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Sample records for 16s-23s intergenic spacer

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

    OpenAIRE

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

    2002-01-01

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

  2. 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.

  3. Identification of Carnobacterium Species by Restriction Fragment Length Polymorphism of the 16S-23S rRNA Gene Intergenic Spacer Region and Species-Specific PCR

    OpenAIRE

    Rachman, Cinta; Kabadjova, Petia; Valcheva, Rosica; Prévost, Hervé; Dousset, Xavier

    2004-01-01

    The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in ord...

  4. Detection of two Bartonella tamiae-like sequences in Amblyomma americanum (Acari: Ixodidae) using 16S-23S intergenic spacer region-specific primers.

    Science.gov (United States)

    Billeter, Sarah A; Miller, Melissa K; Breitschwerdt, Edward B; Levy, Michael G

    2008-01-01

    Four hundred and sixty-six questing Amblyomma americanum (L.) (Acari: Ixodidae) from Carolina County, VA, and 98 questing A. americanum from Chatham County, NC, were screened by polymerase chain reaction (PCR) for the Bartonella 16S-23S intergenic spacer region. Two amplicons, approximately 270-280 bp, were detected in two ticks from Virginia. Based upon PCR and sequencing, an adult male and adult female tick harbored DNA sequences closely related to Bartonella tamiae (DQ395180). Bartonella DNA was not detected in A. americanum from North Carolina. Potential transmission of Bartonella spp. by A. americanum should be the focus of future experimental studies.

  5. 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

    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...... 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....... 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....

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. Sequence Analysis and Comparison of 16S rRNA, 23S rRNA and 16S/23S Intergenic Spacer Region of Greening Bacterium Associated with Yellowing Disease (Huanglongbing) of Kinnow Mandarin.

    Science.gov (United States)

    Gupta, K N; Baranwal, V K; Haq, Q M R

    2012-03-01

    High incidence (up to 40%) of symptoms of yellowing and yellow mottling was observed in 5-8 years old orchards of kinnow mandarin {Citrus reticulate Balanco ('King' × 'Willow mandarin')} in the Punjab state of India during a survey in January 2007. These symptoms are often confused with nutrient deficiency and other stress related disorders. However, a greening bacterium has been attributed to cause the disease. The disease was graft transmissible and sequencing of 16S rRNA, 16S/23S intergenic spacer region and 23S rRNA of the greening bacterium associated with yellowing disease in kinnow mandarin confirmed it to be Candidatus Liberibacter asiaticus ('Ca L. asiaticus') showing maximum identity of 95.9% with 'Ca L. asiaticus' from USA and Brazil in 16S rRNA. The study indicates definite association of 'Ca L. asiaticus' with yellowing/chlorotic mottling symptoms of greening disease of kinnow mandarin in Punjab state of India.

  14. RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions.

    Science.gov (United States)

    García-Martínez, J; Bescós, I; Rodríguez-Sala, J J; Rodríguez-Valera, F

    2001-01-01

    A novel database, under the acronym RISSC (Ribosomal Intergenic Spacer Sequence Collection), has been created. It compiles more than 1600 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and is accessible through the Internet (http://ulises.umh.es/RISSC), where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches. Additionally, a characteristic feature of this region, the presence/absence and nature of tRNA genes within the spacer, is included in all the entries, even when not previously indicated in the original database. All these combined features could provide a useful documentation tool for studies on evolution, identification, typing and strain characterization, among others.

  15. 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.

  16. Heterogeneity within the gram-positive anaerobic cocci demonstrated by analysis of 16S-23S intergenic ribosomal RNA polymorphisms.

    Science.gov (United States)

    Hill, K E; Davies, C E; Wilson, M J; Stephens, P; Lewis, M A O; Hall, V; Brazier, J; Thomas, D W

    2002-11-01

    Peptostreptococci are gram-positive, strictly anaerobic bacteria which, although regarded as members of the commensal human microflora, are also frequently isolated from sites of clinical infection. The study of this diverse group of opportunist pathogens has been hindered by an inadequate taxonomy and the lack of a valid identification scheme. Recent re-classification of the Peptostreptococcus family into five distinct genus groups has helped to clarify the situation. However, this has been on the basis of 16S rRNA sequence determinations, which are both time-consuming and expensive. The aim of the present study was to evaluate the use of PCR-amplified ribosomal DNA spacer polymorphisms for the rapid differentiation of the currently recognised taxa within the group of anaerobic gram-positive cocci. A collection comprising 19 reference strains with representatives of each of the 15 species, two close relatives and two of the well-characterised groups, together with 38 test strains was studied. All strains were identified to species group level by phenotypic means. Amplification of the 16S-23S intergenic spacer region (ISR) with universal primers produced distinct banding patterns for all the 19 reference strains and the patterns could be differentiated easily visually. However, of the 38 test strains, less than half could be speciated from ISR analysis alone. Only five groups produced correlating banding patterns for all members tested (Peptoniphilus lacrimalis, P. ivorii, Anaerococcus octavius, Peptostreptococcus anaerobius and Micromonas micros). For other species, either the type strain differed significantly from other species members (e.g., A. hydrogenalis) or there appeared to be considerable intra-species variation (e.g., A. vaginalis). Partial 16S rRNA gene sequences for the 'trisimilis' and 'betaGAL' groups showed that both are most closely related to the Anaerococcus group. This work highlights the heterogeneous nature of a number of Peptostreptococcus

  17. Analysis of the 16S-23S rRNA gene internal transcribed spacer region in Klebsiella species.

    Science.gov (United States)

    Wang, Min; Cao, Boyang; Yu, Qunfang; Liu, Lei; Gao, Qili; Wang, Lei; Feng, Lu

    2008-11-01

    The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of Klebsiella spp., including Klebsiella pneumoniae subsp. pneumoniae, Klebsiella pneumoniae subsp. ozaenae, Klebsiella pneumoniae subsp. rhinoscleromatis, Klebsiella oxytoca, Klebsiella planticola, Klebsiella terrigena, and Klebsiella ornithinolytica, were characterized, and the feasibility of using ITS sequences to discriminate Klebsiella species and subspecies was explored. A total of 336 ITS sequences from 21 representative strains and 11 clinical isolates of Klebsiella were sequenced and analyzed. Three distinct ITS types-ITS(none) (without tRNA genes), ITS(glu) [with a tRNA(Glu (UUC)) gene], and ITS(ile+ala) [with tRNA(Ile (GAU)) and tRNA(Ala (UGC)) genes]-were detected in all species except for K. pneumoniae subsp. rhinoscleromatis, which has only ITS(glu) and ITS(ile+ala). The presence of ITS(none) in Enterobacteriaceae had never been reported before. Both the length and the sequence of each ITS type are highly conserved within the species, with identity levels from 0.961 to 1.000 for ITS(none), from 0.967 to 1.000 for ITS(glu), and from 0.968 to 1.000 for ITS(ile+ala). Interspecies sequence identities range from 0.775 to 0.989 for ITS(none), from 0.798 to 0.997 for ITS(glu), and from 0.712 to 0.985 for ITS(ile+ala). Regions with significant interspecies variations but low intraspecies polymorphisms were identified; these may be targeted in the design of probes for the identification of Klebsiella to the species level. Phylogenetic analysis based on ITS regions reveals the relationships among Klebsiella species similarly to that based on 16S rRNA genes.

  18. Restrição do 16S-23S DNAr intergênico para avaliação da diversidade de Azospirillum amazonense isolado de Brachiaria spp. Restriction of 16S-23S intergenic rDNA for diversity evaluation of Azospirillum amazonense isolated from different Brachiaria spp.

    Directory of Open Access Journals (Sweden)

    Fábio Bueno dos Reis Junior

    2006-03-01

    Full Text Available O objetivo deste trabalho foi avaliar a diversidade intra-específica de isolados de Azospirillum amazonense e estabelecer a possível influência de diferentes espécies de Brachiaria ssp. e diferentes condições edafoclimáticas. A caracterização da diversidade desses isolados foi conduzida, utilizando-se a análise de restrição da região intergênica 16S-23S DNAr. As estirpes estudadas separaram-se em dois grupos, definidos a 56% de similaridade. As espécies de Brachiaria ssp. influenciaram a diversidade de estirpes. A maioria dos isolados oriundos de B. decumbens e B. brizantha está inserida no primeiro grupo, enquanto os oriundos de B. humidicola concentram-se no segundo grupo.The aim of this work was to study the intra-specific diversity of Azospirillum amazonense isolates and to establish possible influences of different Brachiaria spp. and edaphoclimatic conditions. The characterization of the diversity among the isolates of A. amazonense studied was conducted using restriction analysis of the 16S-23S rDNA intergenic spacer region. The evaluated strains were separated in two groups, defined at 56% of similarity. Brachiaria spp. showed effects on strain diversity. Most part of the isolates from B. decumbens and B. brizantha are inserted in the first group, while B. humidicola isolates concentrate in the second group.

  19. Differentiation of acetic acid bacteria based on sequence analysis of 16S-23S rRNA gene internal transcribed spacer sequences.

    Science.gov (United States)

    González, Angel; Mas, Albert

    2011-06-30

    The 16S-23S gene internal transcribed spacer sequence of sixty-four strains belonging to different acetic acid bacteria genera were analyzed, and phylogenetic trees were generated for each genera. The topologies of the different trees were in accordance with the 16S rRNA gene trees, although the similarity percentages obtained between the species was shown to be much lower. These values suggest the usefulness of including the 16S-23S gene internal transcribed spacer region as a part of the polyphasic approach required for the further classification of acetic acid bacteria. Furthermore, the region could be a good target for primer and probe design. It has also been validated for use in the identification of unknown samples of this bacterial group from wine vinegar and fruit condiments.

  20. 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

  1. Analysis of 16S-23S rRNA internal transcribed spacer regions in Pasteurellaceae isolated from laboratory rodents.

    Science.gov (United States)

    Benga, Laurentiu; Benten, W Peter M; Engelhardt, Eva; Christensen, Henrik; Sager, Martin

    2012-09-01

    The internal transcribed spacer (ITS) regions of members of Pasteurellaceae isolated from rodents, including the [Pasteurella] pneumotropica biotypes Jawetz and Heyl, [Actinobacillus] muris, "Hemophilus influenzaemurium" and Bisgaard taxon 17 were studied and their feasibility to discriminate these species was analyzed. The reference strains of all species analyzed showed unique species-specific ITS patterns which were further present in 49 clinical isolates of [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris allowing their identification by comparison to the reference strains pattern. Sequence analysis of the amplified fragments revealed in all species, with exception of "H. influenzaemurium", a larger ITS(ile+ala) which contained the genes for tRNA(Ile(GAU)) and tRNA(Ala(UGC)) and a smaller ITS(glu) with the tRNA(Glu(UUC)) gene. "H. influenzaemurium" revealed two each of the larger and respectively the smaller ITS fragments. Both the length and the sequence of each ITS type were highly conserved within the [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris strains tested. On the contrary, ITS sequences revealed significant interspecies variations with identity levels ranging from 61.2 to 89.5% for ITS(ile+ala) and 56.5 to 86.8% for ITS(glu). Sequences regions with significant interspecies variation but highly conserved within the species were identified and might be used to design probes for the identification of rodent Pasteurellaceae to the species level. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Improved identification of rapidly growing mycobacteria by a 16S-23S internal transcribed spacer region PCR and capillary gel electrophoresis.

    Directory of Open Access Journals (Sweden)

    Timothy J Gray

    Full Text Available The identification of rapidly growing mycobacteria (RGM remains problematic because of evolving taxonomy, limitations of current phenotypic methods and absence of a universal gene target for reliable speciation. This study evaluated a novel method of identification of RGM by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS followed by resolution of amplified fragments by capillary gel electrophoresis (CGE. Nineteen American Type Culture Collection (ATCC Mycobacterium strains and 178 clinical isolates of RGM (12 species were studied. All RGM ATCC strains generated unique electropherograms with no overlap with slowly growing mycobacteria species, including M. tuberculosis. A total of 47 electropherograms for the 178 clinical isolates were observed allowing the speciation of 175/178 (98.3% isolates, including the differentiation of the closely related species, M. massiliense (M. abscessus subspecies bolletii and M. abscessus (M. abscessus sensu stricto. ITS fragment size ranged from 332 to 534 bp and 33.7% of clinical isolates generated electropherograms with two distinct peaks, while the remainder where characterized with a single peak. Unique peaks (fragment lengths were identified for 11/12 (92% RGM species with only M. moriokaense having an indistinguishable electropherogram from a rarely encountered CGE subtype of M. fortuitum. We conclude that amplification of the 16S-23S ITS gene region followed by resolution of fragments by CGE is a simple, rapid, accurate and reproducible method for species identification and characterization of the RGM.

  3. Establishment and analysis of specific DNA patterns in 16S-23S rRNA gene spacer regions for differentiating different bacteria

    Institute of Scientific and Technical Information of China (English)

    尚世强; 付君芬; 董关萍; 洪文澜; 杜立中; 俞锡林

    2003-01-01

    Objective To establish the specific 16S-23S rRNA gene spacer regions in different bacteria using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), DNA cloning and sequences analysis. Methods A pair of primers were selected from highly conserved sequences adjacent to the 16S-23S rRNA spacer region. Bacterial DNA from sixty-one strains of standard bacteria and corresponding clinical isolates representative of 20 genera and 26 species was amplified by PCR, and further analyzed by RFLP, DNA cloning and sequences analysis. Furthermore, all specimens were examined by bacterial culturing and PCR-RFLP analysis. The evaluation of these assays in practical clinic practice was also discussed.Results Restriction enzyme analysis revealed one, two or three bands or more observed among the 26 different standard strains. The sensitivity of PCR reached 2.5 colony-forming unit (CFU), and there was no cross reaction with human genomic DNA, fungus or virus. Fourteen species could be distinguished immediately by PCR, while another 10 species were further identified by Hinf Ⅰ or Alu Ⅰ digestion. The only difference between K.pneumoniae and E.durans was located at the site of the 779th nucleotide according to the sequence analysis and only XmaⅢ digestion could distinguish one from another. Of 42 specimens from septicemic neonates, 15 were identified as positive by blood culture at a rate of 35.7%. However, 27 specimens identified as positive by PCR, with a rate of 64.2%, a method significantly more effective than blood culture (P<0.01). Of 6 cerebrospinal fluid (CSF) specimens, one tested positive for S.epidermidis was also positive by PCR, two culture negative were positive by PCR and diagnosed as S.epidermidis according to the DNA pattern. One positive for C.neoformans was negative by PCR. The other two specimens were negative by both PCR and culture.Conclusions The method of detecting bacterial 16S-23S rRNA spacer regions using PCR

  4. Phylogenetic diversity of rhizobia associated with horsegram [Macrotyloma uniflorum (Lam.) Verdc.] grown in South India based on glnII, recA and 16S-23S intergenic sequence analyses.

    Science.gov (United States)

    Appunu, Chinnaswamy; Ganesan, Govindan; Kalita, Michał; Kaushik, Raghavan; Saranya, Balamurugan; Prabavathy, Vaiyapuri Ramalingam; Sudha, Nair

    2011-04-01

    Horsegram [Macrotyloma uniflorum (Lam.) Verdc.) is an important grain legume and fodder crop in India. Information on root nodule endosymbionts of this legume in India is limited. In the present study, 69 isolates from naturally occurring root nodules of horsegram collected from two agro-eco-climatic regions of South India was analyzed by generation rate, acid/alkali reaction on YMA medium, restriction fragment length polymorphism analysis of 16S-23S rDNA intergenic spacer region (IGS), and sequence analyses of IGS and housekeeping genes glnII and recA. Based on the rDNA IGS RFLP by means of three restriction enzymes rhizobia were grouped in five clusters (I-V). By sequence analysis of 16S-23S rDNA IGS identified genotypes of horsegram rhizobia were distributed into five divergent lineages of Bradyrhizobium genus which comprised (I) the IGS type IV rhizobia and valid species B. yuanmingense, (II) the strains of IGS type I and Bradyrhizobium sp. ORS 3257 isolated from Vigna sp., (III) the strains of the IGS type II and Bradyrhizobium sp. CIRADAc12 from Acacia sp., (IV) the IGS type V strains and Bradyrhizobium sp. genospecies IV, and (V) comprising genetically distinct IGS type III strains which probably represent an uncharacterized new genomic species. Nearly, 87% of indigenous horsegram isolates (IGS types I, II, III, and V) could not be related to any other species within the genus Bradyrhizobium. Phylogeny based on housekeeping glnII and recA genes confirmed those results found by the analysis of the IGS sequence. All the isolated rhizobia nodulated Macrotyloma sp. and Vigna spp., and only some of them formed nodules on Arachis hypogeae. The isolates within each IGS type varied in their ability to fix nitrogen. Selection for high symbiotic effective strains could reward horsegram production in poor soils of South India where this legume is largely cultivated.

  5. Molecular analysis of the 16S-23S rDNA internal spacer region (ISR) and truncated tRNA(Ala) gene segments in Campylobacter lari.

    Science.gov (United States)

    Hayashi, K; Tazumi, A; Nakanishi, S; Nakajima, T; Matsubara, K; Ueno, H; Moore, J E; Millar, B C; Matsuda, M

    2012-06-01

    Following PCR amplification and sequencing, nucleotide sequence alignment analyses demonstrated the presence of two kinds of 16S-23S rDNA internal spacer regions (ISRs), namely, long length ISRs of 837-844 base pair (bp) [n = six for urease-negative (UN) Campylobacter lari isolates, UN C. lari JCM2530(T), RM2100, 176, 293, 299 and 448] and short length ISRs of 679-725 bp [n = six for UN C. lari: n = 14 for urease-positive thermophilic Campylobacter (UPTC) isolates]. The analyses also indicated that the short length ISRs mainly lacked the 156 bp sequence from the nucleotide positions 122-277 bp in long length ISRs for UN C. lari JCM2530(T). The 156 bp sequences shared 94.9-96.8 % sequence similarity among six isolates. Surprisingly, atypical tRNA(Ala) gene segment (5' end 35 bp), which was extremely truncated, occurred within the 156 bp sequences in the long length ISRs, as an unexpected tRNA(Ala) pseudogene. An order of the intercistronic tRNA genes within the short nucleotide spacer of 5'-16S rDNA-tRNA(Ala)-tRNA(Ile)-23S rDNA-3' occurred in all the C. lari isolates examined.

  6. Diversity of 16S-23S rDNA internal transcribed spacer (ITS reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors.

    Directory of Open Access Journals (Sweden)

    Andrew P Liguori

    Full Text Available Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.

  7. Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru.

    Science.gov (United States)

    Santillana, Nery; Ramírez-Bahena, Martha Helena; García-Fraile, Paula; Velázquez, Encarna; Zúñiga, Doris

    2008-03-01

    In this study 17 isolates from effective nodules of Vicia faba and Pisum sativum var. macrocarpum growing in different soils from Peru were isolated and characterized. The isolates, presenting 11 different RAPD profiles, were distributed in three groups on the basis of their 16S-RFLP patterns. The 16S rRNA gene sequences of strains from 16S-RFLP groups I, II and III were closely related (identities higher than 99.5%) to Rhizobium leguminosarum bv. trifolii DSM 30141 (=ATCC 14480), R. leguminosarum bv. viciae DSM 30132(T) and Rhizobium etli CFN42(T) (=USDA 9032(T)), respectively. The analysis of the 16S-23S intergenic spacer (ITS) and two housekeeping genes, atpD and recA, confirmed the identification of strains from group I, however those from groups II and III were phylogenetically divergent to strains DSM 30132(T) and CFN42(T). These results support the fact that the 16S rRNA gene is not adequate for identification at species level within genus Rhizobium and suggest the existence of putative new species within the phylogenetic group of R. leguminosarum. They also confirm the need of a taxonomic revision of R. leguminosarum since the reference strains of the three biovars included in this study are phylogenetically divergent according to their ITS, atpD and recA gene sequences.

  8. Development of a multiplex PCR assay based on the 16S-23S rRNA internal transcribed spacer for the detection and identification of rodent Pasteurellaceae.

    Science.gov (United States)

    Benga, Laurentiu; Benten, W Peter M; Engelhardt, Eva; Bleich, André; Gougoula, Christina; Sager, Martin

    2013-11-01

    The rodents Pasteurellaceae have to be excluded from the specified pathogen free experimental animal facilities. Despite the biological and economic importance of Pasteurellaceae in relation to experimental animals just a few molecular based methods are available for their detection and identification. The aim of the present investigation was to develop a multiplex PCR assay allowing detection of all rodent Pasteurellaceae and identification of [Pasteurella] pneumotropica biotype Jawetz, [P.] pneumotropica biotype Heyl and [Actinobacillus] muris, as the most prevalent members of the group. For this, a Pasteurellaceae common forward primer located on the 16S rRNA gene was used in conjunction with four different reverse primers specific for [P.] pneumotropica biotype Jawetz, [P.] pneumotropica biotype Heyl, [A.] muris and a common reverse primer for all rodent Pasteurellaceae, all targeting the 16S-23S rRNA internal transcribed spacer sequences. The performance characteristics of the assay were tested against 125 Pasteurellaceae isolates belonging to eleven different species and including 34 strains of [P.] pneumotropica biotype Jawetz, 44 strains of [P.] pneumotropica biotype Heyl and 37 strains of [A.] muris. Additionally, eight other mouse associated bacterial species which could pose a diagnostic problem were included. The assay showed 100% sensitivity and specificity. Identification of the clinical isolates was validated by ITS profiling and when necessary by 16S rRNA gene sequencing. This multiplex PCR represents the first molecular tool able to detect and differentiate in a single assay among the Pasteurellaceae found in laboratory mouse and may become a reliable alternative to the present diagnostic methods. © 2013.

  9. 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

    OpenAIRE

    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 speci...

  10. 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

    We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68°C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming). Fluorescence microscopy and microsensor measurements of O2 and oxygenic photosynth......We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68°C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming). Fluorescence microscopy and microsensor measurements of O2 and oxygenic...... 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...

  11. 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

  12. 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.

  13. Quick identification of acetic acid bacteria based on nucleotide sequences of the 16S-23S rDNA internal transcribed spacer region and of the PQQ-dependent alcohol dehydrogenase gene.

    Science.gov (United States)

    Trcek, Janja

    2005-10-01

    Acetic acid bacteria (AAB) are well known for oxidizing different ethanol-containing substrates into various types of vinegar. They are also used for production of some biotechnologically important products, such as sorbose and gluconic acids. However, their presence is not always appreciated since certain species also spoil wine, juice, beer and fruits. To be able to follow AAB in all these processes, the species involved must be identified accurately and quickly. Because of inaccuracy and very time-consuming phenotypic analysis of AAB, the application of molecular methods is necessary. Since the pairwise comparison among the 16S rRNA gene sequences of AAB shows very high similarity (up to 99.9%) other DNA-targets should be used. Our previous studies showed that the restriction analysis of 16S-23S rDNA internal transcribed spacer region is a suitable approach for quick affiliation of an acetic acid bacterium to a distinct group of restriction types and also for quick identification of a potentially novel species of acetic acid bacterium (Trcek & Teuber 2002; Trcek 2002). However, with the exception of two conserved genes, encoding tRNAIle and tRNAAla, the sequences of 16S-23S rDNA are highly divergent among AAB species. For this reason we analyzed in this study a gene encoding PQQ-dependent ADH as a possible DNA-target. First we confirmed the expression of subunit I of PQQ-dependent ADH (AdhA) also in Asaia, the only genus of AAB which exhibits little or no ADH-activity. Further we analyzed the partial sequences of adhA among some representative species of the genera Acetobacter, Gluconobacter and Gluconacetobacter. The conserved and variable regions in these sequences made possible the construction of A. acetispecific oligonucleotide the specificity of which was confirmed in PCR-reaction using 45 well-defined strains of AAB as DNA-templates. The primer was also successfully used in direct identification of A. aceti from home made cider vinegar as well as for

  14. 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

  15. 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.

  16. Phylogenetic study of Geitlerinema and Microcystis (Cyanobacteria) using PC-IGS and 16S-23S ITS as markers: investigation of horizontal gene transfer.

    Science.gov (United States)

    Piccin-Santos, Viviane; Brandão, Marcelo Mendes; Bittencourt-Oliveira, Maria Do Carmo

    2014-08-01

    Selection of genes that have not been horizontally transferred for prokaryote phylogenetic inferences is regarded as a challenging task. The markers internal transcribed spacer of ribosomal genes (16S-23S ITS) and phycocyanin intergenic spacer (PC-IGS), based on the operons of ribosomal and phycocyanin genes respectively, are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the phycocyanin operon may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of PC-IGS, phylogenetic trees of Geitlerinema and Microcystis strains were generated using PC-IGS and 16S-23S ITS and compared. Phylogenetic trees based on the two markers were mostly congruent for Geitlerinema and Microcystis, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Thus, PC-IGS is a suitable marker, along with 16S-23S ITS for phylogenetic studies of cyanobacteria.

  17. 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.

  18. 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

  19. Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events.

    Science.gov (United States)

    Maslunka, Christopher; Gürtler, Volker; Seviour, Robert

    2015-02-01

    The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.

  20. Specific Detection of Yersinia enterocolitica by Loop-mediated Isothermal Amplification(LAMP)Targeting 16S-23S rDNA Internal Transcribed Spacer(ITS)%利用环介导恒温扩增方法特异性鉴定食品中小肠结肠炎耶尔森氏菌

    Institute of Scientific and Technical Information of China (English)

    赵玉龙; 张宏伟; 刘伟; 刘寅; 郑文杰; 魏亚东; 叶露萌; 黄熙泰

    2010-01-01

    介绍一种便捷、灵敏而又特异的用于检测治病细菌小肠结肠炎耶尔森氏菌(Yersinia enterocolitica)的 环介导恒温扩增基因检测技术(loop-mediated isothermal amplification,LAMP),该技术分别使用特异对应于16S-23S rDNA间区(16S-23S rDNA internal transcribed spacer,ITS)靶序列中6个基因区段的3对引物,在Bst 聚合酶的作用下对靶序列进行恒温扩增,整个检测反应只需1 h.利用这种技术检测小肠结肠炎耶尔森氏菌基因,阳性结果可通过直接观察反应液中有无焦磷酸镁白色沉淀,而无需经电泳检测.试验结果表明,LAMP对Y.enterocolitica的检测灵敏度可达到8 CFU/反应.

  1. 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.

  2. Comparison of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer Analysis

    Directory of Open Access Journals (Sweden)

    CECILIA ANNA SEUMAHU

    2012-06-01

    Full Text Available Tempe fermentation involved complex microbial communities which are only revealed partially through culture dependent methods. Culture-independent methods would be potential to unravel this complex microbial fermentation. Appropriate DNA extraction is an essential tool to obtain reliable data from culture independent method. In this study, we employed two commercial DNA extraction methods to find the best one for microbial community characterization employing amplified ribosomal intergenic spacer analysis (ARISA. Our result showed that PowerFood Microbial DNA Isolation Kit-MOBIO (PFMDIK is an excellent method for microbial DNA extraction from tempe. It gave high quantity and quality of DNA suitable for PCR amplification of 16S-23S rRNA intergenic spacer to yield a diverse and reproducible ARISA profile.

  3. Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains.

    Science.gov (United States)

    Cejková, Darina; Zobaníková, Marie; Pospísilová, Petra; Strouhal, Michal; Mikalová, Lenka; Weinstock, George M; Smajs, David

    2013-02-01

    This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S-23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S-23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.

  4. 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.

  5. 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’.

  6. 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.

  7. Genotyping of Salmonella spp.by 16S-23S rRNA assay%沙门菌PCR-dHPLC基因分型方法建立

    Institute of Scientific and Technical Information of China (English)

    张东方; 袁飞; 王娉; 杨海荣; 胡玥; 赵勇胜; 陈颖; 葛毅强

    2012-01-01

    Objective To develop a polymerase chain reaction-denaturing high performance liquid chromatography (PCR-dHPLC) genotyping method for genotyping of Salmonella spp. Methods Specific primers of 16S-23S rRNA in-tergenic spacer sequence (ITS) region were used to subtype Salmonella spp. The PCR amplification products of experimental strains were separated by dHPLC. The results of genotyping achieved through the differences between dHPLC peaks and were comparaed to the results obtained by serological typing and biochemical typing. Results Totally 89 Salmonella spp. strains were successfully genotyped into 12 dHPLC types(D type). All the Salmonella spp. strains had one same chromatographic peak,while other food-born pathogens showed no similar peak. DNA sequence analysis showed that the sequence was 600bp. The results indicate that the chromatographic peak is specific to Salmonella spp. Comparing the dHPLC genotyping results with those of serological typing and biochemical typing, we found dHPLC genotyping results were significantly differ from the serological typing results, while were consistent with that of the biochemical typing. Conclusion DHPLC is a novel, rapid, highly accurate, and cost-effective genotyping method for genotyping of Salmonella spp.%目的 建立沙门菌聚合酶链反应-变性高效液相色谱(PCR-dHPLC)基因分型方法.方法 采用16S ~23S rRNA内转录间隔(ITS)作为沙门菌分型目的基因,确定特异性扩增引物,进行PCR扩增,扩增产物经dHPLC分离,根据dHPLC图谱峰型差异进行分型,并与血清学和生化分型结果比较.结果 89株沙门菌共分为12个dHPLC型(D型);所有沙门菌均有1个相同色谱峰,克隆测序结果表明,其片断大小为600 bp,其他8种食源性致病菌对照株无此色谱峰,应为沙门菌16S~23S rRNA基因序列的特征性条带,分型结果与血清学差异较大,与生化分型结果有一定一致性.结论 所建立的沙门菌PCR-dHPLC基因分型方法具快速

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Optimisation of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil

    Directory of Open Access Journals (Sweden)

    Karin Jacobs

    2010-07-01

    Full Text Available Automated ribosomal intergenic spacer analysis (ARISA has become a commonly used molecular technique for the study of microbial populations in environmental samples. The reproducibility and accuracy of ARISA, with and without the polymerase chain reaction (PCR are important aspects that influence the results and effectiveness of these techniques. We used the primer set ITS4/ITS5 for ARISA to assess the fungal community composition of two sites situated in the Sand Fynbos. The primer set proved to deliver reproducible ARISA profiles of the fungal community composition with little variation observed between ARISA-PCRs. Variation that occurred in a sample due to repeated DNA extraction is expected for ecological studies. This reproducibility made ARISA a useful tool for the assessment and comparison of diversity in ecological samples. In this paper, we also offered particular suggestions concerning the binning strategy for the analysis of ARISA profiles.

  13. Application of rps16 Intron and trnL-trnF Intergenic Spacer Sequences to Identify Rengas Clone Riau

    Directory of Open Access Journals (Sweden)

    Dewi Indriyani Roslim

    2017-07-01

    Full Text Available Rengas clone Riau has been identified using morphological characters and molecular technique with a psbA-trnH intergenic spacer, however, this method can only determine its taxonomic status at genus level, namely Gluta sp.  This study reports application two DNA barcodes, i.e. rps16 intron and trnL-trnF intergenic spacer, to identify Rengas clone Riau.  The methods included collection of the leaves from Kajuik Lake, total DNA isolation, electrophoresis, PCR (polymerase chain reaction, gel purification and sequencing.  The rps16 intron size was 659 bp and the trnL-trnF intergenic spacer was 527 bp. The BLASTn analysis showed that sequences of the rps16 intron and the trnL-trnF intergenic spacer of Gluta sp clone Riau had 100% similarity to those of G. renghas deposited in GenBank.  These results were supported by high max score, high total score, query cover = 100%, and E-value = 0.  The dendrograms also showed the closest relationship of Gluta sp clone Riau with G. renghas deposited in GenBank compared to other species of Gluta.  In conclusion, this study succeeded in identifying Rengas clone Riau as Gluta renghas by using sequences of the rps16 intron and the trnL-trnF intergenic spacer. A combination of DNA barcodes could be applied to identify various plants as long as the database for the DNA barcodes is available in public database such as GenBank. 

  14. Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic Archaea changes in an anaerobic digester.

    Science.gov (United States)

    Ciesielski, Slawomir; Bułkowska, Katarzyna; Dabrowska, Dorota; Kaczmarczyk, Dariusz; Kowal, Przemyslaw; Możejko, Justyna

    2013-08-01

    The applicability of a newly-designed PCR primer pair in examination of methanogenic Archaea in a digester treating plant biomass was evaluated by Ribosmal Intergenic Spacer Analysis (RISA). To find a suitable approach, three variants of RISA were tested: (1) standard, polyacrylamide gel-based, (2) automated, utilized capillary electrophoresis (GA-ARISA), and (3) automated microfluidics-based (MF-ARISA). All three techniques yielded a consistent picture of archaeal community structure changes during anaerobic digestion monitored for more than 6 weeks. While automated variants were more practical for handling and rapid analysis of methanogenic Archaea, the gel-based technique was advantageous when micro-organism identification was required. A DNA-sequence analysis of dominant bands extracted from the gel revealed that the main role in methane synthesis was played by micro-organisms affiliated with Methanosarcina barkeri. The obtained results revealed that RISA is a robust method allowing for detailed analysis of archaeal community structure during organic biomass conversion into biogas. In addition, our results showed that GA-ARISA has a higher resolution and reproducibility than other variants of RISA and could be used as a technique for tracking changes in methanogenic Archaea in an anaerobic digester.

  15. Ribosomal Intergenic Spacer 1 Based Characterization of Button Mushroom (Agaricus bisporus) Strains.

    Science.gov (United States)

    Kwon, Hyuk Woo; Choi, Min Ah; Kim, Dae Wook; Oh, Youn-Lee; Hyun, Min Woo; Kong, Won-Sik; Kim, Seong Hwan

    2016-12-01

    Breeding the button mushroom requires genetic information about its strains. This study was undertaken to genetically characterize four domestically bred button mushroom strains (Saea, Saejung, Saedo, Saeyeon cultivars) and to assess the possibility of using the intergenic spacer 1 (IGS1) region of rDNA as a genetically variable region in the genetic characterization. For the experiment, 34 strains of Agaricus bisporus, two strains of A. bitorquis, and one strain of A. silvaticus, from 17 countries were used. Nucleotide sequence analysis of IGS1 rDNA in these 37 Agaricus strains confirmed that genetic variations exist, not only among the four domestic strains, but also between the four domestic strains and foreign strains. Crossing two different haploid strains of A. bisporus seems to generate genetic variation in the IGS1 region in their off-spring haploid strains. Phylogenetic analysis based on the IGS1 sequence revealed all A. bisporus strains could be differentiated from A. silvaticus and A. bitorquis strains. Five genetic groups were resolved among A. bisporus strains. Saejung and Saeyeon cultivars formed a separate genetic group. Our results suggest that IGS1 could be complementarily applied in the polymorphism analysis of button mushroom.

  16. Sequences in the intergenic spacer influence RNA Pol I transcription from the human rRNA promoter

    Energy Technology Data Exchange (ETDEWEB)

    Li, W.M.; Sylvester, J.E. [Hahnemann Univ., Philadelphia, PA (United States)

    1994-09-01

    In most eucaryotic species, ribosomal genes are tandemly repeated about 100-5000 times per haploid genome. The 43 Kb human rDNA repeat consists of a 13 Kb coding region for the 18S, 5.8S, 28S ribosomal RNAs (rRNAs) and transcribed spacers separated by a 30 Kb intergenic spacer. For species such as frog, mouse and rat, sequences in the intergenic spacer other than the gene promoter have been shown to modulate transcription of the ribosomal gene. These sequences are spacer promoters, enhancers and the terminator for spacer transcription. We are addressing whether the human ribosomal gene promoter is similarly influenced. In-vitro transcription run-off assays have revealed that the 4.5 kb region (CBE), directly upstream of the gene promoter, has cis-stimulation and trans-competition properties. This suggests that the CBE fragment contains an enhancer(s) for ribosomal gene transcription. Further experiments have shown that a fragment ({approximately}1.6 kb) within the CBE fragment also has trans-competition function. Deletion subclones of this region are being tested to delineate the exact sequences responsible for these modulating activities. Previous sequence analysis and functional studies have revealed that CBE contains regions of DNA capable of adopting alternative structures such as bent DNA, Z-DNA, and triple-stranded DNA. Whether these structures are required for modulating transcription remains to be determined as does the specific DNA-protein interaction involved.

  17. Serotyping, ribotyping, PCR-mediated ribosomal 16S-23S spacer analysis and arbitrarily primed PCR for epidemiological studies on Legionella pneumophila

    NARCIS (Netherlands)

    A.F. van Belkum (Alex); H. Maas (Hugo); H.A. Verbrugh (Henri); N. van Leeuwen (N.)

    1996-01-01

    textabstractFifty clinical and environmental isolates of Legionella pneumophila were typed serologically and by DNA fingerprinting using arbitrarily primed polymerase chain reaction (AP-PCR). Furthermore, variability in and around ribosomal operons was assessed by conventional ribotyping and

  18. Serotyping, ribotyping, PCR-mediated ribosomal 16S-23S spacer analysis and arbitrarily primed PCR for epidemiological studies on Legionella pneumophila

    NARCIS (Netherlands)

    A.F. van Belkum (Alex); H. Maas (Hugo); H.A. Verbrugh (Henri); N. van Leeuwen (N.)

    1996-01-01

    textabstractFifty clinical and environmental isolates of Legionella pneumophila were typed serologically and by DNA fingerprinting using arbitrarily primed polymerase chain reaction (AP-PCR). Furthermore, variability in and around ribosomal operons was assessed by conventional ribotyping and PCR-med

  19. Unusual structure of ribosomal DNA in the copepod Tigriopus californicus: intergenic spacer sequences lack internal subrepeats.

    Science.gov (United States)

    Burton, R S; Metz, E C; Flowers, J M; Willett, C S

    2005-01-03

    Eukaryotic nuclear ribosomal DNA (rDNA) is typically arranged as a series of tandem repeats coding for 18S, 5.8S, and 28S ribosomal RNAs. Transcription of rDNA repeats is initiated in the intergenic spacer (IGS) region upstream of the 18S gene. The IGS region itself typically consists of a set of subrepeats that function as transcriptional enhancers. Two important evolutionary forces have been proposed to act on the IGS region: first, selection may favor changes in the number of subrepeats that adaptively adjust rates of rDNA transcription, and second, coevolution of IGS sequence with RNA polymerase I transcription factors may lead to species specificity of the rDNA transcription machinery. To investigate the potential role of these forces on population differentiation and hybrid breakdown in the intertidal copepod Tigriopus californicus, we have characterized the rDNA of five T. californicus populations from the Pacific Coast of North America and one sample of T. brevicornicus from Scotland. Major findings are as follows: (1) the structural genes for 18S and 28S are highly conserved across T. californicus populations, in contrast to other nuclear and mitochondrial DNA (mtDNA) genes previously studied in these populations. (2) There is extensive differentiation among populations in the IGS region; in the extreme, no homology is observed across the IGS sequences (>2 kb) from the two Tigriopus species. (3) None of the Tigriopus IGS sequences have the subrepeat structure common to other eukaryotic IGS regions. (4) Segregation of rDNA in laboratory crosses indicates that rDNA is located on at least two separate chromosomes in T. californicus. These data suggest that although IGS length polymorphism does not appear to play the adaptive role hypothesized in some other eukaryotic systems, sequence divergence in the rDNA promoter region within the IGS could lead to population specificity of transcription in hybrids.

  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. Absence of DNA sequence diversity of the intergenic spacer 1 region in Malassezia nana isolates from cats.

    Science.gov (United States)

    de Bellis, Filippo; Castellá, Gemma; Cabañes, F Javier; Bond, Ross

    2010-03-01

    Malassezia nana is a recently-described lipophilic yeast that has been isolated from the ear canals and skin of cats in Japan and Europe and from Brazilian cattle with or without otitis externa. Previous reports have demonstrated that significant intra-species variability exists in the DNA sequence of the intergenic spacer 1 region (IGS1), particularly amongst M. globosa, M. restricta and M. pachydermatis, and that certain IGS genotypes are associated with various epidemiological factors, including host disease status. In the present study, we demonstrated that the IGS1 sequences of 12 UK isolates of M. nana from cats and of six isolates from Spain (5 cat, 1 dog) were identical to each other and to CBS 9557, the M. nana type culture originally obtained from a Japanese cat with otitis externa. Further studies are needed to determine whether other genotypes of M. nana can be identified and associated with geographical regions and the species and disease status of mammalian hosts.

  3. The mitochondrial genome of the leaf-cutter ant Atta laevigata: a mitogenome with a large number of intergenic spacers.

    Directory of Open Access Journals (Sweden)

    Cynara de Melo Rodovalho

    Full Text Available In this paper we describe the nearly complete mitochondrial genome of the leaf-cutter ant Atta laevigata, assembled using transcriptomic libraries from Sanger and Illumina next generation sequencing (NGS, and PCR products. This mitogenome was found to be very large (18,729 bp, given the presence of 30 non-coding intergenic spacers (IGS spanning 3,808 bp. A portion of the putative control region remained unsequenced. The gene content and organization correspond to that inferred for the ancestral pancrustacea, except for two tRNA gene rearrangements that have been described previously in other ants. The IGS were highly variable in length and dispersed through the mitogenome. This pattern was also found for the other hymenopterans in particular for the monophyletic Apocrita. These spacers with unknown function may be valuable for characterizing genome evolution and distinguishing closely related species and individuals. NGS provided better coverage than Sanger sequencing, especially for tRNA and ribosomal subunit genes, thus facilitating efforts to fill in sequence gaps. The results obtained showed that data from transcriptomic libraries contain valuable information for assembling mitogenomes. The present data also provide a source of molecular markers that will be very important for improving our understanding of genomic evolutionary processes and phylogenetic relationships among hymenopterans.

  4. High prevalence of spotted fever group rickettsiae in Amblyomma variegatum from Uganda and their identification using sizes of intergenic spacers.

    Science.gov (United States)

    Nakao, Ryo; Qiu, Yongjin; Igarashi, Manabu; Magona, Joseph W; Zhou, Lijia; Ito, Kimihito; Sugimoto, Chihiro

    2013-12-01

    The spotted fever group (SFG) rickettsiae are obligate intracellular bacteria transmitted by ticks that cause several tick-borne rickettsioses in humans worldwide. This study was intended to determine the prevalence of SFG rickettsiae in Amblyomma variegatum from 7 districts across Uganda. In addition to sequencing of gltA and ompA genes, identification of Rickettsia species based on the sizes of highly variable intergenic spacers, namely, dksA-xerC, mppA-purC, and rpmE-tRNA(fMet) was carried out. Application of multiplex PCR for simultaneous amplification of 3 spacers combined with capillary electrophoresis separation allowed simple, accurate, and high-throughput fragment sizing with considerable time and cost savings. Rickettsia genus-specific real-time PCR detected 136 positives out of 140 samples, giving an overall prevalence of 97.1%. Most samples (n=113) had a size combination of 225, 195, and 341 bp for dksA-xerC, mppA-purC, and rpmE-tRNA(fMet), respectively, which was identical to that of R. africae, a causative agent of African tick bite fever. In addition, several samples had size variants in either dksA-xerC or rpmE-tRNA(fMet). Nonetheless, the partial sequences of gltA and ompA genes of samples of all size combinations showed the greatest similarity to R. africae (99.3-100% for gltA and 98.1-100% for ompA). Given these results, it is highly possible that the tested ticks were infected with R. africae or closely related species. This is a first report on molecular genetic detection of R. africae and its high endemicity in Uganda. Clinicians in this country should be aware of this pathogen as a cause of non-malarial febrile illness. This study provided a starting point for the development of Rickettsia species identification based on the sizes of intergenic spacers. The procedure is simple, rapid, and cost-effective to perform; hence it might be particularly well suited for preliminary species identification in epidemiological investigations. The results

  5. 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.

  6. 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.

  7. 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.

  8. Detection of Clostridium tyrobutyricum in milk to prevent late blowing in cheese by automated ribosomal intergenic spacer analysis.

    Science.gov (United States)

    Panelli, Simona; Brambati, Eva; Bonacina, Cesare; Feligini, Maria

    2013-10-01

    Clostridium tyrobutyricum has been identified as the main causal agent of the late blowing defect in cheese, with major effects on quality and commercial value. In this work, for the first time, we applied automated ribosomal intergenic spacer analysis (ARISA) approach to diagnose the presence of C. tyrobutyricum in raw milk before cheesemaking. A species-specific primer set was designed and used for this original application of the ARISA. Sensitivity of detection, reproducibility of the fluorescent PCR assay, and repeatability of the capillary electrophoretic analysis of amplicons were evaluated using DNA extracted from milk added with known amounts of C. tyrobutyricum genome copies, ranging from 3 × 10(6) to 3. Results indicated that the sensitivity of the technique permits to detect the bacterium in all the samples. The reproducibility, evaluated by analyzing 3 sets of serial dilutions, resulted satisfactory, with little deviation within PCR reactions amplifying the same starting amount of template (standard deviations ≤ 0.1, coefficients of variation ≤ 3%). The peaks' fluorescence displayed an evident correspondence with the number of genome copies contained in each dilution. The capillary electrophoretic analysis, tested by running a single PCR product per dilution point in 10 repeats, resulted efficient and highly repeatable, with excellent coefficients of variation ≤ 2% and standard deviations ≤ 0.1 in all the sample sets. This application of ARISA gives good estimates of the total C. tyrobutyricum DNA content allowing a specific, fine-scale resolution of this pollutant species in a complex system as milk. A further advantage linked to the automatization of the process.

  9. Ribosomal RNA gene silencing in interpopulation hybrids of Tigriopus californicus: nucleolar dominance in the absence of intergenic spacer subrepeats.

    Science.gov (United States)

    Flowers, Jonathan M; Burton, Ronald S

    2006-07-01

    A common feature of interspecific animal and plant hybrids is the uniparental silencing of ribosomal RNA gene transcription, or nucleolar dominance. A leading explanation for the genetic basis of nucleolar dominance in animal hybrids is the enhancer-imbalance model. The model proposes that limiting transcription factors are titrated by a greater number of enhancer-bearing subrepeat elements in the intergenic spacer (IGS) of the dominant cluster of genes. The importance of subrepeats for nucleolar dominance has repeatedly been supported in competition assays between Xenopus laevis and X. borealis minigene constructs injected into oocytes. However, a more general test of the importance of IGS subrepeats for nuclear dominance in vivo has not been conducted. In this report, rRNA gene expression was examined in interpopulation hybrids of the marine copepod Tigriopus californicus. This species offers a rare opportunity to test the role of IGS subrepeats in nucleolar dominance because the internal subrepeat structure, found in the IGS of virtually all animal and plant species, is absent in T. californicus. Our results clearly establish that nucleolar dominance occurs in F1 and F2 interpopulation hybrids of this species. In the F2 generation, nucleolar dominance appears to break down in some hybrids in a fashion that is inconsistent with a transcription factor titration model. These results are significant because they indicate that nucleolar dominance can be established and maintained without enhancer-bearing repeat elements in the IGS. This challenges the generality of the enhancer-imbalance model for nucleolar dominance and suggests that dominance of rRNA transcription in animals may be determined by epigenetic factors as has been established in plants.

  10. A one-step reaction for the rapid identification of Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti using oligonucleotide primers designed from the 16S-23S rRNA intergenic sequences

    National Research Council Canada - National Science Library

    Ferchichi, M; Valcheva, R; Prévost, H; Onno, B; Dousset, X

    2008-01-01

    ...) were designed to rapidly discriminate between Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti species recently isolated from French sourdough...

  11. 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.

  12. 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.

  13. Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.

    Science.gov (United States)

    Gago, Sara; Alastruey-Izquierdo, Ana; Marconi, Marco; Buitrago, María José; Kerhornou, Arnaud; Kersey, Paul J; Mellado, Emilia; Cuenca-Estrella, Manuel; Rodríguez-Tudela, Juan Luis; Cuesta, Isabel

    2014-07-01

    The epidemiology of Candida parapsilosis and the closely related species C. orthopsilosis and C. metapsilosis has changed in recent years, justify the need to identify this complex at the species level. In this study we investigate the intergenic spacer 1 (IGS1) of the ribosomal DNA (rDNA) to evaluate the utility of this gene region as a phylogenetic molecular marker and the suitability of a high-resolution melting (HRM) strategy based on this region for identification of members of the C. parapsilosis spp. complex. We sequenced the IGS1 and the internal transcribed spacer (ITS) regions of the rDNA from 33 C. parapsilosis sensu lato strains. Although both regions are useful in identifying species, comparative sequence analysis showed that the diversity in the IGS1 region was higher than in the ITS sequences. We also developed an HRM analysis that reliably identifies C. parapsilosis spp. complex based on the amplification of 70 bp in the IGS1 region. All isolates were correctly identified with a confidence interval >98%. Our results demonstrate that HRM analysis based on the IGS1 region is a powerful tool for distinguishing C. parapsilosis from cryptic species.

  14. Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

    Directory of Open Access Journals (Sweden)

    Natalia Borowska-Zuchowska

    2016-10-01

    Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

  15. Population genetic structure and phylogeographical pattern of a relict tree fern, Alsophila spinulosa (Cyatheaceae), inferred from cpDNA atpB- rbcL intergenic spacers.

    Science.gov (United States)

    Su, Yingjuan; Wang, Ting; Zheng, Bo; Jiang, Yu; Chen, Guopei; Gu, Hongya

    2004-11-01

    Sequences of chloroplast DNA (cpDNA) atpB- rbcL intergenic spacers of individuals of a tree fern species, Alsophila spinulosa, collected from ten relict populations distributed in the Hainan and Guangdong provinces, and the Guangxi Zhuang region in southern China, were determined. Sequence length varied from 724 bp to 731 bp, showing length polymorphism, and base composition was with high A+T content between 63.17% and 63.95%. Sequences were neutral in terms of evolution (Tajima's criterion D=-1.01899, P>0.10 and Fu and Li's test D*=-1.39008, P>0.10; F*=-1.49775, P>0.10). A total of 19 haplotypes were identified based on nucleotide variation. High levels of haplotype diversity (h=0.744) and nucleotide diversity (Dij=0.01130) were detected in A. spinulosa, probably associated with its long evolutionary history, which has allowed the accumulation of genetic variation within lineages. Both the minimum spanning network and neighbor-joining trees generated for haplotypes demonstrated that current populations of A. spinulosa existing in Hainan, Guangdong, and Guangxi were subdivided into two geographical groups. An analysis of molecular variance indicated that most of the genetic variation (93.49%, Phistory. Gene genealogies together with coalescent theory provided significant information for uncovering phylogeography of A. spinulosa.

  16. 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.

  17. 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.

  18. The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor.

    Science.gov (United States)

    Schnare, M N; Collings, J C; Spencer, D F; Gray, M W

    2000-09-15

    In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from approximately 11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an approximately 55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A' pre-rRNA processing sites within the 5' external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5' ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C. fasciculata and Trypanosoma brucei involves 3'-terminal addition of three A residues that are not present in the corresponding DNA sequences.

  19. 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.

  20. 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.

  1. 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.

  2. Trypanosoma cruzi I genotypes in different geographic 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; Silva, Alex Da; Russomando, Graciela; Cuba Cuba, Cesar A.; Aznar, Christine; Abate, Teresa; Levin, Mariano J.; Osuna, Antonio; Gürtler, Ricardo E.; Diosque, Patricio; Solari, Aldo; Triana-Chávez, Omar; Schijman, Alejandro G.

    2011-01-01

    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 harboring 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. PMID:20670628

  3. Genetic variability within Borrelia burgdorferi sensu lato genospecies established by PCR-single-strand conformation polymorphism analysis of the rrfA-rrlB intergenic spacer in ixodes ricinus ticks from the Czech Republic.

    Science.gov (United States)

    Derdáková, Markéta; Beati, Lorenza; Pet'ko, Branislav; Stanko, Michal; Fish, Durland

    2003-01-01

    In Europe the Borrelia burgdorferi sensu lato complex is represented by five distinct genospecies: Borrelia burgdorferi sensu stricto, Borrelia afzelii, Borrelia garinii, Borrelia valaisiana, and Borrelia lusitaniae. These taxonomic entities are known to differ in their specific associations with vertebrate hosts and to provoke distinct clinical manifestations in human patients. However, exceptions to these rules have often been observed, indicating that strains belonging to a single genospecies may be more heterogeneous than expected. It is, therefore, important to develop alternative identification tools which are able to distinguish Borrelia strains not only at the specific level but also at the intraspecific level. DNA from a sample of 370 Ixodes ricinus ticks collected in the Czech Republic was analyzed by PCR for the presence of a approximately 230-bp fragment of the rrfA-rrlB intergenic spacer of Borrelia spp. A total of 20.5% of the ticks were found to be positive. The infecting genospecies were identified by analyzing the amplified products by the restriction fragment length polymorphism (RFLP) method with restriction enzyme MseI and by single-strand conformation polymorphism (SSCP) analysis. The two methods were compared, and PCR-SSCP analysis appeared to be a valuable tool for rapid identification of spirochetes at the intraspecific level, particularly when large samples are examined. Furthermore, by using PCR-SSCP analysis we identified a previously unknown Borrelia genotype, genotype I-77, which would have gone unnoticed if RFLP analysis alone had been used.

  4. Assessment of the genetic diversity of Frankia microsymbionts of Elaeagnus angustifolia L. plants growing in a Tunisian date-palm oasis by analysis of PCR amplified nifD-K intergenic spacer.

    Science.gov (United States)

    Gtari, Maher; Daffonchio, Daniele; Boudabous, Abdellatif

    2007-03-01

    Diversity of Frankia microsymbionts of non-native Elaeagnus angustifolia L. plants spontaneously growing in a Tunisian desertic retreat area, the date-palm oasis of Tozeur, was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR-sequencing techniques targeting the nifD-K intergenic spacer. Three PCR-RFLP haplotypes (I, II, and III) were detected among collected nodules. Haplotype I was detected at all five sampling sites and dominated the other haplotypes present at these sites. This haplotype was also exhibited by strain BMG5.10, which was isolated by a plant-capturing assay in 1998 from soil collected in the same locality, qualifying it to be the most competitive haplotype in the edapho-climatic condition of the studied desertic date-palm oasis. nifD-K sequences of the three haplotypes formed a closely related phylogenetic subgroup. These results suggest that Frankia variability is constrained by severe edapho-climatic conditions of retreated desert in Tunisian area.

  5. 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.

  6. Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals.

    Science.gov (United States)

    Kakumanu, Madhavi L; Ponnusamy, Loganathan; Sutton, Haley T; Meshnick, Steven R; Nicholson, William L; Apperson, Charles S

    2016-04-01

    A novel nested PCR assay was developed to detectRickettsiaspp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) ofRickettsiaspp. The newly designed primers were evaluated using genomic DNA from 11Rickettsiaspecies belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to otherRickettsia-specific PCR targets (ompA,gltA, and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11Rickettsiaspp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from "CandidatusRickettsia amblyommii." Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adultDermacentor variabilisticks. The nested 23S-5S IGS assay detectedRickettsiaDNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species ofRickettsia The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species ofRickettsiain the ticks. "CandidatusRickettsia amblyommii,"R. montanensis,R. felis, andR. belliiwere frequently identified species, along with some potentially novelRickettsiastrains that were closely related toR. belliiandR. conorii. Copyright © 2016 Kakumanu et al.

  7. Short communication: Identification of coagulase-negative staphylococcus species from goat milk with the API Staph identification test and with transfer RNA-intergenic spacer PCR combined with capillary electrophoresis.

    Science.gov (United States)

    Koop, G; De Visscher, A; Collar, C A; Bacon, D A C; Maga, E A; Murray, J D; Supré, K; De Vliegher, S; Haesebrouck, F; Rowe, J D; Nielen, M; van Werven, T

    2012-12-01

    Coagulase-negative staphylococci (CNS) are the most commonly isolated bacteria from goat milk, but they have often been identified with phenotypic methods, which may have resulted in misclassification. The aims of this paper were to assess the amount of misclassification of a phenotypic test for identifying CNS species from goat milk compared with transfer RNA intergenic spacer PCR (tDNA-PCR) followed by capillary electrophoresis, and to apply the tDNA-PCR technique on different capillary electrophoresis equipment. Milk samples were collected from 416 does in 5 Californian dairy goat herds on 3 occasions during lactation. In total, 219 CNS isolates were identified at the species level with tDNA-PCR and subjected to the API 20 Staph identification test kit (API Staph; bioMérieux, Durham, NC). If the same species was isolated multiple times from the same udder gland, only the first isolate was used for further analyses, resulting in 115 unique CNS isolates. According to the tDNA-PCR test, the most prevalent CNS species were Staphylococcus epidermidis, Staphylococcus caprae, and Staphylococcus simulans. Typeability with API staph was low (72%). Although the API Staph test was capable of identifying the majority of Staph. epidermidis and Staph. caprae isolates, sensitivity for identification of Staph. simulans was low. The true positive fraction was high for the 3 most prevalent species. It was concluded that the overall performance of API Staph in differentiating CNS species from goat milk was moderate to low, mainly because of the low typeability, and that genotypic methods such as tDNA-PCR are preferred.

  8. 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.

  9. Influence of detachment procedure and diet on recovery of solid-associated bacteria from sheep ruminal digesta and representativeness of bacterial isolates as assessed by automated ribosomal intergenic spacer analysis-polymerase chain reaction.

    Science.gov (United States)

    Ramos, S; Tejido, M L; Ranilla, M J; Martínez, M E; Saro, C; Carro, M D

    2009-11-01

    Six ruminally and duodenally cannulated sheep were used in a partially replicated 4 x 4 Latin square experiment designed to evaluate the efficiency of 3 detachment procedures (DP) to recover solid-associated bacteria (SAB) from ruminal digesta. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Bacterial biomass was labeled with 15NH4Cl. The DP were 1) MET: digesta was incubated at 38 degrees C for 15 min with saline solution (0.9% NaCl) containing 0.1% methylcellulose under continuous shaking; 2) STO: digesta was mixed with cold saline solution and homogenized with a stomacher for 5 min at 230 rpm; 3) FRE: digesta was immediately frozen at -20 degrees C for 72 h, thawed at 4 degrees C, mixed with saline solution and subjected to STO procedure. Common to all treatments was storing at 4 degrees C for 24 h after the treatment, homogenization, filtration, and resuspension of digesta 2 times in the treatment solutions. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the similarity between bacterial communities attached to the digesta and those in the pellet obtained after each DP. There were no significant F:C x DP or forage x DP interactions for any variable. On average, STO treatment detached 65.8% of SAB from ruminal digesta, about 1.2 and 1.5 times more than FRE and MET treatments, respectively. Total recovery of SAB in STO pellets (48.9%) was greater compared with FRE (31.7%) and MET (33.1%), values being greater for high-forage compared with high-concentrate diets. Similarity index between the bacteria attached to digesta and those in the pellets were lower for FRE (48.2%) compared with MET (54.1%) and STO (54.1%), which suggests that FRE could have destroyed cell integrity of some bacterial species, thus reducing the bacterial diversity present in the pellets. The STO method was the most effective removing SAB from digesta, but

  10. 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。

  11. New species in the genus Francisella (Gammaproteobacteria; Francisellaceae); Francisella piscicida sp. nov. isolated from cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Ottem, Karl F; Nylund, Are; Karlsbakk, Egil

    2007-01-01

    A Francisella strain, GM2212, previously isolated from moribund farmed Atlantic cod (Gadus morhua) in Norway, is closely related to Francisella philomiragia among Francisella spp. according to its complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, Fop...

  12. Characterization of Francisella sp., GM2212, the first Francisella isolate from marine fish, Atlantic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Ottem, Karl F; Nylund, Are; Karlsbakk, Egil;

    2007-01-01

    A Francisella sp., isolate GM2212(T), previously isolated from diseased farmed Atlantic cod Gadus morhua in Norway is characterized. The complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, FopA, lipoprotein TUL4 (LpnA), malate dehydrogenase and a hypothetical...

  13. 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.

  14. 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.

  15. 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.

  16. Comparative phylogenetic analysis of intergenic spacers and small ...

    African Journals Online (AJOL)

    a

    2016-11-23

    Nov 23, 2016 ... 24˚28'49.88N/86˚42'0.00E/249.8. 5.10±0.20 3.20±0.01. 2 .... agarose gel were eluted using the QIA quick gel extraction kit. (Qiagen, Hilden ... Genomic DNA from the two microsporidian isolates was amplified with primers ... DNA from transformed Escherichia coli cells, the plasmids were digested with.

  17. Molecular Method for Bartonella Species Identification in Clinical and Environmental Samples▿

    Science.gov (United States)

    García-Esteban, Coral; Gil, Horacio; Rodríguez-Vargas, Manuela; Gerrikagoitia, Xeider; Barandika, Jesse; Escudero, Raquel; Jado, Isabel; García-Amil, Cristina; Barral, Marta; García-Pérez, Ana L.; Bhide, Mangesh; Anda, Pedro

    2008-01-01

    A new, efficient molecular method for detection of Bartonella, based on the 16S-23S rRNA intergenic spacer and 16S rRNA amplification by multiplex PCR combined with reverse line blotting, was designed. This assay could simultaneously detect 20 different known species and other Bartonella species not described previously. PMID:18094134

  18. 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.

  19. 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.

  20. 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

  1. 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.

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

    Science.gov (United States)

    Wang, Deguo; Liu, Yanhong

    2015-05-26

    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.

  3. Molecular Evidence of Bartonella Infection in Domestic Dogs from Algeria, North Africa, by Polymerase Chain Reaction (PCR)

    OpenAIRE

    Kernif, Tahar; Aissi, Meriem; DOUMANDJI, Salah-eddine; Chomel, Bruno B; Raoult, Didier; Bitam, Idir

    2010-01-01

    Bartonella species are being recognized as important bacterial human and canine pathogens, and are associated with multiple arthropod vectors. Bartonella DNA extracted from blood samples was obtained from domestic dogs in Algiers, Algeria. Polymerase chain reaction (PCR) and DNA sequence analyses of the ftsZ gene and the 16S-23S intergenic spacer region (ITS) were performed. Three Bartonella species: Bartonella vinsonii subsp. berkhoffii, Bartonella clarridgeiae, and Bartonells elizabethae we...

  4. Phylogeny and Virulence of Naturally Occurring Type III Secretion System-Deficient Pectobacterium Strains▿

    OpenAIRE

    Kim, Hye-Sook; Ma, Bing; Perna, Nicole T.; Charkowski, Amy O.

    2009-01-01

    Pectobacterium species are enterobacterial plant-pathogenic bacteria that cause soft rot disease in diverse plant species. Previous epidemiological studies of Pectobacterium species have suffered from an inability to identify most isolates to the species or subspecies level. We used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis,...

  5. New species in the genus Francisella (Gammaproteobacteria; Francisellaceae); Francisella piscicida sp. nov. isolated from cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Ottem, Karl F; Nylund, Are; Karlsbakk, Egil;

    2007-01-01

    A Francisella strain, GM2212, previously isolated from moribund farmed Atlantic cod (Gadus morhua) in Norway, is closely related to Francisella philomiragia among Francisella spp. according to its complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, FopA, lip...... the establishment of GM2212 as a novel species, for which the name Francisella piscicida sp. nov. is proposed (=CNCM I-3511(T) = DSM 18777(T) = LMG registration number not yet available)....

  6. Phylogenetic Study of Mangifera laurina and its Related Species Using cpDNA trnL-F Spacer Markers

    Directory of Open Access Journals (Sweden)

    FITMAWATI

    2010-03-01

    Full Text Available Phylogenetic study of cpDNA intergenic spacer trnL-F of Mangifera laurina and their related species within the genus Mangifera in Indonesia was conducted using Rutaceae as the outgroup. This study was to reconstruct phylogenetic relationships and to understand infraspecific relationships within Mangifera based on cpDNA trnL-F intergenic spacer sequences. The results showed that Mangifera sp. Hiku (mangga hiku as the basic cultivar in the clade, and it supported the monophyletic group in Mangifera. And phylogenetic construction indicated that Mangifera sp. Hiku was the progenitor of M. laurina and their related species.

  7. Structural Stator Spacers

    DEFF Research Database (Denmark)

    Rasmussen, Peter Omand; Andreasen, Jens H.; Pijanowski, J. M.

    2001-01-01

    This paper presents a powerful new design aspect to reduce acoustic noise and vibration of electro-magnetic origin for electrical machines, by introducing improved slot wedges referred to as "Structural Stator Spacers". These spacers, by using a very stiff dielectric and non magnetic material...... drawbacks usually associated with other noise reduction methods or interdict other noise control methods. Design models and practical prototypes are detailed which are used to verify the effectiveness of the spacers......., a modified shape and small modifications to the stator laminations not only secure the windings and reduce windage losses but also make it possible to increase the stiffness of the stator structure significantly thereby reducing the generation of audible noise. This new method does not incur the significant...

  8. RFLP of analyses of an intergenic spacer region of chloroplast DNA ...

    African Journals Online (AJOL)

    user

    2006-11-16

    Nov 16, 2006 ... Several studies are being made to get high productive wheats throughout the world ... using SAHN clustering unweighted pair group method using arith- ..... report, 353 College of Agriculture University of Missouri, Columbia.

  9. Identifikacija ocetnokislinskih bakterij iz industrijske proizvodnje jabolčnega kisa na osnovi medgenske regije 16S-23S rDNA

    OpenAIRE

    2016-01-01

    Zavedanje ljudi o pomembnosti uživanja zdrave hrane postaja vedno močnejše, zato se v zadnjih letih povečuje trend uživanja živil, pridobljenih iz surovin, ki so čim manj izpostavljene kemikalijam, npr. s škropljenjem. Tudi kis, kot eden izmed pogosto uporabljenih dodatkov k hrani, se lahko pridobiva iz jabolk, ki so pridelana na konvencionalen način, s škropljenjem, ali pa brez škropljenja, s čimer pridobimo bio-jabolčni kis. V okviru te magistrske naloge smo primerjali mikrobioto iz industr...

  10. 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

  11. Identification of Swertia mussotii and its adulterant Swertia species by 5S rRNA gene spacer.

    Science.gov (United States)

    Yu, Man-Tang; Wong, Ka-Lok; Zong, Yu-Ying; Shaw, Pang-Chui; Che, Chun-Tao

    2008-03-01

    This research focused on analyzing the differences of 5S rRNA gene spacer sequences on Swertia mussotii and its commonly used adulterants, including S. franchetiana, S. wolfangiana and S. chirayita. DNA was extracted from the collected Swertia samples. 5S rRNA intergenic spacers were amplified by PCR, sequenced and analyzed. 5S rRNA gene spacer sequences were different between S. mussotii and its other three adulterants. Sequence divergence among species ranged from 30.6% to 65.0%. 5S rRNA spacers may be used as molecular authentication markers to differentiate S. mussotii and other commonly used Swertia adulterants. This result provides reliable and simple reference for the authentication of Swertia genus species.

  12. Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants.

    Science.gov (United States)

    Lee, Chunghee; Wen, Jun

    2004-06-01

    Sequences of the chloroplast trnC-trnD region and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were obtained for all species of Panax L. (the ginseng plant genus, Araliaceae) to reconstruct phylogenetic relationships. The trnC-trnD phylogeny is congruent with the ITS phylogeny for the diploid taxa of Panax. This study is the first use of the trnC-trnD sequence data for phylogenetic analysis at the interspecific level. We evaluated this DNA region for its phylogenetic utility at the lower taxonomic level for flowering plants. The trnC-trnD region includes the trnC-petN intergenic spacer, the petN gene, the petN-psbM intergenic spacer, the psbM gene, and the psbM-trnD intergenic spacer. The petN and psbM genes are small, 90 and 104-114 bp across angiosperms, respectively, and have conserved sequences. We have designed universal amplification and sequencing primers within these two genes. Using these primers, we have successfully amplified the entire trnC-trnD region for a diversity of flowering plant groups, including Aralia L. (Araliaceae), Calycanthus L. (Calycanthaceae), Corylus L. (Betulaceae), Hamamelis L. (Hamamelidaceae), Hydrocotyle L. (Apiaceae), Illigera Blume (Hernandiaceae), Nelumbo Adans. (Nelumbonaceae), Nolana L. ex L.f. (Solanaceae), Prunus L. (Rosaceae), and Staphylea L. (Staphyleaceae). In Panax, the trnC-trnD region provides a similar number of informative phylogenetic characters as the ITS regions and a slightly higher number of informative characters than the chloroplast ndhF gene. We thus demonstrate the utility of the trnC-trnD region for lower-level phylogenetic studies in flowering plants.

  13. Analysis of the 16S–23S rRNA Gene Internal Transcribed Spacer Region in Klebsiella Species▿

    Science.gov (United States)

    Wang, Min; Cao, Boyang; Yu, Qunfang; Liu, Lei; Gao, Qili; Wang, Lei; Feng, Lu

    2008-01-01

    The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of Klebsiella spp., including Klebsiella pneumoniae subsp. pneumoniae, Klebsiella pneumoniae subsp. ozaenae, Klebsiella pneumoniae subsp. rhinoscleromatis, Klebsiella oxytoca, Klebsiella planticola, Klebsiella terrigena, and Klebsiella ornithinolytica, were characterized, and the feasibility of using ITS sequences to discriminate Klebsiella species and subspecies was explored. A total of 336 ITS sequences from 21 representative strains and 11 clinical isolates of Klebsiella were sequenced and analyzed. Three distinct ITS types—ITSnone (without tRNA genes), ITSglu [with a tRNAGlu (UUC) gene], and ITSile+ala [with tRNAIle (GAU) and tRNAAla (UGC) genes]—were detected in all species except for K. pneumoniae subsp. rhinoscleromatis, which has only ITSglu and ITSile+ala. The presence of ITSnone in Enterobacteriaceae had never been reported before. Both the length and the sequence of each ITS type are highly conserved within the species, with identity levels from 0.961 to 1.000 for ITSnone, from 0.967 to 1.000 for ITSglu, and from 0.968 to 1.000 for ITSile+ala. Interspecies sequence identities range from 0.775 to 0.989 for ITSnone, from 0.798 to 0.997 for ITSglu, and from 0.712 to 0.985 for ITSile+ala. Regions with significant interspecies variations but low intraspecies polymorphisms were identified; these may be targeted in the design of probes for the identification of Klebsiella to the species level. Phylogenetic analysis based on ITS regions reveals the relationships among Klebsiella species similarly to that based on 16S rRNA genes. PMID:18753345

  14. 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.

  15. Use of PCR primers and probes based on the 23S rRNA and internal transcription spacer (ITS) gene sequence for the detection and enumerization of Lactobacillus acidophilus and Lactobacillus plantarum in feed supplements.

    Science.gov (United States)

    Tsai, Cheng-Chih; Lai, Chieh-Hsien; Yu, Bi; Tsen, Hau-Yang

    2010-06-01

    Novel polymerase chain reaction (PCR) primers designed from the 16S-23S internal transcription spacer (ITS) rRNA and 23S rRNA genes, respectively, were used for the specific detection of Lactobacillus acidophilus and Lactobacillus plantarum. Molecular weights of the PCR products were 221 and 599 bp, respectively. Strains of L. acidophilus and L. plantarum obtained from the culture center, dairy products, infant stool and other samples, could be identified with these PCR primers. DNAs from other lactic acid bacteria (LAB) species including strains of Lactobacillus pentosus which was closely related to L. plantarum, and bacteria species other than LAB, would not generate the false positive results. When this PCR primer set was used for the detection of L. acidophilus and L. plantarum in feed supplement or feed starter samples, reliable results were obtained. Furthermore, when these L. acidophilus or L. plantarum specific primers were used as DNA probes for the colony hybridization of L. acidophilus and L. plantarum, the viable cells of these LAB species in culture and feed supplements or starter products could be identified and enumerized. The method described here thus offers a rapid and economic way to inspect and assure the quality of the feed supplements or fermentation starters.

  16. 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.

  17. Low abundant spacer 5S rRNA transcripts are frequently polyadenylated in Nicotiana.

    Science.gov (United States)

    Fulnecek, Jaroslav; Kovarik, Ales

    2007-11-01

    In plants, 5S rRNA genes (5S rDNA) encoding 120-nt structural RNA molecules of ribosomes are organized in tandem arrays comprising thousands of units. Failure to correctly terminate transcription would generate longer inaccurately processed transcripts interfering with ribosome biogenesis. Hence multiple termination signals occur immediately after the 5S rRNA coding sequence. To obtain information about the efficiency of termination of 5S rDNA transcription in plants we analyzed 5S rRNA pools in three Nicotiana species, N. sylvestris, N. tomentosiformis and N. tabacum. In addition to highly abundant 120-nt 5S rRNA transcripts, we also detected RNA species composed of a genic region and variable lengths of intergenic sequences. These genic-intergenic RNA molecules occur at a frequency severalfold lower than the mature 120-nt transcripts, and are posttranscriptionally modified by polyadenylation at their 3' end in contrast to 120-nt transcripts. An absence of 5S small RNAs (smRNA) argue against a dominant role for the smRNA biosynthesis pathway in the degradation of aberrant 5S rRNA in Nicotiana. This work is the first description of polyadenylated 5S rRNA species in higher eukaryotes originating from a read-through transcription into the intergenic spacer. We propose that polyadenylation may function in a "quality control" pathway ensuring that only correctly processed molecules enter the ribosome biogenesis.

  18. 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...

  19. Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA.

    OpenAIRE

    Williams, D W; Wilson, M.J.; Lewis, M A; Potts, A.J.

    1995-01-01

    The PCR was used to amplify a targeted region of the ribosomal DNA from 84 Candida isolates. Unique product sizes were obtained for Candida guilliermondii, Candida (Torulopsis) glabrata, and Candida pseudotropicalis. Isolates of Candida albicans, Candida tropicalis, Candida stellatoidea, Candida parapsilosis, and Candida krusei could be identified following restriction digestion of the PCR products.

  20. The molecular diversity analysis of Auricularia auricula-judae in China by nuclear ribosomal DNA intergenic spacer

    Directory of Open Access Journals (Sweden)

    Li Li

    2014-01-01

    Conclusion: The grouping information obtained in the present work provides significant information for further genetic improvement in A. auricula-judae, and suggested that the IGS region can be used as an excellent tool for identification of genetic variation.

  1. Spacer lock of roof bolting

    Energy Technology Data Exchange (ETDEWEB)

    Shirokov, A.P.; Boronov, N.N.; Isachenko, V.M.; Kuntsevich, V.I.

    1980-04-05

    The object of the invention is a spacer joint of anchor bolting, which includes a wedge-shaped head and half-coupling, which are beveled on the inner side of the walls, and have ribs on the outer sides of the walls. It is characterized in that in order to reduce cost of the joint by reducing the amount of steel and manufacturing costs, the walls of the half-couplings hae identical thickness lengthwise, and the ribs are of varying height with corresponding projections on the inner side of the half-couplings.

  2. CRISPR interference directs strand specific spacer acquisition.

    Directory of Open Access Journals (Sweden)

    Daan C Swarts

    Full Text Available BACKGROUND: CRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference. RESULTS: We describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A co-occurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner. CONCLUSIONS: The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the

  3. 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.

  4. 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.

  5. LISA telescope spacer design investigations

    Science.gov (United States)

    Sanjuan, Josep; Mueller, Guido; Livas, Jeffrey; Preston, Alix; Arsenovic, Petar; Castellucci, Kevin; Generie, Joseph; Howard, Joseph; Stebbins, Robin

    ) and materials such as Silicon Carbide (SiC) and Carbon Fiber Reinforced Plastic (CFRP) are considered to be used in the telescope spacer structure. We will describe our experimental efforts to understand and quantify the behavior of different materials and also discuss a first investigation of a specific on-axis SiC telescope spacer for LISA. This work is supported by NASA contract 00069955.

  6. Phylogenetic relationships in the Gesnerioideae (Gesneriaceae) based on nrDNA ITS and cpDNA trnL-F and trnE-T spacer region sequences.

    Science.gov (United States)

    Zimmer, Elizabeth A; Roalson, Eric H; Skog, Laurence E; Boggan, John K; Idnurm, Alexander

    2002-02-01

    The Gesnerioideae includes most of the New World members of the Gesneriaceae family and is currently considered to include five tribes: Beslerieae, Episcieae, Gesnerieae, Gloxinieae, and Napeantheae. This study presents maximum parsimony and maximum likelihood phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer regions (ITS), and the chloroplast DNA trnL intron, trnL-trnF intergenic spacer region, and trnE-trnT intergenic spacer region sequences. The ITS and cpDNA data sets strongly support the monophyly of a Beslerieae/Napeantheae clade; an Episcieae clade; a Gesnerieae clade; a Gloxinieae clade minus Sinningia, Sinningia relatives, and Gloxinia sarmentiana; and a Sinningia/Paliavana/Vanhouttea clade. This is the first study to provide strong statistical support for these tribes/clades. These analyses suggest that Sinningia and relatives should be considered as a separate tribe. Additionally, generic relationships are explored, including the apparent polyphyly of Gloxinia. Chromosome number changes are minimized on the proposed phylogeny, with the exception of the n = 11 taxa of the Gloxinieae. Scaly rhizomes appear to have been derived once in the Gloxinieae sensu stricto. The number of derivations of the inferior ovary is unclear: either there was one derivation with a reversal to a superior ovary in the Episcieae, or there were multiple independent derivations of the inferior ovary.

  7. Investigation and analysis of dual-k spacer with different materials and spacer lengths for nanowire-FET performance

    Science.gov (United States)

    Ko, Hyungwoo; Kim, Jongsu; Kang, Myounggon; Shin, Hyungcheol

    2017-10-01

    In this work, dual-k spacer structures are investigated using a variety of materials along the high-k spacer length in detail. It is known that not only the higher permittivity materials of high-k spacer boost the on-current but also lower permittivity materials of low-k spacer effectively reduce the off-current. By compared the results of other various single spacers and dual-k spacers, it is HfO2/Vacuum dual-k spacer that shows relatively higher ION, ION/IOFF, better immunity of short channel effects and outstanding device performances.

  8. The ribosomal gene spacer region in archaebacteria

    Science.gov (United States)

    Achenbach-Richter, L.; Woese, C. R.

    1988-01-01

    Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.

  9. 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.

  10. 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.

  11. The structure of a single unit of ribosomal RNA gene (rDNA) including intergenic subrepeats in the Australian bulldog ant Myrmecia croslandi (Hymenoptera: Formicidae).

    Science.gov (United States)

    Ohnishi, Hitoshi; Yamamoto, Masa-Toshi

    2004-02-01

    A complete single unit of a ribosomal RNA gene (rDNA) of M. croslandi was sequenced. The ends of the 18S, 5.8S and 28S rRNA genes were determined by using the sequences of D. melanogaster rDNAs as references. Each of the tandemly repeated rDNA units consists of coding and non-coding regions whose arrangement is the same as that of D. melanogaster rDNA. The intergenic spacer (IGS) contains, as in other species, a region with subrepeats, of which the sequences are different from those previously reported in other insect species. The length of IGSs was estimated to be 7-12 kb by genomic Southern hybridization, showing that an rDNA repeating unit of M. croslandi is 14-19 kb-long. The sequences of the coding regions are highly conserved, whereas IGS and ITS (internal transcribed spacer) sequences are not. We obtained clones with insertions of various sizes of R2 elements, the target sequence of which was found in the 28S rRNA coding region. A short segment in the IGS that follows the 3' end of the 28S rRNA gene was predicted to form a secondary structure with long stems.

  12. 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.

  13. Quantitative modeling of a gene's expression from its intergenic sequence.

    Directory of Open Access Journals (Sweden)

    Md Abul Hassan Samee

    2014-03-01

    Full Text Available Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1 combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2 independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference

  14. 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.

  15. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Robb, F.T.

    1998-06-01

    '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 idedntified 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.'

  17. Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters.

    Science.gov (United States)

    Ghanem, Noël; Jarinova, Olga; Amores, Angel; Long, Qiaoming; Hatch, Gary; Park, Byung Keon; Rubenstein, John L R; Ekker, Marc

    2003-04-01

    Dlx homeobox genes of vertebrates are generally arranged as three bigene clusters on distinct chromosomes. The Dlx1/Dlx2, Dlx5/Dlx6, and Dlx3/Dlx7 clusters likely originate from duplications of an ancestral Dlx gene pair. Overlaps in expression are often observed between genes from the different clusters. To determine if the overlaps are a result of the conservation of enhancer sequences between paralogous clusters, we compared the Dlx1/2 and the Dlx5/Dlx6 intergenic regions from human, mouse, zebrafish, and from two pufferfish, Spheroides nephelus and Takifugu rubripes. Conservation between all five vertebrates is limited to four sequences, two in Dlx1/Dlx2 and two in Dlx5/Dlx6. These noncoding sequences are >75% identical over a few hundred base pairs, even in distant vertebrates. However, when compared to each other, the four intergenic sequences show a much more limited similarity. Each intergenic sequence acts as an enhancer when tested in transgenic animals. Three of them are active in the forebrain with overlapping patterns despite their limited sequence similarity. The lack of sequence similarity between paralogous intergenic regions and the high degree of sequence conservation of orthologous enhancers suggest a rapid divergence of Dlx intergenic regions early in chordate/vertebrate evolution followed by fixation of cis-acting regulatory elements.

  18. 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.

  19. 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.

  20. [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.

  1. Phenotypic and genotypic diversity of rhizobia nodulating Pterocarpus erinaceus and P. lucens in Senegal.

    Science.gov (United States)

    Sylla, Samba Ndao; Samba, Ramatoulaye Thiaba; Neyra, Marc; Ndoye, Ibrahima; Giraud, Eric; Willems, Anne; de Lajudie, Philippe; Dreyfus, Bernard

    2002-12-01

    A total of fifty root nodules isolates of fast-growing and slow growing rhizobia from Pterocarpus ennaceus and Pterocarpus lucens respectively native of sudanean and sahelian regions of Senegal were characterized. These isolates were compared to representative strains of known rhizobial species. Twenty-two new isolates were slow growers and twenty-eight were fast growers. A polyphasic approach was performed including comparative total protein sodium dodecyl sulphate polyacrylamide gel (SDS-PAGE) profile analysis; 16S rDNA and 16S-23S rDNA intergenic spacer (IGS) sequence analysis. By SDS-PAGE the slow growing isolates grouped in one major cluster containing reference strains of Bradyrhizobium sp. including strains isolated in Africa, in Brazil and in New Zealand. Most of the fast-growing rhizobia grouped in four different clusters or were separate strains related to Rhizobium and Mesorhizobium strains. The 16S rDNA and 16S-23S rDNA IGS sequences analysis showed accurately the differentiation of fast growing rhizobia among the Rhizobium and Mesorbizobium genospecies. The representative strains of slow growing rhizobia were identified as closely related to Bradyrbizobium elkanii and Bradyrhizobium japonicum. Based on 16S rDNA sequence analysis, one slow growing strain (ORS199) was phylogenetically related to Bradyrbizobium sp. (Lupinus) and Blastobacter denitrificans. This position of ORS 199 was not confirmed by IGS sequence divergence. We found no clear relation between the diversity of strains, the host plants and the ecogeographical origins.

  2. Molecular detection and identification of Bartonella species in rat fleas from northeastern Thailand.

    Science.gov (United States)

    Billeter, Sarah A; Colton, Leah; Sangmaneedet, Somboon; Suksawat, Fanan; Evans, Brian P; Kosoy, Michael Y

    2013-09-01

    The presence of Bartonella species in Xenopsylla cheopis fleas collected from Rattus spp. (R. exulans, R. norvegicus, and R. rattus) in Khon Kaen Province, Thailand was investigated. One hundred ninety-three fleas obtained from 62 rats, were screened by polymerase chain reaction using primers specific for the 16S-23S intergenic spacer region, and the presence of Bartonella DNA was confirmed by using the citrate synthase gene. Bartonella DNA was detected in 59.1% (114 of 193) of fleas examined. Sequencing demonstrated the presence of Bartonella spp. similar to B. elizabethae, B. rattimassiliensis, B. rochalimae, and B. tribocorum in the samples tested with a cutoff for sequence similarity ≥ 96% and 4 clustered together with the closest match with B. grahamii (95.5% identity). If X. cheopis proves to be a competent vector of these species, our results suggest that humans and animals residing in this area may be at risk for infection by several zoonotic Bartonella species.

  3. Molecular detection of Bartonella species in ticks from Peru.

    Science.gov (United States)

    Billeter, Sarah A; Cáceres, Abraham G; Gonzales-Hidalgo, James; Luna-Caypo, Deysi; Kosoy, Michael Y

    2011-11-01

    A total of 103 ticks, collected from canines, horses, donkeys, and snakes from Peru, were screened for the presence of Bartonella DNA by polymerase chain reaction analysis. Bartonella DNA was detected in two ticks using Bartonella 16S-23S intergenic spacer region primers and in an additional two ticks using Bartonella NADH dehydrogenase gamma subunit gene (nuoG) primers. Bartonella rochalimae Eremeeva et al., B. quintana Schmincke, and B. elizabethae Daly et al. DNA was detected in a Rhipicephalus sanguineus Latreille (Acari: Ixodidae) female tick removed from a dog and B. quintana DNA was present in a Dermacentor nitens Neumann (Acari: Ixodidae) pool of five larvae, one nymph, and one adult male tick collected from donkeys. This is the first study to report the detection of B. rochalimae, B. quintana, and B. elizabethae DNA in ticks from Peru. Further investigations must be performed to decipher the role ticks may play in the transmission of Bartonella species.

  4. 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.

  5. 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.

  6. 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.

  7. Effect of Spacer and the Enzyme-Linked Immunosorbent Assay

    Directory of Open Access Journals (Sweden)

    Manisha Sathe

    2016-09-01

    Full Text Available The effect of spacers and the enzyme-linked immunosorbent assay (ELISA formats on the functional parameters of assays such as lower detection limit, inhibitory concentration at 50 per cent (IC50, and specificity were studied. Enzyme conjugates having hydrophobic and hydrophilic spacers were prepared using O-isopropyl methylphosphonic acid (IMPA and horseradish peroxidase (HRP as an enzyme label. Comparison was made with reference to enzyme conjugate without any spacer. The present investigation revealed that the presence of a hydrophilic spacer in the enzyme conjugate significantly improves the sensitivity of assays. An enhanced IC50 value achieved was 0.01 μg mL−1 for free antigen detection by direct immunoassay using hydrophilic spacers and precoating of ELISA plates by secondary antibody. The use of a hydrophilic spacer might have helped in projecting the hapten in the aqueous phase, leading to enhanced antibody binding signal and improved sensitivity of the assay.

  8. Comparaison de la structure bactérienne du caecum, du colon et des fèces équin par ARISA (Automated Ribosomal Intergenic Spacer Analysis)

    OpenAIRE

    Sadet-Bourgeteau, Sophie; Philippeau, Christelle; Lelievre, Mélanie; Julliand, Véronique

    2012-01-01

    Le cheval est un herbivore monogastrique. L’hydrolyse et la fermentation des composés fibrolytiques de la ration en acides organiques se déroulent essentiellement au niveau du gros intestin (caecum et côlon) grâce à une flore et une faune microbienne dense et diverse. Parmi les microorganismes présents à ce niveau du tractus digestif, les bactéries ont été les plus étudiées. Il est connu que des régimes alimentaires riches en concentré, distribués aux chevaux à l’exercice pour couvrir leurs b...

  9. 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

  10. Ribosomal operon intergenic sequence region (ISR) heterogeneity in Campylobacter coli and Campylobacter jejuni

    Science.gov (United States)

    Campylobacter jejuni and Campylobacter coli are closely related species that can not be distinguished by their 16S or 23S rRNA gene sequences. However, the intergenic sequence region (ISR) that is between the 16S and 23S genes is markedly different and characteristic for each species. A peculiarit...

  11. Use of the CP and CPm Intergene Sequences to Discriminate CTV Strains

    Science.gov (United States)

    There is a need to develop a rapid assay to distinguish potentially mild vs severe strains of Citrus tristeza virus. Multiple alignment performed on the coat protein (CP) and the minor coat protein (CPm) intergene sequences (~80-100 bp) from different CTV isolates revealed that severe strains (VT, ...

  12. 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.

  13. Mask specification guidelines in spacer patterning technology

    Science.gov (United States)

    Hashimoto, Kohji; Mukai, Hidefumi; Miyoshi, Seiro; Yamaguchi, Shinji; Mashita, Hiromitsu; Kobayashi, Yuuji; Kawano, Kenji; Hirano, Takashi

    2008-11-01

    We have studied both the mask CD specification and the mask defect specification for spacer patterning technology (SPT). SPT has the possibility of extending optical lithography to below 40nm half-pitch devices. Since SPT necessitates somewhat more complicated wafer process flow, the CD error and mask defect printability on wafers involve more process factors compared with conventional single-exposure process (SEP). This feature of SPT implies that it is very important to determine mask-related specifications for SPT in order to select high-end mask fabrication strategies; those are for mask writing tools, mask process development, materials, inspection tools, and so on. Our experimental studies reveal that both mask CD specification and mask defect specification are somehow relaxed from those in ITRS2007. This is most likely because SPT reduces mask CD error enhanced factor (MEF) and the reduction of line-width roughness (LWR).

  14. Stress Analysis of Single Spacer Grid Support considering Fuel Rod

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Y. G.; Jung, D. H.; Kim, J. H. [Chungnam National University, Daejeon (Korea, Republic of); Park, J. K.; Jeon, K. L. [Korea Nuclear Fuel, Daejeon (Korea, Republic of)

    2010-10-15

    Pressurized water reactor (PWR) nuclear fuel assembly is mainly composed of a top-end piece, a bottom-end piece, lots of fuel rods, and several spacer grids. Among them, the main function of spacer grid is protecting fuel rods from Fluid Induced Vibration (FIV). The cross section of spacer grid assembled by laser welding in upper and lower point. When the fuel rod inserted in spacer gird, spring and dimple and around of welded area got a stresses. The main hypothesis of this analysis is the boundary area of HAZ and base metal can get a lot of damage than other area by FIV. So, design factors of spacer grid mainly considered to preventing the fatigue failure in HAZ and spring and dimple of spacer grid. From previous researching, the environment in reactor verified. Pressure and temperature of light water observed 15MPa and 320 .deg. C, and vibration of the fuel rod observed within 0 {approx} 50Hz. In this study, mechanical properties of zirconium alloy that extracted from the test and the spacer grid model which used in the PWR were applied in stress analyzing. General-purpose finite element analysis program was used ANSYS Workbench 12.0.1 version. 3-D CAD program CATIA was used to create spacer grid model

  15. Orthognathic model surgery with LEGO key-spacer.

    Science.gov (United States)

    Tsang, Alfred Chee-Ching; Lee, Alfred Siu Hong; Li, Wai Keung

    2013-12-01

    A new technique of model surgery using LEGO plates as key-spacers is described. This technique requires less time to set up compared with the conventional plaster model method. It also retains the preoperative setup with the same set of models. Movement of the segments can be measured and examined in detail with LEGO key-spacers.

  16. Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

    Science.gov (United States)

    Jiao, Tifeng; Gao, Fengqing; Zhang, Qingrui; Zhou, Jingxin; Gao, Faming

    2013-10-01

    In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures.

  17. Advanced hole patterning technology using soft spacer materials (Conference Presentation)

    Science.gov (United States)

    Park, Jong Keun; Hustad, Phillip D.; Aqad, Emad; Valeri, David; Wagner, Mike D.; Li, Mingqi

    2017-03-01

    A continuing goal in integrated circuit industry is to increase density of features within patterned masks. One pathway being used by the device manufacturers for patterning beyond the 80nm pitch limitation of 193 immersion lithography is the self-aligned spacer double patterning (SADP). Two orthogonal line space patterns with subsequent SADP can be used for contact holes multiplication. However, a combination of two immersion exposures, two spacer deposition processes, and two etch processes to reach the desired dimensions makes this process expensive and complicated. One alternative technique for contact hole multiplication is the use of an array of pillar patterns. Pillars, imaged with 193 immersion photolithography, can be uniformly deposited with spacer materials until a hole is formed in the center of 4 pillars. Selective removal of the pillar core gives a reversal of phases, a contact hole where there was once a pillar. However, the highly conformal nature of conventional spacer materials causes a problem with this application. The new holes, formed between 4 pillars, by this method have a tendency to be imperfect and not circular. To improve the contact hole circularity, this paper presents the use of both conventional spacer material and soft spacer materials. Application of soft spacer materials can be achieved by an existing coating track without additional cost burden to the device manufacturers.

  18. 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.

  19. Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction

    Science.gov (United States)

    Tang, Le; Zhu, Songling; Mastriani, Emilio; Fang, Xin; Zhou, Yu-Jie; Li, Yong-Guo; Johnston, Randal N.; Guo, Zheng; Liu, Gui-Rong; Liu, Shu-Lin

    2017-01-01

    Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment. PMID:28262684

  20. Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction

    Science.gov (United States)

    Tang, Le; Zhu, Songling; Mastriani, Emilio; Fang, Xin; Zhou, Yu-Jie; Li, Yong-Guo; Johnston, Randal N.; Guo, Zheng; Liu, Gui-Rong; Liu, Shu-Lin

    2017-03-01

    Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.

  1. α-MSH regulates intergenic splicing of MC1R and TUBB3 in human melanocytes

    OpenAIRE

    Dalziel, Martin; Kolesnichenko, Marina; das Neves, Ricardo Pires; Iborra, Francisco; Goding, Colin; Furger, André

    2010-01-01

    Alternative splicing enables higher eukaryotes to increase their repertoire of proteins derived from a restricted number of genes. However, the possibility that functional diversity may also be augmented by splicing between adjacent genes has been largely neglected. Here, we show that the human melanocortin 1 receptor (MC1R) gene, a critical component of the facultative skin pigmentation system, has a highly complex and inefficient poly(A) site which is instrumental in allowing intergenic spl...

  2. The Mitochondrial Genome of Conus textile, coxI-coxII Intergenic Sequences and Conoidean Evolution

    OpenAIRE

    2007-01-01

    The cone snails belong to the superfamily Conoidea, comprising ∼10,000 venomous marine gastropods. We determined the complete mitochondrial DNA sequence of Conus textile. The gene order is identical in Conus textile, Lophiotoma cerithiformis (another Conoidean gastropod), and the neogastropod Ilyanassa obsoleta, (not in the superfamily Conoidea). However, the intergenic interval between the coxI/coxII genes, was much longer in C. textile (165 bp) than in any other previously analyzed gastropo...

  3. 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.

  4. Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs

    Directory of Open Access Journals (Sweden)

    Delihas Nicholas

    2009-03-01

    Full Text Available Abstract Background Borrelia species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and/or maintain stable motifs such as small RNA genes. Results In an in silico study, intergenic regions of Borrelia plasmids were scanned for phylogenetically conserved stem loop structures that may represent functional units at the RNA level. Five repeat sequences were found that could fold into stable RNA-type stem loop structures, three of which are closely linked to protein genes, one of which is a member of the Borrelia lipoprotein_1 super family genes and another is the complement regulator-acquiring surface protein_1 (CRASP-1 family. Modeled secondary structures of repeat sequences display numerous base-pair compensatory changes in stem regions, including C-G→A-U transversions when orthologous sequences are compared. Base-pair compensatory changes constitute strong evidence for phylogenetic conservation of secondary structure. Conclusion Intergenic regions of Borrelia species carry evolutionarily stable RNA secondary structure motifs. Of major interest is that some motifs are associated with protein genes that show large sequence variability. The cell may conserve these RNA motifs whereas allow a large flux in amino acid sequence, possibly to create new virulence factors but with associated RNA motifs intact.

  5. Technique for adapting a spacer for a custom impression tray.

    Science.gov (United States)

    Kaur, Harsimran; Nanda, Aditi; Verma, Mahesh; Koli, Dheeraj

    2016-12-01

    A method of adapting a spacer for the custom trays used to make a definite impression for complete dentures is presented. The technique can be used under a variety of conditions and offers several advantages.

  6. 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...

  7. 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.

  8. 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.

  9. Multilocus spacer analysis revealed highly homogeneous genetic background of Asian type of Borrelia miyamotoi.

    Science.gov (United States)

    Mukhacheva, Tatyana A; Salikhova, Irina I; Kovalev, Sergey Y

    2015-04-01

    Borrelia miyamotoi, a member of the relapsing fever group borreliae, was first isolated in Japan and subsequently found in Ixodes ticks in North America, Europe and Russia. Currently, there are three types of B. miyamotoi: Asian or Siberian (transmitted mainly by Ixodes persulcatus), European (Ixodesricinus) and American (Ixodesscapularis and Ixodespacificus). Despite the great genetic distances between B. miyamotoi types, isolates within a type are characterised by an extremely low genetic variability. In particular, strains of B. miyamotoi of Asian type, isolated in Russia from the Baltic sea to the Far East, have been shown to be identical based on the analysis of several conventional genetic markers, such as 16S rRNA, flagellin, outer membrane protein p66 and glpQ genes. Thus, protein or rRNA - coding genes were shown not to be informative enough in studying genetic diversity of B. miyamotoi within a type. In the present paper, we have attempted to design a new multilocus technique based on eight non-coding intergenic spacers (3686bp in total) and have applied it to the analysis of intra-type genetic variability of В. miyamotoi detected in different regions of Russia and from two tick species, I. persulcatus and Ixodespavlovskyi. However, even though potentially the most variable loci were selected, no genetic variability between studied DNA samples was found, except for one nucleotide substitution in two of them. The sequences obtained were identical to those of the reference strain FR64b. Analysis of the data obtained with the GenBank sequences indicates a highly homogeneous genetic background of B. miyamotoi from the Baltic Sea to the Japanese Islands. In this paper, a hypothesis of clonal expansion of B. miyamotoi is discussed, as well as possible mechanisms for the rapid dissemination of one B. miyamotoi clone over large distances.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. A non-electrostatic spacer for aerosol delivery

    DEFF Research Database (Denmark)

    Bisgaard, H; Anhøj, J; Klug, B;

    1995-01-01

    A pear shaped non-electrostatic spacer, composed of steel with a volume of 250 ml and equipped with a facemask containing integrated inlet and outlet valves for inspiration and expiration, was compared with three plastic spacers. The plastic spacers were primed with repeated puffs from a budesonide...... 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...... was 27 seconds and independent of the use of p-MDI. In vitro the maximum dose of budesonide from a p-MDI, expressed as a percentage of the nominal dose, was 56% from the non-electrostatic spacer, 61% from the Nebuhaler, 45% from the Babyhaler, and 30% from the AeroChamber. In 124 children, age 6 months...

  17. Disruption of a Large Intergenic Noncoding RNA in Subjects with Neurodevelopmental Disabilities

    OpenAIRE

    Talkowski, Michael E.; Maussion, Gilles; Crapper, Liam; Rosenfeld, Jill A.; Blumenthal, Ian; Hanscom, Carrie; Chiang, Colby; Lindgren, Amelia; Pereira, Shahrin; Ruderfer, Douglas; Diallo, Alpha B.; Lopez, Juan Pablo; Turecki, Gustavo; Chen, Elizabeth S.; Gigek, Carolina

    2012-01-01

    Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA ...

  18. 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.

  19. 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.)

  20. Partial Deletion of the L-Segment Intergenic Region Produces an Attenuated Machupo Virus that Protects Guinea Pigs Against Lethal Guanarito Virus Infection

    Science.gov (United States)

    2017-01-11

    1 Golden, J.W. et al. Machupo virus live-attenuated vaccine Partial deletion of the L-segment intergenic region produces an attenuated Machupo...had a 35 nucleotide deletion in the L-segment non-coding intergenic region . Contrary to Car91, Car68 produced a lethal infection in guinea pigs with...Keywords: Arenavirus, Machupo virus, Guanarito virus, intergenic region , live-attenuated vaccines, cross-protection 45 TR-17-030 DISTRIBUTION

  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. Characterization of IS6110 insertions in the dnaA-dnaN intergenic region of Mycobacterium tuberculosis clinical isolates.

    Science.gov (United States)

    Turcios, L; Casart, Y; Florez, I; de Waard, J; Salazar, L

    2009-02-01

    Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to be clonally related. The presence of IS6110 in the dnaA-dnaN intergenic region, one preferential locus for the integration of IS6110, was evaluated in 125 M. tuberculosis isolates. Five isolates had IS6110 inserted in this region, and two consisted of a mix of isogenic strains that putatively have evolved during a single infection. Strains from the same isolate had identical spoligo and mycobacterial interspersed repetitive unit-variable-number tandem repeat profiles, but had slight variations in IS6110 RFLP patterns, due to the presence of IS6110 in the dnaA-dnaN intergenic region. Duplication of the dnaA-dnaN intergenic region was found in one isogenic strain.

  3. PCR-Internal Transcribed Spacer (ITS) genes sequencing and ...

    African Journals Online (AJOL)

    2. Department of Pure and Applied Zoology, Federal University of Agriculture, Abeokuta, Nigeria. 3. ... Keywords: Internal transcribed spacer genes, phylogenetic, genetic ... ization of fungi by polymerase chain reaction (PCR) am- .... Basic Local Alignment search Tool (BLAST) to establish ..... Population structure and.

  4. 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

  5. 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.

  6. 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

  7. Filter holder assembly having extended collar spacer ring

    Science.gov (United States)

    Alvin, Mary Anne; Bruck, Gerald J.

    2002-01-01

    A filter holder assembly is provided that utilizes a fail-safe regenerator unit with an annular spacer ring having an extended metal collar for containment and positioning of a compliant ceramic gasket used in the assembly. The filter holder assembly is disclosed for use with advanced composite, filament wound, and metal candle filters.

  8. 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.

  9. 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.

  10. Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Hao

    Full Text Available Long intergenic noncoding RNAs (lincRNAs are intergenic transcripts with a length of at least 200 nt that lack coding potential. Emerging evidence suggests that lincRNAs from animals participate in many fundamental biological processes. However, the systemic identification of lincRNAs has been undertaken in only a few plants. We chose to use cucumber (Cucumis sativus as a model to analyze lincRNAs due to its importance as a model plant for studying sex differentiation and fruit development and the rich genomic and transcriptome data available. The application of a bioinformatics pipeline to multiple types of gene expression data resulted in the identification and characterization of 3,274 lincRNAs. Next, 10 lincRNAs targeted by 17 miRNAs were also explored. Based on co-expression analysis between lincRNAs and mRNAs, 94 lincRNAs were annotated, which may be involved in response to stimuli, multi-organism processes, reproduction, reproductive processes, and growth. Finally, examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, while 16 lincRNAs are under natural selection. Our results provide a rich resource for further validation of cucumber lincRNAs and their function. The identification of lincRNAs targeted by miRNAs offers new clues for investigations into the role of lincRNAs in regulating gene expression. Finally, evaluation of the lincRNAs suggested that some lincRNAs are under positive and balancing selection.

  11. Cotranscription and intergenic splicing of the PPARG and TSEN2 genes in cattle

    Directory of Open Access Journals (Sweden)

    Amarger Valérie

    2006-04-01

    Full Text Available Abstract Background Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptional termination bypass. Results We identified bovine chimeric transcripts resulting from cotranscription and intergenic splicing of two neighboring genes, PPARG and TSEN2. These two genes encode the Peroxisome Proliferator Activated Receptors γ1 and γ2 and the tRNA Splicing Endonuclease 2 homolog and are situated in the same orientation about 50 kb apart on bovine chromosome 22q24. Their relative position is conserved in human and mouse. We identified two types of chimeric transcripts containing all but the last exon of the PPARG gene followed by all but the first exon of the TSEN2 gene. The two chimers differ by the presence/absence of an intermediate exon resulting from transcription of a LINE L2 sequence situated between the two genes. Both transcripts use canonical splice sites for all exons coming from both genes, as well as for the LINE L2 sequence. One of these transcripts harbors a premature STOP codon and the other encodes a putative chimeric protein combining most of the PPARγ protein and the entire TSEN2 protein, but we could not establish the existence of this protein. Conclusion By showing that both individual and chimeric transcripts are transcribed from PPARG and TSEN2, we demonstrated regulation of transcription termination. Further, the existence and functionality of a chimeric protein harboring active motifs that are a priori unrelated is hypothesized.

  12. Biofouling Control in Spiral-Wound Membrane Systems: Impact of Feed Spacer Modification and Biocides

    KAUST Repository

    Siddiqui, Amber

    2016-12-01

    High-quality drinking water can be produced with membrane-based filtration processes like reverse osmosis and nanofiltration. One of the major problems in these membrane systems is biofouling that reduces the membrane performance, increasing operational costs. Current biofouling control strategies such as pre-treatment, membrane modification, and chemical cleaning are not sufficient in all cases. Feed spacers are thin (0.8 mm), complex geometry meshes that separate membranes in a module. The main objective of this research was to evaluate whether feed spacer modification is a suitable strategy to control biofouling. Membrane fouling simulator studies with six feed spacers showed differences in biofouled spacer performance, concluding that (i) spacer geometry influences biofouling impact and (ii) biofouling studies are essential for evaluation of spacer biofouling impact. Computed tomography (CT) was found as a suitable technique to obtain three-dimensional (3D) measurements of spacers, enabling more representative mathematical modeling of hydraulic behavior of spacers in membrane systems. A strategy for developing, characterizing, and testing of spacers by numerical modeling, 3D printing of spacers and experimental membrane fouling simulator studies was developed. The combination of modeling and experimental testing of 3D printed spacers is a promising strategy to develop advanced spacers aiming to reduce the impact of biofilm formation on membrane performance and to improve the cleanability of spiral-wound membrane systems.

  13. Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)

    Science.gov (United States)

    Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergeni...

  14. A small intergenic region drives exclusive tissue-specific expression of the adjacent genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Valle Estela M

    2009-10-01

    Full Text Available Abstract Background Transcription initiation by RNA polymerase II is unidirectional from most genes. In plants, divergent genes, defined as non-overlapping genes organized head-to-head, are highly represented in the Arabidopsis genome. Nevertheless, there is scarce evidence on functional analyses of these intergenic regions. The At5g06290 and At5g06280 loci are head-to-head oriented and encode a chloroplast-located 2-Cys peroxiredoxin B (2CPB and a protein of unknown function (PUF, respectively. The 2-Cys peroxiredoxins are proteins involved in redox processes, they are part of the plant antioxidant defence and also act as chaperons. In this study, the transcriptional activity of a small intergenic region (351 bp shared by At5g06290 and At5g06280 in Arabidopsis thaliana was characterized. Results Activity of the intergenic region in both orientations was analyzed by driving the β-glucuronidase (GUS reporter gene during the development and growth of Arabidopsis plants under physiological and stressful conditions. Results have shown that this region drives expression either of 2cpb or puf in photosynthetic or vascular tissues, respectively. GUS expression driven by the promoter in 2cpb orientation was enhanced by heat stress. On the other hand, the promoter in both orientations has shown similar down-regulation of GUS expression under low temperatures and other stress conditions such as mannitol, oxidative stress, or fungal elicitor. Conclusion The results from this study account for the first evidence of an intergenic region that, in opposite orientation, directs GUS expression in different spatially-localized Arabidopsis tissues in a mutually exclusive manner. Additionally, this is the first demonstration of a small intergenic region that drives expression of a gene whose product is involved in the chloroplast antioxidant defence such as 2cpb. Furthermore, these results contribute to show that 2cpb is related to the heat stress defensive system

  15. DNA barcode and identification of the varieties and provenances of Taiwan's domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences.

    Science.gov (United States)

    Lee, Shih-Chieh; Wang, Chia-Hsiang; Yen, Cheng-En; Chang, Chieh

    2017-04-01

    The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0.379-0.994. In this polymerase chain reaction-amplified noncoding region, no varieties possessed identical sequences. Compared with the trnL intron and trnL-trnF intergenic sequence fragments of chloroplast cpDNA, the proportion of ITS2 nucleotide sequence variation was large and is more suitable for establishing a DNA barcode database to identify tea plant varieties. After establishing the database, 30 imported teas and 35 domestic made teas were used in this model system to explore the feasibility of using ITS2 sequences to identify the varieties and provenances of made teas. A phylogenetic tree was constructed using ITS2 sequences with the unweighted pair group method with arithmetic mean, which indicated that the same variety of tea plant is likely to be successfully categorized into one cluster, but contamination from other tea plants was also detected. This result provides molecular evidence that the similarity between important tea varieties in Taiwan remains high. We suggest a direct, wide collection of made tea and original samples of tea plants to establish an ITS2 sequence molecular barcode identification database to identify the varieties and provenances of tea plants. The DNA barcode comparison method can satisfy the need for a rapid, low-cost, frontline differentiation of the large amount of made teas from Taiwan and abroad, and can provide molecular evidence of their varieties and provenances. Copyright © 2016. Published by Elsevier B.V.

  16. 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...

  17. 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.

  18. 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.

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

    KAUST Repository

    Siddiqui, Amber Siddiqui Shahnawaz

    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

  20. 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

  1. Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.

    Science.gov (United States)

    Talkowski, Michael E; Maussion, Gilles; Crapper, Liam; Rosenfeld, Jill A; Blumenthal, Ian; Hanscom, Carrie; Chiang, Colby; Lindgren, Amelia; Pereira, Shahrin; Ruderfer, Douglas; Diallo, Alpha B; Lopez, Juan Pablo; Turecki, Gustavo; Chen, Elizabeth S; Gigek, Carolina; Harris, David J; Lip, Va; An, Yu; Biagioli, Marta; Macdonald, Marcy E; Lin, Michael; Haggarty, Stephen J; Sklar, Pamela; Purcell, Shaun; Kellis, Manolis; Schwartz, Stuart; Shaffer, Lisa G; Natowicz, Marvin R; Shen, Yiping; Morton, Cynthia C; Gusella, James F; Ernst, Carl

    2012-12-07

    Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  2. 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.

  3. Computational identification of human long intergenic non-coding RNAs using a GA-SVM algorithm.

    Science.gov (United States)

    Wang, Yanqiu; Li, Yang; Wang, Qi; Lv, Yingli; Wang, Shiyuan; Chen, Xi; Yu, Xuexin; Jiang, Wei; Li, Xia

    2014-01-01

    Long intergenic non-coding RNAs (lincRNAs) are a new type of non-coding RNAs and are closely related with the occurrence and development of diseases. In previous studies, most lincRNAs have been identified through next-generation sequencing. Because lincRNAs exhibit tissue-specific expression, the reproducibility of lincRNA discovery in different studies is very poor. In this study, not including lincRNA expression, we used the sequence, structural and protein-coding potential features as potential features to construct a classifier that can be used to distinguish lincRNAs from non-lincRNAs. The GA-SVM algorithm was performed to extract the optimized feature subset. Compared with several feature subsets, the five-fold cross validation results showed that this optimized feature subset exhibited the best performance for the identification of human lincRNAs. Moreover, the LincRNA Classifier based on Selected Features (linc-SF) was constructed by support vector machine (SVM) based on the optimized feature subset. The performance of this classifier was further evaluated by predicting lincRNAs from two independent lincRNA sets. Because the recognition rates for the two lincRNA sets were 100% and 99.8%, the linc-SF was found to be effective for the prediction of human lincRNAs.

  4. A novel intergenic ETnII-β insertion mutation causes multiple malformations in polypodia mice.

    Directory of Open Access Journals (Sweden)

    Jessica A Lehoczky

    Full Text Available Mouse early transposon insertions are responsible for ~10% of spontaneous mutant phenotypes. We previously reported the phenotypes and genetic mapping of Polypodia, (Ppd, a spontaneous, X-linked dominant mutation with profound effects on body plan morphogenesis. Our new data shows that mutant mice are not born in expected Mendelian ratios secondary to loss after E9.5. In addition, we refined the Ppd genetic interval and discovered a novel ETnII-β early transposon insertion between the genes for Dusp9 and Pnck. The ETn inserted 1.6 kb downstream and antisense to Dusp9 and does not disrupt polyadenylation or splicing of either gene. Knock-in mice engineered to carry the ETn display Ppd characteristic ectopic caudal limb phenotypes, showing that the ETn insertion is the Ppd molecular lesion. Early transposons are actively expressed in the early blastocyst. To explore the consequences of the ETn on the genomic landscape at an early stage of development, we compared interval gene expression between wild-type and mutant ES cells. Mutant ES cell expression analysis revealed marked upregulation of Dusp9 mRNA and protein expression. Evaluation of the 5' LTR CpG methylation state in adult mice revealed no correlation with the occurrence or severity of Ppd phenotypes at birth. Thus, the broad range of phenotypes observed in this mutant is secondary to a novel intergenic ETn insertion whose effects include dysregulation of nearby interval gene expression at early stages of development.

  5. A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster.

    Science.gov (United States)

    Gao, Ge; Vibranovski, Maria D; Zhang, Li; Li, Zheng; Liu, Ming; Zhang, Yong E; Li, Xinmin; Zhang, Wenxia; Fan, Qichang; VanKuren, Nicholas W; Long, Manyuan; Wei, Liping

    2014-04-01

    Recent studies have revealed key roles of noncoding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these noncoding RNAs. Profiling the transcriptome of Drosophila melanogaster with whole-genome tiling arrays found that 15% of male-biased transcribed fragments are intergenic noncoding RNAs (incRNAs), suggesting a potentially important role for incRNAs in sex-related biological processes. Statistical analysis revealed a paucity of male-biased incRNAs and coding genes on the X chromosome, suggesting that similar evolutionary forces could be affecting the genomic organization of both coding and noncoding genes. Expression profiling across germline and somatic tissues further suggested that both male meiotic sex chromosome inactivation (MSCI) and sexual antagonism could contribute to the chromosomal distribution of male-biased incRNAs. Comparative sequence analysis showed that the evolutionary age of male-biased incRNAs is a significant predictor of their chromosomal locations. In addition to identifying abundant sex-biased incRNAs in the fly genome, our work unveils a global picture of the complex interplay between noncoding RNAs and sexual chromosome evolution.

  6. 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.

  7. LOC100287225, novel long intergenic non-coding RNA, misregulates in colorectal cancer.

    Science.gov (United States)

    Kazemzadeh, Mina; Safaralizadeh, Reza; Feizi, Mohammad Ali Hosseinpour; Ravanbakhsh, Reyhaneh; Somi, Mohammad Hossein; Hashemzadeh, Shahryar

    2016-01-01

    Colorectal cancer (CRC) is one of the most common cancers in the world; therefore, extensive research is needed to find new molecular therapeutic targets and biomarkers. LncRNA (long non-coding RNA), a new class of non-coding RNAs, has a crucial role in the onset and progression of various cancers including colorectal cancer. Research on lncRNA is still at initial stages and underlying molecular mechanisms of the vast majority of lncRNA have remained unclear. LOC100287225 is one of these novel lncRNAs (long intergenic non-coding RNA) located in the long arm of the chromosome 18. The purpose of this study was to determine the expression of LOC100287225 in colorectal tissue, and its misregulation in CRC patients. Quantitative real-time-PCR (qRT-PCR) was used to investigate the LOC100287225 expression in pairs of tumorous and adjacent tumor-free tissues of 39 colorectal cancer patients. Also, the relationship between the clinicopathology and expression of LOC100287225 was determined. QRT-PCR results revealed that not only is LOC100287225 expressed in the intestinal tissue, but has also been misregulated during tumorigenesis. Moreover, LOC100287225 RNA relative expression levels were significantly lower in tumor tissues compared with adjacent tumor-free tissues (P< 0.001). RNA expression level of LOC100287225 did not show significant correlation with clinical characteristics. In conclusion, our study demonstrated that LOC100287225 misregulation could be a potential target for gene therapy in colorectal cancer.

  8. 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.

  9. Impact of ZnO embedded feed spacer on biofilm development in membrane systems.

    Science.gov (United States)

    Ronen, Avner; Semiat, Raphael; Dosoretz, Carlos G

    2013-11-01

    The concept of suppressing biofouling formation using an antibacterial feed spacer was investigated in a bench scale-cross flow system mimicking a spiral wound membrane configuration. An antibacterial composite spacer containing zinc oxide-nanoparticles was constructed by modification of a commercial polypropylene feed spacer using sonochemical deposition. The ability of the modified spacers to repress biofilm development on membranes was evaluated in flow-through cells simulating the flow conditions in commercial spiral wound modules. The experiments were performed at laminar flow (Re = 300) with a 200 kDa molecular weight cut off polysulfone ultrafiltration membrane using Pseudomonas putida S-12 as model biofilm bacteria. The modified spacers reduced permeate flux decrease at least by 50% compared to the unmodified spacers (control). The physical properties of the modified spacer and biofilm development were evaluated using high resolution/energy dispersive spectrometry-scanning electron microscopy, atomic force microscopy and confocal laser scanning microscopy imaging (HRSEM, EDS, AFM and CLSM). HRSEM images depicted significantly less bacteria attached to the membranes exposed to the modified spacer, mainly scattered and in a sporadic monolayer structure. AFM analysis indicated the influence of the modification on the spacer surface including a phase change on the upper surface. Dead-live staining assay by CLSM indicated that most of the bacterial cells attached on the membranes exposed to the modified spacer were dead in contrast to a developed biofilm which was predominant in the control samples.

  10. Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis

    Directory of Open Access Journals (Sweden)

    Zhengyu eJiang

    2012-12-01

    Full Text Available Recent high-throughput transcript discoveries have yielded a growing recognition of long intergenic non-coding RNAs (lincRNAs, a class of arbitrarily defined transcripts (>200 nt that are primarily produced from the intergenic space. LincRNAs have been increasingly acknowledged for their expressional dynamics and likely functional associations with cancers. However, differential gene dosage of lincRNA genes between cancer genomes is less studied. By using the high-density Human Omni5-Quad BeadChips (Illumina, we investigated genomic copy number aberrations in a set of seven tumor-normal paired primary human mammary epithelial cells (HMECs established from patients with invasive ductal carcinoma. This Beadchip platform includes a total of 2,435,915 SNP loci dispersed at an average interval of ~700 nt throughout the intergenic region of the human genome. We mapped annotated or putative lincRNA genes to a subset of 332,539 SNP loci, which were included in our analysis for lincRNA-associated copy number variations (CNV. We have identified 122 lincRNAs, which were affected by somatic CNV with overlapped aberrations ranging from 0.14% to 100% in length. LincRNA-associated aberrations were detected predominantly with copy number losses and preferential clustering to the ends of chromosomes. Interestingly, lincRNA genes appear to be much less susceptible to CNV in comparison to both protein-coding and intergenic regions (CNV affected segments in percentage: 1.8%, 37.5% and 60.6%, respectively. In summary, our study established a novel approach utilizing high-resolution SNP array to identify lincRNA candidates, which could functionally link to tumorigenesis, and provide new strategies for the diagnosis and treatment of breast cancer.

  11. Definitive Treatment of Infected Shoulder Arthroplasty With a Cement Spacer.

    Science.gov (United States)

    Mahure, Siddharth A; Mollon, Brent; Yu, Stephen; Kwon, Young W; Zuckerman, Joseph D

    2016-09-01

    Infection in the setting of shoulder arthroplasty can result in significant pain, loss of function, and the need for additional surgery. As the use of shoulder arthroplasty increases, the medical and economic burdens of periprosthetic joint infection increase as well. The ideal management of infected shoulder prostheses has not been established. This report describes 9 patients from a single institution who had an infected shoulder arthroplasty that was definitively managed with a cement spacer. All patients had a minimum of 2 years of follow-up. Of the 9 patients in this study, 6 were men. Mean age was 73±9 years. Of the study patients, 1 had diabetes, 2 presented with Parkinson's disease, and 5 had a history of tobacco use. Average body mass index was 27.9±7 kg/m(2). After mean follow-up of 4 years, none of the patients had clinical or radiographic evidence of infection. Functional outcomes, as measured by American Shoulder and Elbow Surgeons scores, were good or fair in 89% of patients, and the average American Shoulder and Elbow Surgeons score was 57. A review of recent literature suggested that the current findings were similar to those in studies reporting 1- or 2-stage revision procedures. Although cement spacers are typically used as part of a 2-stage revision procedure, the current findings suggest that cement spacers can be used effectively to eradicate infection and allow for acceptable functional recovery and range of motion in patients who have severe medical comorbidities and cannot tolerate additional surgery. [Orthopedics. 2016; 39(5):e924-e930.].

  12. 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.

  13. An insulating grid spacer for large-area MICROMEGAS chambers

    CERN Document Server

    Bernard, D; D'Enterria, D G; Le Guay, M; Martínez, G; Mora, M J; Pichot, P; Roy, D; Schutz, Y; Gandi, A; De Oliveira, R

    2002-01-01

    We present an original design for large area gaseous detectors based on the MICROMEGAS technology. This technology incorporates an insulating grid, sandwiched between the micro-mesh and the anode-pad plane, which provides an uniform 200 $\\mu$m amplification gap. The uniformity of the amplification gap thickness has been verified under several experimental conditions. The gain performances of the detector are presented and compared to the values obtained with detectors using cylindrical micro spacers. The new design presents several technical and financial advantages.

  14. 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.

  15. 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...

  16. 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...... 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...... log transformed and expressed as geometric mean fold difference for the average plasma salbutamol concentration (Cav) over 20 min. RESULTS: There were significant differences (P Primed1 vs NewRinsed 1.92 fold (95% CI 1.15, 3...

  17. 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

    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......, 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...... 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...

  18. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  19. Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs.

    Science.gov (United States)

    Managadze, David; Rogozin, Igor B; Chernikova, Diana; Shabalina, Svetlana A; Koonin, Eugene V

    2011-01-01

    Mammalian genomes contain numerous genes for long noncoding RNAs (lncRNAs). The functions of the lncRNAs remain largely unknown but their evolution appears to be constrained by purifying selection, albeit relatively weakly. To gain insights into the mode of evolution and the functional range of the lncRNA, they can be compared with much better characterized protein-coding genes. The evolutionary rate of the protein-coding genes shows a universal negative correlation with expression: highly expressed genes are on average more conserved during evolution than the genes with lower expression levels. This correlation was conceptualized in the misfolding-driven protein evolution hypothesis according to which misfolding is the principal cost incurred by protein expression. We sought to determine whether long intergenic ncRNAs (lincRNAs) follow the same evolutionary trend and indeed detected a moderate but statistically significant negative correlation between the evolutionary rate and expression level of human and mouse lincRNA genes. The magnitude of the correlation for the lincRNAs is similar to that for equal-sized sets of protein-coding genes with similar levels of sequence conservation. Additionally, the expression level of the lincRNAs is significantly and positively correlated with the predicted extent of lincRNA molecule folding (base-pairing), however, the contributions of evolutionary rates and folding to the expression level are independent. Thus, the anticorrelation between evolutionary rate and expression level appears to be a general feature of gene evolution that might be caused by similar deleterious effects of protein and RNA misfolding and/or other factors, for example, the number of interacting partners of the gene product.

  20. 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.

  1. Molecular profiling of microbial communities from contaminated sources: Use of substractive cloning methods and rDNA spacer sequences. 1997 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-01

    'This project is to develop molecular methods for rapid characterization of microbial communities in contaminated ecosystems. The authors are exploring the use of {sup 16}s ribosomal DNA intergenic spacer regions (ISRs) to profile community composition. The choice proves to be a good one: there are 200--550 bases of 1 to 3 variable regions from which to choose species-specific probes, as well as 2--4 stretches of conserved sequence from which to develop universal PCR (polymerase chain reaction) primers. Preliminary community characterization is complete, and several types of arrays are under development to determine the types of bacteria present and the status of the ground water. Profiling the community composition of polluted groundwater will impact the broad field of microbial ecology as well as mixed-waste bioremediation. Results The samples the authors have been analysing were provided by Dr. Fred Brockman from Pacific Northwest Laboratory, and were collected at the US DOE Hanford site, Washington state. The samples were microbial filtrates from ground water polluted with 2 mg/L carbon tetrachloride and 250 mg/L nitrate and subjected to enrichment (acetate + nitrate) and recirculation. This project is described in some detail in PNNL-11113, Accelerated In Situ Bioremediation of Groundwater, by M.J. Truex, B.S. Hooker, and D.B. Anderson, July 1996.'

  2. ERIC and REP-PCR banding patterns and sequence analysis of the internal transcribed spacer of rDNA of Stemphylium solani isolates from cotton.

    Science.gov (United States)

    Mehta, Yeshwant R; Mehta, Angela; Rosato, Yoko B

    2002-05-01

    The genetic diversity of the Stemphylium solani isolates from cotton was assessed by Enterobacterial Repetitive Intergenic Consensus (ERIC) and Repetitive Extragenic Palindromes (REP)-PCR fingerprinting. Twenty eight monosporic isolates of S. solani from cotton were used along with five isolates from tomato and one isolate of Alternaria macrospora from cotton for comparison. The dendrogram obtained revealed clear differences between the cotton and tomato isolates as well as between the tomato isolates from different geographic regions. The genetic relationships among S. solani isolates were also analyzed by sequencing the internal transcribed spacer (ITS) region of four isolates representing the three ERIC and REP groups. The tomato isolate from the State of São Paulo showed a distinct ITS sequence from that of the cotton isolates and tomato isolate from the State of Goiás, giving evidence that it belongs to a different genotype of S. solani. This is the first report of the entire sequence of the ITS1-5.8S-ITS2 regions of S. solani.

  3. 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

  4. Cervical interfacet spacers and maintenance of cervical lordosis.

    Science.gov (United States)

    Tan, Lee A; Straus, David C; Traynelis, Vincent C

    2015-05-01

    OBJECT The cervical interfacet spacer (CIS) is a relatively new technology that can increase foraminal height and area by facet distraction. These offer the potential to provide indirect neuroforaminal decompression while simultaneously enhancing fusion potential due to the relatively large osteoconductive surface area and compressive forces exerted on the grafts. These potential benefits, along with the relative ease of implantation during posterior cervical fusion procedures, make the CIS an attractive adjuvant in the management of cervical pathology. One concern with the use of interfacet spacers is the theoretical risk of inducing iatrogenic kyphosis. This work tests the hypothesis that interfacet spacers are associated with loss of cervical lordosis. METHODS Records from patients undergoing posterior cervical fusion at Rush University Medical Center between March 2011 and December 2012 were reviewed. The FacetLift CISs were used in all patients. Preoperative and postoperative radiographic data were reviewed and the Ishihara indices and cervical lordotic angles were measured and recorded. Statistical analyses were performed using STATA software. RESULTS A total of 64 patients were identified in whom 154 cervical levels were implanted with machined allograft interfacet spacers. Of these, 15 patients underwent anterior-posterior fusions, 4 underwent anterior-posterior-anterior fusions, and the remaining 45 patients underwent posterior-only fusions. In the 45 patients with posterior-only fusions, a total of 110 levels were treated with spacers. There were 14 patients (31%) with a single level treated, 16 patients (36%) with two levels treated, 5 patients (11%) with three levels treated, 5 patients (11%) with four levels treated, 1 patient (2%) with five levels treated, and 4 patients (9%) with six levels treated. Complete radiographic data were available in 38 of 45 patients (84%). On average, radiographic follow-up was obtained at 256.9 days (range 48-524 days

  5. 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.

  6. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Directory of Open Access Journals (Sweden)

    Tran Duc

    2010-05-01

    Full Text Available Abstract Background Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the

  7. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable

  8. 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.

  9. 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.

  10. 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.

  11. Solution-processed organic tandem solar cells with embedded optical spacers

    NARCIS (Netherlands)

    Hadipour, Afshin; de Boer, Bert; Blom, Paul W. M.

    2007-01-01

    We demonstrate a solution-processed polymer tandem solar cell in which the two photoactive single cells are separated by an optical spacer. The use of an optical spacer allows for an independent optimization of both the electronic and optical properties of the tandem cell. The optical transmission

  12. Variability of aerosol delivery via spacer devices in young asthmatic children in daily life

    NARCIS (Netherlands)

    H.M. Janssens (Hettie); S.G. Devadason; W.C.J. Hop (Wim); P.N. LeSouef; J.C. de Jongste (Johan); H.A.W.M. Tiddens (Harm)

    1999-01-01

    textabstractPressurized metered dose inhalers (pMDI) are widely used together with spacers for the treatment of asthma in children. However, the variability of daily medication dose for pMDI/spacer combinations is not known. Electrostatic charge is a potential source of

  13. 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.

  14. A Study of Neutronics Effects of the Spacer Grids in a Typical PWR via Monte Carlo Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Bach, Tran Xuan; Cho, Nam Zin [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2014-10-15

    Neutronics analysis, the spacer grids which support fuel rods are not explicitly described, but they are homogenized with coolant. However, the effects of neglecting or simplifying the spacer grids are not reported in the literature to the best of our knowledge. In this paper, to investigate the effects of spacer grids in neutronics analysis, a detailed description of spacer grids is added to the KAIST benchmark problem 1B. Then, the effective multiplication factor, spatial distributions of neutron flux, and its energy spectrum are obtained for the two cases (with and without spacer grids). Numerical results show that the effects of spacer grids are not negligible. In this paper, to investigate the effect of spacer grids, the spacer grid geometry is described in detail in the Monte Carlo calculation. In the numerical test, the two cases are compared in the context of a modified KAIST benchmark problem 1B. Case 1 does not have spacer grids, while the space is filled by coolant instead. Case 2 includes the spacer grids. The difference in neutron flux spectra is also observed. Thus, the effect of the spacer grids should be considered in the whole-core reactor analysis. In practice, the spacer grids are homogenized into coolant to consider its effect. As a further study, therefore, it would be worthwhile to investigate the differences between the homogenization and the explicit description of the spacer grids.

  15. 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

  16. Hydrophobic spacers enhance the helicity and lectin binding of synthetic, pH-responsive glycopolypeptides.

    Science.gov (United States)

    Mildner, Robert; Menzel, Henning

    2014-12-08

    The influence of different hydrophobic spacers on the structural and lectin binding properties of well-defined glycopolypeptides decorated with galactose moieties was investigated. All glycopolypeptides were prepared from a poly(α,l-glutamic acid) (PGA) precursor via a polymer-analogous aqueous amide coupling reaction. Thereby, two alkyl spacers of different length (C6 and C11) as well as an aromatic spacer were introduced between the backbone and the galactose moieties, as confirmed by (1)H NMR spectroscopy. The secondary structure was investigated as a function of the sugar density and the pH by circular dichroism (CD) spectroscopy. It was found that the helicity in acidic medium and thus the typical coil-to-helix transition is strongly enhanced by the hydrophobic spacers. Preliminary lectin binding tests via turbidimetric assay revealed that the spacers also significantly enhance the interaction of the glycopolypeptides with the lectin RCA120.

  17. Replication intermediate analysis confirms that chromosomal replication origin initiates from an unusual intergenic region in Caulobacter crescentus.

    Science.gov (United States)

    Brassinga, A K; Marczynski, G T

    2001-11-01

    The alpha-proteobacterium Caulobacter crescentus possesses a developmental cell cycle that restricts chromosome replication to a stalked cell type. The proposed C.crescentus chromosome replication origin (Cori) lies between hemE and RP001, an unusual intergenic region not previously associated with bacterial replication origins, although a similar genomic arrangement is also present at the putative replication origin in the related bacterium Rickettsia prowazekii. The cloned Cori supports autonomous plasmid replication selectively in the stalked cell type implying that replication of the entire chromosome also initiates between hemE and RP001. To confirm this location, we applied the 2-D (N/N) agarose gel electrophoresis technique to resolve and identify chromosome replication intermediates throughout a 30 kb region spanning Cori. Replication initiation in Cori was uniquely characterized by an 'origin bubble and Y-arc' pattern and this observation was supported by simple replication fork 'Y-arc' patterns that characterized the regions flanking Cori. These replication forks originated bi-directionally from within Cori as determined by the fork direction assay. Therefore, chromosomal replication initiates from the unusual hemE/RP001 intergenic region that we propose represents a new class of replication origins.

  18. Effects of structural changes in the dsdA-dsdC intergenic region on D-serine deaminase synthesis.

    Science.gov (United States)

    McFall, E; Nikam, S S; Palchaudhuri, S

    1991-02-01

    Single-base-pair changes well upstream of its transcription initiation site resulted in partially to fully constitutive expression of the D-serine deaminase structural gene, dsdA, independently of the cyclic AMP-cyclic AMP-binding protein complex and of the specific D-serine deaminase activator protein. These promoter mutations appear to define a consensus sequence that is repeated several times. Basal expression of dsdA+ was also strongly enhanced by subcloning on multicopy plasmids, by the DNA gyrase inhibitor novobiocin, and in dsdC(Con) mutants by increasing growth temperature. These results suggest that activation of dsdA+ expression by the dsdC-encoded protein involves distortion of promoter DNA. A dsdA translation start at bp -731 was verified by subcloning of dsdC+. Plasmid-specified activator at a high concentration interfered with chromosomal dsdC(Con) expression, and the interference was enhanced by deletion of most of the intergenic region from the plasmid. Even at a high concentration, however, plasmid-specified activator did not activate expression of chromosomal dsdA+, and in one case it was actually repressive. These results confirm the strong cis tropism of plasmid-specified dsdC-encoded protein and suggest that it is mediated by multiple sites in the dsdA-dsdC intergenic region.

  19. Genome-assisted development of nuclear intergenic sequence markers for entomopathogenic fungi of the Metarhizium anisopliae species complex.

    Science.gov (United States)

    Kepler, R M; Rehner, S A

    2013-03-01

    Entomopathogenic fungi in the genus Metarhizium are useful for biological control programmes against economically important arthropod pests worldwide. However, understanding the true diversity and ecology of these organisms is hampered by convergent morphologies between species. The application of molecular techniques has enabled greater resolution of species than allowed by morphology alone. In particular, the commonly used biocontrol agent M. anisopliae was found to be a species complex composed of nine species. This prior work was conducted with commonly used markers in fungal phylogenetics (BTUB, RPB1, RPB2 and TEF), which likely under-represent diversity in the M. anisopliae complex. Using sequence data from nuclear genomes of M. acridum and M. robertsii we identified regions of conserved gene synteny and developed primers to amplify intergenic regions of seven loci. Using ex-type and authenticated tissue specimens for species in the M. anisopliae complex, we demonstrate that sequence data derived from intergenic loci is more variable and phylogenetically informative than previously available markers. These new markers will facilitate investigations at or below the species level for the M. anisopliae complex. The method of marker development employed here should be extendable to any group with sufficiently divergent genome data available.

  20. 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 performance of pressurized metered dose inhalers (pMDIs) and spacers in correct dose recommendations is important, but limited information on dose delivery and fine-particle dose from different combinations of spacers and pMDIs is available. In this study, three combinations of spacers and pM...

  1. Occult spinous process fractures associated with interspinous process spacers.

    Science.gov (United States)

    Kim, David H; Tantorski, Mark; Shaw, Jeremy; Martha, Juli; Li, Ling; Shanti, Nael; Rencu, Tal; Parazin, Stephen; Kwon, Brian

    2011-07-15

    Prospective observational study. To provide a more accurate estimate of the rate of acute spinous process fractures associated with IPS surgery. Biomechanical cadaveric studies have suggested adequate spinous process strength to support placement of interspinous process spacers (IPS). Postoperative spinous process fractures have been reported in one%-to 5.8% of patients in previous series based on routine biplanar radiographic evaluation. However, most fractures occur between the base and midportion of the spinous process in an area that is typically difficult to visualize on plain radiographs due to device design. All patients underwent preoperative biplanar plain radiographs and computed tomography (CT) of the lumbar spine to confirm anatomy favorable for IPS placement and rule out fracture or spondylolysis. Postoperatively, all patients underwent repeat CT imaging within six months of surgery, biplanar radiographs at two weeks, six weeks, three months, six months, and one year. All studies were reviewed independently by a neuroradiologist and two orthopedic spine surgeons. Fifty implants (38 L4-5, 12 L3-4) were placed in 38 patients who completed follow-up and were included in final analysis. Three IPS designs were included (34 Medtronic X-STOP titanium, 8 X-STOP PEEK, 8 Lanx Aspen). Postoperative CT revealed 11 nondisplaced spinous process fractures in 11 patients (28.9% of patients, 22% of levels). Five fractures were associated with mild to moderate lumbar back pain and six fractures were asymptomatic. No patient reported a traumatic incident. No fracture was identifiable on plain radiographs. One fracture displaced during follow-up evaluation. Three patients underwent IPS removal and laminectomy. Three fractures healed by CT in one year. Overall, patients with fractures tended toward poorer outcomes by Zurich Claudication Questionnaire (ZCQ) (28.5% vs. 34.8% improvement in symptom severity, P = 0.496; 21.4% vs. 30.7% improvement in physical function, P = 0

  2. Characterization of feed channel spacer performance using geometries obtained by X-ray computed tomography

    KAUST Repository

    Haaksman, Viktor A.

    2016-09-09

    Spiral-wound membrane modules used in water treatment for water reuse and desalination make use of spacer meshes for keeping the membrane leaves apart and for enhancing the mass transfer. Computational fluid dynamics (CFD) has gained importance in the design of new spacers with optimized hydrodynamic characteristics, but this requires a precise description of the spacer geometry. This study developed a method to obtain accurate three-dimensional (3-D) geometry representations for any given spacer design from X-ray computed tomography (CT) scans. The method revealed that the filaments of industrial spacers have a highly variable cross-section size and shape, which impact the flow characteristics in the feed channel. The pressure drop and friction factors were calculated from numerical simulations on five commercially available feed spacers used in practice. Model solutions compared well to experimental data measured using a flow cell for average velocities up to 0.2 m/s, as used in industrial reverse osmosis and nanofiltration membrane operations. A newly-proposed spacer geometry with alternating strand thickness was tested, which was found to yield a lower pressure drop while being highly efficient in converting the pumping power into membrane shear. Numerical model solutions using CFD with geometries from CT scans were closer to measurements than those obtained using the traditional circular cross-section strand simplification, indicating that CT scans are very well suitable to approximate real feed spacer geometries. By providing detailed insight on the spacer filament shape, CT scans allow better quantification of local distribution of velocity and shear, possibly leading to more accurate estimations of fouling and concentration polarization. © 2016 Elsevier B.V.

  3. Optimization of Radiation Therapy Techniques for Prostate Cancer With Prostate-Rectum Spacers: A Systematic Review

    Energy Technology Data Exchange (ETDEWEB)

    Mok, Gary [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Department of Radiation Oncology, Centre Intégré de Cancérologie de Laval, Centre de Santé et de Services Sociaux de Laval, Laval, Québec (Canada); Department of Radiology, Radiation Oncology, and Nuclear Medicine, Centre Hospitalier Universitaire de Montréal, Montréal, Québec (Canada); Benz, Eileen [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Vallee, Jean-Paul [Department of Radiology, Geneva University Hospital, Geneva (Switzerland); Miralbell, Raymond [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland); Zilli, Thomas, E-mail: Thomas.Zilli@hcuge.ch [Department of Radiation Oncology, Geneva University Hospital, Geneva (Switzerland)

    2014-10-01

    Dose-escalated radiation therapy for localized prostate cancer improves disease control but is also associated with worse rectal toxicity. A spacer placed between the prostate and rectum can be used to displace the anterior rectal wall outside of the high-dose radiation regions and potentially minimize radiation-induced rectal toxicity. This systematic review focuses on the published data regarding the different types of commercially available prostate-rectum spacers. Dosimetric results and preliminary clinical data using prostate-rectum spacers in patients with localized prostate cancer treated by curative radiation therapy are compared and discussed.

  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. 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".

  6. [Interspinous spacers and disc herniation. Geomorphometric and clinical study of 71 cases treated by L4-L5 microdiscectomy associated to spacer placement].

    Science.gov (United States)

    Aso Escario, José; Aso Vizán, Alberto; Martínez Quiñones, José Vicente; Consolini, Fabian; Martín Gallego, Álvaro; Arregui Calvo, Ricardo

    2015-01-01

    A controversial indication of interspinous spacers is their use as a complement to discectomy. At the present time, there is no solid clinical evidence of effectiveness of that association, which might result from variability in spacer positioning, restricting its correct biomechanical actions. In this study our goal was to identify and analyse the variability in the placement of an interspinous spacer, and to investigate its relationship with the clinical results. We performed a retrospective study on X-ray films from 71 patients suffering from disc herniation in L4-L5 who underwent surgery in our hospital, consisting of: microdiscectomy and biomed interspinous spacer implantation. The geomorphometric techniques used to analyse the data were procrustes superimposition and principal components analysis. We compared the clinical results (using the Herron and Turner scale), segmental lordosis and surgical distraction with the geomorphometric parameters. Significant morphological variability was found in the implant position showing cephalo-caudal translation and clockwise-counterclockwise rotations. This variability did not correlate with clinical results. A relationship with anatomical features (lordosis) and additional surgical distraction was identified. A different morphology of implant-segment configuration was identified in cases with recurrence of disc herniation. Geometric morphometrics allowed identifying high variability in the final placement of interspinous spacers. Nevertheless, it seems not to be related to the clinical outcome, depending rather on the degree of lordosis and distraction. Some differences in segment-implant morphology were identified in cases with recurrences. To assess the effectiveness of spacers, larger studies including morphological and clinical variables are required. Copyright © 2013 Sociedad Española de Neurocirugía. Published by Elsevier España. All rights reserved.

  7. Effects of grid spacer with mixing vane on entrainments and depositions in two-phase annular flows

    Directory of Open Access Journals (Sweden)

    Akimaro Kawahara

    2015-06-01

    Full Text Available The effects of mixing vanes (MVs attached to a grid spacer on the characteristics of air–water annular flows were experimentally investigated. To know the effects, a grid spacer with or without MV was inserted in a vertical circular pipe of 16-mm internal diameter. For three cases (i.e., no spacer, spacer without MV, and spacer with MV, the liquid film thickness, liquid entrainment fraction, and deposition rate were measured by the constant current method, single liquid film extraction method, and double liquid film extraction method, respectively. The MVs significantly promote the re-deposition of liquid droplets in the gas core flow into the liquid film on the channel walls. The deposition mass transfer coefficient is three times higher for the spacer with MV than for the spacer without MV, even for cases 0.3-m downstream from the spacer. The liquid film thickness becomes thicker upstream and downstream for the spacer with MV, compared with the thickness for the spacer without MV and for the case with no spacer.

  8. 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.

  9. 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.

  10. Cholesterol-containing liquid crystal dimmers with ether linkages between the spacer and mesogenic units

    NARCIS (Netherlands)

    Marcelis, A.T.M.; Koudijs, A.; Karczmarzyk, Z.; Sudhölter, E.J.R.

    2003-01-01

    Three series of chiral liquid crystalline dimers were investigated, having a cholesteryl and a cyanobiphenylyl, butoxybiphenylyl or hexyloxybiphenylyl group connected to a variable alkyl spacer through ether linkages. Their properties were compared with those of the corresponding ester derivatives.

  11. Very strong antiferromagnetic interlayer exchange coupling with iridium spacer layer for perpendicular magnetic tunnel junctions

    Science.gov (United States)

    Yakushiji, Kay; Sugihara, Atsushi; Fukushima, Akio; Kubota, Hitoshi; Yuasa, Shinji

    2017-02-01

    We systematically studied the interlayer exchange coupling (IEC) in a perpendicular synthetic antiferromagnetically coupled structure having an Ir spacer layer for perpendicular magnetic tunnel junctions (p-MTJs). We found a broader peak in IEC energy density (Jex) versus spacer thickness (tIr) compared with the case of using a Ru spacer. The highest IEC energy density was 2.6 erg/cm2 at a tIr of about 5 nm. The p-MTJ nanopillars had a high magnetoresistance ratio (131%) as well as a high spin-transfer torque (STT) switching efficiency (about 2). An Ir spacer can be used to make a stable reference layer for STT magnetoresistive random access memory.

  12. Cholesterol-containing liquid crystal dimmers with ether linkages between the spacer and mesogenic units

    NARCIS (Netherlands)

    Marcelis, A.T.M.; Koudijs, A.; Karczmarzyk, Z.; Sudhölter, E.J.R.

    2003-01-01

    Three series of chiral liquid crystalline dimers were investigated, having a cholesteryl and a cyanobiphenylyl, butoxybiphenylyl or hexyloxybiphenylyl group connected to a variable alkyl spacer through ether linkages. Their properties were compared with those of the corresponding ester derivatives.

  13. 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.

  14. 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.

  15. 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.

  16. The effect of flexible spacers on the h-shaped dimesogenic liquid crystalline compounds

    Energy Technology Data Exchange (ETDEWEB)

    Park, Joo Hoon; Lee, Hwan Myoung; Choi, Ok Byung; Lee, Chang Joon [Hoseo Univ., Asan (Korea, Republic of); So, Bong Keun; Lee, Soo Min [Hannam Univ., Daejon (Korea, Republic of)

    2001-12-01

    A homologous series of new H-shaped twin liquid crystal molecules (PPPA-n) with flexible spacers, oxypolymethyleneoxy, has been prepared by esterification of acid chloride of {alpha}, {omega}-bis(2,5-dicar-boxyphenoxy)alkanes with p-phenylphenol. The length of spacer was varied from oxyethyleneoxy (n=2) to oxydecamethyleneoxy (n=10). Their thermodynamic data were measured by differential scanning calorimetry and liquid crystalline properties were investigated by a hot-stage polarizing microscope.

  17. Biofouling patterns in spacer filled channels: High resolution imaging for characterization of heterogeneous biofilms

    KAUST Repository

    Staal, Marc

    2017-08-15

    Biofilms develop in heterogeneous patterns at a µm scale up to a cm scale, and patterns become more pronounced when biofilms develop under complex hydrodynamic flow regimes. Spatially heterogeneous biofilms are especially known in spiral wound reverse osmosis (RO) and nanofiltration (NF) membrane filtration systems used for desalination and wastewater reuse to produce high quality (drinking) water. These spiral wound membrane modules contain mesh-like spacer structures used to create an intermembrane space and improve water mixing. Spacers create inhomogeneous water flow patterns resulting in zones favouring biofilm growth, possibly leading to biofouling thus hampering water production. Oxygen sensing planar optodes were used to visualize variations in oxygen decrease rates (ODR). ODR is an indication of biofilm activity. In this study, ODR images of multiple repetitive spacer areas in a membrane fouling simulator were averaged to produce high resolution, low noise ODR images. Averaging 40 individual spacer areas improved the ODR distribution image significantly and allowed comparison of biofilm patterning over a spacer structure at different positions in an RO filter. This method clearly showed that most active biofilm accumulated on and in direct vicinity of the spacer. The averaging method was also used to calculate the deviation of ODR patterning from individual spacer areas to the average ODR pattern, proposing a new approach to determine biofilm spatial heterogeneity. This study showed that the averaging method can be applied and that the improved, averaged ODR images can be used as an analytical, in-situ, non-destructive method to assess and quantify the effect of membrane installation operational parameters or different spacer geometries on biofilm development in spiral wound membrane systems characterized by complex hydrodynamic conditions.

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

    OpenAIRE

    Vergnaud Gilles; Grissa Ibtissem; Pourcel Christine

    2007-01-01

    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 t...

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

    Directory of Open Access Journals (Sweden)

    Diana Chernikova

    2016-07-01

    Full Text Available 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.

  20. Capturing intergenerativity: the use of student reflective journals to identify learning within an undergraduate course in gerontological nursing.

    Science.gov (United States)

    Davies, Susan M; Reitmaier, Amy B; Smith, Linda Reveling; Mangan-Danckwart, Deborah

    2013-03-01

    The benefits of intergenerational contact between older and young adults have been demonstrated; yet, nursing programs have underexplored the potential of such relationships for enhancing student learning. This article presents an analysis of student reflective journals as part of an evaluation of an undergraduate gerontological nursing course. The course aims to create positive learning experiences by involving older adults as partners in student learning. Older adults are recruited to receive visits from a designated student to share aspects of their life and experiences. Students write reflective journals based on these visits as a method of evaluating their learning. A framework analysis of 80 journals completed by 59 students identified four major themes representing the impact of these visits on student learning: becoming aware, making connections, seeing the unique person, and valuing intergenerational relationships. The analysis suggests the relevance of the concept of intergenerativity in illuminating shared benefits of the practicum experience.

  1. Modulation of Re-initiation of Measles Virus Transcription at Intergenic Regions by PXD to NTAIL Binding Strength.

    Science.gov (United States)

    Bloyet, Louis-Marie; Brunel, Joanna; Dosnon, Marion; Hamon, Véronique; Erales, Jenny; Gruet, Antoine; Lazert, Carine; Bignon, Christophe; Roche, Philippe; Longhi, Sonia; Gerlier, Denis

    2016-12-01

    Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication. Transcription of the six genes occurs sequentially. This implies ending and re-initiating mRNA synthesis at each intergenic region (IGR). We explored here to which extent the binding of the X domain of P (XD) to the C-terminal region of the N protein (NTAIL) is involved in maintaining the P/L complex anchored to the nucleocapsid template during the sequential transcription. Amino acid substitutions introduced in the XD-binding site on NTAIL resulted in a wide range of binding affinities as determined by combining protein complementation assays in E. coli and human cells and isothermal titration calorimetry. Molecular dynamics simulations revealed that XD binding to NTAIL involves a complex network of hydrogen bonds, the disruption of which by two individual amino acid substitutions markedly reduced the binding affinity. Using a newly designed, highly sensitive dual-luciferase reporter minigenome assay, the efficiency of re-initiation through the five measles virus IGRs was found to correlate with NTAIL/XD KD. Correlatively, P transcript accumulation rate and F/N transcript ratios from recombinant viruses expressing N variants were also found to correlate with the NTAIL to XD binding strength. Altogether, our data support a key role for XD binding to NTAIL in maintaining proper anchor of the P/L complex thereby ensuring transcription re-initiation at each intergenic region.

  2. Bartonella melophagi in Melophagus ovinus (sheep ked) collected from sheep in northern Oromia, Ethiopia.

    Science.gov (United States)

    Kumsa, Bersissa; Parola, Philippe; Raoult, Didier; Socolovschi, Cristina

    2014-01-01

    Melophagus ovinus (sheep ked) is one of the most common ectoparasites that contributes to enormous economic losses in the productivity of sheep in many countries. The present study was conducted from January 2012 to July 2013 on M. ovinus collected from sheep at three sites in Ethiopia. Of the sheep studied, 65.7% (88/134) were infested with M. ovinus. The prevalence of M. ovinus was 76% (76/100), 47% (8/17) and 23.5% (4/17) at the Kimbibit, Chacha and Shano sites, respectively. An overall number of 229 M. ovinus specimens (138 females, 86 males and five pupae) and 554 M. ovinus specimens (272 females, 282 males) were collected from young and adult sheep, respectively. Bartonella DNA was detected in 89% (694/783) of M. ovinus using a quantitative Bartonella genus-specific PCR assay targeting the 16S/23S rRNA intergenic spacer region. The sequencing of the PCR products of fragments of the gltA and rpoB genes showed 99.6-100% and 100% homology, respectively, with B. melophagi. Statistically significant variation was not noted in the overall prevalence of Bartonella DNA between female and male M. ovinus. All of the sheep infested with M. ovinus 100% (88/88) harbored at least one M. ovinus specimen that contained Bartonella DNA. This study highlights that B. melophagi in M. ovinus from sheep in highlands in Ethiopia possibly has certain zoonotic importance.

  3. Characterization of Vibrio cholerae isolated from the aquatic basins of the State of Pernambuco, Brazil.

    Science.gov (United States)

    Leal, Nilma Cintra; de Araújo Figueiroa, Angela Cristina Torres; Cavalcanti, Valdelúcia Oliveira; da Silva, Soraya Cavalcante; Leal-Balbino, Tereza Cristina; de Almeida, Alzira Maria Paiva; Hofer, Ernesto

    2008-03-01

    Through a continuous bacteriological monitoring programme carried out by the Health Secretariat of the State of Pernambuco, Brazil, two isolates of Vibrio cholerae O1 El Tor Ogawa were discovered in an endemic area in 2001, during a cholera inactive period, along with six V. cholerae non-O1/non-O139 strains and two Aeromonas veronii biovar sobria strains showing an unusual characteristic of agglutination with O1 antiserum. Between that time and 2005, eight other O1 isolates were found. The virulence genes present in the V. cholerae differed among strains, with only three O1 strains harboring the ctxA gene. The O1 and some non-O1/non-O139 strains displayed identical patterns of amplification of the 16S-23S intergenic spacer region. RAPD of the 10 V. cholerae O1 strains, with the two primers used, revealed heterogeneity. The presence of V. cholerae carrying virulence genes in the aquatic basins examined confirms that they constitute a vibrio reservoir during a cholera inactive period, thus strengthening the argument for a continuous monitoring programme and preventative measures for cholera, mainly in the areas where the supply of drinking water is deficient.

  4. Molecular characterization of Aeromonas spp. and Vibrio cholerae O1 isolated during a diarrhea outbreak

    Directory of Open Access Journals (Sweden)

    Carina Lucena Mendes-Marques

    2012-12-01

    Full Text Available This work aimed to assess pathogenic potential and clonal relatedness of Aeromonas sp. and Vibrio cholerae isolates recovered during a diarrhea outbreak in Brazil. Clinical and environmental isolates were investigated for the presence of known pathogenic genes and clonal relatedness was assessed by intergenic spacer region (ISR 16S-23S amplification. Four Aeromonas genes (lip, exu, gcat, flaA/B were found at high overall frequency in both clinical and environmental isolates although the lip gene was specifically absent from selected species. A fifth gene, aerA, was rarely found in A. caviae, the most abundant species. The ISR profile revealed high heterogeneity among the Aeromonas isolates and no correlation with species identification. In contrast, in all the V. cholerae isolates the four genes investigated (ctxA, tcpA, zot and ace were amplified and revealed homogeneous ISR and RAPD profiles. Although Aeromonas isolates were the major enteric pathogen recovered, their ISR profiles are not compatible with a unique cause for the diarrhea events, while the clonal relationship clearly implicates V. cholerae in those cases from which it was isolated. These results reinforce the need for a better definition of the role of aeromonads in diarrhea and whether they benefit from co-infection with V. cholerae.

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

    Science.gov (United States)

    Mendes-Marques, Carina Lucena; Silveira Filho, Vladimir da Mota; da Costa, Ana Paula Rocha; Nunes, Mariana de Lira; da Silva Filho, Sandoval Vieira; Figueirôa, Ângela Cristina Torres de Araújo; Hofer, Ernesto; de Almeida, Alzira Maria Paiva; Leal, Nilma Cintra

    2013-01-01

    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. PMID:23533357

  6. Properties of an Arcanobacterium haemolyticum strain isolated from a donkey.

    Science.gov (United States)

    Sammra, Osama; Balbutskaya, Anna; Nagib, Samy; Alber, Jörg; Lämmler, Christoph; Abdulmawjood, Amir; Timke, Markus; Kostrzewa, Markus; Prenger-Berninghoff, Ellen

    2014-01-01

    The present study was designed to characterize phenotypically and genotypically an Arcanobacterium haemolyticum strain (A. haemolyticum P646) isolated from a purulent nasal discharge of a donkey. A. haemolyticum P646 showed, compared to sheep blood, an enhanced hemolytic reaction on rabbit blood agar, a synergistic CAMP-like reaction with Streptococcus agalactiae and Rhodococcus equi as indicator strains, a reverse CAMP reaction in the zone of Staphylococcus aureus beta-hemolysin and the typical biochemical properties of this species. The species identity could be confirmed by MALDI-TOF MS analysis, by sequencing the 16S rDNA and glyceraldehyde-3-phosphate dehydrogenase encoding gene gap and by amplification of A. haemolyticum specific parts of 16S-23S rDNA intergenic spacer region and 23S rDNA. A. haemolyticum P646 and the reference strain A. haemolyticum DSM 20595 were further characterized by amplification of the putative virulence genes encoding arcanolysin, phospholipase D, hemolysin A, CAMP factor family protein, a collagen binding protein and two neuraminidases which were present for A. haemolyticum DSM 20595. A. haemolyticum P646 showed a comparable gene spectrum but was negative for the genes encoding collagen binding protein and neuraminidase H. To our knowledge, the present study is the first phenotypic and genotypic characterization of an A. haemolyticum strain isolated from a donkey.

  7. PCR monitoring of Lactobacillus and Bifidobacterium dynamics in fermentations by piglet intestinal microbiota.

    Science.gov (United States)

    Moura, Patrícia; Simões, Fernanda; Gírio, Francisco; Loureiro-Dias, Maria C; Esteves, M Paula

    2007-04-01

    A new group-specific primer (Lact71R), targeting the 16S-23S rDNA intergenic spacer region of Lactobacillus, was tested in its specificity to amplify rDNA of lactobacilli from piglet intestinal origin by polymerase chain reaction (PCR). Lact71R and Lab0677F, a Lactobacillus group-specific primer targeting the 16S rDNA, generated a common amplicon by PCR with DNA from Lactobacillus and Pediococcus reference strains, but not from Weissella strains. Sequence analysis of clones obtained by PCR amplification with Lact71R and Lab0677F and total DNA isolated from the ileal, caecal and colonic contents of one piglet resulted in Lactobacillus and Lactobacillus-like sequences mainly retrieved from intestinal environments. The primer pair was further validated in a culture independent PCR-analysis to monitor broad fluctuations of lactobacilli populations in fructo-oligosaccharides (FOS) fermentations by piglet intestinal microbiota. Bifidobacterium genus-specific primers were also used for PCR titre determination throughout FOS fermentations, in parallel with lactate and short chain fatty acids (SCFA) quantification. Increases between PCR titres were correlated with lactate detection in early stages of fermentation. Based on the obtained results, a simple monitoring PCR approach is proposed, foreseeing its application to the study of the dynamics of specific bacterial populations in complex environments.

  8. 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.

  9. Development of a quantitative PCR assay for monitoring Streptococcus agalactiae colonization and tissue tropism in experimentally infected tilapia.

    Science.gov (United States)

    Su, Y-L; Feng, J; Li, Y-W; Bai, J-S; Li, A-X

    2016-02-01

    Streptococcus agalactiae has become one of the most important emerging pathogens in the aquaculture industry and has resulted in large economic losses for tilapia farms in China. In this study, three pairs of specific primers were designed and tested for their specificities and sensitivities in quantitative real-time polymerase chain reactions (qPCRs) after optimization of the annealing temperature. The primer pair IGS-s/IGS-a, which targets the 16S-23S rRNA intergenic spacer region, was finally chosen, having a detection limit of 8.6 copies of S. agalactiae DNA in a 20 μL reaction mixture. Bacterial tissue tropism was demonstrated by qPCR in Oreochromis niloticus 5 days post-injection with a virulent S. agalactiae strain. Bacterial loads were detected at the highest level in brain, followed by moderately high levels in kidney, heart, spleen, intestines, and eye. Significantly lower bacterial loads were observed in muscle, gill and liver. In addition, significantly lower bacterial loads were observed in the brain of convalescent O. niloticus 14 days post-injection with several different S. agalactiae strains. The qPCR for the detection of S. agalactiae developed in this study provides a quantitative tool for investigating bacterial tissue tropism in infected fish, as well as for monitoring bacterial colonization in convalescent fish.

  10. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds.

    Science.gov (United States)

    Alvarez-Martínez, Estela R; Valverde, Angel; Ramírez-Bahena, Martha Helena; García-Fraile, Paula; Tejedor, Carmen; Mateos, Pedro F; Santillana, Nery; Zúñiga, Doris; Peix, Alvaro; Velázquez, Encarna

    2009-08-01

    In this work, we analysed the core and symbiotic genes of rhizobial strains isolated from Vicia sativa in three soils from the Northwest of Spain, and compared them with other Vicia endosymbionts isolated in other geographical locations. The analysis of rrs, recA and atpD genes and 16S-23S rRNA intergenic spacer showed that the Spanish strains nodulating V. sativa are phylogenetically close to those isolated from V. sativa and V. faba in different European, American and Asian countries forming a group related to Rhizobium leguminosarum. The analysis of the nodC gene of strains nodulating V. sativa and V. faba in different continents showed they belong to a phylogenetically compact group indicating that these legumes are restrictive hosts. The results of the nodC gene analysis allow the delineation of the biovar viciae showing a common phylogenetic origin of V. sativa and V. faba endosymbionts in several continents. Since these two legume species are indigenous from Europe, our results suggest a world distribution of strains from R. leguminosarum together with the V. sativa and V. faba seeds and a close coevolution among chromosome, symbiotic genes and legume host in this Rhizobium-Vicia symbiosis.

  11. 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.

  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. 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.

  14. Detection of Campylobacter jejuni in rectal swab samples from Rousettus amplexicaudatus in the Philippines.

    Science.gov (United States)

    Hatta, Yuki; Omatsu, Tsutomu; Tsuchiaka, Shinobu; Katayama, Yukie; Taniguchi, Satoshi; Masangkay, Joseph S; Puentespina, Roberto; Eres, Eduardo; Cosico, Edison; Une, Yumi; Yoshikawa, Yasuhiro; Maeda, Ken; Kyuwa, Shigeru; Mizutani, Tetsuya

    2016-09-01

    Bats are the second diversity species of mammals and widely distributed in the world. They are thought to be reservoir and vectors of zoonotic pathogens. However, there is scarce report of the evidence of pathogenic bacteria kept in bats. The precise knowledge of the pathogenic bacteria in bat microbiota is important for zoonosis control. Thus, metagenomic analysis targeting the V3-V4 region of the 16S rRNA of the rectal microbiota in Rousettus amplexicaudatus was performed using high throughput sequencing. The results revealed that 103 genera of bacteria including Camplyobacter were detected. Campylobacter was second predominant genus, and Campylobacter coli and Campylobacter jejuni were identified in microbiome of R. amplexicaudatus. Campylobacteriosis is one of the serious bacterial diarrhea in human, and the most often implicated species as the causative agent of campylobacteriosis is C. jejuni. Therefore, we investigated the prevalence of C. jejuni in 91 wild bats with PCR. As a result of PCR assay targeted on 16S-23S intergenic spacer, partial genome of C. jejuni was detected only in five R. amplexicaudatus. This is the first report that C. jejuni was detected in bat rectal swab samples. C. jejuni is the most common cause of campylobacteriosis in humans, transmitted through water and contact with livestock animals. This result indicated that R. amplexicaudatus may be a carrier of C. jejuni.

  15. 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.

  16. 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.

  17. Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa.

    Science.gov (United States)

    Zhang, X X; Kosier, B; Priefer, U B

    2001-09-01

    A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv. viciae genotypes in the absence of its host plant.

  18. Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.

    Science.gov (United States)

    Ren, Da Wei; Chen, Wen Feng; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2011-03-01

    A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8  % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176(T) and R. galegae ATCC 43677(T), R. huautlense S02(T) and R. alkalisoli CCBAU 01393(T) were 22.6  %, 8.9  % and 15.9  %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176(T) (=HAMBI 3039(T)=LMG 25447(T)).

  19. Microcosm enrichment of biphenyl-degrading microbial communities from soils and sediments

    Energy Technology Data Exchange (ETDEWEB)

    Wagner-Doebler, I.; Bennasar, A.; Stroempl, C.; Bruemmer, I.; Eichner, C.; Grammel, I.; Moore, E.R.B. [GBF National Research Inst. for Biotechnology, Braunschweig (Germany). Dept. of Microbiology; Vancanneyt, M. [Univ. Gent, Ghent (Belgium). Lab. voor Microbiologie

    1998-08-01

    A microcosm enrichment approach was employed to isolate bacteria which are representative of long-term biphenyl-adapted microbial communities. Growth of microorganisms was stimulated by incubating soil and sediment samples from polluted and nonpolluted sites with biphenyl crystals. After 6 months, stable population densities between 8 {times} 10{sup 9} and 2 {times} 10{sup 11} CFU/ml were established in the microcosms, and a large percentage of the organisms were able to grow on biphenyl-containing minimal medium plates. A total of 177 biphenyl-degrading strains were subsequently isolated and characterized by their ability to grow on biphenyl in liquid culture and to accumulate a yellow meta cleavage product when they were sprayed with dihydroxy-biphenyl. Isolates were identified by using a polyphasic approach, including fatty acid methyl ester (FAME) analysis, 16S rRNA gene sequence comparison, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, and genomic fingerprinting based on sequence variability in the 16S-23S ribosomal DNA intergenic spacer region. In all of the microcosms, isolates identified as Rhodococcus opacus dominated the cultivable microbial community, comprising a cluster of 137 isolates with very similar FAME profiles (Euclidean distances, <10) and identical 16S rRNA gene sequences.

  20. Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains.

    Science.gov (United States)

    Kim, Hye-Sook; Ma, Bing; Perna, Nicole T; Charkowski, Amy O

    2009-07-01

    Pectobacterium species are enterobacterial plant-pathogenic bacteria that cause soft rot disease in diverse plant species. Previous epidemiological studies of Pectobacterium species have suffered from an inability to identify most isolates to the species or subspecies level. We used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis, to examine isolates from diseased stems and tubers and found that MLSA provided the most reliable classification of isolates. We found that strains belonging to at least two Pectobacterium clades were present in each field examined, although representatives of only three of five Pectobacterium clades were isolated. Hypersensitive response and DNA hybridization assays revealed that strains of both Pectobacterium carotovorum and Pectobacterium wasabiae lack a type III secretion system (T3SS). Two of the T3SS-deficient strains assayed lack genes adjacent to the T3SS gene cluster, suggesting that multiple deletions occurred in Pectobacterium strains in this locus, and all strains appear to have only six rRNA operons instead of the seven operons typically found in Pectobacterium strains. The virulence of most of the T3SS-deficient strains was similar to that of T3SS-encoding strains in stems and tubers.

  1. Phylogeny and Virulence of Naturally Occurring Type III Secretion System-Deficient Pectobacterium Strains▿

    Science.gov (United States)

    Kim, Hye-Sook; Ma, Bing; Perna, Nicole T.; Charkowski, Amy O.

    2009-01-01

    Pectobacterium species are enterobacterial plant-pathogenic bacteria that cause soft rot disease in diverse plant species. Previous epidemiological studies of Pectobacterium species have suffered from an inability to identify most isolates to the species or subspecies level. We used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis, to examine isolates from diseased stems and tubers and found that MLSA provided the most reliable classification of isolates. We found that strains belonging to at least two Pectobacterium clades were present in each field examined, although representatives of only three of five Pectobacterium clades were isolated. Hypersensitive response and DNA hybridization assays revealed that strains of both Pectobacterium carotovorum and Pectobacterium wasabiae lack a type III secretion system (T3SS). Two of the T3SS-deficient strains assayed lack genes adjacent to the T3SS gene cluster, suggesting that multiple deletions occurred in Pectobacterium strains in this locus, and all strains appear to have only six rRNA operons instead of the seven operons typically found in Pectobacterium strains. The virulence of most of the T3SS-deficient strains was similar to that of T3SS-encoding strains in stems and tubers. PMID:19411432

  2. Phylogenetic analysis of the pathogenic bacteria Spiroplasma penaei based on multilocus sequence analysis.

    Science.gov (United States)

    Heres, Allan; Lightner, Donald V

    2010-01-01

    A pathogenic Spiroplasma penaei strain was isolated from the hemolymph of moribund Pacific white shrimp, Penaeus vannamei. The shrimp sample originated from a shrimp farm near Cartagena, Colombia, that was suffering from high mortalities in ponds with very low salinity and high temperatures. This new emerging disease in a marine crustacean in the Americas is described as a systemic infection. The multilocus phylogenetic analysis suggests that S. penaei strain has a terrestrial origin. Evolutionary relationship trees, based on five partial DNA sequences of 16S rDNA, 23S rDNA, 5S rDNA, gyrB, rpoB genes and two complete DNA sequences of 16S-23S rDNA and 23S-5S rDNA intergenic spacer region, were reconstructed using the distance-based Neighboring-Joining (NJ) method with Kimura-2-parameter substitution model. The NJ trees based on all DNA sequences investigated in this study positioned S. penaei in the Citri-Poulsonii clade and corroborate the observations by other investigators using the 16S rDNA gene. Pairwise genetic distance calculation between sequences of spiroplasmas showed S. penaei to be closely related to Spiroplasma insolitum and distantly related to Spiroplasma sp. SHRIMP from China.

  3. Genetic diversity of indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two different host plants during soil restoration with alfalfa

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, X.X.; Kosier, B.; Priefer, U.B. [Rheinisch-Westfaelische TH Aachen, Aachen (Germany)

    2001-09-01

    A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv, viciae genotypes in the absence of its host plant.

  4. Detection of Bartonella henselae and Bartonella clarridgeiae DNA in hepatic specimens from two dogs with hepatic disease.

    Science.gov (United States)

    Gillespie, Tracey N; Washabau, Robert J; Goldschmidt, Michael H; Cullen, John M; Rogala, Allison R; Breitschwerdt, Edward B

    2003-01-01

    A 4-year-old Basset Hound and a 6-year-old Doberman Pinscher were referred for diagnostic evaluation following documentation of persistently increased hepatic enzyme activities and hepatic dysfunction. Histologic evaluation of hepatic biopsy specimens from the 2 dogs revealed granulomatous hepatitis in the Basset Hound and lymphocytic hepatitis with fibrosis and copper accumulation in the Doberman Pinscher. No etiologic agents were identified histologically. Bartonella henselae DNA was subsequently amplified from hepatic tissue from the Basset Hound and Bartonella clarridgeiae was amplified from hepatic tissue from the Doberman Pinscher. Amplification was performed with a polymerase chain reaction assay incorporating primers that target a portion of the 16S-23S rRNA intergenic spacer region. Both dogs were treated with azithromycin, in combination with a variety of other medications and herbal treatments, and improved clinically. Identification of Bartonella DNA in these dogs indicates the need for future prospective studies to determine the clinical relevance of Bartonella spp infection in dogs with hepatic disease.

  5. Prevalence of Bartonella species infections in cats in Southern Germany.

    Science.gov (United States)

    Bergmann, M; Englert, T; Stuetzer, B; Hawley, J R; Lappin, M R; Hartmann, K

    2017-04-01

    Bartonella species are zoonotic pathogens, and infections in cats are common. However, prevalence in cats in Southern Germany is still unknown. Therefore, prevalence of Bartonella species DNA in blood of 479 Southern German cats was determined using a previously published conventional PCR targeting a fragment of the 16S-23S rRNA intergenic spacer region. Associations between Bartonella bacteraemia, housing conditions, feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) status, including progressive, regressive and abortive FeLV infection, were evaluated using Fisher's exact test. Prevalence of Bartonella species bacteraemia was 2.5 per cent (12/479; CI 0.01-0.04 per cent). Bartonella henselae DNA was amplified in 11 of the 12 cats. One cat was positive for Bartonella clarridgeiae DNA. Of the infected cats, 2/12 cats were ill; 6/12 cats had thrombocytopenia. There was a significantly higher risk of Bartonella species infection in young and shelter cats, but not in FIV-infected or FeLV-infected cats. Prevalence of Bartonella species bacteraemia is low in Southern German cats, but there is still a risk of zoonotic transmission associated with ownership of young cats. Most of the infected cats did not show clinical signs. Thrombocytopenia was common in Bartonella species-infected cats and further studies are required to define its clinical relevance. British Veterinary Association.

  6. Aliterella atlantica gen. nov., sp. nov., and Aliterella antarctica sp. nov., novel members of coccoid Cyanobacteria.

    Science.gov (United States)

    Rigonato, Janaina; Gama, Watson Arantes; Alvarenga, Danillo Oliveira; Branco, Luis Henrique Zanini; Brandini, Frederico Pereira; Genuário, Diego Bonaldo; Fiore, Marli Fatima

    2016-09-01

    Two Cyanobacteria isolated from South Atlantic Ocean continental shelf deep water and from a marine green algae inhabiting the Admiralty Bay, King George Island, Antarctica were investigated based on morphological and ultrastructural traits, phylogeny of 16S rRNA gene sequences, secondary structure of the 16S-23S internal transcribed spacer regions and phylogenomic analyses. The majority of these evaluations demonstrated that both strains differ from the genera of cyanobacteria with validly published names and, therefore, supported the description of the novel genus as Aliterella gen. nov. The identity and phylogeny of 16S rRNA gene sequences, together with the secondary structure of D1D1' and BoxB intergenic regions, further supported the two strains representing distinct species: Aliterella atlantica gen. nov., sp. nov. (type SP469036, strain CENA595T) and Aliterella antarctica sp. nov. (type SP469035, strain CENA408T). The phylogenomic analysis of A. atlantica sp. nov. CENA595T, based on 21 protein sequences, revealed that this genus belongs to the cyanobacterial order Chroococcidiopsidales. The isolation and cultivation of two geographically distant unicellular members of a novel cyanobacterial genus and the sequenced genome of the type strain bring new insights into the current classification of the coccoid group, and into the reconstruction of their evolutionary history.

  7. 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.

  8. 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.

  9. [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.

  10. Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must.

    Science.gov (United States)

    Mañes-Lázaro, Rosario; Ferrer, Sergi; Rodas, Ana María; Urdiain, Mercedes; Pardo, Isabel

    2008-12-01

    A Lactobacillus strain, designated 203(T), previously isolated from Bobal grape must was characterized phylogenetically, genotypically and phenotypically in order to establish whether it represents a novel species. On the basis of the 16S rRNA gene sequence, strain 203(T) was shown to belong to the genus Lactobacillus, falling within the Lactobacillus alimentarius-Lactobacillus farciminis group and being closely related to the type strains of L. alimentarius, Lactobacillus kimchii and Lactobacillus paralimentarius. DNA-DNA hybridization results confirmed the separate status of strain 203(T) at the species level. To establish the similarities and differences between 203(T) and the three aforementioned closest species, the following methods were used: amplified rDNA restriction analysis, analysis of the 16S-23S rDNA intergenic spacer region, random amplification of polymorphic DNA (RAPD) profiling, ribotyping, carbohydrate fermentation and physiological tests. Strain 203(T) could be differentiated genetically using RAPD analysis and ribotyping. Phenotypically, it can be distinguished from its closest relatives by its ability to grow at pH 3.3, by gas production from gluconate and by certain carbohydrate fermentations. On the basis of these data, strain 203(T) represents a novel species of the genus Lactobacillus, for which the name Lactobacillus bobalius sp. nov. is proposed. The type strain is 203(T) (=CECT 7310(T) =DSM 19674(T)).

  11. 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.

  12. Shape memory alloy smart knee spacer to enhance knee functionality: model design and finite element analysis.

    Science.gov (United States)

    Gautam, Arvind; Rani, A Bhargavi; Callejas, Miguel A; Acharyya, Swati Ghosh; Acharyya, Amit; Biswas, Dwaipayan; Bhandari, Vasundhra; Sharma, Paresh; Naik, Ganesh R; Gautam, Arvind; Rani, A Bhargavi; Callejas, Miguel A; Acharyya, Swati Ghosh; Acharyya, Amit; Biswas, Dwaipayan; Bhandari, Vasundhra; Sharma, Paresh; Naik, Ganesh R; Acharyya, Swati Ghosh; Sharma, Paresh; Bhandari, Vasundhra; Rani, A Bhargavi; Gautam, Arvind; Biswas, Dwaipayan; Callejas, Miguel A; Acharyya, Amit

    2016-08-01

    In this paper we introduce Shape Memory Alloy (SMA) for designing the tibial part of Total Knee Arthroplasty (TKA) by exploiting the shape-memory and pseudo-elasticity property of the SMA (e.g. NiTi). This would eliminate the drawbacks of the state-of-the art PMMA based knee-spacer including fracture, sustainability, dislocation, tilting, translation and subluxation for tackling the Osteoarthritis especially for the aged people of 45-plus or the athletes. In this paper a Computer Aided Design (CAD) model using SolidWorks for the knee-spacer is presented based on the proposed SMA adopting the state-of-the art industry-standard geometry that is used in the PMMA based spacer design. Subsequently Ansys based Finite Element Analysis is carried out to measure and compare the performance between the proposed SMA based model with the state-of-the art PMMA ones. 81% more bending is noticed in the PMMA based spacer compared to the proposed SMA that would eventually cause fracture and tilting or translation of spacer. Permanent shape deformation of approximately 58.75% in PMMA based spacer is observed compared to recoverable 11% deformation in SMA when same load is applied on both separately.

  13. Dual detection of Legionella pneumophila and Legionella species by real-time PCR targeting the 23S-5S rRNA gene spacer region.

    Science.gov (United States)

    Yang, G; Benson, R; Pelish, T; Brown, E; Winchell, J M; Fields, B

    2010-03-01

    Although the majority of cases of Legionnaires' disease (LD) are caused by Legionella pneumophila, an increasing number of other Legionella species have been reported to cause human disease. There are no clinical presentations unique to LD and hence accurate laboratory tests are required for early diagnosis. Therefore, we designed a real-time PCR assay that targets the 23S-5S rRNA intergenic spacer region (23S-5S PCR) and allows for detection of all Legionella species and discrimination of L. pneumophila from other Legionella species. In total, 271 isolates representing 50 Legionella species were tested and the assay was validated using 39 culture-positive and 110 culture-negative patient specimens collected between 1989 and 2006. PCR-positive results were obtained with all 39 culture-positive samples (100% sensitivity). Specimens that tested positive according to 23S-5S PCR, but were culture-negative, were further analysed by DNA sequencing of the amplicon or the macrophage infectivity potentiator (mip) gene. In addition to L. pneumophila, Legionella longbeachae, Legionella cincinnatiensis and Legionella micdadei were identified in the specimens. The assay showed a 7-log dynamic range displaying a sensitivity of 7.5 CFU/mL or three genome equivalents per reaction. Sixty-one specimens containing viruses or bacteria other than Legionellae were negative according to 23S-5S PCR, demonstrating its specificity. Use of this assay should contribute to the earlier detection of respiratory disease caused by Legionella species, as well as to increased rates of detection.

  14. 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.

  15. 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

  16. Predicting the impact of feed spacer modification on biofouling by hydraulic characterization and biofouling studies in membrane fouling simulators

    KAUST Repository

    Siddiqui, A.

    2016-12-22

    Feed spacers are an essential part of spiral-wound reverse osmosis (RO) and nanofiltration (NF) membrane modules. Geometric modification of feed spacers is a potential option to reduce the impact of biofouling on the performance of membrane systems. The objective of this study was to evaluate the biofouling potential of two commercially available reference feed spacers and four modified feed spacers. The spacers were compared on hydraulic characterization and in biofouling studies with membrane fouling simulators (MFSs). The virgin feed spacer was characterized hydraulically by their resistance, measured in terms of feed channel pressure drop, performed by operating MFSs at varying feed water flow rates. Short-term (9 days) biofouling studies were carried out with nutrient dosage to the MFS feed water to accelerate the biofouling rate. Long-term (96 days) biofouling studies were done without nutrient dosage to the MFS feed water. Feed channel pressure drop was monitored and accumulation of active biomass was quantified by adenosine tri phosphate (ATP) determination. The six feed spacers were ranked on pressure drop (hydraulic characterization) and on biofouling impact (biofouling studies). Significantly different trends in hydraulic resistance and biofouling impact for the six feed spacers were observed. The same ranking for biofouling impact on the feed spacers was found for the (i) short-term biofouling study with nutrient dosage and the (ii) long-term biofouling study without nutrient dosage. The ranking for hydraulic resistance for six virgin feed spacers differed significantly from the ranking of the biofouling impact, indicating that hydraulic resistance of clean feed spacers does not predict the hydraulic resistance of biofouled feed spacers. Better geometric design of feed spacers can be a suitable approach to minimize impact of biofouling in spiral wound membrane systems.

  17. [Our experiences with anterior cervical cages and spacer].

    Science.gov (United States)

    Szabó, József; Lapis, István; Marik, László; Kondacs, András; Rusznyák, Csaba

    2007-11-30

    Between 2001 and 2005 86 patients were treated for cervical disc herniations and spondylosis at our department. Stabilization was performed with different cervical cages or spacer after discectomy and decompression. The aim of the study was to examine the changes of the patients' pain, quality of life and work ability, fusion rate, the intervertebral disc height, changes of under and upper segments and finally curvature of cervical spine. Patients were followed by the authors, clinical examination, lateral and antero-posterior radiographic examinations were performed. They were asked to fill in a questionnaire, concerning their pre- and postoperative pain, quality of life and work ability. The patients' pain was graded using a 10-point analog scale (VAS) and with a simplified, McGill-Melzak analog scale. The quality of life was measured with a 10-graduated analog scale as well. More than 77% of our patients appeared at follow up examination. The fusion rate was 89.3%, operated spaces were held in 61%. In the upper segment of operated space 7%, and in the under-segment 14% were found increasingly degenerated. The curvature of cervical spine of the patients' were 64.51% lordotic, 27.42% straight and 8.07% kyphotic. On average the patients' pain changed on VAS from 8.179 to 5.015; on McGill-Melzak scale from 3.89 to 2.80; quality of life changed from 8.045 to 5.463. By the advantage of using cages, the operative approach has become smaller than before, consequently the operative pain has become less too. In addition operation time and hospital stay were significantly shorter (p work and 5 patients do easier work. The majority of our patients were disabled before the operation, but from that time many of them became disabled, in some cases the grade of disability increased. There can be some reasons for it: the majority of the patients have other diseases for example: lumbar spondylosis and disc herniation, hypertension, diabetes, asthma and depression. There is just a

  18. A functional analysis of the spacer of V(DJ recombination signal sequences.

    Directory of Open Access Journals (Sweden)

    Alfred Ian Lee

    2003-10-01

    Full Text Available During lymphocyte development, V(DJ recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS, which serves as the binding site for the recombination machinery. The murine Jbeta2.6 gene segment is a recombinationally inactive pseudogene, but examination of its RSS reveals no obvious reason for its failure to recombine. Mutagenesis of the Jbeta2.6 RSS demonstrates that the sequences of the heptamer, nonamer, and spacer are all important. Strikingly, changes solely in the spacer sequence can result in dramatic differences in the level of recombination. The subsequent analysis of a library of more than 4,000 spacer variants revealed that spacer residues of particular functional importance are correlated with their degree of conservation. Biochemical assays indicate distinct cooperation between the spacer and heptamer/nonamer along each step of the reaction pathway. The results suggest that the spacer serves not only to ensure the appropriate distance between the heptamer and nonamer but also regulates RSS activity by providing additional RAG:RSS interaction surfaces. We conclude that while RSSs are defined by a "digital" requirement for absolutely conserved nucleotides, the quality of RSS function is determined in an "analog" manner by numerous complex interactions between the RAG proteins and the less-well conserved nucleotides in the heptamer, the nonamer, and, importantly, the spacer. Those modulatory effects are accurately predicted by a new computational algorithm for "RSS information content." The interplay between such binary and multiplicative modes of interactions provides a general model for analyzing protein-DNA interactions in various biological systems.

  19. Knitting Technologies And Tensile Properties Of A Novel Curved Flat-Knitted Three-Dimensional Spacer Fabrics

    Directory of Open Access Journals (Sweden)

    Li Xiaoying

    2015-09-01

    Full Text Available This paper introduces a knitting technique for making innovative curved three-dimensional (3D spacer fabrics by the computer flat-knitting machine. During manufacturing, a number of reinforcement yarns made of aramid fibres are inserted into 3D spacer fabrics along the weft direction to enhance the fabric tensile properties. Curved, flat-knitted 3D spacer fabrics with different angles (in the warp direction were also developed. Tensile tests were carried out in the weft and warp directions for the two spacer fabrics (with and without reinforcement yarns, and their stress–strain curves were compared. The results showed that the reinforcement yarns can reduce the fabric deformation and improve tensile stress and dimensional stability of 3D spacer fabrics. This research can help the further study of 3D spacer fabric when applied to composites.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

    2014-01-01

    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. PMID:24920831

  10. Towards a rational spacer design for bivalent inhibition of estrogen receptor

    Science.gov (United States)

    Bujotzek, Alexander; Shan, Min; Haag, Rainer; Weber, Marcus

    2011-03-01

    Estrogen receptors are known drug targets that have been linked to several kinds of cancer. The structure of the estrogen receptor ligand binding domain is available and reveals a homodimeric layout. In order to improve the binding affinity of known estrogen receptor inhibitors, bivalent compounds have been developed that consist of two individual ligands linked by flexible tethers serving as spacers. So far, binding affinities of the bivalent compounds do not surpass their monovalent counterparts. In this article, we focus our attention on the molecular spacers that are used to connect the individual ligands to form bivalent compounds, and describe their thermodynamic contribution during the ligand binding process. We use computational methods to predict structural and entropic parameters of different spacer structures. We find that flexible spacers introduce a number of effects that may interfere with ligand binding and possibly can be connected to the low binding affinities that have been reported in binding assays. Based on these findings, we try to provide guidelines for the design of novel molecular spacers.

  11. 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

  12. 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.

  13. Stable inverted small molecular organic solar cells using a p-doped optical spacer.

    Science.gov (United States)

    Lee, Sang-Hoon; Seo, Ji-Won; Lee, Jung-Yong

    2015-01-07

    We report inverted small molecular organic solar cells using a doped window layer as an optical spacer. The optical spacer was used to shift the optical field distribution inside the active layers, generating more charge carriers from sunlight. In this report, N,N,N',N'-tetrakis(4-methoxyphenyl)-benzidine (MeO-TPD) was doped with 2,2-(perfluoronaphthalene-2,6-diylidene)dimalononitrile (F6-TCNNQ), a p-type dopant material. P-doped MeO-TPD was adopted as an optical spacer because it has a large energy band gap, and its conductivity can be increased by several orders of magnitude through a doping process. As a result, a power conversion efficiency of 4.15% was achieved with the doped window layer of optimized thickness. Lastly, we present significantly improved stability of the inverted devices with the MeO-TPD layer.

  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. Binding of Streptavidin to Surface-attached Biotin with Different Spacer Thicknesses

    Institute of Scientific and Technical Information of China (English)

    LI Yifei; ZHANG Haining

    2015-01-01

    The specific binding of receptor to ligand covalently attached to surface with different surface densities was studied using streptavidin-biotin model pair. Biotinylated substrates with different spacer thicknesses as formed through a simple reaction between amine immobilized surfaces and N-hydroxysucciimide groups at the end of biotin modiifed PEG in anhydrous organic solutions (“grafting to”technique). The amount of the speciifcally adsorbed protein was measured as a function of spacer thickness between hard surface and biotin moieties. It has been shown that the amount of specifically adsorbed streptavidin decreases with the increase spacer thickness and the protein adsorbs onto the functionalized surfaces in a single molecular manner. It provides an interesting model system for studying single molecular interactions.

  16. 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

    2015-01-01

    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

  17. The Xis2d protein of CTnDOT binds to the intergenic region between the mob and tra operons.

    Science.gov (United States)

    Hopp, Crystal M; Gardner, Jeffrey F; Salyers, Abigail A

    2015-09-01

    CTnDOT is a 65kbp integrative and conjugative element (ICE) that carries genes encoding both tetracycline and erythromycin resistances. The excision operon of this element encodes Xis2c, Xis2d, and Exc proteins involved in the excision of CTnDOT from host chromosomes. These proteins are also required in the complex transcriptional regulation of the divergently transcribed transfer (tra) and mobilization (mob) operons of CTnDOT. Transcription of the tra operon is positively regulated by Xis2c and Xis2d, whereas, transcription of the mob operon is positively regulated by Xis2d and Exc. Xis2d is the only protein that is involved in the excision reaction, as well as the transcriptional regulation of both the mob and tra operons. This paper helps establish how Xis2d binds the DNA in the mob and tra region. Unlike other excisionase proteins, Xis2d binds a region of dyad symmetry. The binding site is located in the intergenic region between the mob and tra promoters, and once bound Xis2d induces a bend in the DNA. Xis2d binding to this region could be the preliminary step for the activation of both operons. Then the other proteins, like Exc, can interact with Xis2d and form higher order complexes. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression.

    Science.gov (United States)

    Ehrlich, Kenneth C; Paterson, Heather L; Lacey, Michelle; Ehrlich, Melanie

    2016-12-01

    Tissue-specific enhancers are critical for gene regulation. In this study, we help elucidate the contribution of muscle-associated differential DNA methylation to the enhancer activity of highly muscle-specific genes. By bioinformatic analysis of 44 muscle-associated genes, we show that preferential gene expression in skeletal muscle (SkM) correlates with SkM-specific intragenic and intergenic enhancer chromatin and overlapping foci of DNA hypomethylation. Some genes, e.g., CASQ1 and FBXO32, displayed broad regions of both SkM- and heart-specific enhancer chromatin but exhibited focal SkM-specific DNA hypomethylation. Half of the genes had SkM-specific super-enhancers. In contrast to simple enhancer/gene-expression correlations, a super-enhancer was associated with the myogenic MYOD1 gene in both SkM and myoblasts even though SkM has < 1 percent as much MYOD1 expression. Local chromatin differences in this super-enhancer probably contribute to the SkM/myoblast differential expression. Transfection assays confirmed the tissue-specificity of the 0.3-kb core enhancer within MYOD1's super-enhancer and demonstrated its repression by methylation of its three CG dinucleotides. Our study suggests that DNA hypomethylation increases enhancer tissue-specificity and that SkM super-enhancers sometimes are poised for physiologically important, rapid up-regulation.

  19. 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.

  20. A New Intergenic α-Globin Deletion (α-αΔ125) Found in a Kabyle Population.

    Science.gov (United States)

    Singh, Amrathlal Rabbind; Lacan, Philippe; Cadet, Estelle; Bignet, Patricia; Dumesnil, Cécile; Vannier, Jean-Pierre; Joly, Philippe; Rochette, Jacques

    2016-01-01

    We have identified a deletion of 125 bp (α-α(Δ125)) (NG_000006.1: g.37040_37164del) in the α-globin gene cluster in a Kabyle population. A combination of singlex and multiplex polymerase chain reaction (PCR)-based assays have been used to identify the molecular defect. Sequencing of the abnormal PCR amplification product revealed a novel α1-globin promoter deletion. The endpoints of the deletion were characterized by sequencing the deletion junctions of the mutated allele. The observed deletion was located 378 bp upstream of the α1-globin gene transcription initiation site and leaves the α2 gene intact. In some patients, the α-α(Δ125) deletion was shown to segregate with Hb S (HBB: c.20A>T) and/or Hb C (HBB: c.19G>A) or a β-thalassemic allele. The α-α(Δ125) deletion has no discernible effect on red cell indices when inherited with no other abnormal globin genes. The family study demonstrated that the deletion is heritable. This is the only example of an intergenic α2-α1 non coding DNA deletion, leaving the α2-globin gene and the α1 coding part intact.

  1. 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.

  2. 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').

  3. Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation.

    Science.gov (United States)

    Finger, S Alison; Velapatiño, Billie; Kosek, Margaret; Santivañez, Livia; Dailidiene, Daiva; Quino, Willi; Balqui, Jacqueline; Herrera, Phabiola; Berg, Douglas E; Gilman, Robert H

    2006-07-01

    We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation.

  4. 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.

  5. An attenuated Machupo virus with a disrupted L-segment intergenic region protects guinea pigs against lethal Guanarito virus infection.

    Science.gov (United States)

    Golden, Joseph W; Beitzel, Brett; Ladner, Jason T; Mucker, Eric M; Kwilas, Steven A; Palacios, Gustavo; Hooper, Jay W

    2017-07-05

    Machupo virus (MACV) is a New World (NW) arenavirus and causative agent of Bolivian hemorrhagic fever (HF). Here, we identified a variant of MACV strain Carvallo termed Car(91) that was attenuated in guinea pigs. Infection of guinea pigs with an earlier passage of Carvallo, termed Car(68), resulted in a lethal disease with a 63% mortality rate. Sequencing analysis revealed that compared to Car(68), Car(91) had a 35 nucleotide (nt) deletion and a point mutation within the L-segment intergenic region (IGR), and three silent changes in the polymerase gene that did not impact amino acid coding. No changes were found on the S-segment. Because it was apathogenic, we determined if Car(91) could protect guinea pigs against Guanarito virus (GTOV), a distantly related NW arenavirus. While naïve animals succumbed to GTOV infection, 88% of the Car(91)-exposed guinea pigs were protected. These findings indicate that attenuated MACV vaccines can provide heterologous protection against NW arenaviruses. The disruption in the L-segment IGR, including a single point mutant and 35 nt partial deletion, were the only major variance detected between virulent and avirulent isolates, implicating its role in attenuation. Overall, our data support the development of live-attenuated arenaviruses as broadly protective pan-arenavirus vaccines.

  6. Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig.

    Science.gov (United States)

    Zou, Cheng; Li, Jingxuan; Luo, Wenzhe; Li, Long; Hu, An; Fu, Yuhua; Hou, Ye; Li, Changchun

    2017-08-18

    Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes. Gene ontology and pathway analyses indicated that many potential target genes (PTGs) of lincRNAs were involved in skeletal-muscle-related processes, such as muscle contraction and muscle system process. Combined our previous studies, we found a potential regulatory mechanism in which the promoter methylation of lincRNAs can negatively regulate lincRNA expression and then positively regulate PTG expression, which can finally result in abnormal phenotypes of cloned piglets through a certain unknown pathway. This work detailed a number of lincRNAs and their target genes involved in skeletal muscle growth and development and can facilitate future studies on their roles in skeletal muscle growth and development.

  7. 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.

  8. 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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. The Effect of Various Fabric Parameters on the Sound Absorption Properties of Circular Knitted Spacer Fabrics

    Directory of Open Access Journals (Sweden)

    Arzu Marmaralı

    2014-07-01

    Full Text Available Spacer fabrics which can be produced through weaving or nonwoven technique beside warp knitting and weft knitting processes, can be used for functional applications such as automotive textiles, medical textiles, geotextiles, sportswear, protective textiles and composites due to the possibility of using a variety of different materials, flexible product range and the three dimensional construction. Additionally they can also be used for sound absorption applications with different pore geometry. In this study, the effect of fabric parameters like material type, fabric thickness and surface structures on the sound absorption properties of circular knitted spacer fabrics was investigated and aimed to determine the optimum fabric parameters for better sound absorption.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia.

    Science.gov (United States)

    Almamun, Md; Kholod, Olha; Stuckel, Alexei J; Levinson, Benjamin T; Johnson, Nathan T; Arthur, Gerald L; Davis, J Wade; Taylor, Kristen H

    2017-01-17

    A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.

  17. 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

  18. 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

    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...

  19. Acetabular spacers in 2-stage hip revision: is it worth it? A single-centre retrospective study.

    Science.gov (United States)

    Burastero, Giorgio; Basso, Marco; Carrega, Giuliana; Cavagnaro, Luca; Chiarlone, Francesco; Salomone, Carlo; Papa, Gabriele; Felli, Lamberto

    2017-03-31

    The aim of this work is to evaluate an acetabular antibiotic loaded bone cement spacer in 2-stage revision surgery as a potential approach able to reduce complications during the inter-stage period (i.e. dislocation, acetabular wear), as well as simplify 2-stage hip revision surgery and improve hip biomechanics. We performed a retrospective comparative study and evaluated clinical, radiological and surgical data of 71 patients affected by periprosthetic hip infection who were treated with 2-stage exchange. 31 patients were treated using an acetabular spacer in addition to the femoral (group A) while 40 underwent a standard revision surgery (femoral spacer only, group B). Mean time of surgery for the first stage was 148 ± 59 minutes and 142 ± 45 minutes for group A and B respectively; we noted a statistically significant reduction (26 min, p = 0.015) in the same parameter for the second stage (83 ± 35 minutes for group A and 109 ± 36 minutes for group B). We observed the following interstage complications: 5 femoral spacer dislocations (1 for group A and 4 for group B); 1 spacer fracture (group B), 1 spacer fracture (group A), 2 periprosthetic fractures (group B) and 2 patients with acetabular spacer instability (group B). Additionally, we observed a significant improvement in leg length restoration for group A (p = 0.03). Our data show that the acetabular spacer technique is able to reduce the interstage complication rate and allow improved hip biomechanics restoration.

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

    NARCIS (Netherlands)

    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.

  1. 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,...

  2. A Study of Neutronics Effects of the Spacer Grids in a Typical PWR via Monte Carlo Calculation

    Directory of Open Access Journals (Sweden)

    Xuan Bach Tran

    2016-02-01

    Full Text Available Spacer grids play an important role in maintaining the proper form of the fuel assembly structure and ensuring the safety of reactor core design. This study applies the Monte Carlo method to the analysis of the neutronics effects of spacer grids in a typical pressurized water reactor (PWR. The core problem used to analyze the neutronics effects of spacer grids is a modified version of Korea Advanced Institute of Science and Technology benchmark problem 1B, based on an Advanced Power Reactor 1400 (APR1400 core model. The spacer grids are modeled and added to this test problem in various ways. Then, by running MCNP5 for all cases of spacer grid modeling, some important numerical results, such as the effective multiplication factor, the spatial distributions of neutron flux, and its energy spectrum are obtained. The numerical results of each case of spacer grid modeling are analyzed and compared to assess which type has more advantages in accuracy of numerical results and effectiveness in terms of geometry building. The conclusion is that the most realistic modeling for Monte Carlo calculation is the “volume-preserving” streamlined heterogeneous spacer grids, but the “banded” dissolution spacer grids modeling is a more practical yet accurate model for routine (deterministic analysis.

  3. Recovery of knee mobility after a static or mobile spacer in total knee infection

    NARCIS (Netherlands)

    Brunnekreef, J.J.; Hannink, G.; Mde, W. Malefijt

    2013-01-01

    The purpose of the study was to compare the recovery of knee mobility after two-stage revision of an infected total knee arthroplasty using a static or mobile spacer. At 12 months follow-up, none of the patients had a recurrent infection of their new prosthesis. Knee flexion was lower in the static

  4. Treatment of an old infection in a total hip replacement with an interim spacer prosthesis.

    Science.gov (United States)

    Zilkens, K W; Casser, H R; Ohnsorge, J

    1990-01-01

    When treating a septic hip-joint prosthesis with bone loss of the proximal femur secondary to osteomyelitis, we implanted a specially designed prosthesis to act as a local antibiotic and spacer between the acetabulum and femur until the infection abated. Arthroplasty could then be carried out with no trouble and there was no recurrence of infection.

  5. 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.

  6. Mechanical Properties Of 3D-Structure Composites Based On Warp-Knitted Spacer Fabrics

    Directory of Open Access Journals (Sweden)

    Chen Si

    2015-06-01

    Full Text Available In this paper, the mechanical properties (compression and impact behaviours of three-dimension structure (3D-structure composites based on warp-knitted spacer fabrics have been thoroughly investigated. In order to discuss the effect of fabric structural parameters on the mechanical performance of composites, six different types of warp-knitted spacer fabrics having different structural parameters (such as outer layer structure, diameter of spacer yarn, spacer yarn inclination angle and thickness were involved for comparison study. The 3D-structure composites were fabricated based on a flexible polyurethane foam. The produced composites were characterised for compression and impact properties. The findings obtained indicate that the fabric structural parameters have strong influence on the compression and impact responses of 3D-structure composites. Additionally, the impact test carried out on the 3D-structure composites shows that the impact loads do not affect the integrity of composite structure. All the results reveal that the product exhibits promising mechanical performance and its service life can be sustained.

  7. 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

  8. Electrochemical behavior and dioxygen reactivity of tripodal dinuclear copper complexes linked by unsaturated rigid spacers.

    Science.gov (United States)

    Gomila, Antoine; Le Poul, Nicolas; Kerbaol, Jean-Michel; Cosquer, Nathalie; Triki, Smaïl; Douziech, Bénédicte; Conan, Françoise; Le Mest, Yves

    2013-02-14

    New dinucleating ligands based on two tripodal tris(2-pyridylmethyl)amine (TMPA) units linked by a series of delocalized π-electrons spacers have been synthesized. Their di-Cu(II) complexes have been prepared and structurally characterized. As compared to the corresponding monotopic complexes, these dinuclear Cu(II) complexes reveal spectroscopic and voltammetric features ascribable to weakly perturbed electronic interactions. In the case of the anthracenyl spacer, observation both in the solid and in solution suggests that the existence of intramolecular π-π stacking interactions influences the geometry of the complex and hence its electronic properties. The bis-Cu(I) complexes were prepared electrochemically. In the specific case of the complex bearing a mono-alkyne spacer, addition of dioxygen in acetonitrile leads to the slow formation of a trans-μ-1,2 peroxo Cu(2) complex which shows good stability at 268 K (t(1/2) = 240 s). Analysis of the kinetics of the peroxo formation by UV-vis spectroscopy suggests that the increased activation barrier for intramolecular binding of dioxygen is due to the rigidity of the spacer.

  9. Usefulness of a radiolucent spacer in radiation therapy for cancer of the tongue

    Energy Technology Data Exchange (ETDEWEB)

    Yokoi, Motoo (Nagoya City Univ. (Japan). Hospital); Ito, Yoshiyuki; Fuwa, Nobukazu; Kato, Eriko; Murao, Takayuki; Morita, Kozo

    1993-05-01

    For the purpose of preventing osteonecrosis following interstitial irradiation for tongue cancer, a Radiolucent Spacer was prepared with the intention of reducing bone dose by keeping the mandible at a distance from the source. Because of its radiolucency, the Spacer made of silicone enables to perform X-P while inserted, and more exact dose calculation. For 6 cases in which 8 mm-spacer was used, dose reduction rate for surface of lower gingiva corresponded to 42.3%, average of tumor dose for TDF. For 51 cases in which the observation of course was practicable for 2 years--9 years and 4 months, averaging 5 years and 7 months, the incidence of osteonecrosis was 0%, and therefore, Spacer of not less than 8 mm-thickness is thought useful as prosthesis. Extraction of the tooth was done at the start of irradiation, but the healing course was always favorable. The most aseptic possible alveolectomy and complete closure of the wound are necessary for tooth extraction. (author).

  10. Development of Finite Element Model for the Static Buckling Behavior of the Spacer Grid

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Young Ik; Park, Nam Gyu; Kim, Kyoung Ju; Suh, Jung Min [Kepco Nuclear Fuel, Daejeon (Korea, Republic of)

    2013-10-15

    In this study, finite element model was proposed to evaluate the buckling characteristics and structural behavior of partial spacer grids. A two-dimensional model was developed to simplify a real spacer gird model and save analysis time. And it was validated for comparison with experimental tests. A non-linear analysis method was introduced to perform realistic simulation. Later, the buckling analysis of the full size grid will be performed based on the analysis results of partial spacer grids. A study was conducted to develop the simplified model of a spacer grid and provide a prediction of buckling behavior. The FE analysis results are quite similar to the experimental tests. · The deformed geometry of FE model after compression is consistent and very similar to that of real situation, and the non-linear analysis method used in this model can simulate buckling and post-buckling behavior well. · The buckling strength obtained by FEM shows a very good agreement with the physical tests.

  11. 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

  12. Effect of spacer dielectric engineering on Asymmetric Source Underlapped Double Gate MOSFET using Gate Stack

    Science.gov (United States)

    Chattopadhyay, Ankush; Dasgupta, Arpan; Das, Rahul; Kundu, Atanu; Sarkar, Chandan K.

    2017-01-01

    In this paper, the use of high-k spacers in a source underlapped nMOSFET is explored. The effects have been reported by varying the dielectric constant of the spacer from 3.9 to 22.5 and the study includes a comparison of analog parameters such as transconductance, transconductance generation factor, intrinsic gain, and RF parameters such as parasitic capacitances, resistances, and cut-off frequency. The RF parameters are calculated using the Non-Quasi Static (NQS) Approach which is required for sub 20 nm technology node. The device with high-k spacers features an improvement of 33% in DIBL, significantly increases the on current and reducing the off current by 60%. However, there is a slight compromise in the RF performance of the device, owing to an increase in intrinsic capacitance by about 0.35 fF. The Voltage Transfer Characteristics (VTC) and AC gain analysis of the circuit is also done in this paper. The circuit performance using single stage amplifier with the proposed device as the driver MOS has been analysed. High-k spacers also account for 19% improvement in small signal gain when used in a single stage amplifier circuit.

  13. 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.

  14. A New Pyrene-Spacer-Maleimide Dyad for Sensing Molecules with One or Two Thiol Groups

    Institute of Scientific and Technical Information of China (English)

    WANG,Zhuo; ZHANG,De-Qing; ZHU,Dao-Ben

    2006-01-01

    A new pyrene-spacer-maleimide dyad 1 was used to selectively detect cysteine in the presence of other amino acids, and sequentially react with dithiols to generate the molecule with two pyrene units showing typical excimer fluorescence. Accordingly, dyad 1 was able to differentiate molecules with one or two thiol groups.

  15. 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.

  16. Response of an annular electrostatic probe for a right cylindrical spacer

    DEFF Research Database (Denmark)

    Johansson, Torben; MacAllister, I. W.

    2002-01-01

    The response of an annular electrostatic probe mounted in an electrode is examined with reference to a right cylindrical spacer. The study involves using the probe λ function to derive characteristic parameters. These parameters enable the response of the probe to different charge distributions...

  17. 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.

  18. Investigations in Number, Data, and Space[R]. What Works Clearinghouse Intervention Report

    Science.gov (United States)

    What Works Clearinghouse, 2013

    2013-01-01

    "Investigations in Number, Data, and Space"[R], published by Pearson Scott Foresman, is an activity-based K-5 mathematics curriculum designed to help students understand number and operations, geometry, data, measurement, and early algebra. Each instructional unit focuses on a particular content area and lasts from two to five-and-a-half…

  19. Investigations in Number, Data, and Space[R]. WWC Intervention Report

    Science.gov (United States)

    What Works Clearinghouse, 2009

    2009-01-01

    Investigations in Number, Data, and Space[R], published by Pearson Scott Foresman, is an activity-based K-5 mathematics curriculum designed to help students understand the fundamental ideas of number and operations, geometry, data, measurement, and early algebra. The curriculum encourages students to use prior knowledge to develop an understanding…

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  6. Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence.

    Directory of Open Access Journals (Sweden)

    Katja Böhme

    2012-02-01

    Full Text Available Expression of all Yersinia pathogenicity factors encoded on the virulence plasmid, including the yop effector and the ysc type III secretion genes, is controlled by the transcriptional activator LcrF in response to temperature. Here, we show that a protein- and RNA-dependent hierarchy of thermosensors induce LcrF synthesis at body temperature. Thermally regulated transcription of lcrF is modest and mediated by the thermo-sensitive modulator YmoA, which represses transcription from a single promoter located far upstream of the yscW-lcrF operon at moderate temperatures. The transcriptional response is complemented by a second layer of temperature-control induced by a unique cis-acting RNA element located within the intergenic region of the yscW-lcrF transcript. Structure probing demonstrated that this region forms a secondary structure composed of two stemloops at 25°C. The second hairpin sequesters the lcrF ribosomal binding site by a stretch of four uracils. Opening of this structure was favored at 37°C and permitted ribosome binding at host body temperature. Our study further provides experimental evidence for the biological relevance of an RNA thermometer in an animal model. Following oral infections in mice, we found that two different Y. pseudotuberculosis patient isolates expressing a stabilized thermometer variant were strongly reduced in their ability to disseminate into the Peyer's patches, liver and spleen and have fully lost their lethality. Intriguingly, Yersinia strains with a destabilized version of the thermosensor were attenuated or exhibited a similar, but not a higher mortality. This illustrates that the RNA thermometer is the decisive control element providing just the appropriate amounts of LcrF protein for optimal infection efficiency.

  7. Mutations in the embC-embA intergenic region contribute to Mycobacterium tuberculosis resistance to ethambutol.

    Science.gov (United States)

    Cui, Zhenling; Li, Yuanyuan; Cheng, Song; Yang, Hua; Lu, Junmei; Hu, Zhongyi; Ge, Baoxue

    2014-11-01

    The rapid increase in Mycobacterium tuberculosis resistance to ethambutol (EMB) threatens the diagnosis and treatment of tuberculosis (TB). We investigated the role of mutations in the embC-embA intergenic region (IGR) in EMB-resistant clinical strains from east China. A total of 767 M. tuberculosis clinical strains were collected and analyzed for their drug susceptibility to EMB using the MGIT 960 system and MIC assay, and the embC-embA IGRs of these strains were sequenced. The transcriptional activity of the embC-embA IGR mutations was examined by reporter gene assays in recombinant Mycobacterium smegmatis strains, and the effect of IGR mutations on its binding to EmbR, a transcription regulator of embAB, was analyzed by gel mobility shift assays. Correlation coefficient analysis showed that the embC-embA IGR mutation is associated with EMB resistance. The clinical strains carrying IGR mutations had a much higher level of embA and embB mRNA as well as higher MICs to EMB. IGR mutations had higher transcriptional activity when transformed into M. smegmatis strains. Mutated IGRs bound to EmbR with much higher affinity than wild-type fragments. The sensitivity of molecular drug susceptibility testing (DST) with IGR mutations as an additional marker increased from 65.5% to 73.5%. Mutations of the embC-embA IGR enhance the binding of EmbR to the promoter region of embAB and increase the expression of embAB, thus contributing to EMB resistance. Therefore, identification of IGR mutations as markers of EMB resistance could increase the sensitivity of molecular DST.

  8. Concerted Actions of a Thermo-labile Regulator and a Unique Intergenic RNA Thermosensor Control Yersinia Virulence

    Science.gov (United States)

    Kortmann, Jens; Seekircher, Stephanie; Heroven, Ann Kathrin; Berger, Evelin; Pisano, Fabio; Thiermann, Tanja; Wolf-Watz, Hans; Narberhaus, Franz; Dersch, Petra

    2012-01-01

    Expression of all Yersinia pathogenicity factors encoded on the virulence plasmid, including the yop effector and the ysc type III secretion genes, is controlled by the transcriptional activator LcrF in response to temperature. Here, we show that a protein- and RNA-dependent hierarchy of thermosensors induce LcrF synthesis at body temperature. Thermally regulated transcription of lcrF is modest and mediated by the thermo-sensitive modulator YmoA, which represses transcription from a single promoter located far upstream of the yscW-lcrF operon at moderate temperatures. The transcriptional response is complemented by a second layer of temperature-control induced by a unique cis-acting RNA element located within the intergenic region of the yscW-lcrF transcript. Structure probing demonstrated that this region forms a secondary structure composed of two stemloops at 25°C. The second hairpin sequesters the lcrF ribosomal binding site by a stretch of four uracils. Opening of this structure was favored at 37°C and permitted ribosome binding at host body temperature. Our study further provides experimental evidence for the biological relevance of an RNA thermometer in an animal model. Following oral infections in mice, we found that two different Y. pseudotuberculosis patient isolates expressing a stabilized thermometer variant were strongly reduced in their ability to disseminate into the Peyer's patches, liver and spleen and have fully lost their lethality. Intriguingly, Yersinia strains with a destabilized version of the thermosensor were attenuated or exhibited a similar, but not a higher mortality. This illustrates that the RNA thermometer is the decisive control element providing just the appropriate amounts of LcrF protein for optimal infection efficiency. PMID:22359501

  9. Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection.

    Directory of Open Access Journals (Sweden)

    Kayvan Etebari

    2016-10-01

    Full Text Available Long intergenic non-coding RNAs (lincRNAs are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae. aegypti genome for lincRNA discovery. This led to the identification of 3,482 putative lincRNAs. These lincRNA genes displayed a slightly lower GC content and shorter transcript lengths compared to protein-encoding genes. Ae. aegypti lincRNAs also demonstrate low evolutionary sequence conservation even among closely related species such as Culex quinquefasciatus and Anopheles gambiae. We examined their expression in dengue virus serotype 2 (DENV-2 and Wolbachia infected and non-infected adult mosquitoes and Aa20 cells. The results revealed that DENV-2 infection increased the abundance of a number of host lincRNAs, from which some suppress viral replication in mosquito cells. RNAi-mediated silencing of lincRNA_1317 led to enhancement in viral replication, which possibly indicates its potential involvement in the host anti-viral defense. A number of lincRNAs were also differentially expressed in Wolbachia-infected mosquitoes. The results will facilitate future studies to unravel the function of lncRNAs in insects and may prove to be beneficial in developing new ways to control vectors or inhibit replication of viruses in them.

  10. Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection

    Science.gov (United States)

    Etebari, Kayvan; Asad, Sultan; Zhang, Guangmei; Asgari, Sassan

    2016-01-01

    Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae. aegypti genome for lincRNA discovery. This led to the identification of 3,482 putative lincRNAs. These lincRNA genes displayed a slightly lower GC content and shorter transcript lengths compared to protein-encoding genes. Ae. aegypti lincRNAs also demonstrate low evolutionary sequence conservation even among closely related species such as Culex quinquefasciatus and Anopheles gambiae. We examined their expression in dengue virus serotype 2 (DENV-2) and Wolbachia infected and non-infected adult mosquitoes and Aa20 cells. The results revealed that DENV-2 infection increased the abundance of a number of host lincRNAs, from which some suppress viral replication in mosquito cells. RNAi-mediated silencing of lincRNA_1317 led to enhancement in viral replication, which possibly indicates its potential involvement in the host anti-viral defense. A number of lincRNAs were also differentially expressed in Wolbachia-infected mosquitoes. The results will facilitate future studies to unravel the function of lncRNAs in insects and may prove to be beneficial in developing new ways to control vectors or inhibit replication of viruses in them. PMID:27760142

  11. 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.

  12. 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

  13. Effect of a spacer on pulmonary aerosol deposition from a jet nebuliser during mechanical ventilation.

    Science.gov (United States)

    Harvey, C. J.; O'Doherty, M. J.; Page, C. J.; Thomas, S. H.; Nunan, T. O.; Treacher, D. F.

    1995-01-01

    BACKGROUND--Several factors have been identified which improve nebulised aerosol delivery in vitro. One of these is the addition of a spacer to the ventilator circuit which improves aerosol delivery from a jet nebuliser to a model lung by approximately 30%. The current study was designed to demonstrate whether similar improvements could be demonstrated in vivo. METHODS--Ten patients (seven men) were studied during mechanical ventilation (Siemens Servo 900C) after open heart surgery. Aerosol was delivered using a Siemens Servo 945 nebuliser system (high setting) driving a System 22 Acorn jet nebuliser (Medic-Aid) containing 3 ml technetium-99m labelled human serum albumin (99mTc-HSA (50 micrograms); activity in the first nebulisation, 90 MBq; in the second nebulisation, 185 MBq). Central and peripheral lung aerosol deposition and the time to complete deposition were measured using a gamma camera and compared when the nebuliser was connected to the inspiratory limb using a simple T-piece or a 600 ml spacer. RESULTS--The addition of the spacer increased total lung deposition (mean (SD) percentage initial nebuliser activity) from 2.2 (0.7)% to 3 (0.8)%. There was no difference in the time required to complete nebulisation (18.2 min v 18.3 min respectively for T-piece and spacer) or in the retention of activity in the nebuliser (46.2% v 47.1% respectively). CONCLUSIONS--The combination of a spacer with a jet nebuliser increased lung deposition by 36% in mechanically ventilated patients and is a simple way of increasing drug deposition or reducing the amount of an expensive drug required for nebulisation. Images PMID:7886649

  14. 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.

  15. Evolutionary relationships among Chlamydophila abortus variant strains inferred by rRNA secondary structure-based phylogeny.

    Science.gov (United States)

    Siarkou, Victoria I; Stamatakis, Alexandros; Kappas, Ilias; Hadweh, Paul; Laroucau, Karine

    2011-01-01

    The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS), and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the "classical" C. abortus strains and the other the "LLG/POS variant", with the type strain B577(T) possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic) characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the "classical" lineage, while three were unique for the "LLG/POS variant". The U277 (E. coli numbering) signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies) of the "classical" and the "LLG/POS variant" lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the "classical", the "LLG/POS variant" lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic inference reveal new

  16. Evolutionary relationships among Chlamydophila abortus variant strains inferred by rRNA secondary structure-based phylogeny.

    Directory of Open Access Journals (Sweden)

    Victoria I Siarkou

    Full Text Available The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS, and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs, two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the "classical" C. abortus strains and the other the "LLG/POS variant", with the type strain B577(T possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the "classical" lineage, while three were unique for the "LLG/POS variant". The U277 (E. coli numbering signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies of the "classical" and the "LLG/POS variant" lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the "classical", the "LLG/POS variant" lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic

  17. Marine mesocosm bacterial colonisation of volcanic ash

    Science.gov (United States)

    Witt, Verena; Cimarelli, Corrado; Ayris, Paul; Kueppers, Ulrich; Erpenbeck, Dirk; Dingwell, Donald; Woerheide, Gert

    2015-04-01

    Volcanic eruptions regularly eject large quantities of ash particles into the atmosphere, which can be deposited via fallout into oceanic environments. Such fallout has the potential to alter pH, light and nutrient availability at local scales. Shallow-water coral reef ecosystems - "rainforests of the sea" - are highly sensitive to disturbances, such as ocean acidification, sedimentation and eutrophication. Therefore, wind-delivered volcanic ash may lead to burial and mortality of such reefs. Coral reef ecosystem resilience may depend on pioneer bacterial colonisation of the ash layer, supporting subsequent establishment of the micro- and ultimately the macro-community. However, which bacteria are involved in pioneer colonisation remain unknown. We hypothesize that physico-chemical properties (i.e., morphology, mineralogy) of the ash may dictate bacterial colonisation. The effect of substrate properties on bacterial colonisation was tested by exposing five substrates: i) quartz sand ii) crystalline ash (Sakurajima, Japan) iii) volcanic glass iv) carbonate reef sand and v) calcite sand of similar grain size, in controlled marine coral reef aquaria under low light conditions for six months. Bacterial communities were screened every month by Automated Ribosomal Intergenic Spacer Analysis of the 16S-23S rRNA Internal Transcribed Spacer region. Multivariate statistics revealed discrete groupings of bacterial communities on substrates of volcanic origin (ash and glass) and reef origin (three sands). Analysis of Similarity supported significantly different communities associated with all substrates (p=0.0001), only quartz did not differ from both carbonate and calcite sands. The ash substrate exhibited the most diverse bacterial community with the most substrate-specific bacterial operational taxonomic units. Our findings suggest that bacterial diversity and community composition during colonisation of volcanic ash in a coral reef-like environment is controlled by the

  18. 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.

  19. Quality of life after intensity-modulated radiotherapy for prostate cancer with a hydrogel spacer. Matched-pair analysis

    Energy Technology Data Exchange (ETDEWEB)

    Pinkawa, M.; Piroth, M.D.; Holy, R.; Escobar-Corral, N.; Caffaro, M.; Djukic, V.; Klotz, J.; Eble, M.J. [RWTH Aachen Univ. (Germany). Dept. of Radiation Oncology

    2012-10-15

    Background: Hydrogel spacer is an innovative method to protect the rectal wall during prostate cancer radiotherapy. Clinical effects are not well known. Methods: Patients have been surveyed before, at the last day, and 2-3 months after radiotherapy using a validated questionnaire (Expanded Prostate Cancer Index Composite). Median dose to the prostate in the spacer subgroup (SP) was 78 Gy in 2 Gy fractions. The results were independently compared with two matched-pair subgroups (treated conventionally without spacer): 3D conformal 70.2 Gy in 1.8 Gy fractions (3DCRT) and intensity-modulated radiotherapy (IMRT) 76 Gy in 2 Gy fractions. There were 28 patients in each of the three groups. Results: Baseline mean bowel bother scores were 96 points in all subgroups. Similar mean changes (SP 16, 3DCRT 14, IMRT 17 points) were observed at the end of radiotherapy. The smallest difference resulted in the spacer subgroup 2-3 months after radiotherapy (SP 2, 3DCRT 8, IMRT 6 points). Bowel bother scores were only significantly different in comparison to baseline levels in the spacer subgroup. The percentage of patients reporting moderate/big bother with specific symptoms did not increase for any item (urgency, frequency, diarrhoea, incontinence, bloody stools, pain). Conclusion: Moderate bowel quality-of-life changes can be expected during radiotherapy irrespective of spacer application or total dose. Advantages with a spacer can be expected a few weeks after treatment. (orig.)

  20. Asymmetric underlap spacer layer enabled nanoscale double gate MOSFETs for design of ultra-wideband cascode amplifiers

    Science.gov (United States)

    Roy, Debapriya; Biswas, Abhijit

    2017-10-01

    Using extensive numerical analysis we investigate effects of asymmetric sidewall spacers on various device parameters of 20-nm double gate MOSFETs associated with analog/RF applications. Our studies show that the device with underlap drain-side spacer length LED of 10 nm and source-side spacer length LES of 5 nm shows improvement in terms of the peak value of transconductance efficiency, voltage gain Av, unity-gain cut-off frequency fT and maximum frequency of oscillations fMAX by 8.6%, 51.7%, 5% and 10.3%, respectively compared to the symmetric 5 nm underlap spacer device with HfO2 spacer of dielectric constant k = 22. Additionally, a higher spacer dielectric constant increases the peak Av while decreasing both peak fT and fMAX. The detailed physical insight is exploited to design a cascode amplifier which yields an ultra-wide gain bandwidth of 2.48 THz at LED = 10 nm with a SiO2 spacer.

  1. An H3-H4 histone gene pair in the marine copepod Tigriopus californicus, contains an intergenic dyad symmetry element.

    Science.gov (United States)

    Porter, D; Brown, D; Wells, D

    1991-01-01

    Histone genes are one of the most widely studied multigene families in eucaryotes. Over 200 histone genes have been sequenced, primarily in vertebrates, echinoderms, fungi and plants. We present here the structure and genomic orientation of an H3-H4 histone gene pair from the marine copepod, Tigriopus californicus. These histone gene sequences are the first to be determined for the class Crustacea and among the first to be determined for protostomes. The H4 and H3 genes in Tigriopus are shown to be adjacent, to have opposite polarity, and to contain a 26 bp region of dyad symmetry centrally located within the spacer region between the two genes. A similarly located dyad element has been found in yeast which contributes to the coordinated cell cycle control of the adjacent histone genes. The Tigriopus H3-H4 histone gene pair is clustered with one H2A and two H2B histone genes on a 15 kb genomic Bam H1 fragment. The H4 gene sequence predicts an H4 protein with an unusual serine to threonine substitution at the amino terminal residue. The H3 gene sequence predicts an H3 protein which is identical to the vertebrate H3.2 histone.

  2. On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

    Directory of Open Access Journals (Sweden)

    Sukrit Silas

    2017-07-01

    Full Text Available Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent to a gene encoding a reverse transcriptase (RT related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium—Arthrospira platensis. Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.

  3. Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa.

    Science.gov (United States)

    Blair, Matthew W; González, Laura F; Kimani, Paul M; Butare, Louis

    2010-07-01

    The Great Lakes region of Central Africa is a major producer of common beans in Africa. The region is known for high population density and small average farm size. The common bean represents the most important legume crop of the region, grown on over a third of the cultivated land area, and the per capita consumption is among the highest in the world for the food crop. The objective of this study was to evaluate the genetic diversity in a collection of 365 genotypes from the Great Lakes region of Central Africa, including a large group of landraces from Rwanda as well as varieties from primary centers of diversity and from neighboring countries of Central Africa, such as the Democratic Republic of Congo and Uganda, using 30 fluorescently labeled microsatellite markers and automated allele detection. In addition, the landraces were evaluated for their seed iron and zinc concentration to determine if genetic diversity influenced nutritional quality. Principal coordinate and neighbor-joining analyses allowed the separation of the landraces into 132 Andean and 195 Mesoamerican (or Middle American) genotypes with 32 landraces and 6 varieties intermediate between the gene pools and representing inter-gene pool introgression in terms of seed characteristics and alleles. Genetic diversity and the number of alleles were high for the collection, reflecting the preference for a wide range of seed types in the region and no strong commercial class preference, although red, red mottled and brown seeded beans were common. Observed heterozygosity was also high and may be explained by the common practice of maintaining seed and plant mixtures, a coping strategy practiced by Central African farmers to reduce the effects of abiotic and biotic stresses. Finally, nutritional quality differed between the gene pools with respect to seed iron and zinc concentration, while genotypes from the intermediate group were notably high in both minerals. In conclusion, this study has shown that

  4. Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency

    Directory of Open Access Journals (Sweden)

    Stanton Lawrence W

    2008-04-01

    Full Text Available Abstract Background Transcriptional control of embryonic stem (ES cell pluripotency has been a subject of intense study. Transcriptional regulators including Oct4 (Oct3/4 index, Sox2 and Nanog are fundamental for maintaining the undifferentiated state. However, the ES cell transcriptome is not limited to their targets, and exhibits considerable complexity when assayed with microarray, MPSS, cDNA/EST sequencing, and SAGE technologies. To identify novel genes associated with pluripotency, we globally searched for ES transcripts not corresponding to known genes, validated their sequences, determined their expression profiles, and employed RNAi to test their function. Results Gene Identification Signature (GIS analysis, a SAGE derivative distinguished by paired 5' and 3' transcript end tags, identified 153 candidate novel transcriptional units (TUs distinct from known genes in a mouse E14 ES mRNA library. We focused on 16 TUs free of artefacts and mapping discrepancies, five of which were validated by RTPCR product sequencing. Two of the TUs were revealed by annotation to represent novel protein-coding genes: a PRY-domain cluster member and a KRAB-domain zinc finger. The other three TUs represented intergenic splicing events involving adjacent, functionally unrelated protein-coding genes transcribed in the same orientation, with one event potentially encoding a fusion protein containing domains from both component genes (Clk2 and Scamp3. Expression profiling using embryonic samples and adult tissue panels confirmed that three of the TUs were unique to or most highly expressed in ES cells. Expression levels of all five TUs dropped dramatically during three distinct chemically induced differentiation treatments of ES cells in culture. However, siRNA knockdowns of the TUs did not alter mRNA levels of pluripotency or differentiation markers, and did not affect cell morphology. Conclusion Transcriptome libraries retain considerable potential for novel

  5. Estimation of the energy flow through the spacer in a DGU during calorimetric g-value measurement

    DEFF Research Database (Denmark)

    Duer, Karsten

    1997-01-01

    The edge-construction of a glazing has an impact on the g-value of the glazing, measured by calorimetric devices. If no insulation is applied on the glazing edges (inside and outside) during measurements, heat will be transferred by conduction through the glass panes and through the spacer....... The amount of energy transferred and the direction of the energy flow depends on the construction of the glazing (types of glass, coatings and spacer) and on the interieur and exterieur temperatures during the measurements. This paper gives an evaluation of the amount of energy transferred through the spacer...

  6. CFD analysis of pressure drop across grid spacers in rod bundles compared to correlations and heavy liquid metal experimental data

    Energy Technology Data Exchange (ETDEWEB)

    Batta, A., E-mail: batta@kit.edu; Class, A.G., E-mail: class@kit.edu

    2017-02-15

    Early studies of the flow in rod bundles with spacer grids suggest that the pressure drop can be decomposed in contributions due to flow area variations by spacer grids and frictional losses along the rods. For these shape and frictional losses simple correlations based on theoretical and experimental data have been proposed. In the OECD benchmark study LACANES it was observed that correlations could well describe the flow behavior of the heavy liquid metal loop including a rod bundle with the exception of the core region, where different experts chose different pressure-loss correlations for the losses due to spacer grids. Here, RANS–CFD simulations provided very good data compared to the experimental data. It was observed that the most commonly applied Rehme correlation underestimated the shape losses. The available correlations relate the pressure drop across a grid spacer to the relative plugging of the spacer i.e. solidity e{sub max}. More sophisticated correlations distinct between spacer grids with round or sharp leading edge shape. The purpose of this study is to (i) show that CFD is suitable to predict pressure drop across spacer grids and (ii) to access the generality of pressure drop correlations. By verification and validation of CFD results against experimental data obtained in KALLA we show (i). The generality (ii) is challenged by considering three cases which yield identical pressure drop in the correlations. First we test the effect of surface roughness, a parameter not present in the correlations. Here we compare a simulation assuming a typical surface roughness representing the experimental situation to a perfectly smooth spacer surface. Second we reverse the flow direction for the spacer grid employed in the experiments which is asymmetric. The flow direction reversal is chosen for convenience, since an asymmetric spacer grid with given blockage ratio, may result in different flow situations depending on flow direction. Obviously blockage

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

    Science.gov (United States)

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

    2000-11-01

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

  8. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Science.gov (United States)

    2011-01-01

    Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD) followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes) and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes) hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease. PMID:21669002

  9. 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

    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 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...

  10. 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.

  11. 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.

  12. 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.

  13. Development and Manufacture of the Coil End Spacers of the LHC Pre-series Dipoles

    CERN Document Server

    Farina, E; Perini, D; Schiappapietra, A; Seneé, L

    2002-01-01

    The coil end spacers play an important role in the performance of superconducting coils, as their shape and location determine the mechanical stability of the conductors in the coil ends (and hence the overall coil training performance) and the local field quality. The dipole end spacers are often of a size and a geometry difficult to be industrially series manufactured and measured. Efficiency of the production and related costs are a key issue to achieve the required production rate of the LHC main dipoles at an affordable price. For the latter reasons, a design approach integrating state-of-the-art CAD/CAM optimization techniques allowing to considerably decrease design and machining time was implemented. This paper gives examples and describes the design criteria, the computation methods, the machining and measuring procedures adopted to carry out the pre-series production.

  14. 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.

  15. Pressurised metered dose inhaler-spacer technique in young children improves with video instruction.

    Science.gov (United States)

    Shaw, Nicole; Le Souëf, Peter; Turkovic, Lidija; McCahon, Lucy; Kicic, Anthony; Sly, Peter D; Devadason, Sunalene; Schultz, André

    2016-07-01

    The importance of good device technique to maximise delivery of aerosolised medications is widely recognised. Pressurised metered dose inhaler (pMDI)-spacer technique was investigated in 122 children, aged 2-7 years, with asthma. Eight individual steps of device technique were evaluated before and after viewing an instructional video for correct device technique. Video measurements were repeated every three months for nine months. Device technique improved directly after video instruction at the baseline study visit (p children scoring maximal (p = 0.02) and near-maximal (p = 0.04) scores. Repeated video instruction over time improves inhaler technique in young children. • Correct device technique is considered essential for sufficient delivery of inhaled medication. • Poor inhaler use is common in young asthmatic children using pressurised metered dose inhalers and spacers. What is New: • Video instruction could be used as a strategy to improve device technique in young children.

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

    DEFF Research Database (Denmark)

    León-Sobrino, Carlos; Kot, Witold P; Garrett, Roger A

    2016-01-01

    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 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...

  17. SYNTHESIS OF NOVEL LIQUID CRYSTALLINE POLY(METH)ACRYLATES CONTAINING SILOXANE SPACER AND TERPHENYLENE MESOGENIC UNIT

    Institute of Scientific and Technical Information of China (English)

    Zhi-qian Zang; Yu-fei Luo; Dong Zhang; Xin-hua Wan; Qi-feng Zhou

    2000-01-01

    Novel side-chain liquid-crystalline poly(meth)acrylates were synthesized using 1-(3-hydroxyl-propyl)-3-[(4"cyano-p-terphenyloxycarbonyl)alkyl]-1, 1,3,3-tetramethyldisiloxane as the key intermediate. The polymers used a disiloxane moiety as decoupling spacer with cyano-p-terphenyl as mesogenic unit. The products were characterized by NMR, GPC,DSC and polarizing optical microscopy. All the polymers with cyano-p-terphenyl mesogens formed a stable mesophase.However, if the mesogenic unit is replaced by cyano-p-biphenyl, the liquid crystalline character will be lost. The results also showed that the decoupling is incomplete even if a complex and very flexible decoupling spacer is deliberately incorporated to obtain the highest possible decoupling effect.

  18. 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...

  19. 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.

  20. 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.

  1. Automatic actuation of a dry powder inhaler into a nonelectrostatic spacer

    DEFF Research Database (Denmark)

    Bisgaard, H

    1998-01-01

    This article describes a new "automatic spacer" device, which has been developed to improve the delivery of inhaled medication to young children. In the device, a dry powder inhaler (DPI) is mechanically actuated into a nonelectrostatic spacer, producing an aerosol cloud of fine drug particles...... of the patient to the additives and propellants used in pressurized metered dose inhalers. Studies with the prototype device show a high yield of fine drug particles in the aerosol (mass median aerodynamic diameter, 2.8 microm), a high repeatability of drug delivery owing to the mechanical nature...... of the actuation (relative standard deviation, 12%), and a prolonged residence time of the fine particle aerosol (half-life of the fallout of the fine particles, 82 s). These features should prove advantageous in the treatment of young children with inhaled medication....

  2. Effect of spacer layer on the magnetization dynamics of permalloy/rare-earth/permalloy trilayers

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Chen, E-mail: ronanluochen@gmail.com; Yin, Yuli; Zhang, Dong; Jiang, Sheng; Yue, Jinjin; Zhai, Ya, E-mail: yazhai@seu.edu.cn [Physics Department, Southeast University, Nanjing 211189 (China); Du, Jun; Zhai, Hongru [National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093 (China)

    2015-05-07

    The permalloy/rare-earth/permalloy trilayers with different types (Gd and Nd) and thicknesses of spacer layer are investigated using frequency dependence of ferromagnetic resonance (FMR) measurements at room temperature, which shows different behaviors with different rare earth spacer layers. By fitting the frequency dependence of the FMR resonance field and linewidth, we find that the in-plane uniaxial anisotropy retains its value for all samples, the perpendicular anisotropy remains almost unchanged for different thickness of Gd layer but the values are tailored by different thicknesses of Nd layer. The Gilbert damping is almost unchanged with different thicknesses of Gd; however, the Gilbert damping is significantly enhanced from 8.4×10{sup −3} to 20.1×10{sup −3} with 6 nm of Nd and then flatten out when the Nd thickness rises above 6 nm.

  3. 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.

  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. The intergenic region between the divergently transcribed niiA and niaD genes of Aspergillus nidulans contains multiple NirA binding sites which act bidirectionally.

    OpenAIRE

    1995-01-01

    The niaD and niiA genes of Aspergillus nidulans, which code, respectively, for nitrate and nitrite reductases, are divergently transcribed, and their ATGs are separated by 1,200 bp. The genes are under the control of the positively acting NirA transcription factor, which mediates nitrate induction. The DNA binding domain of NirA was expressed as a fusion protein with the glutathione S-transferase of Schistosoma japonicum. Gel shift and footprint experiments have shown that in the intergenic r...

  6. 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.

  7. Stimulation of the mouse rRNA gene promoter by a distal spacer promoter.

    OpenAIRE

    Paalman, M H; Henderson, S L; Sollner-Webb, B

    1995-01-01

    We show that the mouse ribosomal DNA (rDNA) spacer promoter acts in vivo to stimulate transcription from a downstream rRNA gene promoter. This augmentation of mammalian RNA polymerase I transcription is observed in transient-transfection experiments with three different rodent cell lines, under noncompetitive as well as competitive transcription conditions, over a wide range of template concentrations, whether or not the enhancer repeats alone stimulate or repress expression from the downstre...

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

    Science.gov (United States)

    Yang, Lixin; Zhou, Mengjun; Tian, Zihao

    2017-01-01

    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.

  10. Relative lung bioavailability of generic sodium cromoglycate inhalers used with and without a spacer device.

    Science.gov (United States)

    Aswania, O; Chrystyn, H

    2001-01-01

    The relative lung bioavailability of sodium cromoglycate following inhalation has been evaluated using urinary drug excretion in nine healthly volunteers. Each inhaled four 5 mg sodium cromoglycate doses from a generic metered dose inhaler (MDI) and when it was attached to large volume spacer (MDI + VOL). A breath-actuated MDI was also evaluated either used on its own (EB) or attached to a small volume spacer tube (EBO). The mean (SD) urinary excretion of sodium cromoglycate in the first 30 min post-inhalation was 34.1 (20.2), 211.7 (123.5), 29.3 (19.5) and 52.8 (36.0) microg following MDI, MDI+VOL, EB and EBO, respectively. The cumulative mean (SD) urinary excretion of sodium cromoglycate over the 24 h post-inhalation was 364.7 (266.2), 1227.1 (459.0), 280.2 (155.4) and 429.5 (176.7) microg. A metered dose inhaler attached to a large volume spacer delivers more sodium cromoglycate to the lungs than any other inhalation method.

  11. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

    Science.gov (United States)

    Moller, Abraham G.

    2017-01-01

    Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST. PMID:28894651

  12. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

    Directory of Open Access Journals (Sweden)

    Abraham G. Moller

    2017-09-01

    Full Text Available Clustered regularly interspaced short palindromic repeat (CRISPR systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST that constrains searches based on user-specified direct repeats (DRs. These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD and enhanced biological phosphorus removal (EBPR metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE, and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.

  13. 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.

  14. FIVPET Flow-Induced Vibration Test Report (1) - Candidate Spacer Grid Type I (Optimized H Type)

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kang Hee; Kang, Heung Seok; Yoon, Kyung Ho; Song, Kee Nam; Kim, Jae Yong

    2006-03-15

    The flow-induced vibration (FIV) test using a 5x5 partial fuel assembly was performed to evaluate mechanical/structural performance of the candidate spacer grid type I (Optimized H shape). From the measured vibration response of the test bundle and the flow parameters, design features of the spacer strap can be analyzed in the point of vibration and hydraulic aspect, and also compared with other spacer strap in simple comparative manner. Furthermore, the FIV test will contributes to understand behaviors of nuclear fuel in operating reactor. The FIV test results will be used to verify the theoretical model of fuel rod and assembly vibration. The aim of this report is to present the results of the FIV test of partial fuel assembly and to introduce the detailed test methodology and analysis procedure. In chapter 2, the overall configuration of test bundle and instrumented tube is remarked and chapter 3 will introduce the test facility (FIVPET) and test section. Chapter 4 deals with overall test condition and procedure, measurement and data acquisition devices, instrumentation equipment and calibration, and error analysis. Finally, test result of vibration and pressure fluctuation is presented and discussed in chapter 5.

  15. Investigation of DNA-cationic bolaform surfactants interaction with different spacer length.

    Science.gov (United States)

    Sohrabi, Beheshteh; Khani, Vahid; Moosavi-Movahedi, Ali Akbar; Moradi, Parviz

    2013-10-01

    In this paper interaction of DNA with cationic bolaform surfactants is investigated. The structural formula for synthesized bolaforms is as follows: bolaform B1 with structural formula Br(-)(CH3)3N(+)(CH2)3N(+)(CH3)Br(-) and bolaform B2 with structural formula of Br(-)(CH3)3N(+)(CH2)12N(+)(CH3)Br(-). There are stronger electrostatic interactions in bolaform B1 due to shorter spacer length, while there are stronger hydrophobic interactions in bolaform B2 compared to bolaform B1 due to existence of 12 carbons in hydrocarbonic chain. The structure of bolaforms consists of two polar head groups which play important role in DNA compaction. Surface tension change in aqueous solution of bolaform surfactants is measured using tensiometer. Electrical conductivity of surfactants aqueous solution is examined with and without DNA. DNA compaction is tracked in the presence of bolaforms by dynamic light scattering (DLS) technique. Results of DLS indicate bolaforms with shorter spacer length (dominant electrostatic interactions) are more influential in compressing DNA compared to bolaforms with longer spacer length (stronger hydrophobic interactions). UV-vis and fluorescence spectroscopies specify the binding mechanism of bolaform surfactants to DNA.

  16. Role of spacer lengths of gemini surfactants in the synthesis of silver nanorods in micellar media.

    Science.gov (United States)

    Bhattacharya, Santanu; Biswas, Joydeep

    2011-07-01

    In this work, we have prepared Ag-nanorods using biscationic gemini surfactant micelles as the media by a seed-mediated wet synthesis method. Towards this end, we first synthesized Ag-nanoseeds of diameter ~7 nm stabilized by trisodium citrate (as the capping agent). Then these Ag-nanoseeds were used to synthesize Ag-nanorods of different aspect ratios. With decreasing Ag-nanoseed concentration, the aspect ratios of the Ag-nanorods stabilized by these gemini surfactants increased gradually. Various Ag-nanoseeds and Ag-nanospecies were characterized using UV-Vis spectroscopy (to know the surface plasmon bands), transmission electron microscopy (to find out their particle sizes and distribution), energy-dispersive X-ray spectroscopy and X-ray diffraction. When we used micelles derived from gemini surfactants of shorter spacer -(CH(2))(n)- (n = 2 or 4) to stabilize the Ag-nanorods, the λ(max) of the longitudinal band shifted more towards the blue region compared to that of the gemini surfactant micelles with a longer spacer -(CH(2))(n)- (n = 5, 12) at a given amount of the Ag-nanoseed solution. So, the growth of Ag-nanorods in the gemini micellar solutions depends on the spacer-chain length of gemini surfactants employed.

  17. Review and Comparison of simulation software for additive manufacturing process: the practical case of dipole End-Spacers

    CERN Document Server

    Vevers, Arturs

    2017-01-01

    Project was made to compare and benchmark simulation software for additive manufacturing. Simulations for End-spacers and HOM crab cavity were made to compare simulation results with 3D scanned data for these parts.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Preclinical investigations towards the first spacer gel application in prostate cancer treatment during particle therapy at HIT

    OpenAIRE

    Ruciński, Antoni; Bauer, Julia; Campbell, Patrick; Brons, Stephan; Unholtz, Daniel; Habl, Gregor; Herfarth, Klaus; Debus, Jürgen; Bert, Christoph; Parodi, Katia; Jäkel, Oliver; Haberer, Thomas

    2013-01-01

    Background The application of spacer gel represents a promising approach to reliably spare the rectal frontal wall during particle therapy (IJROBP 76:1251-1258, 2010). In order to qualify the spacer gel for the clinical use in particle therapy, a variety of measurements were performed in order to ensure the biological compatibility of the gel, its physical stability during and after the irradiation, and a proper definition of the gel in terms of the Hounsfield Unit (HU) values for the treatme...

  4. 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...

  5. Linking of Microorganisms to Phenanthrene Metabolism in Soil by Analysis of 13C-Labeled Cell Lipids

    OpenAIRE

    Johnsen, Anders R.; Winding, Anne; Karlson, Ulrich; Roslev, Peter

    2002-01-01

    Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [14C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [13C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), ...

  6. 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.

  7. Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm.

    Science.gov (United States)

    Gioia, Tania; Logozzo, Giuseppina; Attene, Giovanna; Bellucci, Elisa; Benedettelli, Stefano; Negri, Valeria; Papa, Roberto; Spagnoletti Zeuli, Pierluigi

    2013-01-01

    Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from "pure" accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with "pure" accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.

  8. Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes hybridization in the European common bean (Phaseolus vulgaris L. germplasm.

    Directory of Open Access Journals (Sweden)

    Tania Gioia

    Full Text Available Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L. in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs were used to complement chloroplast microsatellite (cpSSRs and nuclear markers (phaseolin and Pv-shatterproof1 data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from "pure" accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2% than in America (12.3%. The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with "pure" accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.

  9. 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.

  10. 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.

  11. 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.

  12. Indirect decompression and vertebral body endplate strength after lateral interbody spacer impaction: cadaveric and foam-block models.

    Science.gov (United States)

    Kwon, Anthony J; Hunter, William D; Moldavsky, Mark; Salloum, Kanaan; Bucklen, Brandon

    2016-05-01

    OBJECTIVE The lateral transpsoas approach to the lumbar spine is a well-defined procedure for the management of discogenic spinal pathology necessitating surgical intervention. Intervertebral device subsidence is a postoperative clinical risk that can lead to recurrence of symptomatic pathology and the need for surgical reintervention. The current study was designed to investigate static versus expandable lateral intervertebral spacers in indirect decompression for preserving vertebral body endplate strength. METHODS Using a cadaveric biomechanical study and a foam-block vertebral body model, researchers compared vertebral body endplate strength and distraction potential. Fourteen lumbar motion segments (7 L2-3 and 7 L4-5 specimens) were distributed evenly between static and expandable spacer groups. In each specimen discectomy was followed by trialing and spacer impaction. Motion segments were axially sectioned through the disc, and a metal stamp was used to apply a compressive load to superior and inferior vertebral bodies to quantify endplate strength. A paired, 2-sample for means t-test was performed to determine statistically significant differences between groups (p ≤ 0.05). A foam-block endplate model was used to control simulated disc tension when a spacer with 2- and 3-mm desired distraction was inserted. One-way ANOVA and a post hoc Student Newman-Keuls test were performed (p ≤ 0.05) to determine differences in distraction. RESULTS Both static and expandable spacers restored intact neural foramen and disc heights after device implantation (p > 0.05). Maximum peak loads at endplate failure for static and expandable spacers were 1764 N (± 966 N) and 2284 N (± 949 N), respectively (p ≤ 0.05). The expandable spacer consistently produced greater desired distraction than was created by the static spacer in the foam-block model (p ≤ 0.05). Distraction created by fully expanding the spacer was significantly greater than the predetermined goals of 2 mm

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. MOLECULAR PHYLOGENETIC ANALYSIS OF MONASCUS FUNGI BASED ON INTERNAL TRANSCRIBED SPACER REGION

    OpenAIRE

    Kikuchi, Y.; N. SUHARNA; Fukatsu, T

    2005-01-01

    A molecular analysis of internal transcribed spacer region has been carried out to reveal the relationship among 16 strains of Monascus spp. A primer set comprised primer ITS1 and ITS4 was used to amplify this region in which they were cloned and scqucnccd. We also compared the sequence result with M. purpureus AF458473, M.ruber AF458470, M. kaoliang AF451859, M. araneous AF458471 and M. pilosus AF451856 and one outgroup species Thermoascus crustaceus U18353. The result showed that 16 M...

  19. Fusion of HMGA1 to the LPP/TPRG1 intergenic region in a lipoma identified by mapping paraffin-embedded tissues.

    Science.gov (United States)

    Wang, Xiaoke; Zamolyi, Renata Q; Zhang, Hongying; Pannain, Vera L; Medeiros, Fabiola; Erickson-Johnson, Michele; Jenkins, Robert B; Oliveira, Andre M

    2010-01-01

    Ordinary lipoma frequently harbors rearrangement of HMGA2. LPP is the most common partner gene to HMGA2, but has not been seen fused to HMGA1. We report the fusion of HMGA1 to the intergenic region between LPP and TPRG1 in a lipoma. Conventional cytogenetic analysis of an abdominal-wall lipoma diagnosed in a 60-year-old woman showed a t(3;6)(q27;p21). Molecular cytogenetic mapping of available paraffin-embedded tissues revealed the fusion of HMGA1 to a 139-kb genomic region between the LPP and TPRG1 loci. No rearrangement of HMGA2 was found. The biological function of this novel fusion could be similar to the role of HMGA2-LPP in tumorigenesis.

  20. 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.

  1. 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.

  2. Comparative study of the contribution of various PWR spacer grid components to hydrodynamic and wall pressure characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharjee, Saptarshi, E-mail: saptarshi.bhattacharjee@outlook.com [Alternative Energies and Atomic Energy Commission (CEA) – Cadarache, DEN/DTN/STCP/LHC, 13108 Saint Paul lez Durance Cedex (France); Laboratoire de Mécanique, Modélisation et Procédés Propres (M2P2), UMR7340 CNRS, Aix-Marseille Université, Centrale Marseille, 13451 Marseille Cedex (France); Ricciardi, Guillaume [Alternative Energies and Atomic Energy Commission (CEA) – Cadarache, DEN/DTN/STCP/LHC, 13108 Saint Paul lez Durance Cedex (France); Viazzo, Stéphane [Laboratoire de Mécanique, Modélisation et Procédés Propres (M2P2), UMR7340 CNRS, Aix-Marseille Université, Centrale Marseille, 13451 Marseille Cedex (France)

    2017-06-15

    Highlights: • Complex geometry inside a PWR fuel assembly is simulated using simplified 3D models. • Structured meshes are generated as far as possible. • Fluctuating hydrodynamic and wall pressure field are analyzed using LES. • Comparative studies between square spacer grid, circular spacer grid and mixing vanes are presented. • Simulations are compared with experimental data. - Abstract: Flow-induced vibrations in a pressurized water reactor (PWR) core can cause fretting wear in fuel rods. These vibrations can compromise safety of a nuclear reactor. So, it is necessary to know the random fluctuating forces acting on the rods which cause these vibrations. In this paper, simplified 3D models like square spacer grid, circular spacer grid and symmetric mixing vanes have been used inside an annular pipe. Hydrodynamic and wall pressure characteristics are evaluated using large eddy simulations (LES). Structured meshes are generated as far as possible. Simulations are compared with an experiment. Results show that the grid and vanes have a combined effect: grid accelerates the flow whereas the vanes contribute to the swirl structures. Spectral analysis of the simulations illustrate vortex shedding phenomenon in the wake of spacer grids. This initial study opens up interesting perspectives towards improving the modeling strategy and understanding the complex phenomenon inside a PWR core.

  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. 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.

  5. 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.

  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. Genetic characterization and antimicrobial resistance of Staphylococcus aureus isolated from bovine milk in Tunisia.

    Science.gov (United States)

    Ben Said, M; Abbassi, M S; Bianchini, V; Sghaier, S; Cremonesi, P; Romanò, A; Gualdi, V; Hassen, A; Luini, M V

    2016-12-01

    Staphylococcus aureus is a major agent of bovine mastitis in dairy herds, causing economic losses in dairy industry worldwide. In addition, milk and milk-products contaminated by Staph. aureus can cause harmful human diseases. The aim of this study was to characterize Staph. aureus strains isolated from dairy farms in Tunisia. Bulk tank milk (n = 32) and individual cow milk (n = 130) samples were collected during the period of 2013-2014. Forty-three Staph. aureus isolates were recovered and typed by spa typing, 16S-23S rRNA intergenic spacer (RS-PCR) and multiplex PCRs for 22 virulence genes. Antimicrobial resistance was also investigated with a disc diffusion test. A selected subsample of 22 strains was additionally genotyped by multilocus sequence typing. Seventeen spa types were recovered, and t2421 (n = 10), t521 (n = 6) and t2112 (n = 5) were the most common. Fourteen different RS-PCR genotypes grouped into 11 clusters were detected in our study, with predominance of the R(VI) genotype (n = 24). Eight sequence types were identified and Clonal Complex 97, corresponding to RS-PCR cluster R, was the most common (n = 10), followed by CC1 (n = 4), CC15 (n = 3) and other four accounting for one or two strains. Different combinations of virulence genes were reported, and enterotoxin genes were present in few strains (seh, n = 4; sea, n = 2; sea and seh, n = 2; sec and sel, n = 2). The majority of strains were resistant only to penicillin; only one strain was found to be multiresistant and no methicillin-resistant Staph. aureus was demonstrated. Our study reported the isolation of CC97 from bovine milk in Tunisia for the first time and confirmed the relevance of this lineage in intramammary infection in cows. This paper describes the characteristics of Staphylococcus aureus isolated from bulk tank and individual cow milk in Tunisia. All strains were genotyped by spa typing and RS-PCR, a method based on the amplification of the 16S-23S r

  8. Identification of a novel DRB1 allele through intergenic recombination between HLA-DRB1 and HLA-DRB3∗02 in a Chinese family.

    Science.gov (United States)

    Huang, Weijin; Liu, Xiangjun; Li, Erwei; Zhao, Chenyan; Liu, Qiang; Liang, Zhenglun; Wang, Youchun; Lu, Fengmin

    2013-12-01

    In this study, a novel DRB1 allele was revealed by routine HLA-SBT typing noted for its extensive mismatches to any known DRB1 alleles within the exon 2. Sequences containing the exons 2, 3 of HLA-DRB1, their surrounding introns, and the full-length cDNA of DRB1 were analyzed to determine a possible recombination event. Interestingly, the sequences of entire exon 2 were characterized as DRB3(∗)02:02:01:01/02; while exon 3 were characterized as DRB1(∗)14 like alleles. Further analysis of the sequences using Simplot software suggested that an intergenic recombinant event (i.e. exchange of sequence between non-allelic genes) may have occurred between DRB3(∗)02 allele and DRB1(∗)14 like allele, and the recombination sites are located at intron 1 and the boundary of exon 2 and intron 2 of DRB1. There are 5 CGGGG sequences flanking each side of exon 2 could serve as potential recombination site. Moreover, the full-length cDNA of the novel allele has been identified. The exon 1 and exon 3 to exon 6 share the same sequence as DRB1(∗)14 like alleles. At the mRNA level, the new allele has no significant difference when compared with the other DRB1 allele. This novel recombinant allele is also found to be paternally inherited. In conclusion, this is the first report of a DRB1 and DRB3 intergenic recombination event involving whole exon 2, which generate a new DRB1(∗)14:141.

  9. Genome-wide Anaplasma phagocytophilum AnkA-DNA interactions are enriched in intergenic regions and gene promoters and correlate with infection-induced differential gene expression.

    Directory of Open Access Journals (Sweden)

    J Stephen Dumler

    2016-09-01

    Full Text Available Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: i intergenic regions predicted to be matrix attachment regions (MARs; ii within predicted lamina-associated domains; and iii at promoters ≤3,000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome re-organizer. AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.

  10. An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression.

    Science.gov (United States)

    Wyszynski, Asaf; Hong, Chi-Chen; Lam, Kristin; Michailidou, Kyriaki; Lytle, Christian; Yao, Song; Zhang, Yali; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Hopper, John L; Southey, Melissa C; Schmidt, Marjanka K; Broeks, Annegien; Muir, Kenneth; Lophatananon, Artitaya; Fasching, Peter A; Beckmann, Matthias W; Peto, Julian; Dos-Santos-Silva, Isabel; Sawyer, Elinor J; Tomlinson, Ian; Burwinkel, Barbara; Marme, Frederik; Guénel, Pascal; Truong, Thérèse; Bojesen, Stig E; Nordestgaard, Børge G; González-Neira, Anna; Benitez, Javier; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Meindl, Alfons; Schmutzler, Rita K; Brauch, Hiltrud; Nevanlinna, Heli; Khan, Sofia; Matsuo, Keitaro; Ito, Hidemi; Dörk, Thilo; Bogdanova, Natalia V; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kosma, Veli-Matti; Wu, Anna H; Van Den Berg, David; Lambrechts, Diether; Wildiers, Hans; Chang-Claude, Jenny; Rudolph, Anja; Radice, Paolo; Peterlongo, Paolo; Couch, Fergus J; Olson, Janet E; Giles, Graham G; Milne, Roger L; Haiman, Christopher A; Henderson, Brian E; Dumont, Martine; Teo, Soo Hwang; Wong, Tien Y; Kristensen, Vessela; Zheng, Wei; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Andrulis, Irene L; Knight, Julia A; Devilee, Peter; Seynaeve, Caroline; García-Closas, Montserrat; Figueroa, Jonine; Klevebring, Daniel; Czene, Kamila; Hooning, Maartje J; van den Ouweland, Ans M W; Darabi, Hatef; Shu, Xiao-Ou; Gao, Yu-Tang; Cox, Angela; Blot, William; Signorello, Lisa B; Shah, Mitul; Kang, Daehee; Choi, Ji-Yeob; Hartman, Mikael; Miao, Hui; Hamann, Ute; Jakubowska, Anna; Lubinski, Jan; Sangrajrang, Suleeporn; McKay, James; Toland, Amanda E; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Swerdlow, Anthony; Orr, Nick; Simard, Jacques; Pharoah, Paul D P; Dunning, Alison M; Chenevix-Trench, Georgia; Hall, Per; Bandera, Elisa; Amos, Chris; Ambrosone, Christine; Easton, Douglas F; Cole, Michael D

    2016-09-01

    Breast cancer is the most diagnosed malignancy and the second leading cause of cancer mortality in females. Previous association studies have identified variants on 2q35 associated with the risk of breast cancer. To identify functional susceptibility loci for breast cancer, we interrogated the 2q35 gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10(-19)) and identify 13 additional linked variants (r(2 )>( )0.8) in the 20Kb linkage block containing the enCNV (P = 3.2 × 10(-15) - 5.6 × 10(-17)). These associations were independent of previously reported 2q35 variants, rs13387042/rs4442975 and rs16857609, and were stronger for ER-positive than ER-negative disease. Together, these results suggest that 2q35 breast cancer risk loci may be mediating their effect through IGFBP5.

  11. 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.

  12. 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.

  13. Evaluation of Interspinous Spacer Outcomes in Degenerative Lumbar Canal Stenosis: Clinical Study.

    Science.gov (United States)

    Abdel Ghany, Walid; Amer, Aboubakr; Saeed, Khaled; Emara, Essam; Hamad, Ahmad; Nosseir, Mohamed; Dawood, Osama; Nada, Mohamed A

    2016-11-01

    Lumbar spinal stenosis is a common diagnosis in elderly individuals, and the rates of surgery have risen all over the world. The optimal approach to provide satisfactory decompression and minimize complications for lumbar spinal stenosis remains controversial. The purpose of this study was to evaluate the surgical outcome of interspinous spacers versus decompressive laminectomy in the management of degenerative lumbar canal stenosis. Our prospective, comparative study included 2 groups of patients who were operated on in Ain Shams University Hospitals between January 2010 and December 2014. In the first group, 28 patients underwent decompression and additional implantation of an interspinous spacer (ISP). In the second group, 25 patients underwent decompressive laminectomy (DL). Our statistical results revealed no significant difference in outcome between the 2 groups regarding visual analog scale score for leg pain and Oswestry Low Back Pain Disability Index. However, the improvement (visual analog scale score) for back pain was better in the DL group. Complication and reoperation rates were higher in the ISP group. Although decompression and additional implantation of an ISP are safe procedures, they do not show better improvement in clinical outcome as compared with decompressive laminectomy. Copyright © 2016 Elsevier Inc. All rights reserved.

  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.

  15. 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.

  16. Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

    Directory of Open Access Journals (Sweden)

    Yuchun Ren

    2015-06-01

    Full Text Available A series of azobenzene–cholesterol organogel compounds (M0–M12 with different spacers were designed and synthesized. The molecular structures were confirmed by 1H NMR and 13C NMR spectroscopy. The rapid and reversible photoresponsive properties of the compounds were investigated by UV–vis spectroscopy. Their thermal phase behaviors were studied by DSC. The length of the spacer plays a crucial role in the gelation. Compound M6 is the only one that can gelate in ethanol, isopropanol and 1-butanol and the reversible gel–sol transitions are also investigated. To obtain visual insight into the microstructure of the gels, the typical structures of the xerogels were studied by SEM. Morphologies of the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure.

  17. Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths

    Science.gov (United States)

    Ren, Yuchun; Zhang, Xiuqing

    2015-01-01

    Summary A series of azobenzene–cholesterol organogel compounds (M 0 –M 12) with different spacers were designed and synthesized. The molecular structures were confirmed by 1H NMR and 13C NMR spectroscopy. The rapid and reversible photoresponsive properties of the compounds were investigated by UV–vis spectroscopy. Their thermal phase behaviors were studied by DSC. The length of the spacer plays a crucial role in the gelation. Compound M 6 is the only one that can gelate in ethanol, isopropanol and 1-butanol and the reversible gel–sol transitions are also investigated. To obtain visual insight into the microstructure of the gels, the typical structures of the xerogels were studied by SEM. Morphologies of the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure. PMID:26199664

  18. 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.

  19. Unexpected Temperature Behavior of Polyethylene Glycol Spacers in Copolymer Dendrimers in Chloroform

    Science.gov (United States)

    Markelov, Denis A.; Matveev, Vladimir V.; Ingman, Petri; Nikolaeva, Marianna N.; Penkova, Anastasia V.; Lahderanta, Erkki; Boiko, Natalia I.; Chizhik, Vladimir I.

    2016-04-01

    We have studied copolymer dendrimer structure: carbosilane dendrimers with terminal phenylbenzoate mesogenic groups attached by poly(ethylene) glycol (PEG) spacers. In this system PEG spacers are additional tuning to usual copolymer structure: dendrimer with terminal mesogenic groups. The dendrimer macromolecules were investigated in a dilute chloroform solution by 1H NMR methods (spectra and relaxations). It was found that the PEG layer in G = 5 generations dendrimer is “frozen” at high temperatures (above 260 K), but it unexpectedly becomes “unfrozen” at temperatures below 250 K (i.e., melting when cooling). The transition between these two states occurs within a small temperature range (~10 K). Such a behavior is not observed for smaller dendrimer generations (G = 1 and 3). This effect is likely related to the low critical solution temperature (LCST) of PEG and is caused by dendrimer conformations, in which the PEG group concentration in the layer increases with growing G. We suppose that the unusual behavior of PEG fragments in dendrimers will be interesting for practical applications such as nanocontainers or nanoreactors.

  20. 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.

  1. 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.

  2. INTERSPINOUS SPACER IN PERSISTENT DISCOGENIC PAIN: PERCUTANEOUS APPROACH OR OPEN TECHNIQUE

    Directory of Open Access Journals (Sweden)

    José Antonio Cruz Ricardez

    Full Text Available ABSTRACT Objective: To compare the postoperative clinical course of placement of interspinous spacer with open technique (ISO with percutaneous interspinous spacer (PIS. Methods: Quasi-experimental, longitudinal study of 42 patients with discogenic pain uncontrolled with analgesics, aged 35-55 years old, 21 women, and 21 men. Clinical history, location of pain, VAS scale before and after surgery, Oswestry Disability Index and Macnab modified scale at 6 months were used. Results: When performing quantitative analysis statistical significance (p = 0.0478, 0.0466, 0.0399 was demonstrated with Student's t test between the results according to VAS scale; in the qualitative analysis with the Oswestry index and Macnab modified scale it was demonstrated the hypothesis that the results is dependent of the surgical technique. Conclusions: According to the results, we can conclude that there is a statistically significant difference depending on the surgical technique used with respect to the rate of disability and functionality in daily life as well as in the improvement of pain symptoms.

  3. 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.

  4. Invariance of the magnetic behavior and AMI in ferromagnetic biphase films with distinct non-magnetic metallic spacers

    Energy Technology Data Exchange (ETDEWEB)

    Silva, E.F. [Departamento de Física, Universidade Federal do Rio Grande do Norte, 59078-900 Natal, RN (Brazil); Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE (Brazil); Gamino, M. [Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE (Brazil); Instituto de Física, Universidade Federal do Rio Grande de Sul, 91501-970 Porto Alegre, RS (Brazil); Andrade, A.M.H. de [Instituto de Física, Universidade Federal do Rio Grande de Sul, 91501-970 Porto Alegre, RS (Brazil); Vázquez, M. [Instituto de Ciencia de Materiales de Madrid, CSIC, 28049 Madrid (Spain); Correa, M.A. [Departamento de Física, Universidade Federal do Rio Grande do Norte, 59078-900 Natal, RN (Brazil); Bohn, F., E-mail: felipebohn@fisica.ufrn.br [Departamento de Física, Universidade Federal do Rio Grande do Norte, 59078-900 Natal, RN (Brazil)

    2017-02-01

    We investigate the quasi-static magnetic, magnetotransport, and dynamic magnetic properties in ferromagnetic biphase films with distinct non-magnetic metallic spacer layers. We observe that the nature of the non-magnetic metallic spacer material does not have significant influence on the overall biphase magnetic behavior, and, consequently, on the magnetotransport and dynamic magnetic responses. We focus on the magnetoimpedance effect and verify that the films present asymmetric magnetoimpedance effect. Moreover, we explore the possibility of tuning the linear region of the magnetoimpedance curves around zero magnetic field by varying the probe current frequency in order to achieve higher sensitivity values. The invariance of the magnetic behavior and the asymmetric magnetoimpedance effect in ferromagnetic biphase films with distinct non-magnetic metallic spacers place them as promising candidates for probe element and open possibilities to the development of lower-cost high sensitivity linear magnetic field sensor devices.

  5. Invariance of the magnetic behavior and AMI in ferromagnetic biphase films with distinct non-magnetic metallic spacers

    Science.gov (United States)

    Silva, E. F.; Gamino, M.; Andrade, A. M. H. de; Vázquez, M.; Correa, M. A.; Bohn, F.

    2017-02-01

    We investigate the quasi-static magnetic, magnetotransport, and dynamic magnetic properties in ferromagnetic biphase films with distinct non-magnetic metallic spacer layers. We observe that the nature of the non-magnetic metallic spacer material does not have significant influence on the overall biphase magnetic behavior, and, consequently, on the magnetotransport and dynamic magnetic responses. We focus on the magnetoimpedance effect and verify that the films present asymmetric magnetoimpedance effect. Moreover, we explore the possibility of tuning the linear region of the magnetoimpedance curves around zero magnetic field by varying the probe current frequency in order to achieve higher sensitivity values. The invariance of the magnetic behavior and the asymmetric magnetoimpedance effect in ferromagnetic biphase films with distinct non-magnetic metallic spacers place them as promising candidates for probe element and open possibilities to the development of lower-cost high sensitivity linear magnetic field sensor devices.

  6. Parylene C-on-photoresist (POP): a low temperature spacer scheme for polymer/metal nanowire fabrication

    Science.gov (United States)

    Li, Yuanhui; Xie, Quan; Wang, Wei; Zheng, Mingxin; Zhang, Hao; Lei, Yinhua; Zhang, Haixia Alice; Wu, Wengang; Li, Zhihong

    2011-06-01

    This work introduced a novel spacer scheme for polymer/metal nanowire preparation by combining Parylene C and photoresist (Parylene C on photoresist, POP, process), both of which possess a low temperature fabrication essence. Adhesion between the Parylene C and the substrate with photoresist onside was improved by introducing a modified silanization pretreatment. Parylene C filled in an undercut generated by regular lithography on a dual-layered photoresist was left as nanometer-sized residues after an isotropic oxygen plasma etching. Parylene C nanowires with the minimal width down to 200 nm were successfully obtained by this POP-based spacer technique, and were then utilized as the etching mask for ion milling of the metal films beneath to realize corresponding chromium/gold nanowires. The present POP scheme will expand the application of the spacer technique in polymer/metal nanowire fabrication for integrated micro/nanoelectromechanical systems.

  7. Multi-Scaled Modeling the Mechanical Properties of Tubular Composites Reinforced with Innovated 3D Weft Knitted Spacer Fabrics

    Science.gov (United States)

    Omrani, Elahe; Hasani, Hossein; Dibajian, Sayed Houssain

    2017-06-01

    Textile composites of 3D integrated spacer configurations have been recently focused by several researchers all over the world. In the present study, newly-designed tubular composites reinforced with 3D spacer weft knitted fabrics were considered and the effects of their structural parameters on some applicable mechanical properties were investigated. For this purpose, two different samples of 3D spacer weft knitted textile types in tubular form were produced on an electronic flat knitting machine, using glass/nylon hybrid yarns. Thermoset tubular-shaped composite parts were manufactured via vacuum infusion molding process using epoxy resin. The mechanical properties of the produced knitted composites in term of external static and internal hydrostatic pressures were evaluated. Resistance of the produced composites against the external static and internal hydrostatic pressures was numerically simulated using multi-scale modeling method. The finding revealed that there is acceptable correlation between experimental and theoretical results.

  8. Survey of Bartonella spp. in U.S. bed bugs detects Burkholderia multivorans but not Bartonella.

    Science.gov (United States)

    Saenz, Virna L; Maggi, Ricardo G; Breitschwerdt, Edward B; Kim, Jung; Vargo, Edward L; Schal, Coby

    2013-01-01

    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.

  9. Bartonella species in invasive rats and indigenous rodents from Uganda.

    Science.gov (United States)

    Billeter, Sarah A; Borchert, Jeff N; Atiku, Linda A; Mpanga, Joseph T; Gage, Kenneth L; Kosoy, Michael Y

    2014-03-01

    The presence of bartonellae in invasive rats (Rattus rattus) and indigenous rodents (Arvicanthis niloticus and Cricetomys gambianus) from two districts in Uganda, Arua and Zombo, was examined by PCR detection and culture. Blood from a total of 228 R. rattus, 31 A. niloticus, and 5 C. gambianus was screened using genus-specific primers targeting the 16S-23S intergenic spacer region. Furthermore, rodent blood was plated on brain heart infusion blood agar, and isolates were verified as Bartonella species using citrate synthase gene- (gltA) specific primers. One hundred and four fleas recovered from R. rattus were also tested for the presence of Bartonella species using the same gltA primer set. An overall prevalence of 1.3% (three of 228) was obtained in R. rattus, whereas 61.3% of 31 A. niloticus and 60% of five C. gambianus were positive for the presence of Bartonella species. Genotypes related to Bartonella elizabethae, a known zoonotic pathogen, were detected in three R. rattus and one C. gambianus. Bartonella strains, similar to bacteria detected in indigenous rodents from other African countries, were isolated from the blood of A. niloticus. Bartonellae, similar to bacteria initially cultured from Ornithodorus sonrai (soft tick) from Senegal, were found in two C. gambianus. Interestingly, bartonellae detected in fleas from invasive rats were similar to bacteria identified in indigenous rodents and not their rat hosts, with an overall prevalence of 6.7%. These results suggest that if fleas are competent vectors of these bartonellae, humans residing in these two districts of Uganda are potentially at greater risk for exposure to Bartonella species from native rodents than from invasive rats. The low prevalence of bartonellae in R. rattus was quite surprising, in contrast, to the detection of these organisms in a large percentage of Rattus species from other geographical areas. A possible reason for this disparity is discussed.

  10. 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

  11. Detection of Bartonella spp. in wild rodents in Israel using HRM real-time PCR.

    Science.gov (United States)

    Morick, Danny; Baneth, Gad; Avidor, Boaz; Kosoy, Michael Y; Mumcuoglu, Kosta Y; Mintz, Dvir; Eyal, Osnat; Goethe, Ralph; Mietze, Andreas; Shpigel, Nahum; Harrus, Shimon

    2009-11-18

    The prevalence of Bartonella spp. in wild rodents was studied in 19 geographical locations in Israel. One hundred and twelve rodents belonging to five species (Mus musculus, Rattus rattus, Microtus socialis, Acomys cahirinus and Apodemus sylvaticus) were included in the survey. In addition, 156 ectoparasites were collected from the rodents. Spleen sample from each rodent and the ectoparasites were examined for the presence of Bartonella DNA using high resolution melt (HRM) real-time PCR. The method was designed for the simultaneous detection and differentiation of eight Bartonella spp. according to the nucleotide variation in each of two gene fragments (rpoB and gltA) and the 16S-23S intergenic spacer (ITS) locus, using the same PCR protocol which allowed the simultaneous amplification of the three different loci. Bartonella DNA was detected in spleen samples of 19 out of 79 (24%) black rats (R. rattus) and in 1 of 4 (25%) Cairo spiny mice (A. cahirinus). In addition, 15 of 34 (44%) flea pools harbored Bartonella DNA. Only rat flea (Xenopsyla cheopis) pools collected from black rats (R. rattus) were positive for Bartonella DNA. The Bartonella sp. detected in spleen samples from black rats (R. rattus) was closely related to both B. tribocorum and B. elizabethae. The species detected in the Cairo spiny mouse (A. cahirinus) spleen sample was closely related to the zoonotic pathogen, B. elizabethae. These results indicate that Bartonella species are highly prevalent in suburban rodent populations and their ectoparasites in Israel. Further investigation of the prevalence and zoonotic potential of the Bartonella species detected in the black rats and the Cairo spiny mouse is warranted.

  12. Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India.

    Science.gov (United States)

    Jeyaram, K; Romi, W; Singh, Th Anand; Devi, A Ranjita; Devi, S Soni

    2010-09-30

    Soidon is a non-salted acidic fermented food prepared from the succulent bamboo shoot tip of Schizostachyum capitatum Munro by using a traditional liquid starter called "soidon mahi" in Manipur state of India. In this study, 163 bacterial isolates associated with this starter samples were identified and their population distribution was investigated by amplified ribosomal DNA restriction analysis (ARDRA), 16S rDNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. This acidic starter (pH 4.5+/-0.15) was dominated by a characteristic association of Bacillus and lactic acid bacteria (LAB) together. The population distribution of dominant species were Bacillus subtilis 29.3%, Bacillus cereus 35.7%, Bacillus pumilus 2.6%, Lactobacillus brevis 9.6%, Lactobacillus plantarum 5.1%, Carnobacterium sp. 11.9%, Enterococcus faecium 1.2% and Pseudomonas fluorescens 4.6%. Alarming population load (10(6)-10(7)cfu/ml) of B. cereus in 87% of starter samples studied should raise concern regarding biosafety of soidon consumption. PCR amplification of 16S-23S rDNA intergenic transcribed spacer (ITS) region and ITS-RFLP profiles revealed a high diversity with eight subgroups in B. subtilis, five subgroups in B. cereus and three subgroups in L. brevis isolates. The most abundant B. subtilis subgroup IB.1 distributed in most of the samples showed very less clonal variability during RAPD analysis. The molecular methods used in this study identified the dominant strains of Bacillus and LAB distributed in most of the starter samples. These dominant strains of B. subtilis, L. brevis and L. plantarum would allow for developing a defined starter culture for the production of quality soidon.

  13. 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.

  14. 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.

  15. 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.

  16. Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.

    Science.gov (United States)

    Ramírez-Bahena, Martha Helena; Peix, Alvaro; Rivas, Raúl; Camacho, María; Rodríguez-Navarro, Dulce N; Mateos, Pedro F; Martínez-Molina, Eustoquio; Willems, Anne; Velázquez, Encarna

    2009-08-01

    Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1% similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S-23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA-DNA hybridization analysis which revealed 21% genetic relatedness between strains PAC48T and PAC68T and 46% and 25%, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.

  17. Isolation, identification and characterisation of three novel probiotic strains (Lactobacillus paracasei CNCM I-4034, Bifidobacterium breve CNCM I-4035 and Lactobacillus rhamnosus CNCM I-4036) from the faeces of exclusively breast-fed infants.

    Science.gov (United States)

    Muñoz-Quezada, Sergio; Chenoll, Empar; Vieites, José María; Genovés, Salvador; Maldonado, José; Bermúdez-Brito, Miriam; Gomez-Llorente, Carolina; Matencio, Esther; Bernal, María José; Romero, Fernando; Suárez, Antonio; Ramón, Daniel; Gil, Angel

    2013-01-01

    The aim of the present study was to isolate, identify and characterise novel strains of lactic acid bacteria and bifidobacteria with probiotic properties from the faeces of exclusively breast-fed infants. Of the 4680 isolated colonies, 758 exhibited resistance to low pH and tolerance to high concentrations of bile salts; of these, only forty-two exhibited a strong ability to adhere to enterocytes in vitro. The identities of the isolates were confirmed by 16S ribosomal RNA (rRNA) sequencing, which permitted the grouping of the forty-two bacteria into three different strains that showed more than 99 % sequence identity with Lactobacillus paracasei, Lactobacillus rhamnosus and Bifidobacterium breve, respectively. The strain identification was confirmed by sequencing the 16S-23S rRNA intergenic spacer regions. Strains were assayed for enzymatic activity and carbohydrate utilisation, and they were deposited in the Collection Nationale de Cultures de Microorganismes (CNCM) of the Institute Pasteur and named L. paracasei CNCM I-4034, B. breve CNCM I-4035 and L. rhamnosus CNCM I-4036. The strains were susceptible to antibiotics and did not produce undesirable metabolites, and their safety was assessed by acute ingestion in immunocompetent and immunosuppressed BALB/c mouse models. The three novel strains inhibited in vitro the meningitis aetiological agent Listeria monocytogenes and human rotavirus infections. B. breve CNCM I-4035 led to a higher IgA concentration in faeces and plasma of mice. Overall, these results suggest that L. paracasei CNCM I-4034, B. breve CNCM I-4035 and L. rhamnosus CNCM I-4036 should be considered as probiotic strains, and their human health benefits should be further evaluated.

  18. Genetic transformation of novel isolates of chicken Lactobacillus bearing probiotic features for expression of heterologous proteins: a tool to develop live oral vaccines

    Science.gov (United States)

    Mota, Rodrigo M; Moreira, João Luiz S; Souza, Marcelo R; Fátima Horta, M; Teixeira, Santuza MR; Neumann, Elisabeth; Nicoli, Jacques R; Nunes, Álvaro C

    2006-01-01

    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 expressing pathogen antigens can

  19. Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes

    Science.gov (United States)

    de las Rivas, Blanca; Marcobal, Ángela; Muñoz, Rosario

    2004-01-01

    Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria. PMID:15574919

  20. 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.

  1. 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.

  2. Diversity and biogeography of rhizobia isolated from root nodules of Glycine max grown in Hebei Province, China.

    Science.gov (United States)

    Li, Qin Qin; Wang, En Tao; Zhang, Yun Zeng; Zhang, Yan Ming; Tian, Chang Fu; Sui, Xin Hua; Chen, Wen Feng; Chen, Wen Xin

    2011-05-01

    A total of 215 rhizobial strains were isolated and analyzed with 16S rRNA gene, 16S-23S intergenic spacer, housekeeping genes atpD, recA, and glnII, and symbiotic genes nifH and nodC to understand the genetic diversity of soybean rhizobia in Hebei province, China. All the strains except one were symbiotic bacteria classified into nine genospecies in the genera of Bradyrhizobium and Sinorhizobium. Surveys on the distribution of these rhizobia in different regions showed that Bradyrhizobium japonicum and Bradyrhizobium elkanii strains were found only in neutral to slightly alkaline soils whereas Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense-related strains and strains of five Sinorhizobium genospecies were found in alkaline-saline soils. Correspondence and canonical correspondence analyses on the relationship of rhizobial distribution and their soil characteristics reveal that high soil pH, electrical conductivity, and potassium content favor distribution of the B. yuanmingense and the five Sinorhizobium species but inhibit B. japonicum and B. elkanii. High contents of available phosphorus and organic matters benefit Sinorhizobium fredii and B. liaoningense-related strains and inhibit the others groups mentioned above. The symbiotic gene (nifH and nodC) lineages among B. elkanii, B. japonicum, B. yuanmingense, and Sinorhizobium spp. were observed in the strains, signifying that vertical gene transfer was the main mechanism to maintain these genes in the soybean rhizobia. However, lateral transfer of symbiotic genes commonly in Sinorhizobium spp. and rarely in Bradyrhizobium spp. was also detected. These results showed the genetic diversity, the biogeography, and the soil determinant factors of soybean rhizobia in Hebei province of China.

  3. Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge.

    Science.gov (United States)

    Zhang, Guo Xia; Ren, Sui Zhou; Xu, Mei Ying; Zeng, Guo Qu; Luo, Hui Dong; Chen, Jin Lin; Tan, Zhi Yuan; Sun, Guo Ping

    2011-04-01

    Three aniline-degrading bacteria, strains DN316(T), DN316-1 and DN365, were isolated from activated sludge. According to 16S rRNA gene sequence-based phylogenetic analysis, the isolates belonged to the genus Rhizobium, with Rhizobium ( = Agrobacterium) radiobacter LMG 140(T) as the closest relative, with 96.5 % sequence similarity. Phylogenetic analysis of the representative strain DN316(T) using sequences of the glnA, thrC and recA genes and the 16S-23S intergenic spacer region confirmed the phylogenetic arrangement obtained from analysis of the 16S rRNA gene. DNA-DNA relatedness between DN316(T) and R. radiobacter LMG 140(T) was 43.7 %, clearly indicating that the representative strain DN316(T) represents a novel species. Phenotypic and biochemical characterization of the isolates and insertion sequence-PCR fingerprinting patterns showed several distinctive features that differentiated them from closely related species. The major components of the cellular fatty acids were C(18 : 1)ω7c (57.10 %), C(16 : 0) (11.31 %) and C(19 : 0) cyclo ω8c (10.13 %). Based on our taxonomic analysis, the three isolates from activated sludge represent a novel species of the genus Rhizobium, for which the name Rhizobium borbori sp. nov. is proposed. The type strain is DN316(T) ( = CICC 10378(T)  = LMG 23925(T)).

  4. Distinguishing bacterial pathogens of potato using a genome-wide microarray approach.

    Science.gov (United States)

    Aittamaa, M; Somervuo, P; Pirhonen, M; Mattinen, L; Nissinen, R; Auvinen, P; Valkonen, J P T

    2008-09-01

    A set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. Gene-specific probes could be designed for all genes of Pectobacterium atrosepticum, c. 50% of the genes of Streptomyces scabies and c. 30% of the genes of Clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. For Streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing important virulence genes. In addition, probes were designed for the virulence-associated nip (necrosis-inducing protein) genes of P. atrosepticum, P. carotovorum and Dickeya dadantii and for the intergenic spacer (IGS) sequences of the 16S-23S rRNA gene region. Ralstonia solanacearum was not included in the study, because it is a quarantine organism and is not presently found in Finland, but a few probes were also designed for this species. The probes contained on average 40 target-specific nucleotides and were synthesized on the array in situ, organized as eight sub-arrays with an identical set of probes which could be used for hybridization with different samples. All bacteria were readily distinguished using a single channel system for signal detection. Nearly all of the c. 1000 probes designed for C. michiganensis ssp. sepedonicus, c. 50% and 40% of the c. 4000 probes designed for the genes of S. scabies and P. atrosepticum, respectively, and over 100 probes for S. turgidiscabies showed significant signals only with the respective species. P. atrosepticum, P. carotovorum and Dickeya strains were all detected with 110 common probes. By contrast, the strains of these species were found to differ in their signal profiles. Probes targeting the IGS region and nip genes could be used to place strains of Dickeya to two groups, which correlated with differences in virulence. Taken together, the approach of using a custom-designed, genome-wide microarray provided a robust means