Mutations in the p53 gene have been recognized in brain tumors, and clonal expansion of p53 mutant cells has been shown to be associated with glioma progression. However, studies on the p53 gene have been limited by the need for frozen tissues. We have developed a method utilizing polymerase chain reaction (PCR) for the direct analysis of p53 mutation by single-strand conformation polymorphism (SSCP) and by direct DNA sequencing of the p53 gene using a single 10-microns paraffin-embedded tissue section. We applied this method to screen for p53 gene mutations in exons 5-8 in human gliomas utilizing paraffin-embedded tissues. Twenty paraffin blocks containing tumor were selected from surgical specimens from 17 different adult patients. Tumors included six anaplastic astrocytomas (AAs), nine glioblastomas (GBs), and two mixed malignant gliomas (MMGs). The tissue section on the stained glass slide was used to guide microdissection of an unstained adjacent tissue section to ensure > 90% of the tumor cell population for p53 mutational analysis. Simultaneously, microdissection of the tissue was also carried out to obtain normal tissue from adjacent areas as a control. Mutations in the p53 gene were identified in 3 of 17 (18%) patients by PCR-SSCP analysis and subsequently confirmed by PCR-based DNA sequencing. Mutations in exon 5 resulting in amino acid substitution were found in one thalamic AA (codon 158, CGC > CTT: Arg > Leu) and one cerebral hemispheric GB (codon 151, CCG > CTG: Pro > Leu).(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Family-Based Association Study of rs17300539 and rs12495941 Polymorphism in Adiponectin Gene and Polycystic Ovary Syndrome in a Chinese Population

    Science.gov (United States)

    Sun, Xianchang; Wu, Xingguo; Duan, Yunmin; Liu, Guanghai; Yu, Xinyan; Zhang, Wenjuan

    2017-01-01

    Backgriond Polycystic ovary syndrome (PCOS) is a complex disease that has both genetic and environmental components. Adiponectin plays an important role in the regulation of insulin sensitivity and insulin resistance (IR) in PCOS. The aim of this study was to determine 2 single-nucleotide polymorphisms (SNPs) variants (rs12495941 and rs17300539) of the adiponectin gene (ADIPOQ) in polycystic ovary syndrome (PCOS) families. Material/Methods We recruited 197 PCOS probands, their biological parents, and 192 controls. Anthropometric variables, including hip circumference (HC) and waist circumference (WC), were measured in all subjects during their first visit to the outpatient department. Serum T, FBG, FINS, TC, TG, LDL, and HDL levels were measured. PCOS patients were divided into 2 groups based on BMI: group A (BMI <25 kg/m2) and group B (BMI ≥25 kg/m2). Parents of PCOS were accordingly categorized into group C and group D (fathers), and group E and group F (mothers). The associations among ADIPOQ rs12495941, rs17300539, and PCOS were analyzed using the transmission disequilibrium test (TDT). Results A significant association was found between SNP rs17300539 and PCOS in our Chinese population. The levels of TG and FINS and the genotype frequencies of rs17300539 are significantly different between overweight and lean PCOS. No significant association was detected for rs12495941. Conclusions TDT confirms that rs17300539 of ADIPOQ is strongly associated with the risk of PCOS in a Chinese Han population, but rs12495941 of ADIPOQ is not associated with the occurrence of PCOS. PMID:28060790

  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.

  19. 长爪沙鼠ApoE基因SNPs的遗传多态性%Evaluation of genetic polymorphisms of ApoE gene in Mongolian gerbils based on single nucleotide polymorphisms

    Institute of Scientific and Technical Information of China (English)

    刘月环; 王志远; 杜江涛; 余强; 余陈欢; 吴旧生; 应华忠

    2014-01-01

    Objective To evaluate the genetic diversity of ApoE gene in Z:ZCLA gerbil closed colony .Methods PCR-SSCP technique was employed to calculate the gene frequency , genotype frequency , heterozygosity , polymorphism information content of three SNPs of ApoE gene , which were reported in our previous work , in a total of 444 ordinary and clean Mongolian gerbils .Results The average allele of 3 SNP site 97, 981 and 1774 was 2.The inheritance pattern was in accordance with Mendel′s law.Expected heterozygosities were 0.063, 0.501, and 0.499, and the average expected heterozygosity of whole group was 0.354.PIC were 0.061, 0375, and 0.374, with an average PIC of 0.270.Conclusion The ApoE gene frequency and genotype distribution in Mongolian gerbils may be to a certain degree associated with the genetic drift caused by long-term closed and selected breeding .%目的:评价ApoE基因在Z:ZCLA长爪沙鼠封闭群中的遗传多样性。方法利用PCR-SSCP技术对前期已筛选到的三个SNP ( single nucleotide polymorphism )位点在普通环境和生物净化后、屏障环境饲养的两个封闭群共444只动物中进行了ApoE等位基因的基因频率,基因型频率,杂合度、多态信息量等参数进行了检测与计算。结果检测结果表明97、781和1774三个SNP位点平均等位基因为2个,遗传方式基本符合孟德尔定律;期望杂合度分别是0.063、0.501、0.499,全群平均为0.354;PIC分别是0.061、0375、0.374,全群平均0.270。结论ApoE基因频率和基因型分布可能与长爪沙鼠的长期封闭和选种方式造成一定程度的遗传漂变相关。

  20. Pathotyping of Australian isolates of Marek's disease virus and association of pathogenicity with meq gene polymorphism.

    Science.gov (United States)

    Renz, Katrin G; Cooke, Julie; Clarke, Nadeene; Cheetham, Brian F; Hussain, Zahid; Fakhrul Islam, A F M; Tannock, Gregory A; Walkden-Brown, Stephen W

    2012-01-01

    We report the pathotyping of six Australian isolates of Marek's disease virus-1 (MDV1) isolated between 1992 and 2004 and association of virulence with meq gene polymorphism. Unvaccinated and herpesvirus of turkeys (HVT)-vaccinated specific pathogen free chickens were challenged at day 5 with 500 plaque forming units of Marek's disease virus. The isolates induced gross Marek's disease lesions in 53 to 94% of unvaccinated chickens, and HVT induced a protective index ranging from 38 to 100% by 56 days post challenge. This experiment provides evidence that current Australian isolates of MDV1 vary significantly in pathogenicity. However, there was no clear evidence that the most virulent recent isolates were more pathogenic than isolates from the 1980s or that any of the isolates belong to the highest pathotype category of very virulent plus. Evidence is presented that virulence can be predicted by measurements taken as early as 13 days post challenge. The meq gene sequences of five of the isolates used in the experiment were determined. When compared with the very virulent US isolate Md5, there was a 177 base-pair insertion and distinct point mutations in each of the five isolates. There were no individual mutations in the meq sequences that correlated with levels of virulence. However, amino acid alignment of the five Australian and 14 international isolates revealed that the number of repeat sequences of four prolines (PPPP repeats) in the meq gene (overall range 2 to 8) was strongly associated with virulence across all isolates, with the most pathogenic isolates having the fewest number of repeats. The results suggest that the presence of the 177 base-pair insertion alone is not an indicator of attenuation. Rather, the number of PPPP repeats, independent of the presence of the insertion, is a better indicator of pathogenicity.

  1. 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...... of their 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...... (using Digital Light Processing) and three traditional methods for the manufacture of inserts (milling of brass, steel, and aluminium) for injection moulds during the pre-production phase....

  2. «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.

  3. Family-based association study of interleukin 6 (IL6) and its receptor (IL6R) functional polymorphisms in schizophrenia in the Polish population.

    Science.gov (United States)

    Kapelski, Pawel; Skibinska, Maria; Maciukiewicz, Malgorzata; Pawlak, Joanna; Permoda-Osip, Agnieszka; Twarowska-Hauser, Joanna

    2015-08-15

    Schizophrenia is a heterogeneous disorder and its etiology remains incompletely elucidated. Among possible causes, immunological factors have been implicated in its pathogenesis and course. The inflammatory system may trigger or modulate the course of schizophrenia through complex mechanisms influencing neurodevelopment, neuroplasticity and neurotransmission. Recent studies indicate a role of excessive interleukin-6 (IL6) signaling in the pathogenesis of schizophrenia. Findings regarding changes in the circulating levels of soluble interleukin-6 receptor (sIL6R) in schizophrenia have been equivocal. The study was performed on a group of 147 trio (patients diagnosed with schizophrenia and their healthy parents). Polymorphisms of IL6 (rs1800795, rs1800797) and IL6R (rs4537545, rs4845617, rs2228145) genes were genotyped with the use of TaqMan SNP Genotyping Assays. No association of the polymorphisms from IL6 and IL6R genes with schizophrenia was found. We also investigated haplotypes in IL6 gene (consisting of rs1800795 and rs1800797) and in IL6R gene (consisting of rs4537545, rs2228145). We also found no preference in transmission of any haplotype. Our results do not support the theory that polymorphisms of IL6 and IL6R genes are involved in the pathogenesis of schizophrenia. It seems advisable to carry out further examinations of the role of these polymorphisms in schizophrenia by means of TDT method and classical (case-control) association method.

  4. Association of glutathione S-transferase polymorphisms (GSTM1 and GSTT1) with primary open-angle glaucoma: an evidence-based meta-analysis.

    Science.gov (United States)

    Huang, Wenbin; Wang, Wei; Zhou, Minwen; Chen, Shida; Zhang, Xiulan

    2013-09-10

    Studies investigating the associations between glutathione S-transferase (GST) genetic polymorphisms and primary open-angle glaucoma (POAG) have reported controversial results. Therefore, a meta-analysis was performed to clarify the effects of GSTM1 and GSTT1 polymorphisms on POAG risk. Published literatures from PubMed, EMBASE, ISI Web of Science and CBM databases were retrieved. All studies evaluating the association between GSTM1/GSTT1 polymorphisms and POAG were included. Pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using fixed- or random-effects model. Eleven studies on GSTM1 (1339 cases and 1412 controls) and seven studies on GSTT1 (958 cases, 1003 controls) were included. Overall analysis showed that the association between GSTM1 and GSTT1 null genotype and POAG risk is not statistically significant. Subgroup analyses showed that the null genotype of GSTM1 increased the risk of POAG in Asians. In GSTM1-GSTT1 interaction analysis, individuals with dual null genotype were associated with a significantly increased risk of POAG when compared with the dual present genotype. In conclusion, the present meta-analysis suggested that GSTM1 null genotypes are associated with increased POAG risk in Asian populations but not in Caucasian and mixed populations. Dual null genotype of GSTM1/GSTT1 is associated with increased risk of POAG. Given the limited sample size, the finding on GST polymorphisms needs further investigation.

  5. Evaluating the X chromosome-specific diversity of Colombian populations using insertion/deletion polymorphisms.

    Directory of Open Access Journals (Sweden)

    Adriana Ibarra

    Full Text Available The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female. This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased.

  6. Angiotensin-converting enzyme insertion/deletion polymorphism in hypertrophic cardiomyopathy: An Egyptian case control study

    Directory of Open Access Journals (Sweden)

    Heba Sh. Kassem

    2014-03-01

    Conclusion: The finding of higher frequency of DD genotype among HCM patients compared to healthy volunteers, particularly so, in sporadic cases suggests that HCM expression is possibly influenced by a genetically predisposed milieu partially determined by the ACE I/D variants. Despite the lack of significant correlation between I/D variants and clinicopathologic characteristics of the HCM patients, however, the higher prevalence of D allele among TNNT2 and MYH7 mutation carriers may contribute to the variable disease outcome among sarcomeric gene positive cases, such a correlation can only be proven through long term follow up studies.

  7. Anionic phospholipids modulate peptide insertion into membranes.

    Science.gov (United States)

    Liu, L P; Deber, C M

    1997-05-06

    While the insertion of a hydrophobic peptide or membrane protein segment into the bilayer can be spontaneous and driven mainly by the hydrophobic effect, anionic lipids, which comprise ca. 20% of biological membranes, provide a source of electrostatic attractions for binding of proteins/peptides into membranes. To unravel the interplay of hydrophobicity and electrostatics in the binding of peptides into membranes, we designed peptides de novo which possess the typical sequence Lys-Lys-Ala-Ala-Ala-X-Ala-Ala-Ala-Ala-Ala-X-Ala-Ala-Trp-Ala-Ala-X-Ala-Al a-Ala-Lys-Lys-Lys-Lys-amide, where X residues correspond to "guest" residues which encompass a range of hydrophobicity (Leu, Ile, Gly, and Ser). Circular dichroism spectra demonstrated that peptides were partially (40-90%) random in aqueous buffer but were promoted to form 100% alpha-helical structures by anionic lipid micelles. In neutral lipid micelles, only the relatively hydrophobic peptides (X = L and I) spontaneously adopted the alpha-helical conformation, but when 25% of negatively charged lipids were mixed in to mimic the content of anionic lipids in biomembranes, the less hydrophobic (X = S and G) peptides then formed alpha-helical conformations. Consistent with these findings, fluorescence quenching by the aqueous-phase quencher iodide indicated that in anionic (dimyristoylphosphatidylglycerol) vesicles, the peptide Trp residue was buried in the lipid vesicle hydrophobic core, while in neutral (dimyristoylphosphatidylcholine) vesicles, only hydrophobic (X = L and I) peptides were shielded from the aqueous solution. Trp emission spectra of peptides in the presence of phospholipids doxyl-labeled at the 5-, 7-, 10-, 12-, and 16-fatty acid positions implied not only a transbilayer orientation for inserted peptides but also that mixed peptide populations (transbilayer + surface-associated) may arise. Overall results suggest that for hydrophobic peptides with segmental threshold hydrophobicity below that which

  8. 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.

  9. Effect of a flow-corrective insert on the flow pattern in a pebble bed reactor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yu; Gui, Nan; Yang, Xingtuan [Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing 100084 (China); Tu, Jiyuan [Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing 100084 (China); School of Aerospace, Mechanical & Manufacturing Engineering, RMIT University, Melbourne 3083, VIC (Australia); Jiang, Shengyao, E-mail: shengyaojiang@sina.com [Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing 100084 (China)

    2016-04-15

    Highlights: • Effect of an insert on improving flow uniformity and eliminating stagnant zone is studied. • Three values concerned with the stagnant zone, radial uniformity and flow sequence are used. • Outlet diameter is a critical parameter that determines balancing mechanism of the insert. • Height/location is varied to let the insert work in unbalanced region and avoid adverse effect. - Abstract: A flow-corrective insert is adopted in the pebble-bed high temperature gas-cooled reactor (HTGR) to improve flow performance of the pebble flow for the first time. 3D discrete element method (DEM) modeling is employed to study this slow and dense granular flow. It is verified that locating a properly designed insert in the bed can help transform unsatisfactory flow field to the preferred flow pattern for pebble bed reactors. Three characteristic values on the stagnant zone, radial uniformity and flow sequence of pebble flow are defined to evaluate uniformity of the overall flow field quantitatively. The results demonstrate that the pebble bed equipped with an insert performs better than normal beds from all these three aspects. Moreover, based on numerical experiments, several universal tips for insert design on height, location and outlet diameter are suggested.

  10. Exclusion of long heterologous insertions and deletions from the pairing synapsis in pneumococcal transformation.

    Science.gov (United States)

    Pasta, F; Sicard, M A

    1996-03-01

    We have studied the mode of recombination of six insertions during genetic transformation of Streptococcus pneumoniae. The six heterologous insertions are located at the same site in the ami locus of the pneumococcal chromosome; insertion sizes range from 4 to 1374 bp. With respect to single-point markers we found that the number of transformants in one-point crosses is reduced, while the number of wild-type transformants in two-point crosses is drastically increased, what we call hyper-recombination. The magnitude of the shift is correlated with the size of the insert. This effect could result either from a special repair pathway of multibase heteroduplexes or from the exclusion of multibase heterologous insertions out of the pairing synapsis. To test these hypotheses we have used insertions in two kinds of three-point crosses. The repair model predicts that the excess of wild-type transformants remains in one set of crosses but is suppressed in the second set. The results we obtained are reversed, ruling out the hypothesis of a repair process, but in agreement with predictions based on the exclusion model. Moreover, we have re-examined the situation of deletions, our previous results suggesting that deletions were likely to be converted at the heteroduplex step. Genetic evidence we obtained in this work no longer supports this hypothesis. Thus, long heterologous insertions are partly excluded at the pairing step.

  11. [Historical evolution of package inserts in Brazil].

    Science.gov (United States)

    Caldeira, Telma Rodrigues; Neves, Eugênio Rodrigo Zimmer; Perini, Edson

    2008-04-01

    In Brazil, package inserts provide key information on pharmaceuticals. The current study analyzes the evolution of package inserts and the impact on this process by scientific research and development, globalization of information, and various health policies. The study began with a retrospective review of Brazilian health legislation until 1920, the year when the National Public Health Department was created. The analysis of documents on the evolution of health regulation in Brazil began with the Brazilian Pharmaceutical Collection-Health Rulings. The second stage of the study involved a search of standards and norms in VISALEGIS: Health Surveillance Legislation, Portal for Legislation from the National Congressional Information System and the Health Legislation System. Package inserts became an important vehicle for information in the country and underwent important regulatory changes in the latter half of the 20th century. From 1946 to 2006, the number of mandatory items increased, with more in-depth description. However, the standardization of information for medicines with the same active ingredient failed to materialize, despite its importance and the various legal initiatives in this direction.

  12. 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.

  13. Association of rs9340799 polymorphism in estrogen receptor alpha gene with the risk of osteoarthritis: evidence based on 8,792 subjects.

    Science.gov (United States)

    Yin, Yan-Wei; Sun, Qian-Qian; Hu, Ai-Min; Wang, Qi; Liu, Hong-Li

    2015-04-01

    Osteoarthritis (OA) is one of the most common skeletal disease, which seriously affects the quality of life of patients, particularly in the middle-aged and elderly individuals. We aimed to explore whether rs9340799 [estrogen receptor alpha (ER-α) XbaI A/G] polymorphism was associated with OA using a meta-analysis. A literature search for eligible studies published before March 28, 2014 was conducted in the PubMed, Web of Science, Embase, Cochrane database, Current Controlled Trials, Clinicaltrials.gov, Chinese Clinical Trial Registry, CBMdisc, CNKI, Google Scholar and Baidu Library. The association between the rs9340799 polymorphism and OA risk was assessed by odds ratios (ORs) together with their 95 % confidence intervals (CIs). A total of 663 articles were found. After article review and quality assessment, 10 articles involving 2,924 OA cases and 5,868 controls were included in the final meta-analysis. The combined evidence suggested that rs9340799 polymorphism contributed significantly to an increased risk of OA (for G allele vs. A allele: OR = 1.21, 95 % CI 1.03-1.43, p = 0.02; for G/G vs. A/A: OR = 1.30, 95 % CI 1.07-1.57, p = 0.009). In the subgroup analyses, significant associations were found between the rs9340799 polymorphism and the OA risk in the European group, Asian group, and knee osteoarthritis group, respectively. These results suggested that the rs9340799 polymorphism might be associated with the risk of OA. However, the results should be interpreted with caution because of the publication bias.

  14. Association of Angiotensin-Converting Enzyme (ACE) Gene Polymorphism with Inflammation and Cellular Cytotoxicity in Vitiligo Patients

    OpenAIRE

    Laila Rashed; Rania Abdel Hay; Rania Mahmoud; Nermeen Hasan; Amr Zahra; Salwa Fayez

    2015-01-01

    Background Vitiligo is a disorder with profound heterogeneity in its aetio-pathophysiology. Angiotensin converting enzyme (ACE) plays an important role in the physiology of the vasculature, blood pressure and inflammation. An insertion/deletion (I/D) polymorphism of the ACE gene was reported be associated with the development of vitiligo. Objective Our aim was to evaluate the ACE I/D polymorphism in vitiligo patients and controls. Our second aim was to find a possible association between ACE ...

  15. Prediction of protein-destabilizing polymorphisms by manual curation with protein structure.

    Directory of Open Access Journals (Sweden)

    Craig Alan Gough

    Full Text Available The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs leading to single amino acid substitutions that change protein structure and function. However, less attention has been paid to more drastic sequence polymorphisms which cause premature termination of a protein's sequence or large changes, insertions, or deletions in the sequence. We have analyzed a large set (n = 512 of insertions and deletions (indels and single nucleotide polymorphisms causing premature termination of translation in disease-related genes. Prediction of protein-destabilization effects was performed by graphical presentation of the locations of polymorphisms in the protein structure, using the Genomes TO Protein (GTOP database, and manual annotation with a set of specific criteria. Protein-destabilization was predicted for 44.4% of the nonsense SNPs, 32.4% of the frameshifting indels, and 9.1% of the non-frameshifting indels. A prediction of nonsense-mediated decay allowed to infer which truncated proteins would actually be translated as defective proteins. These cases included the proteins linked to diseases inherited dominantly, suggesting a relation between these diseases and toxic aggregation. Our approach would be useful in identifying potentially aggregation-inducing polymorphisms that may have pathological effects.

  16. Polymorphic Endpoint Types for Copyless Message Passing

    Directory of Open Access Journals (Sweden)

    Viviana Bono

    2011-07-01

    Full Text Available We present PolySing#, a calculus that models process interaction based on copyless message passing, in the style of Singularity OS. We equip the calculus with a type system that accommodates polymorphic endpoint types, which are a variant of polymorphic session types, and we show that well-typed processes are free from faults, leaks, and communication errors. The type system is essentially linear, although linearity alone may leave room for scenarios where well-typed processes leak memory. We identify a condition on endpoint types that prevents these leaks from occurring.

  17. 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.

  18. Prion protein polymorphisms in white-tailed deer influence susceptibility to chronic wasting disease.

    Science.gov (United States)

    Johnson, Chad; Johnson, Jody; Vanderloo, Joshua P; Keane, Delwyn; Aiken, Judd M; McKenzie, Debbie

    2006-07-01

    The primary sequence of the prion protein affects susceptibility to transmissible spongiform encephalopathies, or prion diseases, in mice, sheep and humans. The Prnp gene sequence of free-ranging, Wisconsin white-tailed deer was determined and the Prnp genotypes of chronic wasting disease (CWD)-positive and CWD-negative deer were compared. Six amino acid changes were identified, two of which were located in pseudogenes. Two alleles, a Q-->K polymorphism at codon 226 and a single octapeptide repeat insertion into the pseudogene, have not been reported previously. The predominant alleles--wild-type (Q95, G96 and Q226) and a G96S polymorphism--comprised almost 98% of the Prnp alleles in the Wisconsin white-tailed deer population. Comparison of the allelic frequencies in the CWD-positive and CWD-negative deer suggested that G96S and a Q95H polymorphism were linked to a reduced susceptibility to CWD. The G96S allele did not, however, provide complete resistance, as a CWD-positive G96S/G96S deer was identified. The G96S allele was also linked to slower progression of the disease in CWD-positive deer based on the deposition of PrP(CWD) in the obex region of the medulla oblongata. Although the reduced susceptibility of deer with at least one copy of the Q95H or G96S allele is insufficient to serve as a genetic barrier, the presence of these alleles may modulate the impact of CWD on white-tailed deer populations.

  19. 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.

  20. Calibration aspects of binaural sound reproduction over insert earphones

    DEFF Research Database (Denmark)

    Hoffmann, Pablo F.; Markovic, Milos; Olesen, Søren Krarup

    2012-01-01

    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......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...

  1. 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.

  2. Polymorphism in Energetic Materials

    Science.gov (United States)

    2008-01-01

    salicylic acid ) was first prepared by Charles Frederic Gerhardt in 1853, a second polymorph of this drug was not discovered until 2005. Studies have...the crystallization conditions post- synthesis were not recorded, reproducing the condi- tions resulting in the analyzed sample was not possible. All

  3. 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.

  4. 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 bri...

  5. 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 oppo...

  6. Polymorphous Perversity in Texts

    Science.gov (United States)

    Johnson-Eilola, Johndan

    2012-01-01

    Here's the tricky part: If we teach ourselves and our students that texts are made to be broken apart, remixed, remade, do we lose the polymorphous perversity that brought us pleasure in the first place? Does the pleasure of transgression evaporate when the borders are opened?

  7. Polymorphism of sorbitol

    Science.gov (United States)

    Nezzal, Amale; Aerts, Luc; Verspaille, Marleen; Henderickx, Geert; Redl, Andreas

    2009-07-01

    The polymorphism of sorbitol was investigated, confirming the existence of four anhydrous crystalline phases plus the hydrate. The crystallised melt (CM), the alpha form, and the gamma form were obtained via a dry route. The CM was confirmed to be a crystalline state with a spherulite morphology. The alpha form was obtained via direct conversion from the CM, in contrast to more complicated routes previously reported, and was found to have a very high crystallinity. Gamma crystals were obtained by seeding the melt at high temperature; however, crystallinity was clearly less than for alpha crystals. Despite its lower crystallinity, the gamma polymorph was found to be the most stable of the anhydrous crystalline forms; this was confirmed by its high melting point and low hygroscopicity. In contrast, the alpha polymorph has a relatively high melting point but lacks moisture stability at high relative humidity. The hydrate form has the same resistance to moisture as the gamma form, but melts at a lower temperature. The combination of both a high melting point and high stability in the presence of water makes the gamma polymorph best suited for confectionary applications.

  8. Difficulties in Learning Inheritance and Polymorphism

    Science.gov (United States)

    Liberman, Neomi; Beeri, Catriel; Kolikant, Yifat Ben-David

    2011-01-01

    This article reports on difficulties related to the concepts of inheritance and polymorphism, expressed by a group of 22 in-service CS teachers with an experience with the procedural paradigm, as they coped with a course on OOP. Our findings are based on the analysis of tests, questionnaires that the teachers completed in the course, as well as on…

  9. 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.

  10. 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.

  11. Classification of Babesia canis strains in Europe based on polymorphism of the Bc28.1-gene from the Babesia canis Bc28 multigene family.

    Science.gov (United States)

    Carcy, B; Randazzo, S; Depoix, D; Adaszek, L; Cardoso, L; Baneth, G; Gorenflot, A; Schetters, T P

    2015-07-30

    the classification of 35 B. canis strains in genotypes A and B using a previously described 18SrDNA-derived PCR-RFLP test revealed a partial but no direct correlation with the classification based on polymorphism of the Bc28.1-gene described here.

  12. 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

  13. Reconciling thermal and structural data from the polymorphic transitions of malonamide

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, Eugene Y. [TransForm Pharmaceuticals, 29 Hartwell Avenue, Lexington, MA 02421 (United States)], E-mail: echeung@its.jnj.com; Peterson, Matthew L. [TransForm Pharmaceuticals, 29 Hartwell Avenue, Lexington, MA 02421 (United States)

    2009-01-15

    Although screening for organic polymorphs has become a hot topic in recent years, polymorph screens continue to be largely based on solution crystallization. Other routes to different crystal forms, such as grinding, annealing, and melt crystallization can also be used to look for polymorphs when chemical stability allows. Thermal analysis is often the first method for identifying polymorphic transitions in solids. However, reconciling the thermal data with the structural data is rarely straightforward without a single crystal X-ray structure. By using differential scanning calorimetry, infrared spectroscopy, and powder X-ray diffraction, the polymorphic transitions of malonamide have now been studied, and two solid state pathways, solid state grinding and annealing, are verified to independently yield the tetragonal polymorph of malonamide from the monoclinic form. In addition, melt recrystallization yields a third polymorph, which has now been confirmed to be the orthorhombic polymorph.

  14. Improved set of short-tandem-repeat polymorphisms for screening the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Bo; Vaske, D.; Weber, J.L. [Marshfield Medical Research Foundation, WI (United States)] [and others

    1997-02-01

    Short-tandem-repeat (microsatellite) DNA polymorphisms are widely used for screening the human and other genomes in initial linkage mapping. Since the average spacing between polymorphisms in genome screens is usually {ge}10 cM and since many thousands of human short-tandem-repeat polymorphisms (STRPs) are now available, optimal subsets of STRPs must be selected for screening. Two screening sets of STRPs for humans have been described in the literature, both of which are based primarily on dinucleotide-repeat polymorphisms. Here we describe our eighth and most recent human screening set, which is based almost entirely on trinucleotide-and tetranucleotide-repeat polymorphisms. 7 refs., 1 tab.

  15. Hardware design for a cable-free fully insertable wireless laparoscopic robotic camera.

    Science.gov (United States)

    Ning Li; Mancini, Gregory J; Jindong Tan

    2016-08-01

    The field of insertable laparoscopic robotic camera is gaining increasing attentions from researchers, surgeons, and also patients. Although many insertable laparoscope prototypes have been introduced, few of them get rid of the encumbrance tethering cable. In this paper, we proposed a hardware architecture for a magnetic actuated robotic surgical (MARS) camera, which facilitates a cable-free fully insertable laparoscopic surgical robotic camera with adequate in-vivo mobility. Modular design and preliminary test of on-board functional payloads have shown feasibility of a cable-free insertable wireless laparoscopic surgical camera based on off-the-shelf electronics and industrial wireless standards operating in ISM frequency bands at 2.4GHz. Potential improvements for laparoscopic surgery benefited from this hardware architecture include more dexterous in-vivo camera mobility and intuitive closed-loop robotic camera control.

  16. New cardiac retractor for epicardial electrode insertion via subxiphoid approach.

    Science.gov (United States)

    Sakamoto, T; Arai, H; Suzuki, A

    1993-04-01

    A new retractor for the insertion of epicardial screw-in electrodes is described. We have found that this instrument can be easily applied to the heart and gives excellent exposure for electrode insertion.

  17. 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

    2016-07-29

    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 tomato lines and to select elite inbred lines, which will accelerate the breeding process.

  18. Intravaginal insertion in KwaZulu Natal: sexual practices and preferences in the context of microbicide gel use

    NARCIS (Netherlands)

    M. Gafos; M. Mzimela; S. Sukazi; R. Pool; C. Montgomery; J. Elford

    2010-01-01

    Intravaginal insertion is often associated with the concept of ‘dry’ sex. All HIV-prevention microbicides tested to date have been vaginally applied lubricant-based gels. In this paper, we examine whether the use of intravaginal insertions could be in conflict with the introduction of vaginal microb

  19. Impact of lux gene insertion on bacterial surface properties and transport.

    Science.gov (United States)

    Chen, Gang; Srinivasa Ranga, Vijay Penagonda; Mao, Yongjun; Chen, Kevin; Qiao, Hanzi

    2008-03-01

    Genetic markers have been in popular use for tracing microbial movement in the environment. However, the impact of genetic marker insertion on microbial surface properties and consequent transport is often ignored. For this research, we investigated the impact of luminescence-based genetic marker insertion on bacterial surface properties and transport. Typical Gram-positive bacterial strains of Lactobacillus casei, Streptococcus mitis and Micrococcus luteus were used as model bacterial strains in this research. We manipulated gene transfer to observe the impact of lux gene insertion on bacterial surface properties based on contact angle measurements, and we conducted column experiments to evaluate the impact of lux gene insertion on bacterial transport. After lux gene insertion, bacterial interactions with the porous media increased, demonstrating stronger deposition potential in the porous media. Accordingly, retention of the daughter strains increased. Lux gene insertion also resulted in an increase in bacterial dispersion and equilibrium adsorption in the porous media. The bacterial deposition coefficient was found to correlate with the free energy of interactions between bacteria and the porous media.

  20. 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.

  1. Experimental testing of exchangeable cutting inserts cutting ability

    OpenAIRE

    Čep, Robert; Janásek, Adam; Čepová Lenka; Petrů, Jana; Ivo HLAVATÝ; Car, Zlatan; Hatala, Michal

    2013-01-01

    The article deals with experimental testing of the cutting ability of exchangeable cutting inserts. Eleven types of exchangeable cutting inserts from five different manufacturers were tested. The tested cutting inserts were of the same shape and were different especially in material and coating types. The main aim was both to select a suitable test for determination of the cutting ability of exchangeable cutting inserts and to design such testing procedure that could make it possible...

  2. MTHFR gene A1298C polymorphisms are associated with breast cancer risk among Chinese population: evidence based on an updated cumulative meta-analysis

    Science.gov (United States)

    Wang, Yadong; Yang, Haiyan; Duan, Guangcai

    2015-01-01

    Objectives: Published studies on the association between methylenetetrahydrofolate reductase (MTHFR) gene A1298C polymorphisms and breast cancer risk among Chinese population have yielded conflicting results. The purpose of this study was to clarify the association between MTHFR gene A1298C polymorphisms and breast cancer risk among Chinese population. Methods: Systematic searches were performed through the database of Medline/PubMed, Science Direct, Elsevier, CNKI and Wanfang Medical Online. Results: Overall, a significantly increased risk of breast cancer was observed among the subjects carrying MTHFR gene A1298C AC+CC genotype (odds ratio [OR]=1.05 with 95% confidence interval [CI]: 1.01-1.10) as compared to those carrying AA genotype among total Chinese population. We did not observe any significant association between MTHFR gene A1298C polymorphisms and the risk of breast cancer under the additional genetic models of AC vs. AA, CC vs. AA and C-allele vs. A-allele (OR=1.00 with 95% CI: 0.97-1.02, OR=1.01 with 95% CI: 1.00-1.02 and OR=1.00 with 95% CI: 0.99-1.02, respectively). The cumulative meta-analysis showed similar results. In subgroup analysis, we observed subjects carrying AC+CC genotype had an increased breast cancer risk compared with those carrying AA genotype among the studies of sample size less than 1000. We did not observe any significant association between MTHFR gene A1298C polymorphisms and breast cancer risk in additional subgroup analyses. Conclusions: Our results suggest that MTHFR gene A1298C AC+CC genotype may be a risk factor for the development of breast cancer among Chinese population. Well-designed studies with a large sample size are needed to further confirm our findings. PMID:26884927

  3. Coupling Neurogenetics (GARS™) and a Nutrigenomic Based Dopaminergic Agonist to Treat Reward Deficiency Syndrome (RDS): Targeting Polymorphic Reward Genes for Carbohydrate Addiction Algorithms

    OpenAIRE

    Kenneth Blum; Thomas Simpatico; Badgaiyan, Rajendra D.; Zsolt Demetrovics; James Fratantonio; Gozde Agan; Marcelo Febo; Gold, Mark S.

    2015-01-01

    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 componen...

  4. Commercial Generic Bioprocessing Apparatus Science Insert - 03

    Science.gov (United States)

    Moreno, Nancy; Sto