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Sample records for 16s-23s intergenic spacer

  1. 16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads.

    Science.gov (United States)

    Tokajian, Sima; Issa, Nahla; Salloum, Tamara; Ibrahim, Joe; Farah, Maya

    2016-01-01

    Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2-57.9 mol%. Five distinct ITS types were identified: ITS(none) (without tRNA genes), ITS(Ala(TGC)), ITS(Ala(TGC)+Ile(GAT)), ITS(Ile(GAT)+Ala(TGC)), and ITS (Ile(GAT)+Pseudo). All of the identified tRNA(Ala(TGC)) molecules consisted of 73 bases, and all of the tRNA(Ile(GAT)) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S-23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.

  2. Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources

    OpenAIRE

    Seurinck, Sylvie; Verstraete, Willy; Siciliano, Steven D.

    2003-01-01

    Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal...

  3. PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species

    Directory of Open Access Journals (Sweden)

    Keys Christine E

    2010-03-01

    Full Text Available Abstract Background The genus Vibrio is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding with the addition of several new species annually. Consequently, it is of paramount importance to have a method which is able to reliably and efficiently differentiate the numerous Vibrio species. Results In this study, a novel and rapid polymerase chain reaction (PCR-based intergenic spacer (IGS-typing system for vibrios was developed that is based on the well-known IGS regions located between the 16S and 23S rRNA genes on the bacterial chromosome. The system was optimized to resolve heteroduplex formation as well as to take advantage of capillary gel electrophoresis technology such that reproducible analyses could be achieved in a rapid manner. System validation was achieved through testing of 69 archetypal Vibrio strains, representing 48 Vibrio species, from which an 'IGS-type' profile database was generated. These data, presented here in several cluster analyses, demonstrated successful differentiation of the 69 type strains showing that this PCR-based fingerprinting method easily discriminates bacterial strains at the species level among Vibrio. Furthermore, testing 36 strains each of V. parahaemolyticus and V. vulnificus, important food borne pathogens, isolated from a variety of geographical locations with the IGS-typing method demonstrated distinct IGS-typing patterns indicative of subspecies divergence in both populations making this technique equally useful for intraspecies differentiation, as well. Conclusion This rapid, reliable and efficient IGS-typing system, especially in combination with 16S rRNA gene sequencing, has the capacity to not only discern and identify vibrios at the species level but, in some cases, at the sub-species level, as well. This procedure is particularly well-suited for preliminary species identification and, lends itself nicely to

  4. Identification of clinically relevant nonhemolytic Streptococci on the basis of sequence analysis of 16S-23S intergenic spacer region and partial gdh gene

    DEFF Research Database (Denmark)

    Nielsen, Xiaohui Chen; Justesen, Ulrik Stenz; Dargis, Rimtas;

    2009-01-01

    for the identification of all species in this group of bacteria. The aim of the present study was to establish a method based on sequence analysis of the 16S-23S intergenic spacer (ITS) region and the partial gdh gene to identify clinical relevant NHS to the species level. Sequence analysis of the ITS region......Nonhemolytic streptococci (NHS) cause serious infections, such as endocarditis and septicemia. Many conventional phenotypic methods are insufficient for the identification of bacteria in this group to the species level. Genetic analysis has revealed that single-gene analysis is insufficient....... A phylogenetic algorithm based on the analysis of partial gdh gene sequences revealed three distinct clusters. We suggest that sequence analysis of the combination of the ITS region and the partial gdh gene can be used in the reference laboratory for the species-level identification of NHS....

  5. Inter- and intraspecific genomic variability of the 16S-23S intergenic spacer regions (ISR) in representatives of Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans.

    Science.gov (United States)

    Ni, Yong-Qing; Yang, Yuan; Bao, Jing-Ting; He, Kai-Yu; Li, Hong-Yu

    2007-05-01

    The complete sequences of 32 intergenic spacer regions (ISR) from Acidithiobacillus strains, including 29 field strains isolated from coal, copper, molybdenum mine wastes or sediment of different geoclimatic regions in China, reference strain ATCC19859 and the type strains of the two species were determined. These data, together with other sequences available in the GenBank database, were used to carry out the first detailed assessment of the inter- and intraspecific genomic variability of the ISR sequences and to infer phylogenetic relationships within the genus. The total length of the 16S-23S rRNA intergenic spacer regions of the Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans strains ranged from 451 to 490 bp, and from 434 to 456 bp, respectively. The degree of intrageneric ISR sequence similarity was higher than the degree of intergeneric similarity, and the overall similarity values of the ISRs varied from 60.49% to 84.71% between representatives of different species of the genus Acidithiobacillus. Sequences from the spacer of the A. thiooxidans and A. ferrooxidans strains ranged from 86.71% to 99.56% and 92.36% to 100% similarity, respectively. All Acidithiobacillus strains were separated into three phylogenetic major clusters and seven phylogenetic groups. ISR may be a potential target for the development of in situ hybridization probe aimed at accurately detecting acidithiobacilli in the various acidic environments.

  6. Length polymorphisms for intergenic spacer regions of 16S-23S rDNA in members of the new hydrogen-producing bacteria

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A method based on PCR amplification of the 16S rRNA gene (rDNA) -23S rDNA intergenic spacer regions (ISR) was developed for the identification of species within the novel group hydrogen-producing anaerobes. The sizes of the PCR products varied from 1264 to 398 bp. Strain of isolate Rennanqilyf 3 was characterized as having products of 1262, 398, 638, 437 and 436 bp. The isolate Rennanqilyf 1 had product of 1264 bp. The isolate Rennanqilyf 13 had products of 1261, 579 and 485 bp. Of the 3 species of the novel group hydrogenproducing anaerobes examined, no one was indistinguishable. Two environmental isolates were identified as hydrogen-producing bacteria, which were new species in present taxon. Rennanqilyf 3 could not be associated With any Clostridium sp. Studied. Rennanqilyf 1 could be classified into Clostridium genus. The combination between 16S rDNA equencing and length polymorphisms of IRS in 16S-23S rDNA is a better method for determining species of the hydrogen-producing bacteria.

  7. Analysis of the 16S-23S rDNA intergenic spacers (IGSs) of marine vibrios for species-specific signature DNA sequences.

    Science.gov (United States)

    Lee, Simon K Y; Wang, H Z; Law, Sheran H W; Wu, Rudolf S S; Kong, Richard Y C

    2002-05-01

    Vibrios are widespread in the marine environment and a few pathogenic species are known to be commonly associated with outbreaks of diarrheal diseases in humans due to the consumption of raw or improperly cooked seafood. However, there are also many Vibrio species which are potentially pathogenic to vertebrate and invertebrate aquatic animals, and of which little is known. In an attempt to develop rapid PCR detection methods for these latter class of vibrios, we have examined the 16S-23S intergenic spacers (IGSs) of 10 lesser-known Vibrio species and successfully developed species-specific primers for eight of them--Vibrio costicola, V. diazotrophicus, V. fluvialis, V. nigripulchritudo, V. proteolyticus, V. salmonicida, V. splendidus and V. tubiashii. The IGS amplicons were amplified using primers complementary to conserved regions of the 16S and 23S rRNA genes, and cloned into plasmid vectors and sequenced. Analysis of the IGS sequences showed that 37 ribosomal RNA (rrn) operons representing seven different IGS types have been cloned from the 10 vibrios. The three IGS types--IGS(0), IGS(IA) and IGS(Glu)--were the most prevalent forms detected. Multiple alignment of representative sequences of these three IGS types from different Vibrio species revealed several domains of high sequence variability, which were used to design species-specific primers for PCR. The specificity of the primers were evaluated using total DNA prepared from different Vibrio species and bacterial genera. The results showed that the PCR method can be used to reliably detect eight of the 10 Vibrio species in marine waters in this study.

  8. Cloning, Sequencing and Analysis of the 16S-23S rDNA Intergenic Spacers (IGSs) of Two Strains of Vibrio vulnificus%2株创伤弧菌的16S-23S rDNA间区的克隆、测序及分析

    Institute of Scientific and Technical Information of China (English)

    邓先余; 陈晓艳; 王智学; 欧普; 何建国

    2006-01-01

    根据细菌的16S rDNA 3'端和23S rDNA 5'端的高度保守区设计引物,PCR扩增了2株创伤弧菌(Vibrio vulnificus)的16S-23S rDNA间区(Intergenic spacer,IGS),克隆到pGEM-T载体上,测序.用BLAST和DNAstar软件对16S-23SrDNA间区序列及其内的tRNA基因进行比较分析.结果表明,2株创伤弧菌共测出9条16S-23S rDNA间区序列,其中ZSU006测出5条,间区类型分别为:IGSGLAV、IGSGLV、IGSIA、IGSA和IGSG.其中IGSGLAV最大,包含tRNAGlu、tRNALys、tRNAAla和tRNAVal基因;IGSGLV包含tRNAGlu、tRNALys和tRNAVal基因;IGSIn,则包含tRNAIle和tRNAAla基因;IGSG仅包含tRNAGlu基因;而IGSA仅包含tRNAAla基因.菌株CG021测出的16S-23S rDNAIGS序列有4条,除缺少IGSA外,其余的IGS类型均与ZSU006的相同.与GenBank内的创伤弧菌ATCC27562的IGS序列比较,发现创伤弧菌所有类型的IGS的tRNA基因两端的非编码区具有较高的种内同源性.16S-23S rDNA间区结构的差异为建立一种新的创伤弧菌检测方法奠定了基础.%According to the conserved sequences flanking the 3' end of the 16S and the 5' end of the 23S rDNAs, PCR primers were designed, and the 16S-23S rDNA intergenic spacers (IGSs) of two strains of Vibrio vulnificus were amplified by PCR and cloned into pGEM-T vector. Different clones were selected to be sequenced and the sequences were analyzed with BLAST and the software DNAstar. Analyses of the IGS sequences suggested that the strain ZSU006 contains five types of polymorphic16S-23S rDNA intergenic spacers, namely, IGSGLAV, IGSGLv, IGSIA, IGSG and IGSA; while the strain CG021 has the same types of IGSs except lacking IGSA. Among these five IGS types, IGSGLAV is the biggest type, including the gene cluster of tRNAGlu - tRNALys - tRNAAla - tRNAVal; IGSGLV includes that of tRNAGlu-tRNALys-tRNAVal; IGSAG, tRNAAla-tRNAGlu; IGSIA, tRNAIle -tRNAAla; IGSG, tRNAGlu and IGSA, tRNAAla. Intraspecies multiple alignment of all the IGS sequences of these two strains with those of V

  9. Identification and phyletic evolution analysis of Proteus mirabilis strains by PCR and restriction fragment length polymorphism of 16S-23S rRNA gene intergenic spacer region%16S-23S rRNA基因间隔序列PCR及RFLP对奇异变形杆菌分离株的鉴别与系统发育分析

    Institute of Scientific and Technical Information of China (English)

    崔国林; 朱瑞良; 左雪梅; 钟世勋; 杨世发; 梁漫飞; 孙婧; 刘静静

    2013-01-01

    根据临床常见致病菌16S-23S rRNA基因间隔序列(ISR)两端的16S及23S rRNA保守序列设计PCR扩增的通用引物,对9株奇异变形杆菌和6株相近菌株应用通用引物PCR扩增16S-23S rRNA ISR序列.通过PCR长度多态性比较、RFLP分析以及部分序列测序比较,分析鉴别奇异变形杆菌.结果显示,PCR长度多态性可以将奇异变形杆菌同其余菌种进行区分;RFLP分析可以将所有试验菌种进行区分;部分序列测序可以对奇异变形杆菌进行分型.由此表明,16S 23S rRNA ISR序列PCR及RFLP分析可以简单、快速、准确的鉴定奇异变形杆菌.%To establish a new method to identify Proteus mirabilis strains, according to the conserved sequences of 16S and 23S which located on both ends of the clinical common pathogenic bacteria 16S-23S rRNA gene intergenic spacer region (ISR),a pair of universal primers was designed. Nine Proteus mirabilis strains and six similar bacteria strains were amplified by PCR and identified by the PCR length polymorphism comparison,restriction fragment length polymorphism (RFLP) analysis and partial sequences sequencing. The result showed that Proteus mirabilis strains could be discriminated from other similar bacteria strains by PCR length polymorphism comparison,all of test organism could be discriminated by RFLP and Proteus mirabilis strains could be typed by partial sequences sequencing. The result indicated that the identification method based on the 16S-23S rRNA ISR, using PCR and PCR-RFLP,is very suitable for the rapid low-cost identification and discrimination of Proteus mirabilis strains from other phylogenetically related bacteria strains.

  10. The Mycoplasma gallisepticum 16S-23S rRNA intergenic spacer region sequence as a novel tool for epizootiological studies.

    Science.gov (United States)

    Raviv, Ziv; Callison, S; Ferguson-Noel, N; Laibinis, V; Wooten, R; Kleven, S H

    2007-06-01

    Mycoplasma gallisepticum (MG) contains two sets of rRNA genes (5S, 16S and 23S) in its genome, but only one of the two is organized in an operon cluster and contains a unique 660-nucleotide intergenic spacer region (IGSR) between the 16S and the 23S rRNA genes. We designed a polymerase chain reaction (PCR) for the specific amplification of the complete MG IGSR segment. The MG IGSR PCR was tested on 18 avian mollicute species and was confirmed as MG specific. The reaction sensitivity was demonstrated by comparing it to the well-established MG mgc2 PCR. The MG IGSR sequence was found to be highly variable (discrimination [D] index of 0.950) among a variety of MG laboratory strains, vaccine strains, and field isolates. The sequencing of the MG IGSR appears to be a valuable single-locus sequence typing (SLST) tool for MG isolate differentiation in diagnostic cases and epizootiological studies. PMID:17626483

  11. Designing PCR Primers from 16S-23S rDNA Intergenic Spacer Region for the Identification of Pasteurella multocida%以 16S-23S rDNA 间区序列为目的基因设计 PCR 引物鉴定多杀巴斯德氏菌

    Institute of Scientific and Technical Information of China (English)

    周浩; 刘寅; 陈一军; 郑泽军; 黄熙泰

    2008-01-01

    多杀巴斯德氏菌是养殖动物(鸡,猪,牛等)的重要致病菌.本研究以16S-23S rDNA间区序列为目的基因设计PCR引物鉴定多杀巴斯德氏菌.通过对多杀巴斯德氏菌ITS-IA(含有tDNA-Ile和tDNA-Ala的16S-23S rDNA间区序列)的测序和与GenBank中序列的BLAST,设计筛选了一对特异引物PS-F/PS-R.对引物的特异性和有效性,用PCR方法进行了验证.结果表明:所有的多杀巴斯德氏菌标准菌株和分离菌株都能被检出,而全部39株非多杀巴斯德氏菌都没有扩增出特异性条带.其检测灵敏度能达到102CFU/mL.研究结果表明,发展了的PCR鉴定方法是省时的和可靠的,整个过程只需要20 h,而传统的鉴定方法需要至少5 d的时间.%Pasteurella multocida is an important pathogen that infects many kinds of animals. In present study, a polymerase chain reaction (PCR) assay using primers derived from the 16S-23S rRNA intergenic spacer (ITS) of P. multocida was developed. One pairs of specific PCR primers were designed by sequencing the ITS-IA (ITS containing tDNA-Ile and tDNA-Ala) of P. multocida and BLAST of GenBank. The specificity and efficiency of the PCR methods were tested against a panel of numerous strains from 39 different bacterial strains. All of the P. multocida strains generated positive signal, and no cross-reaction was observed with non-P, multocida strains in the PCR detection. Sensitivity of the detection is 102 CFU/mL cultures. The newly developed PCR array procedures take only 20 hours for each time, whereas the conventional methods required at least five days. This study demonstrated that the PCR detection for P. multocida is time-saved and reliable.

  12. Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O 139 outbreak based on the inter-genomic heterogeneity of the 16S-23S rRNA intergenic spacer regions.

    Science.gov (United States)

    Ghatak, Atreyi; Majumdar, Anasuya; Ghosh, Ranajit K

    2005-12-01

    We have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eight rrn operons (rrna-rrnh) of Vibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O 139 outbreak. ISR classes 'a' and 'g' were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O 139 serogroup and post-O 139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

  13. USE OF 16S-23S INTERGENIC TRANSCRIBED SPACER IN IDENTIFICATION AND COMMUNITY ANALYSIS OF BACTERIA%基因间隔序列(ITS)在细菌分类鉴定和种群分析中的应用

    Institute of Scientific and Technical Information of China (English)

    郑雪松; 杨虹; 李道棠; 韩文卿

    2003-01-01

    Use of 16S -23S intergenic transcribed spacer (ITS) variability, as a relatively new method, is becoming an important supplement to the molecular methods based on 16S rRNA for which has a fairly constant size and is not divergent enough to give good separation in close relationships. This paper summarizes the structures and characteristics of ITS regions that are extremely variable in copy number, length and sequence per genome. The ITS region can be amplified easily taking advantage of conserved nucleotide stretches at the 5′of the 16S and 3′of the 23S gene, and the amplicon can contain different amounts of the 16S rDNA by choosing primers at different conserved areas within this gene. These primers are listed and discussed for perfecting the methodology of ITS. Furthermore, some recent progresses on the taxonomy, identification and community analysis of bacteria by means of ITS in epidemiology, ecology and artificial environment are reviewed, as well, the virtues and limitations of that method are discussed. Fig 2, Tab 1, Ref 51

  14. Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O139 outbreak based on the intergenomic heterogeneity of the 16S-23S rRNA intergenic spacer regions

    Indian Academy of Sciences (India)

    Atreyi Ghatak; Anasuya Majumdar; Ranajit K Ghosh

    2005-12-01

    We have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eight rrn operons (rrna-rrnh) of Vibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O139 outbreak. ISR classes ‘a’ and ‘g’ were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O139 serogroup and post-O139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

  15. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    OpenAIRE

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repeti...

  16. 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.

  17. A molecular biological study on identification of common septicemia bacteria using 16s-23s rRNA gene spacer regions

    Institute of Scientific and Technical Information of China (English)

    傅君芬; 虞和永; 尚世强; 洪文澜; 陆淼泉; 李建平

    2002-01-01

    In the search for a rapid and reliable method for identification of bacteria in blood and cerebrospinal fluid , we developed a unified set of primers and used them under polymerase chain reaction(PCR) to amplify the spacer regions between the 16s and 23s genes in the prokaryotic rRNA genetic loci . Spacer regions within these loci showed a significant level of length and sequence polymorphism across most of the species lines. A generic pair of priming sequences was selected from highly conserved sequences in the 16s and 23s genes occurring adjacent to these polymorphic regions. This single set of primers and reaction conditions were used for the amplification of the 16s-23s spacer regions for 61 strains of standard bacteria and corresponding clinical isolates belonging to 20 genera and 27 species, including Listeria, Staphylococcus and Salmonella species, et al. When the spacer amplification products were resolved by electrophoresis, the resulting patterns could be used to distinguish most of the bacteria species within the test group, and the amplification products of the clinical isolates clustered at the standard species level. Some species presenting similar pattern were further analyzed by HinfI or AluI digestion or DNA clone and sequences analysis in order to establish the specific 16s-23s rRNA gene spacer regions map. Analysis of 42 blood specimens from septicemic neonates and 6 CSF specimens from suspected purulent meningitis patients by bacterial culture and PCR-RFLP(Restriction Fregament Length Polymorphism) showed that 15 specimens of blood culture were positive(35.7%) in the 42 septicemic neonates; 27 specimens were positive(64.2%) by PCR, and that the positive rate by PCR was significantly higher than that by blood culture(P<0.01). Among the 6 CSF specimens, one specimen found positive by blood culture was also positive by PCR, two found negative by blood culture showed positive by PCR; all three were S.epidermidis according to the DNA map. One C

  18. Cyanobacterial ecotypes in different optical microenvironments of a 68 C hot spring mat community revealed by 16S-23S rRNA internal transcribed spacer region variation

    DEFF Research Database (Denmark)

    Ferris, Mike J.; Kühl, Michael; Wieland, Andrea;

    2003-01-01

    distinct populations over the vertical interval. We were unable to identify patterns in genetic variation in Synechococcus 16S rRNA sequences that correlate with different vertically distributed populations. However, patterns of variation at the internal transcribed spacer locus separating 16S and 23S r......RNA genes suggested the existence of closely related but genetically distinct populations corresponding to different functional populations occurring at different depths....

  19. Modified 16S-23S rRNA intergenic region restriction endonuclease analysis for species identification of Enterococcus strains isolated from pigs, compared with identification using classical methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Nowakiewicz, Aneta; Ziółkowska, Grażyna; Zięba, Przemysław; Trościańczyk, Aleksandra; Banach, Tomasz; Kowalski, Cezary

    2015-03-01

    Fast and reliable identification of bacteria to at least the species level is currently the basis for correct diagnosis and appropriate treatment of infections. This is particularly important in the case of bacteria of the genus Enterococcus, whose resistance profile is often correlated with their species (e.g. resistance to vancomycin). In this study, we evaluated restriction endonuclease analysis of the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region for species identification of Enterococcus. The utility of the method was compared with that of phenotypic methods [biochemical profile evaluation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)]. Identification was based on 21 Enterococcus reference strains, of the species E. faecalis, E. faecium, E. hirae, E. durans, E. casseliflavus, E. gallinarum, E. avium, E. cecorum and E. columbae, and 47 Enterococcus field strains isolated from pigs. Restriction endonuclease analysis of the ITS-PCR product using HinfI, RsaI and MboI, in the order specified, enabled species differentiation of the Enterococcus reference and field strains, and in the case of the latter, the results of species identification were identical (47/47) to those obtained by MALDI-TOF MS. Moreover, as a result of digestion with MboI, a unique restriction profile was also obtained for the strains (3/3) identified by MALDI-TOF MS as E. thailandicus. In our opinion, restriction endonuclease analysis of the 16S-23S rRNA gene ITS region of Enterococcus may be a simple and relatively fast (less than 4 h) alternative method for identifying the species occurring most frequently in humans and animals.

  20. Diversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences Diversidad de las picocianobacterias marinas Prochlorococcus y Synechococcus por medio de polimorfismos de longitud de fragmentos de restricción terminal en secuencias del espaciador transcrito interno del ARNr 16S - 23S

    Directory of Open Access Journals (Sweden)

    PARIS LAVIN

    2008-12-01

    Full Text Available In order to assess the appropriateness of the use of internal transcribed spacer (ITS sequences for the study of population genetics of marine cyanobacteria, we amplified and cloned the 16S rRNA gene plus the 16S-23S ITS regions of six strains of Prochlorococcus and Synechococcus. We analyzed them by denaturing gradient gel electrophoresis (DGGE and terminal restriction fragment length polymorphisms (T-RFLP. When using the standard application of these techniques, we obtained more than one band or terminal restriction fragment (T-RF per strain or cloned sequence. Reports in literature have suggested that these anomalies can result from the formation of secondary structures. Secondary structures of the ITS sequences of Prochlorococcus and Synechococcus strains were computationally modelled at the different temperatures that were used during the polymerase chain reaction (PCR. Modelling results predicted the existence of hairpin loops that would still be present at the extensión temperature; it is likely that these loops produced incomplete and single stranded PCR products. We modified the standard T-RFLP procedure by adding the labelled ITS primer in the last two cycles of the PCR reaction; this resulted, in most cases, in only one T-RF per ribotype. Application of this technique to a natural picoplankton community in marine waters off northern Chile, showed that it was possible to identify the presence, and determine the relative abundance, of several phylogenetic lineages within the genera Prochlorococcus and Synechococcus inhabiting the euphotic zone. Phylogenetic analysis of ITS sequences obtained by cloning and sequencing DNA from the same sample confirmed the presence of the different genotypes. With the proposed modification, T-RFLP profiles should therefore be suitable for studying the diversity of natural populations of cyanobacteria, and should become an important tool to study the factors influencing the genetic structure and

  1. 16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria

    Science.gov (United States)

    Subedi, Shradha; Kong, Fanrong; Jelfs, Peter; Gray, Timothy J.; Xiao, Meng; Sintchenko, Vitali; Chen, Sharon C-A

    2016-01-01

    Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included. Identification was compared with that achieved by high performance liquid chromatography (HPLC), in-house PCR and 16S/ITS sequencing. Isolates of all species yielded a SCGE profile comprising a single fragment length (or peak) except for M. scrofulaceum (two peaks). SCGE peaks of ATCC strains were distinct except for peak overlap between Mycobacterium kansasii and M. marinum. Of clinical/environmental strains, unique peaks were seen for 7/17 (41%) species (M. haemophilum, M. kubicae, M. lentiflavum, M. terrae, M. kansasii, M. asiaticum and M. triplex); 3/17 (18%) species were identified by HPLC. There were five SCGE fragment length types (I–V) each of M. avium, M. intracellulare and M. gordonae. Overlap of fragment lengths was seen between M. marinum and M. ulcerans; for M. gordonae SCGE type III and M. paragordonae; M. avium SCGE types III and IV, and M. intracellulare SCGE type I; M. chimaera, M. parascrofulaceum and M. intracellulare SCGE types III and IV; M. branderi and M. avium type V; and M. vulneris and M. intracellulare type V. The ITS-SCGE method was able to provide the first line rapid and reproducible species identification/screening of SG-NTM and was more discriminatory than HPLC. PMID:27749897

  2. Identification of Lactobacillus strains of goose origin using MALDI-TOF mass spectrometry and 16S-23S rDNA intergenic spacer PCR analysis.

    Science.gov (United States)

    Dec, Marta; Urban-Chmiel, Renata; Gnat, Sebastian; Puchalski, Andrzej; Wernicki, Andrzej

    2014-04-01

    The objective of our study was to identify Lactobacillus sp. strains of goose origin using MALDI-TOF mass spectrometry, ITS-PCR and ITS-PCR/RFLP. All three techniques proved to be valuable tools for identification of avian lactobacilli and produced comparable classification results. Lactobacillus strains were isolated from 100% of geese aged 3 weeks to 4 years, but from only 25% of chicks aged 1-10 days. Among the 104 strains isolated, we distinguished 14 Lactobacillus species. The dominant species was Lactobacillus salivarius (35.6%), followed by Lactobacillus johnsonii (18.3%), Lactobacillus ingluviei (11.5%) and Lactobacillus agilis (7.7%). The intact-cell MALDI-TOF mass spectrometry enabled rapid species identification of the lactobacilli with minimal pretreatment. However, it produced more than one identification result for 11.5% examined strains (mainly of the species L. johnsonii). ITS-PCR distinguished 12 genotypes among the isolates, but was not able to differentiate closely related strains, i.e. between Lactobacillus amylovorus and Lactobacillus kitasatonis and between Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus zeae. These species were differentiated by ITS-PCR/RFLP using the restriction enzymes TaqI and MseI. The results obtained indicate that ITS-PCR and ITS-PCR/RFLP assays could be used not only for interspecific, but also for intraspecific, typing.

  3. A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil

    NARCIS (Netherlands)

    de Oliveira, VM; Manfio, GP; Coutinho, HLD; Keijzer-Wolters, AC; van Elsas, JD

    2006-01-01

    A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was

  4. The use of 16S and 16S-23S rDNA to easily detect and differentiate common Gram-negative orchard epiphytes.

    Science.gov (United States)

    Jeng, R S; Svircev, A M; Myers, A L; Beliaeva, L; Hunter, D M; Hubbes, M

    2001-02-01

    The identification of Gram-negative pathogenic and non-pathogenic bacteria commonly isolated from an orchard phylloplane may result in a time consuming and tedious process for the plant pathologist. The paper provides a simple "one-step" protocol that uses the polymerase chain reaction (PCR) to amplify intergenic spacer regions between 16S and 23S genes and a portion of 16S gene in the prokaryotic rRNA genetic loci. Amplified 16S rDNA, and restriction fragment length polymorphisms (RFLP) following EcoRI digestion produced band patterns that readily distinguished between the plant pathogen Erwinia amylovora (causal agent of fire blight in pear and apple) and the orchard epiphyte Pantoea agglomerans (formerly E. herbicola). The amplified DNA patterns of 16S-23S spacer regions may be used to differentiate E. amylovora at the intraspecies level. Isolates of E. amylovora obtained from raspberries exhibited two major fragments while those obtained from apples showed three distinct amplified DNA bands. In addition, the size of the 16S-23S spacer region differs between Pseudomonas syringae and Pseudomonas fluorescens. The RFLP pattern generated by HaeIII digestion may be used to provide a rapid and accurate identification of these two common orchard epiphytes. PMID:11166101

  5. 116S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

    Directory of Open Access Journals (Sweden)

    Sima eTokajian

    2016-02-01

    Full Text Available Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 to 849 bp, while their G+C content was 42.2 mol% to 57.9 mol%. Five distinct ITS types were identified: ITSnone (without tRNA genes, ITSAla(TGC, ITSAla (TGC+Ile (GAT, ITSIle (GAT+Ala (TGC and ITS Ile (GAT+Pseudo. All of the identified tRNAAla (TGC molecules consisted of 73 bases, and all of the tRNAIle (GAT molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2.

  6. Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling

    Directory of Open Access Journals (Sweden)

    Neumann Elisabeth

    2005-03-01

    Full Text Available Abstract Background The accurate identification of Lactobacillus and other co-isolated bacteria during microbial ecological studies of ecosystems such as the human or animal intestinal tracts and food products is a hard task by phenotypic methods requiring additional tests such as protein and/or lipids profiling. Results Bacteria isolated in different probiotic prospecting studies, using de Man, Rogosa and Sharpe medium (MRS, were typed at species level by PCR amplification of 16S-23S rRNA intergenic spacers using universal primers that anneal within 16S and 23S genes, followed by restriction digestion analyses of PCR products. The set of enzymes chosen differentiates most species of Lactobacillus genus and also co-isolated bacteria such as Enterococcus, Streptococcus, Weissella, Staphylococcus, and Escherichia species. The in silico predictions of restriction patterns generated by the Lactobacillus shorter spacers digested with 11 restriction enzymes with 6 bp specificities allowed us to distinguish almost all isolates at the species level but not at the subspecies one. Simultaneous theoretical digestions of the three spacers (long, medium and short with the same set of enzymes provided more complex patterns and allowed us to distinguish the species without purifying and cloning of PCR products. Conclusion Lactobacillus isolates and several other strains of bacteria co-isolated on MRS medium from gastrointestinal ecosystem and fermented food products could be identified using DNA fingerprints generated by restriction endonucleases. The methodology based on amplified ribosomal DNA restriction analysis (ARDRA is easier, faster and more accurate than the current methodologies based on fermentation profiles, used in most laboratories for the purpose of identification of these bacteria in different prospecting studies.

  7. Intergenic spacer length variants in Old Portuguese bread wheat cultivars

    Indian Academy of Sciences (India)

    Ana Carvalho; Henrique Guedes-Pinto; José Lima-Brito

    2011-08-01

    The intergenic spacer of the ribosomal DNA is highly variable, but is location specific in the nucleolar organizer region of the chromosomes. This study provides an event of high level of polymorphism / size variation and occurrence of 14 unique phenotypes in 48 landraces of Portuguese bread wheat cultivars for IGS-amplified products obtained by PCR-RFLP technique performed with TaqI. The attendant IGS polymorphism has been used to deduce affinities between landraces. Some of the high molecular weight IGS allelic variants were also probed for their chromosomal localization by sequential silver nitrate staining and fluorescence in situ hybridization. However, only the intergenic spacer allelic variant of 3.1 kb could be successfully hybridized, and was observed to be physically located on the chromosome pair 1B in the NOR loci of the cultivar ‘Magueija’.

  8. Analysis of the genotypes among different strains of common Mycobacteria based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences%常见分枝杆菌种内不同株之间16S rRNA基因和16S-23SrRNA ITS序列分析结果的比较

    Institute of Scientific and Technical Information of China (English)

    黄至澄; 徐黔宁; 闫李侠; 陈保文; 王国治

    2011-01-01

    目的 针对常见分枝杆菌不同株对其基因序列进行分析,比较分析结果.方法 利用16S rRNA Gene和16S-23S rRNAITS(转录间隔区序列)分析法分别对97株共7种DSMZ/ATCC引进的常见分枝杆菌进行种内不同株之间基因差异性分析,对比两种分型结果的异同.结果 16S rRNA基因可将13株草分枝杆菌分为3个型别,18株偶发分枝杆菌分为6个型别,17株耻垢分枝杆菌分为4个型别,8株戈登分枝杆菌分为3个型别,9株龟分枝杆菌龟亚种分为3个型别,15株堪萨斯分枝杆菌分为2个型别,17株产鼻疽分枝杆菌分为1个型别;而16S-23S rRNA ITS可依次将上述分枝杆菌分为3个、15个、7个、3个、4个、3个、5个型别.结论 16S rRNA G ene分析和16S-23S rRNA ITS分析均是分枝杆菌基因型分析的可靠方法,此外,16S-23SrRNA ITS的种内多态性高于16S rRNA Gene.

  9. 山羊奇异变形杆菌分离鉴定及其16S-23S rRNA ISR序列RFLP分析%Isolation and Identification of Proteus mirabilis from Goat and the Analysis of Its 16S-23S rRNA ISR Sequence by RFLP

    Institute of Scientific and Technical Information of China (English)

    崔国林; 钟世勋; 杨世发; 左雪梅; 朱瑞良

    2013-01-01

    2012年初,山东菏泽某羊场的羊群发病,从发病羊器官分离到2株病原细菌.对病原细菌进行鉴定,并对其与已知同种异源菌株相似性差异进行分析.从患病山羊内脏器官分离细菌,经形态特征、培养特性、生化试验、血清学试验及致病性试验进行鉴定;再通过设计通用引物扩增16S-23S rRNA ISR (intergenie spacer region)序列,将PCR产物经HinfⅠ单酶切获得3条可视条带,同时对扩增条带中的主带测序并进行系统发育分析.结果表明,分离菌株为奇异变形杆菌;分离菌株同本实验室保存的兔源与鸡源奇异变形杆菌PCR-RFLP结果一致;分离菌株PCR产物同GenBank收录的HI4320株奇异变形杆菌及本实验室保存的兔源与鸡源奇异变形杆菌进行序列比较,分离羊源菌株与兔源菌株相似性为94.8%、与鸡源菌株相似性为96.0%~98.2%,与人源HI4320株相似性为96.9%.研究证实发病羊致病病原为奇异变形杆菌,其与鸡源、兔源和人源奇异变形杆菌的亲缘关系较近.%At the beginning of 2012,a disease occurred in a goat farm in Heze City and two strains of pathogen were isolated from the infected goats.In order to identify the infected bacteria and analyze the homology between isolated strains and heterologous strains,bacteria were isolated from infected goats internal organs and were identified by morphologic characteristics,cultural characteristic,biochemistry test,serologic test and pathogenicity test; A pair of universal primers was designed to amplify 16S-23S rRNA ISR (intergenic spacer region) gene.and three visible straps were observed when PCR products were cut by Hinf Ⅰ,at the same time the main strap of PCR straps was sequenced and analyzed by phyletic evolution.The results showed that isolated strains were Proteus mirabilis ; the result of PCR-RFLP of isolated strains and Proteus mirabilis from rabbit and chicken was the same; The homology was 94.8% between

  10. 16s-23S rDNA: polymorphisms and their use for detection and identification of Xylella fastidiosa strains 16S-23S rDNA: polimorfismos e sua aplicação na detecção e identificação de linhagens de Xylella fastidiosa

    Directory of Open Access Journals (Sweden)

    Juliana Camargo Martinati

    2007-03-01

    Full Text Available Strains of Xylella fastidiosa from several hosts (coffee, citrus, grape, almond, oleander, peach, plum, etc. were characterized by analyzing the content of the nucleotide sequences of 16S-23S rDNA (coding for a small subunit ribosomal RNA spacer region (ITS. Current methods for sequencing the ITS region yields partial sequences that do not contribute with significant information. According to this fact, new primers have been designed in order to obtain a complete sequence and facilitate the sequencing. The complete 16S-23S sequences from 08 strains were amplified through PCR using the primers designed in our lab. The 16S-23S sequences obtained were compared with 52 others sequences entries in GenBank database. The results revealed a higher level of variation than that found in 16S gene sequences, with similarity values ranging from 0.79-1.00. The dendogram based on similarity data revealed 5 main groups. This spacer sequence contains two genes for tRNA (tRNAala and tRNAile. The sequence analysis of the tRNA content showed a conserved region with a few differences in the nucleotide composition.Linhagens de Xylella fastidiosa de diferentes hospedeiros (café, uva, amêndoa, ameixa, etc. foram caracterizados analisando as sequências de nucleotídeos do espaço intergênico 16S-23S (ITS. Os métodos atuais para o sequenciamento da região ITS produzem fragmentos parciais das sequências que não contribuem com informações significantes. Em vista disso, novos primers foram desenhados a fim de obter uma sequência completa e facilitar o sequenciamento. A sequencia completa da região ITS de 08 linhagens de X. Fastidiosa foram amplificadas via PCR, sequenciadas e comparadas com outras 52 sequencias depositadas no GenBank. Os resultados revelaram um alto nível de variação sendo maior que os níveis encontrados quando se utiliza o gene 16S para este tipo de análise, com valores variando entre 0.79 a 1.00. O dendograma baseado em dados de

  11. Cladistic biogeography of Juglans (Juglandaceae) based on chloroplast DNA intergenic spacer sequences

    Science.gov (United States)

    The phylogenetic utility of sequence variation from five chloroplast DNA intergenic spacer (IGS) regions: trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM was examined in the genus Juglans. A total of seventeen taxa representing the four sections within Juglans and an outgroup taxon, ...

  12. Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa.

    Science.gov (United States)

    Lakshmikumaran, M; Negi, M S

    1994-03-01

    Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.

  13. Sequence analysis of rDNA intergenic spacer region (IGS) as a tool for phylogenetic studies in Trichoderma spp.

    Institute of Scientific and Technical Information of China (English)

    Mercatelli Elisabetta; Pecchia Susanna; Ciliegi Sandro; Vannacci Giovanni

    2004-01-01

    @@ Different from ribosomal genes, which contain highly conserved sequences that are detected in all organisms, the intergenic spacer of rDNA (IGS) appears to be the most rapidly-evolving spacer region. For this reason we tested this region for phylogenetic studies.

  14. Sequence analysis of the rDNA intergenic spacer of Metarhizium strains isolated in Brazil

    Directory of Open Access Journals (Sweden)

    Fabiana Y. Yanaka-Schäfer

    2008-01-01

    Full Text Available To assess the extent of genetic variability of rDNA intergenic spacer (IGS in Metarhizium sp., 34 strains (27 isolated in Brazil were sequenced and analyzed together with an additional 20 Metarhizium anisopliae var. anisopliae sequences retrieved from GenBank. Overall, the global nucleotide diversity for the region under study was of 0.090, while for the Brazilian isolates it was only 0.016. Phylogenetic analyses showed four well-supported groups (A, B, C, and D, one of which (D has not been previously identified. All but one of the Brazilian strains cluster in this novel D phylogroup, suggesting that the genetic variation found in Brazil is a subset of the worldwide M. anisopiliae var. anisopliae variation.

  15. Detection of the new cosmopolitan genus Thermoleptolyngbya (Cyanobacteria, Leptolyngbyaceae) using the 16S rRNA gene and 16S-23S ITS region.

    Science.gov (United States)

    Sciuto, Katia; Moro, Isabella

    2016-12-01

    Cyanobacteria are widespread prokaryotes that are able to live in extreme conditions such as thermal springs. Strains attributable to the genus Leptolyngbya are among the most common cyanobacteria sampled from thermal environments. Leptolyngbya is a character-poor taxon that was demonstrated to be polyphyletic based on molecular analyses. The recent joining of 16S rRNA gene phylogenies with 16S-23S ITS secondary structure analysis is a useful approach to detect new cryptic taxa and has led to the separation of new genera from Leptolyngbya and to the description of new species inside this genus and in other related groups. In this study, phylogenetic investigations based on both the 16S rRNA gene and the 16S-23S ITS region were performed alongside 16S rRNA and 16S-23S ITS secondary structure analyses on cyanobacteria of the family Leptolyngbyaceae. These analyses focused on filamentous strains sampled from thermal springs with a morphology ascribable to the genus Leptolyngbya. The phylogenetic reconstructions showed that the Leptolyngbya-like thermal strains grouped into a monophyletic lineage that was distinct from Leptolyngbya. The 16S-23S ITS secondary structure results supported the separation of this cluster. A new genus named Thermoleptolyngbya was erected to encompass these strains, and two species were described inside this new taxon: T. albertanoae and T. oregonensis.

  16. PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea.

    Science.gov (United States)

    Pecchia, S; Mercatelli, E; Vannacci, G

    1998-09-01

    Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes Apal, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates. PMID:9741081

  17. Subfamilial relationships within solanaceae as inferred from atp beta-rbcl intergenic spacer

    International Nuclear Information System (INIS)

    A phylogenetic analysis of family Solanaceae was conducted using sequence data from the chloroplast intergenic atp beta-rbcL spacer. Sequence data was generated from 17 species representing 09 out of 14 genera of Solanaceae from Pakistan. Cladogram was constructed using maximum parsimony method and results indicate that Solanaceae is mainly divided into two subfamilies; Solanoideae and Cestroideae. Four major clades within Solanoideae represent tribes; Physaleae, Capsiceae, Datureae and Solaneae are supported by high bootstrap value and the relationships among them are not corroborating with the previous studies. The findings established that subfamily Cestroideae comprised of three genera; Cestrum, Lycium and Nicotiana with high bootstrap support. Position of Nicotiana inferred with atp beta-rbcL sequence is congruent with traditional classification, which placed the taxa in Cestroideae. In the current study Lycium unexpectedly nested with Nicotiana with 100% bootstrap support and identified as a member of tribe Nicotianeae. Expanded sampling of other genera from Pakistan could be valuable towards improving our understanding of intrafamilial relationships within Solanaceae. (author)

  18. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens).

    Science.gov (United States)

    Kakou, Bidénam; Angers, Bernard; Glémet, Hélène

    2016-03-01

    The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish. PMID:26841134

  19. Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling

    OpenAIRE

    Neumann Elisabeth; Teixeira Santuza MR; Horta Maria F; Mota Rodrigo M; Moreira João; Nicoli Jacques R.; Nunes Álvaro C

    2005-01-01

    Abstract Background The accurate identification of Lactobacillus and other co-isolated bacteria during microbial ecological studies of ecosystems such as the human or animal intestinal tracts and food products is a hard task by phenotypic methods requiring additional tests such as protein and/or lipids profiling. Results Bacteria isolated in different probiotic prospecting studies, using de Man, Rogosa and Sharpe medium (MRS), were typed at species level by PCR amplification of 16S-23S rRNA i...

  20. An improved PCR method for direct identification of Porphyra (Bangiales, Rhodophyta) using conchocelis based on a RUBISCO intergenic spacer

    Institute of Scientific and Technical Information of China (English)

    WANG Chao; DONG Dong; WANG Guangce; ZHANG Baoyu; PENG Guang; XU Pu; TANG Xiaorong

    2009-01-01

    An improved method of PCR in which the small segment of conchocelis is amplified directly without DNA extraction was used to amplify a RUBISCO intergenic spacer DNA fragment from nine species of red algal genus Porphyra (Bangiales, Rhodophyta), including Porphyra yezoensis (Jiangsu, China), P. haitanensis (Fujian, China), P. oligospermatangia (Qingdao, China), P. katadai (Qingdao, China), P. tenera (Qingdao, China), P. suborboculata (Fujian, China), P. pseudolinearis (Kogendo, Korea), P. linearis (Devon, England), and P. fallax (Seattle, USA). Standard PCR and the method developed here were both conducted using primers specific for the RUBISCO spacer region, after which the two PCR products were sequenced. The sequencing data of the amplicons obtained using both methods were identical, suggesting that the improved PCR method was functional. These findings indicate that the method developed here may be useful for the rapid identification of species of Porphyra in a germplasm bank. In addition, a phylogenetic tree was constructed using the RUBISCO spacer and partial rbcS sequence, and the results were in concordant with possible alternative phylogenies based on traditional morphological taxonomic characteristics, indicating that the RUBISCO spacer is a useful region for phylogenetic studies.

  1. 16S rRNA、16S-23S rRNA基因测序分析检测主要血流感染病原菌比较%Comparison of the role of 16S rRNA and 16S-23S rRNA gene sequence-based identification of bacteria in bloodsteam infection

    Institute of Scientific and Technical Information of China (English)

    金中淦; 葛平; 徐蓉; 陈蓉; 宣瑛; 刘学杰; 王庆忠

    2012-01-01

    目的 比较细菌16S rRNA、16S-23S rRNA基因测序分析在血流感染病原菌检测中的作用.方法 提取临床上血流感染常见的金黄色葡萄菌、表皮葡萄球菌、大肠埃希菌、粪肠球菌、肺炎链球菌、铜绿假单胞菌、阴沟肠杆菌、鲍曼不动杆菌、洛菲不动杆菌、肺炎克雷伯杆菌、化脓性链球菌、奇异变形杆菌、潘尼变形杆菌、屎肠球菌、粘质沙雷菌、宋内志贺菌、产气肠杆菌、小肠结肠炎耶尔森菌、腐生葡萄球菌基因组DNA,运用16S rRNA、16S-23S rRNA基因进行PCR扩增.扩增产物经测序后在美国国家生物技术中心( NCBI)上进行比对分析,确定菌种.结果 在所分析的19种临床血流感染常见细菌中,16S rRNA基因测序分析可将除粘质沙雷菌外的细菌鉴定到种的水平,但无法完全区分近缘种属;16S-23SrRNA成功鉴定17种细菌,除大肠埃希菌、宋内志贺菌外所有细菌均成功鉴定到单一种的水平.结论 16S-23S rRNA基因可作为血流感染细菌检测较好的分子靶标.

  2. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    Science.gov (United States)

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.

  3. Characterization of mitochondrial control region, two intergenic spacers and tRNAs of Zaprionus indianus (Diptera: Drosophilidae).

    Science.gov (United States)

    da Silva, Norma Machado; de Souza Dias, Aline; da Silva Valente, Vera Lúcia; Valiati, Victor Hugo

    2009-12-01

    The control region in insects is the major noncoding region in animal mitochondrial DNA (mtDNA), and is responsible for a large part of the variation in the DNA sequence and size of the genome of this organelle. In this study, the mtDNA control region, two intergenic spacers and tRNA genes of a Zaprionus indianus strain were cloned, sequenced and compared with other Drosophila species. The overall A+T content in the Z. indianus control region is 94.3%, and a comparison with other Drosophila species demonstrated that the most conserved region appears to be the 420 base pairs nearest to the tRNA(ile), similar to the findings of other authors. We also describe conserved sequence blocks, including a poly-T involved in the replication process of Drosophila mtDNA; a putative secondary structure also involved in the replication process and repeated sequences. tRNA(ile) sequence demonstrated the greatest variability when the tRNA sequences of species were compared.

  4. A comparison of fungal communities from four salt marsh plants using automated ribosomal intergenic spacer analysis (ARISA).

    Science.gov (United States)

    Torzilli, Albert P; Sikaroodi, Masoumeh; Chalkley, David; Gillevet, Patrick M

    2006-01-01

    Fungal decomposers are important contributors to the detritus-based food webs of salt marsh ecosystems. Knowing the composition of salt marsh fungal communities is essential in understanding how detritus processing is affected by changes in community dynamics. Automated ribosomal intergenic spacer analysis (ARISA) was used to examine the composition of fungal communities associated with four temperate salt marsh plants, Spartina alterniflora (short and tall forms), Juncus roemerianus, Distichlis spicata and Sarcocornia perennis. Plant tissues were homogenized and subjected to a particle-filtration protocol that yielded 106 microm particulate fractions, which were used as a source of fungal isolates and fungal DNA. Genera identified from sporulating cultures demonstrated that the 106 microm particles from each host plant were reliable sources of fungal DNA for ARISA. Analysis of ARISA data by principal component analysis (PCA), principal coordinate analysis (PCO) and species diversity comparisons indicated that the fungal communities from the two grasses, S. alterniflora and D. spicata were more similar to each other than they were to the distinct communities associated with J. roemerianus and S. perennis. Principal component analysis also showed no consistent, seasonal pattern in the composition of these fungal communities. Comparisons of ARISA fingerprints from the different fungal communities and those from pure cultures of selected Spartina ascomycetes supported the host/substrate specificity observed for the fungal communities.

  5. Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples.

    Directory of Open Access Journals (Sweden)

    Witoon Purahong

    Full Text Available Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub. Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.

  6. Phylogenetic analysis of the genus Avena based on chloroplast intergenic spacer psbA-trnH and single-copy nuclear gene Acc1.

    Science.gov (United States)

    Yan, Hong-Hai; Baum, Bernard R; Zhou, Ping-Ping; Zhao, Jun; Wei, Yu-Ming; Ren, Chang-Zhong; Xiong, Fang-Qiu; Liu, Gang; Zhong, Lin; Zhao, Gang; Peng, Yuan-Ying

    2014-05-01

    Two uncorrelated nucleotide sequences, chloroplast intergenic spacer psbA-trnH and acetyl CoA carboxylase gene (Acc1), were used to perform phylogenetic analyses in 75 accessions of the genus Avena, representing 13 diploids, seven tetraploid, and four hexaploids by maximum parsimony and Bayesian inference. Phylogenic analyses based on the chloroplast intergenic spacer psbA-trnH confirmed that the A genome diploid might be the maternal donor of species of the genus Avena. Two haplotypes of the Acc1 gene region were obtained from the AB genome tetraploids, indicating an allopolyploid origin for the tetraploid species. Among the AB genome species, both gene trees revealed differences between Avena agadiriana and the other species, suggesting that an AS genome diploid might be the A genome donor and the other genome diploid donor might be the Ac genome diploid Avena canariensis or the Ad genome diploid Avena damascena. Three haplotypes of the Acc1 gene have been detected among the ACD genome hexaploid species. The haplotype that seems to represent the D genome clustered with the tetraploid species Avena murphyi and Avena maroccana, which supported the CD genomic designation instead of AC for A. murphyi and A. maroccana.

  7. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

    Science.gov (United States)

    Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

  8. Differentiation between Aspergillus flavus and Aspergillus parasiticus from Pure Culture and Aflatoxin-Contaminated Grapes Using PCR-RFLP Analysis of aflR-aflJ Intergenic Spacer

    International Nuclear Information System (INIS)

    Aflatoxins (AFs) represent the most important single mycotoxin-related food safety problem in developed and developing countries as they have adverse effects on human and animal health. They are produced mainly by Aspergillus flavus and A. parasiticus. Both species have different aflatoxinogenic profile. In order to distinguish between A. flavus and A. parasiticus, gene-specific primers were designed to target the intergenic spacer (IGS) for the AF biosynthesis genes, aflJ and aflR. Polymerase chain reaction (PCR) products were subjected to restriction endonuclease analysis using BglII to look for restriction fragment length polymorphisms (RFLPs). Our result showed that both species displayed different PCR-based RFLP (PCR-RFLP) profile. PCR products from A. flavus cleaved into 3 fragments of 362, 210, and 102 bp. However, there is only one restriction site for this enzyme in the sequence of A. parasiticus that produced only 2 fragments of 363 and 311 bp. The method was successfully applied to contaminated grapes samples. This approach of differentiating these 2 species would be simpler, less costly, and quicker than conventional sequencing of PCR products and/or morphological identification. (author)

  9. Identification of Staphylococcus saprophyticus isolated from patients with urinary tract infection using a simple set of biochemical tests correlating with 16S-23S interspace region molecular weight patterns.

    Science.gov (United States)

    Ferreira, Adriano Martison; Bonesso, Mariana Fávero; Mondelli, Alessandro Lia; da Cunha, Maria de Lourdes Ribeiro de Souza

    2012-12-01

    The emergence of Staphylococcus spp. not only as human pathogens, but also as reservoirs of antibiotic resistance determinants, requires the development of methods for their rapid and reliable identification in medically important samples. The aim of this study was to compare three phenotypic methods for the identification of Staphylococcus spp. isolated from patients with urinary tract infection using the PCR of the 16S-23S interspace region generating molecular weight patterns (ITR-PCR) as reference. All 57 S. saprophyticus studied were correctly identified using only the novobiocin disk. A rate of agreement of 98.0% was obtained for the simplified battery of biochemical tests in relation to ITR-PCR, whereas the Vitek I system and novobiocin disk showed 81.2% and 89.1% agreement, respectively. No other novobiocin-resistant non-S. saprophyticus strain was identified. Thus, the novobiocin disk is a feasible alternative for the identification of S. saprophyticus in urine samples in laboratories with limited resources. ITR-PCR and the simplified battery of biochemical tests were more reliable than the commercial systems currently available. This study confirms that automated systems are still unable to correctly differentiate CoNS species and that simple, reliable and inexpensive methods can be used for routine identification.

  10. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

    Directory of Open Access Journals (Sweden)

    Su Ying-Juan

    2011-04-01

    Full Text Available Abstract Background The rpoB-psbZ (BZ region of some fern plastid genomes (plastomes has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. Results A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii the trnY-trnE intergenic spacer (IGS of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv ycf66 has independently lost at least four times in ferns. Conclusions Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.

  11. Application of the Sequences Analysis of the 16S rRNA Gene and ITS of 16S-23S rRNA to the Systematic Study of the Genus Arthrospira and Spirulina%16S rRNA基因与16S-23S rRNA转录单元内间隔区序列分析及其在节旋藻和螺旋藻分类鉴定中的应用

    Institute of Scientific and Technical Information of China (English)

    茅云翔; 杨官品; 张宝红; 张学成

    2001-01-01

    测定了节旋藻属3个品系和螺旋藻属1个品系的全长16S rRNA基因和16S-23S rRNA转录单元内间隔区序列(ITS),分析了已知的节旋藻、螺旋藻和相关品系的相应序列的同源性,构建了系统发生树,并评价了这两段DNA序列在节旋藻、螺旋藻种属分类和种质鉴定中的意义.结果表明:(1)16S rRNA基因序列和ITS序列均可用于节旋藻属和螺旋藻属的属间分类,以两序列为基础的系统学分析结果一致;(2)ITS序列变异程度高于16S rDNA序列,适用于节旋藻和螺旋藻属内品系或种质鉴定;(3)节旋藻属可明确界定,16S rRNA基因序列相似性大于98%,ITS序列相似性大于88%;(4)螺旋藻属某些品系间16S rDNA序列和ITS序列相似性较低,与不同属间的序列相似性程度为同一水平.

  12. 巴戟天及其伪品的psbA-trnH序列鉴定%Molecular identification of psbA-trnH intergenic spacers' sequences of Morinda officinalis How and its counterfeit species

    Institute of Scientific and Technical Information of China (English)

    姬生国; 王东; 张春荣; 张宏意

    2011-01-01

    Objective To perform the molecular identification for Morinda officinalis and its counterfeit species based on psbA-trnH intergenic spacers' sequences. Methods Total DNA was extracted and gene sequence was amplified by PCR. PCR product was directly sequenced after purification. Sequences were analyzed with Clustral X and MEGA 3.1 software. Results The length of psbA-trnH intergenic spacers'sequences was 306 bp. Distinctive variation sites among them can be observed. Conclusion The psbA-trnH intergenic spacers' sequences could be used to identificate Morinda officinalis and its counterfeit species.%目的 利用叶绿体基因psbA-trnH间区序列探讨巴戟天及其常见伪品大果巴戟、樟叶巴戟、羊角藤、虎刺的分子鉴定方法.方法 分别提取巴戟天及其伪品植物的总DNA,经PCR扩增纯化后,测序,利用Clustal X和MEGA 3.1软件对序列进行分析.结果 各样品psbA-trnH序列长度为306 bp,巴戟天及其伪品之间存在多个特异性信息位点.结论 psbA-trnH序列可作为巴戟天分子鉴定的依据.

  13. Identification of Trichosporon spp. Strains by Sequencing D1/D2 Region and Sub-typing by Sequencing Ribosomal Intergenic Spacer Region of Ribosomal DNA

    Institute of Scientific and Technical Information of China (English)

    Jingsi ZENG; Cristina Maria de Souza Motta; Kazutaka Fukushima; Kayoko Takizawa; Oliane Maria Correia Magalhes; Rejane Pereira Neves; Kazuko Nishimura

    2009-01-01

    To re-identify and further group 25 isolates of Trichosporon spp. identified morphologically previously, sequences of D1/D2 region of large subunit (LSU) of ribosomal DNA (rDNA) of 25 tested strains for identification and those of ribosomal intergenic space 1 (IGS1) region of 11 strains for sub-grouping were detected. The identifications of tested strains were changed except 6 strains. According to the alignment of the IGS1 region, 6 T. asahii isolates tested fell into 4 groups and 5 T. faecale isolates into 3 groups. Polymorphism of 2 T.japonicum isolates was found in 10 positions. With the alignments obtained in this research compared with the relative GenBank entries, it was found that T. asahii, T.faecale and T.japonicum species were divided into 7, 3 and 2 subtypes respectively. Morphological and biophysical methods are not sufficient for Trichosporon spp. identification. Sequencing becomes neces-sary for Trichosporon diagnosis. There is obvious diversity within a species.

  14. Identification of Biomphalaria havanensis and Biomphalaria obstructa populations from Cuba using polymerase chain reaction and restriction fragment length polymorphism of the ribosomal RNA intergenic spacer

    Directory of Open Access Journals (Sweden)

    Teofânia HDA Vidigal

    2001-07-01

    Full Text Available In Cuba, several Biomphalaria species have been reported such as B. orbignyi, B. schrammi, B. helophila, B. havanensis and B. peregrina; only the latter three are considered as potential hosts of Schistosoma mansoni. The specific identification of Biomphalaria species is based on anatomical and morphological characters of genital organs and shells. The correct identification of these snails is complicated by the high variation in these characters, similarity among species and in some cases by the small size of the snails. In this paper, we reported the classical morphological identification, the use of PCR and RFLP analysis of the internal transcribed spacer region of the ribosomal RNA genes for molecular identification of seven snail populations from different localities in Cuba. Using morphological and molecular analysis, we showed that among the studied Cuban Biomphalaria populations only B. havanensis and B. obstructa species were found.

  15. Trypanosoma cruzi I genotypes in different geographical regions and transmission cycles based on a microsatellite motif of the intergenic spacer of spliced-leader genes.

    Science.gov (United States)

    Cura, Carolina I; Mejía-Jaramillo, Ana M; Duffy, Tomás; Burgos, Juan M; Rodriguero, Marcela; Cardinal, Marta V; Kjos, Sonia; Gurgel-Gonçalves, Rodrigo; Blanchet, Denis; De Pablos, Luis M; Tomasini, Nicolás; da Silva, Alexandre; Russomando, Graciela; Cuba, Cesar A Cuba; Aznar, Christine; Abate, Teresa; Levin, Mariano J; Osuna, Antonio; Gürtler, Ricardo E; Diosque, Patricio; Solari, Aldo; Triana-Chávez, Omar; Schijman, Alejandro G

    2010-12-01

    The intergenic region of spliced-leader (SL-IR) genes from 105 Trypanosoma cruzi I (Tc I) infected biological samples, culture isolates and stocks from 11 endemic countries, from Argentina to the USA were characterised, allowing identification of 76 genotypes with 54 polymorphic sites from 123 aligned sequences. On the basis of the microsatellite motif proposed by Herrera et al. (2007) to define four haplotypes in Colombia, we could classify these genotypes into four distinct Tc I SL-IR groups, three corresponding to the former haplotypes Ia (11 genotypes), Ib (11 genotypes) and Id (35 genotypes); and one novel group, Ie (19 genotypes). Genotypes harbouring the Tc Ic motif were not detected in our study. Tc Ia was associated with domestic cycles in southern and northern South America and sylvatic cycles in Central and North America. Tc Ib was found in all transmission cycles from Colombia. Tc Id was identified in all transmission cycles from Argentina and Colombia, including Chagas cardiomyopathy patients, sylvatic Brazilian samples and human cases from French Guiana, Panama and Venezuela. Tc Ie gathered five samples from domestic Triatoma infestans from northern Argentina, nine samples from wild Mepraia spinolai and Mepraia gajardoi and two chagasic patients from Chile and one from a Bolivian patient with chagasic reactivation. Mixed infections by Tc Ia+Tc Id, Tc Ia+Tc Ie and Tc Id+Tc Ie were detected in vector faeces and isolates from human and vector samples. In addition, Tc Ia and Tc Id were identified in different tissues from a heart transplanted Chagas cardiomyopathy patient with reactivation, denoting histotropism. Trypanosoma cruzi I SL-IR genotypes from parasites infecting Triatoma gerstaeckeri and Didelphis virginiana from USA, T. infestans from Paraguay, Rhodnius nasutus and Rhodnius neglectus from Brazil and M. spinolai and M. gajardoi from Chile are to our knowledge described for the first time.

  16. Molecular organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural features and evolution of piscine 5S rRNA genes and nontranscribed intergenic spacers.

    Science.gov (United States)

    Pasolini, Paola; Costagliola, Domenico; Rocco, Lucia; Tinti, Fausto

    2006-05-01

    The genomic and gene organisation of 5S rDNA clusters have been extensively characterized in bony fish and eukaryotes, providing general issues for understanding the molecular evolution of this multigene DNA family. By contrast, the 5S rDNA features have been rarely investigated in cartilaginous fish (only three species). Here, we provide evidence for a dual 5S rDNA gene system in the Rajidae by sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) in five Mediterranean species of rays (Rajidae), and in a large number of piscine taxa including lampreys and bony fish. As documented in several bony fish, two functional 5S rDNA types were found here also in the rajid genome: a short one (I) and a long one (II), distinguished by distinct 5S and NTS sequences. That the ancestral piscine genome had these two 5S rDNA loci might be argued from the occurrence of homologous dual gene systems that exist in several fish taxa and from 5S phylogenetic relationships. An extensive analysis of NTS-II sequences of Rajidae and Dasyatidae revealed the occurrence of large simple sequence repeat (SSR) regions that are formed by microsatellite arrays. The localization and organization of SSR within the NTS-II are conserved in Rajiformes since the Upper Cretaceous. The direct correlation between the SSRs extension and the NTS length indicated that they might play a role in the maintenance of the larger 5S rDNA clusters in rays. The phylogenetic analysis indicated that NTS-II is a valuable systematic tool limited to distantly related taxa of Rajiformes. PMID:16612546

  17. Molecular phylogeny of several common Gracilaria species in-ferred from 18S rRNA, cox2-3 intergenic spacer and RUBISCO spacer sequence comparisons%几种江蓠属海藻3个分子序列的系统学分析

    Institute of Scientific and Technical Information of China (English)

    赵小波; 逄少军; 刘峰

    2013-01-01

      分析了我国沿海几种常见的江蓠属(Gracilaria)海藻的18S rRNA 基因、cox2-3间隔区以及RUBISCO间隔区的分子序列,并结合GenBank现有的相关数据进行了分子系统学关系分析,为江蓠属的系统进化和分类地位提供了新的佐证。结果表明,基于cox2-3间隔区、以及 RUBISCO间隔区序列构建的MP (Maximum parsimony)进化树较为相似,而与基于18S rRNA构建的进化树略有不同。这主要是由于18S rRNA更为保守的原因;扁江蓠与脆江蓠在3个系统树中均聚合成支,显示了它们之间具有较近的亲缘关系;龙须菜与江蓠属海藻具有较远的遗传距离,在3个进化树中,龙须菜也均位于进化树的基部,单独成支,证实龙须菜并不隶属于江蓠属,且分化相对较早。%Sequences of three molecular markers (18S rRNA, cox2-3 intergenic spacer and RUBISCO spacer), in combination with data from GenBank, were used to analyze the phylogentic relations of Gracilaria species col-lected from the coast of China. Phylogenetic trees that were constructed using cox2-3 and RUBISCO spacer se-quences exhibited the same pattern but differed slightly from that of the 18S rRNA-based phylogenetic tree due to a higher degree of conservation of the latter. Gracilaria textorii was sister to G. chouae in all three trees showing the close relationship between the two species. The results further confirm that the Gracilariopsis lemaneiformis does not belong to the genus Gracilaria. Results also indicate an earlier evolution status of G.lemaneiformis based on these three sequence comparisons.

  18. DEVELOPMENT OF INTERGENIC SPACERS BASED PCR ASSAY FOR DETECTION OF GIARDIALAMBLIA%犬猫贾第虫IGS序列特异性检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    李雅文; 刘远佳; 郑国超; 谭立娉; 胡伟; 罗琴; 林丽琴; 路鹏云; 李国清

    2013-01-01

    The intergenic spacers (IGS) were amplified in PCR from nuclear ribosomal DNAs of two Giardialamblia strains (assemble D from dog and assemble F from cat) isolated from feces of naturally infected pets in Guangzhou. The PCR products were purified, cloned and sequenced. The resulting nucleotide sequences were compared with related sequences in the GenBank databases. The IGS sequences were 1355 bp for the canine Giardia strain and 1388 bp for the feline Giardia strain. The interspecific difference in the IGS sequence might serve as a genetic marker for the identification and differentiation of Giardia lamblia. Furthermore, a PCR detection method was developed based on IGS sequence. The established PCR assay specifically amplified IGS sequence of G. lamblia but not all control parasites such as Toxocaracanis etc. The minimum detection limit of G.lamblia was 82 fg. Total 84 clinical samples were tested using this method. The positive rate of clinical samples was 3.57%, higher than 2.38%by traditional method.%应用PCR技术对广州市某宠物寄养所采集的一株D型犬源贾第虫和一株F型猫源贾第虫的核糖体IGS序列进行了扩增、克隆、测序,将测序结果与GenBank已上传的贾第虫相应序列进行比对分析,基于贾第虫IGS序列建立了具有良好特异性和敏感性的PCR检测方法,并对84份临床粪样进行了检测。结果显示,D型犬源贾第虫和F型猫源贾第虫的IGS序列长分别为1355 bp和1388 bp,贾第虫IGS序列存在多态性现象,种间差异明显,可以作为区分不同基因型的分子标记;建立的PCR方法能特异性扩增犬源贾第虫核糖体IGS序列,而犬蛔虫等对照虫体DNA均不能扩增,该方法对贾第虫DNA的最小检测量为82 fg,对84份临床粪样的检出率为3.57%,比传统镜检法高出2.38%,具有一定的临床应用价值。

  19. Sequence length variation of internal genic space of 16S rDNA-23S rDNA in biohydrogen-bacterium%产氢菌的16S -23S rDNA间隔区的长度变异性分析

    Institute of Scientific and Technical Information of China (English)

    李永峰; 郑国香; 张文启; 李建政; 胡立杰

    2005-01-01

    生物制氢细菌Rennanqilyf3的16S rRNA gene (rDNA)-23S rDNA间隔区碱基序列被测定.利用PCR扩增间隔区DNA,间隔区碱基序列存在长度多态现象.用这一长度多态现象进行产氢发酵细菌的辨认和识别.产氢发酵细菌Rennanqilyf3的16S rRNA gene (rDNA)-23S rDNA间隔区的PCR产品从1 270 到398 bp,共有5个序列.碱基数目分别为1 270、398、638、437 和 436 bp.%A method based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions was developed for the identification of species for fermentative biohydrogen-producing bacterium. The sizes of the PCR products varied from 1 270 to 398 bp. Strain of Rennanqilyf3 were characterized as having products of 1 270,398,638, 437 and 436bp.

  20. Local repeat sequence organization of an intergenic spacer in the chloroplast genome of Chlamydomonas reinhardtii leads to DNA expansion and sequence scrambling: a complex mode of “copy-choice replication”?

    Indian Academy of Sciences (India)

    Mahendra D Wagle; Subhojit Sen; Basuthkar J Rao

    2001-12-01

    Parent-specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA of Chlamydomonas reinhardtii. Such parent-specific RAPD bands (genomic fingerprints) segregated uniparentally (through mt+) in a cross between a pair of polymorphic interfertile strains of Chlamydomonas (C. reinhardtii and C. minnesotti), suggesting that they originated from the chloroplast genome. Southern analysis mapped the RAPD-markers to the chloroplast genome. One of the RAPD-markers, ``P2” (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3′ end of 23S, full 5S and intergenic region between 5S and psbA. This region seems divergent enough between the two parents, such that a specific PCR designed for a parental specific chloroplast sequence within this region, amplified a marker in that parent only and not in the other, indicating the utility of RAPD-scan for locating the genomic regions of sequence divergence. Remarkably, the RAPD-product, ``P2” seems to have originated from a PCR-amplification of a much smaller (about 600 bp), but highly repeat-rich (direct and inverted) domain of the 3 kb region in a manner that yielded no linear sequence alignment with its own template sequence. The amplification yielded the same uniquely ``sequence-scrambled” product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product, a ``unique” new sequence, had lost the repetitive organization of the template genome where it had originated from and perhaps represented a ``complex path” of copy-choice replication.

  1. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.

    Science.gov (United States)

    Nguyen, Huu-Vang; Gaillardin, Claude; Neuvéglise, Cécile

    2009-06-01

    The intergenic spacer rDNA amplification and AluI fingerprinting (IGSAF) method detected four distinct groups among 170 Debaryomyces hansenii strains: D. hansenii var. hansenii; Candida famata var. famata; D. hansenii var. fabryi and C. famata var. flareri. IGS sequence comparison of representative strains showed that D. hansenii var. hansenii and C. famata var. famata belonged to one species, whereas D. hansenii var. fabryi and C. famata var. flareri belonged to two different ones. This confirmed the following three species recently reinstated: D. hansenii (=C. famata), Debaryomyces fabryi and Debaryomyces subglobosus (=Candida flareri). Accordingly, growth at 37 degrees C may no longer be used to differentiate D. hansenii from D. fabryi. Riboflavin production is more specific for D. fabryi and D. subglobosus strains. IGSAF identified all the other 17 species of the genus Debaryomyces, six of them sharing with D. hansenii an rRNA gene unit harbouring two 5S rRNA genes. The phylogenetic tree established with IGS sequences was congruent with the one based on ACT1, GPD1 and COX2 sequences depicting a distinct D. hansenii clade close to the D. subglobosus, Debaryomyces prosopidis and D. fabryi clade. Description of Debaryomyces vietnamensis sp. nov. (type strain CBS 10535(T), MUCL 51648(T)), closely related to Debaryomyces nepalensis is given. PMID:19385997

  2. The Origin of Garden Chrysanthemums and Molecular Phylogeny of Dendranthema in China based on Nucleotide Sequences of nrDNA ITS, trnT-trnL and trnL-trnF Intergenic Spacer Regions in cpDNA%基于核糖体DNA的ITS序列和叶绿体trnT-trnL及trnL-trnF基因间区的菊花起源与中国菊属植物分子系统学研究

    Institute of Scientific and Technical Information of China (English)

    赵惠恩; 汪小全; 陈俊愉; 洪德元

    2003-01-01

    Several sequences were applied to resolve phylogenetic relationships within Dendranthema and clarify the origin of garden chrysanthemums including sequences of nrDNA ITS, trnT-trnL and trnL-trnF intergenic spacer regions in cpDNA. The relationships among the species are so close that the three sequences could only provide limited information. From the evidence presented, we suggest that: ① D.rhmobifolium be the chloroplast donor of D.vestitum (HN) with the resembling morphology and the same trnT/L IGS sequence. ② D.vestitum, a putative ancestor, may be not the chloroplast donor of garden chrysanthemums. D.lavand-ulifolium might be the chloroplast donor of the type population of D.indicum (HN) or the direct chloroplast donor of the ancient garden chrysanthemum cultivar. ③ D.zawaskii might be not the ancestor of garden chrysanthemums.

  3. Identification of Streptococcus species and Haemophilus influenzae by direct sequencing of PCR products from 16S-23SrDNA intergenic spacer regions%16S-23SrDNA间区序列在链球菌和流感嗜血杆菌分类的应用

    Institute of Scientific and Technical Information of China (English)

    鲁辛辛; 杨持; 黎琳; 杨宏欣

    2002-01-01

    Objective To set up a rapid and simple method for identificating bacteria by 16S-23SrDNA intergenic spacer regions (ISRs). Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning. Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program.Results There was only a single product in streptococcus genus after PCR amplification of 16S-23SrDNA ISRs. Five streptococcal species were obtained from 7 strains of streptococcus. Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H. influenzae). The sequence data showed that they all belonged to H. influenzae type b on GenBank databases.Conclusion PCR and direct sequencing of 16S-23SrDNA ISRs were very successful methods for bacterial species identification.%目的利用16S-23SrRNA间区的特征建立一种简单、快速的细菌分类方法.方法以化脓性链球菌16SrRNA的3'端和23SrRNA的5'端的保守区中合成3对引物,PCR扩增16S-23SrDNA ISRs,纯化后直接测序,在GenBank上查找对应细菌的ISRs序列.用DNAMAN软件进行系统进化分析.结果链球菌属为单拷贝16S-23SrRNA ISRs片段,编码1个tRNAAla基因.流感嗜血杆菌各生物型出现2个大小相似的ISRs片段.与GenBank上的资料比较,7株链球菌归属5个种,流感嗜血杆菌均为b型.结论 ISRs作为细菌分类新的目标基因具有属、种、型和株特异性与灵敏性.

  4. Molecular identfication and virulence of three Aeromonas hydrophila isolates cultured from infected channel catfish during a disease outbreak in West Alabama (USA) in 2009

    Science.gov (United States)

    Three isolates (AL09-71, AL09-72, and AL09-73) of Aeromonas hydrophila were cultured from infected channel catfish during a disease outbreak in West Alabama in August 2009. Sequence analysis of 16S-23S rDNA intergenic spacer region (ISR), cpn60, gyrB, and rpoD genes of the three strains revealed tha...

  5. Differentiation of Actinobacillus pleuropneumoniae strains by sequence analysis of 16S rDNA and ribosomal intergenic regions, and development of a species specific oligonucleotide for in situ detection

    DEFF Research Database (Denmark)

    Fussing, Vivian; Paster, Bruce J.; Dewhirst, Floyd E.;

    1998-01-01

    . The larger RIS's were different between the 3 species tested. The sequence of the 16S ribosomal gene was determined for 8 serotypes of A. pleuropneumoniae. These sequences showed only minor base differences, indicating a close genetic relatedness of these serotypes within the species. An oligonucleotide DNA...... probe designed from the 16S rRNA gene sequence of A. pleuropneumoniae was specific for all strains of the target species and did not cross react with A. lignieresii, the closest known relative of A. pleuropneumoniae. This species-specific DNA probe labeled with fluorescein was used for in situ....... pleuropneumoniae. Amplification and sequence analysis of the 16S-23S rDNA ribosomal intergenic sequence (RIS) from the three species showed the existence of two RIS's, differing by about 100 bp. Both sequences contained a region resembling the ribonuclease III cleavage site found in Escherichia coli. The smaller...

  6. Intragenomic heterogeneity of the 16S rRNA-23S rRNA internal transcribed spacer among Pseudomonas syringae and Pseudomonas fluorescens strains.

    Science.gov (United States)

    Milyutina, Irina A; Bobrova, Vera K; Matveeva, Eugenia V; Schaad, Norman W; Troitsky, Alexey V

    2004-10-01

    The 16S-23S rRNA internal transcribed spacer regions (ITS1) from 14 strains of Pseudomonas syringae and P. fluorescens were sequenced. ITS1 exhibited significant sequence variability among different operons within a single genome. From 1 to 4 types of ITS1 were found in individual genomes of the P. syringae and P. fluorescens strains. A total of eight ITS1 types were identified among strains studied. The ITS1 nucleotide sequences consisted of conserved blocks including, among others, a stem-forming region of box B, tRNAIle and tRNAAla genes and several variable blocks. The differences in the variable regions were mostly due to insertions and/or deletions of nucleotide blocks. The intragenomic heterogeneity of ITS1 was brought about by different combinations of variable blocks, which possibly have resulted from recombination and horizontal transfer.

  7. Functionality of intergenic transcription: an evolutionary comparison.

    Directory of Open Access Journals (Sweden)

    Philipp Khaitovich

    2006-10-01

    Full Text Available Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.

  8. Functionality of Intergenic Transcription: An Evolutionary Comparison

    Science.gov (United States)

    Visagie, Johann; Giger, Thomas; Joerchel, Sabrina; Petzold, Ekkehard; Green, Richard E; Lachmann, Michael; Pääbo, Svante

    2006-01-01

    Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts. PMID:17040132

  9. Development of Primer Sets for Loop-Mediated Isothermal Amplification that Enables Rapid and Specific Detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae

    Directory of Open Access Journals (Sweden)

    Deguo Wang

    2015-05-01

    Full Text Available Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as targets, four sets of LAMP primers were designed for identification and differentiation of S. dysgalactiae, S. uberis and S. agalactiae. The detection limit of all four LAMP primer sets were 0.1 pg DNA template per reaction, the LAMP method with 16S rRNA gene and 16S-23S rRNA intergenic spacers as the targets can differentiate the three pathogens, which is potentially useful in epidemiological studies.

  10. Development of Primer Sets for Loop-Mediated Isothermal Amplification that Enables Rapid and Specific Detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae

    OpenAIRE

    Deguo Wang; Yanhong Liu

    2015-01-01

    Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as targets, four sets of LAMP primers were designed for identification and differentiation of S. dysgalactia...

  11. Intraspecific diversity within Diaporthe helianthi: evidence from rDNA intergenic spacer (IGS) sequence analysis.

    Science.gov (United States)

    Pecchia, Susanna; Mercatelli, Elisabetta; Vannacci, Giovanni

    2004-04-01

    Diaporthe helianthi is the causal agent of sunflower stem canker, a serious pathogen of sunflower in Europe but recorded sporadically in Italy. The genetic diversity of D. helianthi isolates from different geographic origins (Argentina, France, Italy, Yugoslavia, Romania) was investigated using IGS sequences. A 400 bp fragment of the portion of the IGS region flanking the 5' end of the 18S gene was amplified from each isolate. The aligned nucleotide sequences showed intraspecific sequence homology from 99-100% among French/Yugoslavian isolates to 95-100% among Italian isolates. French/Yugoslavian isolates shared 90-92% sequence homology with Italian isolates. The phylogenetic tree obtained from the aligned data revealed three separate groups. Group 1 included all isolates from France and former Yugoslavia and one isolate from Argentina; Group 2 included all Italian isolates and one isolate from Argentina. The most distantly related isolate was that from Romania (Group 3). The average genetic distances among isolates within Group 1 and within Group 2 were 0.22 and 3.29 respectively. The analysis showed that all isolates originating from countries where severe outbreaks of the disease are reported annually (France and former Yugoslavia) form a well defined taxon characterized by relatively low variability. This group is distinct from the group formed by isolates originating from Italy, whose variability is relatively much higher. Results obtained revealed a marked differentiation among pathogen isolates, and members of Group 1 seem not yet to have spread into Italian sunflower-growing areas. PMID:15180160

  12. Mixing vane grid spacer

    International Nuclear Information System (INIS)

    A spacer for a nuclear fuel reactor grid is described having intersecting spring retaining strips for forming fuel element receiving openings and mixing vanes formed at selected ones of the intersections of the strips. The vanes are angularly disposed relative to the strips and overlie predetermined openings at the intersections; each has an opening located above the intersection for improving its coolant flow mixing capability

  13. Caracterização da região espaçadora 16-23S rDNA para diferenciação de estirpes de rizóbios utilizadas na produção de inoculantes comerciais no Brasil Characterization of the spacer region 16-23S rDNA for differentiation of strains of rhizobia used in the production of commercial inoculants in Brazil

    Directory of Open Access Journals (Sweden)

    Andréia Mara Rotta Oliveira

    2012-08-01

    Full Text Available A identificação de estirpes de rizóbio tem sido feita pela especificidade por hospedeiros e ensaios microbiológicos tradicionais. Por constituírem um grupo filogeneticamente heterogêneo, diferentes técnicas moleculares têm sido empregadas para auxiliar na caracterização genética e na identificação de estirpes eficientes e competitivas para a produção de inoculantes. Este trabalho teve por objetivos caracterizar a região espaçadora 16S-23S rDNA das estirpes de rizóbios utilizadas nos inoculantes comercializados no Brasil para espécies leguminosas, utilizando a técnica da PCR em combinação com a de RFLP, e avaliar a possibilidade do uso desse marcador molecular como método auxiliar para identificação das estipes. A amplificação da região espaçadora 16-23 S rDNA das estirpes de rizóbios gerou fragmentos com tamanhos que variaram entre 700pb e 1350pb. Os produtos resultantes da amplificação foram submetidos à digestão com as endonucleases. Mps I, Dde I e Hae III. Os resultados obtidos neste estudo indicam a possibilidade do uso da técnica de PCR-RFLP da região espaçadora 16S-23S rDNA como marcador molecular para a diferenciar as estirpes de rizóbios, em complemento às técnicas microbiológicas tradicionais. Contudo, este marcador não é suficientemente discriminatório para ser usado na identificação das estirpes recomendadas para a produção de inoculantes comerciais.The identification of strains of rhizobia has been made by host specificity and regular microbiological tests. By forming a phylogenetically heterogeneous group, different molecular techniques have been employed to assist in the genetic characterization and identification of efficient and competitive strains for production of inoculants. This study aimed to characterize the spacer region 16S-23S rDNA of the strains of rhizobia used in commercial inoculants in Brazil for legume species, using PCR combined with RFLP, and assess the possibility

  14. Phylogenetic analysis of encapsulated and non-encapsulated Trichinella species by studying the 5S rDNA tandemly repeated intergenic region.

    Science.gov (United States)

    van der Giessen, J W B; Fonville, M; Briels, I; Pozio, E

    2005-09-01

    The identification of sequence regions in the genomes of pathogens which can be useful to distinguish among species and genotypes, is of great importance for epidemiological, molecular, and phylogenetic studies. The 5S ribosomal DNA intergenic spacer region has been identified as a good target to distinguish among eight Trichinella species and genotypes. The recent discovery of two non-encapsulated species in this genus, Trichinella papuae and Trichinella zimbabwensis, which can infect both mammals and reptiles, has suggested analyzing their 5S rDNA. Amplification of the tandem repeats of the 5S rDNA intergenic region of encapsulated species of Trichinella shows a 751bp fragment, whereas the three non-encapsulated species show a fragment of 800bp with T. pseudospiralis showing an additional fragment of 522bp. Although the size of the 800bp PCR fragments of T. papuae and T. zimbabwensis are similar to that of T. pseudospiralis, there are differences in the 5S rDNA intergenic regions among the three non-encapsulated species. Phylogenetic analysis of the 5S rDNA intergenic regions shows a clustering together of the three non-encapsulated Trichinella species that is well separated from the encapsulated ones. In addition, a single PCR-based method allows distinguishing non-encapsulated and encapsulated species. PMID:16076532

  15. Fleas and Flea-Associated Bartonella Species in Dogs and Cats from Peru.

    Science.gov (United States)

    Rizzo, M F; Billeter, S A; Osikowicz, L; Luna-Caipo, D V; Cáceres, A G; Kosoy, M

    2015-11-01

    In the present study, we investigated 238 fleas collected from cats and dogs in three regions of Peru (Ancash, Cajamarca, and Lima) for the presence of Bartonella DNA. Bartonella spp. were detected by amplification of the citrate synthase gene (16.4%) and the 16S-23S intergenic spacer region (20.6%). Bartonella rochalimae was the most common species detected followed by Bartonella clarridgeiae and Bartonella henselae. Our results demonstrate that dogs and cats in Peru are infested with fleas harboring zoonotic Bartonella spp. and these infected fleas could pose a disease risk for humans.

  16. First description of Trueperella (Arcanobacterium) bernardiae of animal origin.

    Science.gov (United States)

    Hijazin, M; Metzner, M; Erhard, M; Nagib, S; Alber, J; Lämmler, C; Hassan, A A; Prenger-Berninghoff, E; Zschöck, M

    2012-10-12

    In the present study a Trueperella (Arcanobacterium) bernardiae strain isolated from an anal swab of a three-day-old piglet could be identified phenotypically, by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and genotypically by sequencing the 16S rDNA, the 16S-23S rDNA intergenic spacer region (ISR) and by sequencing the superoxide dismutase A encoding gene sodA. The present study gives the first information about the presence of T. (A.) bernardiae in specimen of animals. PMID:22608102

  17. Strains of Mesorhizobium amorphae and M. tianshanense carrying symbiotic genes of common chickpea endosymbiotic species constitute a novel biovar (ciceri) able to nodulate Cicer arietinum

    OpenAIRE

    Rivas, Raul; Laranjo, Marta; Mateos, Pedro; Oliveira, Solange; Martínez-Molina, Eustoquio; Velázquez, Encarna

    2007-01-01

    Aims: To identify several strains of Mesorhizobium amorphae and Mesorhizobium tianshanense nodulating Cicer arietinum in Spain and Portugal, and to study the symbiotic genes carried by these strains. Methods and Results: The sequences of 16S-23S intergenic spacer (ITS), 16S rRNA gene and symbiotic genes nodC and nifH were analysed. According to their 16S rRNA gene and ITS sequences, the strains from this study were identified as M. amorphae and M. tianshanense. The type stra...

  18. Potential use of molecular-typing methods for the identification and characterization of salmonella enterica serotypes isolated in the poultry production chain

    Directory of Open Access Journals (Sweden)

    CM Baratto

    2012-09-01

    Full Text Available Salmonella is widespread in nature and can be found in all links of the poultry production chain. Due to its high impact on meat processing, techniques for the rapid detection and reproducible characterization of Salmonella serotypes in foods are needed. The present study investigated the potential of molecular profiling to identify and differentiate 15 Salmonella serotypes isolated from the poultry production chain, based on 5 primers by random amplified polymorphic DNA (RAPD, enterobacterial repetitive intergenic consensus (ERIC-PCR, amplification of rDNA internal spacer analysis (RISA, and amplified ribosomal DNA restriction analysis (ARDRA of 16S-23S rRNA internal spacer region (ISR cleaved with Alu I and Hha I restriction enzymes. Three isolates of each serotype were analyzed for the identification of similar and different profiles. Dendrograms were constructed from molecular profiles using the UPGMA method (unweighted pair-group method for the arithmetic averages and the software program WinBoot. The present study indicates the usefulness of RISA and ARDRA of the 16S-23S rRNA intergenic spacer region (ISR for systematic, epidemiological, and diagnostic purposes. Since these techniques can be used for the differentiation of serotypes, they are highly promising for the characterization of Salmonella serotypes and intra-serotypes. Data indicate that these techniques may be used to produce more consistent, reliable, and reproducible results in the identification and epidemiological study (traceability of Salmonella in the poultry industry.

  19. Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes

    DEFF Research Database (Denmark)

    Caro, Albert Pallejà; García-Vallvé, Santiago; Romeu, Antoni

    2009-01-01

    influence the stop codon usage or the spacing lengths between co-directional genes. RESULTS: The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large......ABSTRACT: BACKGROUND: In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may...... number of genes with the SD sequence concentrate this regulatory motif from 4 to 11 bps before the start codon. However, not all genes seem to have the SD sequence. Genes separated from 1 to 4 bps from a co-directional upstream gene show a high SD presence, though this regulatory signal is located...

  20. Spacer for a fuel element

    International Nuclear Information System (INIS)

    Spacers for fuel pins arranged to form congish fuel elements can be shaped as plates with openings in accordance with the fuel pin grid. Such a plate that covers the cross section of a fuel element consists according to the invention of at least two parts that are offset in the fuel element's longitudinal direction and joint hinge-like in at least one grid position. Thus, one has smaller parts that are easier to work on with due accuracy. The invention is designed in particular for breeder reactors and high-conversion reactors. (orig.)

  1. Detection of Chlamydophila psittaci from pigeons by polymerase chain reaction in Ahvaz

    Directory of Open Access Journals (Sweden)

    Masoud Ghorbanpoor

    2015-10-01

    Full Text Available Background and Objective: Chlamydophila psittaci is a lethal bacterium that causes endemic avian chlamydiosis, and respiratory psittacosis. Laboratory diagnosis of Chlamydophila psittaci is difficult by culture. This study was design to investigate the presence of Chlamydophila psittaci in collected pharyngeal swabs from asyptomatic pigeons by PCR.Materials and Methods: Pharyngeal samples from pigeons with no symptoms of disease (n=280 were collected during hot and cold seasons in different parts of Ahvaz. DNA was extracted from specimens and subjected to PCR targeting pmp genes and 16s-23s rRNA intergenic spacer of Cp. psittaci and chlamydiales specific primers.Results: Of 280 samples 2 (0.7% harbor were positive for chlamydiales (16s-23s intergenic spacer and Cp. psittaci specific genes (pmp gene.Conclusions: In this research the pigeons were asymptomatic carriers for Cp. psittaci in their respiratory discharges. These results suggest that Cp. psittaci infection of human can occur in very close and continuous contact with pigeons.

  2. Development of a High Performance Spacer Grid

    Energy Technology Data Exchange (ETDEWEB)

    Song, Kee Nam; Song, K. N.; Yoon, K. H. (and others)

    2007-03-15

    A spacer grid in a LWR fuel assembly is a key structural component to support fuel rods and to enhance the heat transfer from the fuel rod to the coolant. In this research, the main research items are the development of inherent and high performance spacer grid shapes, the establishment of mechanical/structural analysis and test technology, and the set-up of basic test facilities for the spacer grid. The main research areas and results are as follows. 1. 18 different spacer grid candidates have been invented and applied for domestic and US patents. Among the candidates 16 are chosen from the patent. 2. Two kinds of spacer grids are finally selected for the advanced LWR fuel after detailed performance tests on the candidates and commercial spacer grids from a mechanical/structural point of view. According to the test results the features of the selected spacer grids are better than those of the commercial spacer grids. 3. Four kinds of basic test facilities are set up and the relevant test technologies are established. 4. Mechanical/structural analysis models and technology for spacer grid performance are developed and the analysis results are compared with the test results to enhance the reliability of the models.

  3. Spacer for supporting fuel element boxes

    International Nuclear Information System (INIS)

    A spacer plate unit arranged externally on each side and at a predetermined level of a polygonal fuel element box for mutually supporting, with respect to one another, a plurality of the fuel element boxes forming a fuel element bundle, is formed of a first and a second spacer plate part each having the same length and the same width and being constituted of unlike first and second materials, respectively. The first and second spacer plate parts of the several spacer plate units situated at the predetermined level are arranged in an alternating continuous series when viewed in the peripheral direction of the fuel element box, so that any two spacer plate units belonging to face-to-face oriented sides of two adjoining fuel element boxes in the fuel element bundle define interfaces of unlike materials

  4. Variation in the Spacer Regions Separating tRNA Genes in Renibacterium salmoninarum Distinguishes Recent Clinical Isolates from the Same Location

    Science.gov (United States)

    Alexander, Sarah M.; Grayson, T. Hilton; Chambers, Edel M.; Cooper, Lynne F.; Barker, Gavin A.; Gilpin, Martyn L.

    2001-01-01

    A means for distinguishing between clinical isolates of Renibacterium salmoninarum that is based on the PCR amplification of length polymorphisms in the tRNA intergenic spacer regions (tDNA-ILPs) was investigated. The method used primers specific to nucleotide sequences of R. salmoninarum tRNA genes and tRNA intergenic spacer regions that had been generated by using consensus tRNA gene primers. Twenty-one PCR products were sequenced from five isolates of R. salmoninarum from the United States, England, and Scotland, and four complete tRNA genes and spacer regions were identified. Sixteen specific PCR primers were designed and tested singly and in all possible pairwise combinations for their potential to discriminate between isolates from recent clinical outbreaks of bacterial kidney disease (BKD) in the United Kingdom. Fourteen of the isolates were cultured from kidney samples taken from fish displaying clinical signs of BKD on five farms, and some of the isolates came from the same farm and at the same time. The tDNA-ILP profiles separated 22 clinical isolates into nine groups and highlighted that some farms may have had more than one source of infection. The grouping of isolates improved on the discriminatory power of previously reported typing methods based on randomly amplified polymorphic DNA analysis and restriction fragment length profiles developed using insertion sequence IS994. Our method enabled us to make divisions between closely related clinical isolates of R. salmoninarum that have identical exact tandem repeat (ETR-A) loci, rRNA intergenic spacer sequences, and IS994 profiles. PMID:11136759

  5. Application of spacer fabrics in composite production

    OpenAIRE

    Mecit, Diren; , Arzu Marmaralı

    2012-01-01

    Developments in the field of textile reinforced composites have been increasing in the last several years. In the first developed composite materials, fibers were used as reinforcement element. Textile materials such as staple fibers, bands, filament yarns, cables and two dimensional textiles are widely used as reinforcement elements in composite materials. Spacer fabrics consist of two outer surfaces and a connection layer between those outer surfaces. Spacer fabrics can be classified in the...

  6. Gemini surfactants with a disaccharide spacer.

    Science.gov (United States)

    Menger, F M; Mbadugha, B N

    2001-02-01

    A gemini surfactant is an amphiphile possessing (in sequence) the following: hydrocarbon tail/polar group/spacer/polar group/hydrocarbon tail. Widespread interest in geminis has emerged recently from both industrial and academic laboratories. In the present contribution, two related families of geminis have been synthesized, both with trehalose, a disaccharide, as a polar spacer. One family, Series-A, is nonionic and has amide groups separating the long chains from the trehalose spacer. The other family, Series-B, has quaternary ammonium ions connecting the long chains to the trehalose spacer. It was found that Series-A geminis are water insoluble despite the two amides and multiple hydroxyls. When hydrated or extruded, these geminis form microscopically visible vesicular and tubular structures above their transition temperatures (which were determined calorimetrically). Insoluble monomolecular films, constructed from these geminis, have interfacial areas that are dominated by the sugar spacer although intermolecular chain/chain interactions seem to stabilize the films. Thus, the behavior of Series-A geminis in many ways parallels that of phospholipids and simple double-chain surfactants. It is as if the trehalose is less of a spacer than a large but conventional headgroup. In contrast, cationic Series-B geminis are water soluble and form micelles with critical micelle concentrations an order of magnitude lower than that of corresponding conventional surfactants. Molecular modeling using the Amber force field explains the difference in properties between the two families of geminis. Series-A are tubular in shape and thus prefer bilayer packing as do other amphiphiles in which the headgroups are similar in width to the sum of the tail diameters. Series-B geminis are conical-shaped and pack more readily into spherical micelles. This work entails synthesis, tensiometry, conductance, microscopy, surface balance studies, calorimetry, light scattering, and molecular

  7. Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes

    Institute of Scientific and Technical Information of China (English)

    Anna-Magdalena BARNISKE; Thomas BORSCH; Kai M(U)LLER; Michael KRUG; Andreas WORBERG; Christoph NEINHUIS; Dietmar QUANDT

    2012-01-01

    Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales,and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns (group Ⅰ:trnL; group Ⅱ:petD,rpll6,trnK) and intergenic spacers (trnL-F,petB-petD,atpB-rbcL,rps3-rpll6) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes.Overall patterns of microstructural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group Ⅱ and group Ⅰ introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions (>14 000 aligned characters) converged to a backbone topology ofeudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales.Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.

  8. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  9. A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions.

    Directory of Open Access Journals (Sweden)

    Leonardo G Panunzi

    2014-05-01

    Full Text Available BACKGROUND: Trypanosoma cruzi is the causal agent of Chagas Disease. Recently, the genomes of representative strains from two major evolutionary lineages were sequenced, allowing the construction of a detailed genetic diversity map for this important parasite. However this map is focused on coding regions of the genome, leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence. METHODOLOGY: Using data from the hybrid CL Brener and Sylvio X10 genomes (from the TcVI and TcI Discrete Typing Units, respectively, we identified intergenic regions that share a common evolutionary ancestry, and are present in both CL Brener haplotypes (TcII-like and TcIII-like and in the TcI genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. The genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes. PRINCIPAL FINDINGS: Based on this analysis we have identified i a core of highly conserved intergenic regions, which remained essentially unchanged in independently evolving lineages; ii intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. A fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats.

  10. Separator-spacer for electrochemical systems

    Science.gov (United States)

    Grimes, Patrick G.; Einstein, Harry; Newby, Kenneth R.; Bellows, Richard J.

    1983-08-02

    An electrochemical cell construction features a novel co-extruded plastic electrode in an interleaved construction with a novel integral separator-spacer. Also featured is a leak and impact resistant construction for preventing the spill of corrosive materials in the event of rupture.

  11. Flow dynamics and concentration polarisation in spacer-filled channels

    DEFF Research Database (Denmark)

    Lipnizki, Jens; Jonsson, Gunnar Eigil

    2002-01-01

    . This phenomenon was also observed in spacer-filled channels. In this case the stripes on the surface depended on the spacer geometry. Furthermore, the experiments were used to calculate the energy consumption vs. the mass transfer coefficient for different spacers. This research can be used as a foundation...

  12. Heterogeneous diversity of spacers within CRISPR

    Science.gov (United States)

    Deem, Michael; He, Jiankui

    2011-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face. 1) J. He and M. W. Deem, Phys. Rev. Lett. 105 (2010) 128102

  13. Molecular profiling of microbial communities from contaminated sources: Use of subtractive cloning methods and rDNA spacer sequences. 1998 annual progress report

    International Nuclear Information System (INIS)

    'The major objective of the research is to provide appropriate sequences and to assemble a high-density DNA array of oligonucleotides that can be used for rapid profiling of microbial populations from polluted areas. The sequences to be assigned to the DNA array are chosen from from cloned genomic DNA sequences (the ribosomal operon, described below) from groundwater at DOE sites containing organic solvents. The sites, Hanford Nuclear Plant and Lawrence Livermore Site 300, have well characterized pollutant histories, which have been provided by the collaborators. At this mid-point of the project, over 60 unique sequence classes of intergenic spacer region have been identified from the first sample site. The use of these sequences as hybridization probes, and their frequency of occurrence, allow a clear distinction between bacterial communities before and after remediation by acetate/nitrate pumping. The authors have developed the hybridization conditions for identifying PCR products in a 96 well format, a versatile alignment and visualization program (acronym: MALIGN) developed by Dr. Dennis Maeder, has been used to align the ISRs, which are variable in length and sometimes in position of the tRNAs. Finally, in collaboration with Dr. W. Chen and Dr. J. Zhou at ORNL, they have significant evidence that mass spectrometer analysis can be used to determine the lengths of PCR amplified intergenic spacer DNA.'

  14. 特异性靶基因在弧菌PCR快速检测中的应用%Application of Specific Target Genes to PCR Rapid Detection for Vibrios

    Institute of Scientific and Technical Information of China (English)

    邵蓬; 汪笑宇; 徐晓丽

    2015-01-01

    快速、准确地确定弧菌种类能够有效防治弧菌病的发生,利用PCR技术对水产养殖动物的弧菌病进行诊断,通常需要采用靶基因作为基础.近年来,常用的细菌诊断靶基因主要有:16S rDNA、16S-23S rDNA基因间区序列、gyrB基因、dnaJ基因等看家基因和某些弧菌特定的毒力基因,如toxR基因、tdh基因、trh基因、vvhA基因、ctxA基因等.%Quick and accurate diagnosis of the types of Vibrio can effectively prevent and control the occurrence of Vibrio disease. It is usually needed to use the target genes as the foundation when diagnosing the Vibrio disease of aquatic animals by PCR technology. In recent years, the common target genes for bacterial diagnosis mainly included some house-keeping genes, such as 16S rDNA, 16S-23S intergenic spacer regions,gyrB gene,dnaJ gene and so on, and some specific virulence genes of Vibrio, such astoxR gene,tdh gene,trh gene,vvhA gene,ctxA gene, et al.

  15. Genetic diversity of root-nodulating bacteria isolated from pea (Pisum sativum) in subtropical regions of China

    Institute of Scientific and Technical Information of China (English)

    YANG ChengYun; YANG JiangKe; LI YouGuo; ZHOU JunOhu

    2008-01-01

    Diversity of 42 isolates from effective nodules of Pisum sativum in different geographical regions of China were studied using 16S rRNA gene RFLP patterns, 16S rRNA sequencing, 16S-23S rRNA inter-genic spacer (IGS) region RFLP patterns and G-C rich random amplified polymorphic DNA (RAPD). The isolates were distributed in two groups on the basis of their 16S rRNA gene RFLP patterns. The 16S rRNA gene sequences of strains from 16S rRNA gene RFLP patterns group Ⅰ were very closely related (identities higher than 99.5%) to Rhizobium leguminosarum USDA 2370. Group Ⅱ consisting of WzP3 and WzP15 was closely related to Rhizobium etli CFN42. The analysis of the 16S-23S IGS RFLP pat-terns divided the isolates into 18 genotypes and four groups. Group Ⅰ was clustered with R. legumino-sarum USDA2370. Group Ⅱ consisted of YcP2, YcP3 and CqP7. The strains of group Ⅲ were distributed abroad. Group Ⅳ consisted of WzP3, WzP15 and R. etli CFN42. RAPD divided the isolates into nine clusters in which group Ⅳ only consisted of YcP2 and the strains of group Ⅴ and Ⅸ were from Wenzhou and Xiantao, respectively. This assay demonstrated the geographical effect on genetic diversity of pea rhizobia.

  16. [Isolation and characterization of new species hydrogen producing bacterium Ethanologenbacterium sp. strain X-1 and its capability of hydrogen production].

    Science.gov (United States)

    Xing, De-Feng; Ren, Nan-Qi; Li, Qiu-Bo

    2004-12-01

    To obtain hydrogen-producing bacterium of high efficiency, a strain X-1 of hydrogen-producing bacteria was isolated from the continuous stirred-tank reactor (CSTR) by anaerobic Hungate technique. The Comparative sequence analysis of 16S rDNA showed that homology of strain X-1 with Clostridium cellulose and Acetanaerobacterium elongatum is less than 94%. All sequence alignment of 16S-23S rDNA intergenic spacer regions (ISR) indicated displayed that consensus region is tRNA(Ala), and tRNA(Ile), variable region is not homologous. Morphological, physic-biochemical character, and comparative sequence analysis of 16S rDNA and 16S-23S rDNA ISR indicated that strain X-1 belong to new genus named Ethanologenbacterium gen. nov.. Strain X-1 is facultative anaerobe bacillus; its main fermentative products are acetic acid, ethanol, H2 and CO2. The metabolic character of strain X-1 is typical ethanol type fermentation. Its capability of hydrogen production was measured in the batch culture experiment. X-1's maximum specific hydrogen producing rate is 28.3 mmol H2/( g dry cell x h) at pH 4.0 and 36 degrees C. Result of identify and analysis of hydrogen production ability demonstrated strain X-1 belong to new genus of high hydrogen-producing bacteria.

  17. High-prevalence Borrelia miyamotoi infection among [corrected] wild turkeys (Meleagris gallopavo) in Tennessee.

    Science.gov (United States)

    Scott, M C; Rosen, M E; Hamer, S A; Baker, E; Edwards, H; Crowder, C; Tsao, J I; Hickling, G J

    2010-11-01

    During spring and fall 2009, 60 wild turkeys (Meleagris gallopavo) harvested by Tennessee hunters were surveyed for Borrelia spp. by sampling their blood, tissue, and attached ticks. In both seasons, 70% of turkeys were infested with juvenile Amblyomma americanum; one spring turkey hosted an adult female Ixodes brunneus. Polymerase chain reaction assays followed by DNA sequencing indicated that 58% of the turkeys were positive for the spirochete Borrelia miyamotoi, with tissue testing positive more frequently than blood (P = 0.015). Sequencing of the 16S-23S rRNA intergenic spacer indicated > or = 99% similarity to previously published sequences of the North American strain of this spirochete. Positive turkeys were present in both seasons and from all seven middle Tennessee counties sampled. No ticks from the turkeys tested positive for any Borrelia spp. This is the first report of B. miyamotoi in birds; the transmission pathways and epidemiological significance of this high-prevalence spirochetal infection remain uncertain.

  18. IDENTIFICATION OF MYCOBACTERIUM GENAVENSE IN A DIANA MONKEY (CERCOPITHECUS DIANA) BY POLYMERASE CHAIN REACTION AND HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY.

    Science.gov (United States)

    Kelly, Kathleen M; Wack, Allison N; Bradway, Dan; Simons, Brian W; Bronson, Ellen; Osterhout, Gerard; Parrish, Nicole M; Montali, Richard J

    2015-06-01

    A 25-yr-old Diana monkey (Cercopithecus diana) with a 1.5-yr history of chronic colitis and diarrhea was found to have disseminated granulomatous disease with intralesional acid fast bacilli. Bacilli were identified as Mycobacterium genavense by polymerase chain reaction, sequencing of the 16S-23S ribosomal RNA intergenic spacer (ITS) gene, and mycolic acid analysis by high-performance liquid chromatography. Mycobacterium genavense is a common cause of mycobacteriosis in free-ranging and captive birds. In addition, recognition of opportunistic infection in human immunodeficiency virus-positive patients is increasing. Disease manifestations of M. genavense are similar to Mycobacterium avium complex (MAC) and include fever, wasting, and diarrhea with disseminated disease. Similar clinical signs and lesions were observed in this monkey. Mycobacterium genavense should be considered as a differential for disseminated mycobacterial disease in nonhuman primates as this agent can mimic MAC and related mycobacteria.

  19. Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China.

    Science.gov (United States)

    Wu, Li Juan; Wang, Hai Qing; Wang, En Tao; Chen, Wen Xin; Tian, Chang Fu

    2011-06-01

    A total of 99 bacterial isolates that originated from root nodules of Glycine soja were characterized with restriction analyses of amplified 16S ribosomal DNA and 16S-23S rDNA intergenic spacers (ITS), and sequence analyses of 16S rRNA, rpoB, atpD, recA and nodC genes. When tested for nodulation of G. soja, 72 of the isolates were effective symbionts, and these belonged to five species: Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense and Sinorhizobium fredii. All of these, except some B. yuanmingense strains, also formed effective nodules on the domesticated soybean Glycine max. The remaining 27 isolates did not nodulate either host, but were identified as Rhizobium. Phylogeny nodC in the G. soja symbionts suggested that this symbiosis gene was mainly maintained by vertical gene transfer. Different nodC sublineages and rrs-ITS clusters reflected the geographic origins of isolates in this study.

  20. Heterogeneous diversity of spacers within CRISPR

    OpenAIRE

    He, Jiankui; Deem, Michael W.

    2010-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement w...

  1. Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

    NARCIS (Netherlands)

    Kumar, Vinod; Westra, Harm-Jan; Karjalainen, Juha; Zhernakova, Daria V.; Esko, Tonu; Hrdlickova, Barbara; Almeida, Rodrigo; Zhernakova, Alexandra; Reinmaa, Eva; Hofker, Marten H.; Fehrmann, Rudolf S. N.; Fu, Jingyuan; Withoff, Sebo; Metspalu, Andres; Franke, Lude; Wijmenga, Cisca; Vosa, Urmo

    2013-01-01

    Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variation

  2. Grid welding fixture for a spacer grid

    International Nuclear Information System (INIS)

    A modular grid welding fixture for a spacer grid that facilitates full grid laser welding of a spacer grid in one setup is disclosed. The modular design allows for partial implementation of each weld type. A base plate is used for mounting to the positioning/rotational plate of the welding system. A removable sub-plate received in the base plate is used to position the grid strips for proper location for welding. A top fixture plate is aligned with the base plate and provides for mounting of a second sub-plate if required. Side plates with spring loaded pressure pads that are hinged to the top fixture plate apply uniform pressure to the outer grid strips during processing. The base plate, top plate, side plate, and pressure pads are provided with a plurality of through holes to allow access of the laser beam for welding. Corner clips are used to insure contact of the overlapping sections of the outer grid strips for proper corner welding. 4 figs

  3. Heat transfer augmentation in rod bundles near grid spacers

    International Nuclear Information System (INIS)

    Heat transfer augmentation by straight grid spacers in rod bundles is studied for single phase flow and for post critical heat flux dispersed flow. The heat transfer effect of swirling grid spacers in single phase flow is also examined. Governing heat transfer mechanisms are analyzed, and predictive formulations are established. For single phase flow, the local heat transfer at a straight spacer and at its upstream or downstream locations are treated separately. 18 refs

  4. Molecular recordings by directed CRISPR spacer acquisition.

    Science.gov (United States)

    Shipman, Seth L; Nivala, Jeff; Macklis, Jeffrey D; Church, George M

    2016-07-29

    The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device.

  5. Improvement of inhaler efficacy by home-made spacer.

    Science.gov (United States)

    Sritara, P; Janvitayanuchit, S

    1993-12-01

    The delivery of aerosol from a metered dose inhaler (MDI) was reported to be more efficient with a spacer. Hence, a home-made spacer modified from a 950 ml low cost plastic bottle, was compared with a MDI and with a 750 ml imported spacer (Nebuhaler). On three consecutive days, at the same time of day, 20 adult patients with chronic asthma inhaled two puffs of terbutaline sulphate (0.5 mg), delivered from MDI alone, MDI with a 750 ml Nebuhlaer and MDI with a home-made spacer. The following measurements were made: forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and pulse rate. These measurements were carried out immediately before and at 5, 20, 60 min after inhalation of terbutaline. FEV1 was significantly increased (P terbutaline with MDI via either spacers than with MDI alone but no significant difference was observed between Nebuhaler and the home-made spacer. FVC and pulse rate showed no significant change with each method of administration. In conclusion, terbutaline delivered by MDI and home-made spacer was more effective in bronchodilatation than by MDI alone and was just as effective as MDI and Nebuhaler. The home-made spacer therefore offers a simple, inexpensive and more effective method for delivering aerosol drug. PMID:7798822

  6. CFD application to advanced design for high efficiency spacer grid

    International Nuclear Information System (INIS)

    Highlights: • A new LDV was developed to investigate the local velocity in a rod bundle and inside a spacer grid. • The design information that utilizes for high efficiency spacer grid has been obtained. • CFD methodology that predicts flow field in a PWR fuel has been developed. • The high efficiency spacer grid was designed using the CFD methodology. - Abstract: Pressurized water reactor (PWR) fuels have been developed to meet the needs of the market. A spacer grid is a key component to improve thermal hydraulic performance of a PWR fuel assembly. Mixing structures (vanes) of a spacer grid promote coolant mixing and enhance heat removal from fuel rods. A larger mixing vane would improve mixing effect, which would increase the departure from nucleate boiling (DNB) benefit for fuel. However, the increased pressure loss at large mixing vanes would reduce the coolant flow at the mixed fuel core, which would reduce the DNB margin. The solution is to develop a spacer grid whose pressure loss is equal to or less than the current spacer grid and that has higher critical heat flux (CHF) performance. For this reason, a requirement of design tool for predicting the pressure loss and CHF performance of spacer grids has been increased. The author and co-workers have been worked for development of high efficiency spacer grid using Computational Fluid Dynamics (CFD) for nearly 20 years. A new laser Doppler velocimetry (LDV), which is miniaturized with fiber optics embedded in a fuel cladding, was developed to investigate the local velocity profile in a rod bundle and inside a spacer grid. The rod-embedded fiber LDV (rod LDV) can be inserted in an arbitrary grid cell instead of a fuel rod, and has the advantage of not disturbing the flow field since it is the same shape as a fuel rod. The probe volume of the rod LDV is small enough to measure spatial velocity profile in a rod gap and inside a spacer grid. According to benchmark experiments such as flow velocity

  7. Heat-transfer augmentation in rod bundles near grid spacers

    International Nuclear Information System (INIS)

    Heat-transfer augmentation by straight grid spacers in rod bundles is studied for single-phase flow and for post-critical heat flux dispersed flow. The heat transfer effect of swirling grid spacers in single-phase flow is also examined. Governing heat-transfer mechanisms are analyzed, and predictive formulations are established. For single-phase flow, the local heat transfer at a straight spacer and at its upstream or downstream locations are treated separately. The effect of local velocity increasing near swirling spacer is considered. For post critical heat flux (CHF) dispersed flow, the heat transfer by thermal radiation, fin cooling, and vapor convection near the spacer are calculated. The predictions are compared with experimental data with satisfactory agreement

  8. Trypanosoma brucei: Enrichment by UV of intergenic transcripts from the variable surface glycoprotein gene expression site

    International Nuclear Information System (INIS)

    The expression site for the variable surface glycoprotein (VSG) gene AnTat 1.3A of Trypanosoma brucei is 45 kilobases long and encompasses seven expression site-associated genes (ESAGs). After UV irradiation, several large transcripts from the putative promoter region were strongly enriched. We report that one such major transcript starts near the poly(A) addition site of the first gene (ESAG 7), spans the intergenic region, and extends to the poly(A) addition site of the second gene (ESAG 6), thus bypassing the normal 3' splice site of the ESAG 6 mRNA. Since this transcript is spliced, we conclude that UV irradiation does not inhibit splicing but stabilizes unstable processing products. This demonstrates that at least some intergenic regions of the VSG gene expression site are continuously transcribed in accordance with a polycistronic transcription model

  9. Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

    Directory of Open Access Journals (Sweden)

    Augix Guohua Xu

    Full Text Available Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ribosomal transcripts correspond to annotated exons and 20-23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40-48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20% represents 3'UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.

  10. Analysis of US patents on spacer grids

    International Nuclear Information System (INIS)

    The total of 137 US patents on spacer grids patented from 1968 through 1993 are analyzed and summarized. Database is constituted with designing the appropriate fields by which each patent can be identified. The fields consist of patent number, inventor, assignee, date of patent, title and major foci of the patent. The major foci are again classified by detailed subjects such as the fretting failure and fuel rod support-related, the strength-related, the fabrication-related as for mechanical subjects, while the cooling performance-related and the pressure drop-related as for thermal-hydraulic one. The 92% of the patents analyzed were issued form nuclear companies of USA, France and Germany. Among the patents dealing with mechanical subjects, the fretting failure and fuel rod support-related is more than the pressure drop-related among the patents of thermal-hydraulic subjects. The number of patents issued from Japan ranks just after Germany i.e., the 4th country. It is thought that much concern as well as investment should be increased in this field, the patent of nuclear components. (author). 2 tabs., 5 figs

  11. Shelf life of pie caps with biodegradable films as spacers

    OpenAIRE

    Daniela Verónica Escobar Gianni; Angelina Sala; Carlos Silvera; Rodrigo Harispe; Rosa Marquez Romero

    2013-01-01

    Commonly pie caps at market use polyethylene films as spacers between them. This paper studies the conventional spacers replacement with edible and biodegradable films made with whey protein isolate (WPI) and potassium sorbate as a preservative. Besides facilitating the separation of pie caps, with this application is intended to increase their shelf life. The films made by the compression molding method were used as spacers in pie caps without preservative in their formula (A) and with prese...

  12. Preclinical Evaluation of Bioabsorbable Polyglycolic Acid Spacer for Particle Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Akasaka, Hiroaki [Division of Radiation Oncology, Kobe University Graduate School of Medicine, Hyogo Japan (Japan); Sasaki, Ryohei, E-mail: rsasaki@med.kobe-u.ac.jp [Division of Radiation Oncology, Kobe University Graduate School of Medicine, Hyogo Japan (Japan); Miyawaki, Daisuke; Mukumoto, Naritoshi; Sulaiman, Nor Shazrina Binti [Division of Radiation Oncology, Kobe University Graduate School of Medicine, Hyogo Japan (Japan); Nagata, Masaaki [Division of Gastroenterology, Kobe University Graduate School of Medicine, Hyogo Japan (Japan); Yamada, Shigeru [Research Center Hospital, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Murakami, Masao [Radiation Oncology Center, Dokkyo Medical University, Tochigi (Japan); Demizu, Yusuke [Department of Radiology, Hyogo Ion Beam Medical Center, Hyogo (Japan); Fukumoto, Takumi [Division of Hepato-Biliary-Pancreatic Surgery, Kobe University Graduate School of Medicine, Hyogo Japan (Japan)

    2014-12-01

    Purpose: To evaluate the efficacy and safety of a polyglycolic acid (PGA) spacer through physical and animal experiments. Methods and Materials: The spacer was produced with surgical suture material made of PGA, forming a 3-dimensional nonwoven fabric. For evaluation or physical experiments, 150-MeV proton or 320-MeV carbon-ion beams were used to generate 60-mm width of spread-out Bragg peak. For animal experiments, the abdomens of C57BL/6 mice, with or without the inserted PGA spacers, were irradiated with 20 Gy of carbon-ion beam (290 MeV) using the spread-out Bragg peak. Body weight changes over time were scored, and radiation damage to the intestine was investigated using hematoxylin and eosin stain. Blood samples were also evaluated 24 days after the irradiation. Long-term thickness retention and safety were evaluated using crab-eating macaques. Results: No chemical or structural changes after 100 Gy of proton or carbon-ion irradiation were observed in the PGA spacer. Water equivalency of the PGA spacer was equal to the water thickness under wet condition. During 24 days' observation after 20 Gy of carbon-ion irradiation, the body weights of mice with the PGA spacer were relatively unchanged, whereas significant weight loss was observed in those mice without the PGA spacer (P<.05). In mice with the PGA spacer, villus and crypt structure were preserved after irradiation. No inflammatory reactions or liver or renal dysfunctions due to placement of the PGA spacer were observed. In the abdomen of crab-eating macaques, thickness of the PGA spacer was maintained 8 weeks after placement. Conclusions: The absorbable PGA spacer had water-equivalent, bio-compatible, and thickness-retaining properties. Although further evaluation is warranted in a clinical setting, the PGA spacer may be effective to stop proton or carbon-ion beams and to separate normal tissues from the radiation field.

  13. Preclinical Evaluation of Bioabsorbable Polyglycolic Acid Spacer for Particle Therapy

    International Nuclear Information System (INIS)

    Purpose: To evaluate the efficacy and safety of a polyglycolic acid (PGA) spacer through physical and animal experiments. Methods and Materials: The spacer was produced with surgical suture material made of PGA, forming a 3-dimensional nonwoven fabric. For evaluation or physical experiments, 150-MeV proton or 320-MeV carbon-ion beams were used to generate 60-mm width of spread-out Bragg peak. For animal experiments, the abdomens of C57BL/6 mice, with or without the inserted PGA spacers, were irradiated with 20 Gy of carbon-ion beam (290 MeV) using the spread-out Bragg peak. Body weight changes over time were scored, and radiation damage to the intestine was investigated using hematoxylin and eosin stain. Blood samples were also evaluated 24 days after the irradiation. Long-term thickness retention and safety were evaluated using crab-eating macaques. Results: No chemical or structural changes after 100 Gy of proton or carbon-ion irradiation were observed in the PGA spacer. Water equivalency of the PGA spacer was equal to the water thickness under wet condition. During 24 days' observation after 20 Gy of carbon-ion irradiation, the body weights of mice with the PGA spacer were relatively unchanged, whereas significant weight loss was observed in those mice without the PGA spacer (P<.05). In mice with the PGA spacer, villus and crypt structure were preserved after irradiation. No inflammatory reactions or liver or renal dysfunctions due to placement of the PGA spacer were observed. In the abdomen of crab-eating macaques, thickness of the PGA spacer was maintained 8 weeks after placement. Conclusions: The absorbable PGA spacer had water-equivalent, bio-compatible, and thickness-retaining properties. Although further evaluation is warranted in a clinical setting, the PGA spacer may be effective to stop proton or carbon-ion beams and to separate normal tissues from the radiation field

  14. Response of an electrostatic probe for a right cylindrical spacer

    DEFF Research Database (Denmark)

    Rerup, T; Crichton, George C; McAllister, Iain Wilson

    1994-01-01

    During the last decade many experimental studies of surface charge phenomena have been undertaken employing right cylindrical spacers. Measurement of the surface charge was performed using small electrostatic field probes to scan across the dielectric surface. Charges are electrostatically induced...

  15. Bioinformatics analyses of Shigella CRISPR structure and spacer classification.

    Science.gov (United States)

    Wang, Pengfei; Zhang, Bing; Duan, Guangcai; Wang, Yingfang; Hong, Lijuan; Wang, Linlin; Guo, Xiangjiao; Xi, Yuanlin; Yang, Haiyan

    2016-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.

  16. Sidewall spacer optimization for steep switching junctionless transistors

    Science.gov (United States)

    Gupta, Manish; Kranti, Abhinav

    2016-06-01

    In this work, we analyze the impact of a high permittivity (high-κ) sidewall spacer and gate dielectric on the occurrence of sub-60 mV/decade subthreshold swing (S-swing) in symmetrical junctionless (JL) double gate (DG) transistors. It is shown that steep S-swing values (≤10 mV/decade) can be achieved in JL devices with a combination of a high permittivity (high-κ) gate dielectric and a narrow low permittivity (low-κ) sidewall spacer. Implementation of a wider high-κ spacer will diminish the degree of impact ionization by the influence of the fringing component of the gate electric field, and will not be useful for steep off-to-on current transition. A wider spacer with low-κ and a narrow spacer with high-κ permittivity will be useful to limit the latching effect that can occur at lower temperatures (250 K). For high temperature operation, the decrease in the impact ionization rate can be compensated by designing a JL transistor with a thicker silicon film. The work demonstrates opportunities to enhance impact ionization at sub bandgap voltages, and proposes optimal guidelines for selecting a sidewall spacer to facilitate steep switching in JL transistors.

  17. Intergenic DNA sequences flanking the pseudo alpha globin genes of human and chimpanzee.

    OpenAIRE

    Sawada, I; Beal, M P; Shen, C K; Chapman, B.; Wilson, A C; Schmid, C.

    1983-01-01

    We have determined the sequence of 2400 base pairs upstream from the human pseudo alpha globin (psi alpha) gene, and for comparison, 1100 base pairs of DNA within and upstream from the chimpanzee psi alpha gene. The region upstream from the promoter of the psi alpha gene shows no significant homology to the intergenic regions of the adult alpha 2 and alpha 1 globin genes. The chimpanzee gene has a coding defect in common with the human psi alpha gene, showing that the product of this gene, if...

  18. Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai)

    Science.gov (United States)

    Kim, W S; Gardan, L; Rhim, S L; Geider, K

    1999-04-01

    A novel pathogen from Asian pears (Pyrus pyrifolia Nakai) was analysed by sequencing the 16S rDNA and the adjacent intergenic region, and the data were compared to related Enterobacteriaceae. The 16S rDNA of the Asian pear pathogen was almost identical with the sequence of Erwinia amylovora, in contrast to the 16S-23S rRNA intergenic transcribed spacer region of both species. A dendrogram was deduced from determined sequences of the spacer regions including those of several related species such as Erwinia amylovora, Enterobacter pyrinus, Pantoea stewartii subsp. stewartii and Escherichia coli. Dendrograms derived from 121 biochemical characteristics including Biotype 100 data placed the Asian pear pathogen close to Erwinia amylovora and more distantly to other members of the species Erwinia and to the species Pantoea and Enterobacter. Another DNA relatedness study was performed by DNA hybridizations and estimation of delta Tm values. The Asian pear strains constituted a tight DNA hybridization group (89-100%) and were barely related to strains of Erwinia amylovora (40-50%) with a delta Tm in the range of 5.2-6.8. The G + C content of DNA from the novel pathogen is 52 mol%. Therefore, it is proposed that strains isolated from Asian pears constitute a new species and the name Erwinia pyrifoliae is suggested; the type strain is strain Ep 16/96T (= CFBP 4172T = DSM 12163T). PMID:10319516

  19. Limitations and benefits of ARISA intra-genomic diversity fingerprinting.

    Science.gov (United States)

    Popa, Radu; Popa, Rodica; Mashall, Matthew J; Nguyen, Hien; Tebo, Bradley M; Brauer, Suzanna

    2009-08-01

    Monitoring diversity changes and contamination in mixed cultures and simple microcosms is challenged by fast community structure dynamics, and the need for means allowing fast, cost-efficient and accurate identification of microorganisms at high phylogenetic resolution. The method we explored is a variant of Automated rRNA Intergenic Spacer Analysis based on Intra-Genomic Diversity Fingerprinting (ARISA-IGDF), and identifies phylotypes with multiple 16S-23S rRNA gene Intergenic Transcribed Spacers. We verified the effect of PCR conditions (annealing temperature, duration of final extension, number of cycles, group-specific primers and formamide) on ARISA-IGD fingerprints of 44 strains of Shewanella. We present a digitization algorithm and data analysis procedures needed to determine confidence in strain identification. Though using stringent PCR conditions and group-specific primers allow reasonably accurate identification of strains with three ARISA-IGD amplicons within the 82-1000 bp size range, ARISA-IGDF is best for phylotypes with >or=4 unambiguously different amplicons. This method allows monitoring the occurrence of culturable microbes and can be implemented in applications requiring high phylogenetic resolution, reproducibility, low cost and high throughput such as identifying contamination and monitoring the evolution of diversity in mixed cultures and low diversity microcosms and periodic screening of small microbial culture libraries. PMID:19538993

  20. The potential of standard and modified feed spacers for biofouling control

    KAUST Repository

    Araújo, Paula A.

    2012-06-01

    The impact of feed spacers on initial feed channel pressure (FCP) drop, FCP increase and biomass accumulation has been studied in membrane fouling simulators using feed spacers applied in commercially available nanofiltration and reverse osmosis spiral wound membrane modules. All spacers had a similar geometry.Our studies showed that biofouling was not prevented by (i) variation of spacer thickness, (ii) feed spacer orientation, (iii) feed spacer coating with silver, copper or gold and (iv) using a biostatic feed spacer. At constant feed flow, a lower FCP and FCP increase were observed for a thicker feed spacer. At constant linear flow velocity, roughly the same FCP development and biomass accumulation were found irrespective of the feed spacer thickness: hydrodynamics and substrate load were more important for development and impact of biofouling than the thickness of currently applied spacers. Use of biostatic and metal coated spacers were not effective for biofouling control. The same small reduction of biofouling rate was observed with copper and silver coated spacers as well as uncoated 45° rotated spacers.The studied modified spacers were not effective for biofouling prevention and control. The impact of biofouling on FCP increase was reduced significantly by a lower linear flow velocity, while spacer orientation and spacer thickness in membrane modules had a smaller but still significant effect. © 2012 Elsevier B.V.

  1. De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Chain, P; Garcia, E; Mcloughlin, K; Ovcharenko, I

    2007-02-20

    This project was begun to implement, test, and experimentally validate the results of a novel algorithm for genome-wide identification of candidate transcription-factor binding sites in prokaryotes. Most techniques used to identify regulatory regions rely on conservation between different genomes or have a predetermined sequence motif(s) to perform a genome-wide search. Therefore, such techniques cannot be used with new genome sequences, where information regarding such motifs has not yet been discovered. This project aimed to apply a de novo search algorithm to identify candidate binding-site motifs in intergenic regions of prokaryotic organisms, initially testing the available genomes of the Yersinia genus. We retrofitted existing nucleotide pattern-matching algorithms, analyzed the candidate sites identified by these algorithms as well as their target genes to screen for meaningful patterns. Using properly annotated prokaryotic genomes, this project aimed to develop a set of procedures to identify candidate intergenic sites important for gene regulation. We planned to demonstrate this in Yersinia pestis, a model biodefense, Category A Select Agent pathogen, and then follow up with experimental evidence that these regions are indeed involved in regulation. The ability to quickly characterize transcription-factor binding sites will help lead to a better understanding of how known virulence pathways are modulated in biodefense-related organisms, and will help our understanding and exploration of regulons--gene regulatory networks--and novel pathways for metabolic processes in environmental microbes.

  2. Cultivar-level phylogeny using chloroplast DNA barcode psbK-psbI spacers for identification of Emirati date palm (Phoenix dactylifera L.) varieties.

    Science.gov (United States)

    Enan, M R; Ahmed, A

    2016-01-01

    The efficacy of genetic material for use as DNA barcodes is under constant evaluation and improvement as new barcodes offering better resolution and efficiency of amplification for specific species groups are identified. In this study, the chloroplast intergenic spacer psbK-psbI was evaluated for the first time as a DNA barcode for distinguishing date palm cultivars. Nucleotide sequences were aligned using MEGA 6.0 to calculate pairwise divergence among the cultivars. The analyzed data illustrated a considerable level of variability in the genetic pool of the selected cultivars (0.009). In fact, five haplotypes were detected among 30 cultivars examined, yielding a haplotype diversity of 0.685. An unweighted pair group method with arithmetic mean phylogenetic tree was constructed and shows a well-defined relationship among date palm cultivar varieties. On the other hand, selective neutrality investigations using Tajima test and Fu and Li tests were negative, providing evidence that date palm has been undergoing rapid expansion and recent population growth. Thus, we suggest that the psbK-psbI spacer can be successfully used to construct reliable phylogenetic trees for P. dactylifera. PMID:27525916

  3. Impact of spacer thickness on biofouling in forward osmosis

    KAUST Repository

    Valladares Linares, Rodrigo

    2014-06-01

    Forward osmosis (FO) indirect desalination systems integrate wastewater recovery with seawater desalination. Niche applications for FO systems have been reported recently, due to the demonstrated advantages compared to conventional high-pressure membrane processes such as nanofiltration (NF) and reverse osmosis (RO). Among them, wastewater recovery has been identified to be particularly suitable for practical applications. However, biofouling in FO membranes has rarely been studied in applications involving wastewater effluents. Feed spacers separating the membrane sheets in cross-flow systems play an important role in biofilm formation. The objective of this study was to determine the influence of feed spacer thickness (28, 31 and 46mil) on biofouling development and membrane performance in a FO system, using identical cross-flow cells in parallel studies. Flux development, biomass accumulation, fouling localization and composition were determined and analyzed. For all spacer thicknesses, operated at the same feed flow and the same run time, the same amount of biomass was found, while the flux reduction decreased with thicker spacers. These observations are in good agreement with biofouling studies for RO systems, considering the key differences between FO and RO. Our findings contradict previous cross-flow studies on particulate/colloidal fouling, where higher cross-flow velocities improved system performance. Thicker spacers reduced the impact of biofouling on FO membrane flux. © 2014 Elsevier Ltd.

  4. Impact of spacer thickness on biofouling in forward osmosis.

    Science.gov (United States)

    Valladares Linares, R; Bucs, Sz S; Li, Z; AbuGhdeeb, M; Amy, G; Vrouwenvelder, J S

    2014-06-15

    Forward osmosis (FO) indirect desalination systems integrate wastewater recovery with seawater desalination. Niche applications for FO systems have been reported recently, due to the demonstrated advantages compared to conventional high-pressure membrane processes such as nanofiltration (NF) and reverse osmosis (RO). Among them, wastewater recovery has been identified to be particularly suitable for practical applications. However, biofouling in FO membranes has rarely been studied in applications involving wastewater effluents. Feed spacers separating the membrane sheets in cross-flow systems play an important role in biofilm formation. The objective of this study was to determine the influence of feed spacer thickness (28, 31 and 46 mil) on biofouling development and membrane performance in a FO system, using identical cross-flow cells in parallel studies. Flux development, biomass accumulation, fouling localization and composition were determined and analyzed. For all spacer thicknesses, operated at the same feed flow and the same run time, the same amount of biomass was found, while the flux reduction decreased with thicker spacers. These observations are in good agreement with biofouling studies for RO systems, considering the key differences between FO and RO. Our findings contradict previous cross-flow studies on particulate/colloidal fouling, where higher cross-flow velocities improved system performance. Thicker spacers reduced the impact of biofouling on FO membrane flux. PMID:24726992

  5. CRISPR interference and priming varies with individual spacer sequences.

    Science.gov (United States)

    Xue, Chaoyou; Seetharam, Arun S; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J J; Severin, Andrew J; Sashital, Dipali G

    2015-12-15

    CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.

  6. Mandrel and spacer engineering based self-aligned triple patterning

    Science.gov (United States)

    Chen, Yijian; Cheng, Qi; Kang, Weiling

    2012-03-01

    Self-aligned triple patterning (SATP) technique offers both improved resolution and quasi-2D design flexibility for scaling integrated circuits down to sub-15nm half pitch. By implementation of active layout decomposition/synthesis using mandrel and spacer engineering, SATP process represents a prospective trend that not only drives up the feature density, but also breaks the 1-D gridded limitations posed to future device design. In this paper, we shall present the research progress made in optimizing SATP process to improve its lithographic performance. To solve the previously reported difficulties in etching small mandrels and removing sacrificial spacers, new materials are tested and a promising scheme (using oxide as the mandrel and poly/amorphous Si as the sacrificial spacer) is identified. In the new process, a diluted HF process is applied to shrink the mandrel (oxide) line CD and a highly selective dry etch (which does not attack the mandrel and structural spacer) is developed to strip the sacrificial Si spacers, resulting in significantly improved process performance. We also address the issue of reducing SATP process complexity by exploring the feasibility of a 2-mask concept for specific types of layout.

  7. Impact of spacer thickness on biofouling in forward osmosis.

    Science.gov (United States)

    Valladares Linares, R; Bucs, Sz S; Li, Z; AbuGhdeeb, M; Amy, G; Vrouwenvelder, J S

    2014-06-15

    Forward osmosis (FO) indirect desalination systems integrate wastewater recovery with seawater desalination. Niche applications for FO systems have been reported recently, due to the demonstrated advantages compared to conventional high-pressure membrane processes such as nanofiltration (NF) and reverse osmosis (RO). Among them, wastewater recovery has been identified to be particularly suitable for practical applications. However, biofouling in FO membranes has rarely been studied in applications involving wastewater effluents. Feed spacers separating the membrane sheets in cross-flow systems play an important role in biofilm formation. The objective of this study was to determine the influence of feed spacer thickness (28, 31 and 46 mil) on biofouling development and membrane performance in a FO system, using identical cross-flow cells in parallel studies. Flux development, biomass accumulation, fouling localization and composition were determined and analyzed. For all spacer thicknesses, operated at the same feed flow and the same run time, the same amount of biomass was found, while the flux reduction decreased with thicker spacers. These observations are in good agreement with biofouling studies for RO systems, considering the key differences between FO and RO. Our findings contradict previous cross-flow studies on particulate/colloidal fouling, where higher cross-flow velocities improved system performance. Thicker spacers reduced the impact of biofouling on FO membrane flux.

  8. Final design of a spacer grid using axiomatic design

    Energy Technology Data Exchange (ETDEWEB)

    Park, Gyung-Jin; Lee, Hyun-Ah; Kim, Chong-Ki [Hanyang Univ., Seoul (Korea, Republic of); Song, Gi-Nam [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2007-03-15

    The spacer grid set is a component in the nuclear fuel assembly. The set supports the fuel rod safely. The spacer grid set must have enough strength to sustain external loads such as earthquake. The fretting wear occurs between the spring of the fuel rod and the spacer grid due to the flow-induced vibration after the fuel rod is inserted to the spacer grid set. Design of the spring is carried out by using the independence axiom in axiomatic design to solve the two problems. The spacer grid is divided into two parts for sustaining the impact load and reducing fretting wear based on the function requirements. The design for the impact load is performed through non-linear analysis and the homology theory is adopted to reduce fretting wear achieved for shape optimization. The objective function to be minimized ids the maximum stress and constraints are defined to increase the contact area between the fuel rod and the spring using the homology theory. In the design results, the contact area becomes large and it is conformed by nonlinear static analysis. The final design shows that larger impact loads can be sustained compared to the current model.

  9. Numerical analysis of the spacer grids' compression strength

    International Nuclear Information System (INIS)

    Among the components of the fuel assembly, the spacer grids play an important structural role during the energy generation process, mainly for their requirement to have enough structural strength to withstand lateral impact loads, due to fuel assembly shipping/handling and due to forces outcome from postulated accidents (earthquake and LOCA). This requirement ensures a proper geometry for cooling and for guide thimble straightness in the fuel assembly. In this way, the understanding of the macroscopic mechanical behavior of this component becomes essential even to any subsequent geometrical modifications to optimize the flue assemblies' structural behavior. In the present work, three-dimensional finite element models destined to provide consistent predictions of 16X16-type spacer grids lateral strength were proposed. Firstly, buckling tests based on results available in the literature were performed to establish a methodology for spacer grid finite element-based modeling. The, by considering a spacer grid interesting geometry and some possible variations associated to its fabrication, tolerance, the proposed numerical models were submitted to compression conditions to calculate the buckling force. Also, these models were validated for comparison with experimental buckling load results. Comparison of buckling predictions combined to observations of actual and simulated deformed spacer grids geometries permitted to verify the consistency and applicability of the proposed models. Thus, these numerical results show a good agreement between the and the experimental results. (author)

  10. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences; FINAL

    International Nuclear Information System (INIS)

    The major objective of this research was to provide appropriate sequences and assemble a DNA array of oligonucleotides to be used for rapid profiling of microbial populations from polluted areas and other areas of interest. The sequences to be assigned to the DNA array were chosen from cloned genomic DNA taken from groundwater sites having well characterized pollutant histories at Hanford Nuclear Plant and Lawrence Livermore Site 300. Glass-slide arrays were made and tested; and a new multiplexed, bead-based method was developed that uses nucleic acid hybridization on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences. The test data revealed considerable strain variation between sample sites showing a striking distribution of sequences. It also suggests that diversity varies greatly with bioremediation, and that there are many bacterial intergenic spacer region sequences that can indicate its effects. The bead method exhibited superior sequence discrimination and has features for easier and more accurate measurement

  11. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences

    Energy Technology Data Exchange (ETDEWEB)

    Robb, Frank T.

    2001-04-10

    The major objective of this research was to provide appropriate sequences and assemble a DNA array of oligonucleotides to be used for rapid profiling of microbial populations from polluted areas and other areas of interest. The sequences to be assigned to the DNA array were chosen from cloned genomic DNA taken from groundwater sites having well characterized pollutant histories at Hanford Nuclear Plant and Lawrence Livermore Site 300. Glass-slide arrays were made and tested; and a new multiplexed, bead-based method was developed that uses nucleic acid hybridization on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences. The test data revealed considerable strain variation between sample sites showing a striking distribution of sequences. It also suggests that diversity varies greatly with bioremediation, and that there are many bacterial intergenic spacer region sequences that can indicate its effects. The bead method exhibited superior sequence discrimination and has features for easier and more accurate measurement.

  12. Effect of a spacer moiety on radiometal labelled Neurotensin derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Mascarin, A.; Valverde, I.E.; Mindt, T.L. [Univ. of Basel Hospital (Switzerland). Div. of Radiopharmaceutical Chemistry

    2013-07-01

    The binding sequence of the regulatory peptide Neurotensin, NT(8-13), represents a promising tumour-specific vector for the development of radiopeptides useful in nuclear oncology for the diagnosis (imaging) and therapy of cancer. A number of radiometal-labelled NT(8-13) derivatives have been reported, however, the effect of the spacer which connects the vector with the radiometal complex has yet not been investigated systematically. Because a spacer moiety can influence potentially important biological characteristics of radiopeptides, we synthesized three [DOTA({sup 177}Lu)]-X-NT(8-13) derivatives and evaluated the effect of a spacer (X) on the physico-chemical properties of the conjugate including lipophilicity, stability, and in vitro receptor affinity and cell internalization. (orig.)

  13. Spacer for fuel rods in nuclear fuel elements

    International Nuclear Information System (INIS)

    Spacers for fuel rods in nuclear reactor fuel elements are described, especially for use aboard ships. Spacers are used in a grid formed by web plates orthogonally intersecting and assembled together in a tooth-comb fashion forming a plurality of channels. The web plates are joined together and each of the web plates includes apertures through which resilient and separator members are joined. The resilient and separator members are joined. The resilient and separator members are in adjacent channels and with other similar members in the same channel, contact a fuel rod in the channel. The contact pressure between the members and fuel rod is radially directed

  14. Shelf life of pie caps with biodegradable films as spacers

    Directory of Open Access Journals (Sweden)

    Daniela Verónica Escobar Gianni

    2013-01-01

    Full Text Available Commonly pie caps at market use polyethylene films as spacers between them. This paper studies the conventional spacers replacement with edible and biodegradable films made with whey protein isolate (WPI and potassium sorbate as a preservative. Besides facilitating the separation of pie caps, with this application is intended to increase their shelf life. The films made by the compression molding method were used as spacers in pie caps without preservative in their formula (A and with preservative (B and they were compared with conventional polyethylene spacers (C. During four months, monthly sensory, microbiological and physicochemical (humidity evaluations were done on the pie caps, together with humidity and solubility evaluations of the films. None of the samples showed microbiological or sensory deterioration. The sensory attributes showed no or slight difference in study time. Between samples the differences were minor: the best scores were for sample A in color, sample C in flavor, and samples B and C in texture and overall liking. The edible films have an interesting potential for this application, although studies in disguise the flavor of serum should be done.

  15. A non-electrostatic spacer for aerosol delivery

    DEFF Research Database (Denmark)

    Bisgaard, H; Anhøj, J; Klug, B;

    1995-01-01

    pressurised metered dose inhaler (p-MDI) to minimise the electrostatic charge on the plastic. The procedure prolonged the half life (t1/2) of the aerosol in the Nebuhaler from nine to 32 seconds. A normal cleaning procedure reduced the aerosol t1/2 back to baseline. The t1/2 of the aerosol in the metal spacer...

  16. CRISPR interference and priming varies with individual spacer sequences

    NARCIS (Netherlands)

    Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J.J.; Severin, Andrew J.; Sashital, Dipali G.

    2015-01-01

    CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destructio

  17. Implementation of spacer therapy for acute asthma in children.

    LENUS (Irish Health Repository)

    Vandeleur, M

    2009-09-01

    The aim was to develop and implement an evidence based guideline for the treatment of acute asthma using a metered dose inhaler and spacer combination. Children admitted to Cork University Hospital Paediatric Department with acute asthma were identified during two identical 2 month seasonal periods before (2005) and after (2006) implementation of the new guidelines in September 2006. Pre-intervention and post-intervention audits by case note review were performed to determine the impact of and compliance with this evidence-based guideline emphasising patient assessment, spacer delivered bronchodilator and specific discharge criteria. Patients had similar characteristics during the two study periods. There was a raised threshold for admission after guideline implementation with 11\\/52 patients having mild exacerbations in 2006, compared to 21\\/36 in 2005. Duration of admission was less in the post-implementation group for equivalent exacerbation severity e.g. for moderate severity; 28 hours in 2005, 23 hours in 2006. Duration of bronchodilator therapy was shorter in 2006 and more likely to be given by spacer device earlier for equivalent levels of severity e.g. for moderate exacerbations, in 2006 the average length of salbutamol therapy was 18 hours with 12 hours by spacer device, in 2005 the average length of therapy was 25 hours with 3 hours by spacer. There was earlier initiation of oral corticosteroids; the average time to administration was 56 minutes in 2006 and 227 minutes in 2005. There was an improved documentation of asthma education in 2006 e.g. inhaler technique was reviewed in 37\\/52 in 2006, 21\\/35 in 2005 and better use of written action plans.

  18. Performance Analysis and Test on the KAERI Devised Spacer Grids for PWRs

    Science.gov (United States)

    Song, Kee-Nam; Lee, Soo-Bum

    Spacer grid which is one of the most important structural components in a pressurized light water reactor fuel assembly supports the fuel rods laterally and vertically. Based on design experiences and by scrutinizing the design features of advanced nuclear fuels and the international patents of spacer grids, KAERI has devised its own spacer grid shapes and acquired patents. In this study, a performance evaluation on two new spacer grid shapes devised by KAERI was carried out from mechanical/structural and thermohydraulic view points. And also a performance evaluation on two commercial spacer grid shapes was carried out for the sake of a comparison. The comparisons included the spring characteristics, fuel rod vibration characteristics, fretting wear resistance, impact strength characteristics, CHF enhancement, and pressure drop level of the spacer grid shapes. The comparison results have shown that the performances of the new spacer grid shapes are better or at least not worse than those of the commercial spacer grid shapes.

  19. Effect of plastic spacer handling on salbutamol lung deposition in asthmatic children

    DEFF Research Database (Denmark)

    Lipworth, Brian J; Lee, Daniel K C; Anhøj, Jacob;

    2002-01-01

    AIMS: To study the effects of electrostatics in a plastic spacer on the lung deposition of salbutamol in asthmatic children. METHODS: Twenty-five children (5-12 years) with mild asthma were given salbutamol hydrofluoroalkane pressurized metered dose inhaler 400 micro g via a 750 ml plastic spacer...... on separate days. Blood samples were taken for plasma salbutamol at 5, 10, 15 and 20 min after inhalation to measure lung bioavailability as a surrogate for relative lung dose. With immediate inhalation following actuation, a new rinsed spacer (NewRinsed ) was compared with a used spacer after repeated daily...... use (Used ), a spacer rinsed after repeated use (UsedRinsed ) and a spacer primed with benzalkonium chloride to avoid electrostatics (Primed1). In addition, spacers were evaluated using a 15 s inhalation delay following actuation with primed (PrimedDelay) and rinsed (RinsedDelay) spacers. Data were...

  20. HYDROELASTIC VIBRATIONS AND LIQUID SLOSHING SUPPRESSION IN A RECTANGULAR TANK WITH ELASTIC SPACER

    Institute of Scientific and Technical Information of China (English)

    CHENG Xu-duo; LIANG Yong; WEN Ji-hua

    2004-01-01

    In this paper, the couple vibration of liquid and elastic spacer in a rectangular tank is investigated. Two different velocity potential functions corresponding respectively to the liquid above and below the elastic spacer are assumed. Complicated boundary conditions corresponding to two velocity potential functions and vibrations of elastic spacer are given. Using the method of energy, the equation of couple frequency is obtained. Through numerical computation the natural frequencies that change according to the location and stiffness of the spacer are shown.

  1. Effect of spacer layers on current-voltage characteristics of resonant-tunneling diode

    International Nuclear Information System (INIS)

    Using the numerical solution to the Schroedinger equation, current-voltage characteristics of the resonant-tunneling diode with spacer layers were obtained. The dependences of the peak current of the resonant-tunneling diode on the emitter spacer width were plotted. It was shown that the peak current depends periodically on the emitter spacer width. The constructed electron density diagrams showed that the increase in the peak current is associated with the resonant level in the emitter spacer region.

  2. Effects of spacer length and terminal group on the crystallization and morphology of biscarbamates: a longer spacer does not reduce the melting temperature.

    Science.gov (United States)

    Khan, Mostofa Kamal; Sundararajan, Pudupadi R

    2013-05-01

    The effects of alkyl side chain and spacer lengths and the type of terminal group on the morphology and crystallization of a homologous series of biscarbamates (model compounds for polyurethanes) were investigated. Biscarbamates were synthesized with alkyl side chains of various lengths ranging from C4 to C18 and an alkyl spacer group with 12 CH2 units (C12 spacer) between the two hydrogen bonding motifs. The crystallization and morphological features are compared with the previously studied biscarbamates with a C6 spacer. As a token example, we also studied a biscarbamate molecule in which the terminal methyl group was replaced by a phenyl group. We stress four important conclusions of the study: (1) A number of studies in the literature found that the longer alkyl spacers reduced the thermal transition temperatures of the molecules, and such behavior was attributed to an increase in the flexibility of the alkyl spacer. However, the results of the present study are to the contrary. With the biscarbamates studied here, the hydrogen-bonding groups on both sides of the C12 spacer act as "anchors", and the longer spacer does not reduce the melting temperatures compared with those with the C6 spacer. (2) The melt viscosity measurements show shear-thinning behavior, which has been mostly observed with polysaccharides and hydrogen-bonded polymers. (3) Avrami analysis shows a two-stage crystallization, which is not commonly observed in organic small molecule systems. (4) The phenyl end group does not add another self-assembly code in terms of π-stacking but acts as a defect. While formation of crystals was observed for biscarbamates with short alkyl side chains with a C6 spacer, an increase in spacer length to C12 induces spherulitic morphology. Although the overall sizes of the spherulites are the same for both spacers, the rate of spherulite growth was higher and the crystallization rate was lower with the C12 spacer compared with the C6 spacer. In contrast with the

  3. DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues.

    Science.gov (United States)

    Zhou, Zhong-Yin; Li, Aimin; Wang, Li-Gang; Irwin, David M; Liu, Yan-Hu; Xu, Dan; Han, Xu-Man; Wang, Lu; Wu, Shi-Fang; Wang, Li-Xian; Xie, Hai-Bing; Zhang, Ya-Ping

    2015-01-01

    Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components of genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize the DNA methylation pattern of pig lincRNA genes in adipose and muscle tissues. Our study showed that the methylation level of lincRNA genes was higher than that of mRNA genes, with similar trends observed in comparisons of the promoter, exon or intron regions. Different methylation pattern were observed across the transcription start sites (TSS) of lincRNA and protein-coding genes. Furthermore, an overlap was observed between many lincRNA genes and differentially methylated regions (DMRs) identified among different breeds of pigs, which show different fat contents, sexes and anatomic locations of tissues. We identify a lincRNA gene, linc-sscg3623, that displayed differential methylation levels in backfat between Min and Large White pigs at 60 and 120 days of age. We found that a demethylation process occurred between days 150 and 180 in the Min and Large White pigs, which was followed by remethylation between days 180 and 210. These results contribute to our understanding of the domestication of domestic animals and identify lincRNA genes involved in adipogenesis and muscle development. PMID:26493951

  4. Epistasis in intra- and inter-gene pool crosses of the common bean.

    Science.gov (United States)

    Borel, J C; Ramalho, M A P; Abreu, A F B

    2016-02-26

    Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses.

  5. Transposable element insertions in long intergenic non-coding RNA genes

    Directory of Open Access Journals (Sweden)

    Sivakumar eKannan

    2015-06-01

    Full Text Available Transposable elements (TE are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences, followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TE-derived sequences in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the RIDL (Repeat Insertion Domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and in particular functional diversification, of lincRNA genes.

  6. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.

    Science.gov (United States)

    Pfingsten, Jennifer S; Kieft, Jeffrey S

    2008-07-01

    In eukaryotes, the canonical process of initiating protein synthesis on an mRNA depends on many large protein factors and the modified nucleotide cap on the 5' end of the mRNA. However, certain RNA sequences can bypass the need for these proteins and cap, using an RNA structure-based mechanism called internal initiation of translation. These RNAs are called internal ribosome entry sites (IRESes), and the cap-independent initiation pathway they support is critical for successful infection by many viruses of medical and economic importance. In this review, we briefly describe and compare mechanistic and structural groups of viral IRES RNAs, focusing on those IRESes that are capable of direct ribosome recruitment using specific RNA structures. We then discuss in greater detail some recent advances in our understanding of the intergenic region IRESes of the Dicistroviridae, which use the most streamlined ribosome-recruitment mechanism yet discovered. By combining these findings with knowledge of canonical translation and the behavior of other IRESes, mechanistic models of this RNA structure-based process are emerging. PMID:18515544

  7. Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes.

    Science.gov (United States)

    Pfingsten, Jennifer S; Costantino, David A; Kieft, Jeffrey S

    2007-07-27

    Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the Dicistroviridae intergenic region (IGR) are an excellent model system to understand the fundamental tenets of IRES function, requiring no protein factors to manipulate the ribosome and initiate translation. Here, we explore the architecture of four members of the IGR IRESes, representative of the two divergent classes of these IRES RNAs. Using biochemical and structural probing methods, we show that despite sequence variability they contain a common three-dimensional fold. The three-dimensional architecture of the ribosome binding domain from these IRESes is organized around a core helical scaffold, around which the rest of the RNA molecule folds. However, subtle variation in the folds of these IRESes and the presence of an additional secondary structure element suggest differences in the details of their manipulation of the large ribosomal subunit. Overall, the results demonstrate how a conserved three-dimensional RNA fold governs ribosome binding and manipulation. PMID:17544444

  8. Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila.

    Science.gov (United States)

    Nyberg, Kevin G; Machado, Carlos A

    2016-01-01

    Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid-the evolutionary model Drosophila pseudoobscura Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster, like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, we identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses. PMID:27189981

  9. The evolutionary landscape of intergenic trans-splicing events in insects.

    Science.gov (United States)

    Kong, Yimeng; Zhou, Hongxia; Yu, Yao; Chen, Longxian; Hao, Pei; Li, Xuan

    2015-11-02

    To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of 'breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.

  10. The polymethylmethacrylate antibiotic spacer for treatment of joint infection

    Directory of Open Access Journals (Sweden)

    Manuel Bondi

    2014-09-01

    Full Text Available Joint prostheses chronic infection requires surgical removal of the implant, in order to eradicate the infection process. The Polymethylmethacrylate (PMMA bone cement is a good carrier for the sustained antibiotic release at the site of infection. PMMA cements pre-loaded with antibiotics are utilized for prophylaxis, primary surgical procedure and the treatment of prosthetic joint infections. The mechanical and functional characteristics of the spacers allow a good joint range of motion, weight-bearing in selected cases and a sustained release of antibiotic at the site of infection. These drug delivery systems offer the advantage of local release of high antibiotic concentrations, which considerably exceed those obtained after systemic administration. Nowadays treatment with a preformed antibiotic loaded spacer can be considered a good option for joint prostheses infection maintaining joint function at the intermediate stage in two-stage treatment.

  11. Inhalational drug delivery from seven different spacer devices.

    OpenAIRE

    Barry, P W; O Callaghan, C.

    1996-01-01

    BACKGROUND: A study was performed to determine in vitro the difference in drug output of seven currently available spacer devices when used with different inhaled medications. METHODS: A glass multistage liquid impinger (MSLI) was used to determine the amount of disodium cromoglycate (DSCG, 5 mg), salbutamol (100 micrograms), or budesonide (200 micrograms) obtained in various particle size ranges from metered dose inhalers (MDIs) actuated directly into the MSLI or via one of seven different s...

  12. Surgical spacer placement and proton radiotherapy for unresectable hepatocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    Shohei; Komatsu; Yuichi; Hori; Takumi; Fukumoto; Masao; Murakami; Yoshio; Hishikawa; Yonson; Ku

    2010-01-01

    Few potentially curative treatment options exist apart from hepatic resection for patients with huge hepatocellular carcinoma (HCC). Proton radiotherapy is a promising new modality which has an inherent antitumor effect against HCC. However, the application of proton radiotherapy for tumors adjacent to the gastrointestinal tract is restricted because the tolerance dose of the intestine is extremely low. A novel two-step treatment was developed with surgical spacer placement and subsequent proton radiotherap...

  13. Effects of interspinous spacers on lumbar degenerative disease.

    Science.gov (United States)

    Zhou, Dong; Nong, Lu-Ming; DU, Rui; Gao, Gong-Ming; Jiang, Yu-Qing; Xu, Nan-Wei

    2013-03-01

    The present study aimed to evaluate the early effects of interspinous spacers on lumbar degenerative disease. The clinical outcomes of 23 patients with lumbar degenerative disease, treated using interspinous spacer implantation alone or combined with posterior lumbar fusion, were retrospectively studied and assessed with a visual analogue scale (VAS) and the Oswestry Disability Index (ODI). Pre-operative and post-operative interspinous distance, disc space height, foraminal width and height and segmental lordosis were determined. The early effects and complications associated with the interspinous spacers were recorded. The surgical procedures performed with the in-space treatment were easy and minimally invasive. The VAS scores and ODI were improved post-operatively compared with pre-operatively. Significant changes in the interspinous distance, disc space height, foraminal width and height and segmental lordosis were noted. In-space treatment for degenerative lumbar disease is easy and safe, with good early effects. The in-space system provides an alternative treatment for lumbar degenerative disease.

  14. Impact of feed spacer and membrane modification by hydrophilic, bactericidal and biocidal coating on biofouling control

    KAUST Repository

    Araújo, Paula A.

    2012-06-01

    The influence of polydopamine- and polydopamine-. graft-poly(ethylene glycol)-coated feed spacers and membranes, copper-coated feed spacers, and commercially-available biostatic feed spacers on biofouling has been studied in membrane fouling simulators. Feed spacers and membranes applied in practical membrane filtration systems were used; biofouling development was monitored by feed channel pressure drop increase and biomass accumulation. Polydopamine and polydopamine-. g-PEG are hydrophilic surface modification agents expected to resist protein and bacterial adhesion, while copper feed spacer coatings and biocides infused in feed spacers are expected to restrict biological growth. Our studies showed that polydopamine and polydopamine-. g-PEG coatings on feed spacers and membranes, copper coatings on feed spacers, and a commercial biostatic feed spacer did not have a significant impact on feed channel pressure drop increase and biofilm accumulation as measured by ATP and TOC content. The studied spacer and membrane modifications were not effective for biofouling control; it is doubtful that feed spacer and membrane modification, in general, may be effective for biofouling control regardless of the type of applied coating. © 2012 Elsevier B.V.

  15. Intergenic transcription, cell-cycle and the developmentally regulated epigenetic profile of the human beta-globin locus.

    Directory of Open Access Journals (Sweden)

    Joanne Miles

    Full Text Available Several lines of evidence have established strong links between transcriptional activity and specific post-translation modifications of histones. Here we show using RNA FISH that in erythroid cells, intergenic transcription in the human beta-globin locus occurs over a region of greater than 250 kb including several genes in the nearby olfactory receptor gene cluster. This entire region is transcribed during S phase of the cell cycle. However, within this region there are approximately 20 kb sub-domains of high intergenic transcription that occurs outside of S phase. These sub-domains are developmentally regulated and enriched with high levels of active modifications primarily to histone H3. The sub-domains correspond to the beta-globin locus control region, which is active at all developmental stages in erythroid cells, and the region flanking the developmentally regulated, active globin genes. These results correlate high levels of non-S phase intergenic transcription with domain-wide active histone modifications to histone H3.

  16. Molecular Epidemiology and Sequencing of the G-L Intergenic Region of Rabies Viruses Isolated in China

    Institute of Scientific and Technical Information of China (English)

    Sheng-Li MENG; QI-You XIAO; Guan-Mu DONG; Ge-Lin XU; Jia-Xin YAN; Ping-Gang MING; Jie WU; Xiao-Ming YANG; He-Tian MING; Feng-Cai ZHU; Dun-Jin ZHOU

    2007-01-01

    A group of 25 rabies viruses (RABVs),recovered from 24 dogs and one human case,were collected from various areas in China between 2004 and 2006.Genetic and phylogenetic analyses of the G-L intergenic region were carried out in 25 street RABV isolates and CTN vaccine strains of 7 generations.The study was based on the comparison of a 519 bp nucleotide sequence,encompassing the G-L intergenic region.The nucleotide sequence homologies of Chinese street strains were from 95.5% to 100%.The phylogenetic analysis showed that all Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and they were distributed according to their geographical origins.All of the Chinese strains were closely related but they could still be divided into two groups:group of street strains and group of CTN strains.This study presents details about the molecular epidemiology of rabies viruses based on the sequences of the G-L Intergenic region.

  17. Analytical investigation of the influence of spacer geometry and position on turbulent flow structure and parameters

    Energy Technology Data Exchange (ETDEWEB)

    Stosic, Z.V.; Stevanovic, V.D. [Framatome ANP GmbH - NBTT, Erlangen (Germany)

    2001-07-01

    Nuclear fuel rod bundle thermal-hydraulics strongly depends on the presence of fuel rod spacers. High Reynolds number coolant flows around spacers of different geometry and position are numerically investigated in two-dimensions. Predicted is the influence of the spacer's geometry and its position within a flow channel, on the recirculation zones formation and corresponding reattachment lengths. The numerical procedure is based on the two-equation k-{epsilon} turbulence model and the control volume procedure. Numerical simulation and analyses of high Reynolds fluid flow over the bluff bodies of the nuclear fuel spacer shapes are performed. Two types of flow channels and conditions are considered: spacers mounted on the wall and spacers in a free fluid stream. The major findings are as follows: 1) In fluid flow over the spacer mounted on the wall, the large recirculation zone is formed behind the spacer's fin. The reattachment length and width of this large vortex are increasing with the spacer's fin inclination angle increase. The reattachment length is rapidly increasing for fin inclination angles greater than 45 degrees. The maximum value of the reattachment length is achieved with fin inclination angle of 75 degrees. For angles from 75 to 90 degrees this length is slightly decreasing (the result with the Re=1.6*10{sup 6}). 2) A small vortex is formed in front of the spacer's fin in case of the flow over wall mounted spacer. 3) In case of fluid flow around the spacer in a free stream, the vortexes are formed behind the fin. Vortex shedding is observed, which is contrary to the formation of a stable vortex behind the wall mounted spacers. No small recirculation zone exists in front of the fin, which is opposite to the flow structure in case of wall mounted spacer. (authors)

  18. Development and characterization of 3D-printed feed spacers for spiral wound membrane systems

    KAUST Repository

    Siddiqui, Amber

    2016-01-02

    Feed spacers are important for the impact of biofouling on the performance of spiral-wound reverse osmosis (RO) and nanofiltration (NF) membrane systems. The objective of this study was to propose a strategy for developing, characterizing, and testing of feed spacers by numerical modeling, three-dimensional (3D) printing of feed spacers and experimental membrane fouling simulator (MFS) studies. The results of numerical modeling on the hydraulic behavior of various feed spacer geometries suggested that the impact of spacers on hydraulics and biofouling can be improved. A good agreement was found for the modeled and measured relationship between linear flow velocity and pressure drop for feed spacers with the same geometry, indicating that modeling can serve as first step in spacer characterization. An experimental comparison study of a feed spacer currently applied in practice and a 3D printed feed spacer with the same geometry showed (i) similar hydraulic behavior, (ii) similar pressure drop development with time and (iii) similar biomass accumulation during MFS biofouling studies, indicating that 3D printing technology is an alternative strategy for development of thin feed spacers with a complex geometry. Based on the numerical modeling results, a modified feed spacer with low pressure drop was selected for 3D printing. The comparison study of the feed spacer from practice and the modified geometry 3D printed feed spacer established that the 3D printed spacer had (i) a lower pressure drop during hydraulic testing, (ii) a lower pressure drop increase in time with the same accumulated biomass amount, indicating that modifying feed spacer geometries can reduce the impact of accumulated biomass on membrane performance. The combination of numerical modeling of feed spacers and experimental testing of 3D printed feed spacers is a promising strategy (rapid, low cost and representative) to develop advanced feed spacers aiming to reduce the impact of biofilm formation on

  19. Development and characterization of 3D-printed feed spacers for spiral wound membrane systems.

    Science.gov (United States)

    Siddiqui, Amber; Farhat, Nadia; Bucs, Szilárd S; Linares, Rodrigo Valladares; Picioreanu, Cristian; Kruithof, Joop C; van Loosdrecht, Mark C M; Kidwell, James; Vrouwenvelder, Johannes S

    2016-03-15

    Feed spacers are important for the impact of biofouling on the performance of spiral-wound reverse osmosis (RO) and nanofiltration (NF) membrane systems. The objective of this study was to propose a strategy for developing, characterizing, and testing of feed spacers by numerical modeling, three-dimensional (3D) printing of feed spacers and experimental membrane fouling simulator (MFS) studies. The results of numerical modeling on the hydrodynamic behavior of various feed spacer geometries suggested that the impact of spacers on hydrodynamics and biofouling can be improved. A good agreement was found for the modeled and measured relationship between linear flow velocity and pressure drop for feed spacers with the same geometry, indicating that modeling can serve as the first step in spacer characterization. An experimental comparison study of a feed spacer currently applied in practice and a 3D printed feed spacer with the same geometry showed (i) similar hydrodynamic behavior, (ii) similar pressure drop development with time and (iii) similar biomass accumulation during MFS biofouling studies, indicating that 3D printing technology is an alternative strategy for development of thin feed spacers with a complex geometry. Based on the numerical modeling results, a modified feed spacer with low pressure drop was selected for 3D printing. The comparison study of the feed spacer from practice and the modified geometry 3D printed feed spacer established that the 3D printed spacer had (i) a lower pressure drop during hydrodynamic testing, (ii) a lower pressure drop increase in time with the same accumulated biomass amount, indicating that modifying feed spacer geometries can reduce the impact of accumulated biomass on membrane performance. The combination of numerical modeling of feed spacers and experimental testing of 3D printed feed spacers is a promising strategy (rapid, low cost and representative) to develop advanced feed spacers aiming to reduce the impact of

  20. Aggregation behavior of a gemini surfactant with a tripeptide spacer.

    Science.gov (United States)

    Wang, Meina; Han, Yuchun; Qiao, Fulin; Wang, Yilin

    2015-02-28

    A peptide gemini surfactant, 12-G(NH2)LG(NH2)-12, has been constructed with two dodecyl chains separately attached to the two terminals of a glutamic acid-lysine-glutamic acid peptide and the aggregation behavior of the surfactant was studied in aqueous solution. The 12-G(NH2)LG(NH2)-12 molecules form fiber-like precipitates around pH 7.0, and the precipitation range is widened on increasing the concentration. At pHs 3.0 and 11.0, 12-G(NH2)LG(NH2)-12 forms soluble aggregates because each molecule carries two positively charged amino groups at the two ends of the peptide spacer at pH 3.0, while each molecule carries one negatively charged carboxyl group in the middle of the peptide spacer at pH 11.0. 12-G(NH2)LG(NH2)-12 displays a similar concentration-dependent process at these two pHs: forming small micelles above the critical micelle concentration and transferring to fibers at pH 3.0 or twisted ribbons at pH 11.0 above the second critical concentration. The fibers formed at pH 3.0 tend to aggregate into bundles with twisted structure. Both the twisted fibers at pH 3.0 and the twisted ribbons at pH 11.0 contain β-sheet structure formed by the peptide spacer. PMID:25588349

  1. Hydrodynamic evidence in support of spacer regions in chromatin.

    Science.gov (United States)

    Schmitz, K S; Shaw, B R

    1977-08-12

    Quasi-elastic light scattering and sedimentation velocity methods were used to study the hydrodynamic properties of purified dimer subunits obtained from partial digestion of chicken erythrocyte chromatin with staphylococcal nuclease. The experimental value of 1.87 +/- 0.08 X 10(-7) gram per second for the friction factor of these dimer subunits in low ionic strength buffer cannot be reasonably interpreted in terms of a contiguous sphere model. Analysis by means of an equivalent dimer method suggests that the spacer region accounts for a maximum of 19 percent of the friction properties of the dimer.

  2. Synthesis and properties of novel gemini surfactant with short spacer

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Cationic gemini surfactant dimethylene-1,2-bis(dodecyldiethylammonium bromide), referred to as C12C2C12(Et) was synthesized, and its surface property and aggregation behavior in aqueous solution were studied. The value of γat the critical micelle concentration (γcmc) is much smaller than that of the surfactant homologues with longer spacer. Spherical and elongated micelles were formed in the aqueous solution of this gemini surfactant,and the spherical micelles were absolutely dominant compared to the elongated micelles at our studied concentration quantitatively.

  3. Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

    DEFF Research Database (Denmark)

    Liu, Tao; Li, Yingjun; Wang, Xiaodi;

    2015-01-01

    , it was demonstrated that the transcription level of csa1, cas1, cas2 and cas4 was significantly enhanced in a csa3a-overexpression strain and, moreover, the Csa1 and Cas1 protein levels were increased in this strain. Furthermore, we demonstrated the hyperactive uptake of unique spacers within both CRISPR loci......Acquisition of de novo spacer sequences confers CRISPR-Cas with a memory to defend against invading genetic elements. However, the mechanism of regulation of CRISPR spacer acquisition remains unknown. Here we examine the transcriptional regulation of the conserved spacer acquisition genes in Type I...... in the presence of the csa3a overexpression vector. The spacer acquisition process is dependent on the CCN PAM sequence and protospacer selection is random and non-directional. These results suggested a regulation mechanism of CRISPR spacer acquisition where a single transcriptional regulator senses the presence...

  4. Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Jianqin Li

    Full Text Available Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8 and 5 are negatively correlated (r<-0.8. The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.

  5. Packaging design criteria modified fuel spacer burial box. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, P.F.

    1994-09-13

    Various Hanford facilities must transfer large radioactively contaminated items to burial/storage. Presently, there are eighteen Fuel Spacer Burial Boxes (FSBBs) available on the Hanford Site for transport of such items. Previously, the FSBBS were transported from a rail car to the burial trench via a drag-off operation. To allow for the lifting of the boxes into the burial trench, it will be necessary to improve the packagings lifting attachments and provide structural reinforcement. Additional safety improvements to the packaging system will be provided by the addition of a positive closure system and package ventilation. FSBBs that are modified in such a manner are referred to as Modified Fuel Spacer Burial Boxes (MFSBs). The criteria provided by this PDC will be used to demonstrate that the transfer of the MFSB will provide an equivalent degree of safety as would be provided by a package meeting offsite transportation requirements. This fulfills the onsite transportation safety requirements implemented in WHC-CM-2-14, Hazardous Material Packaging and Shipping. A Safety Analysis Report for Packaging (SARP) will be prepared to evaluate the safety of the transfer operation. Approval of the SARP is required to authorize transfer. Criteria are also established to ensure burial requirements are met.

  6. Genomic organization of Tropomodulins 2 and 4 and unusual intergenic and intraexonic splicing of YL-1 and Tropomodulin 4

    Directory of Open Access Journals (Sweden)

    Zoghbi Huda Y

    2001-10-01

    Full Text Available Abstract Background The tropomodulins (TMODs are a family of proteins that cap the pointed ends of actin filaments. Four TMODs have been identified in humans, with orthologs in mice. Mutations in actin or actin-binding proteins have been found to cause several human diseases, ranging from hypertrophic cardiomyopathy to immunodefiencies such as Wiskott-Aldrich syndrome. We had previously mapped Tropomodulin 2 (TMOD2 to the genomic region containing the gene for amyotrophic lateral sclerosis 5 (ALS5. We determined the genomic structure of Tmod2 in order to better analyze patient DNA for mutations; we also determined the genomic structure of Tropomodulin 4 (TMOD4. Results In this study, we determined the genomic structure of TMOD2 and TMOD4 and found the organization of both genes to be similar. Sequence analysis of TMOD2 revealed no mutations or polymorphisms in ALS5 patients or controls. Interestingly, we discovered that another gene, YL-1, intergenically splices into TMOD4. YL-1 encodes six exons, the last of which is 291 bp from a 5' untranslated exon of TMOD4. We used 5' RACE and RT-PCR from TMOD4 to identify several intergenic RACE products. YL-1 was also found to undergo unconventional splicing using non-canonical splice sites within exons (intraexonic splicing to produce several alternative transcripts. Conclusions The genomic structure of TMOD2 and TMOD4 have been delineated. This should facilitate future mutational analysis of these genes. In addition, intergenic splicing at TMOD4/YL-1 was discovered, demonstrating yet another level of complexity of gene organization and regulation.

  7. Nanoparticle-Based Brachytherapy Spacers for Delivery of Localized Combined Chemoradiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Rajiv, E-mail: r.kumar@neu.edu [Nanomedicine Science and Technology Center, Northeastern University, Boston, Massachusetts (United States); Department of Radiation Oncology, Brigham and Women' s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts (United States); Belz, Jodi [Nanomedicine Science and Technology Center, Northeastern University, Boston, Massachusetts (United States); Markovic, Stacey [Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts (United States); Jadhav, Tej; Fowle, William [Nanomedicine Science and Technology Center, Northeastern University, Boston, Massachusetts (United States); Niedre, Mark [Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts (United States); Cormack, Robert; Makrigiorgos, Mike G. [Department of Radiation Oncology, Brigham and Women' s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts (United States); Sridhar, Srinivas [Nanomedicine Science and Technology Center, Northeastern University, Boston, Massachusetts (United States); Department of Radiation Oncology, Brigham and Women' s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts (United States)

    2015-02-01

    Purpose: In radiation therapy (RT), brachytherapy-inert source spacers are commonly used in clinical practice to achieve high spatial accuracy. These implanted devices are critical technical components of precise radiation delivery but provide no direct therapeutic benefits. Methods and Materials: Here we have fabricated implantable nanoplatforms or chemoradiation therapy (INCeRT) spacers loaded with silica nanoparticles (SNPs) conjugated containing a drug, to act as a slow-release drug depot for simultaneous localized chemoradiation therapy. The spacers are made of poly(lactic-co-glycolic) acid (PLGA) as matrix and are physically identical in size to the commercially available brachytherapy spacers (5 mm × 0.8 mm). The silica nanoparticles, 250 nm in diameter, were conjugated with near infrared fluorophore Cy7.5 as a model drug, and the INCeRT spacers were characterized in terms of size, morphology, and composition using different instrumentation techniques. The spacers were further doped with an anticancer drug, docetaxel. We evaluated the in vivo stability, biocompatibility, and biodegradation of these spacers in live mouse tissues. Results: The electron microscopy studies showed that nanoparticles were distributed throughout the spacers. These INCeRT spacers remained stable and can be tracked by the use of optical fluorescence. In vivo optical imaging studies showed a slow diffusion of nanoparticles from the spacer to the adjacent tissue in contrast to the control Cy7.5-PLGA spacer, which showed rapid disintegration in a few days with a burst release of Cy7.5. The docetaxel spacers showed suppression of tumor growth in contrast to control mice over 16 days. Conclusions: The imaging with the Cy7.5 spacer and therapeutic efficacy with docetaxel spacers supports the hypothesis that INCeRT spacers can be used for delivering the drugs in a slow, sustained manner in conjunction with brachytherapy, in contrast to the rapid clearance of the drugs when

  8. Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis

    Directory of Open Access Journals (Sweden)

    Bose Mridula

    2010-04-01

    Full Text Available Abstract Background The mce operons play an important role in the entry of M. tuberculosis into macrophages and non-phagocytic cells. Their non-redundant function as well as complex regulation is implied by the phenotype of mce mutants. Recently, mce1 operon was found to extend over 13 genes, fadD5 (Rv0166 being the first gene of the operon. The presence of a non-coding sequence of 200 base pairs between Rv0166 and Rv0167 is peculiar to mce1 among the four mce operons of M.tuberculosis. We have examined the function of this region. Results We predicted putative promoter activity of the 200 base pairs of non-coding, intergenic region between Rv0166 and Rv0167 in silico using MEME software and designate it as intergenic promoter, IGPr. We demonstrate both promoter activity and a putative negative regulatory function of this fragment by reporter assays carried out in the surrogate host M.smegmatis. We find that the repressive elements not only control the native promoter but also repress a heterologous promoter of M.smegmatis. The higher activity of the intergenic promoter in a clinical isolate in comparison with the wild type sequence from M.tuberculosis H37Rv could be correlated with a point mutation within the negative element. We have mapped two transcription start sites for mce1 operon both of which are utilized in M.tuberculosis H37Rv as well as the clinical isolate VPCI591. Our studies show that the promoter activity in the non-coding region is relevant not only in reporter gene expression but also in the expression of mce1 operon in M. tuberculosis cells grown in synthetic medium. Conclusion The mce operon of M.tuberculosis H37Rv potentially can be transcribed from two promoters P1 and P2, former mapping upstream of Rv0166 and the latter in the non-coding intergenic region between Rv0166 and Rv0167. The transcription initiation from P1 results in a transcript with Rv0166 while that from P2 will be without it. The sequences between the

  9. Measurement and CFD calculation of spacer loss coefficient for a tight-lattice fuel bundle

    International Nuclear Information System (INIS)

    Highlights: • Experiment and CFD analysis evaluated the pressure drop in a spacer grid. • The measurement and CFD errors for the spacer loss coefficient were estimated. • The spacer loss coefficient for the dual-cooled annular fuel bundle was determined. • The CFD prediction agrees with the measured spacer loss coefficient within 8%. - Abstract: An experiment and computational fluid dynamics (CFD) analysis were performed to evaluate the pressure drop in a spacer grid for a dual-cooled annular fuel (DCAF) bundle. The DCAF bundle for the Korean optimum power reactor (OPR1000) is a 12 × 12 tight-lattice rod array with a pitch-to-diameter ratio of 1.08 owing to a larger outer diameter of the annular fuel rod. An experiment was conducted to measure the pressure drop in spacer grid for the DCAF bundle. The test bundle is a full-size 12 × 12 rod bundle with 11 spacer grid. The test condition covers a Reynolds number range of 2 × 104–2 × 105 by changing the temperature and flow rate of water. A CFD analysis was also performed to predict the pressure drop through a spacer grid using the full-size and partial bundle models. The pressure drop and loss coefficient of a spacer grid were predicted and compared with the experimental results. The CFD predictions of spacer pressure drop and loss coefficient agree with the measured values within 8%. The spacer loss coefficient for the DCAF bundle is estimated to be approximately 1.50 at a nominal operating condition of OPR1000, i.e., Re = 4 × 105

  10. Synthesis and Properties of Gemini Cationic Surfactants with Amide Spacers

    Institute of Scientific and Technical Information of China (English)

    DENG Qi-gang; YU Hong-wei; LIN Hong; JIA Li-hua; GUO Xiang-feng; ZHOU De-rui

    2005-01-01

    Four gemini cationic surfactants {N,N'-di[2-(lauryldimethylamino)acetyl]polymethylenediamine dichloride, LAA-s-LAA, s=2,3,4,6} were synthesized by using four bis(α-chloroacetamide)s and N,N-dimethyllaurylamine, respectively. The molecular structures were characterized by means of IR, 1H NMR, 13C NMR and MS, and the behavior of their aqueous solutions was studied. The critical micell concentrations(CMC) of LAA-s-LAA were one order of magnitude lower than that of dodecyltrimethyl ammonium chloride(DTAC). With the change of the length of spacer chain(s), their CMC values change, and CMC reaches the top value at s=4.

  11. Vibration of the Package of Rods Linked by Spacer Grids

    Science.gov (United States)

    Zeman, V.; Hlaváč, Z.

    This paper deals with modelling and vibration analysis of the large package of identical parallel rods which are linked by transverse springs (spacer grids) placed on several level spacings. The vibration of rods is caused by the support plate motion. The rod discretization by FEM is based on Rayleigh beam theory. With respect to cyclic and central package rod symmetry, the system is decomposed to identical revolved rod segments. The modal synthesis method with condensation of the rod segments is used for modelling and determination of steady forced vibration of the whole system. The presented method is the first step to modelling of the nuclear fuel assembly vibration caused by kinematical excitation determined by motion of the support plates which are part of the reactor core.

  12. All-Trans Retinoic Acid Induces Expression of a Novel Intergenic Long Noncoding RNA in Adult rat Primary Hippocampal Neurons.

    Science.gov (United States)

    Kour, Sukhleen; Rath, Pramod C

    2016-02-01

    Around 90% of the mammalian genome undergoes pervasive transcription into various types of small and long regulatory noncoding RNAs, whereas only ∼ 1.5% codes for proteins. Long noncoding RNAs (lncRNAs) constitute diverse classes of sense- and antisense transcripts that are abundantly expressed in the mammalian central nervous system (CNS) in cell type- and developmental stage-specific manners. They are implicated in brain development, differentiation, neuronal plasticity, and other cognitive functions. Mammalian brain requires the vitamin A metabolite all-trans retinoic acid (atRA) for its normal development, differentiation, and cell-fate determination. However, its role in adult brain function is less understood. Here, we report atRA-mediated transcriptional upregulation of endogenous expression of a novel long intergenic noncoding RNA-rat brain expressed (LINC-RBE) in cultured primary hippocampal neurons from adult rat. We have previously reported LINC-RBE as an intergenic, simple repeat sequence containing lncRNA highly expressed in the rat brain. This is a first-time report of involvement of atRA in transcriptional upregulation of lncRNA expression in rat hippocampal neurons. Therefore, it may be involved in regulation of brain function and disease. PMID:26572536

  13. Development of a new spacer grid form to enhance the integrity of fuel rod support and the crush strength of a spacer grid assembly

    International Nuclear Information System (INIS)

    A spacer grid is one of the most important structural components in a PWR fuel assembly. The spacer grid, which supports nuclear fuel rods laterally and vertically with a friction grip, is an interconnected array of slotted grid straps welded at the intersections to form an egg crate structure. Dimples and springs are stamped into each grid strap to support the fuel rods. The form of grid straps and spring form is known to be closely related with the crush strength of spacer grid assembly and the integrity of fuel rod support, respectively. Zircaloy is prevailing as the material of the spacer grid because of its low neutron absorption characteristic and its successful extensive in reactor use. The primary considerations are to provide a Zircaloy spacer grid with crush strength sufficient to resist design basis loads, without significantly increasing pressure drop across the reactor core. Generally, the thickness and height of the Zircaloy grid strap have been the main design variables in order to meet the above considerations. Recently, it was reported that a dimple location is also a design variable that affects the crush strength of a spacer grid. In this study, a new spacer grid form was developed in order to enhance the integrity of the fuel rod support and the crush strength of the spacer grid assembly by using a systematic optimization technique. The enhancement of fuel rod support was confirmed by comparisons of contact area, peak stresses, plastic deformation and etc. while the enhancement of crush strength was investigated for a 3x3 and 7x7 sub size support grid as a preliminary parameter study for a 16x16 full size support grid. The 3x3 model is chosen to facilitate quick computation for optimization and the 7x7 model is chosen to verify the enhancement

  14. Ertapenem Articulating Spacer for the Treatment of Polymicrobial Total Knee Arthroplasty Infection.

    Science.gov (United States)

    Radoicic, Dragan; Milanovic, Milomir; Marinkovic, Jugoslav; Radoicic, Danica

    2016-01-01

    Introduction. Periprosthetic joint infections (PJIs) are the primary cause of early failure of the total knee arthroplasty (TKA). Polymicrobial TKA infections are often associated with a higher risk of treatment failure. The aim of the study was to assess the efficacy of ertapenem loaded spacers in the treatment of polymicrobial PJI. Methods. There were 18 patients enrolled; nine patients with polymicrobial PJI treated with ertapenem loaded articulating spacers were compared to the group of 9 patients treated with vancomycin or ceftazidime loaded spacers. Results. Successful reimplantation with revision implants was possible in 66.67%. Ertapenem spacers were used in 6 cases in primary two-stage procedure and in 3 cases in secondary spacer exchange. Successful infection eradication was achieved in all cases; final reimplantation with revision knee arthroplasty implants was possible in 6 cases. Conclusion. Ertapenem can be successfully used as antimicrobial addition to the cement spacers in two-stage revision treatment of polymicrobial PJIs. However, this type of spacer may also be useful in the treatment of infections caused by monomicrobial extended spectrum beta-lactamases producing gram-negative bacilli. Further clinical studies are required to evaluate the efficacy and safety of ertapenem spacers in the treatment of polymicrobial and monomicrobial PJIs. PMID:27366173

  15. Ertapenem Articulating Spacer for the Treatment of Polymicrobial Total Knee Arthroplasty Infection

    Directory of Open Access Journals (Sweden)

    Dragan Radoicic

    2016-01-01

    Full Text Available Introduction. Periprosthetic joint infections (PJIs are the primary cause of early failure of the total knee arthroplasty (TKA. Polymicrobial TKA infections are often associated with a higher risk of treatment failure. The aim of the study was to assess the efficacy of ertapenem loaded spacers in the treatment of polymicrobial PJI. Methods. There were 18 patients enrolled; nine patients with polymicrobial PJI treated with ertapenem loaded articulating spacers were compared to the group of 9 patients treated with vancomycin or ceftazidime loaded spacers. Results. Successful reimplantation with revision implants was possible in 66.67%. Ertapenem spacers were used in 6 cases in primary two-stage procedure and in 3 cases in secondary spacer exchange. Successful infection eradication was achieved in all cases; final reimplantation with revision knee arthroplasty implants was possible in 6 cases. Conclusion. Ertapenem can be successfully used as antimicrobial addition to the cement spacers in two-stage revision treatment of polymicrobial PJIs. However, this type of spacer may also be useful in the treatment of infections caused by monomicrobial extended spectrum beta-lactamases producing gram-negative bacilli. Further clinical studies are required to evaluate the efficacy and safety of ertapenem spacers in the treatment of polymicrobial and monomicrobial PJIs.

  16. Optimized spacer layer thickness for plasmonic-induced enhancement of photocurrent in a-Si:H

    Energy Technology Data Exchange (ETDEWEB)

    Saleh, Z. M., E-mail: zaki.saleh@aauj.edu, E-mail: zakimsaleh@yahoo.com; Nasser, H.; Özkol, E.; Günöven, M.; Abak, K. [Middle East Technical University, Center for Solar Energy Research and Applications (GÜNAM) (Turkey); Canli, S. [Middle East Technical University, Central Laboratory (Turkey); Bek, A.; Turan, R. [Middle East Technical University, Center for Solar Energy Research and Applications (GÜNAM) (Turkey)

    2015-10-15

    Plasmonic interfaces consisting of silver nanoparticles of different sizes (50–100 nm) have been processed by the self-assembled dewetting technique and integrated to hydrogenated amorphous silicon (a-Si:H) using SiNx spacer layers to investigate the dependence of optical trapping enhancement on spacer layer thickness through the enhancements in photocurrent. Samples illuminated from the a-Si:H side exhibit a localized surface plasmon resonance (LSPR) that is red-shifted with the increasing particle size and broadened into the red with the increasing spacer layer thickness. The photocurrent measured in a-Si:H is not only consistent with the red-shift and broadening of the LSPR, but exhibits critical dependence on the spacer layer thickness also. The samples with plasmonic interfaces and a SiNx spacer layer exhibit appreciable enhancement of photocurrent compared with flat a-Si:H reference depending on the size of the Ag nanoparticle. Simulations conducted on one-dimensional square structures exhibit electric fields that are localized near the plasmonic structures but extend appreciably into the higher refractive index a-Si:H. These simulations produce a clear red-shift and broadening of extinction spectra for all spacer layer thicknesses and predict an enhancement in photocurrent in agreement with experimental results. The spectral dependence of photocurrent for six plasmonic interfaces with different Ag nanoparticle sizes and spacer layer thicknesses are correlated with the optical spectra and compared with the simulations to predict an optimal spacer layer thickness.

  17. Optimized spacer layer thickness for plasmonic-induced enhancement of photocurrent in a-Si:H

    International Nuclear Information System (INIS)

    Plasmonic interfaces consisting of silver nanoparticles of different sizes (50–100 nm) have been processed by the self-assembled dewetting technique and integrated to hydrogenated amorphous silicon (a-Si:H) using SiNx spacer layers to investigate the dependence of optical trapping enhancement on spacer layer thickness through the enhancements in photocurrent. Samples illuminated from the a-Si:H side exhibit a localized surface plasmon resonance (LSPR) that is red-shifted with the increasing particle size and broadened into the red with the increasing spacer layer thickness. The photocurrent measured in a-Si:H is not only consistent with the red-shift and broadening of the LSPR, but exhibits critical dependence on the spacer layer thickness also. The samples with plasmonic interfaces and a SiNx spacer layer exhibit appreciable enhancement of photocurrent compared with flat a-Si:H reference depending on the size of the Ag nanoparticle. Simulations conducted on one-dimensional square structures exhibit electric fields that are localized near the plasmonic structures but extend appreciably into the higher refractive index a-Si:H. These simulations produce a clear red-shift and broadening of extinction spectra for all spacer layer thicknesses and predict an enhancement in photocurrent in agreement with experimental results. The spectral dependence of photocurrent for six plasmonic interfaces with different Ag nanoparticle sizes and spacer layer thicknesses are correlated with the optical spectra and compared with the simulations to predict an optimal spacer layer thickness

  18. Effect of Structure on the Mechanical Behaviors of Three-Dimensional Spacer Fabric Composites

    Science.gov (United States)

    Li, Min; Wang, Shaokai; Zhang, Zuoguang; Wu, Boming

    2009-02-01

    Three-dimensional (3-D) spacer fabric composite is a newly developed sandwich structure, the reinforcement of which is integrally woven by advanced textile technique. Two facesheets of 3-D spacer fabric are connected by continuous fibers, named pile in the core, providing excellent properties like outstanding integrity, debonding resistance, light weight, good designability and so on. Usually the 3-D spacer fabric composite without extra reinforcement is a kind of core material. In comparison with the facesheet reinforced spacer fabric composite, here the composite without additional weaves is called mono-spacer fabric composite. In this paper, two kinds of mono-spacer fabric composites with integrated hollow cores have been developed, one with 8-shaped piles and the other with corrugated piles. The mechanical characteristics and the damage modes of these mono-spacer fabric composites under different load conditions have been investigated. Besides, effects of pile height, pile distribution density and pile structure on the composites mechanical performances were analyzed. It is shown that the mechanical performances of mono-spacer fabric composites can be widely adapted to the respective requirements through the choice of the structural factors.

  19. Barriers and supports to implementation of MDI/spacer use in nine Canadian pediatric emergency departments: a qualitative study

    OpenAIRE

    Graham Ian D; O'Leary Kathy A; Osmond Martin H; Scott Shannon D; Grimshaw Jeremy; Klassen Terry

    2009-01-01

    Abstract Background Despite recent research supporting the use of metered dose inhalers with spacer devices (MDI/spacers) in pediatric emergency departments (PEDs) for acute exacerbations of asthma, uptake of this practice has been slow. The objectives of this study were to determine the barriers and supports to implementing MDI/spacer research and to identify factors associated with early and late adoption of MDI/spacers in Canadian PEDs. Methods Using a comparative case study design, we cla...

  20. Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals

    Science.gov (United States)

    Chernikova, Diana; Managadze, David; Glazko, Galina V.; Makalowski, Wojciech; Rogozin, Igor B.

    2016-01-01

    The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. PMID:27429005

  1. Antibiotic-impregnated articulating cement spacer for infected total knee arthroplasty

    Directory of Open Access Journals (Sweden)

    Parag Garg

    2011-01-01

    Full Text Available Background : Standard treatment of chronic infected total knee arthroplasty (TKA is a two-stage revision, the first step being placement of an antibiotic-impregnated cement spacer. Here we describe the results of a new technique (modification of the Goldstien′s technique for intraoperative manufacture of a customized articulating spacer at minimal cost and with relatively good conformity and longevity. Materials and Methods : Thirty-six infected knees underwent this procedure from June 2002 to May 2007. The technique consists of using the freshened femur and tibia interface as molds wrapped in a tin foil for manufacturing the two components of the spacer with antibiotic-impregnated methyl methycrylate cement. We used the spacer and the femoral component of the trial set of a TKA system to mold them to perfect articulation. We also reinforced the spacer with a K-wire scaffold to prevent fracture of the cement mantle in the last 21 cases. Results : All 36 knees showed excellent results in terms of infection control, mobility, and stability. There was significant improvement in the WOMAC and Knee Society Scores (20 and 39 points respectively. There were two fractures of the spacers in the initial 15 cases that did not have K-wire scaffolding but none in the last 21 that had reinforcement. Conclusion : This technique provides a more conforming spacer, with good range of motion and stability. The reinforcement helps in preventing the fracture of the cement mantle and is cost effective.

  2. Modulation of porphyrin photoluminescence by nanoscale spacers on silicon substrates

    Science.gov (United States)

    Fang, Y. C.; Zhang, Y.; Gao, H. Y.; Chen, L. G.; Gao, B.; He, W. Z.; Meng, Q. S.; Zhang, C.; Dong, Z. C.

    2013-11-01

    We investigate photoluminescence (PL) properties of quasi-monolayered tetraphenyl porphyrin (TPP) molecules on silicon substrates modulated by three different nanoscale spacers: native oxide layer (NOL), hydrogen (H)-passivated layer, and Ag nanoparticle (AgNP) thin film, respectively. In comparison with the PL intensity from the TPP molecules on the NOL-covered silicon, the fluorescence intensity from the molecules on the AgNP-covered surface was greatly enhanced while that for the H-passivated surface was found dramatically suppressed. Time-resolved fluorescence spectra indicated shortened lifetimes for TPP molecules in both cases, but the decay kinetics is believed to be different. The suppressed emission for the H-passivated sample was attributed to the weaker decoupling effect of the monolayer of hydrogen atoms as compared to the NOL, leading to increased nonradiative decay rate; whereas the enhanced fluorescence with shortened lifetime for the AgNP-covered sample is attributed not only to the resonant excitation by local surface plasmons, but also to the increased radiative decay rate originating from the emission enhancement in plasmonic "hot-spots".

  3. Modulation of porphyrin photoluminescence by nanoscale spacers on silicon substrates

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Y.C. [Department of Vacuum Science and Engineering, Hefei University of Technology, Hefei, Anhui, 230009 (China); HFNL, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Zhang, Y.; Gao, H.Y.; Chen, L.G.; Gao, B.; He, W.Z.; Meng, Q.S.; Zhang, C. [HFNL, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Dong, Z.C., E-mail: zcdong@ustc.edu.cn [HFNL, University of Science and Technology of China, Hefei, Anhui, 230026 (China)

    2013-11-15

    We investigate photoluminescence (PL) properties of quasi-monolayered tetraphenyl porphyrin (TPP) molecules on silicon substrates modulated by three different nanoscale spacers: native oxide layer (NOL), hydrogen (H)-passivated layer, and Ag nanoparticle (AgNP) thin film, respectively. In comparison with the PL intensity from the TPP molecules on the NOL-covered silicon, the fluorescence intensity from the molecules on the AgNP-covered surface was greatly enhanced while that for the H-passivated surface was found dramatically suppressed. Time-resolved fluorescence spectra indicated shortened lifetimes for TPP molecules in both cases, but the decay kinetics is believed to be different. The suppressed emission for the H-passivated sample was attributed to the weaker decoupling effect of the monolayer of hydrogen atoms as compared to the NOL, leading to increased nonradiative decay rate; whereas the enhanced fluorescence with shortened lifetime for the AgNP-covered sample is attributed not only to the resonant excitation by local surface plasmons, but also to the increased radiative decay rate originating from the emission enhancement in plasmonic “hot-spots”.

  4. APPLICATIONS OF SPACERS MADE WITH DOUBLE BAR RASCHEL MACHINE

    Directory of Open Access Journals (Sweden)

    DÍAZ-GARCÍA Pablo

    2016-05-01

    Full Text Available Nowadays, textile technologies develop to adapt their different techniques for creating new products for the different sectors of application every day. Particularly, warp knitted fabrics and warp-knitting technology have applications in all different groups of technical textiles. It could be the most applied technique, the most versatile technology to develop new textile products for the new textile market. Warp knitted fabrics play the most important role among the technical textile fabrics. This technology is used in different product groups such as mobile textiles (car seat covers, dashboard cover, industrial textiles (composites, medical textiles (anti-decubitus blankets, sports textiles and foundation garments (bra cups, pads for swimwear. This study presents some examples of the application of this technology in some markets Within the market of technical textile, medical textile has an increasing relevance and knitted fabrics and knitting technology, at the same time, play a very important role in the fields of technical and medical textiles. Studies have demonstrated that knitted structures possess excellent mechanical properties and can promote more effective regenerative medicine, tissue repair, ligament, tendon cartilage, reconstruction, etc. The aim of this paper is to present different possibilities of textiles developed with this kind of structures, to present different alternatives, different examples of products obtained with this kind of textile structure combined with the correct kind of textile fiber. In this kind of technology, double-bar Raschel machines used for producing three-dimensional textiles, spacers, play an important role.

  5. Enterobacterial repetitive intergenic consensus 1R PCR assay for detection of Raoultella sp. isolates among strains identified as Klebsiella oxytoca in the clinical laboratory.

    Science.gov (United States)

    Granier, Sophie A; Leflon-Guibout, Véronique; Goldstein, Fred W; Nicolas-Chanoine, Marie-Hélène

    2003-04-01

    The enterobacterial repetitive intergenic consensus 1R PCR method, which provided recognizable profiles for reference strains of the three species of Raoultella and the two genetic groups of Klebsiella oxytoca, was applied to 19 clinical isolates identified as K. oxytoca. By this method, as confirmed by species-specific gene sequencing, two Raoultella ornithinolytica and two unclassifiable K. oxytoca isolates were identified.

  6. A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoter.

    Science.gov (United States)

    Lehmeyer, Mona; Hanko, Erik K R; Roling, Lena; Gonzalez, Lilian; Wehrs, Maren; Hehl, Reinhard

    2016-06-01

    The high gene density in Arabidopsis thaliana leaves only relatively short intergenic regions for potential cis-regulatory sequences. To learn more about the regulation of genes harbouring only very short upstream intergenic regions, this study investigates a recently identified novel microbe-associated molecular pattern (MAMP)-responsive cis-sequence located within the 101 bp long intergenic region upstream of the At1g13990 gene. It is shown that the cis-regulatory sequence is sufficient for MAMP-responsive reporter gene activity in the context of its native promoter. The 3' UTR of the upstream gene has a quantitative effect on gene expression. In context of a synthetic promoter, the cis-sequence is shown to achieve a strong increase in reporter gene activity as a monomer, dimer and tetramer. Mutation analysis of the cis-sequence determined the specific nucleotides required for gene expression activation. In transgenic A. thaliana the synthetic promoter harbouring a tetramer of the cis-sequence not only drives strong pathogen-responsive reporter gene expression but also shows a high background activity. The results of this study contribute to our understanding how genes with very short upstream intergenic regions are regulated and how these regions can serve as a source for MAMP-responsive cis-sequences for synthetic promoter design. PMID:26833485

  7. Alfalfa microsymbionts from different ITS and nodC lineages of Ensifer meliloti and Ensifer medicae symbiovar meliloti establish efficient symbiosis with alfalfa in Spanish acid soils.

    Science.gov (United States)

    Ramírez-Bahena, Martha-Helena; Vargas, Margarita; Martín, María; Tejedor, Carmen; Velázquez, Encarna; Peix, Álvaro

    2015-06-01

    Alfalfa (Medicago sativa L.) is an important crop worldwide whose cropping in acid soils is hampered by the poor nodulation and yield commonly attributed to the sensitivity of its endosymbionts to acid pH. In this work, we isolated several acid-tolerant strains from alfalfa nodules in three acid soils in northwestern Spain. After grouping by RAPD fingerprinting, most strains were identified as Ensifer meliloti and only two strains as Ensifer medicae according to their 16S-23S intergenic spacer (ITS) sequences that allowed the differentiation of two groups within each one of these species. The two ITS groups of E. meliloti and the ITS group I of E. medicae have been previously found in Medicago nodules; however, the group II of E. medicae has been only found to date in Prosopis alba nodules. The analysis of the nodC gene showed that all strains isolated in this study belong to the symbiovar meliloti, grouping with the type strains of E. meliloti or E. medicae, but some harboured nodC gene alleles different from those found to date in alfalfa nodules. The strains of E. medicae belong to the symbiovar meliloti which should be also recognised in this species, although they harboured a nodC allele phylogenetically divergent to those from E. meliloti strains. Microcosm experiments showed that inoculation of alfalfa with selected acid-tolerant strains significantly increased yields in acid soils representing a suitable agricultural practice for alfalfa cropping in these soils. PMID:25586575

  8. Identification of Arcanobacterium pyogenes isolated by post mortem examinations of a bearded dragon and a gecko by phenotypic and genotypic properties

    Science.gov (United States)

    Ülbegi-Mohyla, H.; Hijazin, M.; Alber, J.; Hassan, A. A.; Abdulmawjood, A.; Prenger-Berninghoff, E.; Weiß, R.; Zschöck, M.

    2010-01-01

    The present study was designed to identify phenotypically and genotypically two Arcanobacterium (A.) pyogenes strains isolated by post mortem examinations of a bearded dragon and a gecko. The A. pyogenes strains showed the typical biochemical properties and displayed CAMP-like synergistic hemolytic activities with various indicator strains. The species identity could be confirmed genotypically by amplification and sequencing of the 16S rDNA gene and, as novel target gene, by sequencing of the beta subunit of RNA polymerase encoding gene rpoB, of both strains and of reference strains representing nine species of the genus Arcanobacterium. The species identity of the two A. pyogenes strains could additionally be confirmed by PCR mediated amplification of species specific parts of the 16S-23S rDNA intergenic spacer region, the pyolysin encoding gene plo and by amplification of the collagen-binding protein encoding gene cbpA. All these molecular targets might help to improve the future identification and further characterization of A. pyogenes which, as demonstrated in the present study, could also be isolated from reptile specimens. PMID:20706035

  9. Identification of Arcanobacterium pyogenes isolated by post mortem examinations of a bearded dragon and a gecko by phenotypic and genotypic properties.

    Science.gov (United States)

    Ulbegi-Mohyla, H; Hijazin, M; Alber, J; Lämmler, C; Hassan, A A; Abdulmawjood, A; Prenger-Berninghoff, E; Weiss, R; Zschöck, M

    2010-09-01

    The present study was designed to identify phenotypically and genotypically two Arcanobacterium (A.) pyogenes strains isolated by post mortem examinations of a bearded dragon and a gecko. The A. pyogenes strains showed the typical biochemical properties and displayed CAMP-like synergistic hemolytic activities with various indicator strains. The species identity could be confirmed genotypically by amplification and sequencing of the 16S rDNA gene and, as novel target gene, by sequencing of the beta subunit of RNA polymerase encoding gene rpoB, of both strains and of reference strains representing nine species of the genus Arcanobacterium. The species identity of the two A. pyogenes strains could additionally be confirmed by PCR mediated amplification of species specific parts of the 16S-23S rDNA intergenic spacer region, the pyolysin encoding gene plo and by amplification of the collagen-binding protein encoding gene cbpA. All these molecular targets might help to improve the future identification and further characterization of A. pyogenes which, as demonstrated in the present study, could also be isolated from reptile specimens. PMID:20706035

  10. Diversity and antimicrobial properties of lactic acid bacteria isolated from rhizosphere of olive trees and desert truffles of Tunisia.

    Science.gov (United States)

    Fhoula, Imene; Najjari, Afef; Turki, Yousra; Jaballah, Sana; Boudabous, Abdelatif; Ouzari, Hadda

    2013-01-01

    A total of 119 lactic acid bacteria (LAB) were isolated, by culture-dependant method, from rhizosphere samples of olive trees and desert truffles and evaluated for different biotechnological properties. Using the variability of the intergenic spacer 16S-23S and 16S rRNA gene sequences, the isolates were identified as the genera Lactococcus, Pediococcus, Lactobacillus, Weissella, and Enterococcus. All the strains showed proteolytic activity with variable rates 42% were EPS producers, while only 10% showed the ability to grow in 9% NaCl. In addition, a low rate of antibiotic resistance was detected among rhizospheric enterococci. Furthermore, a strong antibacterial activity against plant and/or pathogenic bacteria of Stenotrophomonas maltophilia, Pantoea agglomerans, Pseudomonas savastanoi, the food-borne Staphylococcus aureus, and Listeria monocytogenes was recorded. Antifungal activity evaluation showed that Botrytis cinerea was the most inhibited fungus followed by Penicillium expansum, Verticillium dahliae, and Aspergillus niger. Most of the active strains belonged to the genera Enterococcus and Weissella. This study led to suggest that environmental-derived LAB strains could be selected for technological application to control pathogenic bacteria and to protect food safety from postharvest deleterious microbiota.

  11. [Outbreak of subclinical mastitis due to beta hemolytic group L streptococci (S. dysgalactiae ssp. equisimilis) in an Austrian dairy herd].

    Science.gov (United States)

    Baumgartner, Martina; Giffinger, Friederike; Hoppe, Jan Christoph; Spergser, Joachim

    2011-01-01

    This study is reporting an outbreak of subclinical mastitis due to beta-hemolytic group L streptococci in an Austrian dairy herd with a history of high somatic cell count. At the first survey 16 of 33 lactating cows (28 quarters of 132) were cultured positive for beta-hemolytic, CAMP and esculin negative cocci that grew on Columbia blood agar with small grey catalase negative colonies. With the commercial API 20 Strep system (bioMerieux, F) isolates were classified as members of streptococci group L. All tested strains (eight of 28) produced acid from ribose, lactose, trehalose, amidon and glycogen; they hydrolysed hippurate and showed beta-glucuronidase, beta-galactosidase, alkaline phosphatase, leucinaminopeptidase and arginindehydrolase activity. Isolates were sensitive to bacitracin but resistant to tetracycline. Using phenotypic characterisation as well as sequence analysis of the 16S-23S intergenic spacer region of a representative strain, recovered isolates were identified as Streptococcus (S.) dysgalactiae ssp. equisimilis. Mastitis was characterized by normal milk secretions and absence of clinical abnormalities but high elevations of somatic cell count. Based on the characteristics of the strains and on the observations during the first herd survey, contagious transmission during milking as a result of poor milking hygiene was assumed. The mastitis was controlled through implementation of a strict hygiene protocol including use of single-use udder towels, post milking teat desinfection and cluster disinfection between milking cows in combination with antibiotic treatment of infected udders.

  12. The Aquatic Environment as a Reservoir of Vibrio cholerae O1 in Hydrographic Basins of the State of Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    Carina Lucena Mendes-Marques

    2013-01-01

    Full Text Available After the worldwide cholera epidemic in 1993, permanent environmental monitoring of hydrographic basins was established in Pernambuco, Brazil, where cholera is endemic. After a quiescent period, 4 rfbN (serogroup O1 positive water samples that were culture negative were detected by multiplex single-tube nested PCR (MSTNPCR; 2 of these were also ctxA (cholera toxin positive. From May to June 2012, 30 V. cholerae O1 isolates were obtained by culturing samples. These isolates were analyzed for the presence of virulence genes by PCR, intergenic spacer region 16S-23S PCR (ISR-PCR, and pulsed field gel electrophoresis (PFGE. The isolates were positive for the rfbN gene and negative for the assessed pathogenic genes and were classified into 2 groups by ISR and the same profile by PFGE. Close genetic similarity was observed between them (2012 and environmental strains from 2004 to 2005, indicating the permanence of endemic V. cholerae O1 in the region.

  13. A pmp genes-based PCR as a valuable tool for the diagnosis of avian chlamydiosis.

    Science.gov (United States)

    Laroucau, Karine; Trichereau, Alain; Vorimore, Fabien; Mahé, Anne-Marie

    2007-03-31

    In a previous study we described the use of a new set of PCR primers (CpsiA/CpsiB) specific of the conserved pmp-family genes of Chlamydophila abortus as an efficient tool for the detection of these bacteria in ruminants including also preliminary results on avian strains. In this work, the use of this set of primers was extended to representative strains of the six major avian serovars (serovars A-F) and to field isolates of C. psittaci. For all the studied representative strains, using purified genomic DNA as a template, CpsiA/CpsiB primers allowed, as observed for C. abortus, a minimal 10-fold PCR signal increase compared to the one observed with ompA specific primers. In comparison to primers targeting the 16S-23S rRNA intergenic spacer, similar or increased sensitivity was observed depending on the strain. All the field isolates were amplified with CpsiA/CpsiB primers. On clinical samples, our primers are the best among those tested for detection of C. psittaci by simple conventional PCR. RFLP experiments performed using PCR fragments amplified with the CpsiA/CpsiB primers gave promising results demonstrating that these primers may provide an interesting tool for molecular typing when the bacterium cannot be grown from pathological samples.

  14. Diversity and Antimicrobial Properties of Lactic Acid Bacteria Isolated from Rhizosphere of Olive Trees and Desert Truffles of Tunisia

    Directory of Open Access Journals (Sweden)

    Imene Fhoula

    2013-01-01

    Full Text Available A total of 119 lactic acid bacteria (LAB were isolated, by culture-dependant method, from rhizosphere samples of olive trees and desert truffles and evaluated for different biotechnological properties. Using the variability of the intergenic spacer 16S-23S and 16S rRNA gene sequences, the isolates were identified as the genera Lactococcus, Pediococcus, Lactobacillus, Weissella, and Enterococcus. All the strains showed proteolytic activity with variable rates 42% were EPS producers, while only 10% showed the ability to grow in 9% NaCl. In addition, a low rate of antibiotic resistance was detected among rhizospheric enterococci. Furthermore, a strong antibacterial activity against plant and/or pathogenic bacteria of Stenotrophomonas maltophilia, Pantoea agglomerans, Pseudomonas savastanoi, the food-borne Staphylococcus aureus, and Listeria monocytogenes was recorded. Antifungal activity evaluation showed that Botrytis cinerea was the most inhibited fungus followed by Penicillium expansum, Verticillium dahliae, and Aspergillus niger. Most of the active strains belonged to the genera Enterococcus and Weissella. This study led to suggest that environmental-derived LAB strains could be selected for technological application to control pathogenic bacteria and to protect food safety from postharvest deleterious microbiota.

  15. Genetic characteristics of Streptococcus dysgalactiae isolated from cage cultured cobia, Rachycentron canadum (L.).

    Science.gov (United States)

    Tsai, M-A; Wang, P-C; Yoshida, T; Chen, S-C

    2015-12-01

    Disease outbreaks occurred during 2007-2013 in Taiwan with 2.5-10% mortality among the cage cultured cobia, Rachycentron canadum (L.), characterized by the presence of polyserositis, pericarditis and peritonitis. The micro-organisms isolated from internal organs were Gram-positive cocci. The isolates were confirmed as Streptococcus dysgalactiae by a polymerase chain reaction assay that yielded the expected specific 259 bp amplicon. Additionally, partial sequence of the 16S-23S rDNA intergenic spacer region of the GCS strain isolates from fish was also compared and produced 100% sequence identity with S. dysgalactiae (GenBank accession number AB252398). The genetic characterization was then determined by pulsed-field gel electrophoresis (PFGE) analysis. Based on PFGE, the Apa I or Sma I digestion patterns of chromosomal DNA of these isolates were grouped into three main clusters. Taiwanese strains were divided into two clusters, and the tet(M) gene was detected in cluster 1 (pulsotypes: A1-A2 and S1-S3), but not in cluster 2 strains (pulsotypes: A3-A4 and S4-S5). Three Japanese strains from amberjack, Seriola dumerili (Risso), were grouped into cluster 3 (pulsotypes: A5-A7 and S6-S8) and displayed no mortality to cobia in the challenge experiment. Conversely, Taiwanese strains from cobia and snubnose pompano, Trachinotus blochii (L.), displayed a mortality rate of 50-87.5% in cobia. PMID:25087459

  16. Physiological, numerical and molecular characterization of alkyl ether-utilizing rhodococci.

    Science.gov (United States)

    Kim, Yong-Hak; Engesser, Karl-Heinrich; Kim, Sang-Jong

    2007-06-01

    Twenty-seven Gram-positive strains were characterized physiologically and numerically and classified them into four groups according to their specific activities for utilization of linear alkyl ethers (AEs), cyclic AEs, monoalkoxybenzenes and 1,4-diethoxybenzene. The comparative analysis of the 16S ribosomal RNA gene and 16S-23S intergenic spacer region showed that they belonged to the genera Rhodococcus and Gordonia. Alkyl ether-utilizing rhodococci appeared to involve various and diverse cytochromes P450 of the families CYP116 (25 positive strains from 27), CYP153 (5/27), CYP249 (1/27) and a new family P450RR1 (27/27). The presence of P450RR1 was strongly related to the specific activity for utilization of 2-methoxyphenol and 2-ethoxyphenol. In addition, 26 of 27 strains contained multiple alkB genes coding for probable non-haem iron containing alkane monooxygenases and hydroxylases. Similar DNA fragments coding for a tetrahydrofuran monooxygenase A subunit (ThmA) were found in all cyclic AE-utilizing strains and nearly identical DNA fragments coding for likely orthologues of a propane monooxygenase A subunit (PrmA) in all linear AE-utilizing strains. The substrate availability in the degradation of aryl AEs, cyclic AEs and linear AEs agreed with the molecular probing of the respective genes encoding cytochrome P450RR1, ThmA and PrmA.

  17. Genotyping of starter cultures of Bacillus subtilis and Bacillus pumilus for fermentation of African locust bean (Parkia biglobosa) to produce Soumbala.

    Science.gov (United States)

    Ouoba, Labia Irène Ivette; Diawara, Bréhima; Amoa-Awua, Wisdom kofi; Traoré, Alfred Sababénedyo; Møller, Peter Lange

    2004-01-15

    Bacillus spp. are the predominant microorganisms in fermented African locust bean called Soumbala in Burkina Faso. Ten strains selected as potential starter cultures were characterised by PCR amplification of the16S-23S rDNA intergenic transcribed spacer (ITS-PCR), restriction fragment length polymorphism of the ITS-PCR (ITS-PCR RFLP), pulsed field gel electrophoresis (PFGE) and sequencing of the 968-1401 region of the 16S rDNA. In previous studies, the isolates were identified by phenotyping as Bacillus subtilis and Bacillus pumilus. The phenotyping was repeated as a reference in the present study. The ITS-PCR and ITS-PCR RLFP allowed a typing at species level. The PFGE was more discriminative and allowed a typing at strain level. Full agreement with the phenotyping was observed in all cases. The sequencing of the 16S rDNA allowed the identification at species level with an identity from 97% to 100% comparing the sequences to those from the GenBank databases. The desired cultures of B. subtilis and B. pumilus from African locust bean fermentation were distinguished by ITS-PCR and ITS-PCR RLFP from Bacillus cereus and Bacillus sphaericus which sometimes occur in the beginning of the fermentation.

  18. Zoonotic Bartonella species in wild rodents in the state of Mato Grosso do Sul, Brazil.

    Science.gov (United States)

    Favacho, Alexsandra Rodrigues de Mendonça; Andrade, Marcelle Novaes; de Oliveira, Renata Carvalho; Bonvicino, Cibele Rodrigues; D'Andrea, Paulo Sergio; de Lemos, Elba Regina Sampaio

    2015-01-01

    Several rodent-associated Bartonella species cause disease in humans but little is known about their epidemiology in Brazil. The presence of Bartonella spp. in wild rodents captured in two municipalities of the Mato Grosso do Sul state was assessed by polymerase chain reaction (PCR). Fragments of heart tissue from 42 wild rodents were tested using primers targeting the Bartonella 16S-23S intergenic transcribed spacer (ITS) region and citrate synthase gltA gene. The wild rodents were identified based on external and cranial morphology and confirmed at species level by mitochondrial DNA (cytochrome B) sequencing and karyotype. Overall, 42.9% (18/42) of the wild rodents were PCR positive for Bartonella spp.: Callomys callosus (04), Cerradomys maracajuensis (04), Hylaeamus megacephalus (01), Necromys lasiurus (06), Nectomys squamipes (01), Oecomys catherinae (01) and Oxymycterus delator (01). Bartonella vinsonii subsp. arupensis was detected in N. lasiurus (46%) and C. callosus (21%) captured in the two study sites. We reported the first molecular detection of B. vinsonii subsp. arupensis in different species of wild rodents collected in the Brazilian territory. Further studies are needed to examine the role of these mammals in the eco-epidemiology of bartonellosis in Brazil.

  19. Spacer geometry and particle deposition in spiral wound membrane feed channels

    KAUST Repository

    Radu, A.I.

    2014-11-01

    Deposition of microspheres mimicking bacterial cells was studied experimentally and with a numerical model in feed spacer membrane channels, as used in spiral wound nanofiltration (NF) and reverse osmosis (RO) membrane systems. In-situ microscopic observations in membrane fouling simulators revealed formation of specific particle deposition patterns for different diamond and ladder feed spacer orientations. A three-dimensional numerical model combining fluid flow with a Lagrangian approach for particle trajectory calculations could describe very well the in-situ observations on particle deposition in flow cells. Feed spacer geometry, positioning and cross-flow velocity sensitively influenced the particle transport and deposition patterns. The deposition patterns were not influenced by permeate production. This combined experimental-modeling approach could be used for feed spacer geometry optimization studies for reduced (bio)fouling. © 2014 Elsevier Ltd.

  20. Computer-Aided Design Method of Warp-Knitted Jacquard Spacer Fabrics

    Directory of Open Access Journals (Sweden)

    Li Xinxin

    2016-06-01

    Full Text Available Based on a further study on knitting and jacquard principles, this paper presents a mathematical design model to make computer-aided design of warp-knitted jacquard spacer fabrics more efficient. The mathematical model with matrix method employs three essential elements of chain notation, threading and Jacquard designing. With this model, the processing to design warp-knitted jacquard spacer fabrics with CAD software is also introduced. In this study, the sports shoes which have separated functional areas according to the feet structure and characteristics of movement are analysed. The results show the different patterns on Jacquard spacer fabrics that are seamlessly stitched with jacquard technics. The computer-aided design method of warp-knitted jacquard spacer fabrics is efficient and simple.

  1. CRISPR Spacer Arrays for Detection of Viral Signatures from Acidic Hot Springs

    Science.gov (United States)

    Snyder, J. C.; Bateson, M. M.; Suciu, D.; Young, M. J.

    2010-04-01

    Viruses are the most abundant life-like entities on the planet Earth. Using CRISPR spacer sequences, we have developed a microarray-based approach to detecting viral signatures in the acidic hot springs of Yellowstone.

  2. Manufacturing and Process-based Property Analysis of Textile-Reinforced Thermoplastic Spacer Composites

    Science.gov (United States)

    Hufenbach, Werner; Adam, Frank; Füßel, René; Krahl, Michael; Weck, Daniel

    2012-12-01

    Novel woven spacer fabrics based on hybrid yarns are suitable for an efficient fabrication of three-dimensional composite structures in high volume production. In this paper, an innovative manufacturing process with short cycle times and high automatisation is introduced for textile-reinforced thermoplastic spacer structures suited for bending load cases. The different process steps hybrid yarn fabrication, weaving technology for three-dimensional textile preforms and consolidation with unique kinematics and hot pressing technology are described in detail. The bending properties of the manufactured spacer structures are evaluated by means of experiments as well as finite element simulations. Numerical parametric studies are performed in order to validate the influence of manufacturing tolerances on the bending stiffness of the spacer structures.

  3. Enhanced charge trapping in bipolar spacer oxides during low-dose-rate irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Fleetwood, D.M.; Reber, R.A. Jr.; Winokur, P.S. [Sandia National Labs., Albuquerque, NM (United States); Kosier, S.L.; Schrimpf, R.D. [Arizona Univ., Tucson, AZ (United States). Dept. of Electrical and Computer Engineering; Nowlin, R.N. [Air Force Phillips Laboratory, Albuquerque, NM (United States); Pease, R.L. [RLP Research, Inc., Albuquerque, NM (United States); DeLaus, M. [Analog Devices, Wilmington, MA (United States)

    1994-03-01

    Thermally-stimulated-current and capacitance-voltage measurements reveal enhanced hole trapping in bipolar spacer-oxide capacitors irradiated at 0 V at low dose rates. Possible mechanisms and implications for bipolar low-rate response are discussed.

  4. THE EQUIVALENT MECHANICAL MODELS OF LIQUID SLOSHING IN A SPHERICAL TANK WITH SPACER UNDER LOW GRAVITY

    Institute of Scientific and Technical Information of China (English)

    CHENG Xu-duo; HU Mei-zhu; WEN Ji-hua

    2005-01-01

    The dynamics of liquid sloshing in a spherical tank with spacer under low gravity was investigated. By extending the characteristic functions, the frequencies of liquid free-sloshing, reaction force and moments on the wall of tank were obtained. By mechanical equivalent principle, the equivalent models of spring-vibrator-damper of liquid sloshing were given. The numerical results obtained show when a spacer is inserted in the tank, the sloshing frequency of liquid and the sloshing mass of liquid will decrease.

  5. Visualization of rDNA spacer transcription in Xenopus oocytes treated with fluorouridine

    OpenAIRE

    Rungger, M.; Crippa, M; Trendelenburg, M F; Scheer, Ulrich; Franke, Werner W

    2009-01-01

    Under the intluence of 5-tluoro-uridine, the ultrastructure of the rDNA transcription units in Xenopus oocytes is altered. Whereas part of the matrix units maintains anormal aspect or shows various degrees of inhibition, in a strong proportion of the transcription units the alternating pattern of matrix units and fibril-free spacer regions is no longer recognized. Transcriptional complexes are found along the entire DNP axis, including the regions of the spacers. These observations support bi...

  6. INFLUENCE OF ELECTRICAL AND STRUCTURAL PARAMETERS ON THE PERFORMANCE OF THE SPACERS IN HOPFED

    Institute of Scientific and Technical Information of China (English)

    Zhong Xuefei; Wilbert van der Poel; Daniel den Engelsen; Yin Hanchun

    2006-01-01

    The HOPping Field Emission Display (HOPFED) is a new architecture for field emission displays.The main difference between a conventional Field Emission Display (FED) device and a HOPFED lies in the spacer structure. In a HOPFED, two dielectric plates, named hop and flu spacer, are sandwiched between the emitter and the front plate. The objective of this spacer structure is to improve the performance of a FED substantially with notable contrast, color purity and luminance uniformity. In order to optimize the structure of the device and to make the electron spot on the screen match the requirement of the phosphor dot dimension,the influence of electrical and structural parameters of the device on the electron spot profile was studied by numerical simulation in this paper. Monte Carlo method was employed to calculate the potential distribution inside hop and flu spacers due to secondary electrons mechanism plays an important role in HOPFED. The results indicated that the potential distribution in the spacers and spot profile depended strongly on the hop voltage, anode voltage and spacer's layout. This study may provide a useful theoretical support for optimizing the structure in HOPFED.

  7. Time spans and spacers : Molecular phylogenetic explorations in the Cladophora complex (Chlorophyta) from the perspective of rDNA gene and spacer sequences

    NARCIS (Netherlands)

    Bakker, Frederik Theodoor

    1995-01-01

    In this study, phylogenetic relationships among genera, species and biogeographic representatives of single Cladophora species within the Cladophorales were analyzed using rDNA gene and spacer sequences. Based on phylogenetic analysis of 18S rRNA gene sequences, the Cladophora complex is shown to be

  8. Effects of various spacer grid modeling on the neutronic parameters of the VVER-1000 reactor

    International Nuclear Information System (INIS)

    Highlights: → In this analysis, we presented the spacer girds modeling along the fuel assembly in their actual position. → In diffusion model, the material type in axial direction of core is different. In a simplified model like shroud model, the core includes the same material in axial direction. → The various modeling of spacer grids on the core reactivity and axial power distributions are studied. - Abstract: The main objective of this paper is to study the effects of various spacer grid models on the neutronic parameters of a VVER-1000 reactor. Specifically, the data of the nuclear power plant at the Bushehr site, which is of a VVER-1000 type, will be studied. Three models, representing the spacer grids along the fuel assemblies are presented. These three models are the homogeneous and the heterogeneous local spacer grid models and the shroud spacer grid model. In the homogeneous and the heterogeneous models, the spacer grids are considered at their actual locations in the axial direction. The only difference between the two models is that in the homogeneous model, the spacer grids are homogenized with the coolant while in the heterogeneous model, the spacer grids are modeled around the fuel cells at their exact axial positions. In the shroud model, the spacer grids are modeled in the shroud region containing the coolant and are not necessarily placed at their appropriate axial positions. The aforementioned models and the core geometry are modeled in 3-D hexagonal geometry and solved by the CITATION code. The required cross sections are obtained from the WIMS code using the associated ENDF/B-7 based library. The visual FORTRAN programming 90 is used for analysis of the whole calculation process and provides a sophisticated link between the WIMS and the CITATION codes during core cycle burnup. The core excess reactivity and the critical boron concentration of the reactor are calculated at normal operating state. In addition, the changes in the critical

  9. Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.

    Science.gov (United States)

    Zhou, Zhong-Yin; Li, Ai-Min; Adeola, Adeniyi C; Liu, Yan-Hu; Irwin, David M; Xie, Hai-Bing; Zhang, Ya-Ping

    2014-06-02

    Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in the human and mouse genomes, some of which play important roles in fundamental biological processes. The pig is an important domesticated animal, however, pig lincRNAs remain poorly characterized and it is unknown if they were involved in the domestication of the pig. Here, we used available RNA-seq resources derived from 93 samples and expressed sequence tag data sets, and identified 6,621 lincRNA transcripts from 4,515 gene loci. Among the identified lincRNAs, some lincRNA genes exhibit synteny and sequence conservation, including linc-sscg2561, whose gene neighbor Dnmt3a is associated with emotional behaviors. Both linc-sscg2561 and Dnmt3a show differential expression in the frontal cortex between domesticated pigs and wild boars, suggesting a possible role in pig domestication. This study provides the first comprehensive genome-wide analysis of pig lincRNAs.

  10. Expressing activity of promoter elements of large intergenic region from cotton leaf curl virus in host plant*

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Cotton leaf curl virus (CLCuV) is a type of single-stranded DNAvirus, belonging to geminivirus of subgroup III. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected cotton leaves was used as template, and fragment of LIR was obtained by PCR and inserted into clone vector. The fragment of LIR was fused with gus reporter gene and nos terminator in the orientation of transcription of virion sense and complementary sense respectively, and the plant expression vectors were constructed. GUS activity of Agrobacterium-mediated transgenic tobacco was measured. The result indicated that LIR showed strong promoter activity in complementary sense gene orientation. Average GUS activity of the complementary sense promoter was 5-6 times that of CaMV 35S promoter, and the highest GUS activity of individual plant was ten times of that of CaMV 35S promoter. Histochemical localization confirmed its activity in both mesophyll and vascular tissues. Activity of virion sense of LIR was rather low. Thus LIR isolated from CLCuV could be used as a novel strong promoter in plant genetic manipulation.

  11. Genetic Diversity in Salmonella Isolates from Ducks and their Environments in Penang, Malaysia using Enterobacterial Repetitive Intergenic Consensus

    Directory of Open Access Journals (Sweden)

    Frederick Adzitey 1, Gulam Rusul Rahmat Ali2*, Nurul Huda2 and Rosma Ahmad3

    2013-07-01

    Full Text Available A total of 107 Salmonella isolates (37 S. typhimurium, 26 S. hadar, 15 S. enteritidis, 15 S. braenderup, and 14 S. albany isolated from ducks and their environments in Penang, Malaysia were typed using enterobacterial repetitive intergenic consensus (ERIC to determine their genetic diversity. Analysis of the Salmonella strains by ERIC produced DNA fingerprints of different sizes for differentiation purposes. The DNA fingerprints or band sizes ranged from 14-8300bp for S. Typhimurium, 146-6593bp for S. hadar, 15-4929bp for S. enteritidis, 14-5142bp for S. braenderup and 7-5712bp for S. albany. Cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. typhimurium were grouped into 10 clusters and 6 singletons, S. Hadar were grouped into 3 clusters and 18 singletons, S. enteritidis were grouped into 3 clusters and 7 singletons, S. braenderup were grouped into 4 clusters and 7 singletons, and S. albany were grouped into 3 clusters and 7 singletons with discriminatory index (D ranging from 0.92-0.98. ERIC proved to be a useful typing tool for determining the genetic diversity of the duck Salmonella strains.

  12. Molecular typing among beef isolates of Escherichia coli using consensus repetitive intergenic enterobacteria-polymerase chain reaction (ERIC-PCR)

    Science.gov (United States)

    Zoolkifli, Nurliyana Wan; Mutalib, Sahilah Abd

    2013-11-01

    Genomic DNA of Escherichia coli were characterized by enterobacterial repetitive intergenic consensus-Polymerase chain reaction (ERIC-PCR) and the presence of Shiga toxin gene-I (Stx1) and Shiga toxin gene-2 (Stx2). These isolates were originated from imported raw beef which are come from two countries namely Australia and India. The isolation of E. coli was conducted by using Eosin Methylene Blue Agar (EMBA). A total of 94 strains had been isolated from 30 samples of imported raw beefand 42 strains had been detected positively E. coli by doing biochemical tests. All strains had been tested and the results of biochemical tests showed that 3 strains were from Australia samples while the other 39 strains were from India samples. The biochemical tests used are Indole test, Methyl Red test, Voges-Proskauer test and Citrate test. All the 42 strains were examined for Shiga toxin (stx1 and stx2) gene detection by two pair primers which are stx2F (5'-TTCTTCGGTATCCTATTCCC-3'), stx2R (5'-ATGCATCTCTGGTCATTGTA-3'), stx1F (5'-CAGTTAATGTGGTGGCGAAG-3'), and stx1R (5'-CTGTCACAGTAACAACCGT-3'). The results showed that none of the strains are positive for Shiga toxin gene. Application of ERIC-PCR method towards E. coli had successfully shown the high diversity polymorphism in 21 different genome types of DNA with primers ERIC1R (5'- CACTTAGGGGTCCTCGAATGTA- 3') and ERIC2R (5'- AAGTAAGTGACTGGGGTGACGC- 3').

  13. Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis

    Directory of Open Access Journals (Sweden)

    Travers Ching

    2016-05-01

    Full Text Available Long intergenic noncoding RNAs (lincRNAs are a relatively new class of non-coding RNAs that have the potential as cancer biomarkers. To seek a panel of lincRNAs as pan-cancer biomarkers, we have analyzed transcriptomes from over 3300 cancer samples with clinical information. Compared to mRNA, lincRNAs exhibit significantly higher tissue specificities that are then diminished in cancer tissues. Moreover, lincRNA clustering results accurately classify tumor subtypes. Using RNA-Seq data from thousands of paired tumor and adjacent normal samples in The Cancer Genome Atlas (TCGA, we identify six lincRNAs as potential pan-cancer diagnostic biomarkers (PCAN-1 to PCAN-6. These lincRNAs are robustly validated using cancer samples from four independent RNA-Seq data sets, and are verified by qPCR in both primary breast cancers and MCF-7 cell line. Interestingly, the expression levels of these six lincRNAs are also associated with prognosis in various cancers. We further experimentally explored the growth and migration dependence of breast and colon cancer cell lines on two of the identified lncRNAs. In summary, our study highlights the emerging role of lincRNAs as potentially powerful and biologically functional pan-cancer biomarkers and represents a significant leap forward in understanding the biological and clinical functions of lincRNAs in cancers.

  14. Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis.

    Science.gov (United States)

    Ching, Travers; Peplowska, Karolina; Huang, Sijia; Zhu, Xun; Shen, Yi; Molnar, Janos; Yu, Herbert; Tiirikainen, Maarit; Fogelgren, Ben; Fan, Rong; Garmire, Lana X

    2016-05-01

    Long intergenic noncoding RNAs (lincRNAs) are a relatively new class of non-coding RNAs that have the potential as cancer biomarkers. To seek a panel of lincRNAs as pan-cancer biomarkers, we have analyzed transcriptomes from over 3300 cancer samples with clinical information. Compared to mRNA, lincRNAs exhibit significantly higher tissue specificities that are then diminished in cancer tissues. Moreover, lincRNA clustering results accurately classify tumor subtypes. Using RNA-Seq data from thousands of paired tumor and adjacent normal samples in The Cancer Genome Atlas (TCGA), we identify six lincRNAs as potential pan-cancer diagnostic biomarkers (PCAN-1 to PCAN-6). These lincRNAs are robustly validated using cancer samples from four independent RNA-Seq data sets, and are verified by qPCR in both primary breast cancers and MCF-7 cell line. Interestingly, the expression levels of these six lincRNAs are also associated with prognosis in various cancers. We further experimentally explored the growth and migration dependence of breast and colon cancer cell lines on two of the identified lncRNAs. In summary, our study highlights the emerging role of lincRNAs as potentially powerful and biologically functional pan-cancer biomarkers and represents a significant leap forward in understanding the biological and clinical functions of lincRNAs in cancers.

  15. Development of an innovative spacer grid model utilizing computational fluid dynamics within a subchannel analysis tool

    Science.gov (United States)

    Avramova, Maria

    In the past few decades the need for improved nuclear reactor safety analyses has led to a rapid development of advanced methods for multidimensional thermal-hydraulic analyses. These methods have become progressively more complex in order to account for the many physical phenomena anticipated during steady state and transient Light Water Reactor (LWR) conditions. The advanced thermal-hydraulic subchannel code COBRA-TF (Thurgood, M. J. et al., 1983) is used worldwide for best-estimate evaluations of the nuclear reactor safety margins. In the framework of a joint research project between the Pennsylvania State University (PSU) and AREVA NP GmbH, the theoretical models and numerics of COBRA-TF have been improved. Under the name F-COBRA-TF, the code has been subjected to an extensive verification and validation program and has been applied to variety of LWR steady state and transient simulations. To enable F-COBRA-TF for industrial applications, including safety margins evaluations and design analyses, the code spacer grid models were revised and substantially improved. The state-of-the-art in the modeling of the spacer grid effects on the flow thermal-hydraulic performance in rod bundles employs numerical experiments performed by computational fluid dynamics (CFD) calculations. Because of the involved computational cost, the CFD codes cannot be yet used for full bundle predictions, but their capabilities can be utilized for development of more advanced and sophisticated models for subchannel-level analyses. A subchannel code, equipped with improved physical models, can be then a powerful tool for LWR safety and design evaluations. The unique contributions of this PhD research are seen as development, implementation, and qualification of an innovative spacer grid model by utilizing CFD results within a framework of a subchannel analysis code. Usually, the spacer grid models are mostly related to modeling of the entrainment and deposition phenomena and the heat

  16. Ion therapy of prostate cancer: daily rectal dose reduction by application of spacer gel

    International Nuclear Information System (INIS)

    Ion beam therapy represents a promising approach to treat prostate cancer, mainly due to its high conformity and radiobiological effectiveness. However, the presence of prostate motion, patient positioning and range uncertainties may deteriorate target dose and increase exposure of organs at risk. Spacer gel injected between prostate and rectum may increase the safety of prostate cancer (PC) radiation therapy by separating the rectum from the target dose field. The dosimetric impact of the application of spacer gel for scanned carbon ion therapy of PC has been analyzed at Heidelberg Ion-Beam Therapy Center (HIT). The robustness of ion therapy treatment plans was investigated by comparison of two data sets of patients treated with and without spacer gel. A research treatment planning system for ion therapy was used for treatment plan optimization and calculation of daily dose distributions on 2 to 9 Computed Tomography (CT) studies available for each of the 19 patients. Planning and daily dose distributions were analyzed with respect to target coverage, maximal dose to the rectum (excluding 1 ml of the greatest dose; Dmax-1 ml) and the rectal volume receiving dose greater than 90% of prescribed target dose (V90Rectum), respectively. The application of spacer gel did substantially diminish rectum dose. Dmax-1 ml on the treatment planning CT was on average reduced from 100.0 ± 1.0% to 90.2 ± 4.8%, when spacer gel was applied. The robustness analysis performed with daily CT studies demonstrated for all analyzed patient cases that application of spacer gel results in a decrease of the daily V90Rectum index, which calculated over all patient cases and CT studies was 10.2 ± 10.4 [ml] and 1.1 ± 2.1 [ml] for patients without and with spacer gel, respectively. The dosimetric benefit of increasing the distance between prostate and rectum using spacer gel for PC treatment with carbon ion beams has been quantified. Application of spacer gel substantially reduced rectal

  17. Ternary DNA chip based on a novel thymine spacer group chemistry.

    Science.gov (United States)

    Yang, Yanli; Yildiz, Umit Hakan; Peh, Jaime; Liedberg, Bo

    2015-01-01

    A novel thymine-based surface chemistry suitable for label-free electrochemical DNA detection is described. It involves a simple two-step sequential process: immobilization of 9-mer thymine-terminated probe DNAs followed by backfilling with 9-mer thymine-based spacers (T9). As compared to commonly used organic spacer groups like 2-mercaptoethanol, 3-mercapto-1-propanol and 6-mercapto-1-hexanol, the 9-mer thymine-based spacers offer a 10-fold improvement in discriminating between complementary and non-complementary target hybridization, which is due mainly to facilitated transport of the redox probes through the probe-DNA/T9 layers. Electrochemical measurements, complemented with Surface Plasmon Resonance (SPR) and Quartz Crystal Microbalance (QCM-D) binding analyses, reveal that optimum selectivity between complementary and non-complementary hybridization is obtained for a sensing surface prepared using probe-DNA and backfiller T9 at equimolar concentration (1:1). At this particular ratio, the probe-DNAs are preferentially oriented and easily accessible to yield a sensing surface with favorable hybridization and electron transfer characteristics. Our findings suggest that oligonucleotide-based spacer groups offer an attractive alternative to short organic thiol spacers in the design of future DNA biochips. PMID:25465760

  18. New titanium spacer for cervical laminoplasty. Initial clinical experience. Technical note

    International Nuclear Information System (INIS)

    Many commercially available hydroxyapatite (HA) spacers for cervical laminoplasty have been introduced but have disadvantages such as lack of plasticity, easy cracking, and occasional difficulty in fixation by sutures. Here we present the short-term results of a newly designed titanium spacer (Laminoplasty Basket) in open-door cervical laminoplasty, and evaluated clinically and radiologically. The titanium box-shaped spacer with two arms for fixation was easily inserted and fixed into the laminoplasty space with 4-mm or 5-mm length screws after the posterior cervical arch was repositioned for the canal expansion. Twenty-one patients with cervical myelopathy due to spondylosis or ossification of the longitudinal ligament or developmental narrow canal observed for more than 6 months postoperatively were enrolled in this study. The neurological condition of these patients improved from 9.4 points on the Japanese Orthopaedic Association scale preoperatively to 13.5 points at 6 months after surgery. Postoperative radiological evaluation showed no laminar closure or implant failure and cervical spine curvature was maintained. These results seemed to have no significant difference compared with those using HA spacers. This titanium spacer is a potential substitute for conventional HA or other similar devices in cervical laminoplasty. (author)

  19. Effect of different commercial feed spacers on biofouling of reverse osmosis membrane systems: A numerical study

    KAUST Repository

    Bucs, Szilard

    2014-06-01

    Feed spacers and hydrodynamics have been found relevant for the impact of biofouling on performance in reverse osmosis (RO) and nanofiltration (NF) membrane systems.The objectives of this study on biofouling development were to determine the impact of (i) linear flow velocity and bacterial cell load, (ii) biomass location and (iii) various feed spacer geometries as applied in practice as well as a modified geometry spacer.A three-dimensional mathematical model for biofouling of feed spacer channels including hydrodynamics, solute mass transport and biofilm formation was developed in COMSOL Multiphysics and MATLAB software.Results of this study indicate that the feed channel pressure drop increase caused by biofilm formation can be reduced by using thicker and/or modified feed spacer geometry and/or a lower flow rate in the feed channel. The increase of feed channel pressure drop by biomass accumulation is shown to be strongly influenced by the location of biomass. Results of numerical simulations are in satisfactory agreement with experimental data, indicating that this micro-scale mechanistic model is representative for practice. The developed model can help to understand better the biofouling process of spiral-wound RO and NF membrane systems and to develop strategies to reduce and control biofouling. © 2013 Elsevier B.V.

  20. Numerical investigation on the characteristics of two-phase flow in fuel assemblies with spacer grid

    Energy Technology Data Exchange (ETDEWEB)

    Chen, D.; Yang, Z.; Zhong, Y.; Xiao, Y.; Hu, L. [Chongqing Univ. (China). Key Lab. of Low-grade Energy Utilization Technologies and Systems

    2016-07-15

    In pressurized water reactors (PWRs), the spacer grids of the fuel assembly has significant impact on the thermal-hydraulic performance of the fuel assembly. Particularly, the spacer grids with the mixing vanes can dramatically enhance the secondary flow and have significant effect on the void distribution in the fuel assembly. In this paper, the CFD study has been carried out to analyze the effects of the spacer grid with the steel contacts, dimples and mixing vanes on the boiling two-phase flow characteristics, such as the two-phase flow field, the void distribution, and so on. Considered the influence of the boiling phase change on two-phase flow, a boiling model was proposed and applied in the CFD simulation by using the UDF (User Defined Function) method. Furthermore, in order to analyze the effects of the spacer grid with mixing vanes, the adiabatic (without boiling) two-phase flow has also been investigated as comparison with the boiling two-phase flow in the fuel assembly with spacer grids. The CFD simulation on two-phase flow in the fuel assembly with the proposed boiling model can predict the characteristics of two-phase flow better.

  1. Using cathode spacers to minimize reactor size in air cathode microbial fuel cells

    KAUST Repository

    Yang, Qiao

    2012-04-01

    Scaling up microbial fuel cells (MFCs) will require more compact reactor designs. Spacers can be used to minimize the reactor size without adversely affecting performance. A single 1.5mm expanded plastic spacer (S1.5) produced a maximum power density (973±26mWm -2) that was similar to that of an MFC with the cathode exposed directly to air (no spacer). However, a very thin spacer (1.3mm) reduced power by 33%. Completely covering the air cathode with a solid plate did not eliminate power generation, indicating oxygen leakage into the reactor. The S1.5 spacer slightly increased columbic efficiencies (from 20% to 24%) as a result of reduced oxygen transfer into the system. Based on operating conditions (1000ς, CE=20%), it was estimated that 0.9Lh -1 of air would be needed for 1m 2 of cathode area suggesting active air flow may be needed for larger scale MFCs. © 2012 Elsevier Ltd.

  2. Influence of length and flexibility of spacers on the binding affinity of divalent ligands

    Directory of Open Access Journals (Sweden)

    Susanne Liese

    2015-05-01

    Full Text Available We present a quantitative model for the binding of divalent ligand–receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.

  3. Influence of length and flexibility of spacers on the binding affinity of divalent ligands.

    Science.gov (United States)

    Liese, Susanne; Netz, Roland R

    2015-01-01

    We present a quantitative model for the binding of divalent ligand-receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.

  4. In Silico Study of Spacer Arm Length Influence on Drug Vectorization by Fullerene C60

    Directory of Open Access Journals (Sweden)

    Haifa Khemir

    2015-01-01

    Full Text Available This work studies theoretically the effect of spacer arm lengths on the characteristics of a fullerene C60-based nanovector. The spacer arm is constituted of a carbon chain including a variable number of methylene groups (n = 2–11. To improve the ability of the fullerene carriage, two arms are presented simultaneously through a malonyl bridge. Then the evolution of selected physicochemical parameters is monitored as a function of the spacer arm length and the angle between the two arms. We show here that while the studied characteristics are almost independent of the spacer arm length or vary monotonically with it, the dipole moment and its orientation vary periodically with the parity of the number of carbon atoms. This periodicity is related to both modules and orientations of dipole moments of the spacer arms. In the field of chemical synthesis, these results highlight the importance of theoretical calculations for the optimization of operating conditions. In the field of drug discovery, they show that theoretical calculations of the chemical properties of a drug candidate can help predict its in vivo behaviour, notably its bioavailability and biodistribution, which are known to be tightly dependent of its polarity.

  5. CFD study of isothermal water flow in rod bundle with split-type spacer grid

    Science.gov (United States)

    Batta, A.; Class, A. G.

    2014-06-01

    The design of rod bundles in nuclear application nowadays is assessed by CFD (computational fluid dynamics). The accuracy of CFD models need validation. Within the OECD/NEA benchmark MATiS-H (Measurement and Analysis of Turbulent Mixing in Sub-channels - Horizontal) a single-phase water flow in a 5x5 rod bundle is studied. In the benchmark, two types of spacer grids are tested, the swirl type and the split type, where the current study focuses on the split type spacer grid. Comparison of CFD results obtained at Karlsruhe Institut of Technology (KIT) with experimental results of KAERI (Korea Atomic Energy Research Institute) are presented. In the benchmark velocities components along selected lines downstream of the spacer grid are measured and compared to CFD results. The CFD code STAR CCM+ with the Realized k-ɛ model is used. Comparisons with experimental results show quantitative and qualitative agreement for the averaged values of velocity components. Comparisons of results to other benchmark partners using different modeling show that the selected mesh size and models for the analysis of the current case gives relatively accurate results. However, the used turbulent model (Realized k-ɛ does not capture the turbulent intensity correctly. Computation shows that the flow has very high mixing due to the spacer grid, which does not decay within the measurements domain (z/ DH =0-10 downstream of spacer grid). The same conclusion can be drawn from experimental data.

  6. Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system.

    Science.gov (United States)

    Arslan, Zihni; Hermanns, Veronica; Wurm, Reinhild; Wagner, Rolf; Pul, Ümit

    2014-07-01

    The adaptation against foreign nucleic acids by the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) depends on the insertion of foreign nucleic acid-derived sequences into the CRISPR array as novel spacers by still unknown mechanism. We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. The results show that the insertion of new spacers occurs by site-specific nicking at both strands of the leader proximal repeat in a staggered way and is accompanied by joining of the resulting 5'-ends of the repeat strands with the 3'-ends of the incoming spacer. This concerted cleavage-ligation reaction depends on the metal-binding center of Cas1 protein and requires the presence of Cas2. By acquisition assays using plasmid-located CRISPR array with mutated repeat sequences, we demonstrate that the primary sequence of the first repeat is crucial for cleavage of the CRISPR array and the ligation of new spacer DNA.

  7. Airflows after inhalation of terbutaline sulphate aerosol from a 750-ml spacer for four weeks.

    Science.gov (United States)

    Eriksson, N E; Hidinger, K G; Rosenhall, L; Hagstad, H; Löfgren, L; Perk, J; Stiksa, G; Ström, K

    1986-01-01

    Terbutaline sulphate was administered to 40 adult asthmatic patients via an ordinary metered-dose inhaler (MDI) or one connected to a 750-ml spacer in an open, randomized, crossover study. Spirometry was obtained before the start of the study and again after four weeks of treatment with each inhaler. The patients recorded on a diary card the severity of their asthma symptoms and the peak expiratory flow rate (PEFR) in the morning before and after drug administration and in the evening. Preinhalation spirometric values were higher after four weeks with the 750-ml spacer than at the start of the study (P less than or equal to 0.05). Daily morning and evening PEFR values were higher after use of the 750-ml spacer than after use of the ordinary MDI (P less than 0.05). Daily symptom scores were generally low. A significantly better effect (P less than or equal to 0.05) with the 750-ml spacer was achieved only in daytime dyspnea. The investigators conclude that the attachment of a 750-ml spacer to an ordinary metered-dose inhaler can improve the efficacy of terbutaline sulphate in the long-term treatment of asthma. PMID:3698068

  8. IDENTIFICACIÓN MOLECULAR DE POBLACIONES BACTERIANAS ASOCIADAS AL CARACOL PALA (Strombus gigas DEL CARIBE COLOMBIANO

    Directory of Open Access Journals (Sweden)

    ROMERO MAGALLY

    2009-08-01

    . However, it is currently catalogued as “vulnerable”; there is limited information concerning the bacterial species associated with conch and important in the management of hatcheries for higher productivity and safety of these gastropods. In this study, we used a microbiology and molecular approach using the 16S-23S intergenic region, the 16S rDNA analysis and sequencing to determine the bacterial populations associated with Queen Conch (S. gigas. Also, the capacity to grow in marine agar and selective culture media was used to evaluate the composition of bacteria associated. The 28 total samples analysed we found the number of bacteria recovered after aerobic culture about 106 cfu mL-1 and most belong to the Vibrionaceae family in the order of 105 ufc mL-1. The molecular results of the spacer regions between the 16 and 23S genes from the different analyzed samples indicated a great complexity in the bacterial population associated to S. gigas. The sequencing of the amplicons of 16S rDNA identifies Pseudoalteromonas sp, Halomonas sp., Psycrobacter sp., Cobetia sp., Pseudomonas sp. and Vibrios sp. This suggests these bacteria can play an important role as components of the bacterial community associated to S. gigas. This information can help to improve both the management of hatcheries for higher productivity and for the implementation for the conservation processes of Colombian S. gigas.

    Key words: Strombus gigas, Queen Conch, Bacteria, 16S-23S intergenic region, 16S rDNA.

  9. Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA

    Directory of Open Access Journals (Sweden)

    MacKenzie Alasdair

    2009-12-01

    Full Text Available Abstract Background Human genetic variation produces the wide range of phenotypic differences that make us individual. However, little is known about the distribution of variation in the most conserved functional regions of the human genome. We examined whether different subsets of the conserved human genome have been subjected to similar levels of selective constraint within the human population. We used set theory and high performance computing to carry out an analysis of the density of Single Nucleotide Polymorphisms (SNPs within the evolutionary conserved human genome, at three different selective stringencies, intersected with exonic, intronic and intergenic coordinates. Results We demonstrate that SNP density across the genome is significantly reduced in conserved human sequences. Unexpectedly, we further demonstrate that, despite being conserved to the same degree, SNP density differs significantly between conserved subsets. Thus, both the conserved exonic and intronic genomes contain a significantly reduced density of SNPs compared to the conserved intergenic component. Furthermore the intronic and exonic subsets contain almost identical densities of SNPs indicating that they have been constrained to the same degree. Conclusion Our findings suggest the presence of a selective linkage between the exonic and intronic subsets and ascribes increased significance to the role of introns in human health. In addition, the identification of increased plasticity within the conserved intergenic subset suggests an important role for this subset in the adaptation and diversification of the human population.

  10. Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

    Science.gov (United States)

    Staals, Raymond H. J.; Jackson, Simon A.; Biswas, Ambarish; Brouns, Stan J. J.; Brown, Chris M.; Fineran, Peter C.

    2016-01-01

    CRISPR–Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR–Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR–Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′–5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition (‘targeted acquisition') is a major contributor to adaptation in type I-F CRISPR–Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome. PMID:27694798

  11. Custom Anatomical 3D Spacer for Temporomandibular Joint Resection and Reconstruction.

    Science.gov (United States)

    Green, John Marshall; Lawson, Sarah T; Liacouras, Peter C; Wise, Edward M; Gentile, Michael A; Grant, Gerald Thomas

    2016-03-01

    Two cases are presented using a two-stage approach and a custom antibiotic spacer placement. Temporomandibular reconstruction can be very demanding and accomplished with a variety of methods in preparation of a total joint and ramus reconstruction with total joint prostheses (TMJ Concepts, Ventura, CA). Three-dimensional reconstructions from diagnostic computed tomography were used to establish a virtually planned resection which included the entire condyle-ramus complex. From these data, digital designs were used to manufacture molds to facilitate intraoperative fabrication of precise custom anatomic spacers from rapidly setting antibiotic-impregnated polymethyl methacrylate. Molds were manufactured using vat polymerization (stereolithography) with a photopolymer in the first case and powder bed fusion (electron beam melting) with Ti6AL4V for the second. Surgical methodology and the use of molds for intraoperative spacer fabrication for each case are discussed. PMID:26889353

  12. Synthesis and liquid crystalline properties of hyperbranched aromatic polyesters consisting of azoxybenzene mesogens and polymethylene spacers

    International Nuclear Information System (INIS)

    A new series of hyperbranched aromatic polyesters containing azoxybenzene mesogens and polymethylene spacers were prepared by polymerizing AB2 type monomers that have the isophthaloyl dicarboxylic acid terminal at one end and the p-oxyphenol terminal at the other end. The monomers contain a built-in azoxybenzene mesogen that is linked to the terminal groups through polymethylene spacers. The polyesters prepared were characterized by solution viscosity , differential scanning calorimetry, X-ray diffractometry and polarizing microscopy. All of the polyesters were found to be thermotropic (nematic). Their glass-transition temperatures and mesophase temperature ranges were very sensitive to the length of the two spacers existing in the repeating unit. The degree of branching of one of the polyesters was determined by the NMR spectroscopy and found to be 0.56

  13. Effect of Weld Properties on the Crush Strength of the PWR Spacer Grid

    Directory of Open Access Journals (Sweden)

    Kee-nam Song

    2012-01-01

    Full Text Available Mechanical properties in a weld zone are different from those in the base material because of different microstructures. A spacer grid in PWR fuel is a structural component with an interconnected and welded array of slotted grid straps. Previous research on the strength analyses of the spacer grid was performed using base material properties owing to a lack of mechanical properties in the weld zone. In this study, based on the mechanical properties in the weld zone of the spacer grid recently obtained by an instrumented indentation technique, the strength analyses considering the mechanical properties in the weld zone were performed, and the analysis results were compared with the previous research.

  14. Staged Custom, Intramedullary Antibiotic Spacers for Severe Segmental Bone Loss in Infected Total Hip Arthroplasty

    Directory of Open Access Journals (Sweden)

    Atul F. Kamath

    2011-01-01

    Full Text Available Introduction. Total hip arthroplasty (THA infections with severe bone loss pose significant reconstructive challenges. We present our experience with two-stage hip reimplantation using an intramedullary, antibiotic-impregnated nail. Methods. Three patients with infected THA with severe proximal femoral bone loss (Mallory type IIIB or greater were treated using a custom antibiotic spacer. Clinical outcomes and any complications were recorded. Average followup was 49 months from final reimplantation. Results. Mean age at spacer placement (stage 1 was 53 years. The mean Harris Hip Score at final followup was 80. Two patients had asymptomatic heterotopic ossification, and one patient had a 2 cm leg-length discrepancy. Conclusions. A custom intramedullary nail antibiotic spacer is a reliable option in the staged management of the infected THA with severe proximal femoral bone loss. Benefits of this technique include limb salvage with maintenance of leg length, soft tissue tension, and functional status.

  15. Increased expression of long intergenic non-coding RNA LINC00152 in gastric cancer and its clinical significance.

    Science.gov (United States)

    Pang, Qianqian; Ge, Jiaxin; Shao, Yongfu; Sun, Weiliang; Song, Haojun; Xia, Tian; Xiao, Bingxiu; Guo, Junming

    2014-06-01

    It has been known that differential expression of long non-coding RNA (lncRNA) plays critical roles in carcinogenesis. However, the significance of lncRNA, especially long intergenic ncRNA (lincRNA, the main type of lncRNA family), in the diagnosis of gastric cancer is largely unknown. The aim of this study was to determine the expression level of LINC00152, a newfound lincRNA, in gastric carcinoma and its clinical association. The expression of LINC00152 in 71 pairs of tumorous and adjacent normal tissues from patients with gastric cancer was detected by quantitative real-time reverse transcription-polymerase chain reaction. And then, the potential associations between its level in gastric cancer tissue and the clinicopathological features were analyzed. Finally, a receiver operating characteristic (ROC) curve was constructed for differentiating patients with gastric cancer from patients with benign gastric diseases. The results showed that the expression level of LINC00152 in gastric carcinoma was significantly increased, compared with matched normal tissue (P=0.045) and normal mucosa from health control (P=0.004), respectively. Levels of LINC00152 in gastric cancer cell lines, BGC-823, MGC-803, and SGC-7901, were significantly higher than those in human normal gastric epithelial cell line GES-1. In addition, high expression of LINC00152 was correlated with invasion (P=0.042). LINC00152 levels in gastric juice from patients with gastric cancer were further found significantly higher than those from normal controls (P=0.002). Moreover, the area under the ROC curve (AUC) was up to 0.645 (95 % CI=0.559-0.740, P=0.003). This study highlights that lincRNA LINC00152 might be a novel biomarker for predicting gastric cancer.

  16. Flunisolide hydrofluoroalkane with integrated spacer for treating asthma: an updated review.

    Science.gov (United States)

    Berger, William E; Tashkin, Donald P

    2015-01-01

    Flunisolide hydrofluoroalkane (HFA) with integrated spacer is the most recent reformulated inhaled corticosteroid (ICS) for asthma available in the United States. It is the only product that combines a corticosteroid extrafine aerosol with a built-in spacer. The potential clinical benefit of the flunisolide HFA formulation and its integrated spacer for treating persistent asthma was assessed through a comprehensive review of the published literature and data from the past 10 years focusing on (1) flunisolide, the molecule, and the impact of the HFA reformulation; (2) updated information on the anti-inflammatory response to flunisolide HFA, particularly in the distal airways; and (3) the usefulness of an integrated spacer. Flunisolide HFA was found effective and safe in clinical studies and comparable with the chlorofluorocarbon (CFC) formulation, but at about one-third the dose of flunisolide CFC, likely reflecting both the device and the particle size of the reformulated product. Compared with the CFC formulation, the extrafine aerosol and smaller particle size of flunisolide HFA substantially increased pulmonary deposition and decreased oropharyngeal deposition. The integrated spacer further enhanced the pulmonary/oropharyngeal deposition ratio. Examination of lung biopsy specimens indicated a favorable anti-inflammatory response to flunisolide HFA in peripheral airways. Pediatric studies showed no significant effects on growth. The data indicate that flunisolide HFA is a safe and effective maintenance therapy for asthma patients. The integrated spacer may provide an added advantage for patients, especially those who may be more likely to experience adverse effects of ICSs, both local and systemic, including children susceptible to adverse effects on growth.

  17. New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.

    Science.gov (United States)

    Li, Hao; Li, Peng; Xie, Jing; Yi, Shengjie; Yang, Chaojie; Wang, Jian; Sun, Jichao; Liu, Nan; Wang, Xu; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Wang, Yong; Jia, Leili; Li, Kaiqin; Qiu, Shaofu; Song, Hongbin

    2014-08-01

    A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections.

  18. Multilayer barrier films comprising nitrogen spacers between free-standing barrier layers

    Science.gov (United States)

    Granstrom, Jimmy Erik

    The air sensitivity of organic electronic devices has delayed the broad commercialization of the printed "plastics" electronics technology. The vacuum deposition methods used to fabricate multi-layers which fulfill the encapsulation requirements for plastic electronic devices are complex and expensive. Fully printed "plastic" electronics requires the development of encapsulation architectures which comprise solution deposited barriers and/or low-cost free-standing barrier films based on polymers, e.g. poly ethylene terephthalate (PET). One way to reach this goal is the insertion of contaminant-free (e.g. pure N2) gas-phase spacers between free-standing barrier films in a multilayer structure. The spacers themselves do not exhibit any barrier properties (diffusion of gas permeants in a gas phase is orders of magnitude faster than in a solid), but they delay the attainment of steady state. The spacer also reduces the chemical potential gradient across downstream barrier layers during the transient regime, reducing permeation rate to the device. Furthermore, if sorption is not fully equilibrated and introduces a kinetic barrier to transport, the additional sorption and desorption steps needed for permeant to reach the device may also slow the steady-state permeation rate. Encapsulation architectures utilizing both single-matrix (without nitrogen spacers) and multiple-matrix structures (with nitrogen spacers) were fabricated in this study, including Russian Doll structures utilizing pairs of free-standing barrier films and epoxy seals separated by nitrogen spacers. This structure enables the use of low-cost epoxy to attach two or more free-standing barrier films to a substrate with improved barrier performance. The performance of various Russian Doll encapsulations was evaluated with the calcium thin film optical transmission test, showing improved performance of the Russian doll configuration relative to a non-nested barrier/spacer architecture, and demonstrating that

  19. Role of the conjugated spacer in the optimization of second-order nonlinear chromophores

    Science.gov (United States)

    Pérez-Moreno, Javier; Clays, Koen; Kuzyk, Mark G.

    2009-08-01

    We investigate the role of the conjugated spacer in the optimization of the first hyperpolarizability of organic chromophores. We propose a novel strategy for the optimization of the first hyperpolarizability that is based on the variation of the degree of conjugation for the bridge that separates the donor and acceptors at the end of push-pull type chromophores. The correlation between the type of conjugated spacer and the experimental nonlinear performance of the chromophores is investigated and interpreted in the context of the quantum limits.

  20. Microbial fuel cells with an integrated spacer and separate anode and cathode modules

    KAUST Repository

    He, Weihua

    2016-01-01

    A new type of scalable MFC was developed based on using alternating graphite fiber brush array anode modules and dual cathode modules in order to simplify construction, operation, and maintenance of the electrodes. The modular MFC design was tested with a single (two-sided) cathode module with a specific surface area of 29 m2 m−3 based on a total liquid volume (1.4 L; 20 m2 m−3 using the total reactor volume of 2 L), and two brush anode modules. Three different types of spacers were used in the cathode module to provide structural stability, and enhance air flow relative to previous cassette (combined anode–cathode) designs: a low-profile wire spacer; a rigid polycarbonate column spacer; and a flexible plastic mesh spacer. The best performance was obtained using the wire spacer that produced a maximum power density of 1100 ± 10 mW m−2 of cathode (32 ± 0.3 W m−3 based on liquid volume) with an acetate-amended wastewater (COD = 1010 ± 30 mg L−1), compared to 1010 ± 10 mW m−2 for the column and 650 ± 20 mW m−2 for the mesh spacers. Anode potentials were unaffected by the different types of spacers. Raw domestic wastewater produced a maximum of 400 ± 8 mW m−2 under fed batch conditions (wire-spacers), which is one of the highest power densities for this fuel. Over time the maximum power was reduced to 300 ± 10 mW m−2 and 275 ± 7 mW m−2 for the two anode compartments, with only slightly less power of 250 ± 20 mW m−2 obtained under continuous flow conditions. In fixed-resistance tests, the average COD removal was 57 ± 5% at a hydraulic retention time of 8 h. These results show that this modular MFC design can both simplify reactor construction and enable relatively high power generation from even relatively dilute wastewater.

  1. Self-structuring of lamellar bridged silsesquioxanes with long side spacers.

    Science.gov (United States)

    Fernandes, Mariana; Nobre, Sónia S; Xu, Qinghong; Carcel, Carole; Cachia, Jean Nicolas; Cattoën, Xavier; Sousa, José M; Ferreira, Rute A S; Carlos, Luís D; Santilli, Celso V; Wong Chi Man, Michel; Bermudez, Verónica de Zea

    2011-09-22

    Diurea cross-linked bridged silsesquioxanes (BSs) C(10)C(n)C(10) derived from organosilane precursors, including decylene chains as side spacers and alkylene chains with variable length as central spacers (EtO)(3)Si-(CH(2))(10)-Y-(CH(2))(n)-Y-(CH(2))(10)-Si(OEt)(3) (n = 7, 9-12; Y = urea group and Et = ethyl), have been synthesized through the combination of self-directed assembly and an acid-catalyzed sol-gel route involving the addition of dimethylsulfoxide (DMSO) and a large excess of water. This new family of hybrids has enabled us to conclude that the length of the side spacers plays a unique role in the structuring of alkylene-based BSs, although their morphology remains unaffected. All the samples adopt a lamellar structure. While the alkylene chains are totally disordered in the case of the C(10)C(7)C(10) sample, a variable proportion of all-trans and gauche conformers exists in the materials with longer central spacers. The highest degree of structuring occurs for n = 9. The inclusion of decylene instead of propylene chains as side spacers leads to the formation of a stronger hydrogen-bonded urea-urea array as evidenced by two dimensional correlation Fourier transform infrared spectroscopic analysis. The emission spectra and emission quantum yields of the C(10)C(n)C(10) materials are similar to those reported for diurea cross-linked alkylene-based BSs incorporating propylene chains as side spacers and prepared under different experimental conditions. The emission of the C(10)C(n)C(10) hybrids is ascribed to the overlap of two distinct components that occur within the urea cross-linkages and within the siliceous nanodomains. Time-resolved photoluminescence spectroscopy has provided evidence that the average distance between the siliceous domains and the urea cross-links is similar in the C(10)C(n)C(10) BSs and in oxyethylene-based hybrid analogues incorporating propylene chains as side spacers (diureasils), an indication that the longer side chains in the

  2. Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

    Science.gov (United States)

    He, Jiankui; Deem, Michael W.

    2010-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.

  3. CALCULATION OF AERIAL CABLE SPACER COMPRESSION FORCES IN BUNDLED PHASES DURING SHORT CIRCUIT FAULT

    Directory of Open Access Journals (Sweden)

    I. I. Sergey

    2014-01-01

    Full Text Available The paper presents an approximate method for calculation of electrodynamic resistance parameters of a flexible bus-bar with bundled phases. Comparison of the approximate calculation results with the computer calculations using a FAZA software tool has been given in the paper. An evaluation of permissible aerial cable spacer compression forces for designed modern standard distribution substations of 330 and 550 kV has been provided in the paper. The paper proposes an algorithm for determination of dynamics parameters in a bundled phase with due account of influence pertaining to viscoelastic characteristics of damping spacers.

  4. Production Principles and Technological Development of Novel Woven Spacer Preforms and Integrated Stiffener Structures

    Science.gov (United States)

    Torun, Ahmet R.; Mountasir, Adil; Hoffmann, Gerald; Cherif, Chokri

    2013-06-01

    3D textile preforms offer a high potential to increase mechanical properties of composites and/or decrease manufacturing costs. Within the scope of this study, production principles were developed for complex spacer preforms and integrated stiffeners. These principles were applied through technological further development of the well-known face-to-face and terry weaving techniques. Various woven preforms were produced with Glass fibre/Polypropylene (GF/PP) Commingled yarns, however, the technology is suitable for any type of reinforcement yarns. U-shaped woven spacer preform was consolidated into a sandwich composite component for lightweight applications.

  5. Hole-transfer induced energy transfer in perylene diimide dyads with a donor-spacer-acceptor motif.

    Science.gov (United States)

    Kölle, Patrick; Pugliesi, Igor; Langhals, Heinz; Wilcken, Roland; Esterbauer, Andreas J; de Vivie-Riedle, Regina; Riedle, Eberhard

    2015-10-14

    We investigate the photoinduced dynamics of perylene diimide dyads based on a donor-spacer-acceptor motif with polyyne spacers of varying length by pump-probe spectroscopy, time resolved fluorescence, chemical variation and quantum chemistry. While the dyads with pyridine based polyyne spacers undergo energy transfer with near-unity quantum efficiency, in the dyads with phenyl based polyyne spacers the energy transfer efficiency drops below 50%. This suggests the presence of a competing electron transfer process from the spacer to the energy donor as the excitation sink. Transient absorption spectra, however, reveal that the spacer actually mediates the energy transfer dynamics. The ground state bleach features of the polyyne spacers appear due to the electron transfer decay with the same time constant present in the rise of the ground state bleach and stimulated emission of the perylene energy acceptor. Although the electron transfer process initially quenches the fluorescence of the donor it does not inhibit energy transfer to the perylene energy acceptor. The transient signatures reveal that electron and energy transfer processes are sequential and indicate that the donor-spacer electron transfer state itself is responsible for the energy transfer. Through the introduction of a Dexter blocker unit into the spacer we can clearly exclude any through bond Dexter-type energy transfer. Ab initio calculations on the donor-spacer and the donor-spacer-acceptor systems reveal the existence of a bright charge transfer state that is close in energy to the locally excited state of the acceptor. Multipole-multipole interactions between the bright charge transfer state and the acceptor state enable the energy transfer. We term this mechanism coupled hole-transfer FRET. These dyads represent a first example that shows how electron transfer can be connected to energy transfer for use in novel photovoltaic and optoelectronic devices. PMID:26347443

  6. 一株植物乳杆菌的鉴定及其抑菌特性研究%Identification of a Lactobacillus plantarum and analysis of its antibacterial properties

    Institute of Scientific and Technical Information of China (English)

    郭颖; 杨相宜; 单艺; 满朝新; 王今雨; 董鑫悦; 姜毓君

    2013-01-01

    从内蒙古传统发酵乳制品中分离筛选到1株具有抑菌活性的乳酸菌.通过API生化反应和16S rDNA、16S-23S rDNA间隔(IGS)序列同源性分析,鉴定该乳酸菌为植物乳杆菌(Laaobacillus plantarum),并命名为植物乳杆菌NDC 75017.利用杯碟法,通过蛋白酶K和胰蛋白酶实验,确定该乳酸菌产生的抑菌物质为蛋白质类.理化性质分析表明该抑菌物质具有良好的热稳定性,100 ℃处理120m in后仍有较好的抑菌活性;其抑菌活性最适pH值范围为2~4;通过排除有机酸、过氧化氢的干扰,该菌的发酵上清液对单增李斯特菌、藤黄微球菌、蜡样芽孢杆菌及福氏志贺氏菌的生长具有良好的抑制作用.%A lactic acid bacteria isolated from traditional dairy products in Inner Mongolia of China exhibited antibacterial ability.By API biochemical methods and analysis of 16S rDNA and 16S-23S intergenic spacer region (IGS) gene sequence,the strain was identified as Lactobacillus plantarum and named as L.plantarum NDC 75017.The reduction in antimicrobial activity was observed after treatment with proteinase K and trypsin by cylinder plate method,demonstrating its proteinaceous nature.The bacteriocin showed high temperature stability up to 100 ℃ for 120 min and had less loss in its activity and stability in the range ofpH 2-4.After eliminating some interference factors including the organic acids and hydrogen peroxides,the bacteriocin still evidenced antibacterial activity against Listeria monocytogenes,Micrococcus luteus,Bacillus cereus and Shigella flexneri.

  7. Molecular Identification of Multilocus of "Candidatus Liberibacter asiaticus" in Psylla citrisuga%柚木虱体内韧皮部杆菌亚洲种多基因位点的分子鉴定

    Institute of Scientific and Technical Information of China (English)

    周汶静; 蒲雪莲; 张丽娜; 岑伊静; 邓晓玲

    2012-01-01

    Four pairs of primers for 16S rDNA gene, β-operon ribosomal protein gene, outer membrane protein gene, and 16S-23S rRNA intergenic transcribed spacer gene of "Candidatus Liberibacter asiaticus", were used to amplify the corresponding baterial genes from Psylla citrisuga, Diaphorina citri collected from lemon orchards in Ruili, Yunnan province. The amplicons were collected, purified, and ligated into PEASY-T3 vector and the constructs were transformed into E. coli Trans 1-T1. Positive clones were sequenced and the sequences were analyzed using NCBI Blastn and MEGA5. 05. Results showed that the sequences on the four gene loci shared 99% of identity with those of "Ca. L. asiaticus" str. psy62 in GenBank, suggesting that Psylla citrisuga is a new host of "Ca. L. asiaticus".%利用与柑桔黄龙病相关的韧皮部杆菌(“Candidatus Liberibacter sp.”,简称Ca.L.sp.)16S rDNA基因、β-操纵子核糖体蛋白基因、外膜蛋白基因以及16S-23S rRNA间隔转录区基因位点的4对特异性引物,对采自云南瑞丽柠檬园的柚木虱(Psylla citrisuga)DNA样品进行PCR扩增,将扩增产物进行纯化、回收,连接至PEASY-T3载体并转化大肠杆菌感受态细胞Trans1-T1,筛选阳性克隆进行测序,利用NCBI Blastn软件以及MEGA5.05软件对所克隆的序列进行同源性分析与聚类分析.结果表明:柚木虱体内韧皮部杆菌亚洲种在这4个基因位点与已报道的Ca.L.asiaticus psy62株系全基因组相应基因位点的同源率均为99%.本研究证实柚木虱能够携带韧皮部杆菌亚洲种,是该菌新的昆虫宿主.

  8. pH-dependent phase behavior of carbohydrate-based gemini surfactants. Effect of the length of the hydrophobic spacer

    NARCIS (Netherlands)

    Klijn, Jaap E.; Stuart, Marc C. A.; Scarzello, Marco; Wagenaar, Anno; Engberts, Jan B. F. N.

    2006-01-01

    The phase behavior of a series of carbohydrate-based gemini surfactants with varying spacer lengths was studied using static and dynamic light scattering between pH 2 and 12. Cryo-electron microscopy pictures provide evidence for the different morphologies present in solution. The spacer length of t

  9. Novel anthracycline-spacer-beta-glucuronide, -beta-glucoside, and -beta-galactoside prodrugs for application in selective chemotherapy

    NARCIS (Netherlands)

    Leenders, RGG; Damen, EWP; Bijsterveld, EJA; Scheeren, HW; Houba, PHJ; van der Meulen-Muileman, IH; Boven, E; Haisma, HJ

    1999-01-01

    A series of anthracycline prodrugs containing an immolative spacer was synthesized for application in selective chemotherapy. The prodrugs having the general structure anthracycline-spacer-beta-glycoside were designed to be activated by beta-glucuronidase or beta-galactosidase. Prodrugs with -chloro

  10. Aerosol delivery from spacers in wheezy infants: a daily life study

    NARCIS (Netherlands)

    H.M. Janssens (Hettie); E.M. Heijnen; V.M. de Jong; W.C.J. Hop (Wim); W.P. Holland (Wim); J.C. de Jongste (Johan); H.A.W.M. Tiddens (Harm)

    2000-01-01

    textabstractThe aims of this study were to assess and compare dose delivery and dose variability of pressurized metered dose inhalers (pMDI)/spacers in wheezy infants in daily life and to investigate factors influencing aerosol delivery. In an open randomized crossover

  11. CFD Turbulence Study of PWR Spacer-Grids in a Rod Bundle

    Directory of Open Access Journals (Sweden)

    C. Peña-Monferrer

    2014-01-01

    the flow dynamics and heat transfer phenomena along the fuel rods. This work presents the analysis of the turbulence effects of a split-type and swirl-type spacer-grid geometries on single phase in a PWR (pressurized water reactor rod bundle. Various computational fluid dynamics (CFD calculations have been performed and the results validated with the experiments of the OECD/NEA-KAERI rod bundle CFD blind benchmark exercise on turbulent mixing in a rod bundle with spacers at the MATiS-H facility. Simulation of turbulent phenomena downstream of the spacer-grid presents high complexity issues; a wide range of length scales are present in the domain increasing the difficulty of defining in detail the transient nature of turbulent flow with ordinary turbulence models. This paper contains a complete description of the procedure to obtain a validated CFD model for the simulation of the spacer-grids. Calculations were performed with the commercial code ANSYS CFX using large eddy simulation (LES turbulence model and the CFD modeling procedure validated by comparison with measurements to determine their suitability in the prediction of the turbulence phenomena.

  12. Synthesis and application of rhodamine-based fluorescent probe dyes with spacer linker arm

    Institute of Scientific and Technical Information of China (English)

    Yong Gao; Jian Li Li; Zhen Shi

    2007-01-01

    When rhodamine-based fluorescent probe dyes are used to track target molecules they always perturb the behavior of target molecules because of steric hindrance effect.In order to minimize potential steric problems, a kind of rhodamine-based fluorescent probe dye with spacer linker arm was designed and synthesized and its application in immunofluorescence histochemistry was investigated.

  13. Influence of the spacer on the inhibitory effect of different polycarbophil-protease inhibitor conjugates.

    Science.gov (United States)

    Marschütz, M K; Veronese, F M; Bernkop-Schnürch, A

    2001-09-01

    Within the present study various polycarbophil (PCP)-serine protease inhibitor conjugates were synthesized and the influence of different spacers on their inhibitory efficacy was evaluated in vitro. Results demonstrated that 4.2+/-0.15 units (n=3; +/-SD) of alpha-chymotrypsin were inhibited by 50% utilizing 0.86% (w/v) of a PCP-tetramethylenediamine (TMDA)-chymostatin 20:1 conjugate. In contrast, only 0.6+/-0.05 units (n=3; +/-SD) of alpha-chymotrypsin were inhibited by a corresponding PCP-poly(ethylene glycol) (PEG)-chymostatin conjugate. Inhibitory effects of PCP-TMDA-antipain and -elastatinal conjugates towards trypsin and elastase, respectively, were also significantly higher (P<0.05) than those of corresponding PCP-PEG-inhibitor conjugates. Hence, the great impact of the molecular size as well as the structure of the spacer on resulting polymer-inhibitor conjugates could be demonstrated. The small and rigid C4-spacer TMDA (molecular weight (MW) 161.1) was thereby shown to be highly advantageous over a long, hydrophilic and flexible PEG-diamine spacer (MW 3400). Results obtained should provide helpful basic knowledge for the development of mucoadhesive polymer-inhibitor conjugates used as auxiliary agents for the oral administration of peptide drugs.

  14. Development and Evaluation of a New Nanometer Based Spacer NMS-I

    Institute of Scientific and Technical Information of China (English)

    Cheng Rongchao; Wang Ruihe; Cao Huilian; Bu Yuhuan; Cheng Yuanfang

    2007-01-01

    In view of the inadequate cementing quality in the cementation for long isolation intervals of oil and gas wells,and considering the field practice in Tarim Oilfield,a nanometer material LC-212 was introduced as the base stock to experimentally develop a new spacer system NMS-I,in combination with other materials,including a chemical gel plugging agent,carboxymethyl cellulose and barite. Experimental results indicated that the system had a wide adjustable range of density,good rheological property,static stability and compatibility with cement slurry. It also showed no flocculating or thickening effect on the water-base drilling fluid and low-density cement system. Meanwhile,the capacity of lost circulation control and the influence of the spacer on the second interfacial cementing strength were evaluated by a self-made lost circulation simulator and shearing test facility. The results showed that the spacer had favorable plugging and flushing effect,and the second interfacial cementing strength can be greatly improved. Moreover,based on the experiments,the mechanisms of spacer function were analyzed. The results obtained from the investigation offer a novel approach to resolving some practical problems in cementing jobs.

  15. Dynamic simulation of universal spacer in Dynesys dynamic stabilization system for human vertebra

    Institute of Scientific and Technical Information of China (English)

    Sung-Min KIM; In-Chul YANG; Seung-Yeol LEE; Sung-Youn CHO

    2009-01-01

    The aim of this study is to analyze the simulated behavior of universal spacer in Dynesys dynamic stabilization system inserted in human vertebra. Dynesys, so-called "Dynamic neutralization system for the spine", dynamic stabilization system is a new concept in the surgical treatment of lower back pain recently. Universal spacer used as flexible material is to stabilize the spine and the material property of universal spacer is polycarbonate urethane. Universal spacer may apply different kinematic behaviors at implanted level in vertebra. Spinal range of motion(SROM) of inter-vertebra with installed Dynesys dynamic stabilization system was studied using Adams+LifeMOD as simulation software package. The vertebra model was set up to closely resemble the in-vivo conditions. Inter-vertebra rotations were measured by post processor of Adams and compared with the intact values. SROMs of the flexion, extension, lateral bending, and axial rotation of human virtual models were measured, where three spinal fixation systems such as rigid system, Dynesys system, and fused system were installed. As a result, the value of SROM is decreased in flexion-extension and lateral bending when the spinal fixation system is implanted. The movement of Dynesys system is similar to that of intact model by allowing the movement of lumbar. This means that the Dynesys system is proved to be safe and effective in the treatment of unstable spinal condition.

  16. The Interspinous Spacer: A New Posterior Dynamic Stabilization Concept for Prevention of Adjacent Segment Disease

    Directory of Open Access Journals (Sweden)

    Antoine Nachanakian

    2013-01-01

    Full Text Available Introduction. Posterior Dynamic stabilization using the interspinous spacer device is a known to be used as an alternative to rigid fusion in neurogenic claudication patients in the absence of macro instability. Actually, it plays an important in the management of adjacent segment disease in previously fused lumbar spine. Materials and Method. We report our experience with posterior dynamic stabilization using an interspinous spacer. 134 cases performed in our institution between September 2008 and August 2012 with different lumbar spine pathologies. The ages of our patients were between 40 and 72 years, with a mean age of 57 years. After almost 4 years of follow up in our patient and comparing their outcome to our previous serious we found that in some case the interspinous distracter has an important role not only in the treatment of adjacent segment disease but also in its prevention. Results and Discussion. Clinical improvement was noted in ISD-treated patients, with high satisfaction rate. At first, radicular pain improves with more than 3/10 reduction of the mean score on visual analog scale (VAS. In addition, disability score as well as disc height and lordotic angle showed major improvement at 3 to 6 months post operatively. And, no adjacent segment disease was reported in the patient operated with interspinous spacer. Conclusion. The interspinous spacer is safe and efficient modality to be used not only as a treatment of adjacent segment disease but also as a preventive measure in patients necessitating rigid fusion.

  17. Bending of the Flexible Spacer Chain of Gemini Surfactant Induced by Hydrophobic Interaction

    Institute of Scientific and Technical Information of China (English)

    YOU,Yi; JIANG,Rong; LING,Tingting; ZHAO,Jianxi

    2009-01-01

    In order to understand the special role of the flexible alkylene spacer of gemini surfactant in the self-assembly,three gemini surfactants,alkylene-α,ω-bis(didodecylmethylammonium bromide)that is designated as 2C12-s-2C12·2Br (s=3,6,8),were synthesized.When the spread films of 2C12-s-2C12·2Br on the surface of water were con-structed,they form the dense layer of the alkyl tails owing to four dodecyl chains per molecule.This induced the bending of the spacer chain toward the air-side at the s smaller than that of C12-s-C12·2Br adsorbed on the air/water interface owing to the enhanced hydrophobic interaction between the alkyl tails and the spacer chain, where C12-s-C12·2Br has only two alkyl tails per molecule. Conclusively.,the enhanced hydrophobic interaction between the alkyl tails and the spacer chain can effectively induce the bending of the latter toward the air-side.

  18. Genotyping of Histomonas meleagridis isolates based on Internal Transcribed Spacer-1 sequences

    NARCIS (Netherlands)

    H.M.J.F. van der Heijden; W.J.M. Landman; S. Greve; R. Peek

    2006-01-01

    C-profiling is a novel genotyping method for protozoan pathogens, based on polymerase chain reaction and sequencing of AT-rich Internal Transcribed Spacer-1 sequences. It was applied to various Histomonas meleagridis isolates originating from outbreaks of histomoniasis in six Dutch turkey and chicke

  19. An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli.

    Science.gov (United States)

    Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Banting, Graham; Edge, Thomas A; Topp, Edward; McAllister, Tim A; Neumann, Norman F

    2016-10-01

    Several studies have demonstrated that E. coli appears to display some level of host adaptation and specificity. Recent studies in our laboratory support these findings as determined by logic regression modeling of single nucleotide polymorphisms (SNP) in intergenic regions (ITGRs). We sought to determine the degree of host-specific information encoded in various ITGRs across a library of animal E. coli isolates using both whole genome analysis and a targeted ITGR sequencing approach. Our findings demonstrated that ITGRs across the genome encode various degrees of host-specific information. Incorporating multiple ITGRs (i.e., concatenation) into logic regression model building resulted in greater host-specificity and sensitivity outcomes in biomarkers, but the overall level of polymorphism in an ITGR did not correlate with the degree of host-specificity encoded in the ITGR. This suggests that distinct SNPs in ITGRs may be more important in defining host-specificity than overall sequence variation, explaining why traditional unsupervised learning phylogenetic approaches may be less informative in terms of revealing host-specific information encoded in DNA sequence. In silico analysis of 80 candidate ITGRs from publically available E. coli genomes was performed as a tool for discovering highly host-specific ITGRs. In one ITGR (ydeR-yedS) we identified a SNP biomarker that was 98% specific for cattle and for which 92% of all E. coli isolates originating from cattle carried this unique biomarker. In the case of humans, a host-specific biomarker (98% specificity) was identified in the concatenated ITGR sequences of rcsD-ompC, ydeR-yedS, and rclR-ykgE, and for which 78% of E. coli originating from humans carried this biomarker. Interestingly, human-specific biomarkers were dominant in ITGRs regulating antibiotic resistance, whereas in cattle host-specific biomarkers were found in ITGRs involved in stress regulation. These data suggest that evolution towards host

  20. 3D laser inspection of fuel assembly grid spacers for nuclear reactors based on diffractive optical elements

    Science.gov (United States)

    Finogenov, L. V.; Lemeshko, Yu A.; Zav'yalov, P. S.; Chugui, Yu V.

    2007-06-01

    Ensuring the safety and high operation reliability of nuclear reactors takes 100% inspection of geometrical parameters of fuel assemblies, which include the grid spacers performed as a cellular structure with fuel elements. The required grid spacer geometry of assembly in the transverse and longitudinal cross sections is extremely important for maintaining the necessary heat regime. A universal method for 3D grid spacer inspection using a diffractive optical element (DOE), which generates as the structural illumination a multiple-ring pattern on the inner surface of a grid spacer cell, is investigated. Using some DOEs one can inspect the nomenclature of all produced grids. A special objective has been developed for forming the inner surface cell image. The problems of diffractive elements synthesis, projecting optics calculation, adjusting methods as well as calibration of the experimental measuring system are considered. The algorithms for image processing for different constructive elements of grids (cell, channel hole, outer grid spacer rim) and the experimental results are presented.

  1. Velocity and turbulence distributions in wall subchannels of a road bundle in three axial planes downstream of a spacer grid

    Science.gov (United States)

    Rehme, K.

    1987-03-01

    The velocity, turbulence, and temperature distributions in nuclear fuel element bundles of nuclear reactors were investigated. The mean velocity, the wall shear stresses, and the turbulence were measured in two wall subchannels of a rod bundle of four parallel rods, arranged in a rectangular channel, for three axial planes. A spacer grid was inserted in the rod bundle, for ratios between the distance spacer grid/measuring plane and the hydraulic diameter (LIDh) of 40.4, 32.8 and 16.9. The Reynolds number was 145,000. The results show that the distributions of the velocity and the turbulence are affected by the spacer grid, already for LIDh = 40.4. The effects of the spacer grid increase with decreasing distance to the spacer grid.

  2. A numerical approach to the simulation of one-phase and two phase reactor coolant flow around nuclear fuel spacers

    Energy Technology Data Exchange (ETDEWEB)

    Stosic, Z.V.; Stevanovic, V.D. [Framatome ANP GmbH - NBTT, Erlangen (Germany)

    2001-07-01

    A methodology for the simulation and analysis of one-phase and two-phase coolant flows around one or a row of spacers is presented. It is based on the multidimensional two-fluid mass, momentum and energy balance equations and application of adequate turbulence models. Necessary closure laws for interfacial transfer processes are presented. The stated general approach enables simulation and analyses of reactor coolant flow around spacers on different scale levels of the rod bundle geometry: detailed modelling of coolant flow around spacers and investigation of the influence of spacer's geometry on the coolant thermal-hydraulics, as well as prediction of global thermal-hydraulic parameters within the whole rod bundle with the investigation of the influence of rows of spacers on the bulk thermal-hydraulic processes. Sample problems are included illustrating these different modelling approaches. (author)

  3. DYNAMIC CHARACTERISTICS OF LIQUID SLOSHING IN A TRANS-VERSELY VIBRATING SPHERICAL TANK WITH A SPACER UNDER LOW GRAVITY

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The dynamic characteristics of liquid sloshing in a transversely vibrating spherical tank with spacer under low gravity were investigated. By expanding the characteristic functions, the frequencies and velocity potentials of liquid free-sloshing were obtained. The dynamic equations and boundary conditions of liquid sloshing in the traverse vibrational spherical tank with spacer under low gravity were derived. By modifying the velocity potentials of liquid free-sloshing, the velocity potentials of liquid sloshing in the traverse vibrating spherical tank with a spacer were obtained. Furthermore, the forces and the moments acting on tank wall were given. The numerical results show when a spacer is inserted in the tank, the sloshing frequencies of liquid and the forces acting on tank wall will decrease, but the moment of force to the centre of the tank which is caused by the force of liquid acting on the spacer will occur.

  4. Modeling the effect of spacers and biofouling on forward osmosis performance

    KAUST Repository

    Mosqueira Santillán, María José

    2014-11-01

    Currently, the most utilized desalination technology is reverse osmosis (RO), where a membrane is used as a physical barrier to separate the salts from the seawater, using high hydraulic pressure as driving force. A major problem in RO systems is biofouling, caused by severe growth of bacterial biofilms. Both, the need of an external energy input, as well as biofouling, impose a high cost on RO operation. Forward osmosis (FO) is an alternative membrane process that uses an osmotic pressure difference as driving force. FO uses a concentrated draw solution to generate high osmotic pressure, which extracts water across a semi permeable membrane from a feed solution. One of the main advantages of FO is the limited amount of external energy required to extract water from the feed solution. The objective of this research is the assessment of the impact of spacers, separating the membrane sheets, and biofouling on the FO system performance. This type of studies allow the optimization of membrane devices and operational conditions. For this, a two dimensional numerical model for FO systems was developed using computational fluid dynamics (CFD). This model allowed the evaluation of the impact of (i) spacers and (ii) biofilm, and (iii) the combined impact of spacers and biofilm on the performance of FO systems. The results obtained showed that the presence of spacers improved the performance of FO systems. Cavity configuration spacer gave the higher water flux across the membrane in clean systems; whereas for biofouled systems, the submerged configuration showed a better performance. In absence of spacers, the thickness or amount of biofilm is inversely proportional with the water flux. Furthermore, membrane surface coverage of the biofilm is more important than the amount of biofilm in terms of the impact on the performance. The numerical model can be adapted with other parameters (e.g. membrane and spacer thickness, feed and draw solution, solution concentration, etc.) to

  5. Rapid Identification of Pathogenic Bacteria by means of Two Conservative Gene Loci' Specific PCR-CE-RFLP

    Institute of Scientific and Technical Information of China (English)

    高鹏; 张卓然; 徐维家; 安万新; 张晓慧; 戴兵; 范艳萍; 王运锋; 李萍; 温杰; 于卫健; 高向仪; 谢凡迪; 王永海

    2003-01-01

    To establish a rapid identification method for common pathogenic bacteria on the basis of molecular biology and to construct a preliminary Polymerase Chain Reaction-Capillary Electrophoresis-Restriction Fragment Length Polymorphism (PCR-CE-RFLP) database of bacteria isolated from clinical specimens frequently, 183 strains collected from clinical samples belonging to 12 genera and 19 species whose biochemical characterizations corresponded to the typical ones were examined.The genomic DNAs were amplified by two pairs of fluorescence labeled primers aiming at 16S rRNA gene and 16S-23S rRNA spacer region gene respectively at the same time. PCR products were then digested by restriction endonuclease Hae Ⅲ in-completely before taking capillary electrophoresis. The results with the PCR-CE-RFLP patterns of 16S rRNA genes were just alike within some genera, but when it comes to 16S-23S rRNA spacer region genes, each bacterium showed a unique pattern, which can be distinguished from each other easily. It seems that PCR-CE-RFLP patterns of 16S rRNA gene could only be used to classify the bacteria into family level, whereas the data of 16S-23S rRNA spacer region gene could be utilized to identify the whole microorganisms as precisely as the species level. In spite of the data of the spacer region gene alone can be sufficiently to verify the whole bacteria, we insist that the 16S rRNA gene could be of some assistant in case that there should be lots of families of bacteria, in which some similar ones, with the same RFLP data of 16S-23S rRNA spacer region gene, may coexist. This study proves that the utility of PCR-CE-RFLP is a convenient, rapid method to identify pathogenic bacteria, and is also a quick diagnosis measure for application to clinical use.

  6. Barriers and supports to implementation of MDI/spacer use in nine Canadian pediatric emergency departments: a qualitative study

    Directory of Open Access Journals (Sweden)

    Graham Ian D

    2009-10-01

    Full Text Available Abstract Background Despite recent research supporting the use of metered dose inhalers with spacer devices (MDI/spacers in pediatric emergency departments (PEDs for acute exacerbations of asthma, uptake of this practice has been slow. The objectives of this study were to determine the barriers and supports to implementing MDI/spacer research and to identify factors associated with early and late adoption of MDI/spacers in Canadian PEDs. Methods Using a comparative case study design, we classified nine tertiary care pediatric hospital PEDs based on their stage of implementation. Data were collected using focus group interviews with physicians, registered nurses (RNs, and respiratory therapists (RTs, and individual interviews with both patient care and medical directors at each site. Initial coding was based on the Ottawa Model of Research Use (OMRU categories of elements known to influence the uptake of innovations. Results One hundred and fifty healthcare professionals from nine different healthcare institutions participated in this study. Lack of leadership in the form of a research champion, a lack of consensus about the benefits of MDI/spacers among staff, perceived resistance from patients/parents, and perceived increased cost and workload associated with MDI/spacer use were the most prevalent barriers to the adoption of the MDI/spacer. Common strategies used by early-adopting sites included the active participation of all professional groups in the adoption process in addition to a well-planned and executed educational component for staff, patients, and families. Early adopter sites were also more likely to have the MDI/spacer included in a clinical protocol/pathway. Conclusion Potential barriers and supports to implementation have been identified that will help EDs adopt MDI/spacer use. Future interventions intended to increase MDI/spacer use in PEDs will need to be sensitive to the barriers identified in this study.

  7. Hydrogel Spacer Prospective Multicenter Randomized Controlled Pivotal Trial: Dosimetric and Clinical Effects of Perirectal Spacer Application in Men Undergoing Prostate Image Guided Intensity Modulated Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Mariados, Neil, E-mail: nmariados@ampofny.com [Associated Medical Professionals of New York, Syracuse, New York (United States); Sylvester, John [21st Century Oncology, East Bradenton, Florida (United States); Shah, Dhiren [Western New York Urology Associates, Cancer Care of WNY, Cheektowaga, New York (United States); Karsh, Lawrence [The Urology Center of Colorado, Denver, Colorado (United States); Hudes, Richard [Chesapeake Urology Research Associates, The Prostate Center, Owings Mills, Maryland (United States); Beyer, David [Arizona Oncology Services Foundation, Phoenix, Arizona (United States); Kurtzman, Steven [Urological Surgeons of Northern California, Campbell, California (United States); Bogart, Jeffrey [The Research Foundation of State University of New York, SUNY Upstate Medical University, Syracuse, New York (United States); Hsi, R. Alex [Peninsula Cancer Center, Poulsbo, Washington (United States); Kos, Michael [Urology Nevada, Reno, Nevada (United States); Ellis, Rodney [University Hospitals Case Medical Center, Cleveland, Ohio (United States); Logsdon, Mark [Sutter Health Sacramento Sierra Region, Sutter Institute for Medical Research, Sacramento, California (United States); Zimberg, Shawn [Advanced Radiation Centers of New York, Lake Success, New York (United States); Forsythe, Kevin [Oregon Urology Institute, Springfield, Oregon (United States); Zhang, Hong [University of Rochester, Rochester, New York (United States); Soffen, Edward [CentraState Medical Center, Freehold, New Jersey (United States); Francke, Patrick [Carolina Regional Cancer Center, 21st Century Oncology, Myrtle Beach, South Carolina (United States); Mantz, Constantine [21st Century Oncology, Fort Meyers, Florida (United States); Rossi, Peter [Emory University, Atlanta, Georgia (United States); DeWeese, Theodore [The Johns Hopkins University, Baltimore, Maryland (United States); and others

    2015-08-01

    Purpose: Perirectal spacing, whereby biomaterials are placed between the prostate and rectum, shows promise in reducing rectal dose during prostate cancer radiation therapy. A prospective multicenter randomized controlled pivotal trial was performed to assess outcomes following absorbable spacer (SpaceOAR system) implantation. Methods and Materials: Overall, 222 patients with clinical stage T1 or T2 prostate cancer underwent computed tomography (CT) and magnetic resonance imaging (MRI) scans for treatment planning, followed with fiducial marker placement, and were randomized to receive spacer injection or no injection (control). Patients received postprocedure CT and MRI planning scans and underwent image guided intensity modulated radiation therapy (79.2 Gy in 1.8-Gy fractions). Spacer safety and impact on rectal irradiation, toxicity, and quality of life were assessed throughout 15 months. Results: Spacer application was rated as “easy” or “very easy” 98.7% of the time, with a 99% hydrogel placement success rate. Perirectal spaces were 12.6 ± 3.9 mm and 1.6 ± 2.0 mm in the spacer and control groups, respectively. There were no device-related adverse events, rectal perforations, serious bleeding, or infections within either group. Pre-to postspacer plans had a significant reduction in mean rectal V70 (12.4% to 3.3%, P<.0001). Overall acute rectal adverse event rates were similar between groups, with fewer spacer patients experiencing rectal pain (P=.02). A significant reduction in late (3-15 months) rectal toxicity severity in the spacer group was observed (P=.04), with a 2.0% and 7.0% late rectal toxicity incidence in the spacer and control groups, respectively. There was no late rectal toxicity greater than grade 1 in the spacer group. At 15 months 11.6% and 21.4% of spacer and control patients, respectively, experienced 10-point declines in bowel quality of life. MRI scans at 12 months verified spacer absorption. Conclusions: Spacer

  8. Hydrogel Spacer Prospective Multicenter Randomized Controlled Pivotal Trial: Dosimetric and Clinical Effects of Perirectal Spacer Application in Men Undergoing Prostate Image Guided Intensity Modulated Radiation Therapy

    International Nuclear Information System (INIS)

    Purpose: Perirectal spacing, whereby biomaterials are placed between the prostate and rectum, shows promise in reducing rectal dose during prostate cancer radiation therapy. A prospective multicenter randomized controlled pivotal trial was performed to assess outcomes following absorbable spacer (SpaceOAR system) implantation. Methods and Materials: Overall, 222 patients with clinical stage T1 or T2 prostate cancer underwent computed tomography (CT) and magnetic resonance imaging (MRI) scans for treatment planning, followed with fiducial marker placement, and were randomized to receive spacer injection or no injection (control). Patients received postprocedure CT and MRI planning scans and underwent image guided intensity modulated radiation therapy (79.2 Gy in 1.8-Gy fractions). Spacer safety and impact on rectal irradiation, toxicity, and quality of life were assessed throughout 15 months. Results: Spacer application was rated as “easy” or “very easy” 98.7% of the time, with a 99% hydrogel placement success rate. Perirectal spaces were 12.6 ± 3.9 mm and 1.6 ± 2.0 mm in the spacer and control groups, respectively. There were no device-related adverse events, rectal perforations, serious bleeding, or infections within either group. Pre-to postspacer plans had a significant reduction in mean rectal V70 (12.4% to 3.3%, P<.0001). Overall acute rectal adverse event rates were similar between groups, with fewer spacer patients experiencing rectal pain (P=.02). A significant reduction in late (3-15 months) rectal toxicity severity in the spacer group was observed (P=.04), with a 2.0% and 7.0% late rectal toxicity incidence in the spacer and control groups, respectively. There was no late rectal toxicity greater than grade 1 in the spacer group. At 15 months 11.6% and 21.4% of spacer and control patients, respectively, experienced 10-point declines in bowel quality of life. MRI scans at 12 months verified spacer absorption. Conclusions: Spacer

  9. Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions.

    Science.gov (United States)

    Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Edge, Thomas; Topp, Edward; Neumann, Norman F

    2015-11-01

    Host specificity in E. coli is widely debated. Herein, we used supervised learning logic-regression-based analysis of intergenic DNA sequence variability in E. coli in an attempt to identify single nucleotide polymorphism (SNP) biomarkers of E. coli that are associated with natural selection and evolution toward host specificity. Seven-hundred and eighty strains of E. coli were isolated from 15 different animal hosts. We utilized logic regression for analyzing DNA sequence data of three intergenic regions (flanked by the genes uspC-flhDC, csgBAC-csgDEFG, and asnS-ompF) to identify genetic biomarkers that could potentially discriminate E. coli based on host sources. Across 15 different animal hosts, logic regression successfully discriminated E. coli based on animal host source with relatively high specificity (i.e., among the samples of the non-target animal host, the proportion that correctly did not have the host-specific marker pattern) and sensitivity (i.e., among the samples from a given animal host, the proportion that correctly had the host-specific marker pattern), even after fivefold cross validation. Permutation tests confirmed that for most animals, host specific intergenic biomarkers identified by logic regression in E. coli were significantly associated with animal host source. The highest level of biomarker sensitivity was observed in deer isolates, with 82% of all deer E. coli isolates displaying a unique SNP pattern that was 98% specific to deer. Fifty-three percent of human isolates displayed a unique biomarker pattern that was 98% specific to humans. Twenty-nine percent of cattle isolates displayed a unique biomarker that was 97% specific to cattle. Interestingly, even within a related host group (i.e., Family: Canidae [domestic dogs and coyotes]), highly specific SNP biomarkers (98% and 99% specificity for dog and coyotes, respectively) were observed, with 21% of dog E. coli isolates displaying a unique dog biomarker and 61% of coyote isolates

  10. Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

    OpenAIRE

    Jayakodi, Murukarthick; Jung, Je Won; Park, Doori; Ahn, Young-Joon; Lee, Sang-Choon; Shin, Sang-Yoon; Shin, Chanseok; Yang, Tae-Jin; Kwon, Hyung Wook

    2015-01-01

    Background Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. Results In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an a...

  11. Fundamental Oscillation up to 1.42 THz in Resonant Tunneling Diodes by Optimized Collector Spacer Thickness

    Science.gov (United States)

    Kanaya, Hidetoshi; Sogabe, Riku; Maekawa, Takeru; Suzuki, Safumi; Asada, Masahiro

    2014-05-01

    We report an increase in the oscillation frequency of terahertz oscillators using AlAs/InGaAs double-barrier resonant tunneling diodes (RTDs) by optimizing the collector spacer thickness. For high-frequency oscillation of RTDs, the electron delay time, which is composed of the dwell time in the resonance region and the transit time in the collector depletion region, must be reduced. Although the transit time is reduced by a thin collector spacer, the capacitance increases. Thus, an optimum thickness of collector spacer layer exists. In this report, we investigate the dependence of oscillation frequency on the collector spacer thickness. The RTDs were integrated with 20-μm-long slot antennas, and oscillations up to 1.1, 1.42, and 1.29 THz were obtained for spacer thicknesses of 25, 12, and 6 nm, respectively. The optimum spacer thickness for high-frequency oscillation was around 12 nm. The highest frequency in this experiment was 1.42 THz oscillation, with an output power of ~1 μW. We also extracted the electron velocity in the collector depletion region and the dwell time from the dependence of the delay time on the collector spacer thickness.

  12. A comparative evaluation of application techniques of a paint-on die spacer in grooves: an in vitro study.

    Science.gov (United States)

    Vaishali, K; Prasad, D Krishna; Shetty, Manoj

    2013-12-01

    The use of paint-on die spacer to improve the seating of casting has become quite popular in the recent years. The generally accepted range of paint-on die spacer is approximately 20-40 μm, which suggests a range of tolerance. The painting of the retentive grooves with die spacer has always been a subject of debate. The primary purpose of this study was to determine if there was a tendency for the paint-on die spacer to accumulate in grooves of tooth preparation in sufficient thickness to exceed this accepted range of tolerance when applied using two different techniques. Eight die stone blocks with three grooves each were prepared. Half the samples were painted in unidirectional method and the other halves were painted using the haphazard method of application. The thickness of the die spacer was measured at different positions using 200× magnification and the mean and standard deviations were calculated. On analysis it was seen that the thickness of the paint-on die spacer in grooves was in the range of 20-40 μm for unidirectional method of application, whereas in haphazard method of application the thickness of the paint-on die spacer was in the range of 28-132 μm. From the above study it was concluded that the method of application influenced the thickness of the paint-on die spacer. The recommended thickness of the die spacer was achieved on unidirectional method of application.

  13. Epidemiology of vampire bat-transmitted rabies virus in Goiás, central Brazil: re-evaluation based on G-L intergenic region

    Directory of Open Access Journals (Sweden)

    Ito Fumio H

    2010-11-01

    Full Text Available Abstract Background Vampire bat related rabies harms both livestock industry and public health sector in central Brazil. The geographical distributions of vampire bat-transmitted rabies virus variants are delimited by mountain chains. These findings were elucidated by analyzing a high conserved nucleoprotein gene. This study aims to elucidate the detailed epidemiological characters of vampire bat-transmitted rabies virus by phylogenetic methods based on 619-nt sequence including unconserved G-L intergenic region. Findings The vampire bat-transmitted rabies virus isolates divided into 8 phylogenetic lineages in the previous nucleoprotein gene analysis were divided into 10 phylogenetic lineages with significant bootstrap values. The distributions of most variants were reconfirmed to be delimited by mountain chains. Furthermore, variants in undulating areas have narrow distributions and are apparently separated by mountain ridges. Conclusions This study demonstrates that the 619-nt sequence including G-L intergenic region is more useful for a state-level phylogenetic analysis of rabies virus than the partial nucleoprotein gene, and simultaneously that the distribution of vampire bat-transmitted RABV variants tends to be separated not only by mountain chains but also by mountain ridges, thus suggesting that the diversity of vampire bat-transmitted RABV variants was delimited by geographical undulations.

  14. Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED

    Directory of Open Access Journals (Sweden)

    Michael Bose

    2006-01-01

    Full Text Available Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm, facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators.

  15. The sequence of spacers between the consensus sequences modulates the strength of procaryotic promoters

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Hammer, Karin

    1998-01-01

    than 2000 relative units, which is among the strongest promoters known for this organism. The ranking of the promoter activities was somewhat different when assayed in E. coli, but the promoters are efficient for modulating gene expression in this bacteria as well. DNA sequencing revealed...... the spacers, at least a 400 fold change in activity can be obtained. Interestingly, the entire range of promoter activities is covered in small steps of activity increase, which makes these promoters very suitable for quantitative physiological studies and for fine tuning of gene expression in industrial bio......A library of synthetic promoters for Lactococcus lactis was constructed, in which the known consensus sequences were kept constant while the sequences of the separating spacers were randomized. The library consists of 38 promoters which differ in strength from 0.3 relative units, and up to more...

  16. Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition

    DEFF Research Database (Denmark)

    León Sobrino, Carlos; Kot, W.P.; Garrett, Roger Antony

    2015-01-01

    transposases were unchanged or enhanced. Antisense RNAs were implicated in the transcriptional regulation of adaptation and interference modules of the type I-A CRISPR-Cas system and evidence was found for the occurrence of functional coordination between the single CRISPR-Cas adaptation module and the......A transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich and basal media over a 6 day period. Spacer acquisition preceded strong host growth retardation, altered transcriptional activity of...... four different CRISPR-Cas modules and changes in viral copy numbers, and with significant differences in the two media. Transcript levels of proteins involved in the cell cycle were reduced, while those of DNA replication, DNA repair, transcriptional regulation, and some antitoxin-toxin pairs and...

  17. Transcriptome changes in STSV2-infected Sulfolobus islandicus REY15A undergoing continuous CRISPR spacer acquisition

    DEFF Research Database (Denmark)

    León Sobrino, Carlos; Kot, W.P.; Garrett, Roger Antony

    2016-01-01

    and transposases were unchanged or enhanced. Antisense RNAs were implicated in the transcriptional regulation of adaptation and interference modules of the type I-A CRISPR-Cas system and evidence was found for the occurrence of functional coordination between the single CRISPR-Cas adaptation module......A transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich and basal media over a 6 day period. Spacer acquisition preceded strong host growth retardation, altered transcriptional activity...... of four different CRISPR-Cas modules and changes in viral copy numbers, and with significant differences in the two media. Transcript levels of proteins involved in the cell cycle were reduced, while those of DNA replication, DNA repair, transcriptional regulation, and some antitoxin-toxin pairs...

  18. Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food.

    Science.gov (United States)

    Chen, Peng; Zhao, Yang; Wu, Zhengrong; Liu, Ronghui; Xu, Ruixiang; Yan, Lei; Li, Hongyu

    2016-03-01

    Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS) regions of rRNA genes from 12 different serofluid dish samples. The metagenome comprised of 50,865 average raw reads with an average of 8,958,220 bp and G + C content is 45.62%. This is the first report on metagenomic data of fungal ITS from serofluid dish employing Illumina platform to profile the fungal communities of this little known fermented food from Gansu Province, China. The Metagenomic data of fungal internal transcribed spacer can be accessed at NCBI, SRA database accession no. SRP067411. PMID:26981389

  19. Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food

    Directory of Open Access Journals (Sweden)

    Peng Chen

    2016-03-01

    Full Text Available Serofluid dish (or Jiangshui, in Chinese, a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS regions of rRNA genes from 12 different serofluid dish samples. The metagenome comprised of 50,865 average raw reads with an average of 8,958,220 bp and G + C content is 45.62%. This is the first report on metagenomic data of fungal ITS from serofluid dish employing Illumina platform to profile the fungal communities of this little known fermented food from Gansu Province, China. The Metagenomic data of fungal internal transcribed spacer can be accessed at NCBI, SRA database accession no. SRP067411.

  20. Analysis of sound absorption of tuck spacer fabrics to reduce automotive noise

    Science.gov (United States)

    Dias, Tilak; Monaragala, Ravindra; Needham, Peter; Lay, Edward

    2007-08-01

    Textiles are widely used in the automotive industry to provide both comfort to the passengers and an aesthetic appearance to the automotive interior. They can also be used to reduce automotive interior noise, which can make automotive travel safer and more comfortable. Knitted fabrics are used widely in automotive upholstery; however, the sound absorbency of a single layer of a knitted fabric is inadequate for the reduction of automotive interior noise. This paper investigates the sound absorbency of a novel knitted spacer fabric, which can be used in automotive upholstery and has the potential for greater sound absorbency than a conventional plain knitted fabric and its derivatives. The spacer fabric is modelled as a porous sound absorber and its sound absorbency is studied with regard to its structural parameters.

  1. MOLECULAR FIELD THEORY FOR NEMATIC LIQUID CRYSTAL POLYMER COMPRISING FLEXIBLE SPACER

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaogong; LIU Deshan; ZHOU Qixiang

    1993-01-01

    Based on the new model and concept of intramolecular orientational order parameter, a molecular field theory was built up for main chain liquid crystalline polymer (MC-LCPs) with flexible spacers. The theory takes account of orientational correlation among all mesogens in a polymer chain and the relationship between the intramolecular orientation and spatial orientation of the mesogens. The free energy, temperature and entropy of the nematic-isotropic transition were determined with the theory and compared with experiments in current work. It was found that many unique transition properties of the MC-LCPs comprising flexible spacer are correctly predicted by the theory and the agreement of the theory with the experiments is impressive.

  2. Influence of Spacer Grid Outer Strap on Fuel Assembly Thermal Hydraulic Performance

    Directory of Open Access Journals (Sweden)

    Jingwen Yan

    2014-01-01

    Full Text Available The outer strap as a typical structure of a spacer grid enhances the mechanical strength, decreases hang-up susceptibility, and also influences thermal hydraulic performance, for example, pressure loss, mixing performance, and flow distribution. In the present study, a typical grid spacer with different outer strap designs is adopted to investigate the influence of outer strap design on fuel assembly thermal hydraulic performance by using a commercial computational fluid dynamics (CFD code, ANSYS CFX, and a subchannel analysis code, FLICA. To simulate the outer straps’ influence between fuel assemblies downstream, four quarter-bundles from neighboring fuel assemblies are constructed to form the computational domain. The results show that the outer strap design has a major impact on cross-flow between fuel assemblies and temperature distribution within the fuel assembly.

  3. Numerical Simulation for Flow Distribution in ACE7 Fuel Assemblies affected by a Spacer Grid Deformation

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jongpil; Jeong, Ji Hwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    In spite of various efforts to understand hydraulic phenomena in a rod bundle containing deformed rods due to swelling and/or ballooning of clad, the studies for flow blockage due to spacer grid deformation have been limited. In the present work, 3D CFD analysis for flow blockage was performed to evaluate coolant flow within ACE7 fuel assemblies (FAs) containing a FA affected by a spacer grid deformation. The real geometry except for inner grids was used in the simulation and the region including inner grid was replaced by porous media. In the present work, the numerical simulation was performed to predict coolant flow within ACE7 FAs affected by a Mid grid deformation. The 3D CFD result shows that approximately 60 subchannel hydraulic diameter is required to fully recover coolant flow under normal operating condition.

  4. TiNi Shape Memory Alloy Foams Synthesized by Spacer Sintering and their Properties

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Titanium (Ti) andnickel (Ni) elemental powders were blended by ball milling and the ball milled powders were employed to fabricate TiNi shape memory alloy (SMA) foams by spacer sintering. Effect of ball milling time on phase constitutes of the sintered TiNi alloy foams was studied by X-ray diffraction (XRD) analysis. Scanning electron microscopy (SEM) was used to characterize the porous structure, and compressive tests were carried out to evaluate the mechanical properties ofthe foams. Results indicate that porosities of the TiNi alloy foams can be controlled by using the spacer sintering method, and the porosities show a significant effect on the mechanical properties and shape memory effect (SME).

  5. Enhanced spin-torque in double tunnel junctions using a nonmagnetic-metal spacer

    Energy Technology Data Exchange (ETDEWEB)

    Chen, C. H.; Cheng, Y. H.; Ko, C. W.; Hsueh, W. J., E-mail: hsuehwj@ntu.edu.tw [Nanomagnetism Group, Department of Engineering Science and Ocean Engineering, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 10660, Taiwan (China)

    2015-10-12

    This study proposes an enhancement in the spin-transfer torque of a magnetic tunnel junction (MTJ) designed with double-barrier layer structure using a nonmagnetic metal spacer, as a replacement for the ferromagnetic material, which is traditionally used in these double-barrier stacks. Our calculation results show that the spin-transfer torque and charge current density of the proposed double-barrier MTJ can be as much as two orders of magnitude larger than the traditional double-barrier one. In other words, the proposed double-barrier MTJ has a spin-transfer torque that is three orders larger than that of the single-barrier stack. This improvement may be attributed to the quantum-well states that are formed in the nonmagnetic metal spacer and the resonant tunneling mechanism that exists throughout the system.

  6. Cyanobacterial Diversity and a New Acaryochloris-Like Symbiont from Bahamian Sea-Squirts

    OpenAIRE

    Susanna López-Legentil; Bongkeun Song; Manel Bosch; Joseph R Pawlik; Xavier Turon

    2011-01-01

    Symbiotic interactions between ascidians (sea-squirts) and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS) and by examining symbiont morphology with transmission electron (TEM) and confocal microscopy (CM). As described previously for other s...

  7. Differentiation of Enterococcus faecium from Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains by PCR and dot-blot hybridisation.

    Science.gov (United States)

    Langa, S; Fernández, A; Martín, R; Reviriego, C; Marín, M L; Fernández, L; Rodríguez, J M

    2003-12-01

    Variations in length and sequence of the 16S/23S spacer region of Enterococcus faecium provided the basis for development of simple PCR and dot-blot hybridisation assays that enabled the differentiation of potentially probiotic Enterococcus faecium strains from Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. Such assays may be useful for differentiation of yoghurt starter cultures and enterococcal strains when they are simultaneously present in probiotic food products.

  8. Fluid dynamics evaluation of split vane grid spacer in a small modular reactor

    Energy Technology Data Exchange (ETDEWEB)

    Nazififard, Mohammad [Kashan Univ (Iran, Islamic Republic of). Dept. of Energy System Engineering; Seoul National Univ. (Korea, Republic of). Dept. of Nuclear Engineering; Philosophia, Seoul (Korea, Republic of); Nematollahi, Mohammadreza [Shiraz Univ. (Iran, Islamic Republic of). Dept. of Nuclear Engineering; Suh, Kune Y. [Seoul National Univ. (Korea, Republic of). Dept. of Nuclear Engineering; Philosophia, Seoul (Korea, Republic of)

    2015-12-15

    This paper numerically evaluates the effect of a split vane grid spacer on thermohydrodynamics in a subchannel of a typical small modular pressurized water reactor. The turbulent convective heat transfer and pressure drop are numerically calculated. Thermohydrodynamics and neutronics coupling would indeed be interesting for more quantitative analyses of the fuel assembly design, heat transfer correlation and mixing coefficient for the System-Integrated Modular Advanced Reactor (SMART) being developed by the Korea Atomic Energy Research Institute (KAERI).

  9. Treatment of persistent extraarticular infection using a temporary cement spacer on the tibia after ACL reconstruction.

    Science.gov (United States)

    Jung, Kwang Am; Lee, Soo Chan; Song, Moon Bok; Lee, Choon Key

    2008-01-01

    Postoperative infection after anterior cruciate ligament (ACL) reconstruction is an uncommon but serious complication. Although several treatments for intraarticular infection have been reported, no report has been recorded on the treatment of persistent extraarticular infections. The authors experienced reconstructed graft removal due to a refractory extraarticular infection on tibia. Early ACL reimplantation was performed using a temporary cement spacer containing antibiotics and a irradiated bone patellar tendon bone allograft.

  10. Numerical study on the effect of design parameters and spacers on RPC signal and timing properties

    CERN Document Server

    Jash, Abhik; Mukhopadhyay, Supratik; Saha, Satyajit; Chattopadhyay, Subhasis

    2016-01-01

    Numerical calculations have been performed to understand the reason for the non-uniform response of a Resistive Plate Chamber (RPC) at few critical regions such as near edge spacers and corners of the device, which was observed experimentally. In this context, the signal from an RPC due to passage of muons through different regions has been computed. Also a straightforward simulation for RPC timing properties has been presented along with the effect of applied field, gas mixture and geometrical components.

  11. Reduction of Parasitic Capacitance in Vertical MOSFETs by Spacer Local Oxidation

    OpenAIRE

    Kunz, V Dominik; Uchino, Takashi; De Groot, C. H. (Kees); Ashburn, Peter; Donaghy, David C.; Hall, Steven; Wang, Yun; Hemment, P L F

    2003-01-01

    Application of double gate or surround-gate vertical metal oxide semiconductor field effect transistors (MOSFETs) is hindered by the parasitic overlap capacitance associated with their layout, which is considerably larger than for a lateral MOSFET on the same technology node. A simple self-aligned process has been developed to reduce the parasitic overlap capacitance in vertical MOSFETs using nitride spacers on the sidewalls of the trench or pillar and a local oxidation. This will result in a...

  12. Imidacloprid and Thiamethoxam Induced Mutations in Internal Transcribed Spacer 2 (ITS2) of Anopheles stephensi

    OpenAIRE

    Bhinder, Preety; Chaudhry, Asha; Barna, Bhupinder; Kaur, Satvinderjeet

    2012-01-01

    The present article deals with the polymerase chain reaction (PCR)-based genotoxicity evaluation of neonicotinoid pesticides, imidacloprid and thiamethoxam, by using the genome of a mosquito Anopheles stephensi taken as an experimental model. After treatment of the second instar larvae with LC20 of the pesticides for 24 h, the induced nucleotide sequence variations in the internal transcribed spacer 2 (ITS2) of freshly hatched unfed control and treated individuals was studied from the sequenc...

  13. Robot welding of spacer/support attachments for Heysham II/Torness steam generation unit platens

    International Nuclear Information System (INIS)

    Boiler support systems, based on spacer-tube attachments, at two United Kingdom power stations have been successfully welded using a non-adaptive robotic system, a world first in robotic welding in boiler platen fabrication. Process monitoring, and precision wire feed equipment for accurate synchronous pulsing were developed with contributions from The Welding Institute. Positional error was compensated for using off-line programming with vision sensing. (UK)

  14. Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food

    OpenAIRE

    Peng Chen; Yang Zhao; Zhengrong Wu; Ronghui Liu; Ruixiang Xu; Lei Yan; Hongyu Li

    2015-01-01

    Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS) regions of rRNA genes from 12 different serofluid dish samples. The metagenome comprised of 50,865 average raw reads with...

  15. Calculation of aerial cable spacer compression forces in bundled phases during short circuit fault

    OpenAIRE

    I. I. Sergey; Ya. V. Potachits

    2014-01-01

    The paper presents an approximate method for calculation of electrodynamic resistance parameters of a flexible bus-bar with bundled phases. Comparison of the approximate calculation results with the computer calculations using a FAZA software tool has been given in the paper. An evaluation of permissible aerial cable spacer compression forces for designed modern standard distribution substations of 330 and 550 kV has been provided in the paper. The paper proposes an algorithm for determinatio...

  16. Treatment of persistent extraarticular infection using a temporary cement spacer on the tibia after ACL reconstruction.

    Science.gov (United States)

    Jung, Kwang Am; Lee, Soo Chan; Song, Moon Bok; Lee, Choon Key

    2008-01-01

    Postoperative infection after anterior cruciate ligament (ACL) reconstruction is an uncommon but serious complication. Although several treatments for intraarticular infection have been reported, no report has been recorded on the treatment of persistent extraarticular infections. The authors experienced reconstructed graft removal due to a refractory extraarticular infection on tibia. Early ACL reimplantation was performed using a temporary cement spacer containing antibiotics and a irradiated bone patellar tendon bone allograft. PMID:17899003

  17. Design, Synthesis and Hydrolytic Behavior of Mutual Prodrugs of NSAIDs with Gabapentin Using Glycol Spacers

    Directory of Open Access Journals (Sweden)

    Hiba Najeh Alsaad

    2012-10-01

    Full Text Available The free –COOH present in NSAIDs is thought to be responsible for the GI irritation associated with all traditional NSAIDs. Exploitation of mutual prodrugs is an approach wherein the NSAID is covalently bounded to a second pharmacologically active carrier/drug with the ultimate aim of reducing the gastric irritation. In this study some NSAIDs were conjugated with gabapentin via ester bonds using glycol spacers with the expectation of reducing gastric adverse effects and obtaining synergistic analgesic effects. The kinetics of ester hydrolysis were studied in two different non enzymatic buffer solutions at pH 1.2 and 7.4, as well as in 80% human plasma using HPLC with chloroform -methanol as mobile phase. Compounds 9a–c with ethylene glycol spacers showed significant stability at buffer solutions with half lives ranging from about 8–25 h, while the underwent a reasonable plasma hydrolysis (49%–88% in 2 h. Compound 9d with a propylene glycol spacer shows a higher rate of enzymatic hydrolysis than the corresponding ethylene glycol compound 9c. The result of compounds 9a-c indicate that these compounds may be stable during their passage through the GIT until reaching the blood circulation.

  18. Heat transfer enhancement with mixing vane spacers using the field synergy principle

    Science.gov (United States)

    Yang, Lixin; Zhou, Mengjun; Tian, Zihao

    2016-08-01

    The single-phase heat transfer characteristics in a PWR fuel assembly are important. Many investigations attempt to obtain the heat transfer characteristics by studying the flow features in a 5´5 rod bundle with a spacer grid. The field synergy principle is used to discuss the mechanism of heat transfer enhancement using mixing vanes according to computational fluid dynamics results, including a spacer grid without mixing vanes, one with a split mixing vane, and one with a separate mixing vane. The results show that the field synergy principle is feasible to explain the mechanism of heat transfer enhancement in a fuel assembly. The enhancement in subchannels is more effective than on the rod's surface. If the pressure loss is ignored, the performance of the split mixing vane is superior to the separate mixing vane based on the enhanced heat transfer. Increasing the blending angle of the split mixing vane improves heat transfer enhancement, the maximum of which is 7.1%. Increasing the blending angle of the separate mixing vane did not significantly enhance heat transfer in the rod bundle, and even prevented heat transfer at a blending angle of 50°. This finding testifies to the feasibility of predicting heat transfer in a rod bundle with a spacer grid by field synergy, and upon comparison with analyzed flow features only, the field synergy method may provide more accurate guidance for optimizing the use of mixing vanes.

  19. Microcalorimetric studies of cationic gemini surfactant with a hydrophilic spacer group

    International Nuclear Information System (INIS)

    The aim of this work is to investigate the micellization thermodynamics for gemini surfactants with a hydrophilic spacer group, i.e. Br- n-C12H25N+Me2 -CH2(CH2OCH2) xCH2N+Me2 - n-C12H25 Br-, referred to as 12-EO x-12, where x = 1, 3, 6, 7. These oligooxaalkanediyl-α,ω-bis(dimethyldodecylammonium bromide) dimeric surfactants were synthesized by a two step reaction. Their physicochemical properties in aqueous solutions have been studied by microcalorimetry at 298 K, electrical conductivity and surface tension measurements. The critical micellar concentration (cmc) and the head-group area (a 0) per molecule at the air-water interface increase with increasing number of oxide ethylene moieties in the spacer and, consequently, with the enhanced hydrophilic character of the molecule. The calorimetric studies of the self-assembly process confirm this trend, since the exothermic values of the differential enthalpy of micellization (Δmic H deg ) decrease as the ethylene oxide moieties are lengthened. Moreover, the values of the free energy and entropy of micellization indicate an entropy driven phenomenon for all surfactants. These results are compared with those obtained for gemini cationic surfactants with a hydrophobic spacer and the differences observed are discussed in terms of the hydrophilic head-group conformation in the micelle

  20. Spacer multi-patterning control strategy with optical CD metrology on device structures

    Science.gov (United States)

    Lee, Jongsu; Lee, Byoung-Hoon; Ma, Won-Kwang; Han, Sang-Jun; Kim, Young-Sik; Kwak, Noh-Jung; Theeuwes, Thomas; Guo, Wei; Song, Yi; Wisse, Baukje; Kruijswijk, Stefan; Cramer, Hugo; Welch, Steven; Verma, Alok; Zhang, Rui; Chai, Yvon; Hsu, Sharon; Miceli, Giacomo; Sun, Kyu-Tae; Byun, Jin-Moo

    2016-03-01

    Spacer multi patterning process continues to be a key enabler of future design shrinks in DRAM and NAND process flows. Improving Critical Dimension Uniformity (CDU) for main features remains high priority for multi patterning technology and requires improved metrology and control solutions. In this paper Spacer Patterning Technology is evaluated using an angle resolved scatterometry tool for both intra field control of the core CD after partition etch (S1) and interfield pitch-walking control after final etch (S1-S2). The intrafield measurements were done directly on device using dense sampling. The inter-field corrections were based on sparse full wafer measurements on biased OCD targets. The CDU improvement after partition-etch was verified by direct scatterometer and CD-SEM measurement on device. The final etch performance across wafer was verified with scatterometer on OCD target. The scatterometer metrology in combination with the control strategy demonstrated a consistent CDU improvement of core (S1) intrafield CD after partition etch between 23-39% and 47-53% on interfield pitch-walking (S1-S2) after final etch. To confirm these improvements with CD-SEM, oversampling of more than 16 times is needed compared to scatterometer. Based on the results it is concluded that scatterometry in combination with the evaluated metrology and control strategy in principle qualifies for a spacer process CDU control loop in a manufacturing environment.

  1. Spacers in radiotherapy treatment of prostate cancer: Is reduction of toxicity cost-effective?

    International Nuclear Information System (INIS)

    Background and purpose: To compare the cost-effectiveness of treating prostate cancer patients with intensity-modulated radiation therapy and a spacer (IMRT+S) versus IMRT-only without a spacer (IMRT-O). Materials and methods: A decision-analytic Markov model was constructed to examine the effect of late rectal toxicity and compare the costs and quality-adjusted Life Years (QALYs) of IMRT-O and IMRT+S. The main assumption of this modeling study was that disease progression, genito-urinary toxicity and survival were equal for both comparators. Results: For all patients, IMRT+S revealed a lower toxicity than IMRT-O. Treatment follow-up and toxicity costs for IMRT-O and IMRT+S amounted to €1604 and €1444, respectively, thus saving €160 on the complication costs at an extra charge of €1700 for the spacer in IMRT+S. The QALYs yielded for IMRT-O and IMRT+S were 3.542 and 3.570, respectively. This results in an incremental cost-effectiveness ratio (ICER) of €55,880 per QALY gained. For a ceiling ratio of €80,000, IMRT+S had a 77% probability of being cost-effective. Conclusion: IMRT+S is cost-effective compared to IMRT-O based on its potential to reduce radiotherapy-related toxicity

  2. Synthetically programmable nanoparticle superlattices using a hollow three-dimensional spacer approach

    Energy Technology Data Exchange (ETDEWEB)

    Auyeung, Evelyn; Cutler, Joshua I.; Macfarlane, Robert J.; Jones, Matthew R.; Wu, Jinsong; Liu, George; Zhang, Ke; Osberg, Kyle D.; Mirkin, Chad A. (NWU)

    2013-04-08

    Crystalline nanoparticle arrays and superlattices with well-defined geometries can be synthesized by using appropriate electrostatic, hydrogen-bonding or biological recognition interactions. Although superlattices with many distinct geometries can be produced using these approaches, the library of achievable lattices could be increased by developing a strategy that allows some of the nanoparticles within a binary lattice to be replaced with 'spacer' entities that are constructed to mimic the behaviour of the nanoparticles they replace, even though they do not contain an inorganic core. The inclusion of these spacer entities within a known binary superlattice would effectively delete one set of nanoparticles without affecting the positions of the other set. Here, we show how hollow DNA nanostructures can be used as 'three-dimensional spacers' within nanoparticle superlattices assembled through programmable DNA interactions. We show that this strategy can be used to form superlattices with five distinct symmetries, including one that has never before been observed in any crystalline material.

  3. Genetic Diversity of Fast-growing Rhizobia Associated with Glycine max in Subtropical Regions of China%我国亚热带地区快生型大豆根瘤菌遗传多样性研究

    Institute of Scientific and Technical Information of China (English)

    杨成运; 周俊初; 杨江科; 段广才

    2011-01-01

    Genetic diversity of 31 isolates from effective nodules of soybean in different geographical regions of China was studied using 16S rDNA gene RELP patterns, 16S rDNA gene sequencing, 16S— 23S rDN A IGS region RE LP patterns and 16S — 23S rDN A IGS sequencing assays. The isolates were clustered into one genospecies with Sinorhizobium fredii USDA205 on the basis of their 16S rDNA gene PCR - RFLP patterns. 16S rDNA gene sequence of strains indicated that the isolates were very closely related (identities higher than 99.5%) to Sinorhizobium fredii USDA205. The analysis of the 16S—23S intergenic spacer (IGS) divided the isolates into 10 genotypes and four groups. The 16S—23S rDNA IGS sequencing assays divided the isolates into two groups. Group Ⅰ was clustered with Sinorhizobium fredii USDA205. Group Ⅱ was less similarity to Sinorhizobium fredii USDA205 than Sinorhizobium xinjiangense. The isolates from the subtropical regions of China had higher genetic similarity.%利用16S rDNA PCR-RELP、16S rDNA基因序列分析以及16S-23S rDNA IGS PCRRELP技术,对分离自我国江苏盐城、浙江温州、湖北仙桃及重庆等亚热带地区的31株大豆快生型根瘤茵(fast-growing rhizobia)进行了群体遗传多样性研究.16S rDNA PCR-RELP分析结果表明,所有供试大豆根瘤菌都与费氏中华根瘤菌USDA205聚成一类.供试代表菌株YcS2的16S rDNA基因序列与费氏中华根瘤菌USDA205的该序列相似性超过99.5%.16S-23S rDNA IGS PCR-RFLP研究结果表明:所有供试菌株分为10个基因型,在87%的相似性上分为4个类群.在此基础上筛选出10个代表菌株进行16S-23S rDNA基因序列分析,结果表明,10个供试菌株分为2个群,群Ⅱ(YcS3、ZzS1、YcS14)与新疆中华根瘤茵CCBAU110聚在一起,群I(其余7个菌株)与费氏中华根瘤茵USDA205聚在一起.中国亚热带地区的快生型大豆根瘤茵具有高度的相似性.

  4. Visible light dynamical diffraction in a 1-D photonic crystal-based interferometer with an extremely thin spacer layer

    Science.gov (United States)

    Prudnikov, I. R.

    2016-01-01

    Properties of light diffraction in a Fabry-Pérot-like interferometer composed of two 1-D photonic crystals and a nanometer-thick spacer layer are analytically investigated. It is shown that the resonant enhancement of light wave intensity in such a layer is possible because of light dynamical diffraction from the photonic crystals of the interferometer. Numerical simulations of (i) light reflectivity and transmittance curves of the interferometer having an ultra-thin spacer layer (its thickness changes from less than 1 nm to about 10 nm) and (ii) the resonant distribution of the light wave intensity in the vicinity of the layer are performed. Based on the numerical simulations, potentialities for the determination of the structural parameters (e.g., thicknesses and refraction indexes) of ultra-thin spacer films are discussed. A difference is found to appear in resonant intensity enhancements inside the ultra-thin spacer layers between s- and p-polarized light waves.

  5. Spacer Thickness-Dependent Electron Transport Performance of Titanium Dioxide Thick Film for Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Reda E. El-Shater

    2015-01-01

    Full Text Available A titanium dioxide (P25 film was deposited by cast coating as conductive photoelectrode and subsequently immersed in dye solution (N719 to fabricate the photoanode of dye-sensitized solar cells (DSSCs. A plastic spacer was used as a separation and sealant layer between the photoanode and the counter electrode. The effect of the thickness of this spacer on the transfer of electrons in the liquid electrolyte of the DSSCs was studied by means of both IV curves and electrochemical impedance. Using a spacer thickness range of 20 μm to 50 μm, efficiency ranges from 3.73% to 7.22%. The highest efficiency of 7.22% was obtained with an optimal spacer thickness of 40 μm.

  6. Review of the correlation developments and a new concept based on mixing mechanism for heat transfer enhancement of spacer grids

    Energy Technology Data Exchange (ETDEWEB)

    Mao, H.; Yang, B.W.; Liu, X. [Xi' an Jiaotong Univ., Shaanxi (China). Science and Technology Center for Advanced Nuclear Fuel Research

    2016-07-15

    Spacer grids could cause heat transfer enhancement both at the spacer grid regions and downstream of the spacer grids as a result of mixing promoted by the spacer grids in the rod bundle. This phenomenon has been demonstrated by many experiments, and several correlations have been developed based on these experimental data. This paper gives a review of the grid-enhanced heat transfer correlation developments in single phase flow. Following the exploration of the correlation development history, a predictive formulation of grid-enhanced heat transfer in single phase flow is established taking into account the effect of both swirl flow and crossflow. With emphasis on modeling of the mixing mechanism associated with the mixing vane grid, the new correlation could better reflect the physical process of the heat transfer augmentation, while a large number of experimental data are needed to determine the coefficients of the new correlation.

  7. Effect of electrostatic charge in plastic spacers on the lung delivery of HFA-salbutamol in children

    DEFF Research Database (Denmark)

    Anhøj, J; Bisgaard, H; Lipworth, B J

    1999-01-01

    AIMS: The effect of the electrostatic charge in plastic spacers in vivo on drug delivery to the lung of hydrofluoroalkane (HFA) salbutamol spray was studied in children. METHODS: Five children, aged 7-12 years, were included in a 3-way crossover randomised single-blind trial. Salbutamol HFA spray...... was delivered on 3 different study days from plastic spacers with mouthpiece. Pre-treatment of the spacers differed between study days: (a) Non-electrostatic 350 ml Babyhaler (coated with benzalkonium chloride) (b) New 350 ml Babyhaler (rinsed in water), and (c) New 145 ml AeroChamber (rinsed in water). Plasma...... delivered a significantly (Pplastic spacers reduces lung dose in children by more than two-fold. This is clinically significant and the use of potentially electrostatically charged...

  8. INFLUENCE OF THE SIZE OF METHYLENE SPACERS ON THE THERMAL BEHAVIOR OF SEVERAL ALIPHATIC-AROMATIC POLYESTERS

    Directory of Open Access Journals (Sweden)

    NATALIA HURDUC

    2014-04-01

    Full Text Available Polyesters have a wide range of technical applications and therefore their processing is of the utmost importance. Since polyesters are usually processed by melting, their thermal stability is an extremely important characteristic for the exact determination of the operational parameters. The thermal analysis was carried out using a MOM-Budapest derivatograph at the 10 C/min heating speed, aluminum oxide the reference material, and the air conditions were static. The study lead to conclusions on the thermal stability and degradation mechanism depending on the number of methylene groups in the spacer. Thermal stability is supported by the increase in the number of methylene groups in the spacer. The degradation mechanism is complex through successive reactions. The spacer size influences the nature of the micromolecules formed by spacer fragmenting and by the number of carbon atoms, respectively.

  9. Binding of 12-s-12 dimeric surfactants to calf thymus DNA: Evaluation of the spacer length influence.

    Science.gov (United States)

    Sarrión, Beatriz; Bernal, Eva; Martín, Victoria Isabel; López-López, Manuel; López-Cornejo, Pilar; García-Calderón, Margarita; Moyá, María Luisa

    2016-08-01

    Several cationic dimeric surfactants have shown high affinity towards DNA. Bis-quaternary ammonium salts (m-s-m) have been the most common type of dimeric surfactants investigated and it is generally admitted that those that posses a short spacer (s≤3) show better efficiency to bind or compact DNA. However, experimental results in this work show that 12-s-12 surfactants with long spacers make the surfactant/ctDNA complexation more favorable than those with short spacers. A larger contribution of the hydrophobic interactions, which control the binding Gibbs energy, as well as a higher average charge of the surfactant molecules bound to the nucleic acid, which favors the electrostatic attractions, could explain the experimental observations. Dimeric surfactants with intermediate spacer length seem to be the less efficient for DNA binding. PMID:27108208

  10. Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

    DEFF Research Database (Denmark)

    Shah, Shiraz Ali; Hansen, Niels R; Garrett, Roger A

    2009-01-01

    Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles, the chromo......Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles...

  11. Sonication of antibiotic-loaded cement spacers in a two-stage revision protocol for infected joint arthroplasty

    OpenAIRE

    Mariconda, Massimo; Ascione, Tiziana; Balato, Giovanni; Rotondo, Renato; Smeraglia, Francesco; Costa, Giovan Giuseppe; Conte, Marco

    2013-01-01

    Background Culturing of the sonication fluid of removed implants has proven to be more sensitive than conventional periprosthetic tissue culture for the microbiological diagnosis of prosthetic joint infection. Since bacteria surviving on antibiotic-loaded cement spacers used in a two-stage exchange protocol for infected arthroplasties may cause the persistence of infection, in this study we asked whether the sonication also could be used to identify bacteria on antibiotic-loaded cement spacer...

  12. A Rationale for Going Back to the Future: Use of Disposable Spacers for Pressurised Metered Dose Inhalers

    Directory of Open Access Journals (Sweden)

    Mark Sanders

    2015-01-01

    Full Text Available The introduction of pressurised metered dose inhalers (MDIs in the mid-1950s completely transformed respiratory treatment. Despite decades of availability and healthcare support and development of teaching aids and devices to promote better use, poor pMDI user technique remains a persistent issue. The main pMDI user aid is the spacer/valved holding chamber (VHC device. Spacer/chamber features (size, shape, configuration, construction material, and hygiene considerations can vie with clinical effectiveness (to deliver the same dose as a correctly used pMDI, user convenience, cost, and accessibility. Unsurprisingly, improvised, low-cost alternatives (plastic drink bottles, paper cups, and paper towel rolls have been pressed into seemingly effective service. A UK law change permitting schools to hold emergency inhalers and spacers has prompted a development project to design a low-cost, user-friendly, disposable, and recyclable spacer. This paper spacer requires neither preuse priming nor washing, and has demonstrated reproducible lung delivery of salbutamol sulphate pMDI, comparable to an industry-standard VHC, an alternative paperboard VHC, and pMDI alone. This new device appears to perform better than these other VHC devices at the low flow rates thought achievable by paediatric patients. The data suggest that this disposable spacer may have a place in the single-use emergency setting.

  13. A Rationale for Going Back to the Future: Use of Disposable Spacers for Pressurised Metered Dose Inhalers

    Science.gov (United States)

    Sanders, Mark; Bruin, Ronald

    2015-01-01

    The introduction of pressurised metered dose inhalers (MDIs) in the mid-1950s completely transformed respiratory treatment. Despite decades of availability and healthcare support and development of teaching aids and devices to promote better use, poor pMDI user technique remains a persistent issue. The main pMDI user aid is the spacer/valved holding chamber (VHC) device. Spacer/chamber features (size, shape, configuration, construction material, and hygiene considerations) can vie with clinical effectiveness (to deliver the same dose as a correctly used pMDI), user convenience, cost, and accessibility. Unsurprisingly, improvised, low-cost alternatives (plastic drink bottles, paper cups, and paper towel rolls) have been pressed into seemingly effective service. A UK law change permitting schools to hold emergency inhalers and spacers has prompted a development project to design a low-cost, user-friendly, disposable, and recyclable spacer. This paper spacer requires neither preuse priming nor washing, and has demonstrated reproducible lung delivery of salbutamol sulphate pMDI, comparable to an industry-standard VHC, an alternative paperboard VHC, and pMDI alone. This new device appears to perform better than these other VHC devices at the low flow rates thought achievable by paediatric patients. The data suggest that this disposable spacer may have a place in the single-use emergency setting. PMID:26491563

  14. A Comparison of Flow Field Characteristics from PIV Experiment Measurement to Numerical Simulation behind a Spacer in a Vertical Pipe

    Directory of Open Access Journals (Sweden)

    Lávička D.

    2010-07-01

    Full Text Available This paper describes the topic of measurement using a modern laser method (PIV in an annular channel of very small dimensions. The annular channel simulates the flow area around a model of a fuel rod in the VVER nuclear reactor. The annular channel holds spacers which create obstacles to fluid flow. The spacers serve a number of important purposes. In the real nuclear reactor, the spacer holds a fuel rod in the fuel rod bundle. Another important function of the spacer is to influence the flow field characteristics, especially turbulence size, by the shape of the spacer. The value of the turbulence regulates the intensity of heat transfer between the fuel rod and the fluid. Therefore, it is very important to provide a correct description and analysis of the flow field behind the obstacle the spacer generates. The paper further looks into the solution of the same task using numerical simulation. The solution of this task consisted of setting the suitable boundary conditions and of setting the turbulence model for the numerical simulation. The result is a comparison of the flow field characteristics from the experimental measurement and the findings of the numerical simulation. The numerical simulation was carried out using commercial CFD software package, FLUENT.

  15. Application of a hydrogel spacer for postoperative salvage radiotherapy of prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Pinkawa, Michael; Schubert, Carolin; Escobar-Corral, Nuria; Holy, Richard; Eble, Michael J. [RWTH Aachen University, Department of Radiation Oncology, Aachen (Germany)

    2015-04-01

    In contrast to primary radiotherapy, no reports are available for a hydrogel spacer application in postoperative salvage radiotherapy for prostate cancer. A 77-year-old patient presented 20 years after radical prostatectomy with a digitally palpable local recurrence at the urethrovesical anastomosis (PSA 5.5 ng/ml). The hydrogel spacer (10 ml, SpaceOAR trademark) was injected between the local recurrence and rectal wall under transrectal ultrasound guidance. Treatment planning was performed with an intensity-modulated technique up to a total dose of 76 Gy in 2-Gy fractions. The same planning was performed based on computed tomography before spacer injection for comparison. The local recurrence, initially directly on the rectal wall, could be displaced more than 1 cm from the rectal wall after hydrogel injection. With a mean total dose of 76 Gy to the planning target volume, rectal wall volumes included in the 70 Gy, 60 Gy, 50 Gy isodoses were 0 cm{sup 3}, 0 cm{sup 3}, and 0.4 cm{sup 3} with a spacer and 2.9 cm{sup 3}, 4.5 cm{sup 3}, and 6.2 cm{sup 3} without a spacer, respectively. The patient reported rectal urgency during radiotherapy, completely resolving after the end of treatment. The PSA level was 5.4 ng/ml a week before the end of radiotherapy and dropped to 0.9 ng/ml 5 months after radiotherapy. A hydrogel spacer was successfully applied for dose-escalated radiotherapy in a patient with macroscopic local prostate cancer recurrence at the urethrovesical anastomosis to decrease the dose at the rectal wall. This option can be considered in specifically selected patients. (orig.) [German] Im Gegensatz zum Einsatz bei der primaeren Radiotherapie gibt es bisher keine Berichte zum Einsatz eines Hydrogel-Abstandhalters bei der postoperativen Salvage-Radiotherapie des Prostatakarzinoms. Ein 77-jaehriger Patient stellte sich 20 Jahre nach radikaler Prostatektomie mit einem digital palpablem Lokalrezidiv im Bereich der urethrovesikalen Anastomose vor (PSA 5,5 ng

  16. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

    Science.gov (United States)

    Treangen, Todd J.; Koren, Sergey; Pop, Mihai; Bhaya, Devaki

    2016-01-01

    The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2–13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics. PMID:27611571

  17. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

    Science.gov (United States)

    Davison, Michelle; Treangen, Todd J; Koren, Sergey; Pop, Mihai; Bhaya, Devaki

    2016-01-01

    The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics. PMID:27611571

  18. CFD Verification of 5x5 Rod Bundle with Mixing Vane Spacer Grids

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sungkew; Jang, Hyungwook; Lim, Jongseon; Park, Eungjun; Nahm, Keeyil [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    Results of the CHF test are used for determining the CHF correlation, which is used to evaluate the thermal margin in the reactor core. Computational fluid dynamics (CFD) has been used to save the time and cost for experimental tests, components design and complicated phenomena in all industries including the reactor coolant system. L. D. Smith et al. applied the CFD methodology in a 5x5 rod bundle with the mixing vane spacer grid using the renormalization group (RNG) k-epsilon model. This CFD model agreed reasonably well with the test data. M. E. Conner et al. conducted experiments to validate the CFD methodology for the single-phase flow conditions in PWR fuel assemblies. In this validation case, the CFD code predicted very similar flow field structures as the test data. In this study, a CFD simulation under single-phase flow condition was conducted for one specific condition in a thermal mixing flow test of 5x5 rod bundle with some mixing vane spacer grids. In this study, a CFD simulation under a single-phase flow condition was conducted for one specific condition in a thermal mixing flow test of 5x5 rod bundle with the mixing vane spacer grids to verify the applicability of the CFD model for predicting the outlet temperature distribution. FLUENT 14.5 Version was used in this CFD analysis. For the successful prediction of the wall bounded turbulent flows, the y+ with 3 prism layers was determined within 5. At this time, k-epsilon standard turbulence model was used. The temperature distribution of CFD for each sub-channel at the outlet region of test bundle showed the difference approximately within 1.1% and 0.2% while comparing to that of test and sub-channel analysis code, respectively.

  19. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

    Directory of Open Access Journals (Sweden)

    Vergnaud Gilles

    2007-05-01

    Full Text Available Abstract Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the

  20. A new device designed for direct yield stress measurements of cement spacer

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, C.L.; Tonmukayakul, P.; Morgan, R.L. [Halliburton Energy Services, Houston, TX (United States)

    2007-07-01

    The rheological properties of spacer fluids and cement slurries have a significant impact on the hydraulic shear stress of well casing walls. This paper described experimental studies and numerical models of a device designed to measure the yield stress and rheological properties of spacer and cement samples. The device was designed using the Couette principle for rheological measurements, and measured the yield stress of particle-laden samples between 4 and 150 degrees C. A sample contained in a gap between a stator and a blade located along the inside wall of a steel cup was analyzed using the device. A stator was attached to a torque device and remained static during the rheological measurement. Yield stress was measured by rotating the device at a low speed at 3 rpm and at steady state torque. Torque was recorded when the rotation stopped. Two aqueous mixtures of titanium oxide (TiO{sub 2}) particles were used for the experiment. A cement spacer comprised of a blend of barite, citric acid and water was also measured. A volume-averaged shear method was used to calculate shear rate and shear stress. Key dimensionless variables were the impeller Reynolds number; the Froude number; the Weber number; and the Weissenberg number. Accuracy was assessed by examining the data obtained with a model fluid where yield stress data was already determined. Results of the comparison showed that values obtained using the device were consistent and comparable with results obtained using other techniques. It was concluded that further research is needed to characterize the elastic fluids in the device. 13 refs., 2 tabs., 3 figs.

  1. CFD Verification of 5x5 Rod Bundle with Mixing Vane Spacer Grids

    International Nuclear Information System (INIS)

    Results of the CHF test are used for determining the CHF correlation, which is used to evaluate the thermal margin in the reactor core. Computational fluid dynamics (CFD) has been used to save the time and cost for experimental tests, components design and complicated phenomena in all industries including the reactor coolant system. L. D. Smith et al. applied the CFD methodology in a 5x5 rod bundle with the mixing vane spacer grid using the renormalization group (RNG) k-epsilon model. This CFD model agreed reasonably well with the test data. M. E. Conner et al. conducted experiments to validate the CFD methodology for the single-phase flow conditions in PWR fuel assemblies. In this validation case, the CFD code predicted very similar flow field structures as the test data. In this study, a CFD simulation under single-phase flow condition was conducted for one specific condition in a thermal mixing flow test of 5x5 rod bundle with some mixing vane spacer grids. In this study, a CFD simulation under a single-phase flow condition was conducted for one specific condition in a thermal mixing flow test of 5x5 rod bundle with the mixing vane spacer grids to verify the applicability of the CFD model for predicting the outlet temperature distribution. FLUENT 14.5 Version was used in this CFD analysis. For the successful prediction of the wall bounded turbulent flows, the y+ with 3 prism layers was determined within 5. At this time, k-epsilon standard turbulence model was used. The temperature distribution of CFD for each sub-channel at the outlet region of test bundle showed the difference approximately within 1.1% and 0.2% while comparing to that of test and sub-channel analysis code, respectively

  2. Structure and function of the nontranscribed spacer regions of yeast rDNA.

    OpenAIRE

    Skryabin, K G; Eldarov, M A; Larionov, V L; Bayev, A A; Klootwijk, J; de Regt, V C; Veldman, G M; Planta, R J; Georgiev, O I; Hadjiolov, A A

    1984-01-01

    The sequences of the nontranscribed spacers (NTS) of cloned ribosomal DNA (rDNA) units from both Saccharomyces cerevisiae and Saccharomyces carlsbergensis were determined. The NTS sequences of both species were found to be 93% homologous. The major disparities comprise different frequencies of reiteration of short tracts of six to sixteen basepairs. Most of these reiterations are found within the 1100 basepairs long NTS between the 3'-ends of 26S and 5S rRNA (NTS1). The NTS between the starts...

  3. Modal properties of the flexural vibrating package of rods linked by spacer grids

    Directory of Open Access Journals (Sweden)

    Zeman V.

    2011-06-01

    Full Text Available The paper deals with the modelling and modal analysis of the large package of identical parallel rods linked by transverse springs (spacer grids placed on several level spacings. The rod discretization by finite element method is based on Rayleigh beam theory. For the cyclic and central symmetric package of rods (such as fuel rods in nuclear fuel assembly the system decomposition on the identical revolved rod segments was applied. A modal synthesis method with condensation is used for modelling of the whole system. The presented method is the first step for modelling the nuclear fuel assembly vibration caused by excitation determined by the support plate motion of the reactor core.

  4. Magnetotransport properties of spin-valve structures with Mg spacer layers

    Science.gov (United States)

    Martinez-Boubeta, C.; Ferrante, Y.; Parkin, S. S. P.

    2015-01-01

    A theoretical prediction by Wang et al. [Phys. Rev. B 82, 054405 (2010)] suggests the preferential transmission of majority-spin states with Δ1 symmetry across a magnesium interlayer in Fe/Mg/MgO/Fe based magnetic tunnel junctions. Here, we report experiments to probe this question in CoFe/Mg/CoFe structures. We find that the strength of the interlayer coupling decays exponentially with increasing the spacer thickness, however, a non-monotonic variation of the magnetoresistance as a function of the Mg layer is observed. These data may help revisit the role of the insertion of a Mg interface layer in MgO-based devices.

  5. Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man.

    Science.gov (United States)

    Perrin-Pecontal, P; Gouy, M; Nigon, V M; Trabuchet, G

    1992-01-01

    A 6.0-kb DNA fragment from Gorilla gorilla including the 5' part of the beta-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque delta-beta intergenic region. This analysis reveals four tandemly repeated sequences (RS), at the same location in the four species, showing a variable number of repeats generating both intraspecific (polymorphism) and interspecific variability. These tandem arrays delimit five regions of unique sequence called IG for intergenic. The divergence for these IG sequences is 1.85 +/- 0.22% between human and gorilla, which is not significantly different from the value estimated in the same region between chimpanzee and human (1.62 +/- 0.21%). The CpG and TpA dinucleotides are avoided. CpGs evolve faster than other sequence sites but do not confuse phylogenetic inferences by producing parallel mutations in different lineages. About 75% of CpG doublets have become TpG or CpA since the common ancestor, in agreement with the methylation/deamination pattern. Comparison of this intergenic region gives information on branching order within Hominoidea. Parsimony and distance-based methods when applied to the delta-beta intergenic region provide evidence (although not statistically significant) that human and chimpanzee are more closely related to each other than to gorilla. CpG sites are indeed rich in information by carrying substitutions along the short internal branch. Combining these results with those on the psi eta-delta intergenic region, shows in a statistically significant way that chimpanzee is the closest relative of human. PMID:1556740

  6. Inter- and intraspecies identification of Bartonella (Rochalimaea) species.

    Science.gov (United States)

    Roux, V; Raoult, D

    1995-06-01

    Species of the genus Rochalimaea, recently renamed Bartonella, are of a growing medical interest. Bartonella quintana was reported as the cause of trench fever, endocarditis, and bacillary angiomatosis. B. henselae has been implicated in symptoms and infections of human immunodeficiency virus-infected patients, such as fever, endocarditis, and bacillary angiomatosis, and is involved in the etiology of cat scratch disease. Such a wide spectrum of infections makes it necessary to obtain an intraspecies identification tool in order to perform epidemiological studies. B. vinsonii, B. elizabethae, seven isolates of B. quintana, and four isolates of B. henselae were studied by pulsed-field gel electrophoresis (PFGE) after restriction with the infrequently cutting endonucleases NotI, EagI, and SmaI. Specific profiles were obtained for each of the four Bartonella species. Comparison of genomic fingerprints of isolates of the same species showed polymorphism in DNA restriction patterns, and a specific profile was obtained for each isolate. A phylogenetic analysis of the B. quintana isolates was obtained by using the Dice coefficient, UPGMA (unweighted pair-group method of arithmetic averages), and Package Philip programming. Amplification by PCR and subsequent sequencing using an automated laser fluorescent DNA sequencer (Pharmacia) was performed on the intergenic spacer region (ITS) between the 16 and 23S rRNA genes. It was found that each B. henselae isolate had a specific sequence, while the B. quintana isolates fell into only two groups. When endonuclease restriction analysis of the ITS PCR product was done, three enzymes, TaqI, HindIII, and HaeIII, allowed species identification of Bartonella spp. Restriction fragment length polymorphism after PCR amplification of the 16S-23S rRNA gene ITS may be useful for rapid species identification, and PFGE could be an efficient method for isolate identification.

  7. Borrelia burgdorferi genetic markers and disseminated disease in patients with early Lyme disease.

    Science.gov (United States)

    Jones, Kathryn L; Glickstein, Lisa J; Damle, Nitin; Sikand, Vijay K; McHugh, Gail; Steere, Allen C

    2006-12-01

    Three genetic markers of Borrelia burgdorferi have been associated with disseminated disease: the OspC type, the 16S-23S rRNA intergenic spacer type (RST), and vlsE. Here, we modified previous methods so as to identify the three markers by PCR and restriction fragment length polymorphism in parallel, analyzed B. burgdorferi isolates from erythema migrans (EM) skin lesions in 91 patients, and correlated the results with evidence of dissemination. OspC type A was found approximately twice as frequently in patients with disseminated disease, whereas type K was identified approximately twice as often in those without evidence of dissemination, but these trends were not statistically significant. The remaining seven types identified were found nearly equally in patients with or without evidence of dissemination. RST 1 strains were significantly associated with dissemination (P=0.03), whereas RST 2 and RST 3 strains tended to have an inverse association with this outcome. The vlsE gene was identified in all 91 cases, using primer sets specific for an N-terminal sequence of B. burgdorferi strain B31 (vlsEB31) or strain 297 (vlsE297), but neither marker was associated with dissemination. Specific combinations of the three genetic markers usually occurred together. OspC type A was always found with RST 1 and vlsEB31, type K was always identified with RST 2 and more often with vlsE297, and types E and I were almost always found with RST 3 and equally often with vlsEB31 and vlsE297. We conclude that B. burgdorferi strains vary in their capacity to disseminate, but almost all strains isolated from EM lesions sometimes caused disseminated disease.

  8. Analysis of Borrelia burgdorferi Genotypes in Patients with Lyme Arthritis: High Frequency of RST 1 Strains in Antibiotic-Refractory Arthritis

    Science.gov (United States)

    Jones, Kathryn L.; McHugh, Gail A.; Glickstein, Lisa J.; Steere, Allen C.

    2009-01-01

    Objective Most of the B. burgdorferi genotypes have been isolated from erythema migrans (EM) skin lesions in patients with Lyme disease; outer-surface protein C (OspC) type K strains, which are 16S-23S rRNA intergenic spacer type 2 (RST 2), are most commonly recovered, but a higher percentage of OspC type A strains (RST 1), the next most common type, are detectable in blood. Our goals were to determine the B. burgdorferi genotypes in the joints of patients with Lyme arthritis. Methods Joint fluid samples from 124 patients seen over a 30-year period were analyzed for OspC types by semi-nested PCR and sequencing, and for RST by nested PCR and RFLP techniques. This information was correlated with clinical outcome. Results OspC and RST genotypes could be determined in 49 of the 124 joint fluid samples (40%). Of the 49 samples, 21 (43%) were OspC type K (RST 2), 11 (22%) were type A (RST 1), and 17 (35%) were distributed among 8 other OspC types and all 3 RSTs. However, among 17 patients who received current antibiotic regimens, all 7 infected with RST 1 strains had antibiotic-refractory arthritis compared with 4 of 6 patients infected with RST 2 strains and only 1 of 4 infected with RST 3 strains (P=0.03). Conclusions Most of the B. burgdorferi genotypes infected the joints of patients with Lyme arthritis, particularly OspC type K (RST 2); and genotype frequencies reflected those in EM skin lesions. However, RST 1 strains were most frequent in patients with antibiotic-refractory arthritis. PMID:19565522

  9. Borrelia burgdorferi Genetic Markers and Disseminated Disease in Patients with Early Lyme Disease▿

    Science.gov (United States)

    Jones, Kathryn L.; Glickstein, Lisa J.; Damle, Nitin; Sikand, Vijay K.; McHugh, Gail; Steere, Allen C.

    2006-01-01

    Three genetic markers of Borrelia burgdorferi have been associated with disseminated disease: the OspC type, the 16S-23S rRNA intergenic spacer type (RST), and vlsE. Here, we modified previous methods so as to identify the three markers by PCR and restriction fragment length polymorphism in parallel, analyzed B. burgdorferi isolates from erythema migrans (EM) skin lesions in 91 patients, and correlated the results with evidence of dissemination. OspC type A was found approximately twice as frequently in patients with disseminated disease, whereas type K was identified approximately twice as often in those without evidence of dissemination, but these trends were not statistically significant. The remaining seven types identified were found nearly equally in patients with or without evidence of dissemination. RST 1 strains were significantly associated with dissemination (P = 0.03), whereas RST 2 and RST 3 strains tended to have an inverse association with this outcome. The vlsE gene was identified in all 91 cases, using primer sets specific for an N-terminal sequence of B. burgdorferi strain B31 (vlsEB31) or strain 297 (vlsE297), but neither marker was associated with dissemination. Specific combinations of the three genetic markers usually occurred together. OspC type A was always found with RST 1 and vlsEB31, type K was always identified with RST 2 and more often with vlsE297, and types E and I were almost always found with RST 3 and equally often with vlsEB31 and vlsE297. We conclude that B. burgdorferi strains vary in their capacity to disseminate, but almost all strains isolated from EM lesions sometimes caused disseminated disease. PMID:17035489

  10. Inter- and intraspecies identification of Bartonella (Rochalimaea) species.

    Science.gov (United States)

    Roux, V; Raoult, D

    1995-06-01

    Species of the genus Rochalimaea, recently renamed Bartonella, are of a growing medical interest. Bartonella quintana was reported as the cause of trench fever, endocarditis, and bacillary angiomatosis. B. henselae has been implicated in symptoms and infections of human immunodeficiency virus-infected patients, such as fever, endocarditis, and bacillary angiomatosis, and is involved in the etiology of cat scratch disease. Such a wide spectrum of infections makes it necessary to obtain an intraspecies identification tool in order to perform epidemiological studies. B. vinsonii, B. elizabethae, seven isolates of B. quintana, and four isolates of B. henselae were studied by pulsed-field gel electrophoresis (PFGE) after restriction with the infrequently cutting endonucleases NotI, EagI, and SmaI. Specific profiles were obtained for each of the four Bartonella species. Comparison of genomic fingerprints of isolates of the same species showed polymorphism in DNA restriction patterns, and a specific profile was obtained for each isolate. A phylogenetic analysis of the B. quintana isolates was obtained by using the Dice coefficient, UPGMA (unweighted pair-group method of arithmetic averages), and Package Philip programming. Amplification by PCR and subsequent sequencing using an automated laser fluorescent DNA sequencer (Pharmacia) was performed on the intergenic spacer region (ITS) between the 16 and 23S rRNA genes. It was found that each B. henselae isolate had a specific sequence, while the B. quintana isolates fell into only two groups. When endonuclease restriction analysis of the ITS PCR product was done, three enzymes, TaqI, HindIII, and HaeIII, allowed species identification of Bartonella spp. Restriction fragment length polymorphism after PCR amplification of the 16S-23S rRNA gene ITS may be useful for rapid species identification, and PFGE could be an efficient method for isolate identification. PMID:7650189

  11. The ipdC, hisC1 and hisC2 genes involved in indole-3-acetic production used as alternative phylogenetic markers in Azospirillum brasilense.

    Science.gov (United States)

    Jijón-Moreno, Saúl; Marcos-Jiménez, Cynthia; Pedraza, Raúl O; Ramírez-Mata, Alberto; de Salamone, I García; Fernández-Scavino, Ana; Vásquez-Hernández, Claudia A; Soto-Urzúa, Lucia; Baca, Beatriz E

    2015-06-01

    Plant growth-promoting bacteria of the genus Azospirillum are present in the rhizosphere and as endophytes of many crops. In this research we studied 40 Azospirillum strains isolated from different plants and geographic regions. They were first characterized by 16S rDNA restriction analysis, and their phylogenetic position was established by sequencing the genes 16S rDNA, ipdC, hisC1, and hisC2. The latter three genes are involved in the indole-3-pyruvic acid (IPyA) biosynthesis pathway of indole-3-acetic acid (IAA). Furthermore, the suitability of the 16S-23S rDNA intergenic spacer sequence (IGS) for the differentiation of closely related Azospirillum taxa and development of PCR protocols allows for specific detection of strains. The IGS-RFLP analysis enabled intraspecies differentiation, particularly of Azospirillum brasilense and Azospirillum lipoferum strains. Results demonstrated that the ipdC, hisC1, and hisC2 genes are highly conserved in all the assessed A. brasilense isolates, suggesting that these genes can be used as an alternative phylogenetic marker. In addition, IAA production determined by HPLC ranged from 0.17 to 98.2 μg mg(-1) protein. Southern hybridization with the A. brasilense ipdC gene probe did not show, a hybridization signal with A. lipoferum, Azospirillum amazonense, Azospirillum halopreferans and Azospirillum irakense genomic DNA. This suggests that these species produce IAA by other pathways. Because IAA is mainly synthesized via the IPyA pathway in A. brasilense strains, a species that is used worldwide in agriculture, the identification of ipdC, hisC1, and hisC2 genes by PCR may be suitable for selecting exploitable strains.

  12. Survey of Bartonella spp. in U.S. bed bugs detects Burkholderia multivorans but not Bartonella.

    Directory of Open Access Journals (Sweden)

    Virna L Saenz

    Full Text Available Bed bugs (Cimex lectularius L. have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S-23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector.

  13. Genetic transformation of novel isolates of chicken Lactobacillus bearing probiotic features for expression of heterologous proteins: a tool to develop live oral vaccines

    Directory of Open Access Journals (Sweden)

    Neumann Elisabeth

    2006-01-01

    Full Text Available Abstract Background The use of lactic acid bacteria as vehicles to delivery antigens to immunize animals is a promising issue. When genetically modified, these bacteria can induce a specific local and systemic immune response against selected pathogens. Gastric acid and bile salts tolerance, production of antagonistic substances against pathogenic microorganisms, and adhesive ability to gut epithelium are other important characteristics that make these bacteria useful for oral immunization. Results Bacteria isolated on de Man, Rogosa and Sharpe medium (MRS from different gastrointestinal portions of broiler chicks were evaluated for their resistance to artificial gastric acid and bile salts, production of hydrogen peroxide, and cell surface hydrophobicity. Thirty-eight isolates were first typed at species level by PCR amplification of 16S-23S rRNA intergenic spacers using universal primers that anneal within 16S and 23S genes, followed by restriction digestion analyses of PCR amplicons (PCR-ARDRA. An expression cassette was assembled onto the pCR2.1-Topo vector by cloning the promoter, leader peptide, cell wall anchor and terminator sequences derived from the laminin binding S-layer protein gene of L. crispatus strain F5.7 (lbs gene. A sequence encoding the green fluorescent protein (GFP was inserted as reporter gene, and an erythromycin resistance gene was added as selective marker. All constructs were able to express GFP in the cloning host E. coli XL1-Blue and different Lactobacillus strains as verified by FACS and laser scanning confocal microscopy. Conclusion Lactobacillus isolated from gastrointestinal tract of broiler chickens and selected for probiotic characteristics can be genetically modified by introducing an expression cassette into the lbs locus. The transformed bacteria expressed on its cell wall surface different fluorescent proteins used as reporters of promoter function. It is possible then that similar bacterial model

  14. Microbial analysis of bite marks by sequence comparison of streptococcal DNA.

    Directory of Open Access Journals (Sweden)

    Darnell M Kennedy

    Full Text Available Bite mark injuries often feature in violent crimes. Conventional morphometric methods for the forensic analysis of bite marks involve elements of subjective interpretation that threaten the credibility of this field. Human DNA recovered from bite marks has the highest evidentiary value, however recovery can be compromised by salivary components. This study assessed the feasibility of matching bacterial DNA sequences amplified from experimental bite marks to those obtained from the teeth responsible, with the aim of evaluating the capability of three genomic regions of streptococcal DNA to discriminate between participant samples. Bite mark and teeth swabs were collected from 16 participants. Bacterial DNA was extracted to provide the template for PCR primers specific for streptococcal 16S ribosomal RNA (16S rRNA gene, 16S-23S intergenic spacer (ITS and RNA polymerase beta subunit (rpoB. High throughput sequencing (GS FLX 454, followed by stringent quality filtering, generated reads from bite marks for comparison to those generated from teeth samples. For all three regions, the greatest overlaps of identical reads were between bite mark samples and the corresponding teeth samples. The average proportions of reads identical between bite mark and corresponding teeth samples were 0.31, 0.41 and 0.31, and for non-corresponding samples were 0.11, 0.20 and 0.016, for 16S rRNA, ITS and rpoB, respectively. The probabilities of correctly distinguishing matching and non-matching teeth samples were 0.92 for ITS, 0.99 for 16S rRNA and 1.0 for rpoB. These findings strongly support the tenet that bacterial DNA amplified from bite marks and teeth can provide corroborating information in the identification of assailants.

  15. A Novel Mycoplasma sp. Associated with Phallus Disease in Goose Breeders: Pathological and Bacteriological Findings.

    Science.gov (United States)

    Carnaccini, S; Ferguson-Noel, N M; Chin, R P; Santoro, T; Black, P; Bland, M; Bickford, A A; Sentíes-Cué, C G

    2016-06-01

    In April 2014, poor fertility in a major commercial goose breeder operation in California triggered the submission of six live affected Toulouse ganders ( Anser anser ) to the California Animal Health and Food Safety Laboratory, Turlock branch (University of California-Davis). Toulouse were principally affected among all breeds, and their egg fertility dropped from 65.7% to less than 33.9% in the first 40 days of the 2014 breeding season. The flock consisted of 410 adult birds, 90 males and 320 females, between 2 and 5 yr of age. Inspection of the flock revealed that 44.4% of the Toulouse ganders had severe phallic deformities that prevented them from mating. At postmortem examination, severe yellowish fibrocaseous exudate disrupted the architecture of the phallus and occasionally produced fistulating tracts through the wall of the organ. Microscopically, multifocal lymphoid nodules were noted in the mucosa and submucosa of the phallus and were associated with extensive granulomatous reaction, intralesional bacteria, and spermatozoa. Mycoplasma spp. were isolated from the phallus of affected and nonaffected birds, and PCR protocols targeting the 16S-23S ribosomal RNA intergenic spacer regions and the RNA polymerase beta subunit gene were performed to identify the isolates. Three distinct species were identified on sequencing and analysis using the National Center for Biotechnology Information basic local alignment search tool: Mycoplasma cloacale , Mycoplasma anseris , and an unknown novel Mycoplasma sp. Additionally, Pasteurella multocida , in combination with other bacteria, was also isolated from the phallic lesions and identified as serotype 3 with a DNA profile of 1511 (National Veterinary Service Laboratory). This is the first report of these Mycoplasma spp. and other bacteria associated with reproductive disease in ganders in the United States. PMID:27309284

  16. Characterization of rhizobia from legumes of agronomic interest grown in semi-arid areas of Central Spain relates genetic differences to soil properties.

    Science.gov (United States)

    Ruiz-Díez, Beatriz; Fajardo, Susana; Felipe, María del Rosario de; Fernández-Pascual, Mercedes

    2012-02-01

    A study of symbiotic bacteria from traditional agricultural legumes from Central Spain was performed to create a collection of rhizobia from soils differing in physicochemical, analytical and/or agroecological properties which could be well-adapted to the environmental conditions of this region, and be used for sustainable agricultural practices. Thirty-six isolates were obtained from root-nodules of fifteen legume species (including Cicer arietinum, Lathyrus sativus, Lens culinaris, Lupinus spp., Medicago sativa, Phaseolus vulgaris, Pisum sativum, and Vicia spp.) from three agriculture areas with soils of different pHs and from a forest area with undisturbed soils. Phenotypical characterization revealed uniformity across the thirty-six isolates, with important exceptions in terms of environmental tolerance (three isolates survived at high temperatures, three at high salinity and three at acid pH). The molecular analysis of 16S rRNA gene showed a close relationship of twenty-nine isolates to Rhizobium leguminosarum, one to Rhizobium gallicum, one to Mesorhizobium ciceri, two to Sinorhizobium (Ensifer) meliloti and three to Bradyrhizobium canariense. The sequence analysis of a symbiosis-specific gene, nod C, showed a correlation with the plant host and grouped twenty-six isolates with Rhizobium leguminosarum bv. viciae, establishing the diversity in relation to legume-host. The 16S-23S rRNA intergenic spacer (IGS) region allowed for intraspecific differentiation, so that strains with equal 16S rRNA were grouped by means of their soil origin. These results indicated that phenotypical and genetically related strains may be widely distributed in this region and that soil abiotic characteristics could have a substantial bearing on the selection of the strains living in each environment. PMID:21953333

  17. Vigna mungo, V. radiata and V. unguiculata plants sampled in different agronomical-ecological-climatic regions of India are nodulated by Bradyrhizobium yuanmingense.

    Science.gov (United States)

    Appunu, Chinnaswamy; N'Zoue, Angèle; Moulin, Lionel; Depret, Géraldine; Laguerre, Gisèle

    2009-10-01

    Vigna mungo, Vigna radiata and Vigna unguiculata are important legume crops cultivated in India, but little is known about the genetic resources in native rhizobia that nodulate these species. To identify these bacteria, a core collection of 76 slow-growing isolates was built from root nodules of V. mungo, V. radiata and V. unguiculata plants grown at different sites within three agro-ecological-climatic regions of India. The genetic diversity of the bacterial collection was assessed by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified DNA fragments of the 16S-23S rDNA intergenic spacer (IGS) region, and the symbiotic genes nifH and nodC. One rDNA IGS type grouped 91% of isolates, but more diversity was found at the symbiotic loci (17 symbiotic genotypes). Overall, no host plant specificity was shown, the three host plant species sharing common bradyrhizobial genotypes that represented 62% of the collection. Similarly, the predominant genotypes were found at most sampling sites and in all agro-ecological-climatic regions. Phylogenies inferred from IGS sequencing and multi-locus sequence analysis of the dnaK, glnII and recA genes indicated that all isolates but one were clustered with the Bradyrhizobium yuanmingense species. The nifH phylogeny also grouped the different nif haplotypes within a cluster including B. yuanmingense, except for one infrequent nif haplotype which formed a new lineage within the Bradyrhizobium genus. These results may reflect a long history of co-evolution between B. yuanmingense and Vigna spp. in India, while intra-species polymorphism detected in the symbiotic loci may be linked with the long history of diversification of B. yuanmingense coinciding with that of its host legumes.

  18. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    Science.gov (United States)

    Vieira Vaz, Marcelo Gomes Marçal; Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Célia Leite; Barbiero, Laurent; Fiore, Marli Fátima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (≤91.6 %) and to other sequences from known pseudanabaenacean genera (≤94.3 and 93.7 %, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99 % bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa. PMID:25351877

  19. Detection of Bartonella spp. in neotropical felids and evaluation of risk factors and hematological abnormalities associated with infection.

    Science.gov (United States)

    Guimaraes, A M S; Brandão, P E; Moraes, W; Kiihl, S; Santos, L C; Filoni, C; Cubas, Z S; Robes, R R; Marques, L M; Neto, R L; Yamaguti, M; Oliveira, R C; Catão-Dias, J L; Richtzenhain, L J; Messick, J B; Biondo, A W; Timenetsky, J

    2010-05-19

    Although antibodies to Bartonella henselae have been described in all neotropical felid species, DNA has been detected in only one species, Leopardus wiedii. The aim of this study was to determine whether DNA of Bartonella spp. could be detected in blood of other captive neotropical felids and evaluate risk factors and hematological findings associated with infection. Blood samples were collected from 57 small felids, including 1 Leopardus geoffroyi, 17 L. wiedii, 22 Leopardus tigrinus, 14 Leopardus pardalis, and 3 Puma yagouaroundi; 10 blood samples from Panthera onca were retrieved from blood banks. Complete blood counts were performed on blood samples from small felids, while all samples were evaluated by PCR. DNA extraction was confirmed by amplification of the cat GAPDH gene. Bartonella spp. were assessed by amplifying a fragment of their 16S-23S rRNA intergenic spacer region; PCR products were purified and sequenced. For the small neotropical felids, risk factors [origin (wild-caught or zoo-born), gender, felid species, and flea exposure] were evaluated using exact multiple logistic regression. Hematological findings (anemia, polycythemia/hyperproteinemia, leukocytosis and leukopenia) were tested for association with infection using Fisher's exact test. The 635bp product amplified from 10 samples (10/67=14.92%) was identified as B. henselae by sequencing. Small neotropical felid males were more likely to be positive than females (95% CI=0.00-0.451, p=0.0028), however other analyzed variables were not considered risk factors (p>0.05). Hematological abnormalities were not associated with infection (p>0.05). This is the first report documenting B. henselae detection by PCR in several species of neotropical felids. PMID:19913372

  20. Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes.

    Science.gov (United States)

    Laguerre, Gisèle; Louvrier, Philippe; Allard, Marie-Reine; Amarger, Noëlle

    2003-04-01

    Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy. PMID:12676710

  1. Impact of Asymmetric Dual-k Spacer in the Underlap Regions of Sub 20 nm NMOSFET with Gate Stack

    Science.gov (United States)

    Chakraborty, Shramana; Dasgupta, Arpan; Das, Rahul; Kundu, Atanu; Sarkar, Chandan K.

    2016-10-01

    This paper shows the systematic study of underlap double gate (U-DG) NMOSFETs with Gate Stack (GS) under the influence of dual-k spacers at the different underlap regions. In highly scaled devices, underlap is used at the Source and Drain side so as to reduce the short channel effects (SCE's) but at the cost of low on current (ION) and increased channel resistance. The high-k spacers are used to counter this problem. The ION is improved but at the cost of highly enhanced parasitic capacitances. This paper explores the possibility of using asymmetric dual-k spacer at the source underlap side so as to counter the shortcomings of high-k spacers in highly scaled devices on the basis of analog parameters: ION, gm, gm/ID, and intrinsic gain, gmRo and RF performance in terms of parasitic gate capacitance (Cgs, Cgd and Cgg),gate to source/drain resistances (Rgs and Rgd), transport delay (τm), the unity current gain cut-off frequency (fT) and the maximum frequency of oscillation (fmax). A single stage amplifier performance is also analyzed where it has been seen that the asymmetric dual-k spacer at the source underlap side gives better performance as compared to the other devices under comparison.

  2. Effect of Charging and Position of Metallic Particle Adhered to Spacer on PDIV and PRPD Characteristics in GIS

    Directory of Open Access Journals (Sweden)

    Y. Khan

    2014-07-01

    Full Text Available Gas Insulated Switchgears (GIS are widely used due to their many benefits. The reliability of GIS is challenged due to the presence of spacer defects and/or metallic particles. Free metallic particles can tremendously reduce the insulation strength of GIS especially when they enter the triple junction region (consisting of the spacer, the electrode and the gaseous medium interface around the spacer. Therefore, there a need to investigate the effect of charged metallic particle on the field intensification produced along the spacer surface and its consequences on the Partial Discharge Inception Voltage (PDIV. In this study, simulation and experimental results are reported for metallic particles adhering to a cylindrical spacer. The effect of particle charging on the resulting field intensification, particle initiated partial discharge inception voltage as well as Phase Resolved Partial Discharge (PRPD characteristics are presented in this study. The particle adversely affects the electric field uniformity in the area between the two electrodes. A particle in contact with the electrode causes the most severe intensification in the electric field, while the effect caused by the particle at the gap centre is the least severe.

  3. Pyrocarbon spacer as a trapezium replacement for arthritis of the trapeziometacarpal joint; a follow-up study of 60 cases.

    Science.gov (United States)

    Szalay, Gabor; Meyer, Christof; Scheufens, Tanja; Schnettler, Reinhard; Christ, Ralph; Schleicher, Iris

    2013-12-01

    Rhizarthrosis is the most common degenerative joint disease of the hand, affecting about 10% of the population. We report our results with trapezium replacement using a pyrocarbon spacer. Between January 2005 and April 2010, 70 patients underwent trapeziectomy with interposition of a pyrocarbon spacer. Sixty patients were examined at an average follow-up of 23.6 (5-64) months after the operation. Six (8.6%) of the 70 implanted pyrocarbon spacers dislocated. Based on the assessment scale devised by Buck-Gramcko, 19 patients achieved a very good outcome (31.6%), 31 patients (51.6%) had a good outcome, six results were satisfactory (10%) and four patients (6.6%) had a poor result. In this study, trapeziectomy and implantation of a pyrocarbon spacer achieved good or very good results in 83.2% of cases. The high cost of the implant and the observed rate of spacer dislocation should however be considered critically. While the short-term results of this method are encouraging, long-term outcomes will show whether this technique can keep up with the good results of suspension arthroplasty.

  4. Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR-Cas I-F systems.

    Science.gov (United States)

    Almendros, Cristóbal; Guzmán, Noemí M; García-Martínez, Jesús; Mojica, Francisco J M

    2016-01-01

    Archaea and bacteria harbour clustered regularly interspaced short palindromic repeats (CRISPR) loci. These arrays encode RNA molecules (crRNA), each containing a sequence of a single repeat-intervening spacer. The crRNAs guide CRISPR-associated (Cas) proteins to cleave nucleic acids complementary to the crRNA spacer, thus interfering with targeted foreign elements. Notably, pre-existing spacers may trigger the acquisition of new spacers from the target molecule by means of a primed adaptation mechanism. Here, we show that naturally occurring orphan CRISPR arrays that contain spacers matching sequences of the cognate (absent) cas genes are able to elicit both primed adaptation and direct interference against genetic elements carrying those genes. Our findings show the existence of an anti-cas mechanism that prevents the transfer of a fully equipped CRISPR-Cas system. Hence, they suggest that CRISPR immunity may be undesired by particular prokaryotes, potentially because they could limit possibilities for gaining favourable sequences by lateral transfer. PMID:27573106

  5. CFD analysis on mixing effects of spacer grids with different dimples and sizes for advanced fuel assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Yang, B.W.; Zhang, H.; Han, B.; Zha, Y.D.; Shan, J.Q. [Xi' an Jiaotong Univ. (China). School of Nuclear Science and Technology

    2016-07-15

    The thermal hydraulic characteristics of a mixing vane grid are largely dependent on the structure of key components, such as strip, spring, dimple, weld nugget, as well as the mixing vane configuration. In this paper, several types of spacer grids with different dimple shapes are modeled under subcooled boiling conditions. Prior to the application of CFD on the dimple shape analysis, the mixing effects of spacer grids were studied. After the dimple shape analysis, the side channel effect is discussed by comparing the simulation results of a 3 x 3 and a 5 x 5 spacer grid. The two phase flow CFD models in this study are validated through simple geometry showing that the calculated void fraction is in good agreement with the experimental data. The dimple comparison result shows that varying dimple structures can result in different temperatures, lateral velocities and void fraction distributions downstream of the spacer grids. Comparison of two sizes of spacer grids demonstrate that the side channel generates different flow distribution pattern in the center channel.

  6. The Construction of Chimeric T-Cell Receptor with Spacer Base of Modeling Study of VHH and MUC1 Interaction

    Directory of Open Access Journals (Sweden)

    Nazanin Pirooznia

    2011-01-01

    Full Text Available Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, VHH and CD8α, and FcgIIα are used as signaling moieties, costimulating domain, antibody, and spacers, respectively. To investigate the influence of the ligation of spacers on the conformational structure of VHH, models of VHH were constructed. Molecular dynamics simulation was run to study the influence of the presence of spacers on the conformational changes in the binding sites of VHH. Root mean square deviation and root mean square fluctuation of critical segments in the binding site showed no noticeable differences with those in the native VHH. Results from molecular docking revealed that the presence of spacer FcgIIα causes an increasing effect on VHH with MUC1 interaction. Each of the constructs was transformed into the Jurkat E6.1. Expression analysis and evaluation of their functions were examined. The results showed good expression and function.

  7. The construction of chimeric T-Cell receptor with spacer base of modeling study of VHH and MUC1 interaction.

    Science.gov (United States)

    Pirooznia, Nazanin; Hasannia, Sadegh; Taghdir, Majid; Rahbarizadeh, Fatemeh; Eskandani, Morteza

    2011-01-01

    Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, VHH and CD8α, and FcgIIα are used as signaling moieties, costimulating domain, antibody, and spacers, respectively. To investigate the influence of the ligation of spacers on the conformational structure of VHH, models of VHH were constructed. Molecular dynamics simulation was run to study the influence of the presence of spacers on the conformational changes in the binding sites of VHH. Root mean square deviation and root mean square fluctuation of critical segments in the binding site showed no noticeable differences with those in the native VHH. Results from molecular docking revealed that the presence of spacer FcgIIα causes an increasing effect on VHH with MUC1 interaction. Each of the constructs was transformed into the Jurkat E6.1. Expression analysis and evaluation of their functions were examined. The results showed good expression and function. PMID:21869862

  8. Use of a New Knee Prosthesis as an Articulating Spacer in Two-Stage Revision of Infected Total Knee Arthroplasty

    Science.gov (United States)

    Fabrin, Jesper; Poulsen, Klaus; Schroder, Henrik Morville

    2016-01-01

    Purpose To report our experience with two-stage revision using a new femoral component (NFC) spacer (Depuy Synthes) as an articulating spacer. Materials and Methods In this retrospective study, we reviewed 22 two-stage revisions that were performed using an NFC spacer in 22 patients suspected of having an infected total knee arthroplasty (TKA) from December 2010 to March 2013. The result was considered successful when eradication of infection was achieved using only one NFC spacer. Results The average time from primary TKA to the first stage procedure was 29.1 months and the average time from the first stage procedure until the final second stage procedure was 12.7 weeks. The average range of motion increased from 82° preoperatively to 104° postoperatively. The American Knee Society Knee score increased from 29.3 points to 66 points. The Function score increased from 29.5 points to 64 points. Four cases were reinfected after two-stage revision. The mean follow-up was 37.6 months. Conclusions The new articulating spacer showed promising short-term results both with regard to eradication of infection and functional improvement. PMID:27595079

  9. DYNAMIC CHARACTERISTICS OF LIQUID FORCED SLOSHING IN A TURNING SPHERICAL TANK WITH A SPACER UNDER LOW GRAVITY

    Institute of Scientific and Technical Information of China (English)

    CHENG Xu-duo; HU Mei-zhu; WEN Ji-hua

    2008-01-01

    Under the condition of low gravity the characteristics of liquid forced sloshing in a turning spherical tank with a spacer were investigated. The static shape of the liquid surface was analyzed. By expanding the characteristic functions, the frequencies and velocity potential of liquid free-sloshing were derived. The governing equations and boundary conditions for the forced sloshing of liquid under the tank turning were established. The transverse force of liquid acting on the tank and the moment of force to the centre of the tank which is caused by the force of liquid acting on the spacer were given. Numerical results were compared with the ones of the spherical tank without a spacer. The results show that when a spacer is inserted in the tank, the sloshing frequency of liquid and the transverse force of liquid acting on the tank will decrease, but the moment of force to the centre of the tank which is caused by the force of liquid acting on the spacer will occur.

  10. Spacer engineered Trigate SOI TFET: An investigation towards harsh temperature environment applications

    Science.gov (United States)

    Mallikarjunarao; Ranjan, Rajeev; Pradhan, K. P.; Artola, L.; Sahu, P. K.

    2016-09-01

    In this paper, a novel N-channel Tunnel Field Effect Transistor (TFET) i.e., Trigate Silicon-ON-Insulator (SOI) N-TFET with high-k spacer is proposed for better Sub-threshold swing (SS) and OFF-state current (IOFF) by keeping in mind the sensitivity towards temperature. The proposed model can achieve a Sub-threshold swing less than 35 mV/decade at various temperatures, which is desirable for designing low power CTFET for digital circuit applications. In N-TFET source doping has a significant effect on the ON-state current (ION) level; therefore more electrons will tunnel from source to channel region. High-k Spacer i.e., HfO2 is used to enhance the device performance and also it avoids overlapping of transistors in an integrated circuits (IC's). We have designed a reliable device by performing the temperature analysis on Transfer characteristics, Drain characteristics and also on various performance metrics like ON-state current (ION), OFF-state current (IOFF), ION/IOFF, Trans-conductance (gm), Trans-conductance Generation Factor (TGF), Sub-threshold Swing (SS) to observe the applications towards harsh temperature environment.

  11. Analysis of high-k spacer on symmetric underlap DG-MOSFET with Gate Stack architecture

    Science.gov (United States)

    Das, Rahul; Chakraborty, Shramana; Dasgupta, Arpan; Dutta, Arka; Kundu, Atanu; Sarkar, Chandan K.

    2016-09-01

    This paper shows the systematic study of underlap double gate (U-DG) NMOSFETs with Gate Stack (GS) under the influence of high-k spacers. In highly scaled devices, underlap is used at the Source and Drain side so as to reduce the short channel effects (SCE's), however, it significantly reduces the on current due to the increased channel resistance. To overcome these drawbacks, the use of high-k spacers is projected as one of the remedies. In this paper, the analog performance of the devices is studied on the basis of parameters like transconductance (gm), transconductance generation factor (gm/Id) and intrinsic gain (gmro). The RF performance is analyzed on the merits of intrinsic capacitance (Cgd, Cgs), resistance (Rgd, Rgs), transport delay (τm), inductance (Lsd), cutoff frequency (fT), and the maximum frequency of oscillation (fmax). The circuit performance of the devices are studied by implementing the device as the driver MOSFET in a Single Stage Common Source Amplifier. The Gain Bandwidth Product (GBW) has been analyzed from the frequency response of the circuit.

  12. π-Spacer effect in dithiafulvenyl-π-phenothiazine dyes for dye-sensitized solar cells

    Science.gov (United States)

    Zhang, Xiaofeng; Gou, Faliang; Zhao, Dongning; Shi, Jian; Gao, Hong; Zhu, Zhenping; Jing, Huanwang

    2016-08-01

    New dithiafulvenyl-π-phenothiazine dyes have been devised and prepared for dye-sensitized solar cells. Various π-spacers have been successfully introduced into the skeleton of dithiafulvenyl and phenothiazine unit to generate novel D-π-D-A dyes (DPP-1 ∼ 4). All dyes have been characterized with NMR, HRMS, UV-vis and fluorescence spectra, and taken into cyclic voltammetry measurements. The devices of new dyes have been determined by photoelectrochemical experiments (IV, IPCE and EIS), in which, solar cell of DPP-4 with biphenyl ring π-spacer enhances obviously its photoelectric conversion efficiency to 7.66% reaching 94% of N719-based standard cell and displays good long-term stability with quasi-solid-state electrolyte. Density functional theory (DFT) calculations of new dyes provide further insight into the molecular geometries and the impacts of the torsion angles on their photovoltaic performance. Large dihedral angles in DPP dyes induce good charge separation for efficient unidirectional flow of electron from donor to acceptor.

  13. Effect of GFRP spacer on local deformation of large superconductor in coil pack

    International Nuclear Information System (INIS)

    Design and construction of the Large Helical Device (LHD) are in progress at the National Institute for Fusion Science (NIFS) in Japan. The LHD has superconducting poloidal and helical coils, and many efforts have been undertaken to develop these large superconductors. When designing a large superconducting magnet, the mechanical behavior of the wound structure becomes a very important factor since the apparent rigidity affects the design of a coil support structure and the superconducting coil needs to endure the large electro-magnetic force it creates. Also, non-linear mechanical behavior should yield the instability of the magnet. In this paper, local deformation in a large conductor caused by GFRP spacers and epoxy adhesives was investigated after compressive rigidity testing. The epoxy adhesive used for attaching the GFRP spacers to the superconductor changed shape from an almost square sheet into a lens-like sheet during deformation, and a dent appeared on the surface of the superconductor. Three-dimensional FEM analysis showed that a compressive stress in the vertical direction of the loading axis existed in the adhesive plane. This stress component makes the adhesive lens-like and it results in the dent created during the compressive testing. This local deformation should yield a part of the permanent deformation observed after the compressive load cycle at 4.2 K

  14. Cationic gemini surfactants with cleavable spacer: chemical hydrolysis, biodegradation, and toxicity.

    Science.gov (United States)

    Tehrani-Bagha, A R; Holmberg, K; van Ginkel, C G; Kean, M

    2015-07-01

    The paper describes synthesis and characterization of a new type of cationic gemini surfactant, which has dodecyl tails and a spacer that contains an ester bond. The nomenclature used to describe the structure is 12Q2OCO1Q12, with Q being a quaternary ammonium group and the numbers indicating the number of methylene or methyl groups. Due to the close proximity to the two quaternary ammonium groups, the ester bond is very stable on the acid side and very labile already at slightly alkaline conditions. The hydrolysis products are two single chain surfactants (i.e. 12Q2OH and 12Q1COOH) which are less surface active than the intact gemini surfactant. 12Q2OCO1Q12 was found to be readily biodegradable, i.e. it gave more than 60% biodegradation after 28 days. This is interesting because similar gemini surfactants but with ester bonds in the tails instead of the spacer, have previously been found not to be readily biodegradable. The gemini surfactant was found to be toxic to aquatic organisms (ErC50 value of 0.27 mg/l), although less toxic than the two hydrolysis products. PMID:25446957

  15. Green Synthesis, Molecular Characterization and Associative Behavior of Some Gemini Surfactants without a Spacer Group

    Directory of Open Access Journals (Sweden)

    Eugenio Caponetti

    2013-04-01

    Full Text Available A series of new gemini surfactants without a spacer group, disodium 2,3-dialkyl-1,2,3,4-butanetetracarboxylates, were synthesized in a green chemistry context minimizing the use of organic solvents and applying microwaves (MW when activation energy was required. Once the desired architecture was confirmed by means of the nuclear magnetic resonance technique (1H-NMR, 1H-1H COSY for all the studied surfactants, the critical micellization concentration was determined by conductance measurements. The diffusion coefficient of micelles formed by the four compounds was characterized using pulsed field gradient (PFG-NMR. Diffusion coefficients were found to be dependent on the concentration and on the number of carbon atoms in the alkyl chain. The absence of the spacer group, peculiar to this new series of gemini surfactants, may confer relatively low flexibility to the molecules, with potential implications on the interfacial properties, namely on micellization. These gemini surfactants might have interesting applications in the preparation of composite materials, in nanotechnology, in gene transfection and mainly, due to the low CMCs, as new interesting ingredients of cosmetics and toiletries.

  16. Role of spacer length in interaction between novel gemini imidazolium surfactants and Rhizopus oryzae lipase.

    Science.gov (United States)

    Adak, Sunita; Datta, Sougata; Bhattacharya, Santanu; Banerjee, Rintu

    2015-11-01

    An insight into the effects of new ionic liquid-type gemini imidazolium cationic surfactants on the structure and function of the lipases is of prime importance for their potential application. Changes in the activity, stability and structure of Rhizopus oryzae lipase in the presence of novel gemini surfactants, [C16-3-C16im]Br2 and [C16-12-C16im]Br2 were probed in the present study. Surfactant with shorter spacer length, [C16-3-C16im]Br2 was found to be better in improving the hydrolytic activity and thermal stability of the lipase. For both the surfactants, activation was concentration dependent. CD spectroscopy results showed a decrease in α-helix and an increase in β-sheet content in the presence of these surfactants. A higher structural change observed in presence of [C16-12-C16im]Br2 correlated with lower enzyme activity. Isothermal titration calorimetric studies showed the binding to be spontaneous in nature based on sequential two site binding model. The forces involved in binding were found to differ for the two surfactants proving that the spacer length is an important factor which governs the interaction. These surfactants could be used as promising components both in enzyme modification and media engineering for attaining the desired goals in biocatalytic reactions.

  17. Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences.

    Science.gov (United States)

    Moller, M; Cronk, Q

    1997-07-01

    Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia. PMID:21708650

  18. A denture-type spacer in interstitial brachytherapy for edentulous patients with T1 and T2 carcinoma of the oral tongue

    Energy Technology Data Exchange (ETDEWEB)

    Fujita, Minoru; Tamamoto, Mitsuhiro; Wada, Takuro [Hiroshima Univ. (Japan). School of Dentistry; Hirokawa, Yutaka; Kashiwado, Kouzo; Akagi, Yukio; Kashimoto, Kazuki; Kiriu, Hiroshi

    1995-06-01

    The contribution of a denture-type spacer, fabricated by a denture duplication technique, in reducing the incidence of radiation bone complication (osteonecrosis) was examined retrospectively. Fifty-five edentulous patients with previously untreated T1 and T2 carcinoma of the oral tongue were treated mainly by interstitial brachytherapy between April, 1978 and November, 1992. A spacer was used in 12 patients who were treated after 1991. Osteonecrosis was found in 3 patients treated without a spacer but in no patient treated with the spacer. However, there was no significant relationship between the incidence of osteonecrosis and the use of the spacer. The failure was attributed to specific procedural alterations, i.e., reduction of the frequency of use of external irradiation and thereby of total dose, during the period in which spacers were applied. Despite the failure to observe any significant contribution of the denture-type spacer to reduction of the incidence of osteonecrosis in this study, a reduction of the dose to the mandible can be expected when a spacer is used. We have therefore adopted this type of spacer as a part of our interstitial brachytherapy procedure. (author).

  19. A denture-type spacer in interstitial brachytherapy for edentulous patients with T1 and T2 carcinoma of the oral tongue

    International Nuclear Information System (INIS)

    The contribution of a denture-type spacer, fabricated by a denture duplication technique, in reducing the incidence of radiation bone complication (osteonecrosis) was examined retrospectively. Fifty-five edentulous patients with previously untreated T1 and T2 carcinoma of the oral tongue were treated mainly by interstitial brachytherapy between April, 1978 and November, 1992. A spacer was used in 12 patients who were treated after 1991. Osteonecrosis was found in 3 patients treated without a spacer but in no patient treated with the spacer. However, there was no significant relationship between the incidence of osteonecrosis and the use of the spacer. The failure was attributed to specific procedural alterations, i.e., reduction of the frequency of use of external irradiation and thereby of total dose, during the period in which spacers were applied. Despite the failure to observe any significant contribution of the denture-type spacer to reduction of the incidence of osteonecrosis in this study, a reduction of the dose to the mandible can be expected when a spacer is used. We have therefore adopted this type of spacer as a part of our interstitial brachytherapy procedure. (author)

  20. The Effects of Spacer Length and Composition on Aptamer-Mediated Cell-Specific Targeting with Nanoscale PEGylated Liposomal Doxorubicin.

    Science.gov (United States)

    Xing, Hang; Li, Ji; Xu, Weidong; Hwang, Kevin; Wu, Peiwen; Yin, Qian; Li, Zhensheng; Cheng, Jianjun; Lu, Yi

    2016-06-16

    Aptamer-based targeted drug delivery systems have shown significant promise for clinical applications. Although much progress has been made in this area, it remains unclear how PEG coating would affect the selective binding of DNA aptamers and thus influence the overall targeting efficiency. To answer this question, we herein report a systematic investigation of the interactions between PEG and DNA aptamers on the surface of liposomes by using a series of nanoscale liposomal doxorubicin formulations with different DNA aptamer and PEG modifications. We investigated how the spatial size and composition of the spacer molecules affected the targeting ability of the liposome delivery system. We showed that a spacer of appropriate length was critical to overcome the shielding from surrounding PEG molecules in order to achieve the best targeting effect, regardless of the spacer composition. Our findings provide important guidelines for the design of aptamer-based targeted drug delivery systems. PMID:27123758

  1. Optimization of spacers placement in metal oxide surge arresters due to the thermal stability increment using genetic algorithm

    Directory of Open Access Journals (Sweden)

    Seyed Meysam Seyedbarzegar

    2015-03-01

    Full Text Available Abstract: in this paper the optimal placement of spacers in surge arrester column is presented in order to achieve temperature reduction and surge arrester thermal stability against power losses due to the overvoltage in power system. The simulation is done by using genetic algorithm in MATLAB software that it is linked by numerical analysis, i.e., Finite Element Method (FEM. First, electro thermal analysis is performed according to the IEC60099-4 standard on selected population in certain interval and, then the required data is applied to the genetic algorithm for the optimal placement of spacers. Simulation results show that the placement of spacers has great influence on surge arrester temperature variations. Finally, the optimal model of surge arrester is simulated in COMSOL software and the results of this model are compared with conventional model results.

  2. Current-perpendicular-to-the-plane giant magnetoresistance in spin-valves with AgSn alloy spacers

    Energy Technology Data Exchange (ETDEWEB)

    Read, J. C.; Nakatani, T. M.; Smith, Neil; Choi, Y.-S.; York, B. R.; Brinkman, E.; Childress, J. R. [San Jose Research Center, HGST, a Western Digital Company, San Jose, California 95135 (United States)

    2015-07-28

    We investigate the use of AgSn alloys as the spacer layer in current-perpendicular-to-the-plane magnetoresistance devices. Alloying with Sn increases resistivity but results in a reasonably long (>10 nm) spin-diffusion length, so large magnetoresistance can be achieved with thin AgSn spacers. Compared to Ag thin films, AgSn forms smaller grain sizes, reduced roughness, and exhibits less interdiffusion upon annealing, resulting in decreased interlayer magnetic coupling in exchange biased spin-valves. AgSn also shows improved corrosion resistance compared to Ag, which is advantageous for nanofabrication, including magnetic recording head sensors. Combining a AgSn spacer with Co-based Heusler alloy ferromagnet in an exchange biased, polycrystalline trilayer thinner than 12 nm results in magnetoresistance values up to 15% at room temperature.

  3. Sequence analysis of the rDNA internal transcribed spacer 2 of five species of South American human malaria mosquitoes.

    Science.gov (United States)

    Fritz, G N

    1998-03-01

    The rDNA internal transcribed spacer 2 (ITS2) was sequenced for 5 species of mosquitoes that may be important vectors of human malaria in certain regions of South America and are difficult to distinguish by morphology: Anopheles evansae, An. nuneztovari, An. rangeli, An. strodei and An. trinkae. ITS2 sequences from samples collected in Ecuador, Bolivia, Venezuela and Brazil were aligned and compared in order to determine the usefulness of this spacer for the elaboration of species specific primers and DNA probes. The ITS2 was found to be different in size (ranging from 333 to 397 bp) and sequence between all pairs of species. Highly variable regions were found primarily at the 3' end of the spacer and were interspersed with relatively conserved sites. Instraspecific sequence variation was limited to a single transversion between specimens of An. rangeli from distant geographic locations suggesting concerted evolution and homogenization of the ITS2. PMID:10520449

  4. Current-perpendicular-to-the-plane giant magnetoresistance in spin-valves with AgSn alloy spacers

    Science.gov (United States)

    Read, J. C.; Nakatani, T. M.; Smith, Neil; Choi, Y.-S.; York, B. R.; Brinkman, E.; Childress, J. R.

    2015-07-01

    We investigate the use of AgSn alloys as the spacer layer in current-perpendicular-to-the-plane magnetoresistance devices. Alloying with Sn increases resistivity but results in a reasonably long (>10 nm) spin-diffusion length, so large magnetoresistance can be achieved with thin AgSn spacers. Compared to Ag thin films, AgSn forms smaller grain sizes, reduced roughness, and exhibits less interdiffusion upon annealing, resulting in decreased interlayer magnetic coupling in exchange biased spin-valves. AgSn also shows improved corrosion resistance compared to Ag, which is advantageous for nanofabrication, including magnetic recording head sensors. Combining a AgSn spacer with Co-based Heusler alloy ferromagnet in an exchange biased, polycrystalline trilayer thinner than 12 nm results in magnetoresistance values up to 15% at room temperature.

  5. Enhanced expression of lmb gene encoding laminin-binding protein in Streptococcus agalactiae strains harboring IS1548 in scpB-lmb intergenic region.

    Directory of Open Access Journals (Sweden)

    Rim Al Safadi

    Full Text Available Group B streptococcus (GBS is the main cause of neonatal sepsis and meningitis. Bacterial surface proteins play a major role in GBS binding to and invasion of different host surfaces. The scpB and lmb genes, coding for fibronectin-binding and laminin-binding surface proteins, are present in almost all human GBS isolates. The scpB-lmb intergenic region is a hot spot for integration of two mobile genetic elements (MGEs: the insertion element IS1548 or the group II intron GBSi1. We studied the structure of scpB-lmb intergenic region in 111 GBS isolates belonging to the intraspecies major clonal complexes (CCs. IS1548 was mostly found (72.2% in CC19 serotype III strains recovered more specifically (92.3% from neonatal meningitis. GBSi1 was principally found (70.6% in CC17 strains, mostly (94.4% of serotype III, but also (15.7% in CC19 strains, mostly (87.5% of serotype II. No MGE was found in most strains of the other CCs (76.0%, notably CC23, CC10 and CC1. Twenty-six strains representing these three genetic configurations were selected to investigate the transcription and expression levels of scpB and lmb genes. Quantitative RT-PCR showed that lmb transcripts were 5.0- to 9.6-fold higher in the group of strains with IS1548 than in the other two groups of strains (P<0.001. Accordingly, the binding ability to laminin was 3.8- to 6.6-fold higher in these strains (P< or =0.001. Moreover, Lmb amount expressed on the cell surface was 2.4- to 2.7-fold greater in these strains (P<0.001. By contrast, scpB transcript levels and fibronectin binding ability were similar in the three groups of strains. Deletion of the IS1548 sequence between scpB and lmb genes in a CC19 serotype III GBS strain substantially reduced the transcription of lmb gene (13.5-fold, the binding ability to laminin (6.2-fold, and the expression of Lmb protein (5.0-fold. These data highlight the importance of MGEs in bacterial virulence and demonstrate the up-regulation of lmb gene by IS

  6. Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

    Directory of Open Access Journals (Sweden)

    Patenge Nadja

    2012-10-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49, employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases. Results We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5′ rapid amplification of cDNA ends-PCR (RACE-PCR analysis. Conclusions In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of s

  7. CHIRAL CONJUGATED OLIGOMER BASED ON 1,1'-BINOL WITH 3,3'-ACETYLENE-PHENYLENE-ACETYLENE SPACER

    Institute of Scientific and Technical Information of China (English)

    Tian-jun Liu; Ke-shen Zhang; Yong-jun Chen; Dong Wang; Chao-jun Li

    2001-01-01

    The 1,1'-binaphthol based oligomers 3 and 7 with 3,3'-acetylene-phenylene-acetylene spacer were prepared from BINOL 1. The high optical rotation value and CD spectra demonstrated the main chain chirality of the oligomer molecule. The UV-VIS and fluorescent spectra evidence the characteristics of conjugated structure. In comparison with oligomer 2 bearing 3,3'-acetylene spacer, the oligomers 3 and 7 have longer efficient conjugation segment, and their fluorescent quantum yields (φ) increased (0.60-0.65 versus 0.14). Extending the effective conjugation segment would improve the photophysical properties of chiral conjugated polymers.``

  8. The spacer arm length in cell-penetrating peptides influences chitosan/siRNA nanoparticle delivery for pulmonary inflammation treatment

    Science.gov (United States)

    Jeong, Eun Ju; Choi, Moonhwan; Lee, Jangwook; Rhim, Taiyoun; Lee, Kuen Yong

    2015-11-01

    Although chitosan and its derivatives have been frequently utilized as delivery vehicles for small interfering RNA (siRNA), it is challenging to improve the gene silencing efficiency of chitosan-based nanoparticles. In this study, we hypothesized that controlling the spacer arm length between a cell-penetrating peptide (CPP) and a nanoparticle could be critical to enhancing the cellular uptake as well as the gene silencing efficiency of conventional chitosan/siRNA nanoparticles. A peptide consisting of nine arginine units (R9) was used as a CPP, and the spacer arm length was controlled by varying the number of glycine units between the peptide (R9Gn) and the nanoparticle (n = 0, 4, and 10). Various physicochemical characteristics of R9Gn-chitosan/siRNA nanoparticles were investigated in vitro. Increasing the spacing arm length did not significantly affect the complex formation between R9Gn-chitosan and siRNA. However, R9G10-chitosan was much more effective in delivering genes both in vitro and in vivo compared with non-modified chitosan (without the peptide) and R9-chitosan (without the spacer arm). Chitosan derivatives modified with oligoarginine containing a spacer arm can be considered as potential delivery vehicles for various genes.Although chitosan and its derivatives have been frequently utilized as delivery vehicles for small interfering RNA (siRNA), it is challenging to improve the gene silencing efficiency of chitosan-based nanoparticles. In this study, we hypothesized that controlling the spacer arm length between a cell-penetrating peptide (CPP) and a nanoparticle could be critical to enhancing the cellular uptake as well as the gene silencing efficiency of conventional chitosan/siRNA nanoparticles. A peptide consisting of nine arginine units (R9) was used as a CPP, and the spacer arm length was controlled by varying the number of glycine units between the peptide (R9Gn) and the nanoparticle (n = 0, 4, and 10). Various physicochemical characteristics of

  9. Role of methylene spacer in the excitation energy transfer in europium 1- and 2- naphthylcarboxylates

    Energy Technology Data Exchange (ETDEWEB)

    Zhuravlev, K. [V.A. Kotelnikov Institute of Radioengineering and Electronics of RAS, 1 Vvedenskii sq., Fryazino Moscow reg. 141190 (Russian Federation); Tsaryuk, V., E-mail: vit225@ire216.msk.s [V.A. Kotelnikov Institute of Radioengineering and Electronics of RAS, 1 Vvedenskii sq., Fryazino Moscow reg. 141190 (Russian Federation); Kudryashova, V.; Pekareva, I. [V.A. Kotelnikov Institute of Radioengineering and Electronics of RAS, 1 Vvedenskii sq., Fryazino Moscow reg. 141190 (Russian Federation); Sokolnicki, J. [Faculty of Chemistry, University of WrocLaw, 14 F. Joliot-Curie str., WrocLaw 50-383 (Poland); Yakovlev, Yu. [V.A. Kotelnikov Institute of Radioengineering and Electronics of RAS, 1 Vvedenskii sq., Fryazino Moscow reg. 141190 (Russian Federation)

    2010-08-15

    A series of compounds Ln(RCOO){sub 3}.Phen (Ln=Eu, Gd, Tb; RCOO{sup -}-1- and 2-naphthoate, 1- and 2-naphthylacetate, 1- and 2-naphthoxyacetate anions, Phen-1,10-phenanthroline) was investigated by methods of optical spectroscopy. Compounds of composition Ln(RCOO){sub 3}.nH{sub 2}O with the same carboxylate ligands are also considered. Results of studies of the effects of methylene spacer decoupling the {pi}-{pi}- or p-{pi}-conjugation in the naphthylcarboxylate ligand on the structure of Eu{sup 3+} coordination centre, on the lifetime of {sup 5}D{sub 0} (Eu{sup 3+}) state, and on processes of the excitation energy transfer to Eu{sup 3+} or Tb{sup 3+} ions are presented. Introduction of the methylene bridge in the ligand weakens the influence of the steric hindrances in forming of a crystal lattice and results in lowering the distortion of the Eu{sup 3+} luminescence centre, and in elongation of the observed {sup 5}D{sub 0} lifetime {tau}{sub obs}. The latter is caused by decrease in contribution of the radiative processes rate 1/{tau}{sub r}. This is confirmed by the correlation between the lifetimes {tau}{sub obs} and the quantities '{tau}{sub r}.const' inversely proportional to the total integral intensities of Eu(RCOO){sub 3}.Phen luminescence spectra. The methylene spacer performs a role of regulator of sensitization of the Ln{sup 3+} luminescence efficiency by means of an influence on mutual location of lowest triplet states of the ligands, the ligand-metal charge transfer (LMCT) states, and the emitting states of Ln{sup 3+} ions. The lowest triplet state in lanthanide naphthylcarboxylate adducts with Phen is related to carboxylate anion. A presence of the methylene spacer in naphthylcarboxylate ligand increases the triplet state energy. At the same time, the energy of 'carboxylic group-Eu{sup 3+} ion' charge transfer states falls, which can promote the degradation of excitation energy. In naphthylcarboxylates investigated a range of the

  10. Minimally invasive treatment of lumbar spinal stenosis with a novel interspinous spacer

    Directory of Open Access Journals (Sweden)

    Shabat S

    2011-09-01

    Full Text Available Shay Shabat1, Larry E Miller2,3, Jon E Block3, Reuven Gepstein11Spinal Care Unit, Sapir Medical Center, Kfar Saba, Israel; 2Miller Scientific Consulting, Inc, Biltmore Lake, NC, USA; 3Jon E Block, PhD, Inc, San Francisco, CA, USAPurpose: To assess the safety and effectiveness of a novel, minimally invasive interspinous spacer in patients with moderate lumbar spinal stenosis (LSS.Methods: A total of 53 patients (mean age, 70 ± 11 years; 45% female with intermittent neurogenic claudication secondary to moderate LSS, confirmed on imaging studies, were treated with the Superion® Interspinous Spacer (VertiFlex, Inc, San Clemente, CA and returned for follow-up visits at 6 weeks, 1 year, and 2 years. Study endpoints included axial and extremity pain severity with an 11-point numeric scale, Zurich Claudication Questionnaire (ZCQ, back function with the Oswestry Disability Index (ODI, health-related quality of life with the Physical Component Summary (PCS and Mental Component Summary (MCS scores from the SF-12, and adverse events.Results: Axial and extremity pain each decreased 54% (both P < 0.001 over the 2-year follow-up period. ZCQ symptom severity scores improved 43% (P < 0.001 and ZCQ physical function improved 44% (P < 0.001 from pre-treatment to 2 years post-treatment. A statistically significant 50% improvement (P < 0.001 also was noted in back function. PCS and MCS each improved 40% (both P < 0.001 from pre-treatment to 2 years. Clinical success rates at 2 years were 83%–89% for ZCQ subscores, 75% for ODI, 78% for PCS, and 80% for MCS. No device infection, implant breakage, migration, or pull-out was observed, although two (3.8% patients underwent explant with subsequent laminectomy.Conclusion: Moderate LSS can be effectively treated with a minimally invasive interspinous spacer. This device is appropriate for select patients who have failed nonoperative treatment measures for LSS and meet strict anatomical criteria.Keywords: Superion, axial

  11. Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster.

    Science.gov (United States)

    Yu, Hong; Zhao, Xuelin; Li, Qi

    2016-01-01

    An increasing amount of evidence suggests that long intergenic noncoding RNAs (lincRNAs) may play diverse roles in many cellular processes. However, little is known about lincRNAs in marine invertebrates. Here, we presented the first identification and characterization of lincRNAs in the Pacific oyster (Crassostrea gigas). We developed a pipeline and identified 11,668 lincRNAs in C. gigas based on RNA-Seq resources available. These lincRNAs exhibited many common characteristics with vertebrate lincRNAs: relatively short length, low exon numbers, low expression, and low sequence conservation. 1,175 lincRNAs were expressed in a tissue-specific manner, with 35.2% preferentially expressed in male gonad. 776 lincRNAs were specifically expressed in juvenile during different developmental stages. In addition, 47 lincRNAs were found to be potentially related to oyster settlement and metamorphosis. Such diverse temporal and spatial patterns of expression suggest that these lincRNAs might function in cell differentiation during early development, as well as sex differentiation and reproduction. Based on a co-expression network analysis, five lincRNAs were detected that have an expression correlation with key hub genes in four modules significantly correlated with larval development. Our study provides the first large-scale identification of lincRNAs in molluscs and offers new insights into potential functions of lincRNAs in marine invertebrates. PMID:26861843

  12. Long intergenic non-coding RNA APOC1P1-3 inhibits apoptosis by decreasing α-tubulin acetylation in breast cancer

    Science.gov (United States)

    Liao, X-H; Wang, J-G; Li, L-Y; Zhou, D-M; Ren, K-H; Jin, Y-T; Lv, L; Yu, J-G; Yang, J-Y; Lu, Q; Zou, Q; Yu, J; Liu, X-P; Zhou, P

    2016-01-01

    Increasing evidence indicates that long non-coding RNAs (lncRNAs) act as important regulatory factors in tumor progression. However, their roles in breast cancer remain largely unknown. In present studies, we identified aberrantly expressed long intergenic non-coding RNA APOC1P1-3 (lincRNA-APOC1P1-3) in breast cancer by microarray, verified it by quantitative real-time PCR, and assessed methylation status in the promoter region by pyrosequencing. We also investigated the biological functions with plasmid transfection and siRNA silencing experiments, and further explored their mechanisms by RNA pull-down and RNA immunoprecipitation to identify binding proteins. We found that 224 lncRNAs were upregulated in breast cancer, whereas 324 were downregulated. The lincRNA-APOC1P1-3 was overexpressed in breast cancer, which was related to tumor size and hypomethylation in its promoter region. We also found that APOC1P1-3 could directly bind to tubulin to decrease α-tubulin acetylation, to inactivate caspase-3, and to inhibit apoptosis. This study demonstrates that overexpression of APOC1P1-3 can inhibit breast cancer apoptosis. PMID:27228351

  13. The Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) Study: Design and Methods for Complex DNA Analysis.

    Science.gov (United States)

    Taylor, Jacquelyn Y; Wright, Michelle L; Crusto, Cindy A; Sun, Yan V

    2016-10-01

    The Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) study aims to delineate the independent and interaction effects of genomic (genetic and epigenetic) and psychological-environmental (maternally perceived racial discrimination, mental health, and parenting behavior) factors on blood pressure (BP) among African American mother-child dyads over time. The purpose of this article is to describe the two-step genetic and epigenetic approach that will be executed to explore Gene × Environment interactions on BP using a longitudinal cohort design. Procedure for the single collection of DNA at Time 1 includes the use of the Oragene 500-format saliva sample collection tube, which provides enough DNA for both the Illumina Multi-Ethnic Genotyping and 850K EPIC methylation analyses. BP readings, height, weight, percentage of body fat, and percentage of body water will be measured on all participants every 6 months for 2 years for a total of 4 time points. Genomic data analyses to be completed include multivariate modeling, assessment of population admixture and structure, and extended analyses including Bonferroni correction, false discovery rate methods, Monte Carlo approach, EIGENSTRAT methods, and so on, to determine relationships among both main and interaction effects of genetic, epigenetic, and psychological environmental factors on BP.

  14. -pyrrole substituted porphyrin-pyrene dyads using vinylene spacer: Synthesis, characterization and photophysical properties

    Indian Academy of Sciences (India)

    P Silviya Reeta; Ravi Kumar Kanaparthi; L Giribabu

    2013-03-01

    We have designed and synthesized donor-acceptor conjugates having donor pyrene at the pyrrole- position of either free-base porphyrin or Zn(II) porphyrin using vinylene spacer. Both the dyads have been completely characterized by elemental analysis,MALDI-MS, UV-Vis., and fluorescence (steady state and timeresolved) spectroscopies as well as cyclic voltammetry. The absorption maxima of both dyads are red-shifted by 8-12 nm. The ground state properties showed that there exist minimum - interaction between the aromatic subunits of these D-A systems. Quenched emission was observed in both the dyads when excited at 290 nm. The quenched emission explained in terms of intramolecular excitation energy transfer competes with the photo-induced electron transfer reaction in these D-A system.

  15. Conotoxins containing nonnatural backbone spacers: cladistic-based design, chemical synthesis, and improved analgesic activity.

    Science.gov (United States)

    Green, Brad R; Catlin, Philip; Zhang, Min-Min; Fiedler, Brian; Bayudan, Wendi; Morrison, Alex; Norton, Raymond S; Smith, Brian J; Yoshikami, Doju; Olivera, Baldomero M; Bulaj, Grzegorz

    2007-04-01

    Disulfide-rich neurotoxins from venomous animals continue to provide compounds with therapeutic potential. Minimizing neurotoxins often results in removal of disulfide bridges or critical amino acids. To address this drug-design challenge, we explored the concept of disulfide-rich scaffolds consisting of isostere polymers and peptidic pharmacophores. Flexible spacers, such as amino-3-oxapentanoic or 6-aminohexanoic acids, were used to replace conformationally constrained parts of a three-disulfide-bridged conotoxin, SIIIA. The peptide-polymer hybrids, polytides, were designed based on cladistic identification of nonconserved loci in related peptides. After oxidative folding, the polytides appeared to be better inhibitors of sodium currents in dorsal root ganglia and sciatic nerves in mice. Moreover, the polytides appeared to be significantly more potent and longer-lasting analgesics in the inflammatory pain model in mice, when compared to SIIIA. The resulting polytides provide a promising strategy for transforming disulfide-rich peptides into therapeutics.

  16. Bulk FinFETs with body spacers for improving fin height variation

    Science.gov (United States)

    Wei, Xing; Zhu, Huilong; Zhang, Yanbo; Zhao, Chao

    2016-08-01

    A novel FinFET structure with body spacers in sub fin (BSSF) is proposed to improve the fin height variation produced in the manufacturing processes. Device simulation results are presented to show the electrical variations improvement. The effective fin height (Heff) of FinFETs with BSSF is well controlled because it only depends on the silicon epi layer thickness (TSi). Taking advantage of the precisely controlled epitaxy process, Heff uniformity of FinFETs with BSSF is much better than conventional bulk FinFETs. Benefit from the smaller Heff variation, FinFETs with BSSF show much smaller electrical characteristics variation. For n-FinFETs, the Ion variation improves from 33.46% for conventional bulk FinFETs to 8.05% for FinFETs with BSSF. Additionally, manufacturing of FinFETs with BSSF is compatible with that of the state-of-the-art bulk FinFETs, promising for its applications in massive production.

  17. Switchable wavelength-selective and diffuse metamaterial absorber/emitter with a phase transition spacer layer

    Science.gov (United States)

    Wang, Hao; Yang, Yue; Wang, Liping

    2014-08-01

    We numerically demonstrate a switchable metamaterial absorber/emitter by thermally turning on or off the excitation of magnetic resonance upon the phase transition of vanadium dioxide (VO2). Perfect absorption peak exists around the wavelength of 5 μm when the excitation of magnetic resonance is supported with the insulating VO2 spacer layer. The wavelength-selective absorption is switched off when the magnetic resonance is disabled with metallic VO2 that shorts the top and bottom metallic structures. The resonance wavelength can be tuned with different geometry, and the switchable metamaterial exhibits diffuse behaviors at oblique angles. The results would facilitate the design of switchable metamaterials for active control in energy and sensing applications.

  18. The effect of spacers on the performance of Micromegas detectors: a numerical investigation

    CERN Document Server

    Bhattacharya, Purba; Majumdar, Nayana; Bhattacharya, Sudeb

    2016-01-01

    Micromegas detector is considered to be a promising candidate for a large variety of high-rate experiments. Micromegas of various geometries have already been established as appropriate for these experiments for their performances in terms of gas gain uniformity, energy and space point resolution, and their capability to efficiently pave large read-out surfaces with minimum dead zone. The present work investigates the effect of spacers on different detector characteristics of Micromegas detectors having various amplification gaps and mesh hole pitches. Numerical simulation has been used as a tool of exploration to evaluate the effect of such dielectric material on detector performance. Some of the important and fundamental characteristics such as electron transparency, gain and signal of the Micromegas detector have been estimated.

  19. Nasal inhalation of budesonide from a spacer in children with perennial rhinitis and asthma

    DEFF Research Database (Denmark)

    Pedersen, W; Hjuler, Inga Merete; Bisgaard, H;

    1998-01-01

    The standard treatment of allergic rhinitis and asthma consists of topical corticosteroids administered intranasally and inhaled through the mouth. Although this therapy is highly effective, and side-effects are few and mild, it may be possible further to improve the therapeutic index and patient...... compliance with the treatment. In the present study, we evaluated a nasal inhalation system used for the simultaneous treatment of rhinitis and asthma. In principle, it results in an airway deposition of the corticosteroid similar to that of inhaled allergens. Twenty-four children with perennial rhinitis and...... asthma inhaled budesonide through the nose from a pressurized aerosol, attached to a spacer device, in a double-blind, placebo-controlled, crossover study. Compared with placebo, budesonide treatment resulted in a significant reduction of nasal symptoms (P<0.01) and of asthma symptoms (P<0.05), and in an...

  20. [A new spacer, Babyhaler, for BDP inhalation therapy in severe infantile asthma].

    Science.gov (United States)

    Yamada, Y; Yoshihara, S; Abe, T; Fukuda, N; Watanabe, M; Ono, M; Arisaka, O

    2000-11-01

    Recently, it has been recognized that airway inflammation is the most important pathogenesis of bronchial asthma, and inhaled corticosteroids therapy is effective for childhood asthma. However, using metered dose inhalers (MDI) of beclomethasone dipropionate (BDP) is difficult for infants. In this study, we administered BDP inhalation therapy with a new spacer, Babyhaler, for five cases of early childhood with severe infantile asthma that we could not control even by combination of theophylline round the clock (RTC) therapy and disodium cromoglycate (DSCG) + beta 2 stimulant (beta 2) regular use. We compared symptom score of asthma attack between the pre-treatment period (prior 2 weeks) and post-treatment period (following 8 weeks) of BDP inhalation therapy with Babyhaler. As a result, symptom score decreased significantly within 4 weeks after treatment of BDP with Babyhaler as compared with the score before treatment of BDP. These findings suggest that Babyhaler is useful for BDP inhalation therapy in infantile asthma. PMID:11193463

  1. Phylogenetic analysis of Bambusa (Poaceae: Bambusoideae) based on internal transcribed spacer sequences of nuclear ribosomal DNA.

    Science.gov (United States)

    Sun, Ye; Xia, Nianhe; Lin, Rushun

    2005-12-01

    Phylogenetic analyses of Bambusa species were performed using internal transcribed spacer sequences of nuclear ribosomal DNA. The 21 species sampled included members of Bambusa (sensu stricto), Dendrocalamopsis, Dendrocalamus, Guadua, Leleba, and Lingnania. Arundinaria gigantea was used as an outgroup. Using the maximum parsimony method with PAUP*, gaps were treated as missing states or new states. Parsimonious analysis revealed that Dendrocalamus latiflorus was closely related to the members of Dendrocalamopsis. Dendrocalamus membranaceus was a sister species to Dendrocalamus strictus. Three Dendrocalamus species were closely related to and nested in a polyphyletic Bambusa. Bambusa subaequalis was a sister species to B. multiplex, B. emeiensis to B. chungii, B. contracta to B. hainanensis, and B. flexuosa was a sister species to B. sinospinosa, B. tuldoides, B. surrecta, B. intermedia, and B. valida group, which raised doubts about the monophyly of the subgenera Bambusa (sensu stricto), Dendrocalamopsis, Leleba, and Lingnania under the genus Bambusa. PMID:16382365

  2. The effect of spacers on the performance of Micromegas detectors: A numerical investigation

    Science.gov (United States)

    Bhattacharya, Purba; Mukhopadhyay, Supratik; Majumdar, Nayana; Bhattacharya, Sudeb

    2015-09-01

    Micromegas detector is considered to be a promising candidate for a large variety of high-rate experiments. Micromegas of various geometries have already been established as appropriate for these experiments for their performances in terms of gas gain uniformity, energy and space point resolution, and their capability to efficiently pave large read-out surfaces with minimum dead zone. The present work investigates the effect of spacers on different detector characteristics of Micromegas detectors having various amplification gaps and mesh hole pitches. Numerical simulation has been used as a tool of exploration to evaluate the effect of such dielectric material on detector performance. Some of the important and fundamental characteristics such as electron transparency, gain and signal of the Micromegas detector have been estimated.

  3. Si/SiGe electron resonant tunneling diodes with graded spacer wells

    International Nuclear Information System (INIS)

    Resonant tunneling diodes have been fabricated using graded Si1-xGex (x=0.3->0.0) spacer wells and strained Si0.4Ge0.6 barriers on a relaxed Si0.7Ge0.3 n-type substrate which demonstrates negative differential resistance at up to 100 K. This design is aimed at reducing the voltage at which the peak current density is achieved. Peak current densities of 0.08A/cm2 with peak-to-valley current ratios of 1.67 have been achieved for a low peak voltage of 40 mV at 77 K. This represents an improvement of over an order of magnitude compared to previous work. [copyright] 2001 American Institute of Physics

  4. Magnetotransport properties of spin-valve structures with Mg spacer layers

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Boubeta, C., E-mail: cboubeta@gmail.com [Departament d' Electrònica and IN2UB, Universitat de Barcelona, 08028 Barcelona (Spain); Ferrante, Y. [Technische Universität Kaiserslautern, 67663 Kaiserslautern (Germany); Graduate School of Excellence, Materials Science in Mainz, 55128 Mainz (Germany); Parkin, S. S. P. [IBM Research Division, Almaden Research Center, San Jose, California 95120 (United States)

    2015-01-19

    A theoretical prediction by Wang et al. [Phys. Rev. B 82, 054405 (2010)] suggests the preferential transmission of majority-spin states with Δ{sub 1} symmetry across a magnesium interlayer in Fe/Mg/MgO/Fe based magnetic tunnel junctions. Here, we report experiments to probe this question in CoFe/Mg/CoFe structures. We find that the strength of the interlayer coupling decays exponentially with increasing the spacer thickness, however, a non-monotonic variation of the magnetoresistance as a function of the Mg layer is observed. These data may help revisit the role of the insertion of a Mg interface layer in MgO-based devices.

  5. CFD prediction of flow and phase distribution in fuel assemblies with spacers

    Energy Technology Data Exchange (ETDEWEB)

    Anglart, H.; Nylund, O. [ABB Atom AB, Vasteras (Switzerland); Kurul, N. [Rensselaer Polytechnic Institute, Troy, NY (United States)] [and others

    1995-09-01

    This paper is concerned with the modeling and computation of multi-dimensional two-phase flows in BWR fuel assemblies. The modeling principles are presented based on using a two-fluid model in which lateral interfacial effects are accounted for. This model has been used to evaluate the velocity fields of both vapor and liquid phases, as well as phase distribution, between fuel elements in geometries similar to BWR fuel bundles. Furthermore, this model has been used to predict, in a detailed mechanistic manner, the effects of spacers on flow and phase distribution between, and pressure drop along, fuel elements. The related numerical simulations have been performed using a CFD computer code, CFDS-FLOW3D.

  6. IMMOBILIZATION OF POTENTIALLY BIOACTIVE MOIETIES ONTO POLYETHER WITH POLY(ETHYLENE GLYCOL)-SULFONATE SPACER

    Institute of Scientific and Technical Information of China (English)

    JI Jian; FENG Linxian; QIU Yongxin; YU Xiaojie; YANG Shilin

    1997-01-01

    A new reactive graft copolymer, poly(tetramethylene glycol)-graft-ω-propyl sodium sulfonate-poly(ethylene glycol) (PTMG-g-PEG-CH2CH2CH2SO-3Na+), was synthesized by the cationic polymerization of α-ω-bifunctional PEG macromonomer ((o)CH2-PEG--CH2CH2CH2SO3Na ) and THF. The obtained copolymer exhibits the expected structure as indicated by the result of characterization. Two amino acids (L-arginine, L-tyrosine) were covalently attached to the copolymer after converting the sulfonate group to sulfonyl chloride. So the new reactive graft copolymer (PTMG-g-PEG-CH2CH2CH2SO-3Na+) is expected to be very useful in attachment of potentially bioactive moieties to polymer via a hydrophilic PEG spacer.

  7. Coupled computational fluid dynamics and MOC neutronic simulations of Westinghouse PWR fuel assemblies with grid spacers

    International Nuclear Information System (INIS)

    Neutronic coupling with Computational Fluid Dynamics (CFD) has been under development within the US DOE sponsored “Nuclear Simulation Hub”. The method of characteristics (MOC) neutronics code DeCART ([Joo, 2004], [Kochunas, 2009]) under development at the University of Michigan was coupled with the CFD code STAR-CCM+ to achieve more accurate predictions of fuel assembly performance. At Westinghouse, lower order, neutronic codes such as the nodal code ANC have been coupled to thermal-hydraulics codes such the subchannel code VIPRE to predict the heat flux and fuel nuclear behavior. However, a more detailed neutronics and temperature / fluid field simulation of fuel assembly models which includes explicit representation of spacer grids would considerably improve the design and assessment of new fuel assembly designs. Coupled STAR-CCM+ / DeCART calculations have been performed for various representative three-dimensional models with explicit representation of spacer grids with mixing vanes. The high fidelity results have been compared to lower order simulations. The coupled CFD/MOC solution has provided a more truthful model which includes a more accurate representation of all the important physics such as fission energy, heat convection, heat conduction, and turbulence. Of particular significance is the ability to assess the effects of the mixing grid on the coolant temperature and density distribution using coupled thermal/fluids and neutronic solutions. A more precise cladding temperature can be derived by this approach which will also enable more accurate prediction of departure from nucleate boiling (DNB), as well as a better understanding of DNB margin and crud build up on the fuel rod. (author)

  8. Preparation of the spacer for narrow electrode gap configuration in ionization-based gas sensor

    Energy Technology Data Exchange (ETDEWEB)

    Saheed, Mohamed Shuaib Mohamed; Mohamed, Norani Muti; Burhanudin, Zainal Arif [Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia); Fundamental and Applied Science, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia); Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, Seri Iskandar, Tronoh, Perak. (Malaysia)

    2012-09-26

    Carbon nanotubes (CNTs) have started to be developed as the sensing element for ionization-based gas sensors due to the demand for improved sensitivity, selectivity, stability and other sensing properties beyond what can be offered by the conventional ones. Although these limitations have been overcome, the problems still remain with the conventional ionization-based gas sensors in that they are bulky and operating with large breakdown voltage and high temperature. Recent studies have shown that the breakdown voltage can be reduced by using nanostructured electrodes and narrow electrode gap. Nanostructured electrode in the form of aligned CNTs array with evenly distributed nanotips can enhance the linear electric field significantly. The later is attributed to the shorter conductivity path through narrow electrode gap. The paper presents the study on the design consideration in order to realize ionization based gas sensor using aligned carbon nanotubes array in an optimum sensor configuration with narrow electrode gap. Several deposition techniques were studied to deposit the spacer, the key component that can control the electrode gap. Plasma spray deposition, electron beam deposition and dry oxidation method were employed to obtain minimum film thickness around 32 {mu}m. For plasma spray method, sand blasting process is required in order to produce rough surface for strong bonding of the deposited film onto the surface. Film thickness, typically about 39 {mu}m can be obtained. For the electron beam deposition and dry oxidation, the film thickness is in the range of nanometers and thus unsuitable to produce the spacer. The deposited multilayer film consisting of copper, alumina and ferum on which CNTs array will be grown was found to be removed during the etching process. This is attributed to the high etching rate on the thin film which can be prevented by reducing the rate and having a thicker conductive copper film.

  9. Enzyme detection by surface plasmon resonance using specially engineered spacers and plasmonic labelling

    Science.gov (United States)

    François, A.; Heng, S.; Kostecki, R.; Monro, T. M.

    2011-05-01

    Surface Plasmon Resonance (SPR) is a powerful label free optical biosensing technology that relies on the measurement of the refractive index or change of mass in close vicinity of the sensor surface. Therefore, there is an experimental limitation in the molecular weight of the molecule that can be detected and consequently small molecules are intrinsically more difficult to detect using SPR. One approach to overcoming this limitation is to first adsorb smaller molecules onto the sensor surface, and to follow this by using their higher molecular weight antibodies counterparts which ensure the specificity (and are easier to detect via SPR due to their higher weight). Although this has been demonstrated with some success, it is not applicable in every case and some biomolecules such as enzyme are still difficult to detect due to their specific reactivity (enzymatic reaction). In this paper, we present a powerful new method that utilises specifically engineered spacers attached on one end to the sensor surface and on the other end to a nanoparticle that behaves as a plasmonic label. These spacers are design to specifically react with the biomolecule to be detected and release the (relatively large) plasmonic label, which in turn results in a measurable SPR shift (which is much larger than the shift that would have been associated with the binding of the relatively small biomolecule). As a proof of concept, this approach was used within a recently developed new form of SPR optical fibre sensor which relies on the measurement of the re-emitted light by surface scattering of the plasmonic wave rather than transmission through the fibre was used to detect an enzyme. Here trypsin (25kDa) was successfully sensed. This molecule is involved in both intestinal and pancreatic diseases.

  10. Controlling the Biomimetic Implant Interface: Modulating Antimicrobial Activity by Spacer Design

    Science.gov (United States)

    Wisdom, Cate; Vanoosten, Sarah Kay; Boone, Kyle W.; Khvostenko, Dmytro; Arnold, Paul M.; Snead, Malcolm L.; Tamerler, Candan

    2016-08-01

    Surgical site infection is a common cause of post-operative morbidity, often leading to implant loosening, ultimately requiring revision surgery, increased costs and worse surgical outcomes. Since implant failure starts at the implant surface, creating and controlling the bio-material interface will play a critical role in reducing infection while improving host cell-to-implant interaction. Here, we engineered a biomimetic interface based upon a chimeric peptide that incorporates a titanium binding peptide (TiBP) with an antimicrobial peptide (AMP) into a single molecule to direct binding to the implant surface and deliver an antimicrobial activity against S. mutans and S. epidermidis, two bacteria which are linked with clinical implant infections. To optimize antimicrobial activity, we investigated the design of the spacer domain separating the two functional domains of the chimeric peptide. Lengthening and changing the amino acid composition of the spacer resulted in an improvement of minimum inhibitory concentration by a three-fold against S. mutans. Surfaces coated with the chimeric peptide reduced dramatically the number of bacteria, with up to a nine-fold reduction for S. mutans and a 48-fold reduction for S. epidermidis. Ab initio predictions of antimicrobial activity based on structural features were confirmed. Host cell attachment and viability at the biomimetic interface were also improved compared to the untreated implant surface. Biomimetic interfaces formed with this chimeric peptide offer interminable potential by coupling antimicrobial and improved host cell responses to implantable titanium materials, and this peptide based approach can be extended to various biomaterials surfaces.

  11. The utility of internally transcribed spacer 2 DNA sequences of the nuclear ribosomal gene for distinguishing sibling species of Trichogramma

    NARCIS (Netherlands)

    Stouthamer, R.; Hu, J.; Kan, van F.J.P.M.; Platner, G.R.; Pinto, J.D.

    1999-01-01

    The usefulness of the internally transcribed spacer 2 (ITS2) of the nuclear ribosomal gene complex is tested for providing taxonomic characters to identify Trichogramma species. The ITS2 sequences of a group of sibling species of the T. deion/T. pretiosum complexes were determined. A simple and prec

  12. Effect of the spacer group nature on the optical and electrical properties of confined poly( p-phenylene vinylene) derivatives

    Science.gov (United States)

    Benzarti-Ghédira, Maha; Zahou, Imen; Hrichi, Haikel; Jaballah, Nejmeddine; Ben Chaâbane, Rafik; Majdoub, Mustapha; Ben Ouada, Hafedh

    2015-09-01

    This study is an investigation about the effect of chemical modification on the morphological, optical and electrical properties of semiconducting organic thin films. Two confined poly( p-phenylene vinylene) (PPV)-type polymers containing different spacer groups were studied: P1 has an isopropylidene spacer group and P2 with hexafluoroisopropylidene spacer. The UV-Vis absorption and PL analysis showed a stronger π- π interaction in the P1 film; in P2, the π-stacking is limited by the introduction of a bulky trifluoromethyl (CF3) groups on the spacer units. The P2 exhibits a better film quality as illustrated by the atomic force microscopy. The HOMO and LUMO energy levels and electrochemical band gap of the polymers were determinate by the cyclic voltammetry. The electrical properties of ITO/PPV derivative/Al diodes were investigated by means of current-voltage and show a space-charge-limited current conduction mechanism with higher mobility in the P2 thin layer. The impedance spectra of the devices can be discussed in terms of an equivalent circuit model designed as a parallel resistance ( R p) and capacitance ( C p) network in series with a resistance.

  13. Epitope DNA vaccines against tuberculosis: spacers and ubiquitin modulates cellular immune responses elicited by epitope DNA vaccine

    Institute of Scientific and Technical Information of China (English)

    Wang QM; Sun SH; Hu ZL; Zhou FJ; Yin M; Xiao CJ; Zhang JC

    2005-01-01

    Cell-mediated immune responses are crucial in the protection against tuberculosis. In this study, we constructed epitope DNA vaccines (p3-M-38) encoding cytotoxic T lymphocyte (CTL) epitopes of MPT64 and 38 kDa proteins of Mycobacterium tuberculosis. In order to observe the influence of spacer sequence (Ala-Ala-Tyr) or ubiquitin (UbGR) on the efficacy of the two CTL epitopes, we also constructed DNA vaccines, p3-M-S(spacer)-38, p3-Ub (UbGR)-M-S-38 and p3-Ub-M-38. The immune responses elicited by the four DNA vaccines were tested in C57BL/6 (H-2b) mice. The cytotoxicity of T cells was detected by LDH-release method and by enzyme-linked immunospot assay for epitope-specific cells secreting interferon-gamma. The results showed that DNA immunization with p3-M-38 vaccine could induce epitope-specific CD8+ CTL response and that the spacer sequence (AAY) only enhanced M epitope presentation. The protein-targeting sequence (UbGR) enhanced the immunogenicity of the two epitopes. The finding that defined spacer sequences at C-terminus and protein-targeting degradation modulated the immune response of epitope string DNA vaccines will be of importance for the further development of multi-epitope DNA vaccines against tuberculosis.

  14. The effect of spacer grid critical component on pressure drop under both single and two phase flow conditions

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.; Yang, B.W.; Zhang, H.; Mao, H.; Zha, Y. [Xi' an Jiaotong Univ., Shaanxi (China). Science and Technology Center for Advanced Nuclear Fuel Research

    2016-07-15

    As pressure drop is one of the most critical thermal hydraulic parameters for spacer grids the accurate estimation of it is the key to the design and development of spacer grids. Most of the available correlations for pressure drop do not contain any real geometrical parameters that characterize the grid effect. The main functions for spacer grid are structural support and flow mixing. Once the boundary sublayer near the rod bundle is disturbed, the liquid forms swirls or flow separation that affect pressure drop. However, under two phase flow conditions, due to the existence of steam bubble, the complexity for spacer grid are multiplied and pressure drop calculation becomes much more challenging. The influence of the dimple location, distance of mixing vane to the nearest strip, and the effect of inter-subchannel mixing among neighboring subchannels on pressure drop and downstream flow fields are analyzed in this paper. Based on this study, more detailed space grid geometry parameters are recommended for adding into the correlation when predicting pressure drop.

  15. Investigation of optical spacer layers from solution based precursors for polymer solar cells using X-ray reflectometry

    DEFF Research Database (Denmark)

    Andersen, Philip Hvidthøft Delff; Skårhøj, Jakob; Andreasen, Jens Wenzel;

    2009-01-01

    Optical spacer layers based on titaniumalkoxide precursor solutions were prepared by spin-coating on top of bulk heterojunction layers based on poly-3-hexylthiophene (P3HT) and phenyl-C61-butyric acid methylester (PCBM). Models and experiment have shown that the performance of polymer solar cells...

  16. Effect of the spacer group on the behavior of the cationic Gemini surfactant monolayer at the air/water interface

    Energy Technology Data Exchange (ETDEWEB)

    Chen Qibin; Zhang Dazhi; Li Rong [State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai 200237 (China); Liu Honglai [State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai 200237 (China)], E-mail: hlliu@ecust.edu.cn; Hu Ying [State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai 200237 (China)

    2008-10-01

    Surface properties of the insoluble cationic bis-(quaternary ammonium halide) surfactants (Gemini) with polymethylene spacer at the air/water interface were investigated. The monolayers were transferred onto mica by the Langmuir-Blodgett (LB) technique and the corresponding LB films were characterized by the atomic force microscopy (AFM) and the contact angle of water. For the Gemini surfactants with the different spacer length, it was found that the surface pressure-molecular area isotherms resemble to each other. The limiting area increases rapidly and almost linearly with the increase of spacer length for the short spacers, but reaches a maximum at s = 10 and decreases slightly at s > 10. The AFM images show that the surface micelles and the multilayer aggregates gradually appear with the increase of surface pressure. No matter what the surface pressures are, the main structure of the monolayer almost keeps the same, which suggested that the major molecules lie nearly flat on the water surface, while the increase of surface pressure forces the minor alkyl chains to turn only partly or completely vertical to the water surface and even to overturn. This is the cause that the contact angle of water on LB film increases slightly with the surface pressure.

  17. Rheological response of methylcellulose toward alkanediyl-α,ω-bis(dimethylcetylammonium bromide) surfactants with varying spacer length.

    Science.gov (United States)

    Shah, Rais Ahmad; Chat, Oyais Ahmad; Maswal, Masrat; Rather, Ghulam Mohammad; Dar, Aijaz Ahmad

    2016-06-25

    The modulation of properties of methylcellulose (MC) by cationic gemini surfactants with varying spacer lengths was studied employing tensiometry, rheometry and turbidimetry. Surface tension measurements anticipate that the gemini surfactant with longer spacer chain length saturates MC at lower concentrations owing to its greater hydrophobicity compared to shorter spacer analogues. Rheometric and turbidimetric measurements suggest that at very low concentrations of gemini surfactants, ion-dipole type of interactions between MC and gemini surfactants promote the extension of polymer chains which is manifested by an initial increase in the low shear viscosity and gelation temperature of MC-gemini surfactant systems, and lowering of turbidity. Such interactions were found to be stronger in case of 16-4-16 than 16-5-16, and almost absent in case of 16-6-16 surfactant system. However at concentrations above CAC, hydrophobic forces operative between MC and gemini surfactants were found to be more for 16-6-16 than that of 16-5-16 and 16-4-16. The final levelling of MC viscosity in presence of all the three gemini surfactants and the variation of gelation temperature suggests the solubilization of network junctions in the surfactant micelles. Moreover, the presence of gemini surfactant strongly affects the interaction of MC with a model hydrophobic drug rifampicin.The results highlight the importance of gemini surfactants and their spacer length in controlling the structural dynamics of MC and its effective use in pharmaceutical and food industry. PMID:27083805

  18. Thiol addition to protected allyl glycosides: an improved method for the preparation of spacer-arm glycosides

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Seeventer, P.B. van; Dorst, J.A.L.M. van; Siemerink, J.F.; Kamerling, J.P.

    1997-01-01

    A useful method for the preparation of differently functionalized sulfide spacer-arm glycosides is presented. Several protected allyl glycosides were variously elongated via a radical addition reaction with pentanethiol, methyl 3-mercaptopropionate, or 2-mercaptoethanol. The hydroxyl function of pro

  19. Superiority of Spacer/Mask Topical Anesthetic Compared with Conventional Spray and Gargle Method for Fibreoptic Bronchoscopy

    Directory of Open Access Journals (Sweden)

    RC Balkissoon

    1996-01-01

    Full Text Available OBJECTIVE: To compare the safety and efficacy of a new spacer-oral nasal mask device with those of the standard needle nozzle spray method for the delivery of aerosolized lidocaine to the upper airway for pre-bronchoscopic anaesthesia in a tertiary care hospital.

  20. Preventing Complications from High-Dose Rate Brachytherapy when Treating Mobile Tongue Cancer via the Application of a Modular Lead-Lined Spacer.

    Directory of Open Access Journals (Sweden)

    Shumei Murakami

    Full Text Available To point out the advantages and drawbacks of high-dose rate brachytherapy in the treatment of mobile tongue cancer and indicate the clinical importance of modular lead-lined spacers when applying this technique to patients.First, all basic steps to construct the modular spacer are shown. Second, we simulate and evaluate the dose rate reduction for a wide range of spacer configurations.With increasing distance to the source absorbed doses dropped considerably. Significantly more shielding was obtained when lead was added to the spacer and this effect was most pronounced on shorter (i.e. more clinically relevant distances to the source.The modular spacer represents an important addition to the planning and treatment stages of mobile tongue cancer using HDR-ISBT.

  1. Turbulent mixing in a rod bundle with vaned spacer grids: OECD/NEA–KAERI CFD benchmark exercise test

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Seok-Kyu; Kim, Seok; Song, Chul-Hwa, E-mail: chsong@kaeri.re.kr

    2014-11-15

    Highlights: • Detailed velocity profiles have been examined in a rod bundle with mixing spacer grids. • Mixing characteristics strongly depend on the type of the mixing vane on a spacer grid. • The swirl in subchannels is elliptic and the cross-flow in gaps is vigorous in the split-type. • Swirl-type vanes generate a circular swirl in a subchannel and a weak cross-flow in gaps. • Mixing performance is superior in the case of the split-type compared to the swirl-type. - Abstract: An experimental study titled the 2nd International Benchmark Exercise (IBE-2) has been conducted to provide high-precision data of detailed turbulent flow mixing in a rod bundle for validating the CFD codes being used widely in the nuclear power industry. A 5 × 5 rod bundle having mixing spacer grids was adopted as a test rig, and was contained in a square flow housing with a 170 mm side length and 4670 mm length. The 25 rods in a bundle have dimensions of 25.4 mm in outer diameter and a 3863 mm length. The benchmark experiments have been performed at the MATiS-H water loop facility in KAERI. The axial bulk velocity in a rod bundle was maintained at about 1.50 m/s (equivalent to Re ∼50,000) with loop conditions of 35 °C and 1.57 bar measured upstream of the spacer during the experiments. Detailed measurements of the turbulent flow in the subchannels were accomplished using 2-D LDA at four different distances (0.5, 1, 4 and 10 D{sub H}) from the downstream of the mixing spacer grid. The upstream flow profiles also have been measured at the inlet of the mixing spacer grid for the inlet boundary condition. Precise measurements of the lateral and axial velocities in the subchannels are presented at four downstream distances, as well as the inlet from the mixing spacer grid of two types. Turbulence intensities and vorticities in the subchannels are also evaluated from the velocity measurements.

  2. The effect of polyethylene glycol spacer chain length on the tumor-targeting potential of folate-modified PPI dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Thakur, Shrikant [Dr. Hari Singh Gour University, Pharmaceutics Research Laboratory, Department of Pharmaceutical Sciences (India); Tekade, Rakesh K., E-mail: rakeshtekade@yahoo.com [University of Hawai' i at Hilo, College of Pharmacy (United States); Kesharwani, Prashant, E-mail: prashant_pharmacy04@rediffmail.com; Jain, Narendra K., E-mail: jnarendr@yahoo.co.in [Dr. Hari Singh Gour University, Pharmaceutics Research Laboratory, Department of Pharmaceutical Sciences (India)

    2013-05-15

    The objective of the present investigation was to assess the tumor-targeting potential of ligand-spacer-engineered poly (propylene imine) (PPI) dendrimers as nanoscale drug delivery units for site-specific delivery of a model anticancer agent, docetaxel (DTX). PPI dendrimers were engineered by direct and indirect conjugation of folic acid (FA) via different types of polyethylene glycols (PEGs) [Mw (molecular weight): 1,000, 4,000, 6,000, 7,500] as spacers. The synthesized nanoconjugates (PPIFA, PPIP1FA, PPIP4FA, PPIP6FA, and PPIP7.5FA) were characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance ({sup 1}H-NMR) and transmission electron microscopic (TEM) studies. Nanoconjugates were evaluated for entrapment, in vitro drug release (under various pH conditions) and hemolytic studies. Cell uptake and cytotoxicity studies were performed on human malignant cell lines (MCF-7) using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide [MTT] assay. This debut study explored the effect of PEG spacer length on the targeting potential of folate-conjugated 5.0 G PPI dendrimer. DTX entrapment and in vitro drug release from nanoconjugates augmented, and hemolytic toxicity of nanoconjugates slashed with the molecular weight of PEGs. Further, nanoconjugates with PEG 4000 displayed highest tumor-targeting potential as compared to other spacer conjugated nanoconjugates due to optimized steric hindrance and receptor mediated endocytosis among other PEGs. This work is expected to shed new light on the role of spacer chain length in targeting potential of folate-anchored dendrimer.Graphical Abstract.

  3. Experimental and numerical characterization of the water flow in spacer-filled channels of spiral-wound membranes

    KAUST Repository

    Bucs, Szilard S.

    2015-09-25

    Micro-scale flow distribution in spacer-filled flow channels of spiral-wound membrane modules was determined with a particle image velocimetry system (PIV), aiming to elucidate the flow behaviour in spacer-filled flow channels. Two-dimensional water velocity fields were measured in a flow cell (representing the feed spacer-filled flow channel of a spiral wound reverse osmosis membrane module without permeate production) at several planes throughout the channel height. At linear flow velocities (volumetric flow rate per cross-section of the flow channel considering the channel porosity, also described as crossflow velocities) used in practice (0.074 and 0.163 m∙s-1) the recorded flow was laminar with only slight unsteadiness in the upper velocity limit. At higher linear flow velocity (0.3 m∙s-1) the flow was observed to be unsteady and with recirculation zones. Measurements made at different locations in the flow cell exhibited very similar flow patterns within all feed spacer mesh elements, thus revealing the same hydrodynamic conditions along the length of the flow channel. Three-dimensional (3-D) computational fluid dynamics simulations were performed using the same geometries and flow parameters as the experiments, based on steady laminar flow assumption. The numerical results were in good agreement (0.85-0.95 Bray-Curtis similarity) with the measured flow fields at linear velocities of 0.074 and 0.163 m∙s-1, thus supporting the use of model-based studies in the optimization of feed spacer geometries and operational conditions of spiral wound membrane systems.

  4. Experimental and numerical characterization of the water flow in spacer-filled channels of spiral-wound membranes.

    Science.gov (United States)

    Bucs, Szilard S; Linares, Rodrigo Valladares; Marston, Jeremy O; Radu, Andrea I; Vrouwenvelder, Johannes S; Picioreanu, Cristian

    2015-12-15

    Micro-scale flow distribution in spacer-filled flow channels of spiral-wound membrane modules was determined with a particle image velocimetry system (PIV), aiming to elucidate the flow behaviour in spacer-filled flow channels. Two-dimensional water velocity fields were measured in a flow cell (representing the feed spacer-filled flow channel of a spiral wound reverse osmosis membrane module without permeate production) at several planes throughout the channel height. At linear flow velocities (volumetric flow rate per cross-section of the flow channel considering the channel porosity, also described as crossflow velocities) used in practice (0.074 and 0.163 m·s(-1)) the recorded flow was laminar with only slight unsteadiness in the upper velocity limit. At higher linear flow velocity (0.3 m·s(-1)) the flow was observed to be unsteady and with recirculation zones. Measurements made at different locations in the flow cell exhibited very similar flow patterns within all feed spacer mesh elements, thus revealing the same hydrodynamic conditions along the length of the flow channel. Three-dimensional (3-D) computational fluid dynamics simulations were performed using the same geometries and flow parameters as the experiments, based on steady laminar flow assumption. The numerical results were in good agreement (0.85-0.95 Bray-Curtis similarity) with the measured flow fields at linear velocities of 0.074 and 0.163 m·s(-1), thus supporting the use of model-based studies in the optimization of feed spacer geometries and operational conditions of spiral wound membrane systems. PMID:26433778

  5. CHIR99021 promotes self-renewal of mouse embryonic stem cells by modulation of protein-encoding gene and long intergenic non-coding RNA expression

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yongyan [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Ai, Zhiying [Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); College of Life Sciences, Northwest A and F University, Yangling 712100, Shaanxi (China); Yao, Kezhen [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Cao, Lixia; Du, Juan; Shi, Xiaoyan [Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); College of Life Sciences, Northwest A and F University, Yangling 712100, Shaanxi (China); Guo, Zekun, E-mail: gzk@nwsuaf.edu.cn [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Zhang, Yong, E-mail: zhylab@hotmail.com [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China)

    2013-10-15

    Embryonic stem cells (ESCs) can proliferate indefinitely in vitro and differentiate into cells of all three germ layers. These unique properties make them exceptionally valuable for drug discovery and regenerative medicine. However, the practical application of ESCs is limited because it is difficult to derive and culture ESCs. It has been demonstrated that CHIR99021 (CHIR) promotes self-renewal and enhances the derivation efficiency of mouse (m)ESCs. However, the downstream targets of CHIR are not fully understood. In this study, we identified CHIR-regulated genes in mESCs using microarray analysis. Our microarray data demonstrated that CHIR not only influenced the Wnt/β-catenin pathway by stabilizing β-catenin, but also modulated several other pluripotency-related signaling pathways such as TGF-β, Notch and MAPK signaling pathways. More detailed analysis demonstrated that CHIR inhibited Nodal signaling, while activating bone morphogenetic protein signaling in mESCs. In addition, we found that pluripotency-maintaining transcription factors were up-regulated by CHIR, while several developmental-related genes were down-regulated. Furthermore, we found that CHIR altered the expression of epigenetic regulatory genes and long intergenic non-coding RNAs. Quantitative real-time PCR results were consistent with microarray data, suggesting that CHIR alters the expression pattern of protein-encoding genes (especially transcription factors), epigenetic regulatory genes and non-coding RNAs to establish a relatively stable pluripotency-maintaining network. - Highlights: • Combined use of CHIR with LIF promotes self-renewal of J1 mESCs. • CHIR-regulated genes are involved in multiple pathways. • CHIR inhibits Nodal signaling and promotes Bmp4 expression to activate BMP signaling. • Expression of epigenetic regulatory genes and lincRNAs is altered by CHIR.

  6. Analysis of stress-induced duplex destabilization (SIDD properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe

    Directory of Open Access Journals (Sweden)

    Yadav Mukesh P

    2012-11-01

    Full Text Available Abstract Background Replication and transcription, the two key functions of DNA, require unwinding of the DNA double helix. It has been shown that replication origins in the budding yeast, Saccharomyces cerevisiae contain an easily unwound stretch of DNA. We have used a recently developed method for determining the locations and degrees of stress-induced duplex destabilization (SIDD for all the reported replication origins in the genome of the fission yeast, Schizosaccharomyces pombe. Results We have found that the origins are more susceptible to SIDD as compared to the non-origin intergenic regions (NOIRs and genes. SIDD analysis of many known origins in other eukaryotes suggests that SIDD is a common property of replication origins. Interestingly, the previously shown deletion-dependent changes in the activities of the origins of the ura4 origin region on chromosome 3 are paralleled by changes in SIDD properties, suggesting SIDD’s role in origin activity. SIDD profiling following in silico deletions of some origins suggests that many of the closely spaced S. pombe origins could be clusters of two or three weak origins, similar to the ura4 origin region. Conclusion SIDD appears to be a highly conserved, functionally important property of replication origins in S. pombe and other organisms. The distinctly low SIDD scores of origins and the long range effects of genetic alterations on SIDD properties provide a unique predictive potential to the SIDD analysis. This could be used in exploring different aspects of structural and functional organization of origins including interactions between closely spaced origins.

  7. Genotypic Characterization of Escherichia coli O157:H7 Isolates from Different Sources in the North-West Province, South Africa, Using Enterobacterial Repetitive Intergenic Consensus PCR Analysis

    Directory of Open Access Journals (Sweden)

    Collins Njie Ateba

    2014-05-01

    Full Text Available In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC polymerase chain reaction (PCR typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003 and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I–VIII were identified. Overall, the remarkable similarities (72% to 91% between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa.

  8. A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination

    Directory of Open Access Journals (Sweden)

    Holt Robert A

    2006-04-01

    Full Text Available Abstract Background Cre-loxP recombination refers to the process of site-specific recombination mediated by two loxP sequences and the Cre recombinase protein. Transgenic experiments exploit integrative recombination, where a donor plasmid carrying a loxP site and DNA of interest integrate into a recipient loxP site in a target genome. Unfortunately, integrative recombination is highly inefficient because the insert is flanked by two loxP sites, which themselves become targets for Cre and lead to subsequent excision of the insert. A small number of mutations have been discovered in parts of the loxP sequence, specifically the spacer and inverted repeat segments, that increase the efficiency of integrative recombination. In this study we introduce a high-throughput in vitro assay to rapidly detect novel loxP spacer mutants and describe the sequence characteristics of successful recombinants. Results We created synthetic loxP oligonucleotides that contained a combination of inverted repeat mutations (the lox66 and lox71 mutations and mutant spacer sequences, degenerate at 6 of the 8 positions. After in vitro Cre recombination, 3,124 recombinant clones were identified by sequencing. Included in this set were 31 unique, novel, self-recombining sequences. Using network visualization tools, we recognized 12 spacer sets with restricted promiscuity. We observed that increased guanine content at all spacer positions save for position 8 resulted in increased recombination. Interestingly, recombination between identical spacers was not preferred over non-identical spacers. We also identified a set of 16 pairs of loxP spacers that reacted at least twice with another spacer, but not themselves. Further, neither the wild-type P1 phage loxP sequence nor any of the known loxP spacer mutants appeared to be kinetically favoured by Cre recombinase. Conclusion This study approached loxP spacer mutant screening in an unbiased manner, assuming nothing about candidate

  9. Intensity Modulated Proton and Photon Therapy for Early Prostate Cancer With or Without Transperineal Injection of a Polyethylen Glycol Spacer: A Treatment Planning Comparison Study

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Damien C., E-mail: damien.weber@unige.ch [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Zilli, Thomas [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Vallee, Jean Paul [Department of Diagnostic Radiology, Geneva University Hospital, Geneva (Switzerland); Rouzaud, Michel; Miralbell, Raymond [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Cozzi, Luca [Oncology Institute of Southern Switzerland, Medical Physics Unit, Bellinzona (Switzerland)

    2012-11-01

    Purpose: Rectal toxicity is a serious adverse effect in early-stage prostate cancer patients treated with curative radiation therapy (RT). Injecting a spacer between Denonvilliers' fascia increases the distance between the prostate and the anterior rectal wall and may thus decrease the rectal radiation-induced toxicity. We assessed the dosimetric impact of this spacer with advanced delivery RT techniques, including intensity modulated RT (IMRT), volumetric modulated arc therapy (VMAT), and intensity modulated proton beam RT (IMPT). Methods and Materials: Eight prostate cancer patients were simulated for RT with or without spacer. Plans were computed for IMRT, VMAT, and IMPT using the Eclipse treatment planning system using both computed tomography spacer+ and spacer- data sets. Prostate {+-} seminal vesicle planning target volume [PTV] and organs at risk (OARs) dose-volume histograms were calculated. The results were analyzed using dose and volume metrics for comparative planning. Results: Regardless of the radiation technique, spacer injection decreased significantly the rectal dose in the 60- to 70-Gy range. Mean V{sub 70Gy} and V{sub 60Gy} with IMRT, VMAT, and IMPT planning were 5.3 {+-} 3.3%/13.9 {+-} 10.0%, 3.9 {+-} 3.2%/9.7 {+-} 5.7%, and 5.0 {+-} 3.5%/9.5 {+-} 4.7% after spacer injection. Before spacer administration, the corresponding values were 9.8 {+-} 5.4% (P=.012)/24.8 {+-} 7.8% (P=.012), 10.1 {+-} 3.0% (P=.002)/17.9 {+-} 3.9% (P=.003), and 9.7 {+-} 2.6% (P=.003)/14.7% {+-} 2.7% (P=.003). Importantly, spacer injection usually improved the PTV coverage for IMRT. With this technique, mean V{sub 70.2Gy} (P=.07) and V{sub 74.1Gy} (P=0.03) were 100 {+-} 0% to 99.8 {+-} 0.2% and 99.1 {+-} 1.2% to 95.8 {+-} 4.6% with and without Spacer, respectively. As a result of spacer injection, bladder doses were usually higher but not significantly so. Only IMPT managed to decrease the rectal dose after spacer injection for all dose levels, generally with no

  10. Cladistic Analysis of Sequences of Chloroplast rbcL Gene and trnL-trnF Intergenic Spacer in Taxaceae and Related Taxa%红豆杉科及相关类群叶绿体rbcL基因与trnL-trnF间隔区序列的分支分析

    Institute of Scientific and Technical Information of China (English)

    王艇; 苏应娟; 郑博; 李雪雁

    2002-01-01

    运用对PCR产物克隆后测序和对PCR产物直接测序的方法对红豆杉科、三尖杉科和罗汉松科16种植物的叶绿体rbcL基因和trnL-trnF基因间隔区序列进行了测定.选用PAUP 软件分别对rbcL基因、trnL-trnF间隔区和rbcL基因-trnL-trnF间隔区联合数据矩阵进行分支分析,结果显示:①穗花杉属以置于红豆杉科内为宜,将穗花杉属独立成科的意见未得到支持;②三尖杉属内篦子三尖杉地位特殊,赞同成立篦子三尖杉组;③罗汉松科属单系群,竹柏类应归属罗汉松科,不同意将其从该科中分离出来成立新科竹柏科;④不支持红豆杉科独立成目,其单生单轴球果可能是由复合双轴球果减化而来.

  11. Interspinous spacer versus traditional decompressive surgery for lumbar spinal stenosis: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Ai-Min Wu

    Full Text Available BACKGROUND: Dynamic interspinous spacers, such as X-stop, Coflex, DIAM, and Aperius, are widely used for the treatment of lumbar spinal stenosis. However, controversy remains as to whether dynamic interspinous spacer use is superior to traditional decompressive surgery. METHODS: Medline, Embase, Cochrane Library, and the Cochrane Controlled Trials Register were searched during August 2013. A track search was performed on February 27, 2014. Study was included in this review if it was: (1 a randomized controlled trial (RCT or non-randomized prospective comparison study, (2 comparing the clinical outcomes for interspinous spacer use versus traditional decompressive surgery, (3 in a minimum of 30 patients, (4 with a follow-up duration of at least 12 months. RESULTS: Two RCTs and three non-randomized prospective studies were included, with 204 patients in the interspinous spacer (IS group and 217 patients in the traditional decompressive surgery (TDS group. Pooled analysis showed no significant difference between the IS and TDS groups for low back pain (WMD: 1.2; 95% CI: -10.12, 12.53; P = 0.03; I2 = 66%, leg pain (WMD: 7.12; 95% CI: -3.88, 18.12; P = 0.02; I2 = 70%, ODI (WMD: 6.88; 95% CI: -14.92, 28.68; P = 0.03; I2 = 79%, RDQ (WMD: -1.30, 95% CI: -3.07, 0.47; P = 0.00; I2 = 0%, or complications (RR: 1.39; 95% CI: 0.61, 3.14; P = 0.23; I2 = 28%. The TDS group had a significantly lower incidence of reoperation (RR: 3.34; 95% CI: 1.77, 6.31; P = 0.60; I2 = 0%. CONCLUSION: Although patients may obtain some benefits from interspinous spacers implanted through a minimally invasive technique, interspinous spacer use is associated with a higher incidence of reoperation and higher cost. The indications, risks, and benefits of using an interspinous process device should be carefully considered before surgery.

  12. Effects of spacer parameters, modified monolayers, and patterned substrate on the capture efficiency of Escherichia coli-antibody based biosensing matrix

    Science.gov (United States)

    Cao, Ting

    2007-12-01

    To overcome the problem of losing bioactivity in covalent coupling in chemical sensor, a potential approach is to employ a long chain spacer to immobilize the antibody indirectly while maintaining separation of the biomolecule from the substrate. In this study, Poly (ethylene glycol) (PEG) spacers were employed for tethering E.Coli K99 pilus antibody to silicon wafer surfaces for the purpose of increasing the flexibility of antibody as well as reducing the steric hindrance. To illustrate the effect of spacer length, a series of spacer lengths were used to covalently attach the antibodies to silicon surfaces. XPS and AFM were used to characterize the surface morphology and chemical composition at each reaction step. The effect of spacer length in improving the specificity of immobilized antibody and the recognition process for bacteria-antibody was investigated by attaching E.Coli on the end of an AFM tip. Distribution of unbinding force and rupture distance from the force-distance curved obtained by AFM showed that the introduction of PEG spacer facilitates bacterial recognition which can improve the detected specific interaction up to 90%. J600 exhibited better flexibility in overcoming the steric hindrance experienced with direct immobilization than other spacer lengths. Moreover, binding efficiency, rupture distance and force distribution of bacteria-antibody pairs can be elucidated with AFM for measurement.

  13. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer.

    Science.gov (United States)

    Richter, Corinna; Dy, Ron L; McKenzie, Rebecca E; Watson, Bridget N J; Taylor, Corinda; Chang, James T; McNeil, Matthew B; Staals, Raymond H J; Fineran, Peter C

    2014-07-01

    Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼ 350 new spacers acquired in priming events and identified a 5'-protospacer-GG-3' protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2-3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.

  14. Purging of a multilayer insulation with dacron tuft spacer by gas diffusion

    Science.gov (United States)

    Sumner, I. E.; Fisk, W. J.

    1976-01-01

    The time and purge gas usage required to purge a multilayer insulation (MLI) panel with gaseous helium by means of gas diffusion to obtain a condensable gas (nitrogen) concentration of less than 1 percent within the panel are stipulated. Two different, flat, rectangular MLI panels, one incorporating a butt joint, were constructed of of 11 double-aluminized Mylar (DAM) radiation shields separated by Dacron tuft spacers. The DAM/Dacron tuft concept is known commercially as Superfloc. The nitrogen gas concentration as a function of time within the MLI panel could be adequately predicted by using a simple, one dimensional gas diffusion model in which the boundary conditions at the edge of the MLI panel were time dependent. The time and purge gas usage required to achieve 1 percent nitrogen gas concentration within the MLI panel varied from 208 to 86 minutes and 34.1 to 56.5 MLI panel purge volumes, respectively, for gaseous helium purge rates from 10 to 40 MLI panel volumes per hour.

  15. Development and Investigation of Evacuated Windows Based on Monolithic Silica Xerogel Spacers

    DEFF Research Database (Denmark)

    Schultz, Jørgen Munthe; Svendsen, Sv Aa Højgaard

    on Monolithic Silica Aerogel Spacers" contract JOU2-CT92-0192. Low density monolithic silica xerogel and monolithic silica aerogel are almost identical, but while the aerogel requires a supercritical drying process, xerogels is dried at atmospheric pressure. Ambient pressure drying is possible due to a chemical...... strengthening of the material prior to drying. This process results in an increased density of xerogels compared to aerogels which leads to a slightly higher thermal conductivity with typical values of 0.030 W/(m K) measured in air at atmospheric pressure. If evacuated below 50-100 hPa the thermal conductivity...... at the cold side and intolerable long term creep.A small scale laboratory assembled glazing (0.15 × 0.15 m2, density = 490 kg/m3, thickness = 10 mm) has been made. The development of a rim seal based on a laminated plastic foil has been carried out in close co-operation with the aerogel project due...

  16. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    Science.gov (United States)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  17. Determination of internal transcribed spacer regions (ITS) in Trichomonas vaginalis isolates and differentiation among Trichomonas species.

    Science.gov (United States)

    Ibáñez-Escribano, Alexandra; Nogal-Ruiz, Juan José; Arán, Vicente J; Escario, José Antonio; Gómez-Barrio, Alicia; Alderete, J F

    2014-04-01

    The nucleotide sequence of the 5.8S rRNA gene and the flanked internal transcribed spacer (ITS) regions of six Trichomonas vaginalis isolates with different metronidazole sensitivity and geographic origin were genotyped. A multiple sequence alignment was performed with different sequences of other isolates available at the GenBank/EMBL/DDBJ databases, which revealed 5 different sequence patterns. Although a stable mutation in position 66 of the ITS1 (C66T) was observed in 26% (9/34) of the T. vaginalis sequences analyzed, there was 99.7% ITS nucleotide sequence identity among isolates for this sequence. The nucleotide sequence variation among other species of the genus Trichomonas ranged from 3.4% to 9.1%. Surprisingly, the % identity between T. vaginalis and Pentatrichomonas hominis was ~83%. There was >40% divergence in the ITS sequence between T. vaginalis and Tritrichomonas spp., including Tritrichomonas augusta, Tritrichomonas muris, and Tritrichomonas nonconforma and with Tetratrichomonas prowazeki. Dendrograms grouped the trichomonadid sequences in robust clades according to their genera. The absence of nucleotide divergence in the hypervariable ITS regions between T. vaginalis isolates suggests the early divergence of the parasite. Importantly, these data show this ITS1-5.8S rRNA-ITS2 region suitable for inter-species differentiation.

  18. Fuel tube spacer-pad spot-weld quality estimation using guided ultrasonic waves

    Science.gov (United States)

    Suresh, P.; Balasubramaniam, Krishnan

    2012-05-01

    A guided wave technique for quality analysis of the spot weld spacer pad on the Pressurized Heavy Water Reactor (PHWR) fuel tubes using the strength of signal energy that is reflected from the welds is discussed here. The development of a real-time ultrasonic system for spot weld quality monitoring for the fuel tube, potentially allows for the elimination of expensive destructive testing, reduce the amount of time-consuming off-line ultrasonic inspections and ensures quality and reliability during operation. Due to the rather small spot size of these welds (less than 2 mm in diameter), the current methods such as ultrasonic scanning were found to be difficult to implement, particularly under production conditions Hence, a guided wave method was explored in this work that has the potential to be implemented in the welding. A fixture was developed in order to generate L (0, 1) mode in the wall of the tube and travelling along the length of the tube. Couplant was not used and instead uniform pressure was applied to ensure the coupling of the wave into the tube. The experimentally obtained guided wave reflected signals were correlated destructive assays. The main goal of such testing systems is to reduce operational time and provide reliable means of quality inspection.

  19. Molecular variation of Sporisorium scitamineum in Mainland China revealed by internal transcribed spacers.

    Science.gov (United States)

    Zhang, Y Y; Huang, N; Xiao, X H; Huang, L; Liu, F; Su, W H; Que, Y X

    2015-01-01

    Sugarcane smut caused by the fungus Sporisorium scitamineum is a worldwide disease and also one of the most prevalent diseases in sugarcane production in mainland China. To study molecular variation in S. scitamineum, 23 S. scitamineum isolates from the 6 primary sugar-cane production areas in mainland, China (Guangxi, Yunnan, Guangdong, Hainan, Fujian, and Jiangxi Provinces), were assessed using internal transcribed spacer (ITS) methods. The results of ITS sequence analysis showed that the organisms can be defined at the genus level, including Ustilago and Sporisorium, and can also differentiate between closely related species. This method was not suitable for phylogenetic relationship analysis of different S. scitamineum isolates and could not provide support regarding their race ascription at the molecular level. The results of the present study will be useful for studies examining the molecular diversity of S. scitamineum and for establishing a genetic foundation for their pathogenicity differentiation and new race detection. In addition, our results can provide useful information for the pathogen selection principle in sugarcane smut resistance breeding and variety distribution. PMID:26214470

  20. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA.

    Science.gov (United States)

    Sun, Y; Skinner, D Z; Liang, G H; Hulbert, S H

    1994-09-01

    The phylogenetic relationships of the genus Sorghum and related genera were studied by sequencing the nuclear ribosomal DNA (rDNA) internal transcribed spacer region (ITS). DNA was extracted from 15 Sorghum accessions, including one accession from each of the sections Chaetosorghum and Heterosorghum, four accessions from Parasorghum, two accessions from Stiposorghum, and seven representatives from three species of the section Sorghum (one accession from each of S. propinquum and S. halepense, and five races of S. bicolor). The maize (Zea mays) line, H95, and an accession from Cleistachne sorghoides were also included in the study. Variable nucleotides were used to construct a strict consensus phylogenetic tree. The analyses indicate that S. propinquum, S. halepense and S. bicolor subsp. arundinaceum race aethiopicum may be the closest wild relatives of cultivated sorghum; Sorghum nitidum may be the closest 2n=10 relative to S. bicolor, the sections Chaetosorghum and Heterosorghum appear closely related to each other and more closely related to the section Sorghum than Parasorghum; and the section Parasorghum is not monophyletic. The results also indicate that the genus Sorghum is a very ancient and diverse group.

  1. Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier

    Science.gov (United States)

    Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

    2003-03-01

    Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  2. The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports.

    Science.gov (United States)

    Salvio, Riccardo

    2015-07-27

    Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.

  3. Phylogenetic analysis of Pectinidae (Bivalvia) based on the ribosomal DNA internal transcribed spacer region

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The ribosomal DNA internal transcribed spacer (ITS) region is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, the molecular phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) was performed using the nucleotide sequences of the nuclear ITS region in nine species of this family. The sequences were obtained from the scallop species Argopecten irradians, Mizuhopecten yessoensis, Amusium pleuronectes and Mimachlamys nobilis, and compared with the published sequences of Aequipecten opercularis, Chlamys farreri, C. distorta, M. varia, Pecten maximus, and an outgroup species Perna viridis. The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods. Phylogenetic analysis based on ITS1, ITS2, or their combination always yielded trees of similar topology. The results support the morphological classifications of bivalve and are nearly consistent with classification of two subfamilies (Chlamydinae and Pectininae) formulated by Waller. However, A. irradians, together with A. opercularis made up of genera Amusium, evidences that they may belong to the subfamily Pectinidae. The data are incompatible with the conclusion of Waller who placed them in Chlamydinae by morphological characteristics. These results provide new insights into the evolutionary relationships among scallop species and contribute to the improvement of existing classification systems.

  4. Definition of Eight Mulberry Species in the Genus Morus by Internal Transcribed Spacer-Based Phylogeny.

    Directory of Open Access Journals (Sweden)

    Qiwei Zeng

    Full Text Available Mulberry, belonging to the order Rosales, family Moraceae, and genus Morus, has received attention because of both its economic and medicinal value, as well as for its important ecological function. The genus Morus has a worldwide distribution, however, its taxonomy remains complex and disputed. Many studies have attempted to classify Morus species, resulting in varied numbers of designated Morus spp. To address this issue, we used information from internal transcribed spacer (ITS genetic sequences to study the taxonomy of all the members of generally accepted genus Morus. We found that intraspecific 5.8S rRNA sequences were identical but that interspecific 5.8S sequences were diverse. M. alba and M. notabilis showed the shortest (215 bp and the longest (233 bp ITS1 sequence length, respectively. With the completion of the mulberry genome, we could identify single nucleotide polymorphisms within the ITS locus in the M. notabilis genome. From reconstruction of a phylogenetic tree based on the complete ITS data, we propose that the Morus genus should be classified into eight species, including M. alba, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. insignis, M. rubra, and M. mesozygia. Furthermore, the classification of the ITS sequences of known interspecific hybrid clones into both paternal and maternal clades indicated that ITS variation was sufficient to distinguish interspecific hybrids in the genus Morus.

  5. Definition of Eight Mulberry Species in the Genus Morus by Internal Transcribed Spacer-Based Phylogeny.

    Science.gov (United States)

    Zeng, Qiwei; Chen, Hongyu; Zhang, Chao; Han, Minjing; Li, Tian; Qi, Xiwu; Xiang, Zhonghuai; He, Ningjia

    2015-01-01

    Mulberry, belonging to the order Rosales, family Moraceae, and genus Morus, has received attention because of both its economic and medicinal value, as well as for its important ecological function. The genus Morus has a worldwide distribution, however, its taxonomy remains complex and disputed. Many studies have attempted to classify Morus species, resulting in varied numbers of designated Morus spp. To address this issue, we used information from internal transcribed spacer (ITS) genetic sequences to study the taxonomy of all the members of generally accepted genus Morus. We found that intraspecific 5.8S rRNA sequences were identical but that interspecific 5.8S sequences were diverse. M. alba and M. notabilis showed the shortest (215 bp) and the longest (233 bp) ITS1 sequence length, respectively. With the completion of the mulberry genome, we could identify single nucleotide polymorphisms within the ITS locus in the M. notabilis genome. From reconstruction of a phylogenetic tree based on the complete ITS data, we propose that the Morus genus should be classified into eight species, including M. alba, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. insignis, M. rubra, and M. mesozygia. Furthermore, the classification of the ITS sequences of known interspecific hybrid clones into both paternal and maternal clades indicated that ITS variation was sufficient to distinguish interspecific hybrids in the genus Morus.

  6. Internal transcribed spacer 2 barcode: A good tool for identifying Acanthopanacis cortex

    Directory of Open Access Journals (Sweden)

    Sha eZhao

    2015-10-01

    Full Text Available Acanthopanacis cortex has been used in clinical applications for a long time. Considering some historical and geographical factors, Acanthopanacis cortex is easily confused with other herbs in medicine markets, thereby causing potential safety issues. In this study, we used the internal transcribed spacer 2 (ITS2 barcode to identify 69 samples belonging to six species, including Acanthopanacis cortex and its adulterants. The nearest distance, single-nucleotide polymorphisms (SNPs, and neighbor-joining (NJ tree methods were used to evaluate the identification ability of the ITS2 barcode. According to the kimura-2-parameter model, the intraspecific distance of Eleutherococcus nodiflorus ITS2 sequences ranged from 0 to 0.0132. The minimum interspecific distance between E. nodiflorus and E. giraldii was 0.0221, which was larger than the maximum intraspecific distance of E. nodiflorus. Three stable SNPs in ITS2 can be used to distinguish Acanthopanacis cortex and its closely related species. The NJ tree indicated that the Acanthopanacis cortex samples clustered into one clade, which can be distinguished clearly from the adulterants of this herb. A secondary structure of ITS2 provided another dimensionality to identify species. In conclusion, the ITS2 barcode effectively identifies Acanthopanacis cortex, and DNA barcoding is a convenient tool for medicine market supervision.

  7. The homology analysis of internal transcribed spacer sequence of ribosomal DNA in common dermatophytes

    Institute of Scientific and Technical Information of China (English)

    QIANG WANG; ZHAO HUI JI; HOU MIN LI; LI JUAN ZHANG; WEI LIU; ZHE WAN; XIAO HONG WANG; DUAN LI WANG; RUO YU LI

    2006-01-01

    In order to analyze the sequences of the internal transcribed spacer (ITS) including the 5.8 S ribosomal DNA (rDNA) of common dermatophytes, so as to obtain a rapid and accurate method to identify the species of dermatophytes and to establish the phylogenetic tree of these species to understand their relationship, 16 strains of dermatophytes were collected and preliminarily identified by morphological characteristics. General primers for fungi ITS1 and ITS4 were used to amplify the ITS rDNA of each strains with PCR. The PCR products after purification were sequenced directly and were analyzed through internet. In the results, 11 strains were identified by means of morphological features, among which 5 strains were Trichophyton, 5 strains were Microsporum and 1 was Epidermophyton,which was consistent with the results by molecular biology. In the 5 unidentifiable strains, 1 strain was proved to be Chrysosporium by molecular biology. These strains studied could be divided into 3 different classes as indicated in the analysis of the phylogenetic tree of the sequences in ITS, which were quite different from those of morphological classification. It is evident from the above observations that the molecular method of analysis on the ITS sequences is a rapid, highly sensitive and accurate approach for the detection of dematophyte species, however, it still exhibits some limitations needing the supplementation with morphological identification.

  8. Utilizing insulating nanoparticles as the spacer in laminated flexible polymer solar cells for improved mechanical stability.

    Science.gov (United States)

    Lu, Yunzhang; Alexander, Clement; Xiao, Zhengguo; Yuan, Yongbo; Zhang, Runyu; Huang, Jinsong

    2012-08-31

    Roll-to-roll lamination is one promising technique to produce large-area organic electronic devices such as solar cells with a large through output. One challenge in this process is the frequent electric point shorting of the cathode and anode by the excess or concentrated applied stress from many possible sources. In this paper, we report a method to avoid electric point shorting by incorporating insulating and hard barium titanate (BaTiO(3)) nanoparticles (NPs) into the active layer to work as a spacer. It has been demonstrated that the incorporated BaTiO(3) NPs in poly(3-hexylthiophene):[6,6]-phenyl-c-61-butyric acid methyl ester (P3HT:PCBM) bulk heterojunction solar cells cause no deleterious effect to the power conversion process of this type of solar cell. The resulting laminated devices with NPs in the active layer display the same efficiency as the devices without NPs, while the laminated devices with NPs can sustain a ten times higher lamination stress of over 6 MPa. The flexible polymer solar cell device with incorporated NPs shows a much smaller survivable curvature radius of 4 mm, while a regular flexible device can only sustain a bending curvature radius of 8 mm before fracture. PMID:22886059

  9. Effect of PEG biofunctional spacers and TAT peptide on dsRNA loading on gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, Vanesa; Conde, Joao; Hernandez, Yulan [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain); Baptista, Pedro V. [Universidade Nova de Lisboa, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Centro de Investigacao em Genetica Molecular Humana (Portugal); Ibarra, M. R.; Fuente, Jesus M. de la, E-mail: jmfuente@unizar.es [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain)

    2012-06-15

    The surface chemistry of gold nanoparticles (AuNPs) plays a critical role in the self-assembly of thiolated molecules and in retaining the biological function of the conjugated biomolecules. According to the well-established gold-thiol interaction the undefined ionic species on citrate-reduced gold nanoparticle surface can be replaced with a self-assembled monolayer of certain thiolate derivatives and other biomolecules. Understanding the effect of such derivatives in the functionalization of several types of biomolecules, such as PEGs, peptides or nucleic acids, has become a significant challenge. Here, an approach to attach specific biomolecules to the AuNPs ({approx}14 nm) surface is presented together with a study of their effect in the functionalization with other specific derivatives. The effect of biofunctional spacers such as thiolated poly(ethylene glycol) (PEG) chains and a positive peptide, TAT, in dsRNA loading on AuNPs is reported. Based on the obtained data, we hypothesize that loading of oligonucleotides onto the AuNP surface may be controlled by ionic and weak interactions positioning the entry of the oligo through the PEG layer. We demonstrate that there is a synergistic effect of the TAT peptide and PEG chains with specific functional groups on the enhancement of dsRNA loading onto AuNPs.

  10. Acute toxicity after a diverting stoma and spacer prior to chemoradiation in locally advanced rectal cancer

    International Nuclear Information System (INIS)

    Background and purpose: Chemoradiotherapy (CRT) followed by surgery is the standard of care for locally advanced rectal cancer (LARC). For grade ⩾3 acute diarrhea there is a relationship between dose and irradiated small bowel volume. The aim of this study was to evaluate whether combined placement of a diverting stoma and sigmoid spacer (DSSS) led to reduced irradiated small bowel volume and less grade ⩾3 acute diarrhea in the treatment of LARC. Materials/methods: Between 2003 and 2010, 54 of 189 LARC patients treated with CRT in two institutions had a DSSS prior to CRT. Data on patient and treatment characteristics and outcomes were collected retrospectively. Delineation of small bowel was performed with planning CT-scans. CTCAE version 4.0 was used for acute toxicity. Results: Patients with a DSSS had significantly less small bowel volume irradiated up to doses of 20 Gy. This difference was not observed for the higher dose levels. CRT induced grade ⩾3 acute diarrhea was not different between the two groups (8.3% vs. 12.8%; p = 0.41). Conclusion: DSSS is not clearly beneficial to reduce grade ⩾3 acute diarrhea, and it must be considered whether placement of a DSSS is justified for this purpose

  11. Exchange coupling and magnetoresistance in CoFe/NiCu/CoFe spin valves near the Curie point of the spacer

    Science.gov (United States)

    Andersson, S.; Korenivski, V.

    2010-05-01

    Thermal control of exchange coupling between two strongly ferromagnetic layers through a weakly ferromagnetic Ni-Cu spacer and the associated magnetoresistance is investigated. The spacer, having a Curie point slightly above room temperature, can be cycled between its paramagnetic and ferromagnetic states by varying the temperature externally or using joule heating. It is shown that the giant magnetoresistance vanishes due to a strong reduction in the mean free path in the spacer at above ˜30% Ni concentration—before the onset of ferromagnetism. Finally, a device is proposed which combines thermally controlled exchange coupling and large magnetoresistance by separating the switching and the readout elements.

  12. A More Uniform Electric Field Distribution on Surge Arresters through the Optimal Design of Spacer and Fiber Glass Layer

    Directory of Open Access Journals (Sweden)

    M.R. Aghaebrahimi

    2013-04-01

    Full Text Available In this study, the optimal design of spacers and fiber glass layer of a metal oxide surge arrester is presented in order to achieve a more uniform electric field distribution, inside and outside the arrester. This is done by using intelligent algorithms and numerical analysis, i.e., Finite Element Method (FEM. The introduced method can be used in order to determine the optimal dimensions of spacers and fiber glass layer so that the electric field distribution is optimized and the lifetime of highly stressed ZnO blocks in the vicinity of HV electrode is increased. In order to verify the results, Differential Evolution (DE and Particle Swarm Optimization (PSO algorithms are used.

  13. Dependence of surface distribution of self-assembled InSb nanodots on surface morphology and spacer layer thickness

    Energy Technology Data Exchange (ETDEWEB)

    Godbole, M., E-mail: mohit.godbole@nmmu.ac.za [Department of Physics, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth 6031 (South Africa); Olivier, E.J. [Department of Physics, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth 6031 (South Africa); Coetsee, E.; Swart, H.C. [Department of Physics, University of the Free State, PO Box 339, Bloemfontein 9300 (South Africa); Neethling, J.H.; Botha, J.R. [Department of Physics, Nelson Mandela Metropolitan University, PO Box 77000, Port Elizabeth 6031 (South Africa)

    2012-05-15

    Self-assembled InSb nanodots (NDs) were grown on a GaSb (1 0 0) substrate using metal-organic vapour phase epitaxy (MOVPE). The effects of etching depth of the substrate and thickness of the GaSb buffer layer on the density and size distribution of single and double layer dots were studied for detector applications. The etch depth of the substrate was varied up to 30 {mu}m. In this particular study, the dots were grown at 450 Degree-Sign C and the GaSb spacer thickness was varied between 50 nm and 200 nm. The optimum substrate etch depth was found to be 30 {mu}m while the best spacer thickness was found to be 200 nm.

  14. Status of the Space-Rated Lithium-Ion Battery Advanced Development Project in Support of the Exploration Vision

    Science.gov (United States)

    Miller, Thomas

    2007-01-01

    The NASA Glenn Research Center (GRC), along with the Goddard Space Flight Center (GSFC), Jet Propulsion Laboratory (JPL), Johnson Space Center (JSC), Marshall Space Flight Center (MSFC), and industry partners, is leading a space-rated lithium-ion advanced development battery effort to support the vision for Exploration. This effort addresses the lithium-ion battery portion of the Energy Storage Project under the Exploration Technology Development Program. Key discussions focus on the lithium-ion cell component development activities, a common lithium-ion battery module, test and demonstration of charge/discharge cycle life performance and safety characterization. A review of the space-rated lithium-ion battery project will be presented highlighting the technical accomplishments during the past year.

  15. Dependence of surface distribution of self-assembled InSb nanodots on surface morphology and spacer layer thickness

    International Nuclear Information System (INIS)

    Self-assembled InSb nanodots (NDs) were grown on a GaSb (1 0 0) substrate using metal-organic vapour phase epitaxy (MOVPE). The effects of etching depth of the substrate and thickness of the GaSb buffer layer on the density and size distribution of single and double layer dots were studied for detector applications. The etch depth of the substrate was varied up to 30 μm. In this particular study, the dots were grown at 450 °C and the GaSb spacer thickness was varied between 50 nm and 200 nm. The optimum substrate etch depth was found to be 30 μm while the best spacer thickness was found to be 200 nm.

  16. Distinguishing plasmonic absorption modes by virtue of inversed architectures with tunable atomic-layer-deposited spacer layer

    International Nuclear Information System (INIS)

    We demonstrated the distinguishing between plasmonic absorption modes by exploiting an inversed architecture with tunable atomic-layer-deposited dielectric spacer layer. The dielectric spacer layer was manipulated between the bottom metal–nanoparticle monolayer and the upper metal film to inspect the contributions of metal nanoparticles and dielectric film in a step-by-step manner. The experimental and simulated differences between the two peak absorption positions (Δf) and between the corresponding half width at half maxima (Δw) confirmed the evolutions of gap plasmon and interference-enhanced local surface plasmon resonance absorption modes in the plasmonic metamaterial absorbers (PMAs), which were useful for understanding the underlying mechanism of amorphous PMAs. (paper)

  17. Molecular authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii by ITS and 5S rRNA spacer sequencing.

    Science.gov (United States)

    Sun, Ye; Shaw, Pang-Chui; Fung, Kwok-Pui

    2007-01-01

    In the present study, we examined nuclear DNA sequences in an attempt to reveal the relationships between Pueraria lobata (Willd). Ohwi, P. thomsonii Benth., and P. montana (Lour.) Merr. We found that internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA are highly divergent in P. lobata and P. thomsonii, and four types of ITS with different length are found in the two species. On the other hand, DNA sequences of 5S rRNA gene spacer are highly conserved across multiple copies in P. lobata and P. thomsonii, they could be used to identify P. lobata, P. thomsonii, and P. montana of this complex, and may serve as a useful tool in medical authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii. PMID:17202681

  18. The Construction of Chimeric T-Cell Receptor with Spacer Base of Modeling Study of VHH and MUC1 Interaction

    OpenAIRE

    Nazanin Pirooznia; Sadegh Hasannia; Majid Taghdir; Fatemeh Rahbarizadeh; Morteza Eskandani

    2011-01-01

    Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, ...

  19. Process development for the manufacturing of flat knitted innovative 3D spacer fabrics for high performance composite applications

    OpenAIRE

    Abounaim, Md.

    2011-01-01

    Innovative 3D spacer fabrics made from individual planes and connecting layers present great potential as complexly shaped textile preforms in lightweight composite applications. As one of the most flexible textile manufacturing methods, flat knitting enables the production of intricately shaped textile structures. The major advantages coupled with flat knitting techniques include the ability to produce multi-layer reinforcements, a diminishing waste, reducing production time and near-net sha...

  20. Impact of biofilm accumulation on transmembrane and feed channel pressure drop: Effects of crossflow velocity, feed spacer and biodegradable nutrient

    KAUST Repository

    Dreszer, C.

    2014-03-01

    Biofilm formation causes performance loss in spiral-wound membrane systems. In this study a microfiltration membrane was used in experiments to simulate fouling in spiral-wound reverse osmosis (RO) and nanofiltration (NF) membrane modules without the influence of concentration polarization. The resistance of a microfiltration membrane is much lower than the intrinsic biofilm resistance, enabling the detection of biofilm accumulation in an early stage. The impact of biofilm accumulation on the transmembrane (biofilm) resistance and feed channel pressure drop as a function of the crossflow velocity (0.05 and 0.20ms-1) and feed spacer presence was studied in transparent membrane biofouling monitors operated at a permeate flux of 20Lm-2h-1. As biodegradable nutrient, acetate was dosed to the feed water (1.0 and 0.25mgL-1 carbon) to enhance biofilm accumulation in the monitors. The studies showed that biofilm formation caused an increased transmembrane resistance and feed channel pressure drop. The effect was strongest at the highest crossflow velocity (0.2ms-1) and in the presence of a feed spacer. Simulating conditions as currently applied in nanofiltration and reverse osmosis installations (crossflow velocity 0.2ms-1 and standard feed spacer) showed that the impact of biofilm formation on performance, in terms of transmembrane and feed channel pressure drop, was strong. This emphasized the importance of hydrodynamics and feed spacer design. Biomass accumulation was related to the nutrient load (nutrient concentration and linear flow velocity). Reducing the nutrient concentration of the feed water enabled the application of higher crossflow velocities. Pretreatment to remove biodegradable nutrient and removal of biomass from the membrane elements played an important part to prevent or restrict biofouling. © 2013 Elsevier Ltd.

  1. RELAP5 model to simulate the thermal-hydraulic effects of grid spacers and cladding rupture during reflood

    Energy Technology Data Exchange (ETDEWEB)

    Nithianandan, C.K.; Klingenfus, J.A.; Reilly, S.S. [B& W Nuclear Technologies, Lynchburg, VA (United States)

    1995-09-01

    Droplet breakup at spacer grids and a cladding swelled and ruptured locations plays an important role in the cooling of nuclear fuel rods during the reflooding period of a loss-of-coolant accident (LOCA) in a pressurized water reactor (PWR). During the reflood phase, a spacer grid affects the thermal-hydraulic system behavior through increased turbulence, droplet breakup due to impact on grid straps, grid rewetting, and liquid holdup due to grid form losses. Recently, models to simulate spacer grid effects and blockage and rupture effects on system thermal hydraulics were added to the B&W Nuclear Technologies (BWNT) version of the RELAP5/MOD2 computer code. Several FLECHT-SEASET forced reflood tests, CCTF Tests C1-19 and C2-6, SCTF Test S3-15, and G2 Test 561 were simulated using RELAP5/MOD2-B&W to verify the applicability of the model at the cladding swelled and rupture locations. The results demonstrate the importance of modeling the thermal-hydraulic effects due to grids, and clad swelling and rupture to correctly predict the clad temperature response during the reflood phase of large break LOCA. The RELAP5 models and the test results are described in this paper.

  2. Biodegradability and aquatic toxicity of quaternary ammonium-based gemini surfactants: Effect of the spacer on their ecological properties.

    Science.gov (United States)

    Garcia, M Teresa; Kaczerewska, Olga; Ribosa, Isabel; Brycki, Bogumił; Materna, Paulina; Drgas, Małgorzata

    2016-07-01

    Aerobic biodegradability and aquatic toxicity of five types of quaternary ammonium-based gemini surfactants have been examined. The effect of the spacer structure and the head group polarity on the ecological properties of a series of dimeric dodecyl ammonium surfactants has been investigated. Standard tests for ready biodegradability assessment (OECD 310) were conducted for C12 alkyl chain gemini surfactants containing oxygen, nitrogen or a benzene ring in the spacer linkage and/or a hydroxyethyl group attached to the nitrogen atom of the head groups. According to the results obtained, the gemini surfactants examined cannot be considered as readily biodegradable compounds. The negligible biotransformation of the gemini surfactants under the standard biodegradation test conditions was found to be due to their toxic effects on the microbial population responsible for aerobic biodegradation. Aquatic toxicity of gemini surfactants was evaluated against Daphnia magna. The acute toxicity values to Daphnia magna, IC50 at 48 h exposure, ranged from 0.6 to 1 mg/L. On the basis of these values, the gemini surfactants tested should be classified as toxic or very toxic to the aquatic environment. However, the dimeric quaternary ammonium-based surfactants examined result to be less toxic than their corresponding monomeric analogs. Nevertheless the aquatic toxicity of these gemini surfactants can be reduced by increasing the molecule hydrophilicity by adding a heteroatom to the spacer or a hydroxyethyl group to the polar head groups. PMID:27045632

  3. Ultrafast photoinduced intramolecular charge separation and recombination processes in the oligothiophene-substituted benzene dyads with an amide spacer.

    Science.gov (United States)

    Oseki, Yosuke; Fujitsuka, Mamoru; Cho, Dae Won; Sugimoto, Akira; Tojo, Sachiko; Majima, Tetsuro

    2005-10-20

    Photoinduced intramolecular charge separation (CS) and recombination (CR) processes of the tetrathiophene-substituted benzene dyads with an amide spacer (4T-PhR, R = 4-H (1), 4-CN (2), 3,4-(CN)2 (3), 4-NO2 (4), 3,5-(NO2)2 (5)) in solvents of different polarities were investigated using various fast spectroscopies. It was revealed that the CS rates depend on the ability of the acceptor and solvent polarity. Ultrafast CS with the rate of 5 x 10(12) s(-1) was revealed for 5 in PhCN and MeCN. The ultrafast CS can be attributed to the large electronic coupling matrix element between the donor and the acceptor despite the relative long donor-acceptor distance. The existence of the state with large electron density on the spacer between 14T*-PhR and LUMO should facilitate the CS process in the present dyad system. It was also revealed that the CR rates in these dyads were rather fast because of the enhanced superexchange interaction through the amide spacer.

  4. Influence of the linking spacer length and type on the enantioseparation ability of β-cyclodextrin functionalized monoliths.

    Science.gov (United States)

    Guo, Jialiang; Xiao, Yuan; Lin, Yuanjing; Zhang, Qiaoxuan; Chang, Yiqun; Crommen, Jacques; Jiang, Zhengjin

    2016-05-15

    In order to investigate the effect of the linking spacer on the enantioseparation ability of β-cyclodextrin (β-CD) functionalized polymeric monoliths, three β-CD-functionalized organic polymeric monoliths with different spacer lengths were prepared by using three amino-β-CDs, i.e. mono-6-amino-6-deoxy-β-CD, mono-6-ethylenediamine-6-deoxy-β-CD, mono-6-hexamethylenediamine-6-deoxy-β-CD, as starting materials. These amino-β-CDs reacted with glycidyl methacrylate to produce functional monomers which were then copolymerized with ethylene dimethacrylate. The enantioseparation ability of the three monoliths was evaluated using 14 chiral acidic compounds, including mandelic acid derivatives, nonsteroidal anti-inflammatory drugs, N-derivatized amino acids, and chiral herbicides under optimum chromatographic conditions. Notably, the poly(GMA-NH2-β-CD-co-EDMA) column provides higher enantioresolution and enantioselectivity than the poly(GMA-EDA-β-CD-co-EDMA) and poly(GMA-HDA-β-CD-co-EDMA) columns for most tested chiral analytes. Furthermore, the enantioseparation performance of triazole-linker containing monoliths was compared to that of ethylenediamine-linker containing monoliths. The results indicate that the enantioselectivity of β-CD monolithic columns is strongly related to the length and type of spacer tethering β-CD to the polymeric support. PMID:26992519

  5. Comparative bioinformatics and experimental analysis of the intergenic regulatory regions of Bacillus cereus hbl and nhe enterotoxin operons and the impact of CodY on virulence heterogeneity

    Directory of Open Access Journals (Sweden)

    Maria-Elisabeth eBöhm

    2016-05-01

    Full Text Available Bacillus cereus is a food contaminant with greatly varying enteropathogenic potential. Almost all known strains harbor the genes for at least one of the three enterotoxins Nhe, Hbl and CytK. While some strains show no cytotoxicity, others have caused outbreaks, in rare cases even with lethal outcome. The reason for these differences in cytotoxicity is unknown. To gain insight into the origin of enterotoxin expression heterogeneity in different strains, the architecture and role of 5’ intergenic regions (5’IGRs upstream of the nhe and hbl operons was investigated. In silico comparison of 142 strains of all seven phylogenetic groups of B. cereus sensu lato proved the presence of long 5’IGRs upstream of the nheABC and hblCDAB operons, which harbor recognition sites for several transcriptional regulators, including the virulence regulator PlcR, redox regulators ResD and Fnr, the nutrient-sensitive regulator CodY as well as the master regulator for biofilm formation SinR. By determining transcription start sites, unusually long 5’ untranslated regions (5’UTRs upstream of the nhe and hbl start codons were identified, which are not present upstream of cytK-1 and cytK-2. Promoter fusions lacking various parts of the nhe and hbl 5’UTR in B. cereus INRA C3 showed that the entire 331 bp 5’UTR of nhe is necessary for full promoter activity, while the presence of the complete 606 bp hbl 5’UTR lowers promoter activity. Repression was caused by a 268 bp sequence directly upstream of the hbl transcription start. Luciferase activity of reporter strains containing nhe and hbl 5’IGR lux fusions provided evidence that toxin gene transcription is upregulated by the depletion of free amino acids. Electrophoretic mobility shift assays showed that the branched-chain amino acid sensing regulator CodY binds to both nhe and hbl 5’UTR downstream of the promoter, potentially acting as a nutrient-responsive roadblock repressor of toxin gene transcription

  6. Comparative Bioinformatics and Experimental Analysis of the Intergenic Regulatory Regions of Bacillus cereus hbl and nhe Enterotoxin Operons and the Impact of CodY on Virulence Heterogeneity.

    Science.gov (United States)

    Böhm, Maria-Elisabeth; Krey, Viktoria M; Jeßberger, Nadja; Frenzel, Elrike; Scherer, Siegfried

    2016-01-01

    Bacillus cereus is a food contaminant with greatly varying enteropathogenic potential. Almost all known strains harbor the genes for at least one of the three enterotoxins Nhe, Hbl, and CytK. While some strains show no cytotoxicity, others have caused outbreaks, in rare cases even with lethal outcome. The reason for these differences in cytotoxicity is unknown. To gain insight into the origin of enterotoxin expression heterogeneity in different strains, the architecture and role of 5' intergenic regions (5' IGRs) upstream of the nhe and hbl operons was investigated. In silico comparison of 142 strains of all seven phylogenetic groups of B. cereus sensu lato proved the presence of long 5' IGRs upstream of the nheABC and hblCDAB operons, which harbor recognition sites for several transcriptional regulators, including the virulence regulator PlcR, redox regulators ResD and Fnr, the nutrient-sensitive regulator CodY as well as the master regulator for biofilm formation SinR. By determining transcription start sites, unusually long 5' untranslated regions (5' UTRs) upstream of the nhe and hbl start codons were identified, which are not present upstream of cytK-1 and cytK-2. Promoter fusions lacking various parts of the nhe and hbl 5' UTR in B. cereus INRA C3 showed that the entire 331 bp 5' UTR of nhe is necessary for full promoter activity, while the presence of the complete 606 bp hbl 5' UTR lowers promoter activity. Repression was caused by a 268 bp sequence directly upstream of the hbl transcription start. Luciferase activity of reporter strains containing nhe and hbl 5' IGR lux fusions provided evidence that toxin gene transcription is upregulated by the depletion of free amino acids. Electrophoretic mobility shift assays showed that the branched-chain amino acid sensing regulator CodY binds to both nhe and hbl 5' UTR downstream of the promoter, potentially acting as a nutrient-responsive roadblock repressor of toxin gene transcription. PlcR binding sites are

  7. Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9.

    Directory of Open Access Journals (Sweden)

    Marie L Harth-Hertle

    2013-09-01

    Full Text Available Epstein-Barr virus (EBV causes a persistent infection in human B cells by establishing specific transcription programs to control B cell activation and differentiation. Transcriptional reprogramming of EBV infected B cells is predominantly driven by the action of EBV nuclear antigens, among them the transcriptional repressor EBNA3A. By comparing gene expression profiles of wt and EBNA3A negative EBV infected B cells, we have previously identified a broad array of cellular genes controlled by EBNA3A. We now find that genes repressed by EBNA3A in these cells are significantly enriched for the repressive histone mark H3K27me3, which is installed by Polycomb group (PcG proteins. This PcG-controlled subset of genes also carries H3K27me3 marks in a variety of other tissues, suggesting that the commitment to PcG silencing is an intrinsic feature of these gene loci that can be used by EBNA3A. In addition, EBNA3A targets frequently reside in co-regulated gene clusters. To study the mechanism of gene repression by EBNA3A and to evaluate the relative contribution of PcG proteins during this process, we have selected the genomic neighbors CXCL10 and CXCL9 as a model for co-repressed and PcG-controlled genes. We show that EBNA3A binds to CBF1 occupied intergenic enhancers located between CXCL10 and CXCL9 and displaces the transactivator EBNA2. This impairs enhancer activity, resulting in a rapid transcriptional shut-down of both genes in a CBF1-dependent manner and initiation of a delayed gain of H3K27me3 marks covering an extended chromatin domain. H3K27me3 marks increase gradually and are maintained by EBNA3A. Our study provides direct evidence that repression by EBNA3A requires CBF1 and that EBNA3A and EBNA2 compete for access to CBF1 at identical genomic sites. Most importantly, our results demonstrate that transcriptional silencing by EBNA3A precedes the appearance of repressive PcG marks and indicate that both events are triggered by loss of enhancer

  8. Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9.

    Science.gov (United States)

    Harth-Hertle, Marie L; Scholz, Barbara A; Erhard, Florian; Glaser, Laura V; Dölken, Lars; Zimmer, Ralf; Kempkes, Bettina

    2013-09-01

    Epstein-Barr virus (EBV) causes a persistent infection in human B cells by establishing specific transcription programs to control B cell activation and differentiation. Transcriptional reprogramming of EBV infected B cells is predominantly driven by the action of EBV nuclear antigens, among them the transcriptional repressor EBNA3A. By comparing gene expression profiles of wt and EBNA3A negative EBV infected B cells, we have previously identified a broad array of cellular genes controlled by EBNA3A. We now find that genes repressed by EBNA3A in these cells are significantly enriched for the repressive histone mark H3K27me3, which is installed by Polycomb group (PcG) proteins. This PcG-controlled subset of genes also carries H3K27me3 marks in a variety of other tissues, suggesting that the commitment to PcG silencing is an intrinsic feature of these gene loci that can be used by EBNA3A. In addition, EBNA3A targets frequently reside in co-regulated gene clusters. To study the mechanism of gene repression by EBNA3A and to evaluate the relative contribution of PcG proteins during this process, we have selected the genomic neighbors CXCL10 and CXCL9 as a model for co-repressed and PcG-controlled genes. We show that EBNA3A binds to CBF1 occupied intergenic enhancers located between CXCL10 and CXCL9 and displaces the transactivator EBNA2. This impairs enhancer activity, resulting in a rapid transcriptional shut-down of both genes in a CBF1-dependent manner and initiation of a delayed gain of H3K27me3 marks covering an extended chromatin domain. H3K27me3 marks increase gradually and are maintained by EBNA3A. Our study provides direct evidence that repression by EBNA3A requires CBF1 and that EBNA3A and EBNA2 compete for access to CBF1 at identical genomic sites. Most importantly, our results demonstrate that transcriptional silencing by EBNA3A precedes the appearance of repressive PcG marks and indicate that both events are triggered by loss of enhancer activity. PMID

  9. Comparative Bioinformatics and Experimental Analysis of the Intergenic Regulatory Regions of Bacillus cereus hbl and nhe Enterotoxin Operons and the Impact of CodY on Virulence Heterogeneity.

    Science.gov (United States)

    Böhm, Maria-Elisabeth; Krey, Viktoria M; Jeßberger, Nadja; Frenzel, Elrike; Scherer, Siegfried

    2016-01-01

    Bacillus cereus is a food contaminant with greatly varying enteropathogenic potential. Almost all known strains harbor the genes for at least one of the three enterotoxins Nhe, Hbl, and CytK. While some strains show no cytotoxicity, others have caused outbreaks, in rare cases even with lethal outcome. The reason for these differences in cytotoxicity is unknown. To gain insight into the origin of enterotoxin expression heterogeneity in different strains, the architecture and role of 5' intergenic regions (5' IGRs) upstream of the nhe and hbl operons was investigated. In silico comparison of 142 strains of all seven phylogenetic groups of B. cereus sensu lato proved the presence of long 5' IGRs upstream of the nheABC and hblCDAB operons, which harbor recognition sites for several transcriptional regulators, including the virulence regulator PlcR, redox regulators ResD and Fnr, the nutrient-sensitive regulator CodY as well as the master regulator for biofilm formation SinR. By determining transcription start sites, unusually long 5' untranslated regions (5' UTRs) upstream of the nhe and hbl start codons were identified, which are not present upstream of cytK-1 and cytK-2. Promoter fusions lacking various parts of the nhe and hbl 5' UTR in B. cereus INRA C3 showed that the entire 331 bp 5' UTR of nhe is necessary for full promoter activity, while the presence of the complete 606 bp hbl 5' UTR lowers promoter activity. Repression was caused by a 268 bp sequence directly upstream of the hbl transcription start. Luciferase activity of reporter strains containing nhe and hbl 5' IGR lux fusions provided evidence that toxin gene transcription is upregulated by the depletion of free amino acids. Electrophoretic mobility shift assays showed that the branched-chain amino acid sensing regulator CodY binds to both nhe and hbl 5' UTR downstream of the promoter, potentially acting as a nutrient-responsive roadblock repressor of toxin gene transcription. PlcR binding sites are

  10. High signal output in current-perpendicular-to-the-plane giant magnetoresistance sensors using In-Zn-O-based spacer layers

    Science.gov (United States)

    Nakatani, Tomoya; Mihajlović, Goran; Read, John C.; Choi, Young-suk; Childress, Jeffrey R.

    2015-09-01

    We report current-perpendicular-to-the-plane giant magnetoresistance (CPP-GMR) sensors with a conductive Ag/In-Zn-O (IZO)/Zn trilayer as the spacer layer. Magnetoresistance ratios as high as 26% at resistance-area product (RA) = 60-120 mΩ µm2 were obtained in thin, polycrystalline spin valves suitable for modern read sensors of hard disk drives (HDDs). The large CPP-GMR values are attributed to the large spin-dependent scattering at the interfaces of the ferromagnet/IZO-based spacer junctions. The maximum voltage output of sensors with Ag/IZO/Zn spacers was ΔVmax = 11.3 mV, significantly larger than that observed for metallic AgSn spacers (2.3 mV). Such improved properties are important for HDD read heads with recording densities larger than 1 Tbit/in.2.

  11. Optimisation of BACE1 inhibition of tripartite structures by modification of membrane anchors, spacers and pharmacophores - development of potential agents for the treatment of Alzheimer's disease.

    Science.gov (United States)

    Linning, Philipp; Haussmann, Ute; Beyer, Isaak; Weidlich, Sebastian; Schieb, Heinke; Wiltfang, Jens; Klafki, Hans-Wolfgang; Knölker, Hans-Joachim

    2012-10-01

    Systematic variation of membrane anchor, spacer and pharmacophore building blocks leads to an optimisation of the inhibitory effect of tripartite structures towards BACE1-induced cleavage of the amyloid precursor protein (APP). PMID:22930158

  12. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    Science.gov (United States)

    Schoch, Conrad L.; Seifert, Keith A.; Huhndorf, Sabine; Robert, Vincent; Spouge, John L.; Levesque, C. André; Chen, Wen; Bolchacova, Elena; Voigt, Kerstin; Crous, Pedro W.; Miller, Andrew N.; Wingfield, Michael J.; Aime, M. Catherine; An, Kwang-Deuk; Bai, Feng-Yan; Barreto, Robert W.; Begerow, Dominik; Bergeron, Marie-Josée; Blackwell, Meredith; Boekhout, Teun; Bogale, Mesfin; Boonyuen, Nattawut; Burgaz, Ana R.; Buyck, Bart; Cai, Lei; Cai, Qing; Cardinali, G.; Chaverri, Priscila; Coppins, Brian J.; Crespo, Ana; Cubas, Paloma; Cummings, Craig; Damm, Ulrike; de Beer, Z. Wilhelm; de Hoog, G. Sybren; Del-Prado, Ruth; Dentinger, Bryn; Diéguez-Uribeondo, Javier; Divakar, Pradeep K.; Douglas, Brian; Dueñas, Margarita; Duong, Tuan A.; Eberhardt, Ursula; Edwards, Joan E.; Elshahed, Mostafa S.; Fliegerova, Katerina; Furtado, Manohar; García, Miguel A.; Ge, Zai-Wei; Griffith, Gareth W.; Griffiths, K.; Groenewald, Johannes Z.; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Guo, Liang-Dong; Hagen, Ferry; Hambleton, Sarah; Hamelin, Richard C.; Hansen, Karen; Harrold, Paul; Heller, Gregory; Herrera, Cesar; Hirayama, Kazuyuki; Hirooka, Yuuri; Ho, Hsiao-Man; Hoffmann, Kerstin; Hofstetter, Valérie; Högnabba, Filip; Hollingsworth, Peter M.; Hong, Seung-Beom; Hosaka, Kentaro; Houbraken, Jos; Hughes, Karen; Huhtinen, Seppo; Hyde, Kevin D.; James, Timothy; Johnson, Eric M.; Johnson, Joan E.; Johnston, Peter R.; Jones, E.B. Gareth; Kelly, Laura J.; Kirk, Paul M.; Knapp, Dániel G.; Kõljalg, Urmas; Kovács, Gábor M.; Kurtzman, Cletus P.; Landvik, Sara; Leavitt, Steven D.; Liggenstoffer, Audra S.; Liimatainen, Kare; Lombard, Lorenzo; Luangsa-ard, J. Jennifer; Lumbsch, H. Thorsten; Maganti, Harinad; Maharachchikumbura, Sajeewa S. N.; Martin, María P.; May, Tom W.; McTaggart, Alistair R.; Methven, Andrew S.; Meyer, Wieland; Moncalvo, Jean-Marc; Mongkolsamrit, Suchada; Nagy, László G.; Nilsson, R. Henrik; Niskanen, Tuula; Nyilasi, Ildikó; Okada, Gen; Okane, Izumi; Olariaga, Ibai; Otte, Jürgen; Papp, Tamás; Park, Duckchul; Petkovits, Tamás; Pino-Bodas, Raquel; Quaedvlieg, William; Raja, Huzefa A.; Redecker, Dirk; Rintoul, Tara L.; Ruibal, Constantino; Sarmiento-Ramírez, Jullie M.; Schmitt, Imke; Schüßler, Arthur; Shearer, Carol; Sotome, Kozue; Stefani, Franck O.P.; Stenroos, Soili; Stielow, Benjamin; Stockinger, Herbert; Suetrong, Satinee; Suh, Sung-Oui; Sung, Gi-Ho; Suzuki, Motofumi; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M. Teresa; Tretter, Eric; Untereiner, Wendy A.; Urbina, Hector; Vágvölgyi, Csaba; Vialle, Agathe; Vu, Thuy Duong; Walther, Grit; Wang, Qi-Ming; Wang, Yan; Weir, Bevan S.; Weiß, Michael; White, Merlin M.; Xu, Jianping; Yahr, Rebecca; Yang, Zhu L.; Yurkov, Andrey; Zamora, Juan-Carlos; Zhang, Ning; Zhuang, Wen-Ying; Schindel, David

    2012-01-01

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups. PMID:22454494

  13. Molecular analysis of fungal populations in patients with oral candidiasis using internal transcribed spacer region.

    Science.gov (United States)

    Ieda, Shinsuke; Moriyama, Masafumi; Takeshita, Toru; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection.

  14. Microstructural evolution of CANDU spacer material Inconel X-750 under in situ ion irradiation

    Science.gov (United States)

    Zhang, He Ken; Yao, Zhongwen; Judge, Colin; Griffiths, Malcolm

    2013-11-01

    Work on Inconel®Inconel® is a registered trademark of Special Metals Corporation that refers to a family of austenitic nickel-chromium-based superalloys.1 X-750 spacers removed from CANDU®CANDU® is a registered trademark of Atomic Energy of Canada Limited standing for ''CANada Deuterium Uranium''.2 reactors has shown that they become embrittled and there is development of many small cavities within the metal matrix and along grain boundaries. In order to emulate the neutron irradiation induced microstructural changes, heavy ion irradiations (1 MeV Kr2+ ions) were performed while observing the damage evolution using an intermediate voltage electron microscope (IVEM) operating at 200 kV. The irradiations were carried out at various temperatures 60-400 °C. The principal strengthening phase, γ‧, was disordered at low doses (˜0.06 dpa) during the irradiation. M23C6 carbides were found to be stable up to 5.4 dpa. Lattice defects consisted mostly of stacking fault tetrahedras (SFTs), 1/2 perfect loops and small 1/3 faulted Frank loops. The ratio of SFT number density to loop number density for each irradiation condition was found to be neither temperature nor dose dependent. Under the operation of the ion beam the SFT production was very rapid, with no evidence for further growth once formed, indicating that they probably formed as a result of cascade collapse in a single cascade. The number density of the defects was found to saturate at low dose (˜0.68 dpa). No cavities were observed regardless of the irradiation temperature between 60 °C and 400 °C for doses up to 5.4 dpa. In contrast, cavities have been observed after neutron irradiation in the same material at similar doses and temperatures indicating that helium, produce during neutron irradiation, may be essential for the nucleation and growth of cavities.

  15. Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker

    Science.gov (United States)

    Stern, Rowena F.; Andersen, Robert A.; Jameson, Ian; Küpper, Frithjof C.; Coffroth, Mary-Alice; Vaulot, Daniel; Le Gall, Florence; Véron, Benoît; Brand, Jerry J.; Skelton, Hayley; Kasai, Fumai; Lilly, Emily L.; Keeling, Patrick J.

    2012-01-01

    Background DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. Methodology/Principal Findings The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. Conclusions/Significance The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would

  16. Evaluating the ribosomal internal transcribed spacer (ITS as a candidate dinoflagellate barcode marker.

    Directory of Open Access Journals (Sweden)

    Rowena F Stern

    Full Text Available BACKGROUND: DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI and Cytochrome b oxidase (COB, have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. METHODOLOGY/PRINCIPAL FINDINGS: The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. CONCLUSIONS/SIGNIFICANCE: The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these

  17. Vibrational and quantum-chemical study of push-pull chromophores for second-order nonlinear optics from rigidified thiophene-based pi-conjugating spacers.

    Science.gov (United States)

    Ruiz Delgado, Mari Carmen; Hernández, Víctor; Casado, Juan; López Navarrete, Juan T; Raimundo, Jean-Manuel; Blanchard, Philippe; Roncali, Jean

    2003-08-01

    Two types of push-pull chromophores built around thiophene-based pi-conjugating spacers rigidified by either covalent bonds or noncovalent intramolecular interactions have been analysed by means of IR and Raman spectroscopical measurements in the solid state as well as in a variety of solvents. Comparison of the Raman features of NLO-phores based on a covalently rigidified dithienylene (DTE) spacer with those of their open chain DTE analogues shows that the bridging of the central double bond of DTE with the nearest beta-positions of the thienyl units through two ethylene bridges significantly improves the intramolecular charge transfer. This also occurs for NLO-phores based on a 2,2'-bi(3,4-ethylenedioxythiophene) (BEDOT) spacer as compared with their corresponding parent compounds based on an unsubstituted bithiophene (BT) spacer. For NLO-phores based on a BEDOT spacer, noncovalent intramolecular interactions between sulfur and oxygen atoms are responsible for the rigidification of the spacer. The Raman spectra of these NLO-phores obtained in the form of solutes in dilute solutions reveal two different behaviours: i) chromophores based on covalently bridged or open chain DTE spacers display Raman spectral profiles in solution quite similar to those of the corresponding solids, with a very little dependence on the polarity of the solvent, while ii) larger spectral changes are noticed for NLO-phores built around BEDOT or BT spacers on going from solids to solutions. In the second case, spectral changes must be ascribed not solely to conformational distortions of the donor and acceptor end groups with respect to the pi-conjugated backbone mean-square-plane (as for the DTE-based NLO-phores) but also to distortions of the thienyl units of the pi-conjugating spacer from coplanarity. The insertion of vinylenic bridges between the thienyl units of the pi-conjugating spacer and between the spacer and the donor and acceptor end groups is a suitable strategy to reach a

  18. Microstructures of NiFe/nonmagnetic metal spacer/FeMn films and their influences on exchange coupling

    Institute of Scientific and Technical Information of China (English)

    LI; Minghua(李明华); YU; Guanghua(于广华); ZHU; Fengwu(朱逢吾); HE; Ke(何珂); LAI; Wuyan(赖武彦)

    2003-01-01

    Ta/NiFe/nonmagnetic metal spacer/FeMn films were prepared by magnetron sputtering. The dependences of the exchange coupling field (Hex) between an antiferromagnetic FeMn layer and a ferromagnetic NiFe layer on the thickness of nonmagnetic metal spacer layers were systematically studied. The results show that the Hex dramatically decreases with the increase in the thicknesses of Bi and Ag spacer layers. However, it gradually decreases with the increase in the thickness of a Cu spacer layer. For a Cu space layer, its crystalline structure is the same as that of NiFe and the lattice parameters of them are close to each other. The Cu layer and FeMn layer will epitaxially grow on the NiFe layer in succession, so the (111) texture of the FeMn layer will not be damaged. As a result, the Hex gradually decreases with the deposition thickness of a Cu layer. For an Ag space layer, its crystalline structure is the same as that of NiFe, but its lattice parameter is very different from that of NiFe. Thus, neither an Ag nor an FeMn layer will epitaxially grow on the NiFe layer and the (111) texture of the FeMn layer will be damaged. The Hex rapidly decreases with the increase in the deposition thickness of an Ag layer. For a Bi spacer layer, not only its crystalline structure but also its lattice parameter is greatly different from that of NiFe. For the same reason, the Bi and FeMn layer cannot epitaxially grow on the NiFe layer. The texture of the FeMn layer will also be damaged. Therefore, the Hex rapidly decreases with the increase in the deposition thickness of a Bi layer as well. However, the research result of X-ray photoelectron spectroscopy indicates that a very small amount of surfactant Bi atoms will migrate to the FeMn layer surface when they are deposited on the NiFe/FeMn interface. Thus, the Hex will hardly decrease.

  19. Titanocene Dichloride Complexes Bonded to Carbosilane Dendrimers Via a Spacer of Variable Length – Molecular Dynamics Calculations and Catalysis of Allylic Coupling Reactions

    OpenAIRE

    Strašák, T. (Tomáš); Jaroschik, F.; M. Malý; Čermák, J.; Sýkora, J.; Fajgar, R. (Radek); Karban, J.; Harakat, D.

    2014-01-01

    Carbosilane metallodendrimers of the first and second generation containing 4, 8 or 16 titanocene dichloride endgroups were prepared by the normal hydrosilylation method. Different chain lengths of the carbon spacer between the dendrimer and the Cp linkage were investigated. Computer atomistic models of the second generation metallodendrimers with the length of carbon spacer n = 1, 3 and 5 carbon atoms were created, parametrized, and consequently simulated in THF solvent using molecular dynam...

  20. Advantages of the AlGaN spacer in InAlN high-electron-mobility transistors grown using metalorganic vapor phase epitaxy

    Science.gov (United States)

    Yamada, Atsushi; Ishiguro, Tetsuro; Kotani, Junji; Tomabechi, Shuichi; Nakamura, Norikazu; Watanabe, Keiji

    2016-05-01

    We demonstrate the advantages of an AlGaN spacer layer in an InAlN high-electron-mobility transistor (HEMT). We investigated the effects of the growth parameters of the spacer layer on electron mobility in InAlN HEMTs grown by metalorganic vapor phase epitaxy, focusing on the surface roughness of the spacer layer and sharpness of the interface with the GaN channel layer. The electron mobility degraded, as evidenced by the formation of a graded AlGaN layer at the top of the GaN channel layer and the surface roughness of the AlN spacer layer. We believe that the short migration length of aluminum atoms is responsible for the observed degradation. An AlGaN spacer layer was employed to suppress the formation of the graded AlGaN layer and improve surface morphology. A high electron mobility of 1550 cm2 V-1 s-1 and a low sheet resistance of 211 Ω/sq were achieved for an InAlN HEMT with an AlGaN spacer layer.

  1. Artifacts in spine magnetic resonance imaging due to different intervertebral test spacers: an in vitro evaluation of magnesium versus titanium and carbon-fiber-reinforced polymers as biomaterials

    International Nuclear Information System (INIS)

    Intervertebral spacers are made of different materials, which can affect the postfusion magnetic imaging (MRI) scans. Susceptibility artifacts especially for metallic implants can decrease the image quality. This study aimed to determine whether magnesium as a lightweight and biocompatible metal is suitable as a biomaterial for spinal implants based on its MRI artifacting behavior. To compare artifacting behaviors, we implanted into one porcine cadaveric spine different test spacers made of magnesium, titanium, and carbon-fiber-reinforced polymers (CFRP). All test spacers were scanned using two T1-TSE MRI sequences. The artifact dimensions were traced on all scans and statistically analyzed. The total artifact volume and median artifact area of the titanium spacers were statistically significantly larger than magnesium spacers (p 0.05). Our results suggest that spinal implants made with magnesium alloys will behave more like CFRP devices in MRI scans. Given its osseoconductive potential as a metal, implant alloys made with magnesium would combine the advantages to the two principal spacer materials currently used but without their limitations, at least in terms of MRI artifacting. (orig.)

  2. Arrangement and number of clustered regularly interspaced short palindromic repeat spacers are associated with erythromycin susceptibility in emm12, emm75 and emm92 of group A streptococcus.

    Science.gov (United States)

    Zheng, P-X; Chiang-Ni, C; Wang, S-Y; Tsai, P-J; Kuo, C-F; Chuang, W-J; Lin, Y-S; Liu, C-C; Wu, J-J

    2014-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of numerous repeat-spacer units and are considered a prokaryotic defence system against foreign nucleic acids. Since antibiotic-resistant genes are frequently encoded in foreign nucleic acids, the aim of this study was to test whether erythromycin susceptibility in group A streptococcus (Streptococcus pyogenes) is associated with characteristics of CRISPR elements. Erythromycin susceptibility of 330 isolates collected between 1997 and 2003 was analysed. Among 29 emm types, emm12, emm75 and emm92 showed significant changes in erythromycin-resistance rates. By sequencing the spacers from two CRISPR loci, spacer contents in emm12, emm75 and emm92 strains were associated with erythromycin susceptibility. Strains with fewer spacers were more resistant to erythromycin. Moreover, in emm4 strains, which showed no significant change in their annual erythromycin-resistance rate, CRISPR type and number of spacers were not correlated with erythromycin susceptibility. These results highlight a novel association between CRISPR spacer content and erythromycin susceptibility in group A streptococcus.

  3. Two-stage revision total hip arthroplasty for periprosthetic infections using antibiotic-impregnated cement spacers of various types and materials.

    Science.gov (United States)

    Uchiyama, Katsufumi; Takahira, Naonobu; Fukushima, Kensuke; Moriya, Mitsutoshi; Yamamoto, Takeaki; Minegishi, Yojiro; Sakai, Rina; Itoman, Moritoshi; Takaso, Masashi

    2013-01-01

    Antibiotic-impregnated hip cement spacers of various types and materials have been used in the treatment of periprosthetic hip infections. We developed a handmade spacer by using polymethylmethacrylate (PMMA) and/or α -tricalcium phosphate ( α -TCP). In this study, we retrospectively reviewed the surgical outcomes in 36 consecutive patients treated with 2-stage revision total hip arthroplasty by using our antibiotic-impregnated hip cement spacers. We aimed to analyze the infection control and reinfection rates after revision surgery. Moreover, we analyzed the possible predictors of postoperative reinfection. After exclusion of 1 patient who died immediately after the first-stage surgery, infection was controlled in 33 of the 36 hips (success rate, 91.7%). Two of these 33 hips underwent resection arthroplasty. Of the 36 hips that had been treated with the antibiotic-cement spacer, 31 hips (86.1%) were eligible for the second-stage prosthesis re-implantation. The 31 protocol hip joints of patients followed up for >6 months (mean, 48.6 months). Ten of these 31 hips (32.3%) became reinfected. No possible predictor examined differed significantly between the reinfection-positive and reinfection-negative groups. However, spacers consisting of PMMA cement alone were associated with the highest risk of reinfection. Therefore, α -TCP-containing antibiotic-impregnated hip cement spacers might decrease the reinfection rate in patients undergoing re-implantation.

  4. A comparative evaluation of tray spacer thickness and repeat pour on the accuracy of monophasic polyvinyl siloxane impression material: In vitro study

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar

    2014-01-01

    Full Text Available Purpose: This study was aimed to determine the effect of various tray spacer thickness and subsequent repeated pours on the accuracy and dimensional stability of the impression made from monophasic polyvinyl siloxane material. Materials and Methods: Custom trays with different spacer thickness (2, 4 and 6 mm were used for making an impression of a master model simulating 3 unit fixed partial denture with monophasic polyvinyl siloxane material. These impressions were poured with die stone and repoured. Distance between the reference points were measured and subjected to statistical analysis. Result: Casts obtained from 1 st , 2 nd and 3 rd pour of the impression in 2, 4 and 6 mm spacer thickness tray have similar dimensional accuracy amongst each other and with the master model except in molar diameter and inter-abutment distances of cast obtained from 6 mm spacer thickness tray. Conclusion: The vertical distance of stone dies were decreased, whereas horizontal distance increased as the thickness of impression material is increased. There were statistically non-significant changes occurring among the repeated pours in 2, 4 and 6 mm spacer thickness. Clinical Implication: 2 and 4 mm spacer thickness are acceptable for making an impression for three unit fixed partial denture with monophasic polyvinyl siloxane material and it was not affected by two subsequent (1 st and 2 nd repeated pours.

  5. Bladder–Rectum Spacer Balloon in High-Dose-Rate Brachytherapy in Cervix Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Rai, Bhavana [Department of Radiotherapy and Oncology, Regional Cancer Centre, Postgraduate Institute of Medical Education and Research, Chandigarh (India); Patel, Firuza D., E-mail: firuzapatel@gmail.com [Department of Radiotherapy and Oncology, Regional Cancer Centre, Postgraduate Institute of Medical Education and Research, Chandigarh (India); Chakraborty, Santam; Sharma, Suresh C.; Kapoor, Rakesh [Department of Radiotherapy and Oncology, Regional Cancer Centre, Postgraduate Institute of Medical Education and Research, Chandigarh (India); Aprem, Abi Santhosh [Corporate R and D Division, HLL Lifecare Limited, Karamana, Trivandrum (India)

    2013-04-01

    Purpose: To compare bladder and rectum doses with the use of a bladder–rectum spacer balloon (BRSB) versus standard gauze packing in the same patient receiving 2 high-dose-rate intracavitary brachytherapy fractions. Methods and Materials: This was a randomized study to compare the reduction in bladder and rectum doses with the use of a BRSB compared with standard gauze packing in patients with carcinoma of the cervix being treated with high-dose-rate intracavitary brachytherapy. The patients were randomized between 2 arms. In arm A, vaginal packing was done with standard gauze packing in the first application, and BRSB was used in the second application. Arm B was the reverse of arm A. The International Commission for Radiation Units and Measurement (ICRU) point doses and doses to 0.1-cm{sup 3}, 1-cm{sup 3}, 2-cm{sup 3}, 5-cm{sup 3}, and 10-cm{sup 3} volumes of bladder and rectum were compared. The patients were also subjectively assessed for the ease of application and the time taken for application. Statistical analysis was done using the paired t test. Results: A total of 43 patients were enrolled; however, 3 patients had to be excluded because the BRSB could not be inserted owing to unfavorable local anatomy. Thus 40 patients (80 plans) were evaluated. The application was difficult in 3 patients with BRSB, and in 2 patients with BRSB the application time was prolonged. There was no significant difference in bladder doses to 0.1 cm{sup 3}, 1 cm{sup 3}, 2 cm{sup 3}, 5 cm{sup 3}, and 10 cm{sup 3} and ICRU bladder point. Statistically significant dose reductions to 0.1-cm{sup 3}, 1-cm{sup 3}, and 2-cm{sup 3} volumes for rectum were observed with the BRSB. No significant differences in 5-cm{sup 3} and 10-cm{sup 3} volumes and ICRU rectum point were observed. Conclusion: A statistically significant dose reduction was observed for small high-dose volumes in rectum with the BRSB. The doses to bladder were comparable for BRSB and gauze packing. Transparent balloons of

  6. Diaminoalkane as Spacer Arm between Polystyrene and - Cylodextrin in Affinity Chromatography for -Amylase Separation

    Directory of Open Access Journals (Sweden)

    Sri Widarti* ,

    2014-02-01

    Full Text Available Stationary phase design in affinity chromatography has to fulfill at least two requirements: non-specific interaction between solid support and or spacer arm and protein target or others is minimal and specific interaction between ligand and protein target is maximal. In this study, stationary phases that consist of polystyrene (PS as solid support, diaminoalkane as spacer arm and with and without βCD as a ligand are performed in α-amylase separation. Therefore, the research was carried out in two steps; stationary phase preparation and adsorption parameter determination towards α-amylase. Stationary phases that consist of PS, 1,6-diaminohexane and βCD (PS–DAH–βCD and without βCD (PS–DAH were synthesized. Stationary phase structure was confirmed by FTIR, 13C NMR solid, 13C dan 1H NMR liquid spectroscopy. Other stationary phases, PS–DAP–βCD and PS–DAP that consist of 1,2-diaminopropane (DAP as spacer arm was synthesized in the previous research. Dynamic α-amylase adsorption isotherm on PS–DAP and PS–DAH shows that both of them did not fix any adsorption isotherm model. The average binding capacity are 0.071 and 0.31 mg/0.1 g resin, respectively. In another hand, PS–DAP–βCD and PS–DAH–βCD fix isotherm adsorption Langmuir model and the adsorption parameters; the maximum binding capacity (qm are 5.5 and 2.1 mg/0.1 g resin, adsorption equilibrium constant (KA are 0.01965 and 0.01925 μL—1 and desorption rate constant (k2 are 0.201 and 0.774 mg s—1 , respectively. Due to adsorption parameters, PS–DAP–βCD offer the best adsorption capacity and selectivity as stationary phase in affinity chromatography for α-amylase separation.

  7. Analysis of the thermal comfort and impact properties of the neoprene-spacer fabric structure for preventing the joint damages

    Directory of Open Access Journals (Sweden)

    Ehsan Ghorbani

    2013-01-01

    Full Text Available Background: Frequent moves at the joint, plus external factors such as trauma, aging, and etc., are all reasons for joint damages. In order to protect and care of joints, the orthopedic textiles are used. To protect the joints, these textiles keep muscles warm to prevent shock. To produce orthopedic textiles, Neoprene foams have been traditionally used. These foams are flexible and resist impact, but are not comfortable enough and might cause problems for the consumer. This study introduces a new structure consisting of perforated Neoprene foam attached to the spacer fabric and also compares the properties of thermal and moisture comfort and impact properties of this structure in comparison with Neoprene foam. Methods: In order to measure the factors related to the samples lateral pressure behavior, a tensile tester was used. A uniform pressure is applied to the samples and a force - displacement curve is obtained. The test continues until the maximum compression force is reached to 50 N. The area under the curve is much greater; more energy is absorbed during the impact. In order to investigate the dynamic heat and moisture transfer of fabrics, an experimental apparatus was developed. This device made the simulation of sweating of human body possible and consisted of a controlled environmental chamber, sweating guarded hot plate, and data acquisition system. Results: The findings show that the Neoprene-spacer fabric structure represents higher toughness values compared to other samples (P ≤ 0.001. Neoprene-spacer fabric structure (A3 has higher rate of moisture transport than conventional Neoprene foam; because of undesirable comfort characteristics in Neoprene. Conclusions: Results of the tests indicate full advantage of the new structure compared with the Neoprene foam for use in orthopedic textiles (P ≤ 0.001.

  8. Cold-neutron tomography of annular flow and functional spacer performance in a model of a boiling water reactor fuel rod bundle

    International Nuclear Information System (INIS)

    Highlights: → Annular flows w/wo functional spacers are investigated by cold neutron imaging. → Liquid film thickness distribution on fuel pins and on spacer vanes is measured. → The influence of the spacers on the liquid film distributions has been quantified. → The cross-sectional averaged liquid hold-up significantly affected by the spacers. → The sapers affect the fraction of the entrained liquid hold up in the gas core. - Abstract: Dryout of the coolant liquid film at the upper part of the fuel pins of a boiling water reactor (BWR) core constitutes the type of heat transfer crisis relevant for the conditions of high void fractions. It is both a safety concern and a limiting factor in the thermal power and thus for the economy of BWRs. We have investigated adiabatic, air-water annular flows in a scaled-up model of two neighboring subchannels as found in BWR fuel assemblies using cold-neutron tomography. The imaging of the double suchannel has been performed at the ICON beamline at the neutron spallation source SINQ at the Paul Scherrer Institute, Switzerland. Cold-neutron tomography is shown here to be an excellent tool for investigating air-water annular flows and the influence of functional spacers of different geometries on such flows. The high-resolution, high-contrast measurements provide the spatial distributions of the coolant liquid film thickness on the fuel pin surfaces as well as on the surfaces of the spacer vanes. The axial variations of the cross-section averaged liquid hold-up and its fraction in the gas core shows the effect of the spacers on the redistribution of the two phases.

  9. Effects of dual-spacer dielectrics on low-power and high-speed performance of sub-10 nm tunneling field-effect transistors

    Science.gov (United States)

    Yoon, Young Jun; Seo, Jae Hwa; Cho, Seongjae; Kwon, Hyuck-In; Lee, Jung-Hee; Kang, In Man

    2016-06-01

    In this paper, we propose and investigate a dual-spacer dielectric structure for realizing a sub-10 nm tunneling field-effect transistors (TFET) with excellent low-power (LP) and switching performance. The effects of the dual-spacer dielectric were assessed by analyzing the direct current (DC) and radio frequency (RF) performance of the GaAs0.5Sb0.5/In0.53Ga0.47As heterojunction-based short channel TFETs. The dual-spacer dielectric that consists of hafnium oxide (HfO2) and silicon dioxide (SiO2) raises an energy-band on drain-side because of the fringe field induced by the high-k spacer dielectric HfO2. The raised energy-band suppresses direct band-to-band tunneling (BBT) through the channel region and drain-induced barrier thinning (DIBT) phenomenon with improvement in the off-state current (I off) and subthreshold swing (S). The dual-spacer dielectric also influences total gate capacitance (C gg) because the HfO2 in the dual-spacer dielectric increases out-fringe capacitance (C of) in gate-to-drain capacitance (C gd). Although the proposed TFET has a high C gd, the optimized TFET with the HfO2 length (L dual-spacer) of 30 nm achieves a lower intrinsic delay time (τ), a higher cut-off frequency (f T), and a higher maximum oscillation frequency (f max) owing to higher current performance and smaller gate-to-source capacitance (C gs).

  10. The Purification of Glucose Type Glycosyl Nitrate and the Synthesis of Spacer-armed N-Acetyllactosamines and Their Dimers

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    3,6-di-O-acetyl-4-O-(2,3,4,6-tetra-O-acetyl-(-D-galactopyranosyl)-2-azido-2-deoxy- (-D-glucoppyranosyl nitrate could be separated from its mannose type isomer by glycosylation according to the reactivity difference of these two compounds.The pure glucose type nitrate can be converted to corresponding trichloroacemidate,which reacted with spacer arms in solution of CH2Cl2 with BF3@Et2O as promoters to give desired glycosides and dimers.

  11. Synthesis and Properties of Bis-Porphyrin Molecular Tweezers: Effects of Spacer Flexibility on Binding and Supramolecular Chirogenesis

    Directory of Open Access Journals (Sweden)

    Magnus Blom

    2015-12-01

    Full Text Available Ditopic binding of various dinitrogen compounds to three bisporphyrin molecular tweezers with spacers of varying conformational rigidity, incorporating the planar enediyne (1, the helical stiff stilbene (2, or the semi-rigid glycoluril motif fused to the porphyrins (3, are compared. Binding constants Ka = 104–106 M−1 reveal subtle differences between these tweezers, that are discussed in terms of porphyrin dislocation modes. Exciton coupled circular dichroism (ECCD of complexes with chiral dinitrogen guests provides experimental evidence for the conformational properties of the tweezers. The results are further supported and rationalized by conformational analysis.

  12. Detection of Vibrio splendidus and related species in Chamelea gallina sampled in the Adriatic along the Abruzzi coastline.

    Science.gov (United States)

    Torresi, Marina; Acciari, Vicdalia A; Piano, Annamaria; Serratore, Patrizia; Prencipe, Vincenza; Migliorati, Giacomo

    2011-01-01

    Vibrio species are an important and widespread component of marine microbial communities. Some Vibrio strains are potentially pathogenic to marine vertebrates and invertebrates. The aim of this study was to identify vibrios, in particular Vibrio splendidus and related species, isolated from clams (Chamelea gallina) collected along the coasts of the Abruzzi region from May to October 2007. The isolates obtained were phenotyped and classified as belonging to the genus Vibrio. The strains underwent biochemical testing in accordance with Alsina's scheme for V. splendidus identification. Molecular analysis of the 16S-23S intergenic space region and recA gene was used to identify V. splendidus and related species. All the samples examined were found to contain halophylic Vibrio species, with V. alginolyticus, V. splendidus-related species and V. mediterranei most commonly found. A polymerase chain reaction of the 16S-23S intergenic space region and sequencing of the recA gene from isolates confirmed that phenotyping of Vibrio species is not sufficient to distinguish between different species. Differentiation of the highly related species among V. splendidus-related clusters remains an important issue. In this regard, our data suggests sequencing the recA genes was far more discriminatory than sequencing 16S rDNA for this purpose.

  13. Development of a new feed channel spacer for reverse osmosis elements. Phase 2 final report, October 1, 1994--December 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Milstead, C.E.; Riley, R.L.

    1998-02-11

    During Phase 1, computer modeling techniques were used as the prime instrument of evaluation of designs for a new feed channel spacer to replace the 30 mil thick standard mesh (Vexar) spacer currently used in ROWPU [Reverse Osmosis Water Processing Unit] spiral-wound elements. A hemispherical peg model, based on a Bed of Nails concept developed in Phase 1, was selected for prototype production of spiral-wound elements for field testing. Evaluation in the See-Thru test cell to observe pressure drops through the spacer, feed mixing patterns and ease of cleaning fouled membrane samples showed considerable benefit over Vexar. This design would be suitable for production by roll embossing (or rotary punching) methods instead of expensive injection molding techniques. A 10{1/2} inch die set was fabricated to prove this concept using a 12 ton press brake. Due to a number of factors, however, the equipment did not work as anticipated and numerous modifications are currently in progress. This work will continue at no cost to the government until completed. A seawater test system has been constructed for field testing of various commercially available feed channel spacers for comparison with the Vexar spacer.

  14. Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harbouring a CRISPR-like Cas4 protein

    Directory of Open Access Journals (Sweden)

    Ian F. Connerton

    2015-01-01

    Full Text Available Campylobacter jejuni is a worldwide cause of human diarrhoeal disease. Clustered Repetitively Interspaced Palindromic Repeats (CRISPRs and associated proteins allow Bacteria and Archaea to evade bacteriophage and plasmid infection. Type II CRISPR systems are found in association with combinations of genes encoding the CRISPR-associated Cas1, Cas2, Cas4 or Csn2, and Cas9 proteins. C. jejuni possesses a minimal subtype II-C CRISPR system containing cas1, cas2, and cas9 genes whilst cas4 is notably absent. Cas4 proteins possess 5ʹ-3ʹ exonuclease activity to create recombinogenic-ends for spacer acquisition. Here we report a conserved Cas4-like protein in Campylobacter bacteriophages that creates a novel split arrangement between the bacteriophage and host that represents a new twist in the bacteriophage/host co-evolutionary arms race. The continuous association of bacteriophage and host in the carrier state life cycle of C. jejuni provided an opportunity to study spacer acquisition in this species. Remarkably all the spacer sequences observed were of host origin. We hypothesise that Campylobacter bacteriophages can use Cas4-like protein to activate spacer acquisition to use host DNA as an effective decoy to bacteriophage DNA. Bacteria that acquire self-spacers and escape phage infection must overcome CRISPR-mediated autoimmunity either by loss of the interference functions leaving them susceptible to foreign DNA incursion or tolerate changes in gene regulation.

  15. Improvement in the Photocurrent of Inverted Organic Solar Cells Using MoO(x)-Doped TAPC as a P-Type Optical Spacer.

    Science.gov (United States)

    Song, Jiyun; Song, Hyung-Jun; Kim, Jun Young; Lee, Yeonkyung; Park, Myeongjin; Kwon, Yongwon; Ko, Youngjun; Lee, Changhee

    2016-05-01

    In this work, we demonstrate enhancement in the short-circuit current of inverted organic photovoltaic cells (OPVs) using a p-type optical spacer. The p-type optical spacer, which consists of molybdenum oxide (MoO(x))-doped 1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC), shows improved transmittance at visible light with high electrical conductivity. The electrical field distribution of incident light at the active layer of OPVs can be controlled by tuning the thickness of the optical spacer in the OPVs. Specifically, the incorporation of the 20-nm optical spacer layer in the OPV leads to enhanced spectral response of the device in the wavelength range of 400-600 nm, which is consistent with the combined results of improved optical absorption and better charge transport characteristics. As a result, the OPV with a 20-nm p-type optical spacer shows improvement in the short-circuit current compared with a device with 10 nm of embedded MoO(x). PMID:27483861

  16. Sub-15 nm nano-pattern generation by spacer width control for high density precisely positioned self-assembled device nanomanufacturing

    KAUST Repository

    Rojas, Jhonathan Prieto

    2012-08-01

    We present a conventional micro-fabrication based thin film vertical sidewall (spacer) width controlled nano-gap fabrication process to create arrays of nanopatterns for high density precisely positioned self-assembled nanoelectronics device integration. We have used conventional optical lithography to create base structures and then silicon nitride (Si 3N4) based spacer formation via reactive ion etching. Control of Si3N4 thickness provides accurate control of vertical sidewall (spacer) besides the base structures. Nano-gaps are fabricated between two adjacent spacers whereas the width of the gap depends on the gap between two adjacent base structures minus width of adjacent spacers. We demonstrate the process using a 32 nm node complementary metal oxide semiconductor (CMOS) platform to show its compatibility for very large scale heterogeneous integration of top-down and bottom-up fabrication as well as conventional and selfassembled nanodevices. This process opens up clear opportunity to overcome the decade long challenge of high density integration of self-assembled devices with precise position control. © 2012 IEEE.

  17. Identification of Pathogens Causing Common Bacterial Blight on Common Bean (Phaseolus vulgaris L.)%菜豆普通细菌性疫病病原菌鉴定

    Institute of Scientific and Technical Information of China (English)

    陈泓宇; 徐新新; 段灿星; 王述民; 朱振东

    2012-01-01

    [目的]明确中国北方地区菜豆普通细菌性疫病病原菌.[方法]应用菌落特征、油菜黄单胞菌菜豆变种诊断试剂检测、致病性测定、16SrDNA和16S-23SrDNA ITS序列分析、特异PCR检测、脂肪酸分析及生理生化反应特征对病原菌分离物进行鉴定.[结果]从病害样品和菜豆种子样品中均分离到类似黄单胞杆菌的细菌分离物,选取25个代表分离物进行致病性测定,有24个分离物在菜豆品种“英国红”上导致典型菜豆普通细菌性疫病症状.结合16S rDNA及16S-23S rDNA ITS序列比对分析、特异性PCR检测及生理生化反应的结果,24个分离物中7株被鉴定为地毯草黄单胞菌菜豆变种,17株为褐色黄单胞菌褐色亚种.[结论]中国北方地区发生的菜豆普通细菌性疫病由地毯草黄单胞菌菜豆变种或(和)褐色黄单胞菌褐色亚种引起;褐色黄单胞菌褐色亚种在中国属首次报道.%[ Objective ] The objective of this study is to identify the pathogens that cause common bacterial blight on common bean in north China. [Method) The causal agents were identified by colony characterization, detection using Xanthomonas campestris pv. phaseoli diagonsis kit (ADGEN EXPRESS, pathogenicity test, sequencing 16 rDNA and 16S-23S rDNA intergenic spacer (ITS) regions, PCR detection using specific primers for X. axonopodis pv. Phaseoli and X. fuscans subsp. Fuscans, fatty acid methyl esters (FAME) analysis and biochemical characterization tests. [Result] Bacterial isolates of Xanthmonads-like were isolated from all diseased plant and seed samples. Twenty-five representative isolates were selected for pathogenicity test, and 24 tested isolates casused typical symptoms of common bacterial blight on the inoculated plants of common bean cutivar 'Yingguohong'. Based on pathenogenicity test, and combined with the results of diagonsis kit and specific PCR detection, biochemical and molecular characterization, 7 isoaltes were

  18. Immobilization of pyrene on quartz plate surface via a flexible long spacer and its sensing properties to dicarboxylic acids

    Institute of Scientific and Technical Information of China (English)

    GAO Lining; FANG Yu; Lü Fengting; DING Liping

    2004-01-01

    A novel photo-induced luminescence film has been prepared by immobilizing pyrene on quartz plate surface via a flexible long spacer, 1,3-diaminopropane and 3-glycidoxypropyl trimethoxysilane. The film shows combined monomer and excimer emission of pyrene in both wet and dry states. Steady-state and time-resolved fluorescence emission measurements demonstrated that the excimer emission mainly came from direct excitation of ground state dimers, and/or monomers in aggregated state. Classical Birks' scheme plays little role in the formation of the excimers. The structures of the excimers formed during the excitation are complex. Both "standard excimer" of sandwich-like fully overlapped structure and "distorted excimer" of partially overlapped structure exist in the excited state of the fluorophore. The emission of the film is sensitive to the presence of dicarboxylic acids, including ethanedioic acid, malonic acid, succinic acid, etc. The emission in the monomer and excimer region increases along with increasing the concentration of the dicarboxylic acids. The time needed for the emission to reach equilibrium depends on the nature of the acids. It has been shown that the longer the chain length of the acids, the more the time needed. This observation is explained by considering the conformational reorganization of the immobilized pyrene due to insertion of the dicarboxylic acids into the space between neighboring spacers. Experimental results from similar studies using formic acid and acetic acid are in support of this explanation. Furthermore, the response of the film to dicarboxylic acids is reversible.

  19. Pyrolysis of Phenethyl Phenyl Ether Tethered in Mesoporous Silica. Effects of Confinement and Surface Spacer Molecules on Product Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Kidder, Michelle [ORNL; Chaffe, Alan [Monash University, Australia; Nguyen, M [Monash University, Australia; Buchanan III, A C [ORNL

    2011-01-01

    There has been expanding interest in exploring porous metal oxides as a confining environment for organic molecules resulting in altered chemical and physical properties including chemical transformations. In this paper, we examine the pyrolysis behavior of phenethyl phenyl ether (PPE) confined in mesoporous silica by covalent tethers to the pore walls as a function of tether density and the presence of co-tethered surface spacer molecules of varying structure (biphenyl, naphthyl, octyl, and hexadecyl). The PPE pyrolysis product selectivity, which is determined by two competitive free-radical pathways cycling through the two aliphatic radical intermediates (PhCH CH2OPh and PhCH2CH OPh), is shown to be dramatically different from that measured in the liquid phase as well as for PPE tethered to the exterior surface of nonporous silica nanoparticles. Tailoring the pore surface with spacer molecules further alters the selectivity such that the PPE reaction channel involving a molecular rearrangement (O-C phenyl shift in PhCH2CH OPh), which accounts for 25 % of the products in the liquid phase, can be virtually eliminated under pore confinement conditions. The origin of this change in selectivity is discussed in the context of steric constraints on the rearrangement path, confinement effects, pore surface curvature, and hydrogen bonding of PPE with residual surface silanols supplemented by nitrogen physisorption data and molecular dynamics simulations.

  20. Spacer-less, decoupled granular L10 FePt magnetic media using Ar–He sputtering gas

    International Nuclear Information System (INIS)

    Spacer materials are often used to fabricate granular L10 FePt media and reduce the grain size, however, at the expense of reduced out-of-plane coercivity. Here, we demonstrate a spacer-less method in which adding 1% helium to argon sputtering gas leads to a substantial improvement in the chemical ordering, as well as the magnetic and microstructural properties of FePt. This change is attributed to the modification in the ion current density of the plasma caused by the excited metastable helium species. Helium plays a pivotal role in providing the Fe and Pt atoms optimal adatom mobility, thereby, producing well-ordered L10 FePt media. This leads to an enhancement of the out-of-plane coercivity from 15 to 22 kOe. Furthermore, exchange decoupled grains with a twofold reduction in their diameter to ∼24 nm are also achieved. These properties are crucial for magnetic media of the future for data storage recording densities beyond 1 Tb/in2.

  1. In vitro performance of three combinations of spacers and pressurized metered dose inhalers for treatment in children

    DEFF Research Database (Denmark)

    Berg, E; Madsen, J; Bisgaard, H

    1998-01-01

    the highest doses, both maximal dose and dose to ventilator. The recovered doses (means+/-SD) were 55+/-6% and 51+/-2%, respectively, of the delivered dose from the pMDI. The corresponding results for the Babyhaler were 41+/-7% and 24+/-4% and for the Aerochamber 27+/-3% and 17+/-3%. The passive fallout......MDIs were investigated: NebuChamber and AeroChamber with budesonide pMDI and Babyhaler with fluticasone propionate pMDI. Doses were withdrawn onto a filter either with a breathing simulator (dose to ventilator) or with constant flow (maximal dose). The fine-particle dose was assessed with a cascade impactor...... (Andersen Sampler). The effect of repeated use and cleaning of the spacers on the passive fallout of aerosol within the spacers was determined by evacuating the dose on a filter 2, 5, 10 and 30 s after actuating the spray. The drugs were quantified by liquid chromatography. The NebuChamber delivered...

  2. Micelle-Vesicle Transition by Cleavage of Disulfide Spacer Chain for Gemini Surfactant in Didodecyldimethylammonium Chloride Aqueous Solutions.

    Science.gov (United States)

    Mizuhashi, Toshinari; Asakawa, Tsuyoshi; Ohta, Akio

    2015-01-01

    We examined the "micelle-vesicle transition" through the mixing effect of single-tailed thiol surfactants produced by the cleavage of gemini surfactants, [C12H25N(CH3)2CH2CH2SSCH2CH2N(CH3)2C12H25] 2Cl (C12SSC12), which have a disulfide bond in the spacer chain. Phase diagrams of C12H25N(CH3)2CH2CH2SHCl-didodecyldimethylammonium chloride (C12SH-DDAC) and C12SSC12-DDAC were determined by conductivity and pyrene fluorescence probe methods. The aggregate diameters were evaluated by dynamic light scattering (DLS). The critical vesicle concentration (CVC) was confirmed by the abrupt increase in the intensity of light scattering with excitation at 335 nm. Vesicle formation was confined to the DDAC-rich region of the C12SSC12-DDAC system, while the vesicle formation region for the C12SH-DDAC system spread out with the addition of dithiothreitol (DTT) to C12SSC12-DDAC. This implies that single-tailed surfactants can induce a more favorable environment for molecular packing of the vesicular surface. The micelle-vesicle transition occurs with disulfide spacer chain cleavage of gemini surfactants at a particular specific concentration range. PMID:26250426

  3. Unusual low-energy near-infrared bands for ferrocenyl-naphthalimide donor-acceptor dyads with aromatic spacer groups

    DEFF Research Database (Denmark)

    Tagg, Tei; Kjærgaard, Henrik Grum; Lane, Joseph R.;

    2015-01-01

    Time-dependent density functional theory (TDDFT) calculations for a series of donor-spacer-acceptor (D-S-A) molecules with phenyl (1), biphenyl (2), and anthryl (3) spacers interpolated between the ferrocenylalkene donor and -C≡C-4-naphthalimido acceptor components predicted the presence of weak,...... 2500 nm correspond to forbidden e1″ → e1″ transitions localized on the ferrocenium subunit with very low oscillator strengths. (Figure Presented.)......, very low energy near-IR (NIR) transitions in the electronic spectra of the oxidized species Fc+-S-A. Subsequent optically transparent thin layer electrolysis (OTTLE) spectroscopy experiments in the spectral range 1500-3200 nm reveal that, in each case, very low energy NIR bands are indeed...... observed at approximately 2500 nm. The TDDFT calculations not only allow the prediction of these low energy bands but also, in concert with recently developed natural transition orbital (NTO) analysis, give detailed insights into the nature of the transitions involved. It is found that these bands around...

  4. CFD simulation of turbulent flow in a rod bundle with spacer grids (MATIS-H) using STAR-CCM+

    Energy Technology Data Exchange (ETDEWEB)

    Cinosi, N., E-mail: n.cinosi@imperial.ac.uk; Walker, S.P.; Bluck, M.J.; Issa, R.

    2014-11-15

    Highlights: • CDF simulation of turbulent flow generated by a typical PWR spacer grid. • Benchmarking against the MATIS-H experiments run at KAERI in Daejeon, Korea. • Deployment of various steady RANS models to compute the turbulence. • Sensitivity analysis of hardware components. - Abstract: This paper presents the CFD simulation of the turbulent flow generated by a model PWR spacer grid within a rod bundle. The investigation was part of the MATIS-H benchmark exercise, organized by the OECD-NEA, with measurements performed at the KAERI facilities in Daejeon, Korea. The study employed the CD-Adapco code Star-CCM+. An initial sensitivity study was conducted to attempt to assess the importance to the overall flow of components such as the outlet plenum and the end support grid; these were shown to be able to be safely neglected, but the tapered end portion of the rods was found to be significant, and this was incorporated in the model analyzed. A RANS model using any of K-epsilon, K-omega and Reynolds-stress turbulence models was found to be adequate for the prediction of mean velocity profiles, but they all three underestimate the time-averaged turbulent velocity components. Vorticity seems to be better predicted, although the measured values of vorticity are only presented via colored contour plots, making quantitative comparison rather difficult. Circulation, calculated via an integral for each channel, seems to be well predicted by all three models.

  5. Density functional theory study of new azo dyes with different π-spacers for dye-sensitized solar cells

    Science.gov (United States)

    Bagheri Novir, Samaneh; Hashemianzadeh, Seyed Majid

    2015-05-01

    Some of new azo-based metal-free dyes with different π-conjugation spacers, such as carbazole, fluorene, pyrrole, thiophene, furan and thiazole, have been investigated with density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. Theoretical calculations allow us to quantify factors such as light harvesting efficiency (LHE), electron injection driving force (ΔGinject) and the weight of the LUMO orbital on the carboxylic group (QLUMO) related to the short-circuit photocurrent density (Jsc), and to evaluate both charge recombination between the semiconductor conduction band electrons and the oxidized dyes and/or electrolyte, and also the shift of the conduction band of the semiconductor as a result of the adsorption of the dyes onto the semiconductor surface, associated with the open-circuit photovoltage (Voc). According to the results, we could predict that how the π-conjugation spacers influence the Jsc as well as the Voc of DSSCs. Among these dyes, the carbazole and fluorene-based dyes (dyes 1 and 2) show the highest LHE, ΔGinject, QLUMO, and the slowest recombination rate. Consequently, the obtained results show that the carbazole and fluorene-based dyes could have the better Jsc and Voc compared to the other dyes.

  6. Diversity of Aphanizomenon flos-aquae (Cyanobacterium) Populations along a Baltic Sea Salinity Gradient

    OpenAIRE

    Laamanen, Maria J.; Forsström, Laura; Sivonen, Kaarina

    2002-01-01

    Colony-forming cyanobacteria of the genus Aphanizomenon form massive blooms in the brackish water of the Baltic Sea during the warmest summer months. There have been recent suggestions claiming that the Baltic Sea Aphanizomenon species may be different from Aphanizomenon flos-aquae found in lakes. In this study, we examined variability in the morphology and 16S-23S rRNA internal transcribed spacer (ITS) sequences of A. flos-aquae populations along a salinity gradient from a string of lakes to...

  7. GenBank blastn search result: AK058973 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK058973 001-020-D03 AY830189.1 Brassica oleracea var. botrytis rrn16S-trnI intergenic spacer..., tRNA-Ile (trnI) gene, trnI-trnA intergenic spacer, and tRNA-Ala (trnA) gene, complete sequence; ...and trnA-rrn23S intergenic spacer, partial sequence; plastid.|PLN PLN 3e-99 Plus Plus ...

  8. GenBank blastn search result: AK288664 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288664 J090058A09 AY555421.1 AY555421 Physocarpus alternans isolate 175 trnD-trnY intergenic spacer..., partial sequence; tRNA-Tyr (trnY) gene, trnY-trnE intergenic spacer, and tRNA-Glu (trnE)... gene, complete sequence; and trnE-trnT intergenic spacer, partial sequence; chloroplast. PLN 5e-79 1 -1 ...

  9. GenBank blastn search result: AK288664 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288664 J090058A09 AY555424.1 AY555424 Physocarpus capitatus isolate 184 trnD-trnY intergenic spacer..., partial sequence; tRNA-Tyr (trnY) gene, trnY-trnE intergenic spacer, and tRNA-Glu (trnE)... gene, complete sequence; and trnE-trnT intergenic spacer, partial sequence; chloroplast. PLN 5e-79 1 -1 ...

  10. GenBank blastn search result: AK288664 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288664 J090058A09 AY555430.1 AY555430 Physocarpus opulifolius isolate 142 trnD-trnY intergenic spacer..., partial sequence; tRNA-Tyr (trnY) gene, trnY-trnE intergenic spacer, and tRNA-Glu (trn...E) gene, complete sequence; and trnE-trnT intergenic spacer, partial sequence; chloroplast. PLN 5e-79 1 -1 ...

  11. GenBank blastn search result: AK288664 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288664 J090058A09 AY555433.1 AY555433 Lyonothamnus floribundus trnD-trnY intergenic spacer..., partial sequence; tRNA-Tyr (trnY) gene, trnY-trnE intergenic spacer, and tRNA-Glu (trnE) gene, co...mplete sequence; and trnE-trnT intergenic spacer, partial sequence; chloroplast. PLN 2e-81 1 -1 ...

  12. GenBank blastn search result: AK288664 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288664 J090058A09 AY555428.1 AY555428 Physocarpus monogynus isolate 269 trnD-trnY intergenic spacer..., partial sequence; tRNA-Tyr (trnY) gene, trnY-trnE intergenic spacer, and tRNA-Glu (trnE)... gene, complete sequence; and trnE-trnT intergenic spacer, partial sequence; chloroplast. PLN 5e-79 1 -1 ...

  13. SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2.

    Science.gov (United States)

    Erdmann, Susanne; Shah, Shiraz A; Garrett, Roger A

    2013-12-01

    Organisms of the crenarchaeal order Sulfolobales carry complex CRISPR (clustered regularly interspaced short palindromic repeats) adaptive immune systems. These systems are modular and show extensive structural and functional diversity, especially in their interference complexes. The primary targets are an exceptional range of diverse viruses, many of which propagate stably within cells and follow lytic life cycles without producing cell lysis. These properties are consistent with the difficulty of activating CRISPR spacer uptake in the laboratory, but appear to conflict with the high complexity and diversity of the CRISPR immune systems that are found among the Sulfolobales. In the present article, we re-examine the first successful induction of archaeal spacer acquisition in our laboratory that occurred exclusively for the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2 that was co-infected with the virus SMV1 (Sulfolobus monocaudavirus 1). Although we reaffirm that protospacer selection is essentially a random process with respect to the pMGB1 genome, we identified single spacer sequences specific for each of CRISPR loci C, D and E that, exceptionally, occurred in many sequenced clones. Moreover, the same sequence was reproducibly acquired for a given locus in independent experiments, consistent with it being the first protospacer to be selected. There was also a small protospacer bias (1.6:1) to the antisense strand of protein genes. In addition, new experiments demonstrated that spacer acquisition in the previously inactive CRISPR locus A could be induced on freeze-thawing of the infected cells, suggesting that environmental stress can facilitate activation. Coincidentally with spacer acquisition, a mobile OrfB element was deleted from pMGB1, suggesting that interplay can occur between spacer acquisition and transposition.

  14. Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus

    Directory of Open Access Journals (Sweden)

    Lovley Derek R

    2010-07-01

    Full Text Available Abstract Background Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences. Results CRISPR spacer #1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is unlikely to compensate for interference with hisS. Spacer #1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which the native hisS was replaced with that of P. carbinolicus. The prediction that interference with hisS would result in an attenuated histidyl-tRNA pool insufficient for translation of proteins with multiple closely spaced histidines, predisposing them to mutation and elimination during evolution, was investigated by comparative genomics of P. carbinolicus and related species. Several ancestral genes with high histidine demand have been lost or modified in the P. carbinolicus lineage, providing an explanation for its physiological differences from other Geobacteraceae. Conclusions The disappearance of multiheme c-type cytochromes and other genes typical of a metal-respiring ancestor from the P. carbinolicus lineage may be the consequence of spacer #1 interfering with hisS, a condition that can be reproduced in a heterologous host. This is the first successful co-introduction of an active CRISPR spacer and its target in the same cell, the first application of a chimeric CRISPR construct consisting of a spacer from one species in the context of repeats of another species, and the first report of

  15. H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3.

    Directory of Open Access Journals (Sweden)

    Richárd Bártfai

    Full Text Available Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however, the epigenetic component of gene expression in P. falciparum is poorly understood. Dynamic or stable association of epigenetic marks with genomic features provides important clues about their function and helps to understand how histone variants/modifications are used for indexing the Plasmodium epigenome. We describe a novel, linear amplification method for next-generation sequencing (NGS that allows unbiased analysis of the extremely AT-rich Plasmodium genome. We used this method for high resolution, genome-wide analysis of a histone H2A variant, H2A.Z and two histone H3 marks throughout parasite intraerythrocytic development. Unlike in other organisms, H2A.Z is a constant, ubiquitous feature of euchromatic intergenic regions throughout the intraerythrocytic cycle. The almost perfect colocalisation of H2A.Z with H3K9ac and H3K4me3 suggests that these marks are preferentially deposited on H2A.Z-containing nucleosomes. By performing RNA-seq on 8 time-points, we show that acetylation of H3K9 at promoter regions correlates very well with the transcriptional status whereas H3K4me3 appears to have stage-specific regulation, being low at early stages, peaking at trophozoite stage, but does not closely follow changes in gene expression. Our improved NGS library preparation procedure provides a foundation to exploit the malaria epigenome in detail. Furthermore, our findings place H2A.Z at the cradle of P. falciparum epigenetic regulation by stably defining intergenic regions and providing a platform for dynamic assembly of epigenetic and other transcription related complexes.

  16. Characterization of the psbH precursor RNAs reveals a precise endoribonuclease cleavage site in the psbT/psbH intergenic region that is dependent on psbN gene expression.

    Science.gov (United States)

    Chevalier, Fabien; Ghulam, Mustafa Malik; Rondet, Damien; Pfannschmidt, Thomas; Merendino, Livia; Lerbs-Mache, Silva

    2015-07-01

    The plastid psbB operon harbours 5 genes, psbB, psbT, psbH, petB and petD. A sixth gene, the psbN gene, is located on the opposite DNA strand in the psbT/psbH intergenic region. Its transcription produces antisense RNA to a large part of the psbB pentacistronic mRNA. We have investigated whether transcription of the psbN gene, i.e. production of antisense RNA, influences psbT/psbH intergenic processing. Results reveal the existence of four different psbH precursor RNAs. Three of them result from processing and one is produced by transcription initiation. One of the processed RNAs is probably created by site-specific RNA cleavage. This RNA is absent in plants where the psbN gene is not transcribed suggesting that cleavage at this site is dependent on the formation of sense/antisense double-stranded RNA. In order to characterize the nuclease that might be responsible for double-stranded RNA cleavage, we analysed csp41a and csp41b knock-out mutants and the corresponding double mutant. Both CSP41 proteins are known to interact physically and CSP41a had been shown to cleave within 3'-untranslated region stem-loop structures, which contain double-stranded RNA, in vitro. We demonstrate that the psbH RNA, that is absent in plants where the psbN gene is not transcribed, is also strongly diminished in all csp41 plants. Altogether, results reveal a site-specific endoribonuclease cleavage event that seems to depend on antisense RNA and might implicate endoribonuclease activity of CSP41a. PMID:26012647

  17. An intergenic region shared by At4g35985 and At4g35987 in Arabidopsis thaliana is a tissue specific and stress inducible bidirectional promoter analyzed in transgenic arabidopsis and tobacco plants.

    Directory of Open Access Journals (Sweden)

    Joydeep Banerjee

    Full Text Available On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985 are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85 showed stronger expression (about 3.5 fold compared to the At4g35987 promoter (P87. The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.

  18. Failure problems in superheater spacers of steam generators; Problematica de fallas en espaciadores de sobrecalentadores de generadores de vapor

    Energy Technology Data Exchange (ETDEWEB)

    Chacon Nava, Jose G.; Martinez Villafane, Alberto [Instituto de Investigaciones Electricas, Cuernavaca (Mexico); Fuentes Samaniego, Raul [Universidad Autonoma de Nuevo Leon (Mexico); Mojica Calderon, Cecilio [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1988-12-31

    In this article the general aspects of the steam generator superheater fixed spacers failures are analyzed, emphasis is made on the influence several aspects such as the operation of the unit have, the appropriate execution of welds and the selection of binding materials. Likewise several recommendations are made to bring the failures to a minimum. [Espanol] En este articulo se analizan aspectos generales de fallas en espaciadores fijos de sobrecalentadores de generadores de vapor, y se hace hincapie en la influencia que tienen diversos aspectos tales como la operacion de la unidad, la adecuada ejecucion de soldaduras y la seleccion del material de aporte. Asimismo, se proponen algunas recomendaciones para reducir al minimo las fallas.

  19. Tailoring the spacer type and length in push-pull chromophores. Insights from a systematic theoretical study

    Science.gov (United States)

    Kerkines, Ioannis S. K.; Lathiotakis, Nektarios N.; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

    2016-06-01

    The predicting ability of Mulliken-type formulae in estimating the charge-transfer (CT) excitation energy in "push-pull" donor-bridge-acceptor (D-B-A) systems is evaluated systematically by tailoring the length of an oligoenic spacer bridge separating an N,N-dimethylanilino (DMA) donor and a dicyanovinyl (DCV) acceptor. In order to achieve satisfactory agreement with time-dependent density functional theory (TDDFT) values, the D⋯A distance and charge separation inside the D-B-A system are replaced with rigorously calculated "effective" values, while using "superdonor-superacceptor" energetics. The proposed modified Mulliken formula has the potential to be of significant assistance for cases when direct TDDFT calculation of the CT state is unfeasible.

  20. The family of N9-adenine: New entry for adenine-benzamide conjugates linked via versatile spacers

    Indian Academy of Sciences (India)

    Prabhpreet Singh

    2014-01-01

    We have prepared 4-nitrobenzamide-adenine conjugates (8, 13 and 14) linked with versatile spacer such as triethylene glycol (TEG), aminocaproic acid and ethyl chains which were eventually reduced to obtain the corresponding 4-aminobenzamide-adenine conjugates (1-3) in good yields. These conjugates bear a nucleobase for DNA recognition or self-assembly through base-pair complementarity, a biocompatible linker for interfacing with biological system, and a p-aminobenzamide moiety for pharmacological applications. The use of hydrophilic or lipophilic linkers may tune the dispersibility of these conjugates in different solvents, as well as impart different properties. In the preliminary experiments the versatility and application of these linkers has been tested for functionalization of SWCNTs.