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Sample records for t-dna insertion line

  1. Brachypodium distachyon T-DNA insertion lines: a model pathosystem to study nonhost resistance to wheat stripe rust.

    PubMed

    An, Tianyue; Cai, Yanli; Zhao, Suzhen; Zhou, Jianghong; Song, Bo; Bux, Hadi; Qi, Xiaoquan

    2016-01-01

    Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases and can cause severe yield losses in many regions of the world. Because of the large size and complexity of wheat genome, it is difficult to study the molecular mechanism of interaction between wheat and PST. Brachypodium distachyon has become a model system for temperate grasses' functional genomics research. The phenotypic evaluation showed that the response of Brachypodium distachyon to PST was nonhost resistance (NHR), which allowed us to present this plant-pathogen system as a model to explore the immune response and the molecular mechanism underlying wheat and PST. Here we reported the generation of about 7,000 T-DNA insertion lines based on a highly efficient Agrobacterium-mediated transformation system. Hundreds of mutants either more susceptible or more resistant to PST than that of the wild type Bd21 were obtained. The three putative target genes, Bradi5g17540, BdMYB102 and Bradi5g11590, of three T-DNA insertion mutants could be involved in NHR of Brachypodium distachyon to wheat stripe rust. The systemic pathologic study of this T-DNA mutants would broaden our knowledge of NHR, and assist in breeding wheat cultivars with durable resistance. PMID:27138687

  2. Brachypodium distachyon T-DNA insertion lines: a model pathosystem to study nonhost resistance to wheat stripe rust

    PubMed Central

    An, Tianyue; Cai, Yanli; Zhao, Suzhen; Zhou, Jianghong; Song, Bo; Bux, Hadi; Qi, Xiaoquan

    2016-01-01

    Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases and can cause severe yield losses in many regions of the world. Because of the large size and complexity of wheat genome, it is difficult to study the molecular mechanism of interaction between wheat and PST. Brachypodium distachyon has become a model system for temperate grasses’ functional genomics research. The phenotypic evaluation showed that the response of Brachypodium distachyon to PST was nonhost resistance (NHR), which allowed us to present this plant-pathogen system as a model to explore the immune response and the molecular mechanism underlying wheat and PST. Here we reported the generation of about 7,000 T-DNA insertion lines based on a highly efficient Agrobacterium-mediated transformation system. Hundreds of mutants either more susceptible or more resistant to PST than that of the wild type Bd21 were obtained. The three putative target genes, Bradi5g17540, BdMYB102 and Bradi5g11590, of three T-DNA insertion mutants could be involved in NHR of Brachypodium distachyon to wheat stripe rust. The systemic pathologic study of this T-DNA mutants would broaden our knowledge of NHR, and assist in breeding wheat cultivars with durable resistance. PMID:27138687

  3. Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection

    PubMed Central

    Gordon, Sean P.; Guttman, Mara E.; Thilmony, Roger; Lazo, Gerard R.; Gu, Yong Q.; Vogel, John P.

    2012-01-01

    The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest. PMID:23028431

  4. Spectrum of T-DNA integrations for insertional mutagenesis of Histoplasma capsulatum

    PubMed Central

    Kemski, Megan M.; Stevens, Bryan; Rappleye, Chad A.

    2012-01-01

    Agrobacterium-mediated transformation is being increasingly used for insertional mutagenesis of fungi. To better evaluate its effectiveness as a mutagen for the fungal pathogen Histoplasma capsulatum, we analyzed a collection of randomly selected T-DNA insertion mutants. Testing of different T-DNA element vectors engineered for transformation of fungi showed that pBHt2 provides the highest transformation efficiency and the lowest rate of vector backbone carryover. Sixty-eight individual T-DNA integrations were characterized by recovery of T-DNA ends and flanking genomic sequences. The right border end of the T-DNA is largely preserved whereas the left border end is frequently truncated. Analysis of T-DNA insertion sites confirms the lack of any integration hotspots in the Histoplasma genome. Relative to genes, T-DNA integrations show significant bias towards promoter regions at the expense of coding sequences. With consideration for potential promoter interruption and the demonstrated efficacy of intronic insertions, 61% of mapped T-DNA insertions should impair gene expression or function. Mapping of T-DNA flanking sequences demonstrates 67% of T-DNA integrations are integrations at a single chromosomal site and 31% of T-DNA integrations are associated with large-scale chromosomal rearrangements. This characterization of T-DNA insertions in mutants selected without regard to phenotype supports application of Agrobacterium-mediated transformation as an insertional mutagen for genome-based screens and functional discovery of genes in Histoplasma. PMID:23332832

  5. T-DNA insertion alters the terpenoid content composition and bioactivity of transgenic Artemisia annua.

    PubMed

    Karaket, Netiya; Wiyakrutta, Suthep; Lacaille-Dubois, Marie-Aleth; Supaibulwatana, Kanyaratt

    2014-03-01

    In this study, the interference of T-DNA insertion upon Agrobacterium-mediated transformation on the biochemical expression of the host genome is discussed. Plant extracts of transgenic Artemisia annua L. with or without an overexpressed famesyl pyrophosphate synthase gene have been investigated for their bioactivity and metabolic profile in comparison with wild type A. annua. The highest antimicrobial activity against Staphylococcus aureus, Bacillus subtilis and Candida albicans was observed in the T253 transgenic lines. Moreover, the crude extract from T253 showed higher antimalarial activity against the Plasmodium faciparum K1 strain than those of the others. The terpenoid constituents and antimicrobial properties of the plant samples were grouped by hierarchical clustering analysis. The clustering showed that squalene is a putative compound that might be involved in increasing the bioactivity of the transgenic line. In addition, T253 had a triterpene content that was about twice as great as that of the T253-2 line, which had a higher content of sesquiterpenes. However, both lines were transformed by the same FPS gene. These results suggested that the different bioactive properties observed in each transgenic line may be caused by variations in their terpenoid composition, which is affected by T-DNA insertion at different positions in the host plant. PMID:24689216

  6. Decreased Expression of a Gene Caused by a T-DNA Insertion in an Adjacent Gene in Arabidopsis

    PubMed Central

    Tamura, Kentaro; Kawabayashi, Takenori; Shikanai, Toshiharu; Hara-Nishimura, Ikuko

    2016-01-01

    ALADIN is a component of the nuclear pore complex in higher eukaryotes. An Arabidopsis knockout line that had a T-DNA insertion in the ALADIN gene was defective in plant growth and thylakoid development and had reduced photosynthetic activity resulting from lower chlorophyll accumulation. The mutation appeared to decrease the level of chloroplast RuBisCO subunits and PSBA and PGL35 proteins. Unexpectedly, the T-DNA insertion in the ALADIN gene decreased the expression of the neighboring gene PSRP5, which functions in translation in chloroplasts. The mutant phenotype was rescued by expressing PSRP5, but not by expressing ALADIN. The abnormal phenotypes were also detected in an artificial microRNA (amiRNA)-mediated PSRPS5 knockdown, but not in an amiRNA-mediated ALADIN knockdown line. Thus, users of T-DNA insertions should be aware that a T-DNA insertion in one gene can have effects on the expression of neighboring genes. PMID:26828726

  7. Generation and analysis of end sequence database for T-DNA tagging lines in rice.

    PubMed

    An, Suyoung; Park, Sunhee; Jeong, Dong-Hoon; Lee, Dong-Yeon; Kang, Hong-Gyu; Yu, Jung-Hwa; Hur, Junghe; Kim, Sung-Ryul; Kim, Young-Hea; Lee, Miok; Han, Soonki; Kim, Soo-Jin; Yang, Jungwon; Kim, Eunjoo; Wi, Soo Jin; Chung, Hoo Sun; Hong, Jong-Pil; Choe, Vitnary; Lee, Hak-Kyung; Choi, Jung-Hee; Nam, Jongmin; Kim, Seong-Ryong; Park, Phun-Bum; Park, Ky Young; Kim, Woo Taek; Choe, Sunghwa; Lee, Chin-Bum; An, Gynheung

    2003-12-01

    We analyzed 6749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3793 genomic sequences flanking the T-DNA. Among the insertions, 1846 T-DNAs were integrated into genic regions, and 1864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd. PMID:14630961

  8. The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism.

    PubMed

    Kleinboelting, Nils; Huep, Gunnar; Appelhagen, Ingo; Viehoever, Prisca; Li, Yong; Weisshaar, Bernd

    2015-11-01

    Transformation by Agrobacterium tumefaciens, an important tool in modern plant research, involves the integration of T-DNA initially present on a plasmid in agrobacteria into the genome of plant cells. The process of attachment of the agrobacteria to plant cells and the transport of T-DNA into the cell and further to the nucleus has been well described. However, the exact mechanism of integration into the host's DNA is still unclear, although several models have been proposed. During confirmation of T-DNA insertion alleles from the GABI-Kat collection of Arabidopsis thaliana mutants, we have generated about 34,000 sequences from the junctions between inserted T-DNA and adjacent genome regions. Here, we describe the evaluation of this dataset with regard to existing models for T-DNA integration. The results suggest that integration into the plant genome is mainly mediated by the endogenous plant DNA repair machinery. The observed integration events showed characteristics highly similar to those of repair sites of double-strand breaks with respect to microhomology and deletion sizes. In addition, we describe unexpected integration events, such as large deletions and inversions at the integration site that are relevant for correct interpretation of results from T-DNA insertion mutants in reverse genetics experiments. PMID:26343971

  9. Intronic T-DNA insertion renders Arabidopsis opr3 a conditional jasmonic acid-producing mutant.

    PubMed

    Chehab, E Wassim; Kim, Se; Savchenko, Tatyana; Kliebenstein, Daniel; Dehesh, Katayoon; Braam, Janet

    2011-06-01

    Jasmonic acid and its derived metabolites (JAs) orchestrate plant defense against insects and fungi. 12-Oxo-phytodienoic acid (OPDA), a JA precursor, has also been implicated in plant defense. We sought to define JAs and OPDA functions through comparative defense susceptibility characteristics of three Arabidopsis (Arabidopsis thaliana) genotypes: aos, lacking JAs and OPDA; opda reductase3 (opr3), deficient in JA production but can accumulate OPDA; and transgenics that overexpress OPR3. opr3, like aos, is susceptible to cabbage loopers (Trichoplusia ni) but, relative to aos, opr3 has enhanced resistance to a necrotrophic fungus. Gas chromatography-mass spectrometry reveals that opr3 produces OPDA but no detectable JAs following wounding and looper infestation; unexpectedly, substantial levels of JAs accumulate in opr3 upon fungal infection. Full-length OPR3 transcripts accumulate in fungal-infected opr3, potentially through splicing of the T-DNA containing intron. Fungal resistance correlates with levels of JAs not OPDA; therefore, opr3 resistance to some pests is likely due to JA accumulation, and signaling activities ascribed to OPDA should be reassessed because opr3 can produce JAs. Together these data (1) reinforce the primary role JAs play in plant defense against insects and necrotrophic fungi, (2) argue for a reassessment of signaling activities ascribed to OPDA, and (3) provide evidence that mutants with intron insertions can retain gene function. PMID:21487047

  10. Analysis of the early-flowering mechanisms and generation of T-DNA tagging lines in Kitaake, a model rice cultivar.

    PubMed

    Kim, Song Lim; Choi, Minkyung; Jung, Ki-Hong; An, Gynheung

    2013-11-01

    As an extremely early flowering cultivar, rice cultivar Kitaake is a suitable model system for molecular studies. Expression analyses revealed that transcript levels of the flowering repressor Ghd7 were decreased while those of its downstream genes, Ehd1, Hd3a, and RFT1, were increased. Sequencing the known flowering-regulator genes revealed mutations in Ghd7 and OsPRR37 that cause early translation termination and amino acid substitutions, respectively. Genetic analysis of F2 progeny from a cross between cv. Kitaake and cv. Dongjin indicated that those mutations additively contribute to the early-flowering phenotype in cv. Kitaake. Because the short life cycle facilitates genetics research, this study generated 10 000 T-DNA tagging lines and deduced 6758 flanking sequence tags (FSTs), in which 3122 were genic and 3636 were intergenic. Among the genic lines, 367 (11.8%) were inserted into new genes that were not previously tagged. Because the lines were generated by T-DNA that contained the promoterless GUS reporter gene, which had an intron with triple splicing donors/acceptors in the right border region, a high efficiency of GUS expression was shown in various organs. Sequencing of the GUS-positive lines demonstrated that the third splicing donor and the first splicing acceptor of the vector were extensively used. The FST data have now been released into the public domain for seed distribution and facilitation of rice research. PMID:23966593

  11. Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library

    PubMed Central

    Larmande, Pierre; Gay, Céline; Lorieux, Mathias; Périn, Christophe; Bouniol, Matthieu; Droc, Gaëtan; Sallaud, Christophe; Perez, Pascual; Barnola, Isabelle; Biderre-Petit, Corinne; Martin, Jérôme; Morel, Jean Benoît; Johnson, Alexander A. T.; Bourgis, Fabienne; Ghesquière, Alain; Ruiz, Manuel; Courtois, Brigitte; Guiderdoni, Emmanuel

    2008-01-01

    To organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB. PMID:17947330

  12. Reduced tillering in Basmati rice T-DNA insertional mutant OsTEF1 associates with differential expression of stress related genes and transcription factors.

    PubMed

    Paul, Priyanka; Awasthi, Anjali; Rai, Amit Kumar; Gupta, Santosh Kumar; Prasad, R; Sharma, T R; Dhaliwal, H S

    2012-06-01

    A T-DNA insertional mutant OsTEF1 of rice gives 60-80% reduced tillering, retarded growth of seminal roots, and sensitivity to salt stress compared to wild type Basmati 370. The insertion occurred in a gene encoding a transcription elongation factor homologous to yeast elf1, on chromosome 2 of rice. Detailed transcriptomic profiling of OsTEF1 revealed that mutation in the transcription elongation factor differentially regulates the expression of more than 100 genes with known function and finely regulates tillering process in rice by inducing the expression of cytochrome P450. Along with different transcription factors, several stress associated genes were also affected due to a single insertion. In silico analysis of the TEF1 protein showed high conservation among different organisms. This transcription elongation factor predicted to interact with other proteins that directly or indirectly positively regulate tillering in rice. PMID:22367482

  13. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source.

    PubMed

    Wei, Fu-Jin; Tsai, Yuan-Ching; Hsu, Yu-Ming; Chen, Yu-An; Huang, Ching-Ting; Wu, Hshin-Ping; Huang, Lin-Tzu; Lai, Ming-Hsin; Kuang, Lin-Yun; Lo, Shuen-Fang; Yu, Su-May; Lin, Yann-Rong; Hsing, Yue-Ie Caroline

    2016-01-01

    Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations. PMID:27186981

  14. Gene expression profile of zeitlupe/lov kelch protein1 T-DNA insertion mutants in Arabidopsis thaliana: Downregulation of auxin-inducible genes in hypocotyls

    PubMed Central

    Saitoh, Aya; Takase, Tomoyuki; Kitaki, Hiroyuki; Miyazaki, Yuji; Kiyosue, Tomohiro

    2015-01-01

    Elongation of hypocotyl cells has been studied as a model for elucidating the contribution of cellular expansion to plant organ growth. ZEITLUPE (ZTL) or LOV KELCH PROTEIN1 (LKP1) is a positive regulator of warmth-induced hypocotyl elongation under white light in Arabidopsis, although the molecular mechanisms by which it promotes hypocotyl cell elongation remain unknown. Microarray analysis showed that 134 genes were upregulated and 204 genes including 15 auxin-inducible genes were downregulated in the seedlings of 2 ztl T-DNA insertion mutants grown under warm conditions with continuous white light. Application of a polar auxin transport inhibitor, an auxin antagonist or an auxin biosynthesis inhibitor inhibited hypocotyl elongation of control seedlings to the level observed with the ztl mutant. Our data suggest the involvement of auxin and auxin-inducible genes in ZTL-mediated hypocotyl elongation. PMID:26237185

  15. High-throughput analysis of T-DNA location and structure using sequence capture

    SciTech Connect

    Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; Comai, Luca

    2015-10-07

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  16. High-throughput analysis of T-DNA location and structure using sequence capture

    DOE PAGESBeta

    Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; Comai, Luca

    2015-10-07

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously,more » using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. As a result, our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.« less

  17. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture

    PubMed Central

    Inagaki, Soichi; Henry, Isabelle M.; Lieberman, Meric C.; Comai, Luca

    2015-01-01

    Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines. PMID:26445462

  18. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source

    PubMed Central

    Wei, Fu-Jin; Tsai, Yuan-Ching; Hsu, Yu-Ming; Chen, Yu-An; Huang, Ching-Ting; Wu, Hshin-Ping; Huang, Lin-Tzu; Lai, Ming-Hsin; Kuang, Lin-Yun; Lo, Shuen-Fang; Yu, Su-May; Lin, Yann-Rong; Hsing, Yue-Ie Caroline

    2016-01-01

    Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources–the relationship between genotype and phenotype–is very low. We used whole-genome sequencing to analyze a T-DNA–tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes–wild type, large grains, and tillering dwarf–in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations. PMID:27186981

  19. Intronic T-DNA Insertion Renders Arabidopsis opr3 a Conditional Jasmonic Acid-Producing Mutant1[C][W][OA

    PubMed Central

    Chehab, E. Wassim; Kim, Se; Savchenko, Tatyana; Kliebenstein, Daniel; Dehesh, Katayoon; Braam, Janet

    2011-01-01

    Jasmonic acid and its derived metabolites (JAs) orchestrate plant defense against insects and fungi. 12-Oxo-phytodienoic acid (OPDA), a JA precursor, has also been implicated in plant defense. We sought to define JAs and OPDA functions through comparative defense susceptibility characteristics of three Arabidopsis (Arabidopsis thaliana) genotypes: aos, lacking JAs and OPDA; opda reductase3 (opr3), deficient in JA production but can accumulate OPDA; and transgenics that overexpress OPR3. opr3, like aos, is susceptible to cabbage loopers (Trichoplusia ni) but, relative to aos, opr3 has enhanced resistance to a necrotrophic fungus. Gas chromatography-mass spectrometry reveals that opr3 produces OPDA but no detectable JAs following wounding and looper infestation; unexpectedly, substantial levels of JAs accumulate in opr3 upon fungal infection. Full-length OPR3 transcripts accumulate in fungal-infected opr3, potentially through splicing of the T-DNA containing intron. Fungal resistance correlates with levels of JAs not OPDA; therefore, opr3 resistance to some pests is likely due to JA accumulation, and signaling activities ascribed to OPDA should be reassessed because opr3 can produce JAs. Together these data (1) reinforce the primary role JAs play in plant defense against insects and necrotrophic fungi, (2) argue for a reassessment of signaling activities ascribed to OPDA, and (3) provide evidence that mutants with intron insertions can retain gene function. PMID:21487047

  20. Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis.

    PubMed Central

    Nacry, P; Camilleri, C; Courtial, B; Caboche, M; Bouchez, D

    1998-01-01

    We show that major chromosomal rearrangements can occur upon T-DNA transformation of Arabidopsis thaliana. In the ACL4 line, two T-DNA insertion loci were found; one is a tandem T-DNA insert in a head-to-head orientation, and the other is a truncated insert with only the left part of the T-region. The four flanking DNA regions were isolated and located on the Arabidopsis chromosomes; for both inserts, one side of the T-DNA maps to chromosome 2, whereas the other side maps to chromosome 3. Both chromosome 3 flanking regions map to the same location, despite a 1.4-kb deletion at this point, whereas chromosome 2 flanking regions are located 40 cM apart on the bottom arm of chromosome 2. These results strongly suggest a reciprocal translocation between chromosomes 2 and 3, with the breakpoints located at the T-DNA insertion sites. The interchanged fragments roughly correspond to the 20-cM distal ends of both chromosomes. Moreover, a large inversion, spanning 40 cM on the genetic map, occurs on the bottom arm of chromosome 2. This was confirmed by genetic analyses that demonstrated a strong reduction of recombination in the inverted region. Models for T-DNA integration and the consequences for T-DNA tagging are discussed in light of these results. PMID:9611180

  1. An Intron Sense Suppression Construct Targeting Soybean FAD2-1 Requires a Double-Stranded RNA-Producing Inverted Repeat T-DNA Insert[OA

    PubMed Central

    Mroczka, Andrew; Roberts, Peter D.; Fillatti, JoAnne J.; Wiggins, B. Elizabeth; Ulmasov, Tim; Voelker, Toni

    2010-01-01

    We demonstrate that the transformation of soybean (Glycine max) with sense suppression constructs using intron sequences from the fatty acid oleyl Δ12 desaturase gene FAD2-1A leads to efficient and specific reduction of FAD2-1 transcripts in developing seeds, increased oleic acid, and decreased polyunsaturated fatty acids. The related FAD2-2 transcripts are only marginally affected. Despite screening a large number of independent transformants, no single-copy efficacious transformants could be found. Invariably, all the least complex transgenic loci have two T-DNA copies in an inverted repeat configuration, centered at the right borders. We show that this T-DNA configuration produces an inverted repeat transcript and that small interfering RNAs accumulate against the target sequence. PMID:20424004

  2. Complementation of the embryo-lethal T-DNA insertion mutant of AUXIN-BINDING-PROTEIN 1 (ABP1) with abp1 point mutated versions reveals crosstalk of ABP1 and phytochromes.

    PubMed

    Effendi, Yunus; Ferro, Noel; Labusch, Corinna; Geisler, Markus; Scherer, Günther F E

    2015-01-01

    The function of the extracytoplasmic AUXIN-BINDING-PROTEIN1 (ABP1) is largely enigmatic. We complemented a homozygous T-DNA insertion null mutant of ABP1 in Arabidopsis thaliana Wassilewskia with three mutated and one wild-type (wt) ABP1 cDNA, all tagged C-terminally with a strepII-FLAG tag upstream the KDEL signal. Based on in silico modelling, the abp1 mutants were predicted to have altered geometries of the auxin binding pocket and calculated auxin binding energies lower than the wt. Phenotypes linked to auxin transport were compromised in these three complemented abp1 mutants. Red light effects, such as elongation of hypocotyls in constant red (R) and far-red (FR) light, in white light supplemented by FR light simulating shade, and inhibition of gravitropism by R or FR, were all compromised in the complemented lines. Using auxin- or light-induced expression of marker genes, we showed that auxin-induced expression was delayed already after 10 min, and light-induced expression within 60 min, even though TIR1/AFB or phyB are thought to act as receptors relevant for gene expression regulation. The expression of marker genes in seedlings responding to both auxin and shade showed that for both stimuli regulation of marker gene expression was altered after 10-20 min in the wild type and phyB mutant. The rapidity of expression responses provides a framework for the mechanics of functional interaction of ABP1 and phyB to trigger interwoven signalling pathways. PMID:25392478

  3. Genetics, structure, and prevalence of FP967 (CDC Triffid) T-DNA in flax.

    PubMed

    Young, Lester; Hammerlindl, Joseph; Babic, Vivijan; McLeod, Jamille; Sharpe, Andrew; Matsalla, Chad; Bekkaoui, Faouzi; Marquess, Leigh; Booker, Helen M

    2015-01-01

    The detection of T-DNA from a genetically modified flaxseed line (FP967, formally CDC Triffid) in a shipment of Canadian flaxseed exported to Europe resulted in a large decrease in the amount of flax planted in Canada. The Canadian flaxseed industry undertook major changes to ensure the removal of FP967 from the supply chain. This study aimed to resolve the genetics and structure of the FP967 transfer DNA (T-DNA). The FP967 T-DNA is thought to be inserted in at single genomic locus. The junction between the T-DNA and genomic DNA consisted of two inverted Right Borders with no Left Border (LB) flanking genomic DNA sequences recovered. This information was used to develop an event-specific quantitative PCR (qPCR) assay. This assay and an existing assay specific to the T-DNA construct were used to determine the genetics and prevalence of the FP967 T-DNA. These data supported the hypothesis that the T-DNA is present at a single location in the genome. The FP967 T-DNA is present at a low level (between 0.01 and 0.1%) in breeder seed lots from 2009 and 2010. None of the 11,000 and 16,000 lines selected for advancement through the Flax Breeding Program in 2010 and 2011, respectively, tested positive for the FP967 T-DNA, however. Most of the FP967 T-DNA sequence was resolved via PCR cloning and next generation sequencing. A 3,720 bp duplication of an internal portion of the T-DNA (including a Right Border) was discovered between the flanking genomic DNA and the LB. An event-specific assay, SAT2-LB, was developed for the junction between this repeat and the LB. PMID:25883881

  4. Forward genetics screening of Medicago truncatula Tnt1 insertion lines.

    PubMed

    Yarce, Juan Carlos Serrani; Lee, Hee-Kyung; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S

    2013-01-01

    A large population of Medicago truncatula insertion lines has been generated using the Tnt1 retrotransposon. More than 21,000 insertion lines have been generated, representing more than 500,000 insertion events. This mutant population is being used by the legume research community to screen for various different mutants using a forward genetics approach. Some of the phenotypes that have been screened using this population include developmentally abnormal phenotypes in leaves, stem, flowers, and roots. In addition to these, mutants with defects in symbiosis with Rhizobium and mycorrhiza, mutants with altered nonhost resistance against Asian Soybean Rust and switch grass rust pathogens, mutants with altered lignin content, mutants with altered cell wall structure, etc. have been identified. Here, we describe the high throughput methodology that is being used to identify these M. truncatula mutants. PMID:23996311

  5. Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing.

    PubMed

    Mlotshwa, Sizolwenkosi; Pruss, Gail J; Gao, Zhihuan; Mgutshini, Nomathamsanqa L; Li, Junjie; Chen, Xuemei; Bowman, Lewis H; Vance, Vicki

    2010-11-01

    The utility of many T-DNA insertion mutant lines of Arabidopsis is compromised by their propensity to trigger transcriptional silencing of transgenes expressed from the CaMV 35S promoter. To try to circumvent this problem, we characterized the genetic requirements for maintenance of 35S promoter homology-dependent transcriptional gene silencing induced by the dcl3-1 (SALK_005512) T-DNA insertion mutant line. Surprisingly, even though DCL3 and RDR2 are known components of the siRNA-dependent transcriptional gene silencing pathway, transcriptional gene silencing of a 35S promoter-driven GUS hairpin transgene did occur in plants homozygous for the dcl3-1 T-DNA insertion and was unaffected by loss of function of RDR2. However, the transcriptional gene silencing was alleviated in dcl2 dcl3 dcl4 triple mutant plants and also by mutations in AGO4, NRPD2, HEN1 and MOM1. Thus, some T-DNA insertion mutant lines induce 35S promoter homology-dependent transcriptional silencing that requires neither DCL3 nor RDR2, but involves other genes known to function in siRNA-dependent transcriptional silencing. Consistent with these results, we detected 35S promoter siRNAs in dcl3-1 SALK line plants, suggesting that the 35S promoter homology-dependent silencing induced by some T-DNA insertion mutant lines is siRNA-mediated. PMID:21070421

  6. Variable T-DNA linkage configuration affects inheritance of carotenogenic transgenes and carotenoid accumulation in transgenic indica rice.

    PubMed

    Rai, Mayank; Datta, Karabi; Parkhi, Vilas; Tan, Jing; Oliva, Norman; Chawla, Harvinder S; Datta, Swapan K

    2007-08-01

    Transgenics for the expression of beta-carotene biosynthetic pathway in the endosperm were developed in indica rice background by introducing phytoene synthase (psy) and phytoene desaturase (crtI) genes through Agrobacterium-mediated transformation, employing non-antibiotic positive selectable marker phosphomannose isomerase (pmi). Twenty-seven transgenic lines were characterized for the structural organization of T-DNA inserts and the expression of transgenes in terms of total carotenoid and beta-carotene accumulation in the endosperm. Ten lines were also studied for the inheritance of transgenic loci to the T(1) progenies. Copy number and sites of integration of the transgenes ranged from one to four. Almost 50% of the transgenic lines showed rearrangement of T-DNA inserts. However, most of the rearrangements occurred in the crtI expression cassette which is adjacent to the right T-DNA border. Differences in copy numbers of psy and crtI were also observed indicating partial T-DNA integration. Beyond T-DNA border transfer was also detected in 25% of the lines. Fifty percent of the lines studied showed single Mendelian locus inheritance, while two lines showed bi-locus inheritance in the T(1) progenies. Some of the lines segregating in 3:1 ratio showed two sites of integration on restriction digestion analysis indicating that the T-DNA insertion sites were tightly linked. Three transgenic lines showed nonparental types in the segregating progenies, indicating unstable transgenic locus. Evidences from the HPLC analysis showed that multiple copies of transgenes had a cumulative effect on the accumulation of carotenoid in the endosperm. T(1) progenies, in general, accumulated more carotenoids than their respective parents, the highest being 6.77 mug/g of polished seeds. High variation in the carotenoid accumulation was observed within the T(1) progenies which could be attributed to the variation in the structural organization and expression of transgenes, minor variations in the genetic background within the progeny plants, or differences in the plant microenvironments. The study identified lines worthy of further multiplication and breeding based on transgene structural integrity in the segregating progeny and high expression levels in terms of the beta-carotene accumulation. PMID:17377795

  7. Generation of insect-resistant and glyphosate-tolerant rice by introduction of a T-DNA containing two Bt insecticidal genes and an EPSPS gene.

    PubMed

    Zhao, Qi-chao; Liu, Ming-hong; Zhang, Xian-wen; Lin, Chao-yang; Zhang, Qing; Shen, Zhi-cheng

    2015-10-01

    Insect resistance and glyphosate tolerance have been two of the most important traits in the genetic improvement of various crops. In this study, two Bacillus thuringiensis (Bt) insecticidal genes, Cry1Ac and Cry1Ig, and a modified glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (G10) were combined into a single transferred DNA (T-DNA) fragment and introduced into rice by Agrobacterium-mediated transformation. A transgenic line with single-copy T-DNA insertion named GAI-14 was found to be highly resistant to striped stem borer and rice leaf roller, and tolerant to glyphosate. Analysis of T-DNA border sequence suggested that the transgenes were inserted at the chromosome 3 and appeared to have not interrupted any known or putative genes. A field trial observed no significant difference in the basic agronomic traits between GAI-14 and the recipient rice. PMID:26465130

  8. Generation of insect-resistant and glyphosate-tolerant rice by introduction of a T-DNA containing two Bt insecticidal genes and an EPSPS gene*

    PubMed Central

    ZHAO, Qi-chao; LIU, Ming-hong; ZHANG, Xian-wen; LIN, Chao-yang; ZHANG, Qing; SHEN, Zhi-cheng

    2015-01-01

    Insect resistance and glyphosate tolerance have been two of the most important traits in the genetic improvement of various crops. In this study, two Bacillus thuringiensis (Bt) insecticidal genes, Cry1Ac and Cry1Ig, and a modified glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (G10) were combined into a single transferred DNA (T-DNA) fragment and introduced into rice by Agrobacterium-mediated transformation. A transgenic line with single-copy T-DNA insertion named GAI-14 was found to be highly resistant to striped stem borer and rice leaf roller, and tolerant to glyphosate. Analysis of T-DNA border sequence suggested that the transgenes were inserted at the chromosome 3 and appeared to have not interrupted any known or putative genes. A field trial observed no significant difference in the basic agronomic traits between GAI-14 and the recipient rice. PMID:26465130

  9. DEVELOPMENT OF A TOOL TO INSERT ABOMASAL INFUSION LINES INTO DAIRY COWS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A tool was developed to aid in ruminal insertion of abomasal infusion lines into dairy cows. The tool consisted of two pieces cut from polyvinyl chloride pipe. The first piece of pipe, the insertion tool, contained a groove that held the flexible plastic flange that was on the end of the infusion ...

  10. Plasma transfusions prior to insertion of central lines for patients with abnormal coagulation

    PubMed Central

    Hall, David P; Estcourt, Lise J; Doree, Carolyn; Hopewell, Sally; Trivella, Marialena; Walsh, Timothy S

    2015-01-01

    This is the protocol for a review and there is no abstract. The objectives are as follows: To assess the effect of different prophylactic plasma transfusion regimens prior to central line insertion in patients with abnormal coagulation.

  11. Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae

    PubMed Central

    Choi, Jaehyuk; Park, Jongsun; Jeon, Junhyun; Chi, Myoung-Hwan; Goh, Jaeduk; Yoo, Sung-Yong; Park, Jaejin; Jung, Kyongyong; Kim, Hyojeong; Park, Sook-Young; Rho, Hee-Sool; Kim, Soonok; Kim, Byeong Ryun; Han, Seong-Sook; Kang, Seogchan; Lee, Yong-Hwan

    2007-01-01

    Agrobacterium tumefaciens-mediated transformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T-DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant-pathogenic fungus, Magnaporthe oryzae, here we report the most comprehensive analysis of T-DNA integration events in fungi and the development of an informatics infrastructure, termed a T-DNA analysis platform (TAP). We identified a total of 1110 T-DNA-tagged locations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T-DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T-DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T-DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T-DNA borders and flanking genomic DNA sequences revealed that T-DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large-scale insertional mutagenesis. PMID:17850257

  12. Comparison of different platelet transfusion thresholds prior to insertion of central lines in patients with thrombocytopenia

    PubMed Central

    Estcourt, Lise J; Desborough, Michael; Hopewell, Sally; Trivella, Marialena; Doree, Carolyn; Stanworth, Simon

    2015-01-01

    This is the protocol for a review and there is no abstract. The objectives are as follows: To assess the effects of different platelet transfusion thresholds prior to the insertion of a central line in patients with thrombocytopenia (low platelet count). PMID:26814707

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

    PubMed

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

    2016-06-01

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

  14. An evaluation of new and established methods to determine T-DNA copy number and homozygosity in transgenic plants.

    PubMed

    Głowacka, Katarzyna; Kromdijk, Johannes; Leonelli, Lauriebeth; Niyogi, Krishna K; Clemente, Tom E; Long, Stephen P

    2016-04-01

    Stable transformation of plants is a powerful tool for hypothesis testing. A rapid and reliable evaluation method of the transgenic allele for copy number and homozygosity is vital in analysing these transformations. Here the suitability of Southern blot analysis, thermal asymmetric interlaced (TAIL-)PCR, quantitative (q)PCR and digital droplet (dd)PCR to estimate T-DNA copy number, locus complexity and homozygosity were compared in transgenic tobacco. Southern blot analysis and ddPCR on three generations of transgenic offspring with contrasting zygosity and copy number were entirely consistent, whereas TAIL-PCR often underestimated copy number. qPCR deviated considerably from the Southern blot results and had lower precision and higher variability than ddPCR. Comparison of segregation analyses and ddPCR of T1 progeny from 26 T0 plants showed that at least 19% of the lines carried multiple T-DNA insertions per locus, which can lead to unstable transgene expression. Segregation analyses failed to detect these multiple copies, presumably because of their close linkage. This shows the importance of routine T-DNA copy number estimation. Based on our results, ddPCR is the most suitable method, because it is as reliable as Southern blot analysis yet much faster. A protocol for this application of ddPCR to large plant genomes is provided. PMID:26670088

  15. Paramutation-Like Interaction of T-DNA Loci in Arabidopsis

    PubMed Central

    Xue, Weiya; Ruprecht, Colin; Street, Nathaniel; Hematy, Kian; Chang, Christine; Frommer, Wolf B.; Persson, Staffan; Niittylä, Totte

    2012-01-01

    In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best understood in plants. Here we describe an unexpected paramutation-like trans SALK T-DNA interaction in Arabidopsis. Unlike most of the previously described paramutations, which led to gene silencing, the trans SALK T-DNA interaction caused an increase in the transcript levels of the endogenous gene (COBRA) where the T-DNA was inserted. This increased COBRA expression state was stably inherited for several generations and led to the partial suppression of the cobra phenotype. DNA methylation was implicated in this trans SALK T-DNA interaction since mutation of the DNA methyltransferase 1 in the suppressed cobra caused a reversal of the suppression. In addition, null mutants of the DNA demethylase ROS1 caused a similar COBRA transcript increase in the cobra SALK T-DNA mutant as the trans T-DNA interaction. Our results provide a new example of a paramutation-like trans T-DNA interaction in Arabidopsis, and establish a convenient hypocotyl elongation assay to study this phenomenon. The results also alert to the possibility of unexpected endogenous transcript increase when two T-DNAs are combined in the same genetic background. PMID:23272131

  16. Short direct repeats flank the T-DNA on a nopaline Ti plasmid

    PubMed Central

    Yadav, Narendra S.; Vanderleyden, Jos; Bennett, Donald R.; Barnes, Wayne M.; Chilton, Mary-Dell

    1982-01-01

    Crown gall disease results from the insertion of a segment of the Agrobacterium Ti plasmid, called T-DNA, into host plant nuclear DNA. We have subjected to sequence analysis the border regions of pTi T37 (ends of T-DNA) and one left T-DNA/plant DNA border fragment isolated from BT37 tobacco teratoma by molecular cloning. These sequence studies, taken together with published sequence of a right T-DNA/plant DNA border fragment, allowed us to identify the positions of left and right borders at the DNA sequence level. Comparison of left and right border regions of the Ti plasmid revealed a “core” direct repeat of 13 of 14 bases (12 contiguous) precisely at the borders of T-DNA. An extended repeat of 21 of 25 bases overlaps this core repeat. T-DNA on the Ti plasmid exhibits no longer direct or inverted repeats in the border regions, based on Southern hybridization studies. The physical structure of T-DNA differs from that of known prokaryotic and eukaryotic transposable elements but bears a structural resemblance to the prophage of bacteriophage λ. Images PMID:16593241

  17. Comparison of different platelet transfusion thresholds prior to insertion of central lines in patients with thrombocytopenia

    PubMed Central

    Estcourt, Lise J; Desborough, Michael; Hopewell, Sally; Doree, Carolyn; Stanworth, Simon J

    2016-01-01

    Background Patients with a low platelet count (thrombocytopenia) often require the insertion of central lines (central venous catheters (CVCs)). CVCs have a number of uses; these include: administration of chemotherapy; intensive monitoring and treatment of critically-ill patients; administration of total parenteral nutrition; and long-term intermittent intravenous access for patients requiring repeated treatments. Current practice in many countries is to correct thrombocytopenia with platelet transfusions prior to CVC insertion, in order to mitigate the risk of serious procedure-related bleeding. However, the platelet count threshold recommended prior to CVC insertion varies significantly from country to country. This indicates significant uncertainty among clinicians of the correct management of these patients. The risk of bleeding after a central line insertion appears to be low if an ultrasound-guided technique is used. Patients may therefore be exposed to the risks of a platelet transfusion without any obvious clinical benefit. Objectives To assess the effects of different platelet transfusion thresholds prior to the insertion of a central line in patients with thrombocytopenia (low platelet count). Search methods We searched for randomised controlled trials (RCTs) in CENTRAL (The Cochrane Library 2015, Issue 2), MEDLINE (from 1946), EMBASE (from 1974), the Transfusion Evidence Library (from 1950) and ongoing trial databases to 23 February 2015. Selection criteria We included RCTs involving transfusions of platelet concentrates, prepared either from individual units of whole blood or by apheresis, and given to prevent bleeding in patients of any age with thrombocytopenia requiring insertion of a CVC. Data collection and analysis We used standard methodological procedures expected by The Cochrane Collaboration. Main results One RCT was identified that compared different platelet transfusion thresholds prior to insertion of a CVC in people with chronic liver disease. This study is still recruiting participants (expected recruitment: up to 165 participants) and is due to be completed in December 2017. There were no completed studies. There were no studies that compared no platelet transfusions to a platelet transfusion threshold. Authors’ conclusions There is no evidence from RCTs to determine whether platelet transfusions are required prior to central line insertion in patients with thrombocytopenia, and, if a platelet transfusion is required, what is the correct platelet transfusion threshold. Further randomised trials with robust methodology are required to develop the optimal transfusion strategy for such patients. The one ongoing RCT involving people with cirrhosis will not be able to answer this review’s questions, because it is a small study that assesses one patient group and does not address all of the comparisons included in this review. To detect an increase in the proportion of participants who had major bleeding from 1 in 100 to 2 in 100 would require a study containing at least 4634 participants (80% power, 5% significance). PMID:26627708

  18. High-frequency T-DNA-mediated gene tagging in plants.

    PubMed

    Koncz, C; Martini, N; Mayerhofer, R; Koncz-Kalman, Z; Körber, H; Redei, G P; Schell, J

    1989-11-01

    An insertion element [transferred DNA (T-DNA)], transferred by soil agrobacteria into the nuclear genome of plants, was used for induction of gene fusions in Arabidopsis thaliana, Nicotiana tabacum, and Nicotiana plumbaginifolia. A promoterless aph(3')II (aminoglycoside phosphotransferase II) reporter gene was linked to the right end of the T-DNA and transformed into plants along with a plasmid replicon and a selectable hygromycin-resistance gene. Transcriptional and translational reporter gene fusions were identified by screening for APH(3')II enzyme activity in diverse tissues of transgenic plants. The frequency of gene fusions, estimated by determination of the copy number of T-DNA insertions, showed that on average 30% of T-DNA inserts induced gene fusions in Arabidopsis and Nicotiana. Gene fusions were rescued from plants by transformation of the T-DNA-linked plasmid and flanking plant DNA into Escherichia coli. By dissection of gene fusions and construction of chimeric genes, callus- and root-specific promoters were identified that showed an altered tissue specificity in the presence of a 3'-downstream-located 35S promoter. Transcript mapping of a gene fusion and expression of a non-frame transcriptional fusion of bacterial luciferase luxA and luxB genes demonstrated that dicistronic transcripts are translated in tobacco. PMID:2554318

  19. Formation of Complex Extrachromosomal T-DNA Structures in Agrobacterium tumefaciens-Infected Plants1[C][W][OA

    PubMed Central

    Singer, Kamy; Shiboleth, Yoel M.; Li, Jianming; Tzfira, Tzvi

    2012-01-01

    Agrobacterium tumefaciens is a unique plant pathogenic bacterium renowned for its ability to transform plants. The integration of transferred DNA (T-DNA) and the formation of complex insertions in the genome of transgenic plants during A. tumefaciens-mediated transformation are still poorly understood. Here, we show that complex extrachromosomal T-DNA structures form in A. tumefaciens-infected plants immediately after infection. Furthermore, these extrachromosomal complex DNA molecules can circularize in planta. We recovered circular T-DNA molecules (T-circles) using a novel plasmid-rescue method. Sequencing analysis of the T-circles revealed patterns similar to the insertion patterns commonly found in transgenic plants. The patterns include illegitimate DNA end joining, T-DNA truncations, T-DNA repeats, binary vector sequences, and other unknown filler sequences. Our data suggest that prior to T-DNA integration, a transferred single-stranded T-DNA is converted into a double-stranded form. We propose that termini of linear double-stranded T-DNAs are recognized and repaired by the plants DNA double-strand break-repair machinery. This can lead to circularization, integration, or the formation of extrachromosomal complex T-DNA structures that subsequently may integrate. PMID:22797657

  20. Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

    PubMed Central

    Wagstaff, Bradley J.; Hedges, Dale J.; Derbes, Rebecca S.; Campos Sanchez, Rebeca; Chiaromonte, Francesca; Makova, Kateryna D.; Roy-Engel, Astrid M.

    2012-01-01

    Alu elements are trans-mobilized by the autonomous non-LTR retroelement, LINE-1 (L1). Alu-induced insertion mutagenesis contributes to about 0.1% human genetic disease and is responsible for the majority of the documented instances of human retroelement insertion-induced disease. Here we introduce a SINE recovery method that provides a complementary approach for comprehensive analysis of the impact and biological mechanisms of Alu retrotransposition. Using this approach, we recovered 226 de novo tagged Alu inserts in HeLa cells. Our analysis reveals that in human cells marked Alu inserts driven by either exogenously supplied full length L1 or ORF2 protein are indistinguishable. Four percent of de novo Alu inserts were associated with genomic deletions and rearrangements and lacked the hallmarks of retrotransposition. In contrast to L1 inserts, 5′ truncations of Alu inserts are rare, as most of the recovered inserts (96.5%) are full length. De novo Alus show a random pattern of insertion across chromosomes, but further characterization revealed an Alu insertion bias exists favoring insertion near other SINEs, highly conserved elements, with almost 60% landing within genes. De novo Alu inserts show no evidence of RNA editing. Priming for reverse transcription rarely occurred within the first 20 bp (most 5′) of the A-tail. The A-tails of recovered inserts show significant expansion, with many at least doubling in length. Sequence manipulation of the construct led to the demonstration that the A-tail expansion likely occurs during insertion due to slippage by the L1 ORF2 protein. We postulate that the A-tail expansion directly impacts Alu evolution by reintroducing new active source elements to counteract the natural loss of active Alus and minimizing Alu extinction. PMID:22912586

  1. Instability of the Arabidopsis mutant csn5a-2 caused by epigenetic modification of intronic T-DNA.

    PubMed

    Jia, Xiaoyan; Chanda, Bidisha; Zhao, Mingzhe; Brunner, Amy M; Beers, Eric P

    2015-09-01

    T-DNA insertion mutants play a crucial role in elucidating Arabidopsis gene function. In some cases, two or more T-DNA mutants are combined to study genetic interactions between homologous genes or genes hypothesized to act in the same pathway. We studied the significance of protein-protein interactions between CSN5A and ROP11 by crossing three independent rop11 T-DNA insertion mutants with csn5a-2, a partial loss-of-function intronic T-DNA insertion mutant. The csn5a-2 single mutant is severely stunted, but double rop11 csn5a-2mutants were rescued and exhibited increased CSN5A transcript and protein levels. The rescued phenotype was maintained in non-Mendelian fashion when the csn5a-2 single mutant was re-isolated from the rop11-1 csn5a-2 double mutant, and was sensitive to two inhibitors of DNA methylation. Loss of kanamycin resistance was also observed in re-isolated csn5a-2. These findings indicate that the rescue of csn5a-2 resulted from a trans T-DNA-mediated epigenetic effect on the csn5a-2 intronic T-DNA, similar to recent reports involving the intronic T-DNA mutants ag-TD, ben1-1, and cob-6. Thus the work reported here provides further support for the recommendation that mutants created through novel combinations of T-DNA alleles should be carefully evaluated for evidence of epigenetic modification of T-DNA before final conclusions are drawn. PMID:26259174

  2. Increased Polyamine Biosynthesis Enhances Stress Tolerance by Preventing the Accumulation of Reactive Oxygen Species: T-DNA Mutational Analysis of Oryza sativa Lysine Decarboxylase-like Protein 1

    PubMed Central

    Jang, Su Jin; Wi, Soo Jin; Choi, Yoo Jin; An, Gynheung; Park, Ky Young

    2012-01-01

    A highly oxidative stress-tolerant japonica rice line was isolated by T-DNA insertion mutation followed by screening in the presence of 50 mM H2O2. The T-DNA insertion was mapped to locus Os09g0547500, the gene product of which was annotated as lysine decarboxylase-like protein (GenBank accession No. AK062595). We termed this gene OsLDC-like 1, for Oryza sativa lysine decarboxylase-like 1. The insertion site was in the second exon and resulted in a 27 amino acid N-terminal deletion. Despite this defect in OsLDC-like 1, the mutant line exhibited enhanced accumulation of the polyamines (PAs) putrescine, spermidine, and spermine under conditions of oxidative stress. The generation of reactive oxygen species (ROS) in the mutant line was assessed by qRT-PCR analysis of NADPH oxidase (RbohD and RbohF), and by DCFH-DA staining. Cellular levels of ROS in osldc-like 1 leaves were significantly lower than those in the wild-type (WT) rice after exposure to oxidative, high salt and acid stresses. Exogenously-applied PAs such as spermidine and spermine significantly inhibited the stress-induced accumulation of ROS and cell damage in WT leaves. Additionally, the activities of ROS-detoxifying enzymes were increased in the homozygous mutant line in the presence or absence of H2O2. Thus, mutation of OsLDC-like 1 conferred an oxidative stress-tolerant phenotype. These results suggest that increased cellular PA levels have a physiological role in preventing stress-induced ROS and ethylene accumulation and the resultant cell damage. PMID:22965749

  3. T-DNA recombination and replication in maize cells.

    PubMed

    Zhao, Xiaoxia; Coats, Isabelle; Fu, Ping; Gordon-Kamm, Bill; Lyznik, L Alexander

    2003-01-01

    T-DNA recombination and replication was analyzed in 'black mexican sweet' (BMS) cells transformed with T-DNAs containing the replication system from wheat dwarf virus (WDV). Upon recombination between the T-DNA ends, a promoterless marker gene (gusA) was activated. Activation of the recombination marker gene was delayed and increased exponentially over time, suggesting that recombination and amplification of the T-DNA occurred in maize cells. Mutant versions of the viral initiator gene (rep), known to be defective in the replication function, failed to generate recoverable recombinant T-DNA molecules. Circularization of T-DNA by the FLP/FRT site-specific recombination system and/or homologous recombination was not necessary to recover circular T-DNAs. However, replicating T-DNAs appeared to be suitable substrates for site-specific and homologous recombination. Among 33 T-DNA border junctions sequenced, only one pair of identical junction sites was found implying that the population of circular T-DNAs was highly heterogenous. Since no circular T-DNA molecules were detected in treatments without rep, it suggested that T-DNA recombination was linked to replication and might have been stimulated by this process. The border junctions observed in recombinant T-DNA molecules were indicative of illegitimate recombination and were similar to left-border recombination of T-DNA into the genome after Agro-mediated plant transformation. However, recombination between T-DNA molecules differed from T-DNA/genomic DNA junction sites in that few intact right borders were observed. The replicating T-DNA molecules did not enhance genomic random integration of T-DNA in the experimental configuration used for this study. PMID:12943549

  4. A simple method to enrich an Agrobacterium-transformed population for plants containing only T-DNA sequences.

    PubMed

    Hanson, B; Engler, D; Moy, Y; Newman, B; Ralston, E; Gutterson, N

    1999-09-01

    A simple modification to standard binary vector design has been utilized to enrich an Agrobacterium-transformed population for plants containing only T-DNA sequences. A lethal gene was incorporated into the non-T-DNA portion of a binary vector, along with a screenable marker. The resulting class of vectors is designated as NTL T-DNA vectors (non-T-DNA lethal gene-containing T-DNA vectors). The lethal gene used here is a CaMV 35S-barnase gene with an intron in the coding sequence (barnase-INT); the screenable marker is a pMAS-luciferase gene with an intron in the coding sequence (LUC-int). To evaluate the utility of this vector design, tobacco plants were transformed with either the NTL T-DNA vector or a control vector from which most of the barnase-INT gene was deleted. Populations of 50 transgenic plants were scored for LUC expression. The results indicated a dramatic reduction in the presence of non-T-DNA sequences in the transgenic population using the NTL T-DNA vector. Only one transgenic plant was found to be LUC+ using the NTL vector, compared with 42 of 50 plants using the control vector. Importantly, the efficiency with which transformed tobacco plants was obtained was reduced by no more than 30%. The reduction in LUC+ transgenics was partially reversed when a barstar-expressing tobacco line was transformed, indicating that barnase expression was responsible for the reduced frequency of incorporating non-T-DNA sequences. Similar transformation results were obtained with tomato and grape. The incorporation of a barnase-INT gene outside the left border appears to provide a generally applicable tool for enriching an Agrobacterium-transformed population for plants containing only T-DNA sequences. PMID:10571858

  5. Characterization and isolation of a T-DNA tagged banana promoter active during in vitro culture and low temperature stress

    PubMed Central

    Santos, Efrén; Remy, Serge; Thiry, Els; Windelinckx, Saskia; Swennen, Rony; Sági, László

    2009-01-01

    Background Next-generation transgenic plants will require a more precise regulation of transgene expression, preferably under the control of native promoters. A genome-wide T-DNA tagging strategy was therefore performed for the identification and characterization of novel banana promoters. Embryogenic cell suspensions of a plantain-type banana were transformed with a promoterless, codon-optimized luciferase (luc+) gene and low temperature-responsive luciferase activation was monitored in real time. Results Around 16,000 transgenic cell colonies were screened for baseline luciferase activity at room temperature 2 months after transformation. After discarding positive colonies, cultures were re-screened in real-time at 26°C followed by a gradual decrease to 8°C. The baseline activation frequency was 0.98%, while the frequency of low temperature-responsive luciferase activity was 0.61% in the same population of cell cultures. Transgenic colonies with luciferase activity responsive to low temperature were regenerated to plantlets and luciferase expression patterns monitored during different regeneration stages. Twenty four banana DNA sequences flanking the right T-DNA borders in seven independent lines were cloned via PCR walking. RT-PCR analysis in one line containing five inserts allowed the identification of the sequence that had activated luciferase expression under low temperature stress in a developmentally regulated manner. This activating sequence was fused to the uidA reporter gene and back-transformed into a commercial dessert banana cultivar, in which its original expression pattern was confirmed. Conclusion This promoter tagging and real-time screening platform proved valuable for the identification of novel promoters and genes in banana and for monitoring expression patterns throughout in vitro development and low temperature treatment. Combination of PCR walking techniques was efficient for the isolation of candidate promoters even in a multicopy T-DNA line. Qualitative and quantitative GUS expression analyses of one tagged promoter in a commercial cultivar demonstrated a reproducible promoter activity pattern during in vitro culture. Thus, this promoter could be used during in vitro selection and generation of commercial transgenic plants. PMID:19552803

  6. Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans

    PubMed Central

    Bourras, Salim; Meyer, Michel; Grandaubert, Jonathan; Lapalu, Nicolas; Fudal, Isabelle; Linglin, Juliette; Ollivier, Benedicte; Blaise, Franoise; Balesdent, Marie-Hlne; Rouxel, Thierry

    2012-01-01

    The ever-increasing generation of sequence data is accompanied by unsatisfactory functional annotation, and complex genomes, such as those of plants and filamentous fungi, show a large number of genes with no predicted or known function. For functional annotation of unknown or hypothetical genes, the production of collections of mutants using Agrobacterium tumefaciensmediated transformation (ATMT) associated with genotyping and phenotyping has gained wide acceptance. ATMT is also widely used to identify pathogenicity determinants in pathogenic fungi. A systematic analysis of T-DNA borders was performed in an ATMT-mutagenized collection of the phytopathogenic fungus Leptosphaeria maculans to evaluate the features of T-DNA integration in its particular transposable element-rich compartmentalized genome. A total of 318 T-DNA tags were recovered and analyzed for biases in chromosome and genic compartments, existence of CG/AT skews at the insertion site, and occurrence of microhomologies between the T-DNA left border (LB) and the target sequence. Functional annotation of targeted genes was done using the Gene Ontology annotation. The T-DNA integration mainly targeted gene-rich, transcriptionally active regions, and it favored biological processes consistent with the physiological status of a germinating spore. T-DNA integration was strongly biased toward regulatory regions, and mainly promoters. Consistent with the T-DNA intranuclear-targeting model, the density of T-DNA insertion correlated with CG skew near the transcription initiation site. The existence of microhomologies between promoter sequences and the T-DNA LB flanking sequence was also consistent with T-DNA integration to host DNA mediated by homologous recombination based on the microhomology-mediated end-joining pathway. PMID:22908038

  7. Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice.

    PubMed

    Kim, Chul Min; Piao, Hai Long; Park, Soon Ju; Chon, Nam Soo; Je, Byoung Il; Sun, Bingyao; Park, Sung Han; Park, Jin Young; Lee, Eun Jin; Kim, Min Jung; Chung, Woo Sik; Lee, Kon Ho; Lee, Young Suk; Lee, Jeung Joo; Won, Yong Jae; Yi, GiHwan; Nam, Min Hee; Cha, Young Soon; Yun, Doh Won; Eun, Moo Young; Han, Chang-deok

    2004-07-01

    Rapid, large-scale generation of a Ds transposant population was achieved using a regeneration procedure involving tissue culture of seed-derived calli carrying Ac and inactive Ds elements. In the F(2) progeny from genetic crosses between the same Ds and Ac starter lines, most of the crosses produced an independent germinal transposition frequency of 10-20%. Also, many Ds elements underwent immobilization even though Ac was expressed. By comparison, in a callus-derived regenerated population, over 70% of plants carried independent Ds insertions, indicating transposition early in callus formation. In the remaining population, the majority of plants carried only Ac. Most of the new Ds insertions were stably transmitted to a subsequent generation. An exceptionally high proportion of independent transposants in the regenerated population means that selection markers for transposed Ds and continual monitoring of Ac/Ds activities may not necessarily be required. By analyzing 1297 Ds-flanking DNA sequences, a genetic map of 1072 Ds insertion sites was developed. The map showed that Ds elements were transposed onto all of the rice chromosomes, with preference not only near donor sites (36%) but also on certain physically unlinked arms. Populations from both genetic crossing and tissue culture showed the same distribution patterns of Ds insertion sites. The information of these mapped Ds insertion sites was deposited in GenBank. Among them, 55% of Ds elements were on predicted open-reading frame (ORF) regions. Thus, we propose an optimal strategy for the rapid generation of a large population of Ds transposants in rice. PMID:15225289

  8. Cloning of an Arabidopsis Patatin-Like Gene, STURDY, by Activation T-DNA Tagging

    PubMed Central

    Huang, Shihshieh; Cerny, R. Eric; Bhat, Deepti S.; Brown, Sherri M.

    2001-01-01

    Activation T-DNA tagging can generate dominant gain-of-function mutants by overexpression of a particular endogenous gene. We identified an activation-tagged mutant, sturdy, exhibiting a stiff inflorescence stem, thicker leaves, shorter siliques, larger seeds, round-shaped flowers, and delayed growth. It is most important that unlike its wild-type counterpart, this mutant is less prone to lodging. Cloning of STURDY revealed that in sturdy, there is an open reading frame containing a single intron encoding a patatin-like homolog. The T-DNA is inserted into the 3′ region of the second exon. The mutant phenotype was shown to be the result of overexpression of STURDY by mRNA analysis and transgenic studies. Preliminary histological studies have revealed an increase in cell number in the inflorescence stem of mutant plants; however, additional studies are needed to better understand the overexpression phenotype. PMID:11161015

  9. Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics.

    PubMed Central

    Tissier, A F; Marillonnet, S; Klimyuk, V; Patel, K; Torres, M A; Murphy, G; Jones, J D

    1999-01-01

    A new system for insertional mutagenesis based on the maize Enhancer/Suppressor-mutator (En/Spm) element was introduced into Arabidopsis. A single T-DNA construct carried a nonautonomous defective Spm (dSpm) element with a phosphinothricin herbicide resistance (BAR) gene, a transposase expression cassette, and a counterselectable gene. This construct was used to select for stable dSpm transpositions. Treatments for both positive (BAR) and negative selection markers were applicable to soil-grown plants, allowing the recovery of new transpositions on a large scale. To date, a total of 48,000 lines in pools of 50 have been recovered, of which approximately 80% result from independent insertion events. DNA extracted from these pools was used in reverse genetic screens, either by polymerase chain reaction (PCR) using primers from the transposon and the targeted gene or by the display of insertions whereby inverse PCR products of insertions from the DNA pools are spotted on a membrane that is then hybridized with the probe of interest. By sequencing PCR-amplified fragments adjacent to insertion sites, we established a sequenced insertion-site database of 1200 sequences. This database permitted a comparison of the chromosomal distribution of transpositions from various T-DNA locations. PMID:10521516

  10. A feasibility study of a PET/MRI insert detector using strip-line and waveform sampling data acquisition

    NASA Astrophysics Data System (ADS)

    Kim, H.; Chen, C.-T.; Eclov, N.; Ronzhin, A.; Murat, P.; Ramberg, E.; Los, S.; Wyrwicz, A. M.; Li, L.; Kao, C.-M.

    2015-06-01

    We are developing a time-of-flight Positron Emission Tomography (PET) detector by using silicon photo-multipliers (SiPM) on a strip-line and high speed waveform sampling data acquisition. In this design, multiple SiPMs are connected on a single strip-line and signal waveforms on the strip-line are sampled at two ends of the strip to reduce readout channels while fully exploiting the fast time response of SiPMs. In addition to the deposited energy and time information, the position of the hit SiPM along the strip-line is determined by the arrival time difference of the waveform. Due to the insensitivity of the SiPMs to magnetic fields and the compact front-end electronics, the detector approach is highly attractive for developing a PET insert system for a magnetic resonance imaging (MRI) scanner to provide simultaneous PET/MR imaging. To investigate the feasibility, experimental tests using prototype detector modules have been conducted inside a 9.4 T small animal MRI scanner (Bruker BioSpec 94/30 imaging spectrometer). On the prototype strip-line board, 16 SiPMs (5.2 mm pitch) are installed on two strip-lines and coupled to 2×8 LYSO scintillators (5.0×5.0×10.0 mm3 with 5.2 mm pitch). The outputs of the strip-line boards are connected to a Domino-Ring-Sampler (DRS4) evaluation board for waveform sampling. Preliminary experimental results show that the effect of interference on the MRI image due to the PET detector is negligible and that PET detector performance is comparable with the results measured outside the MRI scanner.

  11. Automatic computation of wing-fuselage intersection lines and fillet inserts with fixed-area constraint

    NASA Technical Reports Server (NTRS)

    Barger, Raymond L.; Adams, Mary S.

    1993-01-01

    Procedures for automatic computation of wing-fuselage juncture geometry are described. These procedures begin with a geometry in wave-drag format. First, an intersection line is computed by extrapolating the wing to the fuselage. Then two types of filleting procedures are described, both of which utilize a combination of analytical and numerical techniques appropriate for automatic calculation. An analytical technique for estimating the added volume due to the fillet is derived, and an iterative procedure for revising the fuselage to compensate for this additional volume is given. Sample results are included in graphical form.

  12. Power electron beam front shortening in magnetically insulated transmission line with inner coaxial dielectric insert

    SciTech Connect

    Galstjan, E.A.; Kazanskiy, L.N.

    1995-12-31

    By now the technology of high-power high-current relativistic electron beams with microsecond duration has been developed. The same technology is used in high-power electric pulse generation. However at present the high-power beams of subnanosecond duration are necessary for some investigations and applications. The maximum power parameter achieved by means of the usual technology is limited by a value in the range of 100-300 MW. For this reason a search for new ways to generate high-power REB (relativistic electron beam) is a topical problem. It is obvious that this problem may be reduced to the generation of pulses with a subnanosecond front duration. There are many methods to shorten a pulse duration to its front duration for instance, by using parts of short-circuited transmission lines.

  13. Identification of Lactobacillus species using tDNA-PCR.

    PubMed

    Baele, Margo; Vaneechoutte, Mario; Verhelst, Rita; Vancanneyt, Marc; Devriese, Luc A; Haesebrouck, Freddy

    2002-08-01

    tDNA intergenic spacer PCR (tDNA-PCR) using consensus primers complementary to the conserved edges of the tRNA genes can amplify the intergenic spacers. Separation of the PCR products with capillary electrophoresis enables discrimination between fragments differing only one basepair in length. This method was applied to a collection of 82 Lactobacillus strains belonging to 37 species in order to evaluate the discriminatory power of this technique within this genus. Twenty-one species could be distinguished to species level on the basis of a unique tDNA fingerprint pattern. The other species grouped by two (e.g. L. fermentum and L. cellobiosus) or three (L. acidophilus, L. gallinarum and L. helveticus). Inclusion of the resulting fingerprints in a numerical database containing fingerprints of numerous other Gram-positive and Gram-negative species makes the identification of unknown strains possible. PMID:12031576

  14. CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds.

    PubMed

    Yan, Fan; Di, Shaokang; Takahashi, Ryoji

    2015-08-01

    The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family. PMID:26360633

  15. Transcultural diabetes nutrition algorithm (tDNA): Venezuelan application.

    PubMed

    Nieto-Martínez, Ramfis; Hamdy, Osama; Marante, Daniel; Marulanda, María Inés; Marchetti, Albert; Hegazi, Refaat A; Mechanick, Jeffrey I

    2014-04-01

    Medical nutrition therapy (MNT) is a necessary component of comprehensive type 2 diabetes (T2D) management, but optimal outcomes require culturally-sensitive implementation. Accordingly, international experts created an evidence-based transcultural diabetes nutrition algorithm (tDNA) to improve understanding of MNT and to foster portability of current guidelines to various dysglycemic populations worldwide. This report details the development of tDNA-Venezuelan via analysis of region-specific cardiovascular disease (CVD) risk factors, lifestyles, anthropometrics, and resultant tDNA algorithmic modifications. Specific recommendations include: screening for prediabetes (for biochemical monitoring and lifestyle counseling); detecting obesity using Latin American cutoffs for waist circumference and Venezuelan cutoffs for BMI; prescribing MNT to people with prediabetes, T2D, or high CVD risk; specifying control goals in prediabetes and T2D; and describing regional differences in prevalence of CVD risk and lifestyle. Venezuelan deliberations involved evaluating typical food-based eating patterns, correcting improper dietary habits through adaptation of the Mediterranean diet with local foods, developing local recommendations for physical activity, avoiding stigmatizing obesity as a cosmetic problem, avoiding misuse of insulin and metformin, circumscribing bariatric surgery to appropriate indications, and using integrated health service networks to implement tDNA. Finally, further research, national surveys, and validation protocols focusing on CVD risk reduction in Venezuelan populations are necessary. PMID:24699193

  16. Transcultural Diabetes Nutrition Algorithm (tDNA): Venezuelan Application

    PubMed Central

    Nieto-Martínez, Ramfis; Hamdy, Osama; Marante, Daniel; Inés Marulanda, María; Marchetti, Albert; Hegazi, Refaat A.; Mechanick, Jeffrey I.

    2014-01-01

    Medical nutrition therapy (MNT) is a necessary component of comprehensive type 2 diabetes (T2D) management, but optimal outcomes require culturally-sensitive implementation. Accordingly, international experts created an evidence-based transcultural diabetes nutrition algorithm (tDNA) to improve understanding of MNT and to foster portability of current guidelines to various dysglycemic populations worldwide. This report details the development of tDNA-Venezuelan via analysis of region-specific cardiovascular disease (CVD) risk factors, lifestyles, anthropometrics, and resultant tDNA algorithmic modifications. Specific recommendations include: screening for prediabetes (for biochemical monitoring and lifestyle counseling); detecting obesity using Latin American cutoffs for waist circumference and Venezuelan cutoffs for BMI; prescribing MNT to people with prediabetes, T2D, or high CVD risk; specifying control goals in prediabetes and T2D; and describing regional differences in prevalence of CVD risk and lifestyle. Venezuelan deliberations involved evaluating typical food-based eating patterns, correcting improper dietary habits through adaptation of the Mediterranean diet with local foods, developing local recommendations for physical activity, avoiding stigmatizing obesity as a cosmetic problem, avoiding misuse of insulin and metformin, circumscribing bariatric surgery to appropriate indications, and using integrated health service networks to implement tDNA. Finally, further research, national surveys, and validation protocols focusing on CVD risk reduction in Venezuelan populations are necessary. PMID:24699193

  17. On-line air-tightness and insertion loss simultaneous detection method of high air-tightness fiber optic penetration connector

    NASA Astrophysics Data System (ADS)

    Zhang, Jingchuan; Yang, Xiaoning; Wang, Jing; Jiang, Junfeng

    2015-08-01

    The high air-tightness multicore fiber optic penetration connector is a core component for the optical fiber sensing and communication technologies applied in the space environment simulator under the vacuum thermal environment. High air-tightness and insertion loss are the two key indexes of the fiber optic penetration connector. The air-tightness and insertion loss on-line synchronous detection method was proposed. First, established hardware-in-the-loop testing platform by using the vacuum pumping system, the vacuum vessel, the helium mass spectrometer leak detector and optical time-domain reflectmeter, then, described the air tightness and insertion loss on-line detection principle, finally, designed a detection test scheme and air-tightness and insertion loss were tested. Experimental results indicate that the leakage rate is lower than 1.0×10-7Pa•L/S, the minimum of which is1.0×10-10Pa•L/S and the insertion loss at wave length window 1550 nm is +/-0.07db, which is less than +/-0.1db. It can lay the data basis for the design of opto-mechanical combination and later period fine processing.

  18. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optim...

  19. Frequent problems and their resolutions by using thermal asymmetric interlaced PCR (TAIL-PCR) to clone genes in Arabidopsis T-DNA tagged mutants

    PubMed Central

    Wu, Lei; Di, Dong-Wei; Zhang, Dan; Song, Bin; Luo, Pan; Guo, Guang-Qin

    2015-01-01

    T-DNA insertional mutagenesis is a powerful tool in Arabidopsis functional genomics research. Previous studies have developed thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) as an efficient strategy in isolation of DNA sequences adjacent to known sequences in T-DNA tagged mutants. However, a number of problems are encountered when attempts are made to clone flanking sequences in T-DNA tagged mutants. Therefore, it is necessary to improve the efficiency of cloning mutagenesis. Here, we present the most frequent problems and provide an improved method to increase TAIL-PCR efficiency. Even then, it is not always possible to successfully obtain flanking sequences; in such cases, we recommend using high-throughput sequencing to determine the mutations. PMID:26019639

  20. Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana.

    PubMed Central

    McElver, J; Tzafrir, I; Aux, G; Rogers, R; Ashby, C; Smith, K; Thomas, C; Schetter, A; Zhou, Q; Cushman, M A; Tossberg, J; Nickle, T; Levin, J Z; Law, M; Meinke, D; Patton, D

    2001-01-01

    The purpose of this project was to identify large numbers of Arabidopsis genes with essential functions during seed development. More than 120,000 T-DNA insertion lines were generated following Agrobacterium-mediated transformation. Transgenic plants were screened for defective seeds and putative mutants were subjected to detailed analysis in subsequent generations. Plasmid rescue and TAIL-PCR were used to recover plant sequences flanking insertion sites in tagged mutants. More than 4200 mutants with a wide range of seed phenotypes were identified. Over 1700 of these mutants were analyzed in detail. The 350 tagged embryo-defective (emb) mutants identified to date represent a significant advance toward saturation mutagenesis of EMB genes in Arabidopsis. Plant sequences adjacent to T-DNA borders in mutants with confirmed insertion sites were used to map genome locations and establish tentative identities for 167 EMB genes with diverse biological functions. The frequency of duplicate mutant alleles recovered is consistent with a relatively small number of essential (EMB) genes with nonredundant functions during seed development. Other functions critical to seed development in Arabidopsis may be protected from deleterious mutations by extensive genome duplications. PMID:11779812

  1. Should nephrologists take a larger role in interventional nephrology, and should central line insertion remain a requirement of nephrology residency training? A debate.

    PubMed

    Mendelssohn, David C

    2015-01-01

    The Canadian Society of Nephrology must soon provide input concerning the future of procedural training in nephrology. While at one time, the ability to insert a central venous catheter (CVC) was an essential skill required by all nephrologists, in 2014, nephrology training and practice has changed in fundamental ways such that it would be both unreasonable, and impractical, to maintain this requirement. Indeed, survey evidence suggests that many current trainees are not achieving this competency. Amongst the reasons that this requirement should be withdrawn include: 1) Not all trainees have the procedural skills to safely learn to insert CVC's. 2) Most nephrologists in training and in practice are intellectually oriented, not procedurally oriented and are not seeking to perform lots of procedures. 3) In most practice settings, interventional radiologists and intensive care doctors perform dialysis line insertions using real time ultrasound guidance frequently, and offer timely, safer, and better service to patients. 4) Most trainees will not enter practice settings where CVC insertion ability is required. 5) Otherwise excellent future trainees may be denied a nephrology certificate of special competence only because they are unable to insert a CVC by the end of their fellowship. 6) Academic nephrology training programs that cannot provide adequate CVC insertion experience to fellows may lose their status as training centres. As a pragmatic way forward, Canadian nephrology training programs must encourage and offer only those nephrology trainees who have the ability and interest in procedural nephrology, a pathway through which they may be provided superb advanced training to become an expert. There is no longer a compelling reason to mandate this for all trainees. PMID:25922687

  2. Improving central line infection rates in the neonatal intensive care unit: Effect of hospital location, site of insertion, and implementation of catheter-associated bloodstream infection protocols

    PubMed Central

    Freeman, Jennifer J.; Gadepalli, Samir K.; Siddiqui, Sabina M.; Jarboe, Marcus D.; Hirschl, Ronald B.

    2016-01-01

    Introduction Catheter associated blood stream infections (CABSI) are morbid and expensive for all ages, including neonates. Thus far, the impact of CABSI prevention protocols, such as insertion and maintenance bundles, in the neonatal intensive care unit (NICU) is largely unknown. We hypothesized that lines placed in the operating room (OR) would have a lower infection rate due to established insertion protocols and a more sterile environment. Methods Retrospective chart review of NICU patients who received a percutaneous or tunneled central venous catheter between 2005 and 2012. ECMO cannulas, PICC and umbilical catheters were excluded. Variables of interest included demographics, anatomical site, hospital location, line days, and line infection. Line infection was defined as a positive blood culture drawn through the catheter. Results A total of 368 catheters were placed in 285 NICU patients. Majority of catheters (65.5%) were placed in OR. Saphenous and femoral veins were most common anatomical sites (50.8%). Twenty-eight catheters were infected (7.6%). After adjusting for pre-operative antibiotics, anatomical site, and SNAPPE-II scores, lines placed in OR were three times less likely to become infected (Odds Ratio=0.32, p=0.038). Although implementation of CABSI prevention protocols resulted in statistically significant reductions in infection (Odds Ratio=0.4, p=0.043), lines placed in the OR remained less likely to become infected. Conclusions NICU line infection rates decreased with implementation of CABSI prevention protocols. Despite this implementation, catheters placed in the NICU continued to have higher infection rates. As a result, when patient status allows it, we recommend that central lines in newborns be placed in the operating room. PMID:25783394

  3. Retrieval of Embolized Intracardiac Peripherally Inserted Central Catheter Line: Novel Percutaneous Technique by Utilizing a Flexible Biopsy Forceps

    PubMed Central

    Pande, Arindam; Sarkar, Achyut; Ahmed, Imran; Patil, Shailesh K.

    2015-01-01

    Peripheral catheter embolization to the heart is common but infrequently reported. In view of the hazardous complications of thrombosis, embolism, infection, arrhythmia and even death, percutaneous retrieval of such foreign bodies is usually attempted. Previously reported percutaneous technique of retrieval mainly involved the snaring technique. Herein, we report a novel nonsurgical retrieval technique for successful removal of a 46 cm long embolized intracardiac peripherally inserted central catheter by utilizing a flexible biopsy forceps. To the best of our knowledge, the use of flexible biopsy forceps for retrieval has hitherto been unreported and this case report therefore adds to the repertoire of percutaneous retrieval techniques for safe and easy removal of embolized catheters to the heart. PMID:26900421

  4. Neonatal late-onset sepsis following peripherally inserted central catheter removal: association with antibiotic use and adverse line events.

    PubMed

    Hoffman, Michelle A; Snowden, Jessica N; Simonsen, Kari A; Nenninger, Tabitha M; Lyden, Elizabeth R; Anderson-Berry, Ann L

    2015-01-01

    The objective of the study was to evaluate incidence of and risk factors for sepsis following peripherally inserted central catheter (PICC) removal. The retrospective cohort study looked at neonatal intensive care unit patients with PICC placement between February 2003 and June 2010 at a single medical center in the United States. Results showed that 14/216 patients (6.5%) had sepsis within 5 days of PICC removal. PICC removal because of adverse events was significantly associated with sepsis (P = .017). Antibiotic use before PICC removal did not have a significant impact on sepsis. The conclusions of the study are that removal of PICCs because of adverse events is significantly associated with late-onset neonatal sepsis and that antibiotic use at the time of PICC removal is not associated with a decline in sepsis rate. PMID:25723835

  5. A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence.

    PubMed

    Wolf, Zena T; Leslie, Elizabeth J; Arzi, Boaz; Jayashankar, Kartika; Karmi, Nili; Jia, Zhonglin; Rowland, Douglas J; Young, Amy; Safra, Noa; Sliskovic, Saundra; Murray, Jeffrey C; Wade, Claire M; Bannasch, Danika L

    2014-04-01

    Cleft palate (CP) is one of the most commonly occurring craniofacial birth defects in humans. In order to study cleft palate in a naturally occurring model system, we utilized the Nova Scotia Duck Tolling Retriever (NSDTR) dog breed. Micro-computed tomography analysis of CP NSDTR craniofacial structures revealed that these dogs exhibit defects similar to those observed in a recognizable subgroup of humans with CP: Pierre Robin Sequence (PRS). We refer to this phenotype in NSDTRs as CP1. Individuals with PRS have a triad of birth defects: shortened mandible, posteriorly placed tongue, and cleft palate. A genome-wide association study in 14 CP NSDTRs and 72 unaffected NSDTRs identified a significantly associated region on canine chromosome 14 (24.2 Mb-29.3 Mb; p(raw?)=?4.64 10(-15)). Sequencing of two regional candidate homeobox genes in NSDTRs, distal-less homeobox 5 (DLX5) and distal-less homeobox 6 (DLX6), identified a 2.1 kb LINE-1 insertion within DLX6 in CP1 NSDTRs. The LINE-1 insertion is predicted to insert a premature stop codon within the homeodomain of DLX6. This prompted the sequencing of DLX5 and DLX6 in a human cohort with CP, where a missense mutation within the highly conserved DLX5 homeobox of a patient with PRS was identified. This suggests the involvement of DLX5 in the development of PRS. These results demonstrate the power of the canine animal model as a genetically tractable approach to understanding naturally occurring craniofacial birth defects in humans. PMID:24699068

  6. Insertional mutagenesis using Tnt1 retrotransposon in potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato is the third most important food crop in the world. However, genetics and genomics research of potato has lagged behind many major crop species due to its autotetraploidy and a highly heterogeneous genome. Insertional mutagenesis using T-DNA or transposable elements, which is available in sev...

  7. Daptomycin cure after cefazolin treatment failure of Methicillin-sensitive Staphylococcus aureus (MSSA) tricuspid valve acute bacterial endocarditis from a peripherally inserted central catheter (PICC) line.

    PubMed

    Cunha, Burke A; Hamid, Naveed; Kessler, Heather; Parchuri, Subha

    2005-01-01

    Right-sided acute bacterial endocarditis (ABE) is an infrequent complication of central intravenous (IV) lines. We report a case of methicillin-sensitive Staphylococcus aureus tricuspid valve (TV) ABE related to a peripherally inserted central catheter line (PICC). Patients with right-sided ABE present with symptoms of fever and chills, and symptoms and signs of pulmonary emboli. In the patient presented, the PICC line was removed and high-dose cefazolin therapy, 2 g (IV) every 8 hours, was initiated. Although the patient's blood cultures became negative during the third week of cefazolin therapy, her erythrocyte sedimentation rate and teichoic acid antibody titers remained high. Pulmonary emboli developed. A large TV vegetation (1 x 2 cm) remained unchanged after 4 weeks of cefazolin therapy. For these reasons, cefazolin treatment was considered a treatment failure. Therapy with daptomycin was initiated at a dose of 6 mg/kg (IV) every 24 hours. During daptomycin therapy, the patient's erythrocyte sedimentation rate and teichoic acid antibody titers gradually returned to normal. Repeat transthoracic echocardiograph revealed the TV vegetation was gone and the methicillin-sensitive Staphylococcus aureus ABE was cured with daptomycin. We conclude daptomycin is a rapidly bactericidal antistaphylococcal antibiotic reliably effective even when other usually effective antistaphylococcal antibiotics have failed. PMID:16324966

  8. Activity of T-DNA borders in plant cell transformation by mini-T plasmids.

    PubMed

    Jen, G C; Chilton, M D

    1986-05-01

    By using a binary vector system, we examined the requirements for border sequences in T-DNA transformation of plant genomes. Mini-T plasmids consisting of small replicons with different extents of pTiT37 T-DNA were tested for plant tumor-inducing ability in Agrobacterium tumefaciens strain LBA4404 containing helper plasmid pAL4404 (which encodes virulence genes needed for T-DNA transfer). Assays of these bacteria on carrot disks, Kalanchoë leaves, and SR1 Nicotiana tabacum plantlets showed that mini-T plasmid containing full length T-DNA including left and right borders was highly virulent, as were mini-T plasmids containing all onc (oncogenicity) genes and only the right border. In contrast, mini-T plasmids containing all onc genes and only the left border induced tumors only rarely, and a mini-T plasmid containing all onc genes but no T-DNA borders was completely avirulent. Southern hybridization analyses of tumor DNA showed that T-DNA border sequences delimited the extent of the two-border mini-T plasmid transferred and integrated into the plant genome. When only one T-DNA border was present, it formed one end of the transferred DNA, and the other end mapped in the vector sequences. The implications of these results for the mechanism of T-DNA transfer and integration are discussed. PMID:3009403

  9. The maternal chromosome set is the target of the T-DNA in the in planta transformation of Arabidopsis thaliana.

    PubMed Central

    Bechtold, N; Jaudeau, B; Jolivet, S; Maba, B; Vezon, D; Voisin, R; Pelletier, G

    2000-01-01

    In planta transformation methods are now commonly used to transform Arabidopsis thaliana by Agrobacterium tumefaciens. The origin of transformants obtained by these methods has been studied by inoculating different floral stages and examining gametophytic expression of an introduced beta-glucuronidase marker gene encoding GUS. We observed that transformation can still occur after treating flowers where embryo sacs have reached the stage of the third division. No GUS expression was observed in embryo sacs or pollen of plants infiltrated with an Agrobacterium strain bearing a GUS gene under the control of a gametophyte-specific promoter. To identify the genetic target we used an insertion mutant in which a gene essential for male gametophytic development has been disrupted by a T-DNA bearing a Basta resistance gene (B(R)). In this mutant the B(R) marker is transferred to the progeny only by the female gametes. This mutant was retransformed with a hygromycin resistance marker and doubly resistant plants were selected. The study of 193 progeny of these transformants revealed 25 plants in which the two resistance markers were linked in coupling and only one plant where they were linked in repulsion. These results point to the chromosome set of the female gametophyte as the main target for the T-DNA. PMID:10924482

  10. Peripherally inserted central catheter - insertion

    MedlinePlus

    PICC - insertion ... A PICC is a long, thin tube (called a catheter) that goes into your body through a vein in ... into a large vein near your heart. The PICC helps carry nutrients and medicines into your body. ...

  11. Feeding tube insertion - gastrostomy

    MedlinePlus

    ... tube insertion; G-tube insertion; PEG tube insertion; Stomach tube insertion; Percutaneous endoscopic gastrostomy tube insertion ... and down the esophagus, which leads to the stomach. After the endoscopy tube is inserted, the skin ...

  12. LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice

    PubMed Central

    Geister, Krista A.; Brinkmeier, Michelle L.; Cheung, Leonard Y.; Wendt, Jennifer; Oatley, Melissa J.; Burgess, Daniel L.; Kozloff, Kenneth M.; Cavalcoli, James D.; Oatley, Jon M.; Camper, Sally A.

    2015-01-01

    Skeletal dysplasias are a common, genetically heterogeneous cause of short stature that can result from disruptions in many cellular processes. We report the identification of the lesion responsible for skeletal dysplasia and male infertility in the spontaneous, recessive mouse mutant chagun. We determined that Poc1a, encoding protein of the centriole 1a, is disrupted by the insertion of a processed Cenpw cDNA, which is flanked by target site duplications, suggestive of a LINE-1 retrotransposon-mediated event. Mutant fibroblasts have impaired cilia formation and multipolar spindles. Male infertility is caused by defective spermatogenesis early in meiosis and progressive germ cell loss. Spermatogonial stem cell transplantation studies revealed that Poc1a is essential for normal function of both Sertoli cells and germ cells. The proliferative zone of the growth plate is small and disorganized because chondrocytes fail to re-align after cell division and undergo increased apoptosis. Poc1a and several other genes associated with centrosome function can affect the skeleton and lead to skeletal dysplasias and primordial dwarfisms. This mouse mutant reveals how centrosome dysfunction contributes to defects in skeletal growth and male infertility. PMID:26496357

  13. An intronic LINE-1 element insertion in the dystrophin gene aborts dystrophin expression and results in Duchenne-like muscular dystrophy in the corgi breed

    PubMed Central

    Smith, Bruce F.; Yue, Yongping; Woods, Philip R.; Kornegay, Joe N.; Shin, Jin-Hong; Williams, Regina R.; Duan, Dongsheng

    2010-01-01

    Duchenne muscular dystrophy (DMD) is a dystrophin-deficient lethal muscle disease. To date, the catastrophic muscle wasting phenotype has only been seen in dystrophin-deficient humans and dogs. While Duchenne-like symptoms have been observed in more than a dozen dog breeds, the mutation is often not known and research colonies are rarely established. Here we report an independent canine DMD model originally derived from the Pembroke Welsh corgi breed. The affected dogs presented clinical signs of muscular dystrophy. Immunostaining revealed the absence of dystrophin and up-regulation of utrophin. Histopathologic examination showed variable fiber size, central nucleation, calcification, fibrosis, neutrophil and macrophage infiltration and cardiac focal vacuolar degeneration. Carrier dogs also displayed mild myopathy. The mutation was identified as a long interspersed repetitive element-1 (LINE-1) insertion in intron 13 which introduced a new exon containing an in-frame stop codon. Similar mutations have been seen in human patients. A colony was generated by crossing carrier females with normal males. Affected puppies had a normal birth weight but they experienced a striking growth delay in the first 5 days. In summary, the new corgi DMD model offers an excellent opportunity to study DMD pathogenesis and to develop novel therapies. PMID:20714321

  14. Regional Fluctuation in the Functional Consequence of LINE-1 Insertion in the Mitf Gene: The Black Spotting Phenotype Arisen from the Mitfmi-bw Mouse Lacking Melanocytes

    PubMed Central

    Yamamoto, Hiroaki; Shibahara, Shigeki

    2016-01-01

    Microphthalmia-associated transcription factor (Mitf) is a key regulator for differentiation of melanoblasts, precursors to melanocytes. The mouse homozygous for the black-eyed white (Mitfmi-bw) allele is characterized by the white-coat color and deafness with black eyes due to the lack of melanocytes. The Mitfmi-bw allele carries LINE-1, a retrotransposable element, which results in the Mitf deficiency. Here, we have established the black spotting mouse that was spontaneously arisen from the homozygous Mitfmi-bw mouse lacking melanocytes. The black spotting mouse shows multiple black patches on the white coat, with age-related graying. Importantly, each black patch also contains hair follicles lacking melanocytes, whereas the white-coat area completely lacks melanocytes. RT-PCR analyses of the pigmented patches confirmed that the LINE-1 insertion is retained in the Mitf gene of the black spotting mouse, thereby excluding the possibility of the somatic reversion of the Mitfmi-bw allele. The immunohistochemical analysis revealed that the staining intensity for beta-catenin was noticeably lower in hair follicles lacking melanocytes of the homozygous Mitfmi-bw mouse and the black spotting mouse, compared to the control mouse. In contrast, the staining intensity for beta-catenin and cyclin D1 was higher in keratinocytes of the black spotting mouse, compared to keratinocytes of the control mouse and the Mitfmi-bw mouse. Moreover, the keratinocyte layer appears thicker in the Mitfmi-bw mouse, with the overexpression of Ki-67, a marker for cell proliferation. We also show that the presumptive black spots are formed by embryonic day 15.5. Thus, the black spotting mouse provides the unique model to explore the molecular basis for the survival and death of developing melanoblasts and melanocyte stem cells in the epidermis. These results indicate that follicular melanocytes are responsible for maintaining the epidermal homeostasis; namely, the present study has provided evidence for the link between melanocyte development and the epidermal microenvironment. PMID:26930598

  15. Regional Fluctuation in the Functional Consequence of LINE-1 Insertion in the Mitf Gene: The Black Spotting Phenotype Arisen from the Mitfmi-bw Mouse Lacking Melanocytes.

    PubMed

    Takeda, Kazuhisa; Hozumi, Hiroki; Ohba, Koji; Yamamoto, Hiroaki; Shibahara, Shigeki

    2016-01-01

    Microphthalmia-associated transcription factor (Mitf) is a key regulator for differentiation of melanoblasts, precursors to melanocytes. The mouse homozygous for the black-eyed white (Mitfmi-bw) allele is characterized by the white-coat color and deafness with black eyes due to the lack of melanocytes. The Mitfmi-bw allele carries LINE-1, a retrotransposable element, which results in the Mitf deficiency. Here, we have established the black spotting mouse that was spontaneously arisen from the homozygous Mitfmi-bw mouse lacking melanocytes. The black spotting mouse shows multiple black patches on the white coat, with age-related graying. Importantly, each black patch also contains hair follicles lacking melanocytes, whereas the white-coat area completely lacks melanocytes. RT-PCR analyses of the pigmented patches confirmed that the LINE-1 insertion is retained in the Mitf gene of the black spotting mouse, thereby excluding the possibility of the somatic reversion of the Mitfmi-bw allele. The immunohistochemical analysis revealed that the staining intensity for beta-catenin was noticeably lower in hair follicles lacking melanocytes of the homozygous Mitfmi-bw mouse and the black spotting mouse, compared to the control mouse. In contrast, the staining intensity for beta-catenin and cyclin D1 was higher in keratinocytes of the black spotting mouse, compared to keratinocytes of the control mouse and the Mitfmi-bw mouse. Moreover, the keratinocyte layer appears thicker in the Mitfmi-bw mouse, with the overexpression of Ki-67, a marker for cell proliferation. We also show that the presumptive black spots are formed by embryonic day 15.5. Thus, the black spotting mouse provides the unique model to explore the molecular basis for the survival and death of developing melanoblasts and melanocyte stem cells in the epidermis. These results indicate that follicular melanocytes are responsible for maintaining the epidermal homeostasis; namely, the present study has provided evidence for the link between melanocyte development and the epidermal microenvironment. PMID:26930598

  16. Translation start sequences affect the efficiency of silencing of Agrobacterium tumefaciens T-DNA oncogenes.

    PubMed

    Lee, Hyewon; Humann, Jodi L; Pitrak, Jennifer S; Cuperus, Josh T; Parks, T Dawn; Whistler, Cheryl A; Mok, Machteld C; Ream, L Walt

    2003-11-01

    Agrobacterium tumefaciens oncogenes cause transformed plant cells to overproduce auxin and cytokinin. Two oncogenes encode enzymes that convert tryptophan to indole-3-acetic acid (auxin): iaaM (tryptophan mono-oxygenase) and iaaH (indole-3-acetamide hydrolase). A third oncogene (ipt) encodes AMP isopentenyl transferase, which produces cytokinin (isopentenyl-AMP). Inactivation of ipt and iaaM (or iaaH) abolishes tumorigenesis. Because adequate means do not exist to control crown gall, we created resistant plants by introducing transgenes designed to elicit posttranscriptional gene silencing (PTGS) of iaaM and ipt. Transgenes that elicit silencing trigger sequence-specific destruction of the inducing RNA and messenger RNAs with related sequences. Although PTGS has proven effective against a variety of target genes, we found that a much higher percentage of transgenic lines silenced iaaM than ipt, suggesting that transgene sequences influenced the effectiveness of PTGS. Sequences required for oncogene silencing included a translation start site. A transgene encoding a translatable sense-strand RNA from the 5' end of iaaM silenced the iaaM oncogene, but deletion of the translation start site abolished the ability of the transgene to silence iaaM. Silencing A. tumefaciens T-DNA oncogenes is a new and effective method to produce plants resistant to crown gall disease. PMID:12972655

  17. Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

    SciTech Connect

    John, Vogel P.

    2015-10-29

    Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge. Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/) and through the Phytozome genome browser (http://phytozome.jgi.doe.gov/pz/portal.html). The collection has been heavily utilized by the research community and, as of October 23, 2015, 223 orders for 12,069 seeds packets have been filled. In addition to creating this resource, we also optimized methods for transformation and sequencing DNA flanking insertion sites.

  18. Percutaneously inserted central catheter - infants

    MedlinePlus

    PICC - infants; PQC - infants; Pic line - infants; Per-Q cath - infants ... A percutaneously inserted central catheter (PICC) is a long, very thin, soft plastic tube that is put into a small blood vessel. This article addresses PICCs in ...

  19. Facility target insert shielding assessment

    SciTech Connect

    Mocko, Michal

    2015-10-06

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

  20. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  1. Arabidopsis genes essential for seedling viability: isolation of insertional mutants and molecular cloning.

    PubMed Central

    Budziszewski, G J; Lewis, S P; Glover, L W; Reineke, J; Jones, G; Ziemnik, L S; Lonowski, J; Nyfeler, B; Aux, G; Zhou, Q; McElver, J; Patton, D A; Martienssen, R; Grossniklaus, U; Ma, H; Law, M; Levin, J Z

    2001-01-01

    We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening approximately 38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype. PMID:11779813

  2. Identification of pathogenicity-related genes in the rice pathogen Ustilaginoidea virens through random insertional mutagenesis.

    TOXLINE Toxicology Bibliographic Information

    Yu M; Yu J; Hu J; Huang L; Wang Y; Yin X; Nie Y; Meng X; Wang W; Liu Y

    2015-03-01

    Agrobacterium tumefaciens-mediated transformation (ATMT) is becoming a popular effective system as an insertional mutagenesis tool in filamentous fungi. To gain more insight into the cellular and molecular mechanisms in the pathogenesis of Ustilaginoidea virens, the causal agent of rice false smut disease, a T-DNA insertion mutant library of U. virens was established using ATMT. We optimized a range of conditions to improve the transformation efficiency. Transformants were most effectively obtained when the optimal co-cultivation time is 72h, with 50μM AS in medium and 100μl A. tumefaciens for co-cultivation, leading to the production of 160-185 hygromycin B resistant transformants per 1×10(5) conidia. Southern blot analysis indicated that 58.14% of transformants had a single T-DNA copy. Among 5600 transformants tested for virulence, 37 mutants with reproducible pathogenic defects were obtained. The flanking sequences of three avirulent tranformants (B20, B1015 and B1465) and two pathogenicity-reduced transformants (B726 and B785) were amplified by high-efficiency thermal asymmetric interlaced PCR. Sequence analyses revealed that single T-DNA insertion in mutant B20 targeted the coding region of a gene encoding a protein highly similar to SUN family protein, and in mutant B726 targeted upstream of a gene with unknown function. The two T-DNA insertion sites in mutant B785 were found in the coding region of a gene encoding C6 transcription factor, but failed in amplified flanking sequence of another T-DNA. Chromosomal rearrangement occurred in the genome of mutant B1016 and B1465 with single T-DNA insertion. Among avirulent mutants, B20 showed altered colony growth and pigmentation. The T-DNA insert in B20 was detected in the coding region of a gene named UvSUN2. Morphophysiological characterization analysis suggested that UvSUN2 might be a virulence factor, and possibly required for proper fungal growth, cell wall construction, and stress responses in U. virens. This study optimize and validate the transformation procedure, maximizing the number of single copy transformants and developing an efficient procedure for rescuing adjacent host sequences along with the inserted T-DNA. This is the first report of identification several candidate virulence factors and validated one in U. virens. Together with identification of avirulent mutants and their associated genes, results suggested that ATMT can effectively be used to identify genes associated with pathogenicity in U. virens, and provided novel insights into molecular mechanisms underlying virulence of this pathogen.

  3. The Genomic Pattern of tDNA Operon Expression in E. coli

    PubMed Central

    Ardell, David H; Kirsebom, Leif A

    2005-01-01

    In fast-growing microorganisms, a tRNA concentration profile enriched in major isoacceptors selects for the biased usage of cognate codons. This optimizes translational rate for the least mass invested in the translational apparatus. Such translational streamlining is thought to be growth-regulated, but its genetic basis is poorly understood. First, we found in reanalysis of the E. coli tRNA profile that the degree to which it is translationally streamlined is nearly invariant with growth rate. Then, using least squares multiple regression, we partitioned tRNA isoacceptor pools to predicted tDNA operons from the E. coli K12 genome. Co-expression of tDNAs in operons explains the tRNA profile significantly better than tDNA gene dosage alone. Also, operon expression increases significantly with proximity to the origin of replication, oriC, at all growth rates. Genome location explains about 15% of expression variation in a form, at a given growth rate, that is consistent with replication-dependent gene concentration effects. Yet the change in the tRNA profile with growth rate is less than would be expected from such effects. We estimated per-copy expression rates for all tDNA operons that were consistent with independent estimates for rDNA operons. We also found that tDNA operon location, and the location dependence of expression, were significantly different in the leading and lagging strands. The operonic organization and genomic location of tDNA operons are significant factors influencing their expression. Nonrandom patterns of location and strandedness shown by tDNA operons in E. coli suggest that their genomic architecture may be under selection to satisfy physiological demand for tRNA expression at high growth rates. PMID:16103901

  4. Pacemaker insertion

    PubMed Central

    Kotsakou, Maria; Kioumis, Ioannis; Lazaridis, George; Pitsiou, Georgia; Lampaki, Sofia; Papaiwannou, Antonis; Karavergou, Anastasia; Tsakiridis, Kosmas; Katsikogiannis, Nikolaos; Karapantzos, Ilias; Karapantzou, Chrysanthi; Baka, Sofia; Mpoukovinas, Ioannis; Karavasilis, Vasilis; Rapti, Aggeliki; Trakada, Georgia; Zissimopoulos, Athanasios; Zarogoulidis, Konstantinos

    2015-01-01

    A pacemaker (PM) (or artificial PM, so as not to be confused with the heart’s natural PM) is a medical device that uses electrical impulses, delivered by electrodes contracting the heart muscles, to regulate the beating of the heart. The primary purpose of this device is to maintain an adequate heart rate, either because the heart’s natural PM is not fast enough, or there is a block in the heart’s electrical conduction system. Modern PMs are externally programmable and allow the cardiologist to select the optimum pacing modes for individual patients. Some combine a PM and defibrillator in a single implantable device. PMs can be temporary or permanent. Temporary PMs are used to treat short-term heart problems, such as a slow heartbeat that’s caused by a heart attack, heart surgery, or an overdose of medicine. Permanent PMs are used to control long-term heart rhythm problems. A PM can relieve some arrhythmia symptoms, such as fatigue and fainting. A PM also can help a person who has abnormal HRs resume a more active lifestyle. In the current mini review we will focus on the insertion of a PM and the possible pneumothorax that can be caused. PMID:25815303

  5. Altered Growth and Wood Characteristics in Transgenic Hybrid Aspen Expressing Agrobacterium tumefaciens T-DNA Indoleacetic Acid-Biosynthetic Genes.

    PubMed

    Tuominen, H.; Sitbon, F.; Jacobsson, C.; Sandberg, G.; Olsson, O.; Sundberg, B.

    1995-12-01

    A key regulator of cambial growth is the plant hormone indoleacetic acid (IAA). Here we report on altered wood characteristics and growth patterns in transgenic hybrid aspen (Populus tremula L. x Populus tremuloides Michx.) expressing Agrobacterium tumefaciens T-DNA IAA-biosynthetic iaaM and iaaH genes. Eighteen lines simultaneously expressing both genes were regenerated. Of these, four lines, verified to be transgenic by northern blot analysis, were selected and raised under controlled growth conditions. All four lines were affected in their growth patterns, including alterations in height and stem diameter growth, internode elongation, leaf enlargement, and degree of apical dominance. Two transgenic lines, showing the most distinct phenotypic deviation from the wild type, were characterized in more detail for free and conjugated IAA levels and for wood characteristics. Both lines showed an altered IAA balance, particularly in mature leaves and roots where IAA levels were elevated. They also exhibited changes in wood anatomy, most notably a reduction in vessel size, an increase in vessel density, and changes in ray development. Thus, the recent development of techniques for gene transfer to forest trees enabled us to investigate the influence of an altered IAA balance on xylem development in an intact experimental system. In addition, the results demonstrate the possibility of manipulating wood properties in a forest tree through controlled changes of IAA concentration and distribution. PMID:12228661

  6. Enhancing T-DNA Transfer Efficiency in Barley (Hordeum vulgare L.) Cells Using Extracellular Cellulose and Lectin.

    PubMed

    Gürel, Filiz; Uçarlı, Cüneyt; Tufan, Feyza; Kalaskar, Deepak M

    2015-06-01

    A major limitation of transforming barley tissues by Agrobacterium tumefaciens is the low frequency of T-DNA transfer due to recalcitrance of barley as a host. The effect of extracellular cellulose and lectin on Agrobacterium transformation efficiency was investigated in this study. Barley callus cultures were transformed with the AGL1 strain containing the vector pBI121 in the presence of 10 mg mL(-1) cellulose or 0.001, 0.05 and 0.1 mg mL(-1) lectin. Addition of cellulose significantly (P ≤ 0.05) increased the number of GUS spots by 50 % compared to standard conditions in the presence of only 200 μM acetosyringone (AS). Frequency of G418-resistant aggregates on the surfaces of callus cultures was 29 and 71.5 %, following AS and AS + cellulose treatments, respectively, after 4 weeks of selection. Presence of 0.05 or 0.1 mg mL(-1) lectin also increased the number of GUS spots and frequency of G418-resistant cells in the selection period, but the increase in blue spots was not significant. We examined the effect of lectin and cellulose on bacterial attachment to callus tissues. Both cellulose and lectin were found to have a significant positive effect on the numbers of bacteria attached to barley callus. Epifluorescence microscopy revealed that Agrobacterium cells had accumulated in the scaffolds of irregular fibrous cellulose with a mean particle size of 200 μm. Expression of nptII in transformed callus lines confirmed the stable transformation of the gene. Our study showed for the first time the binding of Agrobacterium cells to fibrous cellulose and also demonstrated how polysaccharides and glycoproteins can be used to improve T-DNA transfer in monocotyledon transformation procedures. PMID:25935223

  7. Chest tube insertion

    MedlinePlus

    Chest drainage tube insertion; Insertion of tube into chest; Tube thoracostomy; Pericardial drain ... When your chest tube is inserted, you will lie on your side or sit partly upright, with one arm over your ...

  8. Dihalocarbene Insertion Experiment

    ERIC Educational Resources Information Center

    Goh, S. H.

    1975-01-01

    Describes the insertion reaction using the insertion of carbenes into carbon-hydrogen bonds as an example. Outlines an experiment that will illustrate dihalocarbene insertions into diisopropyl ether. (GS)

  9. Genetic analysis of the virD operon of Agrobacterium tumefaciens: a search for functions involved in transport of T-DNA into the plant cell nucleus and in T-DNA integration.

    PubMed Central

    Koukolíková-Nicola, Z; Raineri, D; Stephens, K; Ramos, C; Tinland, B; Nester, E W; Hohn, B

    1993-01-01

    The transferred DNA (T-DNA) is transported from Agrobacterium tumefaciens to the nucleus and is stably integrated into the genome of many plant species. It has been proposed that the VirD2 protein, tightly attached to the T-DNA, pilots the T-DNA into the plant cell nucleus and that it is involved in integration. Using agroinfection and beta-glucuronidase expression as two different very sensitive transient assays for T-DNA transfer, together with assays for stable integration, we have shown that the C-terminal half of the VirD2 protein and the VirD3 protein are not involved in T-DNA integration. However, the bipartite nuclear localization signal, which is located within the C terminus of the VirD2 protein and which has previously been shown to be able to target a foreign protein into the plant cell nucleus, was shown to be required for efficient T-DNA transfer. virD4 mutants were shown by agroinfection to be completely inactive in T-DNA transfer. Images PMID:8380800

  10. Registration of the barley transposon-tagged population I:seventy lines each with a single, unique site of Ds insertion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Agricultural Research Service, U.S. Dept. of Agriculture (USDA-ARS), has developed and released a new genetic stock resource, a transposon-tagging barley (Hordeum vulgare L.) population comprised of 70 lines, TNP 200-TNP 207, TNP 210—TNP 229, TNP 232, TNP 233, TNP 235, TNP 237—TNP 262, TNP 264—T...

  11. M-31 mutant (virA::Tn5) of Agrobacterium tumefaciens is capable of transferring its T-DNA into the nucleus of host cell, but incapable of integrating it into the chromosome.

    PubMed

    Majumder, P; Yoshida, H; Shioiri, H; Nozue, M; Kojima, M

    2000-01-01

    An avirulent mutant (M-31 strain) was produced by the transposon (Tn5) mutagenesis of Agrobacterium tumefaciens (A-208 strain). A binary vector, pIG121-Hm, containing a kanamycin resistance gene (nptII) and beta-glucuronidase (GUS) gene with an intron, was introduced into M-31 and A-208 strains. The resultant Agrobacteria were inoculated onto leaves of Kalanchoe daigremontiana and to tobacco BY-2 cells to assay GUS activity to monitor the T-DNA transfer into the nuclei of host cells. The results indicated that T-DNA was transferred into the nuclei of cells of both host plants inoculated with the M-31 mutant. The M-31 mutant strain had an insertion of Tn5 in the virA gene on its Ti plasmid. The introduction of the virA gene in the M-31 mutant complemented its avirulent phenotype. No kanamycin-resistant cells were observed when the M-31 mutant harboring the pIG121-Hm was inoculated to tobacco BY-2 cells. The M-31 mutant (virA::Tn5) seems to transfer T-DNA into the nucleus of the host cell, but is unable to integrate it to the chromosome. PMID:16232864

  12. The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregulation of the Normande Agouti gene.

    PubMed

    Girardot, Michael; Guibert, Sylvain; Laforet, Marie-Pierre; Gallard, Yves; Larroque, Hélène; Oulmouden, Ahmad

    2006-08-01

    Mammalian pigmentation is controlled by the concerted action of Tyr, Tyrp1 and Dct producing eumelanin and/or pheomelanin in melanocytes. The ratio of these two pigments is determined by the agonist alpha-melanocyte stimulating hormone and the antagonist Agouti protein acting on the Mc1r. Here we show that the Agouti gene is over-expressed in Normande breed compared with Prim'Holstein breed. The Normande cattle have a characteristic coat color phenotype with a variable presence of black (eumelanin) hair over a red/brown background. We have found a previously undescribed full-length L1-BT element inserted in the 5'-genomic sequence of the Agouti gene in Normande cattle which promotes the over-expression of alternative transcripts. The variable expression of the alternative transcript directed by the long interspersed nuclear element promoter may be the origin of the brindle coat color pattern of the Normande breed. This new bovine Agouti allele isolated in Normande breed has been named Abr. Finally, as ectopic over-expression of Agouti in Ay mice is responsible for the obesity syndrome, we discuss the possible consequences of Abr for meat and milk production in cattle. PMID:16827753

  13. Transgene-specific and event-specific molecular markers for characterization of transgenic papaya lines resistant to Papaya ringspot virus.

    PubMed

    Fan, Ming-Jen; Chen, Shu; Kung, Yi-Jung; Cheng, Ying-Huey; Bau, Huey-Jiunn; Su, Tien-Tsai; Yeh, Shyi-Dong

    2009-12-01

    The commercially valuable transgenic papaya lines carrying the coat protein (CP) gene of Papaya ringspot virus (PRSV) and conferring virus resistance have been developed in Hawaii and Taiwan in the past decade. Prompt and sensitive protocols for transgene-specific and event-specific detections are essential for traceability of these lines to fulfill regulatory requirement in EU and some Asian countries. Here, based on polymerase chain reaction (PCR) approaches, we demonstrated different detection protocols for characterization of PRSV CP-transgenic papaya lines. Transgene-specific products were amplified using different specific primer pairs targeting the sequences of the promoter, the terminator, the selection marker, and the transgene, and the region across the promoter and transgene. Moreover, after cloning and sequencing the DNA fragments amplified by adaptor ligation-PCR, the junctions between plant genomic DNA and the T-DNA insert were elucidated. The event-specific method targeting the flanking sequences and the transgene was developed for identification of a specific transgenic line. The PCR patterns using primers designed from the left or the right flanking DNA sequence of the transgene insert in three selected transgenic papaya lines were specific and reproducible. Our results also verified that PRSV CP transgene is integrated into transgenic papaya genome in different loci. The copy number of inserted T-DNA was further confirmed by real-time PCR. The event-specific molecular markers developed in this investigation are crucial for regulatory requirement in some countries and intellectual protection. Also, these markers are helpful for prompt screening of a homozygote-transgenic progeny in the breeding program. PMID:19526355

  14. Morphogenesis and Auxin Sensitivity of Transgenic Tobacco with Different Complements of Ri T-DNA 1

    PubMed Central

    Spanò, Laura; Mariotti, Domenico; Cardarelli, Maura; Branca, Camillo; Costantino, Paolo

    1988-01-01

    Leaf explants of hairy root tobacco (Nicotiana tabacum) regenerants characteristically differentiate roots from the wound margins on hormonefree medium. The same response can be elicited on normal tobacco by culturing the explants in the presence of auxin. We show here that the spontaneous rooting of transformed plants is neither due to the activity of right T-DNA-borne auxin genes nor to a substantially altered balance of endogenous hormones. Rather, an increased sensitivity to auxin is conferred to transformed cells by the left T-DNA (TL-DNA). Analysis of the morphogenetic behavior of transgenic tobacco plants obtained by transferring segments of TL-DNA cloned in a binary vector system allowed us to pinpoint TL-DNA genes responsible for this increased auxin sensitivity of hairy root tissues. Three genes (open reading frames 10, 11, 12) are responsible for the spontaneous rooting of leaf explants and confer to transgenic plants an exaggerated response to auxin. Images Fig. 1 Fig. 2 PMID:16666168

  15. Analysis of the T-DNA structure in a large number of transgenic petunias generated by Agrobacterium-mediated transformation.

    PubMed

    Deroles, S C; Gardner, R C

    1988-05-01

    Southern hybridisation was performed on ninety-six transgenic petunias that had been selected for resistance to kanamycin. Just over half of the plants contained intact copies of the T-DNA. The most common rearrangements (at least 24 plants out of 96) were simple deleted derivatives that had lost one or both ends of the T-DNA. T-DNAs lacking the left border occurred at a frequency of 20%, and estimates of the frequency of T-DNAs lacking the right border were at least this high. Three plants contained grossly rearranged T-DNAs, of which all expressed the kanamycin resistance gene but only one transmitted the gene to progeny. Two plants lacked T-DNA homology altogether and did not express kanamycin resistance in their leaves or their progeny. Circumstantial evidence suggests that plants containing a chimaeric kanamycin resistance gene driven by the ocs promoter do not root efficiently in the presence of kanamycin. There was no correlation between intactness of the T-DNA and Mendelian inheritance of the kanamycin-resistance phenotype. However, a disproportionate number of plants showing non-Mendelian inheritance had a high copy number of their T-DNA. PMID:24272349

  16. Agrobacterium T-DNA-encoded protein Atu6002 interferes with the host auxin response

    PubMed Central

    Lacroix, Benoît; Gizatullina, Diana I.; Babst, Benjamin A.; Gifford, Andrew N.; Citovsky, Vitaly

    2013-01-01

    Summary Several genes in the Agrobacterium tumefaciens transferred (T) DNA encode proteins that are involved in developmental alterations leading to the formation of tumors in infected plants. We investigated the role of the protein encoded by the Atu6002 gene, the function of which is completely unknown. The Atu6002 expression occurs in Agrobacterium-induced tumors, and is also activated upon activation of plant cell division by growth hormones. Within the expressing plant cells, the Atu6002 protein is targeted to the plasma membrane. Interestingly, constitutive ectopic expression of Atu6002 in transgenic tobacco plants lead to a severe developmental phenotype characterized by stunted growth, shorter internodes, lanceolate leaves, increased branching, and modified flower morphology. These Atu6002-expressing plants also displayed impaired response to auxin. However, auxin cellular uptake and polar transport were not significantly inhibited in these plants, suggesting that Atu6002 interferes with auxin perception or signaling pathways. PMID:24128370

  17. The T-DNA-linked VirD2 protein contains two distinct functional nuclear localization signals.

    PubMed Central

    Tinland, B; Koukolíková-Nicola, Z; Hall, M N; Hohn, B

    1992-01-01

    Agrobacterium tumefaciens causes neoplastic growth in plants by transferring a piece of DNA, called T-DNA, into the nucleus of the plant cell. The virulence protein VirD2 of A. tumefaciens is tightly linked to the T-DNA and is thought to direct it to the plant genome. Here we show that the VirD2 protein contains two nuclear localization signals that are functional both in yeast and in plant cells. One signal is located in the N-terminal part of the protein and resembles a single-cluster-type nuclear localization signal. The second signal is near the C terminus and is a bipartite-type nuclear localization signal. The involvement of these sequences in the entry of the T-DNA into the nucleus is discussed. Images PMID:1502156

  18. Lines

    ERIC Educational Resources Information Center

    Mires, Peter B.

    2006-01-01

    National Geography Standards for the middle school years generally stress the teaching of latitude and longitude. There are many creative ways to explain the great grid that encircles our planet, but the author has found that students in his college-level geography courses especially enjoy human-interest stories associated with lines of latitude…

  19. Turbomachinery shaft insert

    NASA Technical Reports Server (NTRS)

    Vonpragenau, George L. (Inventor)

    1989-01-01

    An insert is presented for a hollow rotatable shaft on the end of which an impeller is mounted, the insert having a first cylindrical portion receivable within the end of the shaft. The insert includes a radially extending portion adjacent the end of the shaft having an annular wall including radially inner and outer surfaces for engaging tightly similar surfaces in a recess formed in the impeller to provide inner and outer pilot surfaces. The insert also includes a tubular extension which is received within a bore in the impeller, the tubular extension having spaced longitudinally extending slits for permitting the extension together with radially extending hook-like tongues thereon to be received within radial slots in the bore of the impeller to lock the impeller to the insert.

  20. [Inserts for foot deformities].

    PubMed

    Stinus, H; Weber, F

    2005-08-01

    Inserts are orthopedic aids in the treatment of foot disorders that result from changes of the static or dynamic situation. Provision of appropriate orthopedic devices can relieve the pain caused by forefoot deformities either in lieu of surgical intervention or in rare cases also following surgical treatment to improve the symptoms of residual pain.Available materials provide support, padding, and cushioning. Inserts are custom-made to measure and/or based on a plaster impression. Determining the indication, prescribing the inlay, and checking the orthosis are the tasks of the physician. One treatment option for relieving the pain of forefoot deformities consists in conservative therapy with an insert combining features of padding and support as well as adjusting a ready-made shoe. The shoe and inlay should constitute a functional unit since often the optimal effect is only achieved with a combination of insert and orthopedic adjustment of the ready-made shoe. PMID:15991037

  1. Cloning quantitative trait loci by insertional mutagenesis.

    PubMed

    Soller, M; Beckmann, J S

    1987-07-01

    This study explores the theoretical potential of "insertional mutagenesis" (i.e., mutagenesis as a result of integration of novel DNA sequences into the germ line), as a means of cloning quantitative trait loci (QTL). The approach presented is based on a direct search for mutagenic effects of a quantitative nature, and makes no assumptions as to the nature of the loci affecting quantitative trait value. Since there are a very large number of potential insertion sites in the genome but only a limited number of target sites that can affect any particular trait, large numbers of inserts will have to be generated and screened. The effects of allelic variants at any single QTL on phenotype value are expected to be small relative to sampling variation. Thus two of three stages of replicate testing will be required for each insert in order to bring overall Type I error down to negligible proportions and yet maintain good statistical power for inserts with true effects on the quantitative traits under consideration. The overall effort involved will depend on the spectrum of mutagenic effects produced by insertional mutagenesis. This spectrum is presently unknown, but using reasonable estimates, about 10,000 inserts would have to be tested, at reasonable replicate numbers (n ? 30) and Type I error (?=0.01) in the first testing stage, to provide a high likelihood of detecting at least one insert with a true effect on a given quantitative trait of interest. Total offspring numbers required per true quantitative mutagenic effect detected decrease strongly with increased number of traits scored and increased number of inserts per initial transformed parent. In fact, it would appear that successful implementation of experiments of this sort will require the introduction of multiple independent inserts in the original parent individuals, by means of repeated transformation, or use of transposable elements as inserts. When biologically feasible, selfing would appear to be the method of choice for insert replication, and in all cases the experiments must be carried out in inbred lines to reduce error variation due to genetic segregation, and avoid confounding mutational effects of the insert with effects due to linkage with nearby segregating QTL. The special qualifications of Arabidopsis thaliana for studies of this sort are emphasized, and problems raised by somaclonal variation are discussed. PMID:24241675

  2. Core Vessel Insert Handling Robot for the Spallation Neutron Source

    SciTech Connect

    Graves, Van B; Dayton, Michael J

    2011-01-01

    The Spallation Neutron Source provides the world's most intense pulsed neutron beams for scientific research and industrial development. Its eighteen neutron beam lines will eventually support up to twenty-four simultaneous experiments. Each beam line consists of various optical components which guide the neutrons to a particular instrument. The optical components nearest the neutron moderators are the core vessel inserts. Located approximately 9 m below the high bay floor, these inserts are bolted to the core vessel chamber and are part of the vacuum boundary. They are in a highly radioactive environment and must periodically be replaced. During initial SNS construction, four of the beam lines received Core Vessel Insert plugs rather than functional inserts. Remote replacement of the first Core Vessel Insert plug was recently completed using several pieces of custom-designed tooling, including a highly complicated Core Vessel Insert Robot. The design of this tool are discussed.

  3. Oxalate-minus mutants of Sclerotinia sclerotiorum via T-DNA insertion accumulate fumarate in culture and retain pathogenicity on plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sclerotinia sclerotiorum is a ubiquitous necrotrophic pathogen capable of infecting over 400 plant species including many economically important crops. Oxalic acid production has been shown in numerous studies to be a pathogenicity factor for S. sclerotiorum through several mechanisms. During our ra...

  4. Identification of pathogenicity-related genes in the vascular wilt fungus verticillium dahliae by agrobacterium tumefaciens-mediated t-DNA insertional mutagenesis.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Verticillium dahliae is the causal agent of vascular wilt in many economically important crops worldwide. Identification of genes that underpin pathogenicity or virulence may suggest targets for alternative control methods for this fungus. In this study, Agrobacterium tumefaciens-mediated transform...

  5. In planta transformation method for T-DNA transfer in orchids

    NASA Astrophysics Data System (ADS)

    Semiarti, Endang; Purwantoro, Aziz; Mercuriani, Ixora S.; Anggriasari, Anida M.; Jang, Seonghoe; Suhandono, Sony; Machida, Yasunori; Machida, Chiyoko

    2014-03-01

    Transgenic plant technology is an efficient tool to study the function of gene(s) in plant. The most popular and widely used technique is Agrobacterium-mediated transformation in which cocultivation was done by immersing the plant tissues/organ in overnight bacterial cultured for about 30 minutes to one hour under in vitro condition. In this experiment, we developed more easier technique that omitted the in vitro step during cocultivation with Agrobacterium, namely in planta transformation method. Pollinaria (compact pollen mass of orchid) of Phalaenopsis amabilis and Spathoglottis plicata orchids were used as target explants that were immersed into bacterial culture for 30 minutes, then dried up the pollinaria, the transformed pollinaria was used to pollinate orchid flowers. The T-DNA used for this experiments were Ubipro∷PaFT/A. tumefaciens GV3101 for P. amabilis and MeEF1α2 pro∷GUS/ A. tumefaciens LBA 4404 for S.plicata. Seeds that were produced from pollinated flowers were grown onto 10 mg/l hygromicin containing NP (New Phalaenopsis) medium. The existance of transgene in putative transformant protocorm (developing orchid embryo) genome was confirmed using PCR with specific primers of either PaFT or GUS genes. Histochemical GUS assay was also performed to the putative transformants. The result showed that transformation frequencies were 2.1 % in P. amabilis, and 0,53% in S. plicata. These results indicates that in planta transformation method could be used for Agrobacterium-mediated genetic transformation, with advantage easier and more secure work from contaminants than that of the in vitro method.

  6. Double-stranded cleavage of T-DNA and generation of single-stranded T-DNA molecules in Escherichia coli by a virD-encoded border-specific endonuclease from Agrobacterium tumefaciens.

    PubMed Central

    Jayaswal, R K; Veluthambi, K; Gelvin, S B; Slightom, J L

    1987-01-01

    The virD locus of Agrobacterium tumefaciens Ti plasmid pTiA6 was sequenced. Computer analysis of the sequence indicated five possible open reading frames (ORFs) within this locus. Two additional ORFs were identified distal to this locus. However, only two polypeptides of apparent molecular masses 16 and 56 kilodaltons, the products of ORFs 1 and 2, were detected in Escherichia coli, both in vivo and in an in vitro coupled transcription-translation system. The virD locus was cloned in expression vector pKK223.3 under control of a tac promoter and introduced into an E. coli strain harboring mini-Ti plasmid pAL1050. When induced with isopropyl-beta-D-thiogalactopyranoside, the virD gene products exhibited double-stranded T-DNA border-specific endonuclease activity. Deletion analysis demonstrated that this activity is encoded within the 5'-proximal 1.7-kilobase-pair portion of the virD locus that carries ORF 1 and most of ORF 2. Neither ORF 1 nor ORF 2 independently showed endonuclease activity; complementation studies indicated that the products of ORFs 1 and 2 together have this activity. The expression of this 1.7-kilobase-pair region of the virD locus caused double-stranded cleavage of the T-DNA at or near the borders and generated single-stranded T-DNA molecules with approximately equal frequencies in E. coli. Images PMID:2822660

  7. ALS insertion devices

    SciTech Connect

    Hoyer, E.; Chin, J.; Halbach, K.; Hassenzahl, W.V.; Humphries, D.; Kincaid, B.; Lancaster, H.; Plate, D.

    1990-11-01

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

  8. Nucleotide sequences of the Pseudomonas savastanoi indoleacetic acid genes show homology with Agrobacterium tumefaciens T-DNA.

    PubMed

    Yamada, T; Palm, C J; Brooks, B; Kosuge, T

    1985-10-01

    We report the nucleotide sequences of iaaM and iaaH, the genetic determinants for, respectively, tryptophan 2-monooxygenase and indoleacetamide hydrolase, the enzymes that catalyze the conversion of L-tryptophan to indoleacetic acid in the tumor-forming bacterium Pseudomonas syringae pv. savastanoi. The sequence analysis indicates that the iaaM locus contains an open reading frame encoding 557 amino acids that would comprise a protein with a molecular weight of 61,783; the iaaH locus contains an open reading frame of 455 amino acids that would comprise a protein with a molecular weight of 48,515. Significant amino acid sequence homology was found between the predicted sequence of the tryptophan monooxygenase of P. savastanoi and the deduced product of the T-DNA tms-1 gene of the octopine-type plasmid pTiA6NC from Agrobacterium tumefaciens. Strong homology was found in the 25 amino acid sequence in the putative FAD-binding region of tryptophan monooxygenase. Homology was also found in the amino acid sequences representing the central regions of the putative products of iaaH and tms-2 T-DNA. The results suggest a strong similarity in the pathways for indoleacetic acid synthesis encoded by genes in P. savastanoi and in A. tumefaciens T-DNA. PMID:16593610

  9. Interfacial insert for electrical connectors

    NASA Technical Reports Server (NTRS)

    Macavay, D.

    1975-01-01

    The development of interfacial inserts for improved electric connectors is discussed. The inserts were manufactured from epoxy resins. The design features of the inserts and the manufacturing equipment are described. The reliability test program is reported. Drawings of the interfacial inserts are provided.

  10. Insertion in Persian

    ERIC Educational Resources Information Center

    Kambuziya, Aliyeh Kord-e Zafaranlu; Dehghan, Masoud

    2011-01-01

    This paper investigates epenthesis process in Persian to catch some results in relating to vowel and consonant insertion in Persian lexicon. This survey has a close relationship to the description of epenthetic consonants and the conditions in which these consonants are used. Since no word in Persian may begin with a vowel, so that hiatus can't be…

  11. Regulation of Oncogene Expression in T-DNA-Transformed Host Plant Cells

    PubMed Central

    Zhang, Yi; Lee, Chil-Woo; Wehner, Nora; Imdahl, Fabian; Svetlana, Veselova; Weiste, Christoph; Dröge-Laser, Wolfgang; Deeken, Rosalia

    2015-01-01

    Virulent Agrobacterium tumefaciens strains integrate their T-DNA into the plant genome where the encoded agrobacterial oncogenes are expressed and cause crown gall disease. Essential for crown gall development are IaaH (indole-3-acetamide hydrolase), IaaM (tryptophan monooxygenase) and Ipt (isopentenyl transferase), which encode enzymes for the biosynthesis of auxin (IaaH, IaaM) and cytokinin (Ipt). Although these oncogenes are well studied as the tumor-inducing principle, nothing is known about the regulation of oncogene expression in plant cells. Our studies show that the intergenic regions (IGRs) between the coding sequences (CDS) of the three oncogenes function as promoters in plant cells. These promoters possess a eukaryotic sequence organization and cis-regulatory elements for the binding of plant transcription factors. WRKY18, WRKY40, WRKY60 and ARF5 were identified as activators of the Ipt promoter whereas IaaH and IaaM is constitutively expressed and no transcription factor further activates their promoters. Consistent with these results, the wrky triple mutant plants in particular, develops smaller crown galls than wild-type and exhibits a reduced Ipt transcription, despite the presence of an intact ARF5 gene. WRKY40 and WRKY60 gene expression is induced by A. tumefaciens within a few hours whereas the ARF5 gene is transcribed later during crown gall development. The WRKY proteins interact with ARF5 in the plant nucleus, but only WRKY40 together with ARF5 synergistically boosts the activation of the Ipt promoter in an auxin-dependent manner. From our data, we propose that A. tumefaciens initially induces WRKY40 gene expression as a pathogen defense response of the host cell. The WRKY protein is recruited to induce Ipt expression, which initiates cytokinin-dependent host cell division. With increasing auxin levels triggered by ubiquitous expression of IaaH and IaaM, ARF5 is activated and interacts with WRKY40 to potentiate Ipt expression and balance cytokinin and auxin levels for further cell proliferation. PMID:25615824

  12. Regulation of oncogene expression in T-DNA-transformed host plant cells.

    PubMed

    Zhang, Yi; Lee, Chil-Woo; Wehner, Nora; Imdahl, Fabian; Svetlana, Veselova; Weiste, Christoph; Dröge-Laser, Wolfgang; Deeken, Rosalia

    2015-01-01

    Virulent Agrobacterium tumefaciens strains integrate their T-DNA into the plant genome where the encoded agrobacterial oncogenes are expressed and cause crown gall disease. Essential for crown gall development are IaaH (indole-3-acetamide hydrolase), IaaM (tryptophan monooxygenase) and Ipt (isopentenyl transferase), which encode enzymes for the biosynthesis of auxin (IaaH, IaaM) and cytokinin (Ipt). Although these oncogenes are well studied as the tumor-inducing principle, nothing is known about the regulation of oncogene expression in plant cells. Our studies show that the intergenic regions (IGRs) between the coding sequences (CDS) of the three oncogenes function as promoters in plant cells. These promoters possess a eukaryotic sequence organization and cis-regulatory elements for the binding of plant transcription factors. WRKY18, WRKY40, WRKY60 and ARF5 were identified as activators of the Ipt promoter whereas IaaH and IaaM is constitutively expressed and no transcription factor further activates their promoters. Consistent with these results, the wrky triple mutant plants in particular, develops smaller crown galls than wild-type and exhibits a reduced Ipt transcription, despite the presence of an intact ARF5 gene. WRKY40 and WRKY60 gene expression is induced by A. tumefaciens within a few hours whereas the ARF5 gene is transcribed later during crown gall development. The WRKY proteins interact with ARF5 in the plant nucleus, but only WRKY40 together with ARF5 synergistically boosts the activation of the Ipt promoter in an auxin-dependent manner. From our data, we propose that A. tumefaciens initially induces WRKY40 gene expression as a pathogen defense response of the host cell. The WRKY protein is recruited to induce Ipt expression, which initiates cytokinin-dependent host cell division. With increasing auxin levels triggered by ubiquitous expression of IaaH and IaaM, ARF5 is activated and interacts with WRKY40 to potentiate Ipt expression and balance cytokinin and auxin levels for further cell proliferation. PMID:25615824

  13. Remote test methods of optical cable short insert losses

    NASA Astrophysics Data System (ADS)

    Burdin, Vladimir A.; Bourdine, Anton V.

    2000-10-01

    During fiber optic communication lines restoration often appear optical cable short insert joint quality control needs. It is problem to measure of short cable insert fiber splice losses on long-haul optical communication lines. This problem is caused by limits of dynamic range and resolution of optical time domain reflectometer (OTDR). We present overview of ways of short cable insert optical power losses control on long- haul optical communication lines. Theoretical and experimental proof some of this methods is considered. Numerical results are represented. A good agreement of theoretically predicted and experimental values is demonstrated.

  14. [Orthopedic shoe treatment : Inserts].

    PubMed

    Schuh, R; Windhager, R

    2016-03-01

    The use of inserts and orthopedic shoe adjustment represents an essential component of the conservative therapy of degenerative diseases and deformities of the musculoskeletal system. Inserts can have supportive, bedding and corrective effects and are used in particular for complaints of the feet and ankles. The combination of diverse materials allows a high level of cushioning and supporting features and corresponding longevity to be accomplished. The production is carried out on an individual basis and if necessary computer-assisted in order to achieve an optimal fit. For severe and rigid deformities the formation of pressure ulcers can be prevented by orthopedic shoe adjustment and by the use of orthopedic tailor-made shoes. PMID:26861757

  15. Hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T-DNA

    SciTech Connect

    Hood, E.E.; Helmer, G.L.; Fraley, R.T.; Chilton, M.D.

    1986-12-01

    A binary-vectory strategy was used to study the hypervirulence of Agrobacterium tumefaciens A281, an L,L-succinamopine strain. Strain A281 is hypervirulent on several solanaceous plants. Plasmids were constructed (pCS65 and pCS277) carrying either the transferred DNA (T-DNA) or the remainder of the tumor-inducing (Ti) plasmid (pEHA101) from this strain and tested each of these constructs were tested in trans with complementary each of regions from heterologous Ti plasmids. Hypervirulence on tobacco could be reconstructed in a bipartite strain with the L,L-succinamopine T-DNA and the vir region on separate plasmids. pEHA101 was able to complement octopine T-DNA to hypervirulence on tobacco and tomato plants. Nopaline T-DNA was complemented better on tomato plants by pEHA101 than it was by its own nopaline vir region, but not to hypervirulence. L,L-Succinamopine T-DNA could not be complemented to hypervirulence on tobacco and tomato plants with either heterologous vir region. From these results the authors suggest that the hypervirulence of strain A281 is due to non-T-DNA sequences on the Ti plasmid.

  16. Ear tube insertion - series (image)

    MedlinePlus

    Ear tube insertion is recommended for: fluid in the middle ear (present for more than 12 weeks) recurrent ear ... the accumulated fluid is suctioned out. A small tube is inserted through the incised eardrum in order ...

  17. Identification of virulence genes in the crucifer anthracnose fungus Colletotrichum higginsianum by insertional mutagenesis.

    PubMed

    Liu, Liping; Zhao, Dian; Zheng, Lu; Hsiang, Tom; Wei, Yangdou; Fu, Yanping; Huang, Junbin

    2013-11-01

    To investigate the molecular and genetic mechanisms underlying virulence of Colletotrichum higginsianum on Arabidopsis thaliana, a T-DNA insertion mutant library of C. higginsianum, the causal agent of crucifer anthracnose, was established using Agrobacterium tumefaciens-mediated transformation. Among 875 transformants tested for virulence on Arabidopsis, six mutants with altered virulence, including an appressorial melanin-deficient mutant T734, two mutants defective in penetration, T45 and B30, and three mutants, T679, T732 and T801, that cause hypersensitive reactions on host Arabidopsis, were obtained. Southern blot analysis indicated that the mutants T732 and T734 harbored single-site T-DNA integrations, while B30 harbored two T-DNA insertions. Border flanking sequences of T-DNAs from these mutants were recovered by inverse polymerase chain reaction (PCR) and thermal asymmetric interlaced PCR. Sequence analyses revealed that single T-DNA insertions in mutant T734 targeted the coding region of a gene with unknown function, and in mutant T732 targeted a gene encoding a copper amine oxidase. The two T-DNA insertion sites in mutant B30 were found in the coding region of a gene encoding an exosome component and in the upstream region of a DUF221-domain gene. None of these genes have previously been implicated in virulence of the phytopathogenic fungi. Among these avirulent mutants, T734 showed altered color in colony growth and produced melanin-deficient, albino appressoria. The T-DNA insert in T734 was detected in the coding region of a gene named C. higginsianum melanin-deficiency gene (Ch-MEL1), which is highly similar to a gene encoding a hypothetical protein in Colletotrichum gloeosporioides (GenBank ELA33048). To validate whether the Ch-MEL1 gene was associated with virulence of the mutant T734, a targeted gene disruption and complementation approach was used. The appressoria of ▵Ch-mel1 null mutants were defective in melanization and failed to penetrate the host epidermal cells. When inoculated onto the wounded leaf tissues, the ▵Ch-mel1 mutants grew on host tissues but failed to cause lesions beyond the wound site. In contrast, both the complement C▵Ch-mel1-2 and the wild type produced melanized appressoria and caused necrosis on leaves of Arabidopsis. Ch-MEL1 is required for both appressorial melanin production in C. higginsianum and post-invasive growth in host tissues. Together with identification of other avirulent mutants and their associated genes, this study provides novel insights into molecular mechanisms underlying virulence of the hemibiotroph, C. higginsianum. PMID:23806215

  18. Insight into the molecular requirements for pathogenicity of Fusarium oxysporum f. sp. lycopersici through large-scale insertional mutagenesis

    PubMed Central

    Michielse, Caroline B; van Wijk, Ringo; Reijnen, Linda; Cornelissen, Ben JC; Rep, Martijn

    2009-01-01

    Background Fusarium oxysporum f. sp. lycopersici is the causal agent of vascular wilt disease in tomato. In order to gain more insight into the molecular processes in F. oxysporum necessary for pathogenesis and to uncover the genes involved, we used Agrobacterium-mediated insertional mutagenesis to generate 10,290 transformants and screened the transformants for loss or reduction of pathogenicity. Results This led to the identification of 106 pathogenicity mutants. Southern analysis revealed that the average T-DNA insertion is 1.4 and that 66% of the mutants carry a single T-DNA. Using TAIL-PCR, chromosomal T-DNA flanking regions were isolated and 111 potential pathogenicity genes were identified. Conclusions Functional categorization of the potential pathogenicity genes indicates that certain cellular processes, such as amino acid and lipid metabolism, cell wall remodeling, protein translocation and protein degradation, seem to be important for full pathogenicity of F. oxysporum. Several known pathogenicity genes were identified, such as those encoding chitin synthase V, developmental regulator FlbA and phosphomannose isomerase. In addition, complementation and gene knock-out experiments confirmed that a glycosylphosphatidylinositol-anchored protein, thought to be involved in cell wall integrity, a transcriptional regulator, a protein with unknown function and peroxisome biogenesis are required for full pathogenicity of F. oxysporum. PMID:19134172

  19. Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-homologous end-joining proteins.

    PubMed

    Park, So-Yon; Vaghchhipawala, Zarir; Vasudevan, Balaji; Lee, Lan-Ying; Shen, Yunjia; Singer, Kamy; Waterworth, Wanda M; Zhang, Zhanyuan J; West, Christopher E; Mysore, Kirankumar S; Gelvin, Stanton B

    2015-03-01

    Non-homologous end joining (NHEJ) is the major model proposed for Agrobacterium T-DNA integration into the plant genome. In animal cells, several proteins, including KU70, KU80, ARTEMIS, DNA-PKcs, DNA ligase IV (LIG4), Ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR), play an important role in 'classical' (c)NHEJ. Other proteins, including histone H1 (HON1), XRCC1, and PARP1, participate in a 'backup' (b)NHEJ process. We examined transient and stable transformation frequencies of Arabidopsis thaliana roots mutant for numerous NHEJ and other related genes. Mutants of KU70, KU80, and the plant-specific DNA Ligase VI (LIG6) showed increased stable transformation susceptibility. However, these mutants showed transient transformation susceptibility similar to that of wild-type plants, suggesting enhanced T-DNA integration in these mutants. These results were confirmed using a promoter-trap transformation vector that requires T-DNA integration into the plant genome to activate a promoterless gusA (uidA) gene, by virus-induced gene silencing (VIGS) of Nicotiana benthamiana NHEJ genes, and by biochemical assays for T-DNA integration. No alteration in transient or stable transformation frequencies was detected with atm, atr, lig4, xrcc1, or parp1 mutants. However, mutation of parp1 caused high levels of T-DNA integration and transgene methylation. A double mutant (ku80/parp1), knocking out components of both NHEJ pathways, did not show any decrease in stable transformation or T-DNA integration. Thus, T-DNA integration does not require known NHEJ proteins, suggesting an alternative route for integration. PMID:25641249

  20. Characterization of pre-insertion loci of de novo L1 insertions

    PubMed Central

    Gasior, Stephen L.; Preston, Graeme; Hedges, Dale J.; Gilbert, Nicolas; Moran, John V.; Deininger, Prescott L.

    2007-01-01

    The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci show a different set of biases than those observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C-neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome. PMID:17067767

  1. Impedance calculation for ferrite inserts

    SciTech Connect

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

    2005-01-01

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

  2. Mars Observer Orbit Insertion Briefing

    NASA Technical Reports Server (NTRS)

    1993-01-01

    For the first part of this briefing, see NONP-NASA-VT-2000081556. Marvin Traxler continues his discussion on signal tracking from the Mars Observer. Julie Webster, Lead Engineer, Telecommunications Subsystem, is introduced. She explains how signals coming back from Mars are detected. Dr. Pasquale Esposito talks about flyby orbits and capture orbits. He says that frequencies coming from the spacecraft can determine if the spacecraft has flown by Mars, or if a capture orbit has occurred. Charles Whetsel, System Engineer Spacecraft Team, presents a computer program. He shows where the signal will appear on the computer from the Spacecraft. Suzanne Dodd presents orbit insertion geometry. Dr. Arden Albee, Project Scientist Mars Observer Project, Cal Tech tech, says that Mars is studied to get more data to confirm their hypotheses derived from previous Mars Missions such as the Viking Mars Program and the Mariner Program. Dr. Albee also describes instrumentation on the Mars Observer such as the Ultra Stable Oscillator, Mars Orbiter Laser Altimeter, and Magnetometer. The camera on the spacecraft is similar to a fax machine because it scans one line at a time as the spacecraft orbits Mars. Dr. Michael Malin, Principle Investigator Mars Observer Camera, Malin Space Science Systems, Inc., describe this process.

  3. Cloning of insertion site flanking sequence and construction of transfer DNA insert mutant library in Stylosanthes colletotrichum.

    PubMed

    Chen, Helong; Hu, Caiping; Yi, Kexian; Huang, Guixiu; Gao, Jianming; Zhang, Shiqing; Zheng, Jinlong; Liu, Qiaolian; Xi, Jingen

    2014-01-01

    Stylosanthes sp. is the most important forage legume in tropical areas worldwide. Stylosanthes anthracnose, which is mainly caused by Colletotrichum gloeosporioides, is a globally severe disease in stylo production. Little progress has been made in anthracnose molecular pathogenesis research. In this study, Agrobacterium tumefaciens-mediated transformation was used to transform Stylosanthes colletotrichum strain CH008. The major factors of the genetic transformation system of S. colletotrichum were optimized as follows: A. tumefaciens' AGL-1 concentration (OD(600)), 0.8; concentration of Colletotrichum conidium, 1 10(6) conidia/mL; acetosyringone concentration, 100 mmol/L; induction time, 6 h; co-culture temperature, 25 C; and co-culture time, 3 d. Thus, the transformation efficiency was increased to 300-400 transformants per 106 conidia. Based on the optimized system, a mutant library containing 4616 mutants was constructed, from which some mutants were randomly selected for analysis. Results show that the mutants were single copies that could be stably inherited. The growth rate, spore amount, spore germination rate, and appressorium formation rate in some mutants were significantly different from those in the wild-type strain. We then selected the most appropriate method for the preliminary screening and re-screening of each mutant's pathogenic defects. We selected 1230 transformants, and obtained 23 strains with pathogenic defects, namely, 18 strains with reduced pathogenicity and five strains with lost pathogenicity. Thermal asymmetric interlaced PCR was used to identify the transfer DNA (T-DNA) integration site in the mutant that was coded 2430, and a sequence of 476 bp was obtained. The flanking sequence of T-DNA was compared with the Colletotrichum genome by BLAST, and a sequence of 401 bp was found in Contig464 of the Colletotrichum genome. By predicting the function of the flanking sequence, we discovered that T-DNA insertion in the promoter region of the putative gene had 79% homology with the aspartate aminotransferase gene in Magnaporthe oryzae (XP_003719674.1). PMID:25361073

  4. Cloning of Insertion Site Flanking Sequence and Construction of Transfer DNA Insert Mutant Library in Stylosanthes Colletotrichum

    PubMed Central

    Huang, Guixiu; Gao, Jianming; Zhang, Shiqing; Zheng, Jinlong; Liu, Qiaolian; Xi, Jingen

    2014-01-01

    Stylosanthes sp. is the most important forage legume in tropical areas worldwide. Stylosanthes anthracnose, which is mainly caused by Colletotrichum gloeosporioides, is a globally severe disease in stylo production. Little progress has been made in anthracnose molecular pathogenesis research. In this study, Agrobacterium tumefaciens-mediated transformation was used to transform Stylosanthes colletotrichum strain CH008. The major factors of the genetic transformation system of S. colletotrichum were optimized as follows: A. tumefaciens’ AGL-1 concentration (OD600), 0.8; concentration of Colletotrichum conidium, 1×106 conidia/mL; acetosyringone concentration, 100 mmol/L; induction time, 6 h; co-culture temperature, 25°C; and co-culture time, 3 d. Thus, the transformation efficiency was increased to 300–400 transformants per 106 conidia. Based on the optimized system, a mutant library containing 4616 mutants was constructed, from which some mutants were randomly selected for analysis. Results show that the mutants were single copies that could be stably inherited. The growth rate, spore amount, spore germination rate, and appressorium formation rate in some mutants were significantly different from those in the wild-type strain. We then selected the most appropriate method for the preliminary screening and re-screening of each mutant’s pathogenic defects. We selected 1230 transformants, and obtained 23 strains with pathogenic defects, namely, 18 strains with reduced pathogenicity and five strains with lost pathogenicity. Thermal asymmetric interlaced PCR was used to identify the transfer DNA (T-DNA) integration site in the mutant that was coded 2430, and a sequence of 476 bp was obtained. The flanking sequence of T-DNA was compared with the Colletotrichum genome by BLAST, and a sequence of 401 bp was found in Contig464 of the Colletotrichum genome. By predicting the function of the flanking sequence, we discovered that T-DNA insertion in the promoter region of the putative gene had 79% homology with the aspartate aminotransferase gene in Magnaporthe oryzae (XP_003719674.1). PMID:25361073

  5. Wider opportunities for IUD insertion.

    PubMed

    Cole, L P; Potts, D M

    1983-02-01

    The timing of IUD insertion has important implications for those who insert the devices as well as the users. In 1978 the US Food and Drug Administration recommended insertion during menstruation but acknowledged that it is also "necessary and proper" to insert IUDs at other times in the cycle. A 1977 study found that 30% of European and North American obstetricians limited insertion to the time of menstruation. Nearly half those in Africa and the Middle East and 13% of those in Asia followed this practice. Consequently, many women are required to make more than 1 visit to a clinic, meaning inconvenience for both the user and provider and some unintended pregnancies. In developing countries women may depend on mobile clinics or infrequent visits by trained personnel and many seek help without an appointment. 1 reason for insertion at or just after menstruation is to ensure that the woman is not pregnant when the IUD is inserted. 2 recent articles attempt to assess the best time for IUD insertion with regard to IUD performance. White et al. found that women whose Copper T IUDs were inserted on days 1-5 of the menstrual cycle had a lower continuation rate in the 1st few months than did those whose IUDs were inserted at a later time in the cycle. Edelman et al. found that Copper T and Copper 7 IUDs could be inserted at any time during the menstrual cycle without any increased risk of subsequent pregnancy, removal for medical reasons or expulsion during the 1st 12 months after insertion. Pooled International Fertility Research Program (IFRP) data indicate that there is no consistent pattern with regard to the time in the cycle that the IUD is inserted and its later performance. In no case is there a distinct advantage for the 1st 5 days of the menstrual cycle. It is much simpler to offer a woman an IUD when she is first seen, provided she is reasonably sure she is not pregnant. New practices are evolving in relation to recently pregnant women. The postabortal use of IUDs has been extensively researched and is a useful option, using a variety of currently available devices. In regard to the postpartum use of IUDs, some programs have reported a high expulsion rate. Provided proper insertion technique is used, IUDs can be inserted immediately postpartum with a high degree of retention. Another use for copper containing IUDs is insertion within 5 days of unprotected sexual intercourse. In sum, women can be provided with IUDs upon request at any time during the menstrual cycle. PMID:12264751

  6. On windscreen insertion loss

    NASA Astrophysics Data System (ADS)

    Buzduga, Mariana; Peppin, Richard J.

    2002-05-01

    Microphone windscreens are used to attenuate wind noise. They add impedance between the source and microphone, not accounted for when the system is checked by acoustical calibrator or when used in the field. The procedure for the characterization of the attenuation has recently been addressed in ANSI S1.17/2000 part 1. But to date, no windscreens have been tested in accordance with that standard. Partially, the reason is that the precision of the procedure has not been determined. As of January 2002 a round robin is addressing just that issue. By June 2002 the results of the uncertainty determination will be available. In the meantime, we have tested some of the samples used and others in a small chamber approaching free-field conditions. We present the results of the tests of insertion loss (not in accordance with S1.17 because we do not have a reverberation room). We will show that, in some cases, the use of a windscreen can easily change a measurement using type 1 instruments to type 2 or worse. Without knowing information about a particular windscreen, the use of a windscreen in still air can drastically change uncertainty of measurement. In moving air conditions we expect even more severe problems.

  7. Efforts to deregulate Rainbow papaya in Japan: Molecular Characterization of Transgene and Vector Inserts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transformation plasmid-derived insert number and insert site sequence in 55-1 line papaya derivatives Rainbow and SunUp was determined as part of a larger petition to allow its import into Japan (Suzuki, et al., 2007, 2008). Three insertions were detected by Southern analysis and their correspondin...

  8. Agrobacterium tumefaciens-mediated transformation of Aspergillus aculeatus for insertional mutagenesis

    PubMed Central

    2011-01-01

    Agrobacterium tumefaciens-mediated transformation (AMT) was applied to Aspergillus aculeatus. Transformants carrying the T-DNA from a binary vector pBIG2RHPH2 were sufficiently mitotically stable to allow functional genomic analyses. The AMT technique was optimized by altering the concentration of acetosyringone, the ratio and concentration of A. tumefaciens and A. aculeatus cells, the duration of co-cultivation, and the status of A. aculeatus cells when using conidia, protoplasts, or germlings. On average, 30 transformants per 104 conidia or 217 transformants per 107 conidia were obtained under the optimized conditions when A. tumefaciens co-cultured with fungi using solid or liquid induction media (IM). Although the transformation frequency in liquid IM was 100-fold lower than that on solid IM, the AMT method using liquid IM is better suited for high-throughput insertional mutagenesis because the transformants can be isolated on fewer selection media plates by concentrating the transformed germlings. The production of two albino A. aculeatus mutants by AMT confirmed that the inserted T-DNA disrupted the polyketide synthase gene AapksP, which is involved in pigment production. Considering the efficiency of AMT and the correlation between the phenotypes and genotypes of the transformants, the established AMT technique offers a highly efficient means for characterizing the gene function in A. aculeatus. PMID:22166586

  9. Chemo-port insertion: A cause of vocal cord palsy.

    PubMed

    Alazzawi, Sarmad; Hindi, Khalid; Malik, Ausama; Wee, Chong Aun; Prepageran, Narayanan

    2015-11-01

    We describe extremely rare cases of vocal cord palsy following surgical insertion of a chemo port. Our cohort consisted of patients with cancer who developed hoarseness immediately after central venous line placement for the administration of chemotherapy, with vocal cord palsy confirmed with flexible laryngoscopy. Given the timing, central venous line placement appears to be the most likely cause. PMID:26108861

  10. Insertion device vacuum system designs

    SciTech Connect

    Hoyer, E.

    1988-05-01

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

  11. Norplant insertions, removals remain low.

    PubMed

    2000-09-01

    Norplant contraceptive implants contain a very low dose of progestin and no estrogen, and offer cumulative 7-year pregnancy rates similar to those characterizing surgical sterilization. But despite its advantages, few women in the US are selecting Norplant implants, say participants in Contraceptive Technology Update's 2000 Contraception Survey. The survey indicated that nearly 72% of surveyed health care providers reported no removals, compared with 69.3% in 1999. Furthermore, under 70% of participants have not performed any Norplant insertions in the year 2000, comparable to the 1999 statistics; 16 performed 1-5 insertions and 7.3% inserted 6-10 implants. Overall, only 1.8% of survey respondents had performed 11-25 insertions, and less than 1% reported 25 or more insertions, declining from 1999's 3.4% and 1.6%, respectively. PMID:12296240

  12. SPONTANEOUS TRANSMEMBRANE HELIX INSERTION THERMODYNAMICALLY MIMICS TRANSLOCON-GUIDED INSERTION

    PubMed Central

    Ulmschneider, Martin B.; Ulmschneider, Jakob P.; Schiller, Nina; Wallace, B. A.; von Heijne, Gunnar; White, Stephen H.

    2014-01-01

    The favorable transfer free energy for a transmembrane (TM) α-helix between the aqueous phase and lipid bilayer underlies the stability of membrane proteins. However, the connection between the energetics and process of membrane protein assembly by the Sec61/SecY translocon complex in vivo is not clear. Here, we directly determine the partitioning free energies of a family of designed peptides using three independent approaches: an experimental microsomal Sec61 translocon assay, a biophysical (spectroscopic) characterization of peptide insertion into hydrated planar lipid bilayer arrays, and an unbiased atomic-detail equilibrium folding-partitioning molecular dynamics simulation. Remarkably, the measured free energies of insertion are quantitatively similar for all three approaches. The molecular dynamics simulations show that TM helix insertion involves equilibrium with the membrane interface, suggesting that the interface may play a role in translocon-guided insertion. PMID:25204588

  13. The T-DNA oncogene A4-orf8 from Agrobacterium rhizogenes A4 induces abnormal growth in tobacco.

    PubMed

    Umber, Marie; Clément, Bernadette; Otten, Léon

    2005-03-01

    The related orf8 and iaaM T-DNA genes from Agrobacterium are each composed of two distinct parts. The 5' parts (called Norf8 or NiaaM) encode a 200-amino-acid (aa) sequence with homology to various T-DNA oncoproteins such as RolB, RolC, and 6b. The 3' parts (Corf8 or CiaaM) encode a 550-aa sequence with homology to IaaM proteins from Pseudomonas and Pantoea spp. Whereas iaaM genes encode flavin adenine dinucleotide (FAD)-dependent tryptophan 2-monooxygenases that catalyze the synthesis of indole-3-acetamide (IAM), A4-orf8 from Agrobacterium rhizogenes A4 does not. Plants expressing a 2x35S-A4-Norf8 construct accumulate soluble sugars and starch. We now have regenerated plants that express the full-size 2x35S-A4-orf8 and the truncated 2x35S-A4-Corf8 gene. 2x35S-A4-Corf8 plants accumulate starch and show reduced growth like 2x35S-A4-Norf8 plants but, in addition, display a novel set of characteristic growth modifications. These consist of leaf hypertrophy and hyperplasia (blisters); thick, dark-green leaves; thick stems; and swollen midveins. Mutations in the putative FAD-binding site of A4-Orf8 did not affect the blister syndrome. Plants expressing 2x35S-A4-Corf8 had a normal phenotype but contained less starch and soluble sugars than did wild-type plants. When 2x35S-A4-Corf8 plants were crossed to starch-accumulating 2x35S-A4-Norf8 plants with reduced growth, A4-Corf8 partially restored growth and reduced starch accumulation. A4-Corf8xA4-Norf8 crosses did not lead to the blister syndrome, suggesting that this requires physical linkage of the A4-NOrf8 and A4-COrf8 sequences. PMID:15782634

  14. Agrobacterium rhizogenes pRi8196 T-DNA: mapping and DNA sequence of functions involved in mannopine synthesis and hairy root differentiation.

    PubMed Central

    Hansen, G; Larribe, M; Vaubert, D; Tempé, J; Biermann, B J; Montoya, A L; Chilton, M D; Brevet, J

    1991-01-01

    This paper presents the map and DNA sequence analysis of pRi8196 transferred DNA (T-DNA) genes encoding root-inducing and mannopine synthesis functions. A canonical 24-base-pair border repeat as well as two "pseudoborders" are present at the functional right T-DNA border. To the left of this border are homologs of the mas1' and mas2' genes of TR pRiA4. Next to these are five open reading frames (ORFs) homologous to ORFs 10-14 of TL of pRiA4. ORFs 10-12 (rolA, rolB, and rolC) are less related to their pRiA4 homologs than are the other large ORFs analyzed here. In contrast to T-DNA genes of pRiA4, pRi8196 T-DNA ORFs 11 and 12 (rolB and rolC) are sufficient to induce hairy roots on carrot disks. Images PMID:1909028

  15. Beamline Insertions Manager at Jefferson Lab

    SciTech Connect

    Johnson, Michael C.

    2015-09-01

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

  16. Sequence and temperature effect on electrical properties of modified poly(dA)-poly(dT) DNA wire

    NASA Astrophysics Data System (ADS)

    Suhendro, Daniel K.; Yudiarsah, Efta; Saleh, Rosari

    2016-03-01

    We studied the effect of thermal fluctuations on charge transport in two types of modified poly(dA)-poly(dT) DNA by calculating the transmission probability and I-V characteristics. The modification is carried out by replacing some of the AT base pairs with CG or GC base pairs placed randomly along the chain. The DNA model is placed in between two metallic electrodes. We used tight binding Hamiltonian to model the DNA molecule and electrodes. The thermal fluctuation is modeled by varying the twist angles of each base in the DNA. The transfer matrix and scattering matrix methods were employed in calculating the transmission probability. Transmission probability is used as an input in calculating I-V characteristics using Landauer-Büttiker formalism. The twist angle disorder is influenced by the temperature and frequency. In order to prevent spurious results, we take the average value transmission probability of 1000 realizations of twist angles. Our results indicate that the DNA modified by CG base pairs has its electrical properties impeded by increasing thermal fluctuation (increasing temperature and decreasing frequency). However, different behavior is observed on the DNA modified by GC base pairs, at low temperature its electrical properties are enhanced by decreasing frequency. Moreover, electrical properties of this DNA at high frequency are also enhanced as temperature increases.

  17. Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification.

    PubMed

    Huang, Hailiang; Shi, Shuo; Zheng, Xuyue; Yao, Tianming

    2015-09-15

    Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers. PMID:25950941

  18. Molecular analysis of high-copy insertion sites in maize

    PubMed Central

    Settles, A. Mark; Latshaw, Susan; McCarty, Donald R.

    2004-01-01

    High-copy transposon mutagenesis is an effective tool for creating gene disruptions in maize. In order to molecularly define transposon-induced disruptions on a genome-wide scale, we optimized TAIL-PCR to amplify genomic DNA flanking maize Robertson’s Mutator insertions. Sample sequencing from 43 Mutator stocks and the W22 inbred line identified 676 non-redundant insertions, and only a small fraction of the flanking sequences showed significant similarity to maize repetitive sequences. We further designed and tested 79 arbitrary primers to identify 12 primers that amplify all Mutator insertions within a DNA sample at 3.1-fold redundancy. Importantly, the products are of sufficient size to use as substrates or probes for hybridization-based identification of gene disruptions. Our adaptation simplifies previously published TAIL-PCR protocols and should be transferable to other high-copy insertional mutagens. PMID:15060129

  19. Gene Insertion Patterns and Sites

    NASA Astrophysics Data System (ADS)

    Vain, Philippe; Thole, Vera

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

  20. Inducible Expression of Agrobacterium Virulence Gene VirE2 for Stringent Regulation of T-DNA Transfer in Plant Transient Expression Systems.

    PubMed

    Denkovskienė, Erna; Paškevičius, Šarūnas; Werner, Stefan; Gleba, Yuri; Ražanskienė, Aušra

    2015-11-01

    Agrotransfection with viral vectors is an effective solution for the transient production of valuable proteins in plants grown in contained facilities. Transfection methods suitable for field applications are desirable for the production of high-volume products and for the transient molecular reprogramming of plants. The use of genetically modified (GM) Agrobacterium strains for plant transfections faces substantial biosafety issues. The environmental biosafety of GM Agrobacterium strains could be improved by regulating their T-DNA transfer via chemically inducible expression of virE2, one of the essential Agrobacterium virulence genes. In order to identify strong and stringently regulated promoters in Agrobacterium strains, we evaluated isopropyl-β-d-thiogalactoside-inducible promoters Plac, Ptac, PT7/lacO, and PT5/lacOlacO and cumic acid-inducible promoters PlacUV5/CuO, Ptac/CuO, PT5/CuO, and PvirE/CuO. Nicotiana benthamiana plants were transfected with a virE2-deficient A. tumefaciens strain containing transient expression vectors harboring inducible virE2 expression cassettes and containing a marker green fluorescent protein (GFP) gene in their T-DNA region. Evaluation of T-DNA transfer was achieved by counting GFP expression foci on plant leaves. The virE2 expression from cumic acid-induced promoters resulted in 47 to 72% of wild-type T-DNA transfer. Here, we present efficient and tightly regulated promoters for gene expression in A. tumefaciens and a novel approach to address environmental biosafety concerns in agrobiotechnology. PMID:26292850

  1. Detection of transformed cells in crown gall tumors using the GUS reporter gene and correlation of GUS stained cells with T-DNA gene activity

    SciTech Connect

    Black, R.C. ); Labriola, J.; Binns, A.N. )

    1990-05-01

    Crown gall tumors are a mixture of transformed hormone producing cells and normal cells. Until now it has not been possible to directly visualize these cell types in situ. We have constructed strains of Agrobacterium tumefaciens that carry the 35S-{beta}-glucuronidase (GUS) reporter gene in either wild type or mutant Ti plasmids. Using histochemical staining for GUS activity, blue (GUS positive) sectors are observed in tumor sections. In order to demonstrate that the blue sectors actually represent cells expressing other T-DNA genes, we have looked for T-DNA gene encoded enzyme activity in the stained and unstained sectors. The blue sectors accumulate octopine (a product of the octopine synthase gene on the T-DNA) while the white (GUS negative) sectors do not. We conclude that the use of the GUS reporter gene provides a sensitive and reliable method for visualizing transformation events in plant tissues. A comparison of the proportion of transformed and nontransformed cells in wild type tumors vs. tumors deficient in auxin or cytokinin encoding genes will be discussed.

  2. Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon–helix–helix DNA-binding fold

    PubMed Central

    Lu, Jun; den Dulk-Ras, Amke; Hooykaas, Paul J. J.; Glover, J. N. Mark

    2009-01-01

    Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-Å X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC282–202, which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DNA but not single-stranded DNA. Mutations that severely affect VirC2 DNA binding are highly deleterious for both T-DNA transfer into yeast and the virulence of A. tumefaciens in different plants including Nicotiana glauca and Kalanchoe daigremontiana. These data suggest that VirC2 enhances T-DNA transfer and virulence through DNA binding with its RHH fold. The RHH fold of VirC2 is the first crystal structure representing a group of predicted RHH proteins that facilitate endonucleolytic processing of DNA for horizontal gene transfer. PMID:19482939

  3. Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.

    PubMed

    Lu, Jun; den Dulk-Ras, Amke; Hooykaas, Paul J J; Glover, J N Mark

    2009-06-16

    Agrobacterium tumefaciens VirC2 stimulates processing of single-stranded T-DNA that is translocated into plants to induce tumor formation, but how VirC2 functions is unclear. Here, we report the 1.7-A X-ray crystal structure of its trypsin-resistant C-terminal domain, VirC2(82-202), which reveals a form of the ribbon-helix-helix (RHH) DNA-binding fold contained within a single polypeptide chain. DNA-binding assays and mutagenesis indicate that VirC2 uses this RHH fold to bind double-stranded DNA but not single-stranded DNA. Mutations that severely affect VirC2 DNA binding are highly deleterious for both T-DNA transfer into yeast and the virulence of A. tumefaciens in different plants including Nicotiana glauca and Kalanchoe daigremontiana. These data suggest that VirC2 enhances T-DNA transfer and virulence through DNA binding with its RHH fold. The RHH fold of VirC2 is the first crystal structure representing a group of predicted RHH proteins that facilitate endonucleolytic processing of DNA for horizontal gene transfer. PMID:19482939

  4. Precise-Conductance Valve Insert

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.; Hoyt, R. F.

    1986-01-01

    Valve modification provides two operating modes fully open and small, precise leak. Copper insert with radially oriented holes allows small, controllable, precise effusion rate when valve closed or nearly unobstructed flow when valve open. Numerous applications in surface physics, vacuum physics, materials science, gas kinetics, thin films, and other areas of research requiring measured flows of gas into or out of system.

  5. Many P-Element Insertions Affect Wing Shape in Drosophila melanogaster

    PubMed Central

    Weber, Kenneth; Johnson, Nancy; Champlin, David; Patty, April

    2005-01-01

    A screen of random, autosomal, homozygous-viable P-element insertions in D. melanogaster found small effects on wing shape in 11 of 50 lines. The effects were due to single insertions and remained stable and significant for over 5 years, in repeated, high-resolution measurements. All 11 insertions were within or near protein-coding transcription units, none of which were previously known to affect wing shape. Many sites in the genome can affect wing shape. PMID:15545659

  6. Biomechanical Analysis of Differing Pedicle Screw Insertion Angles

    PubMed Central

    Sterba, William; Kim, Do-Gyoon; Fyhrie, David P.; Yeni, Yener N.; Vaidya, Rahul

    2007-01-01

    Background Pedicle screw fixation to stabilize lumbar spinal fusion has become the gold standard for posterior stabilization. A significant percentage of surgical candidates are classified as obese or morbidly obese. For these patients, the depth of the incisions and soft tissue makes it extremely difficult to insert pedicle screws along the pedicle axis. As such, the pedicle screws could only be inserted in a much more sagittal axis. However, biomechanical stability of the angled screw insertion has been controversial. We hypothesized that the straight or parallel screw was a more stable construct compared to the angled or axially inserted screw when subjected to caudal cyclic loading. Methods We obtained 12 fresh frozen lumbar vertebrae from L3 to L5 from five cadavers. Schantz screws (6.0mm) were inserted into each pedicle, one angled and along the axis of the pedicle and the other parallel to the spinous process. Fluoroscopic imaging was used to guide insertion. Each screw was then subjected to caudal cyclic loads of 50N for 2000 cycles at 2Hz. Analysis of initial damage, initial rate, and total damage during cyclic loading was undertaken. Findings Average total fatigue damage for straight screws measured 0.3980.38 mm, and 0.6890.96 mm for angled screws. Statistical analysis for total fatigue damage ratio of angled to straight screws revealed that a significant stability was achieved in straight- screw construct (p<0.03). Interpretation This study showed that straight screw insertion results in a more stable pedicle-screw construct. The angled screw insertion technique resulted in more scattered values of damage indicating that the outcome from the angled screw fixation is less predictable. This validates the use of this technique to implant pedicle screws across the axis of the pedicle rather than along the axis, (parallel to the midline sagittal line), and has broad implications in instrumented posterior lumbar spinal surgery. PMID:17208340

  7. Ultrasound guided spine needle insertion

    NASA Astrophysics Data System (ADS)

    Chen, Elvis C. S.; Mousavi, Parvin; Gill, Sean; Fichtinger, Gabor; Abolmaesumi, Purang

    2010-02-01

    An ultrasound (US) guided, CT augmented, spine needle insertion navigational system is introduced. The system consists of an electromagnetic (EM) sensor, an US machine, and a preoperative CT volume of the patient anatomy. Three-dimensional (3D) US volume is reconstructed intraoperatively from a set of two-dimensional (2D) freehand US slices, and is coregistered with the preoperative CT. This allows the preoperative CT volume to be used in the intraoperative clinical coordinate. The spatial relationship between the patient anatomy, surgical tools, and the US transducer are tracked using the EM sensor, and are displayed with respect to the CT volume. The pose of the US transducer is used to interpolate the CT volume, providing the physician with a 2D "x-ray vision" to guide the needle insertion. Many of the system software components are GPU-accelerated, allowing real-time performance of the guidance system in a clinical setting.

  8. Insertional mutagenesis in transgenic mice

    SciTech Connect

    Woychik, R.P.; Bultman, S.J.; Schrick, J.J.; Moyer, J.H.; Beatty, B.R.; Godfrey, V.L.; Selby, P.B. )

    1991-03-11

    The molecular analysis of mutations in the mouse is an ideal way of establishing structure-function relationships between individual genes and complex developmental phenotypes. Insertional mutations, caused by the integration of a transgene, are advantageous because the mutant locus is tagged' with the exogenously added DNA and can be accessed with existing cloning and molecular analysis techniques. The authors have implemented a large-scale insertional mutagenesis program at the Oak Ridge National Laboratory in an effort to identify numerous mutations with developmental phenotypes. Several of these mutations are currently being subjected to an in-depth molecular analysis involving the characterization of the structure and expression of the mutant locus. Additionally, the authors are mapping transgene integration sites with in situ hybridization procedures, which will result in additional well-characterized molecular access points for the mouse genome.

  9. Magnetic counterforce for insertion devices.

    PubMed

    Carr, Roger

    2003-05-01

    In a standard insertion device, such as a wiggler or undulator, the force between two rows of magnets increases exponentially as the gap between the rows decreases. This force is usually managed by a powerful mechanical gap adjustor, sometimes with the aid of springs at small values of gap. This paper is a description of how the magnetic forces can be nulled using auxiliary counterforce magnets. PMID:12714760

  10. A coumaroyl-ester-3-hydroxylase Insertion Mutant Reveals the Existence of Nonredundant meta-Hydroxylation Pathways and Essential Roles for Phenolic Precursors in Cell Expansion and Plant Growth1[W][OA

    PubMed Central

    Abdulrazzak, Nawroz; Pollet, Brigitte; Ehlting, Jürgen; Larsen, Kim; Asnaghi, Carole; Ronseau, Sebastien; Proux, Caroline; Erhardt, Mathieu; Seltzer, Virginie; Renou, Jean-Pierre; Ullmann, Pascaline; Pauly, Markus; Lapierre, Catherine; Werck-Reichhart, Danièle

    2006-01-01

    Cytochromes P450 monooxygenases from the CYP98 family catalyze the meta-hydroxylation step in the phenylpropanoid biosynthetic pathway. The ref8 Arabidopsis (Arabidopsis thaliana) mutant, with a point mutation in the CYP98A3 gene, was previously described to show developmental defects, changes in lignin composition, and lack of soluble sinapoyl esters. We isolated a T-DNA insertion mutant in CYP98A3 and show that this mutation leads to a more drastic inhibition of plant development and inhibition of cell growth. Similar to the ref8 mutant, the insertion mutant has reduced lignin content, with stem lignin essentially made of p-hydroxyphenyl units and trace amounts of guaiacyl and syringyl units. However, its roots display an ectopic lignification and a substantial proportion of guaiacyl and syringyl units, suggesting the occurrence of an alternative CYP98A3-independent meta-hydroxylation mechanism active mainly in the roots. Relative to the control, mutant plantlets produce very low amounts of sinapoyl esters, but accumulate flavonol glycosides. Reduced cell growth seems correlated with alterations in the abundance of cell wall polysaccharides, in particular decrease in crystalline cellulose, and profound modifications in gene expression and homeostasis reminiscent of a stress response. CYP98A3 thus constitutes a critical bottleneck in the phenylpropanoid pathway and in the synthesis of compounds controlling plant development. CYP98A3 cosuppressed lines show a gradation of developmental defects and changes in lignin content (40% reduction) and structure (prominent frequency of p-hydroxyphenyl units), but content in foliar sinapoyl esters is similar to the control. The purple coloration of their leaves is correlated to the accumulation of sinapoylated anthocyanins. PMID:16377748

  11. Lipid-insertion enables targeting functionalization of erythrocyte membrane-cloaked nanoparticles.

    PubMed

    Fang, Ronnie H; Hu, Che-Ming J; Chen, Kevin N H; Luk, Brian T; Carpenter, Cody W; Gao, Weiwei; Li, Shulin; Zhang, Dong-Er; Lu, Weiyue; Zhang, Liangfang

    2013-10-01

    RBC membrane-cloaked polymeric nanoparticles represent an emerging nanocarrier platform with extended circulation in vivo. A lipid-insertion method is employed to functionalize these nanoparticles without the need for direct chemical conjugation. Insertion of both folate and the nucleolin-targeting aptamer AS1411 shows receptor-specific targeting against model cancer cell lines. PMID:23907698

  12. Characterization of insertion sites in Rainbow papaya, the first commercialized transgenic tree-fruit crop

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inserts and insert sites in transgenic, commercial papaya line 55-1 derivatives Rainbow and SunUp were characterized as part of a petition to Japan to allow import of fresh fruit of these cultivars from the U.S. and to provide data for a larger study aimed at understanding the global impact of DNA t...

  13. Agrobacterium tumefaciens oncogenic suppressors inhibit T-DNA and VirE2 protein substrate binding to the VirD4 coupling protein

    PubMed Central

    Cascales, Eric; Atmakuri, Krishnamohan; Liu, Zhenying; Binns, Andrew N.; Christie, Peter J.

    2009-01-01

    Summary Agrobacterium tumefaciens uses a type IV secretion (T4S) system composed of VirB proteins and VirD4 to deliver oncogenic DNA (T-DNA) and protein substrates to susceptible plant cells during the course of infection. Here, by use of the Transfer DNA Immuno-Precipitation (TrIP) assay, we present evidence that the mobilizable plasmid RSF1010 (IncQ) follows the same translocation pathway through the VirB/D4 secretion channel as described previously for the T-DNA. The RSF1010 transfer intermediate and the Osa protein of plasmid pSa (IncW), related in sequence to the FiwA fertility inhibition factor of plasmid RP1 (IncPα), render A. tumefaciens host cells nearly avirulent. By use of a semi-quantitative TrIP assay, we show that both of these ‘oncogenic suppressor factors’ inhibit binding of T-DNA to the VirD4 substrate receptor. Both factors also inhibit binding of the VirE2 protein substrate to VirD4, as shown by coimmunoprecipitation and bimolecular fluorescence complementation assays. Osa fused to the green fluorescent protein (GFP) also blocks T-DNA and VirE2 binding to VirD4, and Osa-GFP colocalizes with VirD4 at A. tumefaciens cell poles. RSF1010 and Osa interfere specifically with VirD4 receptor function and not with VirB channel activity, as shown by (i) TrIP and (ii) a genetic screen for effects of the oncogenic suppressors on pCloDF13 translocation through a chimeric secretion channel composed of the pCloDF13-encoded MobB receptor and VirB channel subunits. Our findings establish that a competing plasmid substrate and a plasmid fertility inhibition factor act on a common target, the T4S receptor, to inhibit docking of DNA and protein substrates to the translocation apparatus. PMID:16194240

  14. Pneumothorax as a complication of central venous catheter insertion.

    PubMed

    Tsotsolis, Nikolaos; Tsirgogianni, Katerina; Kioumis, Ioannis; Pitsiou, Georgia; Baka, Sofia; Papaiwannou, Antonis; Karavergou, Anastasia; Rapti, Aggeliki; Trakada, Georgia; Katsikogiannis, Nikolaos; Tsakiridis, Kosmas; Karapantzos, Ilias; Karapantzou, Chrysanthi; Barbetakis, Nikos; Zissimopoulos, Athanasios; Kuhajda, Ivan; Andjelkovic, Dejan; Zarogoulidis, Konstantinos; Zarogoulidis, Paul

    2015-03-01

    The central venous catheter (CVC) is a catheter placed into a large vein in the neck [internal jugular vein (IJV)], chest (subclavian vein or axillary vein) or groin (femoral vein). There are several situations that require the insertion of a CVC mainly to administer medications or fluids, obtain blood tests (specifically the "central venous oxygen saturation"), and measure central venous pressure. CVC usually remain in place for a longer period of time than other venous access devices. There are situations according to the drug administration or length of stay of the catheter that specific systems are indicated such as; a Hickman line, a peripherally inserted central catheter (PICC) line or a Port-a-Cath may be considered because of their smaller infection risk. Sterile technique is highly important here, as a line may serve as a port of entry for pathogenic organisms, and the line itself may become infected with organisms such as Staphylococcus aureus and coagulase-negative Staphylococci. In the current review we will present the complication of pneumothorax after CVC insertion. PMID:25815301

  15. Pneumothorax as a complication of central venous catheter insertion

    PubMed Central

    Tsotsolis, Nikolaos; Tsirgogianni, Katerina; Kioumis, Ioannis; Pitsiou, Georgia; Baka, Sofia; Papaiwannou, Antonis; Karavergou, Anastasia; Rapti, Aggeliki; Trakada, Georgia; Katsikogiannis, Nikolaos; Tsakiridis, Kosmas; Karapantzos, Ilias; Karapantzou, Chrysanthi; Barbetakis, Nikos; Zissimopoulos, Athanasios; Kuhajda, Ivan; Andjelkovic, Dejan; Zarogoulidis, Konstantinos

    2015-01-01

    The central venous catheter (CVC) is a catheter placed into a large vein in the neck [internal jugular vein (IJV)], chest (subclavian vein or axillary vein) or groin (femoral vein). There are several situations that require the insertion of a CVC mainly to administer medications or fluids, obtain blood tests (specifically the “central venous oxygen saturation”), and measure central venous pressure. CVC usually remain in place for a longer period of time than other venous access devices. There are situations according to the drug administration or length of stay of the catheter that specific systems are indicated such as; a Hickman line, a peripherally inserted central catheter (PICC) line or a Port-a-Cath may be considered because of their smaller infection risk. Sterile technique is highly important here, as a line may serve as a port of entry for pathogenic organisms, and the line itself may become infected with organisms such as Staphylococcus aureus and coagulase-negative Staphylococci. In the current review we will present the complication of pneumothorax after CVC insertion. PMID:25815301

  16. Insert metering plates for gas turbine nozzles

    SciTech Connect

    Burdgick, Steven S.; Itzel, Gary; Chopra, Sanjay; Abuaf, Nesim; Correia, Victor H.

    2004-05-11

    The invention comprises a metering plate which is assembled to an impingement insert for use in the nozzle of a gas turbine. The metering plate can have one or more metering holes and is used to balance the cooling flow within the nozzle. A metering plate with multiple holes reduces static pressure variations which result from the cooling airflow through the metering plate. The metering plate can be assembled to the insert before or after the insert is inserted into the nozzle.

  17. Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

    PubMed Central

    Gohl, Daryl M.; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J.; Horowitz, Mark; Clandinin, Thomas R.

    2014-01-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools. PMID:24374352

  18. JT/LJT connector insert material evaluation

    SciTech Connect

    Baca, J.R.F.

    1991-10-01

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

  19. Chassis unit insert tightening-extract device

    NASA Technical Reports Server (NTRS)

    Haerther, L. W.; Zimmerman, P. A. (Inventor)

    1964-01-01

    The invention relates to the insertion and extraction of rack mounted electronic units and in particular to a screw thread insert tightening and extract device, for chassis units having a collar which may be rotatably positioned manually for the insert tightening or extraction of various associated chassis units, as desired.

  20. Electromagnetically tracked placement of a peripherally inserted central catheter

    NASA Astrophysics Data System (ADS)

    Sacolick, Laura; Patel, Neilesh; Tang, Jonathan; Levy, Elliot; Cleary, Kevin R.

    2004-05-01

    This paper describes a computer program to utilize electromagnetic tracking guidance during insertion of peripherally inserted central catheters. Placement of a Peripherally Inserted Central Catheter (PICC) line is a relatively simple, routine procedure in which a catheter is inserted into the veins of the lower arm and threaded up the arm to the vena cava to sit just above the heart. However, the procedure requires x-ray verification of the catheter position and is usually done under continuous fluoroscopic guidance. The computer program is designed to replace fluoroscopic guidance in this procedure and make PICC line placement a bedside procedure. This would greatly reduce the time and resources dedicated to this procedure. The physician first goes through a quick registration procedure to register the patient space with the computer screen coordinates. Once registration is completed, the program provides a continuous, real-time display of the position of the catheter tip overlaid on an x-ray image of the patient on an adjacent computer screen. Both the position and orientation of the catheter tip is shown. The display is very similar to that shown when using fluoroscopy.

  1. Placement of a peripherally inserted central catheter into the azygous vein

    SciTech Connect

    Franklin, Iain Gilmore, Christopher

    2015-06-15

    Peripherally inserted central catheters (PICC) are used for a variety of infusion therapies. They are indicated in patients requiring long-term venous access. Incorrect positioning of the insertion of a PICC line is one of the known complications when inserting the device in clinical practice. Radiographers once performing imaging will commonly check if the tip of a PICC has entered the superior vena cava. This case study will report on a lesser known incorrect placement of a PICC line into the azygous vein and how this can be detected on radiographic imaging. This outcome for the patient can be detrimental as it has an increased risk of perforation, thrombus, and fistula formation.

  2. Analysis of inserts in prokaryote genomes

    NASA Astrophysics Data System (ADS)

    Cristea, Paul Dan; Tuduce, Rodica Aurora

    2008-02-01

    Nucleotide genomic signals satisfy regularities that reveal restrictions in the distribution of nucleotides and pairs of nucleotides along DNA sequences. Structurally, a chromosome appears to be more than a plain text, by satisfying symmetry constrains that evoke the rhythm and rhyme in poems. These regularities make it easy to identify exogenous inserts in the genomes of prokaryotes, because such inserts obey different regularities than the background sequence. The paper presents instances of inserts found in the genomes of Bacillus subtilis, Mycobacterium tuberculosis and other prokaryotes. Inserts of exogenous material are frequently accompanied by complementary inserts tending to restore the original constrains.

  3. Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) Furnace Development

    NASA Technical Reports Server (NTRS)

    Crouch, Myscha; Carswell, William; Farmer, Jeff; Rose, Fred; Tidwell, Paul

    2000-01-01

    This paper presents, in viewgraph form, QMI (Quench Module Insert) and DMI (Diffusion Module Insert) furnace development. The topics include: 1) Furnace Module in Rack; 2) Quench Module Insert; 3) QMI in MSL Core; 4) Diffusion Module Insert; 5) QMI; and 6) QMI Development and Testing.

  4. Insertion sequence elements of Pseudomonas savastanoi: Nucleotide sequence and homology with Agrobacterium tumefaciens transfer DNA.

    PubMed

    Yamada, T; Lee, P D; Kosuge, T

    1986-11-01

    Two types of transposable elements, IS51 and IS52 (IS, insertion sequence), were found in Pseudomonas syringae subsp. savastanoi (P. savastanoi) that spontaneously insert into and inactivate iaaM; the insertion results in the loss of indoleacetic acid production and attenuation of virulence. The nucleotide sequences of both IS elements have sizes and structural features common to other prokaryotic IS elements; IS51 is 1311 base pairs (bp) long and has terminal inverted repeats of 26 bp; IS52 is 1209 bp long and has terminal inverted repeats of 10 bp with a 1 bp mismatch. In the insertion involving IS51, the trinucleotide sequence CAG is duplicated within iaaM sequences at the recombination junction; in those involving IS52 the tetranucleotide sequences TTAG or CTAG are duplicated within iaaM sequences at the recombination junction. A copy of IS51 occurs 2.5 kilobases downstream from IaaH. In contrast to the high copy number of IS51 in the genome of the bacterium, only a few copies of IS52 are present. No nucleotide sequence homology was found between IS51 and IS52. However, a striking nucleotide sequence homology was found between a 531-bp region of IS51 and a portion of the central region of transfer DNA (T-DNA) in the octopine plasmid pTi15955 from Agrobacterium tumefaciens. These observations, together with our earlier finding on the homology between iaaM and iaaH and between gene 1 and gene 2 of transfer DNA, further suggest that genes for indoleacetic acid production in the two systems have a common origin. PMID:16593778

  5. Focus on peripherally inserted central catheters in critically ill patients

    PubMed Central

    Cotogni, Paolo; Pittiruti, Mauro

    2014-01-01

    Venous access devices are of pivotal importance for an increasing number of critically ill patients in a variety of disease states and in a variety of clinical settings (emergency, intensive care, surgery) and for different purposes (fluids or drugs infusions, parenteral nutrition, antibiotic therapy, hemodynamic monitoring, procedures of dialysis/apheresis). However, healthcare professionals are commonly worried about the possible consequences that may result using a central venous access device (CVAD) (mainly, bloodstream infections and thrombosis), both peripherally inserted central catheters (PICCs) and centrally inserted central catheters (CICCs). This review aims to discuss indications, insertion techniques, and care of PICCs in critically ill patients. PICCs have many advantages over standard CICCs. First of all, their insertion is easy and safe -due to their placement into peripheral veins of the arm- and the advantage of a central location of catheter tip suitable for all osmolarity and pH solutions. Using the ultrasound-guidance for the PICC insertion, the risk of hemothorax and pneumothorax can be avoided, as well as the possibility of primary malposition is very low. PICC placement is also appropriate to avoid post-procedural hemorrhage in patients with an abnormal coagulative state who need a CVAD. Some limits previously ascribed to PICCs (i.e., low flow rates, difficult central venous pressure monitoring, lack of safety for radio-diagnostic procedures, single-lumen) have delayed their start up in the intensive care units as common practice. Though, the recent development of power-injectable PICCs overcomes these technical limitations and PICCs have started to spread in critical care settings. Two important take-home messages may be drawn from this review. First, the incidence of complications varies depending on venous accesses and healthcare professionals should be aware of the different clinical performance as well as of the different risks associated with each type of CVAD (CICCs or PICCs). Second, an inappropriate CVAD choice and, particularly, an inadequate insertion technique are relevant-and often not recognized-potential risk factors for complications in critically ill patients. We strongly believe that all healthcare professionals involved in the choice, insertion or management of CVADs in critically ill patients should know all potential risk factors of complications. This knowledge may minimize complications and guarantee longevity to the CVAD optimizing the risk/benefit ratio of CVAD insertion and use. Proper management of CVADs in critical care saves lines and lives. Much evidence from the medical literature and from the clinical practice supports our belief that, compared to CICCs, the so-called power-injectable peripherally inserted central catheters are a good alternative choice in critical care. PMID:25374804

  6. Nucleotide sequence of an insertion sequence (IS) element identified in the T-DNA region of a spontaneous variant of the Ti-plasmid pTiT37.

    PubMed Central

    Vanderleyden, J; Desair, J; De Meirsman, C; Michiels, K; Van Gool, A P; Chilton, M D; Jen, G C

    1986-01-01

    We have identified and determined the nucleotide sequence of an IS element (IS136) of Agrobacterium tumefaciens. This is the first IS element isolated and sequenced from a nopaline type Ti-plasmid. Our IS element has 32/30 bp inverted repeats with 6 mismatches, is 1,313 bp long and generates 9 bp direct repeats upon integration. IS136 has 3 main open reading frames (ORF's). Only ORF1 (159 codons) is preceded by sequences that are proposed to serve functional roles in transcriptional and translational initiation. No DNA sequence homology was found between IS136 and IS66, an IS element isolated from an octopine type Ti-plasmid. PMID:3018677

  7. Nozzle insert for mixed mode fuel injector

    DOEpatents

    Lawrence, Keith E.

    2006-11-21

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

  8. Preoperative measurement of ACL insertion sites.

    PubMed

    Schwartzberg, Randy; Snyder, Kevin; Reuss, Bryan

    2015-02-01

    This study was designed to evaluate preoperative predictions of the femoral and tibial ACL insertion lengths. Intraoperative measurements were made of the femoral and tibial ACL insertion lengths with an arthroscopic ruler. A musculoskeletal radiologist and a sports medicine orthopedic surgeon measured the ACL insertions from preoperative magnetic resonance imagings (MRIs) in a blinded fashion. Correlations between height, weight, body mass index, and gender with intraoperative ACL insertion length measures were also evaluated. Patient height and male gender demonstrated strong correlations with intraoperative ACL insertion measures. A moderate correlation was seen between patient weight and intraoperative ACL insertion measures. When evaluating the frequency with which the raters' respective MRI measures were exactly the same as the intraoperative measures, moderate correlations were seen. The radiologist and orthopedic surgeons' MRI measures were within 3 mm of the intraoperative measures 98 and 75% of the time, respectively, for the femur and 92 and 83% of the time, respectively, for the tibia. This study concludes that preoperative MRI measures of ACL insertion lengths can be used to predict intraoperative ACL insertion lengths. Also, it is expected that taller patients and male patients should have greater ACL insertion lengths seen arthroscopically. PMID:24622911

  9. Lipid-insertion enables targeting functionalization of erythrocyte membrane-cloaked nanoparticles

    NASA Astrophysics Data System (ADS)

    Fang, Ronnie H.; Hu, Che-Ming J.; Chen, Kevin N. H.; Luk, Brian T.; Carpenter, Cody W.; Gao, Weiwei; Li, Shulin; Zhang, Dong-Er; Lu, Weiyue; Zhang, Liangfang

    2013-09-01

    RBC membrane-cloaked polymeric nanoparticles represent an emerging nanocarrier platform with extended circulation in vivo. A lipid-insertion method is employed to functionalize these nanoparticles without the need for direct chemical conjugation. Insertion of both folate and the nucleolin-targeting aptamer AS1411 shows receptor-specific targeting against model cancer cell lines.RBC membrane-cloaked polymeric nanoparticles represent an emerging nanocarrier platform with extended circulation in vivo. A lipid-insertion method is employed to functionalize these nanoparticles without the need for direct chemical conjugation. Insertion of both folate and the nucleolin-targeting aptamer AS1411 shows receptor-specific targeting against model cancer cell lines. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03064d

  10. Central Solenoid Insert Technical Specification

    SciTech Connect

    Martovetsky, Nicolai N; Smirnov, Alexandre

    2011-09-01

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

  11. Insertion sequence elements in Lactococcus garvieae.

    PubMed

    Eraclio, Giovanni; Ricci, Giovanni; Fortina, Maria Grazia

    2015-01-25

    Insertion sequences are the simplest intracellular Mobile Genetic Elements which can occur in very high numbers in prokaryotic genomes, where they play an important evolutionary role by promoting genome plasticity. As such, the studies on the diversity and distribution of insertion sequences in genomes not yet investigated can contribute to improve the knowledge on a bacterial species and to identify new transposable elements. The present work describes the occurrence of insertion sequences in Lactococcus garvieae, an opportunistic emerging zoonotic and human pathogen, also associated with different food matrices. To date, no insertion elements have been described for L. garvieae in the IS element database. The analysis of the twelve published L. garvieae genomes identified 15 distinct insertion sequences that are members of the IS3, IS982, IS6, IS21 and IS256 families, including five new elements. Most of the insertion sequences in L. garvieae show substantial homology to the Lactococcus lactis elements, suggesting the movement of IS between these two species phylogenetically closely related. ISLL6 elements belonging to IS3 family were most abundant, with several copies distributed in 9 of the 12 genomes analyzed. An alignment analysis of two complete genomes carrying multi-copies of this insertion sequence indicates a possible involvement of ISLL6 in chromosomal rearrangement. PMID:25447909

  12. IUD insertion immediately after incomplete abortion.

    PubMed

    Goldsmith, A; Goldberg, R; Eyzaguirre, H; Lizana, L

    1972-04-01

    All women who were admitted to the Felix Bulnes Hospital, Santiaog, Chile, for incomplete abortion between July 1968 and June 1969 were given instruction in family planning and contraceptive services. A total of 584 women chose to have an IUD insertion. Although all the women thought they had received an IUD, 1 group had a Lippes loop D inserted immediately after curettage and the other group had no insertion. The attending doctor had no prior knowledge as to which women were to receive the device nor did the doctor at the follow-up know until after the physical exam had taken place. 30 days after discharge from the hospital, the women returned from check-up and follow-up. At this time the women who had not received an IUD were given an insertion. Differences between the group with insertion and the one without were significant only for the interval between curettage and first menses and for the quantity of flow in relation to previous menstruation. The difference between the 2 groups for duration of menstrual flow was of borderline significance at the .05 significance level. It is concluded from the study that in the absence of psychologi cal bias of the patient to the IUD insertion, and possibly bias in its use by the doctor, there are no serious complications in the first month following immediate postabortal IUD insertion even where the abortion was a septic incomplete one. PMID:12333065

  13. Sequential cooling insert for turbine stator vane

    SciTech Connect

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

    2014-11-04

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

  14. Sequential cooling insert for turbine stator vane

    SciTech Connect

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

    2014-04-01

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

  15. Elliptically polarizing adjustable phase insertion device

    DOEpatents

    Carr, Roger

    1995-01-01

    An insertion device for extracting polarized electromagnetic energy from a beam of particles is disclosed. The insertion device includes four linear arrays of magnets which are aligned with the particle beam. The magnetic field strength to which the particles are subjected is adjusted by altering the relative alignment of the arrays in a direction parallel to that of the particle beam. Both the energy and polarization of the extracted energy may be varied by moving the relevant arrays parallel to the beam direction. The present invention requires a substantially simpler and more economical superstructure than insertion devices in which the magnetic field strength is altered by changing the gap between arrays of magnets.

  16. Effects of Single P-Element Insertions on Olfactory Behavior in Drosophila Melanogaster

    PubMed Central

    Anholt, RRH.; Lyman, R. F.; Mackay, TFC.

    1996-01-01

    Single P-element (P[lArB]) insertional mutagenesis of an isogenic strain was used to identify autosomal loci affecting odor-guided behavior of Drosophila melanogaster. The avoidance response to benzaldehyde of 379 homozygous P[lArB] element-containing insert lines was evaluated quantitatively. Fourteen smell impaired (smi) lines were identified in which P[lArB] element insertion caused different degrees of hyposmia in one or both sexes. The smi loci map to different cytological locations and probably are novel olfactory genes. Enhancer trap analysis of the smi lines indicates that expression of at least 10 smi genes is controlled by olfactory tissue-specific promoter/enhancer elements. PMID:8722782

  17. Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays

    PubMed Central

    Mahalingam, Ramamurthy; Fedoroff, Nina

    2001-01-01

    We describe a method to screen pools of DNA from multiple transposon lines for insertions in many genes simultaneously. We use thermal asymmetric interlaced–PCR, a hemispecific PCR amplification protocol that combines nested, insertion-specific primers with degenerate primers, to amplify DNA flanking the transposons. In reconstruction experiments with previously characterized Arabidopsis lines carrying insertions of the maize Dissociation (Ds) transposon, we show that fluorescently labeled, transposon-flanking fragments overlapping ORFs hybridize to cognate expressed sequence tags (ESTs) on a DNA microarray. We further show that insertions can be detected in DNA pools from as many as 100 plants representing different transposon lines and that all of the tested, transposon-disrupted genes whose flanking fragments can be amplified individually also can be detected when amplified from the pool. The ability of a transposon-flanking fragment to hybridize declines rapidly with decreasing homology to the spotted DNA fragment, so that only ESTs with >90% homology to the transposon-disrupted gene exhibit significant cross-hybridization. Because thermal asymmetric interlaced–PCR fragments tend to be short, use of the present method favors recovery of insertions in and near genes. We apply the technique to screening pools of new Ds lines using cDNA microarrays containing ESTs for ≈1,000 stress-induced and -repressed Arabidopsis genes. PMID:11416215

  18. Insertion Homo- and Copolymerization of Diallyl Ether.

    PubMed

    Jian, Zhongbao; Mecking, Stefan

    2015-12-21

    The previously unresolved issue of polymerization of allyl monomers CH2 ?CHCH2 X is overcome by a palladium-catalyzed insertion polymerization of diallyl ether as a monomer. An enhanced 2,1-insertion of diallyl ether as compared to mono-allyl ether retards the formation of an unreactive five-membered cyclic O-chelate (after 1,2-insertion) that otherwise hinders further polymerization, and also enhances incorporation in ethylene polymers (20.4?mol?%). Cyclic ether repeat units are formed selectively (96?%-99?%) by an intramolecular insertion of the second allyl moiety of the monomer. These features even enable a homopolymerization to yield polymers (poly-diallyl ether) with degrees of polymerization of DPn ?44. PMID:26564774

  19. Shoe Inserts and Prescription Custom Orthotics

    MedlinePlus

    ... supports that you can order online or at retail stores. Unless the device has been prescribed by ... cost more than shoe inserts purchased in a retail store, but the additional cost is usually well ...

  20. Insertable fluid flow passage bridgepiece and method

    DOEpatents

    Jones, Daniel O.

    2000-01-01

    A fluid flow passage bridgepiece for insertion into an open-face fluid flow channel of a fluid flow plate is provided. The bridgepiece provides a sealed passage from a columnar fluid flow manifold to the flow channel, thereby preventing undesirable leakage into and out of the columnar fluid flow manifold. When deployed in the various fluid flow plates that are used in a Proton Exchange Membrane (PEM) fuel cell, bridgepieces of this invention prevent mixing of reactant gases, leakage of coolant or humidification water, and occlusion of the fluid flow channel by gasket material. The invention also provides a fluid flow plate assembly including an insertable bridgepiece, a fluid flow plate adapted for use with an insertable bridgepiece, and a method of manufacturing a fluid flow plate with an insertable fluid flow passage bridgepiece.

  1. Peripherally inserted central catheter - dressing change

    MedlinePlus

    PICC - dressing change ... You have a peripherally inserted central catheter (PICC). This is a tube that goes into a vein in your arm. It carries nutrients and medicines into your body. It may also ...

  2. Modeling and characterization of partially inserted electrical connector faults

    NASA Astrophysics Data System (ADS)

    Tokgöz, ćaǧatay; Dardona, Sameh; Soldner, Nicholas C.; Wheeler, Kevin R.

    2016-03-01

    Faults within electrical connectors are prominent in avionics systems due to improper installation, corrosion, aging, and strained harnesses. These faults usually start off as undetectable with existing inspection techniques and increase in magnitude during the component lifetime. Detection and modeling of these faults are significantly more challenging than hard failures such as open and short circuits. Hence, enabling the capability to locate and characterize the precursors of these faults is critical for timely preventive maintenance and mitigation well before hard failures occur. In this paper, an electrical connector model based on a two-level nonlinear least squares approach is proposed. The connector is first characterized as a transmission line, broken into key components such as the pin, socket, and connector halves. Then, the fact that the resonance frequencies of the connector shift as insertion depth changes from a fully inserted to a barely touching contact is exploited. The model precisely captures these shifts by varying only two length parameters. It is demonstrated that the model accurately characterizes a partially inserted connector.

  3. Efficient instruction sequencing with Inline Target Insertion

    NASA Technical Reports Server (NTRS)

    Hwu, Wen-Mei W.; Chang, Pohua P.

    1992-01-01

    Inline target insertion, a specific compiler and pipeline implementation method for delayed branches with squashing, is defined. The method is shown to offer two important features not discovered in previous studies. First, branches inserted into branch slots are correctly executed. Second, the execution returns correctly from interrupts or exceptions with only one program counter. These two features result in better performance and less software/hardware complexity than conventional delayed branching mechanisms.

  4. Rectal suppository: commonsense and mode of insertion.

    PubMed

    Abd-el-Maeboud, K H; el-Naggar, T; el-Hawi, E M; Mahmoud, S A; Abd-el-Hay, S

    1991-09-28

    Rectal suppository is a well-known form of medication and its use is increasing. The commonest shape is one with an apex (pointed end) tapering to a base (blunt end). Because of a general lack of information about mode of insertion, we asked 360 lay subjects (Egyptians and non-Egyptians) and 260 medical personnel (physicians, pharmacists, and nurses) by questionnaire which end they inserted foremost. Apart from 2 individuals, all subjects suggested insertion with the apex foremost. Commonsense was the most frequent basis for this practice (86.9% of lay subjects and 84.6% of medical personnel) followed by information from a relative, a friend, or medical personnel, or from study at medical school. Suppository insertion with the base or apex foremost was compared in 100 subjects (60 adults, 40 infants and children). Retention with the former method was more easily achieved in 98% of the cases, with no need to introduce a finger in the anal canal (1% vs 83%), and lower expulsion rate (0% vs 3%). The designer of the "torpedo-shaped" suppository suggested its insertion with apex foremost. Our data suggest that a suppository is better inserted with the base foremost. Reversed vermicular contractions or pressure gradient of the anal canal might press it inwards. PMID:1681170

  5. Strength of inserts in titanium alloy machining

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  6. Earth boring tool with improved inserts

    SciTech Connect

    Dill, H.; Scales, S.

    1980-07-08

    A description is given of an improved earth boring tool of the type having at least one sintered tungsten carbide insert with a substantially cylindrical retaining surface interferringly secured to the wall of a retaining hole, the improvement comprising said retaining surface roughened such that in any lineal increment of at least 010 inch, there are at least three asperities at least 0.001 in ch long and at least 0.00005 inch deep when measured with a stylus point with a 0.00005 inch radius. An improved method of retaining tungsten carbide inserts in an earth boring tool, said method comprising the steps of: drilling and reaming a plurality of holes in selected locations on the earth boring tool; sintering a plurality of tungsten carbide inserts with a binder selected from the group consisting of cobalt, nickel or iron; grinding a substantially cylindrical wall surface on the inserts that are nominally larger in diameter than the drilled and reamed holes; roughening the wall surface of the inserts such that any lineal increment of at least 0.010 inch has at least three asperities which are at least 0.001 inch long and at least 00005 inch deep when measured with a stylus point with a 0.00005 inch radius; and forcing the inserts interferringly into the mating drilled and reamed holes.

  7. Post-placental insertion of IUDs.

    PubMed

    Aznar, R; Reynoso, L; Montemayor, G; Giner, J

    1980-04-01

    A study was conducted into the efficacy of high fundal insertion of IUDs immediately postplacental delivery. 1008 women who were delivered at 5 large hospitals in Mexico during 1978 accepted this method of contraception. 5 different types of IUD were inserted by approximately 75 persons (ranging from medical students through interns and residents to certified gynecologists) by 3 different insertion techniques. Age and parity of the acceptors are tabulated. Life table follow-up analysis is used to cover cumulative pregnancy, expulsion, removal and continuation events at 3, 6, 9, and 12 months postinsertion. The continuation rate at the end of a year was 61.8 and this rate may rise as the study is completed. There were no differences as to any of these events or in the extent of postinsertion bleeding among the groups using the 5 different devices or with the 3 different techniques. High fundus placement seems to have improved the retention of IUDs inserted immediately after delivery. Rates for accidental pregnancy and medical removal were the same as those obtained with interval IUD insertion. Infection rates did not increase with this timing of insertion. Patient acceptance of this method was high. PMID:12336241

  8. Z-2 Threaded Insert Design and Testing

    NASA Technical Reports Server (NTRS)

    Ross, Amy; Rhodes, Richard; Jones, Robert J.; Graziosi, David; Ferl, Jinny; Sweeny, Mitch; Scarborough, Stephen

    2016-01-01

    NASA's Z-2 prototype space suit contains several components fabricated from an advanced hybrid composite laminate consisting of IM10 carbon fiber and fiber glass. One requirement was to have removable, replaceable helicoil inserts to which other suit components would be fastened. An approach utilizing bonded in inserts with helicoils inside of them was implemented. During initial assembly, cracking sounds were heard followed by the lifting of one of the blind inserts out of its hole when the screws were torqued. A failure investigation was initiated to understand the mechanism of the failure. Ultimately, it was determined that the pre-tension caused by torqueing the fasteners is a much larger force than induced from the pressure loads of the suit which was not considered in the insert design. Bolt tension is determined by dividing the torque on the screw by a k value multiplied by the thread diameter of the bolt. The k value is a factor that accounts for friction in the system. A common value used for k for a non-lubricated screw is 0.2. The k value can go down by as much as 0.1 if the screw is lubricated which means for the same torque, a much larger tension could be placed on the bolt and insert. This paper summarizes the failure investigation that was performed to identify the root cause of the suit failure and details how the insert design was modified to resist a higher pull out tension.

  9. Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers.

    PubMed

    Yamada, H; Starikov, E B; Hennig, D; Archilla, J F R

    2005-06-01

    We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small. PMID:15906117

  10. Cassini/Huygens nears insertion into Saturn's orbit

    NASA Astrophysics Data System (ADS)

    2004-06-01

    On 1 July CEST (30 June Pacific Daylight Time), after a journey of almost seven years and four gravity-assist swing-by manoeuvres, the spacecraft will be inserted into its orbit around Saturn and will reach its closest approach to the planet. The Huygens probe will be detached from the mother ship on 25 December and is due to land on Titan in January next year. The Saturn orbit insertion event can be followed at ESA’s European Space Operations Centre (ESOC) at Darmstadt, Germany, on 1 July, from 05:00 to 09:00. Several project representatives will be present. The event can also be followed at ESA HQ in Paris and at ESA/ESRIN, Frascati, in Italy. At each site, ESA specialists will be available for interviews. Those wishing to attend are asked to complete the attached reply form and fax it to the communications office at the establishment of their choice. The ESA TV service will provide extensive live coverage of all international press conferences, the orbital insertion operations on the night of 30 June to 1 July, and the presentation of the first images and results at JPL. All transmission and satellite details are published online and will be continuously updated at http://television.esa.int. The ESA live TV line transmission of the orbital insertion will also be transmitted on Astra 2C, the satellite reception details being as follows: Astra 2C at 19 degrees East Transponder 57, horizontal, MPEG-2, MCPC Frequency 10832 MHz, Symbol rate 22000 MS/sec. FEC=5/6. (*) The Cassini-Huygens mission is a cooperation between NASA, ESA (European Space Agency) and ASI (Italian Space Agency). The Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, is managing the mission for NASA’s Office of Space Science, Washington

  11. Determining common insertion sites based on retroviral insertion distribution across tumors.

    PubMed

    Chen, Feng; Li, Zhoufang; Chen, Yi-Ping Phoebe

    2014-08-01

    A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not require any prior knowledge of underlying insertion distribution; (2) it can resolve the insertion biases caused by hotspots; (3) it can detect CISs of any biological width; (4) it can identify noises resulting from statistic mistakes and non-CIS insertions; and (5) it can identify the widths of CISs as accurately as possible. We develop a method to resolve these difficulties. We verify a region's significance from two perspectives: distribution width and distribution depth. The former indicates how many insertions in a region while the latter evaluates the insertion distribution across the tumors in a region. We compare our method with kernel density estimation and sliding window on the simulated data, showing that our method not only identifies cancer-related insertions effectively, but also filters noises correctly. The experiments on the real data show that taking insertion distribution into account can highlight significant CISs. We detect 53 novel CISs, some of which have been proven correct by the biological literature. PMID:24675070

  12. Cancer gene discovery: exploiting insertional mutagenesis

    PubMed Central

    Ranzani, Marco; Annunziato, Stefano; Adams, David J.; Montini, Eugenio

    2013-01-01

    Insertional mutagenesis has been utilized as a functional forward genetics screen for the identification of novel genes involved in the pathogenesis of human cancers. Different insertional mutagens have been successfully used to reveal new cancer genes. For example, retroviruses (RVs) are integrating viruses with the capacity to induce the deregulation of genes in the neighborhood of the insertion site. RVs have been employed for more than 30 years to identify cancer genes in the hematopoietic system and mammary gland. Similarly, another tool that has revolutionized cancer gene discovery is the cut-and-paste transposons. These DNA elements have been engineered to contain strong promoters and stop cassettes that may function to perturb gene expression upon integration proximal to genes. In addition, complex mouse models characterized by tissue-restricted activity of transposons have been developed to identify oncogenes and tumor suppressor genes that control the development of a wide range of solid tumor types, extending beyond those tissues accessible using RV-based approaches. Most recently, lentiviral vectors (LVs) have appeared on the scene for use in cancer gene screens. LVs are replication defective integrating vectors that have the advantage of being able to infect non-dividing cells, in a wide range of cell types and tissues. In this review, we describe the various insertional mutagens focusing on their advantages/limitations and we discuss the new and promising tools that will improve the insertional mutagenesis screens of the future. PMID:23928056

  13. Peptide partitioning properties from direct insertion studies

    SciTech Connect

    Ulmschneider, Martin; Smith, Jeremy C; Ulmschneider, Jakob

    2010-06-01

    Partitioning properties of polypeptides are at the heart of biological membrane phenomena and their precise quantification is vital for ab-initio structure prediction and the accurate simulation of membrane protein folding and function. Recently the cellular translocon machinery has been employed to determine membrane insertion propensities and transfer energetics for a series of polyleucine segments embedded in a carrier sequence. We show here that the insertion propensity, pathway, and transfer energetics into synthetic POPC bilayers can be fully described by direct atomistic peptide partitioning simulations. The insertion probability as a function of peptide length follows two-state Boltzmann statistics, in agreement with the experiments. The simulations expose a systematic offset between translocon-mediated and direct insertion free energies. Compared to the experiment the insertion threshold is shifted toward shorter peptides by 2 leucine residues. The simulations reveal many hitherto unknown atomic-resolution details about the partitioning process and promise to provide a powerful tool for urgently needed calibration of lipid parameters to match experimentally observed peptide transfer energies.

  14. Rack Insertion End Effector (RIEE) automation

    NASA Technical Reports Server (NTRS)

    Malladi, Narasimha

    1993-01-01

    NASA is developing a mechanism to manipulate and insert Racks into the Space Station Logistic modules. The mechanism consists of the following: a base with three motorized degrees of freedom, a 3 section motorized boom that goes from 15 to 44 feet in length, and a Rack Insertion End Effector (RIEE) with 5 hand wheels for precise alignment. The robotics section was tasked with the automation of the RIEE unit. In this report, for the automation of the RIEE unit, application of the Perceptics Vision System was conceptually developed to determine the position and orientation of the RIEE relative to the logistic module, and a MathCad program is written to display the needed displacements for precise alignment and final insertion of the Rack. The uniqueness of this report is that the whole report is in fact a MathCad program including text, derivations, and executable equations with example inputs and outputs.

  15. Elliptically polarizing adjustable phase insertion device

    DOEpatents

    Carr, R.

    1995-01-17

    An insertion device for extracting polarized electromagnetic energy from a beam of particles is disclosed. The insertion device includes four linear arrays of magnets which are aligned with the particle beam. The magnetic field strength to which the particles are subjected is adjusted by altering the relative alignment of the arrays in a direction parallel to that of the particle beam. Both the energy and polarization of the extracted energy may be varied by moving the relevant arrays parallel to the beam direction. The present invention requires a substantially simpler and more economical superstructure than insertion devices in which the magnetic field strength is altered by changing the gap between arrays of magnets. 3 figures.

  16. Interactive simulation of needle insertion models.

    PubMed

    DiMaio, Simon P; Salcudean, Septimiu E

    2005-07-01

    A novel interactive virtual needle insertion simulation is presented. The simulation models are based on measured planar tissue deformations and needle insertion forces. Since the force-displacement relationship is only of interest along the needle shaft, a condensation technique is shown to reduce the computational complexity of linear simulation models significantly. As the needle penetrates or is withdrawn from the tissue model, the boundary conditions that determine the tissue and needle motion change. Boundary condition and local material coordinate changes are facilitated by fast low-rank matrix updates. A large-strain elastic needle model is coupled to the tissue models to account for needle deflection and bending during simulated insertion. A haptic environment, based on these novel interactive simulation techniques, allows users to manipulate a three-degree-of-freedom virtual needle as it penetrates virtual tissue models, while experiencing steering torques and lateral needle forces through a planar haptic interface. PMID:16041980

  17. Placement of a peripherally inserted central catheter into the azygous vein

    PubMed Central

    Franklin, Iain; Gilmore, Christopher

    2015-01-01

    Peripherally inserted central catheters (PICC) are used for a variety of infusion therapies. They are indicated in patients requiring long-term venous access. Incorrect positioning of the insertion of a PICC line is one of the known complications when inserting the device in clinical practice. Radiographers once performing imaging will commonly check if the tip of a PICC has entered the superior vena cava. This case study will report on a lesser known incorrect placement of a PICC line into the azygous vein and how this can be detected on radiographic imaging. This outcome for the patient can be detrimental as it has an increased risk of perforation, thrombus, and fistula formation. PMID:26229681

  18. Placement of a peripherally inserted central catheter into the azygous vein.

    PubMed

    Franklin, Iain; Gilmore, Christopher

    2015-06-01

    Peripherally inserted central catheters (PICC) are used for a variety of infusion therapies. They are indicated in patients requiring long-term venous access. Incorrect positioning of the insertion of a PICC line is one of the known complications when inserting the device in clinical practice. Radiographers once performing imaging will commonly check if the tip of a PICC has entered the superior vena cava. This case study will report on a lesser known incorrect placement of a PICC line into the azygous vein and how this can be detected on radiographic imaging. This outcome for the patient can be detrimental as it has an increased risk of perforation, thrombus, and fistula formation. PMID:26229681

  19. Mosaic retroposon insertion patterns in placental mammals.

    PubMed

    Churakov, Gennady; Kriegs, Jan Ole; Baertsch, Robert; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

    2009-05-01

    One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The "presence" of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its "absence" in more distant species. To resolve the placental origin controversy we extracted approximately 2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a "soft" polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy. PMID:19261842

  20. Mosaic retroposon insertion patterns in placental mammals

    PubMed Central

    Churakov, Gennady; Kriegs, Jan Ole; Baertsch, Robert; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

    2009-01-01

    One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The “presence” of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its “absence” in more distant species. To resolve the placental origin controversy we extracted ∼2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a “soft” polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy. PMID:19261842

  1. Mosaic retroposon insertion patterns in placental mammals.

    TOXLINE Toxicology Bibliographic Information

    Churakov G; Kriegs JO; Baertsch R; Zemann A; Brosius J; Schmitz J

    2009-05-01

    One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The "presence" of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its "absence" in more distant species. To resolve the placental origin controversy we extracted approximately 2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a "soft" polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.

  2. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-14

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  3. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  4. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2008-06-24

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  5. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  6. RERTR-12 Insertion 2 Irradiation Summary Report

    SciTech Connect

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

    2012-09-01

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

  7. Active interlock for storage ring insertion devices

    SciTech Connect

    Rochman, J.L.; Nawrocky, R.J.

    1989-01-01

    The insertion devices in the NSLS x-ray ring produce such intense photon beams that passive measures alone are not adequate to protect the vacuum chamber. An active interlock is used to prevent thermal damage from improperly steered electron beams. The interlock system measures the position of the electron beam on both sides of the insertion devices using pick-up electrodes and interrupts the rf if the beam moves outside a safe window. The interlock features redundant circuitry as well as an automatic testing procedure. 1 ref., 4 figs.

  8. Defining peripherally inserted central catheter tip position and an evaluation of insertions in one unit.

    PubMed

    Johnston, A J; Bishop, S M; Martin, L; See, T C; Streater, C T

    2013-05-01

    Peripherally inserted central catheters are increasingly used to provide access to the central venous circulation. They are commonly positioned 'blind' using a variety of anthropometric techniques and operator experience to direct insertion length. Malposition rates are poorly defined because of differing insertion techniques, difficulties defining anatomical tip position on chest radiographs, controversy over what constitutes an adequate catheter position and possible differences between patient groups. We have developed a reproducible method to define catheter positions on chest radiograph and have applied this in a retrospective analysis of 256 ICU and 243 non-ICU catheter insertions over a 6-month period. Two different definitions were used for adequate position. 'Blind' positioning of peripherally inserted central catheters was associated with a definition-dependent malposition rate of 42-76%. Malposition rates were significantly higher in ICU patients. Emerging technologies may assist in reducing these high rates. PMID:23488895

  9. The BDGP gene disruption project: Single transposon insertions associated with 40 percent of Drosophila genes

    SciTech Connect

    Bellen, Hugo J.; Levis, Robert W.; Liao, Guochun; He, Yuchun; Carlson, Joseph W.; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P. Robin; Schulze, Karen L.; Rubin, Gerald M.; Hoskins, Roger A.; Spradling, Allan C.

    2004-01-13

    The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in more than 30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6,300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7,140 lines. It now includes individual lines predicted to disrupt 5,362 of the 13,666 currently annotated Drosophila genes (39 percent). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene mis-expression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

  10. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.

    PubMed Central

    Bellen, Hugo J; Levis, Robert W; Liao, Guochun; He, Yuchun; Carlson, Joseph W; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P Robin; Schulze, Karen L; Rubin, Gerald M; Hoskins, Roger A; Spradling, Allan C

    2004-01-01

    The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool. PMID:15238527

  11. PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice

    PubMed Central

    Sun, Ling V.; Jin, Ke; Liu, Yiming; Yang, Wenwei; Xie, Xing; Ye, Lin; Wang, Li; Zhu, Lin; Ding, Sheng; Su, Yi; Zhou, Jie; Han, Min; Zhuang, Yuan; Xu, Tian; Wu, Xiaohui; Gu, Ning; Zhong, Yang

    2008-01-01

    DNA transposon piggyBac (PB) is a newly established mutagen for large-scale mutagenesis in mice. We have designed and implemented an integrated database system called PBmice (PB Mutagenesis Information CEnter) for storing, retrieving and displaying the information derived from PB insertions (INSERTs) in the mouse genome. This system is centered on INSERTs with information including their genomic locations and flanking genomic sequences, the expression levels of the hit genes, and the expression patterns of the trapped genes if a trapping vector was used. It also archives mouse phenotyping data linked to INSERTs, and allows users to conduct quick and advanced searches for genotypic and phenotypic information relevant to a particular or a set of INSERT(s). Sequence-based information can be cross-referenced with other genomic databases such as Ensembl, BLAST and GBrowse tools used in PBmice offer enhanced search and display for additional information relevant to INSERTs. The total number and genomic distribution of PB INSERTs, as well as the availability of each PB insertional LINE can also be viewed with user-friendly interfaces. PBmice is freely available at http://www.idmshanghai.cn/PBmice or http://www.scbit.org/PBmice/. PMID:17932058

  12. 21 CFR 886.5420 - Contact lens inserter/remover.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Contact lens inserter/remover. 886.5420 Section... (CONTINUED) MEDICAL DEVICES OPHTHALMIC DEVICES Therapeutic Devices § 886.5420 Contact lens inserter/remover. (a) Identification. A contact lens inserter/remover is a handheld device intended to insert or...

  13. Immediate postabortal insertion of intrauterine devices.

    PubMed

    Okusanya, Babasola O; Oduwole, Olabisi; Effa, Emmanuel E

    2014-01-01

    Background The use of an effective contraceptive may be necessary after an abortion. Insertion of an intrauterine device (IUD) may be done the same day or later. Immediate IUD insertion is an option since the woman is not pregnant, pain of insertion is less because the cervical os is open, and her motivation to use contraception may be high. However, insertion of an IUD immediately after a pregnancy ends carries risks, such as spontaneous expulsion.Objectives To assess the safety and efficacy of IUD insertion immediately after spontaneous or induced abortion.Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, POPLINE, ClinicalTrials.gov,and ICTRP in January 27, 2014. We also contacted investigators to identify other trials.Selection criteria We sought all randomised controlled trials (RCTs) with at least one treatment arm that involved IUD insertion immediately after an induced abortion or after curettage for spontaneous abortion.Data collection and analysis We evaluated the methodological quality of each report and abstracted the data. We focused on discontinuation rates for accidental pregnancy, perforation, expulsion, and pelvic inflammatory disease.We computed the weighted average of the rate ratios.We compute drisk ratios (RRs) with 95% Confidence Intervals (CIs).We performed an intention-to-treat (ITT) analysis by including all randomised participants in the analysis according to the Cochrane Handbook for Systematic Reviews of Interventions.Main results We identified 12 trials most of which are of moderate risk of bias involving 7,119 participants which described random assignment.Five trials randomised to either immediate or delayed insertion of IUD. One of them randomised to immediate versus delayed insertion of Copper 7 showed immediate insertion of the Copper 7 was associated with a higher risk of expulsion than was delayed insertion(RR 11.98, 95% CI 1.61 to 89.35,1 study, 259 participants); the quality of evidence was moderate. Moderate quality of evidence also suggests that use and expulsion of levonorgestrel-releasing intrauterine system or CuT380A was more likely for immediate compared to delayed insertion risk ratio (RR) 1.40 (95% CI 1.24 to 1.58; 3 studies; 878 participants) and RR 2.64 ( 95% CI 1.16 to 6.00; 3 studies; 878 participants) respectively. Another trial randomised to the levonorgestrel IUD or Nova T showed discontinuation rates due to pregnancy were likely to be higher for women in the Nova T group. (MD 8.70, 95% CI 3.92 to 13.48;1 study; 438 participants);moderate quality evidence.Seven trials examined immediate insertion of IUD only. From meta-analysis of two multicentre trials, pregnancy was less likely for the TCu 220C versus the Lippes Loop (RR 0.43, 95% CI 0.24 to 0.75; 2 studies; 2257 participants ) as was expulsion (RR 0.61, 95% CI0.46 to 0.81; 2 studies; 2257 participants). Estimates for the TCu 220 versus the Copper 7 were RR 0.42 ( 95% CI 0.23 to 0.77; 2 studies, 2,274 participants) and RR 0.68, (95% CI 0.51 to 0.91); 2 studies, 2,274 participants), respectively. In other work, adding copper sleeves to the Lippes Loop improved efficacy (RR 3.40, 95% CI 1.28 to 9.04, 1 study, 400 participants) and reduced expulsion(RR 3.00, 95% CI 1.51 to 5.97; 1 study, 400 participants).Authors' conclusions Moderate quality evidence shows that insertion of an IUD immediately after abortion is safe and practical. IUD expulsion rates appear higher immediately after abortions compared to delayed insertions. However, at six months postabortion, IUD use is higher following immediate insertion compared to delayed insertion. PMID:25101364

  14. Mars Observer Lecture: Mars Orbit Insertion

    NASA Technical Reports Server (NTRS)

    Dodd, Suzanne R. (Personal Name)

    1993-01-01

    The Mars Observer mission spacecraft was primarily designed for exploring Mars and the Martian environment. The Mars Observer was launched on September 25, 1992. The spacecraft was lost in the vicinity of Mars on August 21, 1993 when the spacecraft began its maneuvering sequence for Martian orbital insertion. This videotape shows a lecture by Suzanne R. Dodd, the Mission Planning Team Chief for the Mars Observer Project. Ms Dodd begins with a brief overview of the mission and the timeline from the launch to orbital insertion. Ms Dodd then reviews slides showing the trajectory of the spacecraft on its trip to Mars. Slides of the spacecraft being constructed are also shown. She then discusses the Mars orbit insertion and the events that will occur to move the spacecraft from the capture orbit into a mapping orbit. During the trip to Mars, scientists at JPL had devised a new strategy, called Power In that would allow for an earlier insertion into the mapping orbit. The talk summarizes this strategy, showing on a slide the planned transition orbits. There are shots of the Martian moon, Phobos, taken from the Viking spacecraft, as Ms Dodd explains that the trajectory will allow the orbiter to make new observations of that moon. She also explains the required steps to prepare for mapping after the spacecraft has achieved the mapping orbit around Mars. The lecture ends with a picture of Mars from the Observer on its approach to the planet.

  15. Lymphatic Leak Complicating Central Venous Catheter Insertion

    SciTech Connect

    Barnacle, Alex M. Kleidon, Tricia M.

    2005-12-15

    Many of the risks associated with central venous access are well recognized. We report a case of inadvertent lymphatic disruption during the insertion of a tunneled central venous catheter in a patient with raised left and right atrial pressures and severe pulmonary hypertension, which led to significant hemodynamic instability. To our knowledge, this rare complication is previously unreported.

  16. Embedded Multiprocessor Technology for VHSIC Insertion

    NASA Technical Reports Server (NTRS)

    Hayes, Paul J.

    1990-01-01

    Viewgraphs on embedded multiprocessor technology for VHSIC insertion are presented. The objective was to develop multiprocessor system technology providing user-selectable fault tolerance, increased throughput, and ease of application representation for concurrent operation. The approach was to develop graph management mapping theory for proper performance, model multiprocessor performance, and demonstrate performance in selected hardware systems.

  17. Inserting new technology into small missions

    NASA Technical Reports Server (NTRS)

    Deutsch, L. J.

    2001-01-01

    Part of what makes small missions small is that they have less money. Executing missions at low cost implies extensive use of cost sharing with other missions or use of existing solutions. Luckily, there are methods for creating new technology and inserting it into faster-better-cheaper missions.

  18. Thermal Performance of the XRS Helium Insert

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  19. Frequency, Gradience, and Variation in Consonant Insertion

    ERIC Educational Resources Information Center

    An, Young-ran

    2010-01-01

    This dissertation addresses the extent to which linguistic behavior can be described in terms of the projection of patterns from existing lexical items, through an investigation of Korean reduplication. Korean has a productive pattern of reduplication in which a consonant is inserted in a vowel-initial base, illustrated by forms such as "alok"--"t…

  20. Electrochemistry of ion inserted vanadium oxide nanosheets

    NASA Astrophysics Data System (ADS)

    Pomeroy, Marc; Ren, Shaola; Yuan, Qifan; Soghomonian, Victoria

    2013-03-01

    Electrochemical energy storage is becoming increasingly important for its high specific power and quick charge and discharge rates. We investigate the electrical properties of hydrothermally synthesized vanadium oxide nanosheets as potential anode component of an electrochemical capacitor. The room temperature resistivity of the as-synthesized and pristine vanadium oxide nanosheets is around 10⌃7 ohm-cm, and variable temperature measurements indicate the semiconducting behavior of the material. Electrodes are fabricated from the nanosheets, and inserted into appropriate chloride solutions of Li, Na and ammonium. Room temperature voltammetry in the solutions are recorded and provide a measure of stored energy relative to each cation. Scanning electron micrographs obtained before and after various cyclic voltammograms provides a visual measure of nanosheet stability and a correlation to its electrochemical activity. Micrographs show that the material is robust towards Li insertion, but after several cycles of ammonium insertion, degradation occurs. Degradation upon Na insertion is minimal. These comparative studies shed light on the interactions between ions and metal oxide nanosheets. We acknowledge support from NSF DMR 0943971 and 1206338.

  1. Insertion Loss of Personal Protective Clothing

    SciTech Connect

    Shull D.J.; Biesel, V.B.; Cunefare, K.A.

    1999-05-13

    'The use of personal protective clothing that covers the head is a common practice in many industries. Such personal protective clothing will impact the sound pressure level and the frequency content of sounds to which the wearer will be exposed. The use of such clothing, then, may impact speech and alarm audibility. A measure of the impact of such clothing is its insertion loss. Insertion loss measurements were performed on four types of personal protective clothing in use by Westinghouse Savannah River Company personnel which utilize cloth and plastic hood configurations to protect the head. All clothing configurations tested at least partially cover the ears. The measurements revealed that insertion loss of the items tested was notable at frequencies above 1000 Hz only and was a function of material stiffness and acoustic flanking paths to the ear. Further, an estimate of the clothing''s noise reduction rating reveals poor performance in that regard, even though the insertion loss of the test articles was significant at frequencies at and above 1000 Hz.'

  2. The Genomic Distribution of L1 Elements: The Role of Insertion Bias and Natural Selection

    PubMed Central

    Graham, Todd; Boissinot, Stephane

    2006-01-01

    LINE-1 (L1) retrotransposons constitute the most successful family of retroelements in mammals and account for as much as 20% of mammalian DNA. L1 elements can be found in all genomic regions but they are far more abundant in AT-rich, gene-poor, and low-recombining regions of the genome. In addition, the sex chromosomes and some genes seem disproportionately enriched in L1 elements. Insertion bias and selective processes can both account for this biased distribution of L1 elements. L1 elements do not appear to insert randomly in the genome and this insertion bias can at least partially explain the genomic distribution of L1. The contrasted distribution of L1 and Alu elements suggests that postinsertional processes play a major role in shaping L1 distribution. The most likely mechanism is the loss of recently integrated L1 elements that are deleterious (negative selection) either because of disruption of gene function or their ability to mediate ectopic recombination. By comparison, the retention of L1 elements because of some positive effect is limited to a small fraction of the genome. Understanding the respective importance of insertion bias and selection will require a better knowledge of insertion mechanisms and the dynamics of L1 inserts in populations. PMID:16877820

  3. Functional Genomics of Eukaryotic Photosynthesis Using Insertional Mutagenesis of Chlamydomonas reinhardtii1

    PubMed Central

    Dent, Rachel M.; Haglund, Cat M.; Chin, Brian L.; Kobayashi, Marilyn C.; Niyogi, Krishna K.

    2005-01-01

    The unicellular green alga Chlamydomonas reinhardtii is a widely used model organism for studies of oxygenic photosynthesis in eukaryotes. Here we describe the development of a resource for functional genomics of photosynthesis using insertional mutagenesis of the Chlamydomonas nuclear genome. Chlamydomonas cells were transformed with either of two plasmids conferring zeocin resistance, and insertional mutants were selected in the dark on acetate-containing medium to recover light-sensitive and nonphotosynthetic mutants. The population of insertional mutants was subjected to a battery of primary and secondary phenotypic screens to identify photosynthesis-related mutants that were pigment deficient, light sensitive, nonphotosynthetic, or hypersensitive to reactive oxygen species. Approximately 9% of the insertional mutants exhibited 1 or more of these phenotypes. Molecular analysis showed that each mutant line contains an average of 1.4 insertions, and genetic analysis indicated that approximately 50% of the mutations are tagged by the transforming DNA. Flanking DNA was isolated from the mutants, and sequence data for the insertion sites in 50 mutants are presented and discussed. PMID:15653810

  4. Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect.

    PubMed

    Cridland, Julie M; Thornton, Kevin R; Long, Anthony D

    2015-01-01

    Transposable elements are a common source of genetic variation that may play a substantial role in contributing to gene expression variation. However, the contribution of transposable elements to expression variation thus far consists of a handful of examples. We used previously published gene expression data from 37 inbred Drosophila melanogaster lines from the Drosophila Genetic Reference Panel to perform a genome-wide assessment of the effects of transposable elements on gene expression. We found thousands of transcripts with transposable element insertions in or near the transcript and that the presence of a transposable element in or near a transcript is significantly associated with reductions in expression. We estimate that within this example population, ∼2.2% of transcripts have a transposable element insertion, which significantly reduces expression in the line containing the transposable element. We also find that transcripts with insertions within 500 bp of the transcript show on average a 0.67 standard deviation decrease in expression level. These large decreases in expression level are most pronounced for transposable element insertions close to transcripts and the effect diminishes for more distant insertions. This work represents the first genome-wide analysis of gene expression variation due to transposable elements and suggests that transposable elements are an important class of mutation underlying expression variation in Drosophila and likely in other systems, given the ubiquity of these mobile elements in eukaryotic genomes. PMID:25335504

  5. LINE-ABOVE-GROUND ATTENUATOR

    DOEpatents

    Wilds, R.B.; Ames, J.R.

    1957-09-24

    The line-above-ground attenuator provides a continuously variable microwave attenuator for a coaxial line that is capable of high attenuation and low insertion loss. The device consists of a short section of the line-above- ground plane type transmission lime, a pair of identical rectangular slabs of lossy material like polytron, whose longitudinal axes are parallel to and indentically spaced away from either side of the line, and a geared mechanism to adjust amd maintain this spaced relationship. This device permits optimum fineness and accuracy of attenuator control which heretofore has been difficult to achieve.

  6. Screw-Thread Inserts As Temporary Flow Restrictors

    NASA Technical Reports Server (NTRS)

    Trimarchi, Paul

    1992-01-01

    Coil-spring screw-thread inserts found useful as temporary flow restrictors. Inserts placed in holes through which flow restricted, effectively reducing cross sections available for flow. Friction alone holds inserts against moderate upstream pressures. Use of coil-spring thread inserts as flow restrictors conceived as inexpensive solution to problem of adjusting flow of oxygen through orifices in faceplate into hydrogen/oxygen combustion chamber. Installation and removal of threaded inserts gentle enough not to deform orifice tubes.

  7. Distal Insertions of the Biceps Femoris

    PubMed Central

    Branch, Eric A.; Anz, Adam W.

    2015-01-01

    Background: Avulsion of the biceps femoris from the fibula and proximal tibia is encountered in clinical practice. While the anatomy of the primary posterolateral corner structures has been qualitatively and quantitatively described, a quantitative analysis regarding the insertions of the biceps femoris on the fibula and proximal tibia is lacking. Purpose: To quantitatively assess the insertions of the biceps femoris, fibular collateral ligament (FCL), and anterolateral ligament (ALL) on the fibula and proximal tibia as well as establish relationships among these structures and to pertinent surgical anatomy. Study Design: Descriptive laboratory study. Methods: Dissections were performed on 12 nonpaired, fresh-frozen cadaveric specimens identifying the biceps femoris, FCL, and ALL, and their insertions on the proximal tibia and fibula. The footprint areas, orientations, and distances from relevant osseous landmarks were measured using a 3-dimensional coordinate measurement device. Results: Dissection produced 6 easily identifiable and reproducible anatomic footprints. Tibial footprints included the insertion of the ALL and an insertion of the biceps femoris (TBF). Fibular footprints included the insertion of the FCL, a distal insertion of the biceps femoris (DBF), a medial footprint of the biceps femoris (MBF), and a proximal footprint of the biceps femoris (PBF). The mean area of these footprints (95% CI) was as follows: ALL, 53.0 mm2 (38.4-67.6); TBF, 93.9 mm2 (72.0-115.8); FCL, 86.8 mm2 (72.3-101.2); DBF, 119 mm2 (91.1-146.9); MBF, 46.8 mm2 (29.0-64.5); and PBF, 215 mm2 (192.4-237.5). The mean distance (95% CI) from the Gerdy tubercle to the center of the ALL footprint was 24.3 mm (21.6-27.0) and to the center of the TBF was 22.5 mm (21.0-24.0). The center of the DBF was 8.68 mm (7.0-10.3) from the anterior border of the fibula, the center of the FCL was 14.6 mm (12.5-16.7) from the anterior border of the fibula and 20.7 mm (19.0-22.4) from the tip of the fibular styloid, and the center of the PBF was 8.96 mm (8.2-9.7) from the tip of the fibular styloid. Conclusion: A tibial footprint, distal fibular footprint, medial fibular footprint, and proximal fibular footprint were all consistent components of the insertion of the biceps femoris. Consistent relationships existed between the biceps femoris and insertions of the ALL and FCL. Clinical Relevance: The size of these footprints and distances from pertinent surgical landmarks will guide repairs of biceps femoris avulsion injuries. PMID:26535398

  8. Toolbox for mobile-element insertion detection on cancer genomes.

    PubMed

    Lee, Wan-Ping; Wu, Jiantao; Marth, Gabor T

    2014-01-01

    Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram. PMID:25452688

  9. Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

    PubMed Central

    Lee, Wan-Ping; Wu, Jiantao; Marth, Gabor T

    2014-01-01

    Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram. PMID:25452688

  10. Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

    PubMed Central

    Lee, Wan-Ping; Wu, Jiantao; Marth, Gabor T

    2015-01-01

    Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram. PMID:25931804

  11. Toolbox for mobile-element insertion detection on cancer genomes.

    PubMed

    Lee, Wan-Ping; Wu, Jiantao; Marth, Gabor T

    2015-01-01

    Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram. PMID:25931804

  12. Effect of Off-Axis Screw Insertion, Insertion Torque, and Plate Contouring on Locked Screw Strength

    PubMed Central

    Gallagher, Bethany; Silva, Matthew J.; Ricci, William M.

    2015-01-01

    Objectives This study quantifies the effects of insertion torque, off-axis screw angulation, and plate contouring on the strength of locking plate constructs. Methods Groups of locking screws (n = 6–11 screws) were inserted at 50%, 100%, 150%, and 200% of the manufacturer-recommended torque (3.2 Nm) into locking compression plates at various angles: orthogonal (control), 5-degree angle off-axis, and 10-degree angle off-axis. Screws were loaded to failure by a transverse force (parallel to the plate) either in the same (“+”) or opposite direction (“−”) of the initial screw angulation. Separately, locking plates were bent to 5 and 10-degree angles, with the bend apex at a screw hole. Locking screws inserted orthogonally into the apex hole at 100% torque were loaded to failure. Results Orthogonal insertion resulted in the highest average load to failure, 2577 ± 141 N (range, 2413–2778 N), whereas any off-axis insertion significantly weakened constructs (165–1285 N, at 100% torque) (P < 0.05). For “+” loading, torque beyond 100% did not increase strength, but 50% torque reduced screw strength (P < 0.05). Loading in the “−” direction consistently resulted in higher strengths than “+” loading (P < 0.05). Plate contouring of 5-degree angle did not significantly change screw strength compared with straight plates but contouring of 10-degree angle significantly reduced load to failure (P < 0.05). Conclusions To maximize the screw plate interface strength, locking screws should be inserted without cross-threading. The mechanical stability of locked screws is significantly compromised by loose insertion, off-axis insertion, or severe distortion of the locking mechanism. PMID:24343255

  13. Symplectic models for general insertion devices

    SciTech Connect

    Wu, Y.; Forest, E.; Robin, D. S.; Nishimura, H.; Wolski, A.; Litvinenko, V. N.

    2001-06-01

    A variety of insertion devices (IDs), wigglers and undulators, linearly or elliptically polarized,are widely used as high brightness radiation sources at the modern light source rings. Long and high-field wigglers have also been proposed as the main source of radiation damping at next generation damping rings. As a result, it becomes increasingly important to understand the impact of IDs on the charged particle dynamics in the storage ring. In this paper, we report our recent development of a general explicit symplectic model for IDs with the paraxial ray approximation. High-order explicit symplectic integrators are developed to study real-world insertion devices with a number of wiggler harmonics and arbitrary polarizations.

  14. Insertion and Management of Temporary Pacemakers.

    PubMed

    Sullivan, Breandan Lawrence; Bartels, Karsten; Hamilton, Natalie

    2016-03-01

    Temporary pacemakers are used in a variety of critical care settings. These life-saving devices are reviewed in 2 major categories in this review: first, the insertion and management of epicardial pacemakers after and during cardiac surgery; and second, the insertion of transvenous temporary pacemakers for the emergent treatment of bradyarrhythmias. Temporary epicardial pacemakers are used routinely in patients recovering from cardiac surgery. Borrowing from advances in cardiac resynchronization therapy there are many theoretical and untested benefits to pacing the postoperative cardiac surgery patient. Temporary transvenous pacing is traditionally an emergency procedure to stabilize patients suffering from hemodynamically unstable bradyarrhythmia. We review the traditional and expanding use of transvenous pacemakers inside and outside the operating room. PMID:26134176

  15. Innovations in central vascular access device insertion.

    PubMed

    Pieger-Mooney, Sandi

    2005-01-01

    The new millennium has brought with it many technological advances that have affected every industry, especially healthcare and nursing. The key to success will be the ability of nurses to acclimate to these changes. To accomplish this, nurses need to advance their individual practice and skills, and to pursue and maintain an education in their respective fields. At no other time in healthcare history have so many changes taken place in such a short time, and nurses must remain abreast of changes to ensure career securement, advancement, and the safety of their patients. This article focuses on peripherally inserted central catheters and the changing technology for their insertion, maintenance, and training requirements. PMID:15965380

  16. Human Diallelic Insertion/Deletion Polymorphisms

    PubMed Central

    Weber, James L.; David, Donna; Heil, Jeremy; Fan, Ying; Zhao, Chengfeng; Marth, Gabor

    2002-01-01

    We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a ⩾2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletion:insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise ∼8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications. PMID:12205564

  17. Electrochemical insertion of sodium into carbon

    SciTech Connect

    Doeff, M.M.; Yanping Ma; Visco, S.J.; De Jonghe, L.C.

    1993-12-01

    Electrochemical insertion of sodium ions into carbon using solid polymer electrolytes or organic liquid electrolytes is described. Cells with the configuration Na/P(EO){sub 8}NaCF{sub 3}SO{sub 3}/C where P(EO) = polyethylene oxide or Na/liquid electrolyte/C were galvanostatically discharged, charged, and cycled. The extent of insertion into C (i.e., x in Na{sup +}C{sub x{minus}}) was found to be a strong function of the type and particle size of the carbon used, and the reversibility of the process was highly dependent upon the type of electrolyte used. The possibility of designing a sodium ion rocking chair cell is discussed, and a first-generation example, using a petroleum coke anode, polymer electrolyte, and sodium cobalt bronze cathode is described.

  18. Perception and Action in Teleoperated Needle Insertion

    PubMed Central

    Nisky, Ilana; Pressman, Assaf; Pugh, Carla M.; Mussa-Ivaldi, Ferdinando A.; Karniel, Amir

    2015-01-01

    We studied the effect of delay on perception and action in contact with a force field that emulates elastic soft tissue with a rigid nonlinear boundary. Such field is similar to forces exerted on a needle during teleoperated needle insertion. We found that delay causes motor underestimation of the stiffness of this nonlinear soft tissue, without perceptual change. These experimental results are supported by simulation of a simplified mechanical model of the arm and neural controller, and a model for perception of stiffness, which is based on regression in the force-position space. In addition, we show that changing the gain of the teleoperation channel cancels the motor effect of delay without adding perceptual distortion. We conclude that it is possible to achieve perceptual and motor transparency in virtual one-dimensional remote needle insertion task. PMID:26379813

  19. A Monte Carlo study of peptide insertion into lipid bilayers: equilibrium conformations and insertion mechanisms.

    PubMed Central

    Maddox, Michael W; Longo, Marjorie L

    2002-01-01

    The membrane insertion behavior of two peptides, Magainin2 and M2 delta, was investigated by applying the Monte Carlo simulation technique to a theoretical model. The model included many novel aspects, such as a new semi-empirical lipid bilayer model and a new set of semi-empirical transfer energies, which reproduced the experimental insertion behavior of Magainin2 and M2 delta without parameter fitting. Additionally, we have taken into account diminished internal (intramolecular) hydrogen bonding at the N- and C-termini of helical peptides. All simulations were carried out at 305 K, above the membrane thermal phase transition temperature, and at pH 7.0. The peptide equilibrium conformations are discussed for a range of bilayers with tail polarities varying from octanol-like to alkane-like. Probability distributions of the individual amino-acid-residue positions show the dynamic nature of these equilibrium conformations. Two different insertion mechanisms for M2 delta, and a translocation mechanism for Magainin2, are described. A study of the effect of bilayer thickness on M2 delta insertion suggests a critical thickness above which insertion is unfavorable. Additionally, we did not need to use an orientational potential or array of hard cylinders to persuade M2 delta to insert perpendicular to the membrane surface. Instead, we found that diminished internal hydrogen bonding in the helical conformation anchored the termini in the headgroups and resulted in a nearly perpendicular orientation. PMID:11751313

  20. Hollow polymer microneedles array resistance and insertion tests.

    PubMed

    Lhernould, Marion Sausse; Deleers, Michel; Delchambre, Alain

    2015-03-01

    Microneedles are developed in order to become the transdermal administration method of the future. They however still face numerous challenges. This paper addresses the challenge to effectively insert the microneedle arrays into membranes. A recently proposed model membrane and test method for microneedles insertion, published in International Journal of Pharmaceutics, is used in this aim. A moulded 4 by 4 hollow polymer microneedle array developed at the Universit Libre de Bruxelles is tested for insertion using this model. Results show that the array is extremely resistant to insertion, it can withstand very high forces and even multiple insertions without blunting. Different insertion tests were performed on a folded in eight Parafilm film because it exhibits excellent similarity to porcine skin. The insertion force, the insertion speed and the holding time of the array against membranes must be optimised in order to get efficient reliable insertions at, at least, 500?m depth. PMID:25595569

  1. Investigation of flexible hose insertion forces and selected factors.

    PubMed

    Drinkaus, P; Armstrong, T; Foulke, J

    2009-01-01

    Flexible hoses are widely used in automobiles. Understanding the force required to insert a hose, independent of worker variation, is important for engineers, designers and health professionals. Various parameters affect the insertion forces including the interference between the hose and flange. Also, it has been observed that workers often add motions during the insertion process, including rotation and oscillation. This paper describes the effects of these parameters on axial insertion forces. A programmable mill was used to isolate the effects of four variables on hose insertion force: fit, insertion speed, rotational velocity and oscillation magnitude. The results show that the magnitude of the interference of the 19 mm inside diameters (ID) heater hose and the flange, and the insertion technique affect the insertion forces; resulting in a range of insertion forces from 11.1+/-0.2 to 128.4+/-11.3N. PMID:18339355

  2. Descemet's Stripping Automated Endothelial Keratoplasty Tissue Insertion Devices.

    PubMed

    Khan, Salman Nasir; Shiakolas, Panos S; Mootha, Venkateswara Vinod

    2015-01-01

    This review study provides information regarding the construction, design, and use of six commercially available endothelial allograft insertion devices applied for Descemet's stripping automated endothelial keratoplasty (DSAEK). We also highlight issues being faced in DSAEK and discuss the methods through which medical devices such as corneal inserters may alleviate these issues. Inserter selection is of high importance in the DSAEK procedure since overcoming the learning curve associated with the use of an insertion device is a time and energy consuming process. In the present review, allograft insertion devices were compared in terms of design, construction material, insertion technique, dimensions, incision requirements and endothelial cell loss to show their relative merits and capabilities based on available data in the literature. Moreover, the advantages/disadvantages of various insertion devices used for allograft insertion in DSAEK are reviewed and compared. The information presented in this review can be utilized for better selection of an insertion device for DSAEK. PMID:27051492

  3. Descemet's Stripping Automated Endothelial Keratoplasty Tissue Insertion Devices

    PubMed Central

    Khan, Salman Nasir; Shiakolas, Panos S.; Mootha, Venkateswara Vinod

    2015-01-01

    This review study provides information regarding the construction, design, and use of six commercially available endothelial allograft insertion devices applied for Descemet's stripping automated endothelial keratoplasty (DSAEK). We also highlight issues being faced in DSAEK and discuss the methods through which medical devices such as corneal inserters may alleviate these issues. Inserter selection is of high importance in the DSAEK procedure since overcoming the learning curve associated with the use of an insertion device is a time and energy consuming process. In the present review, allograft insertion devices were compared in terms of design, construction material, insertion technique, dimensions, incision requirements and endothelial cell loss to show their relative merits and capabilities based on available data in the literature. Moreover, the advantages/disadvantages of various insertion devices used for allograft insertion in DSAEK are reviewed and compared. The information presented in this review can be utilized for better selection of an insertion device for DSAEK. PMID:27051492

  4. Inserting new technology into small missions

    NASA Technical Reports Server (NTRS)

    Deutsch, L. J.

    2001-01-01

    Part of what makes small missions small is that they have less money. Executing missions at low cost implies extensive use of cost sharing with other missions or use of existing solutions. However, in order to create many small missions, new technology must be developed, applied, and assimilated. Luckily, there are methods for creating new technology and inserting it into faster-better-cheaper (FBC) missions.

  5. Comparison of Insertional RNA Editing in Myxomycetes

    PubMed Central

    Chen, Cai; Frankhouser, David; Bundschuh, Ralf

    2012-01-01

    RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871

  6. Comparison of insertional RNA editing in Myxomycetes.

    PubMed

    Chen, Cai; Frankhouser, David; Bundschuh, Ralf

    2012-01-01

    RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871

  7. DEVICE FOR CONTROLLING INSERTION OF ROD

    DOEpatents

    Beaty, B.J.

    1958-10-14

    A device for rapidly inserting a safety rod into a nuclear reactor upon a given signal or in the event of a power failure in order to prevent the possibility of extensive damage caused by a power excursion is described. A piston is slidably mounted within a vertical cylinder with provision for an electromagnetic latch at the top of the cylinder. This assembly, with a safety rod attached to the piston, is mounted over an access port to the core region of the reactor. The piston is normally latched at the top of the cylinder with the safety rod clear of the core area, however, when the latch is released, the piston and rod drop by their own weight to insert the rod. Vents along the side of the cylinder permit the escape of the air entrapped under the piston over the greater part of the distance, however, at the end of the fall the entrapped air is compressed thereby bringing the safety rod gently to rest, thus providing for a rapid automatic insertion of the rod with a minimum of structural shock.

  8. One-piece rocker arm with insert

    SciTech Connect

    Patel, R.L.; Wherry, J.L.

    1988-04-19

    A one-piece, cold-formed rocker arm of the cam-follower type is described comprising a one-piece metal body having a rounded recess in a first end portion thereof to receive an end of a lifter post on which the rocker arm can pivot. The end portion thereof has an opening extending therethrough communicating with the rounded recess and the opening being flared outwardly in a direction away from the recess to form an oil reservoir. The body has an additional recess of rectangular transverse cross-sectional shape at a second end portion thereof to receive an end of a valve stem. The body has an intermediate generally convex portion facing away from the recesses. The convex portion has a shallow rectangular recess therein defined by four peripheral side walls. The body has a shallow projection of rectangular shape in longitudinal cross section on the side directly opposite the shallow recess, a long-wearing metal insert in the shallow recess to be engaged by a cam, the metal insert being prevented from sideways movement by the side walls of the body, and means affixing the metal insert in the shallow recess.

  9. Genetic transformation and gene silencing mediated by multiple copies of a transgene in eastern white pine.

    PubMed

    Tang, Wei; Newton, Ronald J; Weidner, Douglas A

    2007-01-01

    An efficient transgenic eastern white pine (Pinus strobus L.) plant regeneration system has been established using Agrobacterium tumefaciens strain GV3850-mediated transformation and the green fluorescent protein (gfp) gene as a reporter in this investigation. Stable integration of transgenes in the plant genome of pine was confirmed by polymerase chain reaction (PCR), Southern blot, and northern blot analyses. Transgene expression was analysed in pine T-DNA transformants carrying different numbers of copies of T-DNA insertions. Post-transcriptional gene silencing (PTGS) was mostly obtained in transgenic lines with more than three copies of T-DNA, but not in transgenic lines with one copy of T-DNA. In situ hybridization chromosome analysis of transgenic lines demonstrated that silenced transgenic lines had two or more T-DNA insertions in the same chromosome. These results suggest that two or more T-DNA insertions in the same chromosome facilitate efficient gene silencing in transgenic pine cells expressing green fluorescent protein. There were no differences in shoot differentiation and development between transgenic lines with multiple T-DNA copies and transgenic lines with one or two T-DNA copies. PMID:17158108

  10. Software-implemented fault insertion: An FTMP example

    NASA Technical Reports Server (NTRS)

    Czeck, Edward W.; Siewiorek, Daniel P.; Segall, Zary Z.

    1987-01-01

    This report presents a model for fault insertion through software; describes its implementation on a fault-tolerant computer, FTMP; presents a summary of fault detection, identification, and reconfiguration data collected with software-implemented fault insertion; and compares the results to hardware fault insertion data. Experimental results show detection time to be a function of time of insertion and system workload. For the fault detection time, there is no correlation between software-inserted faults and hardware-inserted faults; this is because hardware-inserted faults must manifest as errors before detection, whereas software-inserted faults immediately exercise the error detection mechanisms. In summary, the software-implemented fault insertion is able to be used as an evaluation technique for the fault-handling capabilities of a system in fault detection, identification and recovery. Although the software-inserted faults do not map directly to hardware-inserted faults, experiments show software-implemented fault insertion is capable of emulating hardware fault insertion, with greater ease and automation.

  11. Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

    PubMed Central

    2014-01-01

    Background Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS. We have developed a program with a new algorithm to detect the transpositions from NGS data. Results In the process of tool development, we used next-generation sequence (NGS) data of derivative lines (ttm2 and ttm5) of japonica rice cv. Nipponbare, regenerated through cell culture. The new program, called a transposon insertion finder (TIF), was applied to detect the de novo transpositions of Tos17 in the regenerated lines. TIF searched 300 million reads of a line within 20min, identifying 4 and 12 de novo transposition in ttm2 and ttm5 lines, respectively. All of the transpositions were confirmed by PCR/electrophoresis and sequencing. Using the program, we also detected new transposon insertions of P-element from NGS data of Drosophila melanogaster. Conclusion TIF operates to find the transposition of any elements provided that target site duplications (TSDs) are generated by their transpositions. PMID:24629057

  12. Estimation of insertion depth angle based on cochlea diameter and linear insertion depth: a prediction tool for the CI422.

    PubMed

    Franke-Trieger, Annett; Mürbe, Dirk

    2015-11-01

    Beside the cochlear size, the linear insertion depth (LID) influences the insertion depth angle of cochlear implant electrode arrays. For the specific implant CI422 the recommended LID is not fixed but can vary continuously between 20 and 25 mm. In the current study, the influence of cochlea size and LID on the final insertion depth angle was investigated to develop a prediction tool for the insertion depth angle by means of cochlea diameter and LID. Preoperative estimation of insertion depth angles might help surgeons avoid exceeding an intended insertion depth, especially with respect to low-frequency residual hearing preservation. Postoperative, high-resolution 3D-radiographs provided by Flat Panel Computed Volume Tomography (FPCT) were used to investigate the insertion depth angle in 37 CI422 recipients. Furthermore, the FPCT images were used to measure linear insertion depth and diameter of the basal turn of the cochlea. A considerable variation of measured insertion depth angles ranging from 306° to 579° was identified. The measured linear insertion depth ranged from -18.6 to 26.2 mm and correlated positively with the insertion depth angle. The cochlea diameter ranged from 8.11 to 10.42 mm and correlated negatively with the insertion depth angle. The results suggest that preoperatively measured cochlea diameter combined with the option of different array positions by means of LID may act as predictors for the final insertion depth angle. PMID:25361895

  13. Commercial Generic Bioprocessing Apparatus Science Insert - 03

    NASA Technical Reports Server (NTRS)

    Moreno, Nancy; Stodieck, Louis; Cushing, Paula; Stowe, Mark; Hamilton, Mary Ann; Werner, Ken

    2008-01-01

    Commercial Generic Bioprocessing Apparatus Science Insert - 03 (CSI-03) is the third set of investigations in the CSI program series. The CSI program provides the K-12 community opportunities to utilize the unique microgravity environment of the International Space Station as part of the regular classroom to encourage learning and interest in science, technology, engineering and math. CSI-03 will examine the complete life cycle of the painted lady butterfly and the ability of an orb weaving spider to spin a web, eat and remain healthy in space.

  14. Phoenix's Probe Inserted in Martian Soil

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Phoenix Mars lander's robotic-arm camera took this image of the spacecraft's thermal and electrical-conductivity probe (TECP) inserted into Martian soil on day 149 of the mission. Phoenix landed on Mars' northern plains on May 25, 2008, landing.

    The robotic-arm camera acquired this image at 16:02:41 local solar time. The camera pointing was elevation -72.6986 degrees and azimuth 2.1093 degrees.

    The Phoenix mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  15. Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) Furnace Development

    NASA Technical Reports Server (NTRS)

    Crouch, Myscha R.; Carswell, William E.; Farmer, Jeff; Rose, Fred; Tidwell, Paul H., II

    2000-01-01

    The Quench Module Insert (QMI) and the Diffusion Module Insert (DMI) are microgravity furnaces under development at Marshall Space Flight Center. The furnaces are being developed for the first Materials Science Research Rack (MSRR-1) of the Materials Science Research Facility (MSRF), one of the first International Space Station (ISS) scientific payloads. QMI is a Bridgman furnace with quench capability for studying interface behavior during directional solidification of metallic and alloy materials. DMI will be a Bridgman-Stockbarger furnace to study diffusion processes in semiconductors. The design for each insert, both QMI and DMI, is driven by specific science, operations and safety requirements, as well as by constraints arising from resource limitations, such as volume, mass and power. Preliminary QMI analysis and testing indicates that the design meets these requirements.

  16. Forceps insertion with incisional anesthesia for Sensar intraocular lenses.

    PubMed

    Dewey, Steven H

    2002-07-01

    This technique to prevent self-adherence of the Sensar acrylic intraocular lens (IOL) optic during forceps insertion with wound stretch includes modifications to the 3-and-9 insertion technique to prevent difficulties that may be encountered with this phenomenon. To decrease patient sensation during IOL insertion and thus improve surgeon control, the corneal tunnel incision is directly anesthetized. PMID:12106716

  17. 21 CFR 310.515 - Patient package inserts for estrogens.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 5 2014-04-01 2014-04-01 false Patient package inserts for estrogens. 310.515... package inserts for estrogens. (a) Requirement for a patient package insert. FDA concludes that the safe and effective use of drug products containing estrogens requires that patients be fully informed...

  18. 21 CFR 310.515 - Patient package inserts for estrogens.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 5 2011-04-01 2011-04-01 false Patient package inserts for estrogens. 310.515... package inserts for estrogens. (a) Requirement for a patient package insert. FDA concludes that the safe and effective use of drug products containing estrogens requires that patients be fully informed...

  19. 21 CFR 310.515 - Patient package inserts for estrogens.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Patient package inserts for estrogens. 310.515... package inserts for estrogens. (a) Requirement for a patient package insert. FDA concludes that the safe and effective use of drug products containing estrogens requires that patients be fully informed...

  20. 21 CFR 310.515 - Patient package inserts for estrogens.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 5 2012-04-01 2012-04-01 false Patient package inserts for estrogens. 310.515... package inserts for estrogens. (a) Requirement for a patient package insert. FDA concludes that the safe and effective use of drug products containing estrogens requires that patients be fully informed...

  1. Insertion torque versus mechanical resistance of mini-implants inserted in different cortical thickness

    PubMed Central

    Santos, Renata de Faria; Ruellas, Antonio Carlos de Oliveira; Fernandes, Daniel Jogaib; Elias, Carlos Nelson

    2014-01-01

    Objective This study aimed to measure insertion torque, tip mechanical resistance to fracture and transmucosal neck of mini-implants (MI) (Conexão Sistemas de PróteseT), as well as to analyze surface morphology. Methods Mechanical tests were carried out to measure the insertion torque of MIs in different cortical thicknesses, and tip mechanical resistance to fracture as well as transmucosal neck of MIs. Surface morphology was assessed by scanning electron microscopy (SEM) before and after the mechanical tests. Results Values of mechanical resistance to fracture (22.14 N.cm and 54.95 N.cm) were higher and statistically different (P < 0.05) from values of insertion torque for 1-mm (7.60 N.cm) and 2-mm (13.27 N.cm) cortical thicknesses. Insertion torque was statistically similar (P > 0.05) to torsional fracture in the tip of MI (22.14 N.cm) when 3 mm cortical thickness (16.11 N.cm) and dense bone (23.95 N.cm) were used. Torsional fracture of the transmucosal neck (54.95 N.cm) was higher and statistically different (P < 0.05) from insertion torsional strength in all tested situations. SEM analysis showed that the MIs had the same smooth surface when received from the manufacturer and after the mechanical tests were performed. Additionally, no significant marks resulting from the manufacturing process were observed. Conclusion All mini-implants tested presented adequate surface morphology. The resistance of mini-implants to fracture safely allows placement in 1 and 2-mm cortical thickness. However, in 3-mm cortical thickness and dense bones, pre-drilling with a bur is recommended before insertion. PMID:25162571

  2. Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping System

    PubMed Central

    Blanchard, Adam M.; Leigh, James A.; Egan, Sharon A.; Emes, Richard D.

    2015-01-01

    The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS PMID:25914720

  3. Lithium Insertion Chemistry of Some Iron Vanadates

    SciTech Connect

    Patoux, Sebastien; Richardson, Thomas J.

    2007-02-02

    Lithium insertion into various iron vanadates has been investigated. Fe{sub 2}V{sub 4}O{sub 13} and Fe{sub 4}(V{sub 2}O{sub 7}){sub 3} {center_dot} 3H{sub 2}O have discharge capacities approaching 200 mAh/g above 2.0 V vs. Li{sup +}/Li. Although the potential profiles change significantly between the first and subsequent discharges, capacity retention is unexpectedly good. Other phases, structurally related to FeVO{sub 4}, containing copper and/or sodium ions were also studied. One of these, {beta}-Cu{sub 3}Fe{sub 4}(VO{sub 4}){sub 6}, reversibly consumes almost 10 moles of electrons per formula unit (ca. 240 mAh g{sup -1}) between 3.6 and 2.0 V vs. Li{sup +}/Li, in a non-classical insertion process. It is proposed that both copper and vanadium are electrochemically active, whereas iron(III) reacts to form LiFe{sup III}O{sub 2}. The capacity of the Cu{sub 3}Fe{sub 4}(VO{sub 4}){sub 6}/Li system is nearly independent of cycling rate, stabilizing after a few cycles at 120-140 mAh g{sup -1}. Iron vanadates exhibit better capacities than their phosphate analogues, whereas the latter display more constant discharge potentials.

  4. Evidence for insertional RNA editing in humans.

    PubMed

    Zougman, Alexandre; Zi?kowski, Piotr; Mann, Matthias; Wi?niewski, Jacek R

    2008-11-25

    Large-scale analysis directly at the protein level holds the promise of uncovering features not apparent or present at the gene level [1-3]. Although mass spectrometry (MS)-based proteomics can now identify and quantify thousands of cellular proteins in large-scale proteomics experiments, much of the peptide information contained in these experiments remains unassigned [4]. Here, we use such information to discover a previously unreported mechanism creating altered protein forms. Linker histones H1 and high-mobility group (HMG) proteins are abundant nuclear proteins that regulate gene expression through modulation of chromatin structure [5-8]. In the high-resolution MS analysis of histone H1 and HMG protein fractions isolated from human cells, we discovered peptides that mapped upstream of the known translation start sites of these genes. No alternative upstream start site exists in the genome, but analysis of Expressed Sequence Tag (EST) databases revealed that these N-terminally extended (ET) proteins are due to in-frame translation of the 5' untranslated region (5'UTR) sequences of the transcripts. The new translation start sites are created by a single uridine insertion between AG, reflecting a previously unreported RNA-editing mechanism. To our knowledge, this is the first report of RNA-insertion editing in humans and may be an example of the type of discoveries possible with modern proteomics methods. PMID:18993075

  5. Radiological Insertion and Management of Peritoneovenous Shunt

    SciTech Connect

    Bratby, M. J.; Hussain, F. F. Lopez, A. J.

    2007-06-15

    The purpose of the study was to report our experience of the management of complications following the insertion of a peritoneovenous shunt for intractable malignant ascites. From June 1999 to January 2006, 26 patients underwent insertion of a peritoneovenous shunt for ascites by interventional radiologists. We have used ultrasound and shuntography to assist in the diagnosis of the cause of shunt blockage. Successful techniques for the restoration of the shunt function include port- pumping, stripping of any fibrin sheath, and revision of either the venous or peritoneal catheter. The procedure was initially successful in all patients with continued patency until death in 17. A further four patients are still alive with a functioning shunt. There was one rapid postprocedure death resulting from pulmonary edema. Two patients developed pneumothorax, managed successfully with either a chest drain or aspiration. Shunt dysfunction occurred eight times in seven patients. There were five successful revisions in four patients. Overall, shunt patency has been maintained in 80.1% of patients. Shunt dysfunction is seen in a significant number of patients, but successful revision of the shunt can be achieved in the majority.

  6. Model of a Hollow Cathode Insert Plasma

    NASA Technical Reports Server (NTRS)

    Mikellides, Ioannis G.; Katz, Ira; Goebel, Dan M.; Polk, James E.

    2004-01-01

    A 2-D axisymmetric fluid model of the plasma in the insert region of a hollow cathode is presented. The level of sophistication included in the model is motivated in part by the need to determine quantitatively plasma fluxes to the emitter surface. The ultimate goal is to assess whether plasma effects can degrade the life of impregnated inserts beyond those documented throughout the 30-50 year history of vacuum cathode technologies. Results from simulations of a 1.2-cm diameter cathode operating at a discharge current of 25 A, and a gas flow rate of 5 sccm, suggest that approximately 10 A of electron current, and 3.5 A of ion current return to the emitter surface. The total emitted electron current computed by the model is about 35 A. Comparisons with plasma measurements suggest that anomalous heating of the plasma due to two-stream instabilities is possible near the orifice region. Solution to the heavy species energy equation, with classical transport and no viscous effects, predicts heavy species temperatures as high as 2640 K.

  7. Mammalian NUMT insertion is non-random

    PubMed Central

    Tsuji, Junko; Frith, Martin C.; Tomii, Kentaro; Horton, Paul

    2012-01-01

    It is well known that remnants of partial or whole copies of mitochondrial DNA, known as Nuclear MiTochondrial sequences (NUMTs), are found in nuclear genomes. Since whole genome sequences have become available, many bioinformatics studies have identified putative NUMTs and from those attempted to infer the factors involved in NUMT creation. These studies conclude that NUMTs represent randomly chosen regions of the mitochondrial genome. There is less consensus regarding the nuclear insertion sites of NUMTs — previous studies have discussed the possible role of retrotransposons, but some recent ones have reported no correlation or even anti-correlation between NUMT sites and retrotransposons. These studies have generally defined NUMT sites using BLAST with default parameters. We analyze a redefined set of human NUMTs, computed with a carefully considered protocol. We discover that the inferred insertion points of NUMTs have a strong tendency to have high-predicted DNA curvature, occur in experimentally defined open chromatin regions and often occur immediately adjacent to A + T oligomers. We also show clear evidence that their flanking regions are indeed rich in retrotransposons. Finally we show that parts of the mitochondrial genome D-loop are under-represented as a source of NUMTs in primate evolution. PMID:22761406

  8. Phoenix Conductivity Probe Inserted in Martian Soil

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This series of six images from the Robotic Arm Camera on NASA's Phoenix Mars Lander records the first time that the four spikes of the lander's thermal and electrical conductivity probe were inserted into Martian soil.

    The images were taken on July 8, 2008, during the Phoenix mission's 43rd Martian day, or sol, since landing. The insertion visible from the shadows cast on the ground on that sol was a validation test of the procedure. The spikes on the probe are about 1.5 centimeters or half an inch long.

    The science team will use the probe tool to assess how easily heat and electricity move through the soil from one spike to another. Such measurements can provide information about frozen or unfrozen water in the soil. The probe is mounted on the 'knuckle' of Phoenix's Robotic Arm. It has already been used for assessing water vapor in the atmosphere when it is held above the ground.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is led by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  9. Deep insertion - round window approach by using SRA electrode.

    PubMed

    Skarżyński, H; Matusiak, M; Furmanek, M; Skarzyński, P H

    2014-05-01

    Hearing preservation surgery requires specially a traumatic technique. Having some preoperative anatomical data of the size of patient's cochlea surgeon can design his or her insertion depth. In the study we have evaluated a relation between hearing preservation rate and angular insertion depth estimated intraoperatively and postoperatively having measured insertion angle from radiological assessment and calculations given by Escude. There has not been no statistically significant difference between insertion depth angle, either estimated intraoperatively and measured and calculated post-operatively, and hearing preservation rate in the group. This analysis confirms a traumaticy of insertion in hearing preservation surgery. PMID:24869441

  10. Insertion of coherence requests for debugging a multiprocessor

    DOEpatents

    Blumrich, Matthias A.; Salapura, Valentina

    2010-02-23

    A method and system are disclosed to insert coherence events in a multiprocessor computer system, and to present those coherence events to the processors of the multiprocessor computer system for analysis and debugging purposes. The coherence events are inserted in the computer system by adding one or more special insert registers. By writing into the insert registers, coherence events are inserted in the multiprocessor system as if they were generated by the normal coherence protocol. Once these coherence events are processed, the processing of coherence events can continue in the normal operation mode.

  11. QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

    PubMed

    Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

    2009-07-01

    Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles. PMID:19387483

  12. Method Of Wire Insertion For Electric Machine Stators

    DOEpatents

    Brown, David L; Stabel, Gerald R; Lawrence, Robert Anthony

    2005-02-08

    A method of inserting coils in slots of a stator is provided. The method includes interleaving a first set of first phase windings and a first set of second phase windings on an insertion tool. The method also includes activating the insertion tool to radially insert the first set of first phase windings and the first set of second phase windings in the slots of the stator. In one embodiment, interleaving the first set of first phase windings and the first set of second phase windings on the insertion tool includes forming the first set of first phase windings in first phase openings defined in the insertion tool, and forming the first set of second phase windings in second phase openings defined in the insertion tool.

  13. A piezoelectric vibration-based syringe for reducing insertion force

    NASA Astrophysics Data System (ADS)

    Huang, Y. C.; Tsai, M. C.; Lin, C. H.

    2012-12-01

    Puncturing of the human skin with a needle is perhaps the most common invasive medical procedure. Clinical studies have revealed that tissue deformation and needle deflection are the primary problem for needle misplacement in percutaneous procedures. To avoid this, various techniques for reducing insertion forces during needle insertion have been considered. This paper presents a piezoelectric vibration-based syringe to reduce insertion force. AC power was applied to the piezoelectric elements to vibrate the needle with high frequency and thereby reduce the friction and cutting forces between the needle and tissue. Vibration mode shapes of the needle were observed by finite element analysis and verified by experimental results. Effects of reducing insertion force via the vibrating needle were also confirmed by inserting the needle into the porcine tissues. The proposed syringe, which minimizes the insertion force and overcomes limitations of needle materials, can be widely utilized in robot-assisted needle insertion systems.

  14. Lithium Insertion Electrodes and Molten Salt Electrolytes.

    NASA Astrophysics Data System (ADS)

    Macklin, W. J.

    Available from UMI in association with The British Library. Requires signed TDF. The development of a new electrolyte for ambient -temperature secondary lithium cells based on insertion -type electrodes is described. Mixtures of aluminium chloride and 1-methyl-3-ethylimidazolium chloride form salts that are liquid at room temperature. Lithium chloride has a maximum solubility of 12 mole percent in the acidic (aluminium chloride rich) melt. The electrochemical window of the lithiated ternary melt was determined by cyclic voltammetry. ^{27}Al NMR and Infrared spectroscopy indicate that the addition of lithium chloride causes a shift in the predominant equilibrium 2AlCl _4^- longleftrightarrow Al_2Cl_7 ^- + Cl^- in favour of the tetrahedral AlCl_4^-^ecies. The addition of LiCl^2 to the binary melts also affects the chemical shifts of the protons on the imidazolium cation. A decrease in melt conductivity was observed on lithiation. The lithium-ion mobility was estimated from a transference experiment based on the Hittorf method. The observed reactivity of the melt with metallic lithium requires the use of two insertion electrodes for use in a practical cell; the electrochemical energy being provided by shuttling lithium ions between the two electrodes. Powder X-ray diffraction and A.C.-impedance measurements demonstrate that the defect cubic spinel Li_{x }Cu_{0.07}Ti _2S_4 is a suitable electrode material; lithium can be successfully inserted electrochemically with a high degree of reversibility from the melt electrolyte. This electrode can be coupled with the layered oxide Li_{x} CoO_2 to give a cell with an open-circuit voltage of 1.71 V. The ionic medium of the molten salt results in higher exchange currents enabling more rapid charge transfer than observed in conventional organic solvent electrolytes. The generation of a surface film on the Li_{x}CoO _2 electrode is responsible for a large fraction of the polarisation losses in the cell.

  15. Intermetallic insertion anodes for lithium batteries.

    SciTech Connect

    Thackeray, M. M.; Vaughey, J.; Johnson, C. S.; Kepler, K. D.

    1999-11-12

    Binary intermetallic compounds containing lithium, or lithium alloys, such as Li{sub x}Al, Li{sub x}Si and Li{sub x}Sn have been investigated in detail in the past as negative electrode materials for rechargeable lithium batteries. It is generally acknowledged that the major limitation of these systems is the large volumetric expansion that occurs when lithium reacts with the host metal. Such large increases in volume limit the practical use of lithium-tin electrodes in electrochemical cells. It is generally recognized that metal oxide electrodes, MO{sub y}, in lithium-ion cells operate during charge and discharge by means of a reversible lithium insertion/extraction process, and that the cells offer excellent cycling behavior when the crystallographic changes to the unit cell parameters and unit cell volume of the Li{sub x}MO{sub y} electrode are kept to a minimum. An excellent example of such an electrode is the spinel Li{sub 4}Ti{sub 5}O{sub 12}, which maintains its cubic symmetry without any significant change to the lattice parameter (and hence unit cell volume) during lithium insertion to the rock-salt composition Li{sub 7}Ti{sub 5}O{sub 12}. This spinel electrode is an example of a ternary Li{sub x}MO{sub y} system in which a binary MO{sub y} framework provides a stable host structure for lithium. With this approach, the authors have turned their attention to exploring ternary intermetallic systems Li{sub x}MM{prime} in the hope of finding a system that is not subject to the high volumetric expansion that typifies many binary systems. In this paper, the authors present recent data of their investigations of lithium-copper-tin and lithium-indium-antimonide electrodes in lithium cells. The data show that lithium can be inserted reversibly into selected intermetallic compounds with relatively small expansion of the lithiated intermetallic structures.

  16. CRUCIBLE LINING METHOD

    DOEpatents

    Bone, W.H.; Schmidt, W.W.

    1958-11-01

    A method is presented for forming refractory liners in cylindrical reaction vessels used for the reductlon of uranium tetrafluoride to metallic uranium. A preliminary form, having positioning lugs attached thereto, is inserted into the reaction vessel and the refractory powder, usually CaO, is put in the annular space between the form and the inner wall of the reaction vessel. A jolting table is used to compact this charge of liner material ln place, and after thls has been done, the preliminary form is removed and the flnal form or plug is lnserted without disturbing the partially completed lining. The remainder of the lining charge is then introduced and compacted by jolting, after which the form is removed.

  17. Stabilization of insertion electrodes for lithium batteries.

    SciTech Connect

    Thackeray, M. M.

    1998-09-03

    This paper discusses the techniques that are being employed to stabilize LiMn{sub 2}O{sub 4} spinel and composite Li{sub x}MnO{sub 2} positive electrodes. The critical role that spinel domains play in stabilizing these electrodes for operation at both 4 V and 3 V is highlighted. The concept of using an intermetallic electrode MM{prime} where M is an active alloying element and M{prime} is an inactive element (or elements) is proposed as an alternative negative electrode (to carbon) for lithium-ion cells. An analogy to metal oxide insertion electrodes, such as MnO{sub 2}, in which Mn is the electrochemically active ion and O is the inactive ion, is made. Performance data are given for the copper-tin electrode system, which includes the intermetallic phases eta-Cu{sub 6}Sn{sub 5} and Li{sub 2}CuSn.

  18. [Integration of AAV vectors and insertional mutagenesis].

    PubMed

    Rossi, Axel; Salvetti, Anna

    2016-02-01

    Recombinant AAV vectors (rAAV) are considered as very efficient tools for in vivo gene transfer. Accordingly, several preclinical and clinical gene therapy trials use these vectors to treat inherited and acquired diseases. rAAV vectors possess the capacity to persist for a long term in the transduced tissue in a transcriptionally active, extra-chromosomal (episomal) form. However, many studies have shown that a significant fraction of the rAAV genomes can also nonspecifically integrate into the host cell genome thus raising the possibility of insertional mutagenesis events. This review summarizes the current knowledge on integration of wild type and rAAV genomes and highlights the major questions which remain unresolved. PMID:26936174

  19. Polymorphic Alu insertions among Mayan populations.

    PubMed

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

    2007-01-01

    The Mayan homeland within Mesoamerica spans five countries: Belize, El Salvador, Guatemala, Honduras and Mexico. There are indications that the people we call the Maya migrated from the north to the highlands of Guatemala as early as 4000 B.C. Their existence was village-based and agricultural. The culture of these Preclassic Mayans owes much to the earlier Olmec civilization, which flourished in the southern portion of North America. In this study, four different Mayan groups were examined to assess their genetic variability. Ten polymorphic Alu insertion (PAI) loci were employed to ascertain the genetic affinities among these Mayan groups. North American, African, European and Asian populations were also examined as reference populations. Our results suggest that the Mayan groups examined in this study are not genetically homogeneous. PMID:17151812

  20. 48 CFR 252.204-7011 - Alternative Line Item Structure.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Structure. 252.204-7011 Section 252.204-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION... of Provisions And Clauses 252.204-7011 Alternative Line Item Structure. As prescribed in 204.7109(b), insert the following provision: ALTERNATIVE LINE-ITEM STRUCTURE (SEP 2011) (a) Line items are the...

  1. 48 CFR 252.204-7011 - Alternative Line Item Structure.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Structure. 252.204-7011 Section 252.204-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION... of Provisions And Clauses 252.204-7011 Alternative Line Item Structure. As prescribed in 204.7109(b), insert the following provision: Alternative Line-Item Structure (SEP 2011) (a) Line items are the...

  2. 48 CFR 252.204-7011 - Alternative Line Item Structure.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Structure. 252.204-7011 Section 252.204-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION... of Provisions And Clauses 252.204-7011 Alternative Line Item Structure. As prescribed in 204.7109(b), insert the following provision: Alternative Line-Item Structure (SEP 2011) (a) Line items are the...

  3. 48 CFR 252.204-7011 - Alternative Line Item Structure.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Structure. 252.204-7011 Section 252.204-7011 Federal Acquisition Regulations System DEFENSE ACQUISITION... of Provisions And Clauses 252.204-7011 Alternative Line Item Structure. As prescribed in 204.7109(b), insert the following provision: Alternative Line-Item Structure (SEP 2011) (a) Line items are the...

  4. Lining up your service lines.

    PubMed

    Bilsky, Steven D; Aber, Jeffrey M

    2007-07-01

    Steps in implementing a service line approach include: Defining the service line. Allocating service line revenue and expense. Analyzing service line contribution margin and profitability. Determining the value of other factors. Creating standards for investment decisions, benchmarking, and ranking. PMID:17687972

  5. Peripherally inserted central catheter: compliance with evidence-based indications for insertion in an inpatient setting.

    PubMed

    Wojnar, Danuta G; Beaman, Margaret L

    2013-01-01

    A randomized, retrospective chart review was conducted at a medium-sized community hospital to verify appropriateness of peripherally inserted central catheter (PICC) use in 49 inpatient patients. Study results support the Infusion Nurses Society recommendation to use PICCs to facilitate either short- or long-term intravenous therapy of vesicants, irritants, and any medications with a pH less than 5 or greater than 9 and osmolarity greater than 600 mOsm/L. All PICC insertion criteria recommended by the Centers for Disease Control and Prevention were met except one--the intended duration of intravenous therapy of more than 6 days. Identical PICC selection criteria are needed to standardize clinical practice. PMID:23823005

  6. Neonatal peripherally inserted central catheters: recommendations for prevention of insertion and postinsertion complications.

    PubMed

    Paulson, Pamela R; Miller, Kellee M

    2008-01-01

    Peripherally inserted central catheters (PICCs) continue to be necessary in neonatal care. They benefit many premature infants and those needing long-term intravenous access. An experienced inserter, early recognition of PICC candidates, early PICC placement, knowledge of anatomy, and correct choice of vein all increase placement success. As with any invasive procedure, there are risks. These include pain, difficulty advancing the catheter, damage to vessels, catheter malposition, and bleeding. Utilizing assessment skills, following the product manufacturer's instructions, and carefully placing the catheter should minimize most of these risks. Additional risks include postinsertion complications such as occlusions, thrombosis, catheter failure, infection, and catheter malposition. Proper nursing care--which includes controlling infection, properly securing the catheter, and changing the dressing as needed--is key to preventing complications and maintaining the PICC until treatment has been completed. PMID:18697655

  7. An evaluation of consumable inserts for gas tungsten arc welding

    SciTech Connect

    Chavez, A.E.; Marburger, S.J.

    1987-03-01

    This study presents information on the use of consumable inserts to make 100% penetration welds in 304 and modified A286 (designated JBK-75) stainless steels. Current and voltage ranges which produced acceptable welds were found for different combinations of joint preparations and inserts. Three third member insert designs were examined: Type A (AWS Class 1), Type G (AWS Class 3), and Type K (AWS Class 5). One joint design incorporated the configuration of the Type G insert into the root face of the joint (termed an ''integral insert''). Joints welded with and without filler wire addition were made for comparison. Metallurgical and radiographic tests were done on all welds. It was found that the consumable insert root pass was comparable to the wire-fed root pass in weld shape and size using the same parameters; it also had additional advantages in ease of use, cleanliness, inspectability and reduced procedure complexity.

  8. Effect of insertion torque on bone screw pullout strength.

    PubMed

    Lawson, K J; Brems, J

    2001-05-01

    The effect of insertion torque on the holding strength of 4.5-mm ASIF/AO cortical bone screws was studied in vitro. Screw holding strength was determined using an Instron materials testing machine (Bristol, United Kingdom) on 55 lamb femora and 30 human tibiocortical bone sections. Holding strength was defined as tensile stress at pullout with rapid loading to construct failure. Different insertion torques were tested, normalizing to the thickness of cortical bone specimen engaged. These represented low, intermediate, high, and thread-damaging insertion torque. All screws inserted with thread-damaging torque and single cortex engaging screws inserted to high torque tightening moments showed diminished holding strength. This loss of strength amounted to 40%-50% less than screws inserted with less torque. PMID:11379993

  9. Assessment of infants with peripherally inserted central catheters: Part 1. Detecting the most frequently occurring complications.

    PubMed

    Pettit, Janet

    2002-12-01

    Inserting, maintaining, and monitoring vascular access are integral components of neonatal care. Advances in vascular access technology have led to the insertion of peripherally inserted central catheters (PICC) to provide stable venous access for early and aggressive parenteral nutrition. Medications that are irritating or damaging, or those with a high osmolality or a nonphysiologic pH, can also be safely administered into the central venous system. The need for repeated peripheral intravenous attempts, as well as the associated pain and physiologic instability, are virtually eliminated once a PICC line is placed. Complications related to PICCs may occur at any phase of therapy: during insertion, while indwelling, or after discontinuing the line. The risk factors associated with PICCs are distinctly different from peripheral intravenous lines because of their long dwell time, central placement, and potential to migrate. Part 1 of Focus on the Physical offers a review of the relevant anatomy of the vascular system and a discussion of the appropriate sites for catheter tip placement. Guidelines for a systematic physical assessment, along with recommendations for standardized PICC documentation, are provided. A review of the signs and symptoms of more frequently occurring complications, such as catheter occlusion and bloodstream infections, is presented to enhance awareness of PICC-specific complications in the neonate and to expedite early detection and treatment. Part 2 of this series will focus on systematic assessment for less common complications such as catheter migration, dislodgement, breakage, and thrombosis, as well as the life-threatening complications of pleural and pericardial effusion. PMID:12881943

  10. A Collection of Ds Insertional Mutants Associated With Defects in Male Gametophyte Development and Function in Arabidopsis thaliana

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional analyses of the Arabidopsis genome require analysis of the gametophytic generation, since 10% of the genes are expressed in the male gametophyte and 9% in the female gametophyte. Here we describe the genetic and molecular characterization of 67 Ds insertion lines that show reduced transmi...

  11. Critical monitoring of the Cassini Saturn Orbit Insertion maneuver

    NASA Technical Reports Server (NTRS)

    Asmar, S. W.; Johnston, D. V.; Maize, E.; Mitchell, R. T.

    2004-01-01

    The Cassini-Huygens spacecraft will have spent seven years since launch by the time it reaches Saturn and its satellites. The primary mission will begin after the Saturn Orbit Insertion (SOI) scheduled for early July 2004. the insertion will require a critical navigational maneuver that involves firing the orbiter's thrusters leading to the capture in the gravity well of the planet. This paper will describe the challenges and plans by the Cassini Program to monitor the Saturn Orbit Insertion Maneuver.

  12. The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

    PubMed Central

    Pereira, Vini; Enard, David; Eyre-Walker, Adam

    2009-01-01

    Background Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ?20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents. PMID:19183808

  13. Topographically grooved gel inserts for aligning epithelial cells during air-liquid-interface culture.

    PubMed

    Soleas, John P; Waddell, Thomas K; McGuigan, Alison P

    2015-01-01

    Epithelial tissues are a critical component of all tubular organs. Engineering artificial epithelium requires an understanding of the polarization of epithelia: both apicobasal and in a planar fashion. Air liquid interface (ALI) culture is typically used to generate apicobasal polarized airway epithelium in vitro; however, this approach does not provide any signalling cues to induce morphological planar polarization of the generated epithelial layer. Here we describe a microgrooved gelatin hydrogel insert that can induce alignment of confluent epithelial cell sheets under ALI conditions to induce both apicobasal and morphologically planar polarized epithelium. Microgrooves are imprinted into the surface of the gelatin insert using elastomeric stamps moulded from a diffraction grating film and gels are stabilized by crosslinking with glutaraldehyde. We show that microgrooved gelatin inserts produce alignment of 3T3 fibroblasts and a number of epithelial cell lines (ARPE-19, BEAS2B and IMCD3 cells). Furthermore, we show that BEAS2B apicobasally polarize and form a similar density of cilia on both gelatin inserts and standard transwell filters used for ALI culture but that as apicobasal polarization progresses cell alignment on the grooves is lost. Our method provides a simple strategy that can easily be adopted by labs without microfabrication expertise for manipulating epithelial organization in transwell culture and studying the interplay of various polarization forces. PMID:26214196

  14. Insertional footprint anatomy of the pectoralis major tendon.

    PubMed

    Carey, Paul; Owens, Brett D

    2010-01-01

    Correct anatomical repair of pectoralis major tendon injuries requires accurate identification of the humeral insertion site. In the absence of residual fibers at the insertion, proper placement requires knowledge of the anatomic relationships in the proximal humerus. This anatomic study attempts to measure these relationships and the dimensions of the insertional footprint to assist in surgical repair and reconstruction. Six matched pairs of cadaver proximal humeri were examined. All specimens were found to be in good condition and none were excluded. The proximal to distal length and maximum width of the pectoralis major tendon were measured at the humeral insertion with a digital caliper. The distance from the superomedial corner of the greater tuberosity to the superior aspect of the tendon insertion was also measured. The mean proximal to distal dimension of the pectoralis major insertion was 72.3+/-12.3 mm. The mean maximal thickness at the humeral insertion was 1.4+/-.2 mm. The distance from the superomedial corner of the greater tuberosity to the bony tendon insertion was 42.2+/-8.5 mm. The anatomic location of the humeral insertion of the pectoralis major tendon can be located in repair of pectoralis tendon injuries by referencing the superomedial corner of the greater tuberosity and the lateral lip of the bicipital groove. Findings in the present study will improve knowledge of the surgical anatomy relevant to repair and reconstruction of the pectoralis major tendon. PMID:20055351

  15. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis.

    PubMed

    Petyuk, Vladislav; McDermott, Jeffrey; Cook, Malcolm; Sauer, Brian

    2004-08-27

    Cre is a site-specific recombinase from bacteriophage P1. It is a member of the tyrosine integrase family and catalyzes reciprocal recombination between specific 34-bp sites called loxP. To analyze the structure-function relationships of this enzyme, we performed large scale pentapeptide insertional mutagenesis to generate insertions of five amino acids at random positions in the protein. The high density of insertion mutations into Cre allowed us to identify an unexpected degree of functional tolerance to insertions into the 4-5 beta-hairpin and into the loop between helices J and K (both of which contact the DNA in the minor groove) and also into helix A. The phenotypes of the majority of inserts allowed us to confirm a variety of predictions made on the basis of sequence conservation, known three-dimensional structure, and proposed catalytic mechanism. In particular, most insertions into conserved regions or secondary structure elements inactivated Cre, and most insertions located in nonconserved, unstructured regions preserved Cre activity. Less expectedly, the non-conserved and poorly structured loops and linkers between helices A-B, E-F, and M-N did not tolerate insertions, thus identifying these as critical regions for recombinase activity. We purified and characterized in vitro several representatives of these "unexpected" Cre insertion mutants. The role of those regions in the recombination process is discussed. PMID:15218019

  16. Optimal needle design for minimal insertion force and bevel length.

    PubMed

    Wang, Yancheng; Chen, Roland K; Tai, Bruce L; McLaughlin, Patrick W; Shih, Albert J

    2014-09-01

    This research presents a methodology for optimal design of the needle geometry to minimize the insertion force and bevel length based on mathematical models of cutting edge inclination and rake angles and the insertion force. In brachytherapy, the needle with lower insertion force typically is easier for guidance and has less deflection. In this study, the needle with lancet point (denoted as lancet needle) is applied to demonstrate the model-based optimization for needle design. Mathematical models to calculate the bevel length and inclination and rake angles for lancet needle are presented. A needle insertion force model is developed to predict the insertion force for lancet needle. The genetic algorithm is utilized to optimize the needle geometry for two cases. One is to minimize the needle insertion force. Using the geometry of a commercial lancet needle as the baseline, the optimized needle has 11% lower insertion force with the same bevel length. The other case is to minimize the bevel length under the same needle insertion force. The optimized design can reduce the bevel length by 46%. Both optimized needle designs were validated experimentally in ex vivo porcine liver needle insertion tests and demonstrated the methodology of the model-based optimal needle design. PMID:24957487

  17. Threaded insert for compact cryogenic-capable pressure vessels

    SciTech Connect

    Espinosa-Loza, Francisco; Ross, Timothy O.; Switzer, Vernon A.; Aceves, Salvador M.; Killingsworth, Nicholas J.; Ledesma-Orozco, Elias

    2015-06-16

    An insert for a cryogenic capable pressure vessel for storage of hydrogen or other cryogenic gases at high pressure. The insert provides the interface between a tank and internal and external components of the tank system. The insert can be used with tanks with any or all combinations of cryogenic, high pressure, and highly diffusive fluids. The insert can be threaded into the neck of a tank with an inner liner. The threads withstand the majority of the stress when the fluid inside the tank that is under pressure.

  18. [Molecular phylogenies and nucleotide insertion-deletion].

    PubMed

    Barriel, V

    1994-07-01

    Molecular trees based on the analysis of sequence data can be obtained through parsimony procedures. Such approaches identify evolutionary events (homologies and homoplasies and their location in the tree). Nevertheless, it is not possible generally to analyze directly the information given by the aligned sequences. Noticeably, gaps ("indel") need special coding. Standard procedures for coding gaps offer alternatives which suffer of several weaknesses. In this article a new strategy of coding the sequences is defined in view to express the potential phylogenetic information contained in complex zones with internested insertion/deletion and substitutions, contrary to what is done up to the present. This strategy applies without loss or distortion of information to any case where gaps are present in aligned sequences. According to the hierarchy of internested states of characters (sites), this strategy introduces in the data matrix question marks, "?", which are optimized in fine in the cladogram based on all data. These "?" are not missing data, they are methodological codes, neutral to a priori phylogenetic hypotheses. PMID:7882153

  19. Phoenix Conductivity Probe Inserted into Martian Soil

    NASA Technical Reports Server (NTRS)

    2008-01-01

    NASA's Phoenix Mars Lander inserted the four needles of its thermal and conductivity probe into Martian soil during the 98th Martian day, or sol, of the mission and left it in place until Sol 99 (Sept. 4, 2008).

    The Robotic Arm Camera on Phoenix took this image on the morning of Sol 99 while the probe's needles were in the ground. The science team informally named this soil target 'Gandalf.'

    The thermal and conductivity probe measures how fast heat and electricity move from one needle to an adjacent one through the soil or air between the needles. Conductivity readings can be indicators about water vapor, water ice and liquid water.

    The probe is part of Phoenix's Microscopy, Electrochemistry and Conductivity suite of instruments.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  20. IYA2009 newspaper insert in your community

    NASA Astrophysics Data System (ADS)

    Harvey, J.

    2008-06-01

    The Gemini PIO (Public Information Officer) offers suggestions on how to approach your local newspaper about a newspaper insert for your community being published during IYA2009. Local government support, articles by astronomers, advertisers, and appointing someone within your organisation to manage the content will be discussed. We will explain the timeline required, the number of personnel hours required, developmental stages and income a local newspaper would have to generate to produce a quality, table-top supplement. In 2003, over 30,000 copies of Stars over Mauna Kea, a special supplement in tabloid format were produced and distributed in the local newspapers in Hilo, Hawaii. The publication, 48 pages in total, featured profiles of the observatories on Mauna Kea, stories about the geology and legends of Mauna Kea, and historical information about the evolution of astronomy in Hawaii. In additionthe publication included a series of essays titled In their own words. These articles were written by key members of the astronomy community. Sixty thousand copies of Stars over Mauna Kea II were printed as a follow-up to the first edition in 2005. This second edition included an article on the `Imiloa Astronomy Education Center, explanations about the types of telescopes on Mauna Kea and columns written by scientists about the fascinating and significant discoveries made on Hawaii. Personal stories about careers in astronomy were also highlighted. In Chile, a similar eight-page supplement, featuring Gemini, CTIO and SOAR telescopes, was published in 2005 and 5000 copies were distributed throughout the country.

  1. Axially Inserted Magnetic/Langmuir Probe

    NASA Astrophysics Data System (ADS)

    Hannum, David; Bergerson, W.; Fiksel, G.; Forest, C. B.; Hegna, C.; Kendrick, R.; Oliva, S.; Sarff, J.

    2006-10-01

    A new probe has been designed to provide internal magnetic and Langmuir diagnostics throughout the rotating wall machine. The machine is a linear screw-pinch built to study the role of different wall boundary conditions on the resistive wall mode (RWM). Individual mode stability depends on the value of the safety factor at the plasma edge (qa). The plasma is produced by an array of nineteen guns, creating a column one meter in length and up to 20 cm in diameter. The central guns in the array can be biased to individually discharge 1 kA of plasma current. Different instabilities are studied by changing the current and density profiles of the guns. But profile measurement has been limited to the top and bottom of the plasma column by radial port access. The new axially-inserted Q-Tip probe can travel along the entire span of the column. The Q-Tip combines ten pickup loops with four triplets of electrodes for simultaneous magnetic and Langmuir measurements. The edge a and safety factor q of the plasma can now be found for different instabilities seen along the column. This poster tracks the change of ne, Te, φp, and q throughout the plasma.

  2. AKATSUKI status after the Venus orbit insertion

    NASA Astrophysics Data System (ADS)

    Nakamura, M.; Ishii, N.; Imamura, T.; Ueno, M.; Yamazaki, A.; Satoh, T.; Suzuki, M.; Iwagami, N.; Taguchi, M.; Watanabe, S.; Takahashi, Y.; Fukuhara, T.; Ohtsuki, S.; PLANET-C Project Team

    2010-12-01

    Japanese Venus Climate Orbiter 'AKATSUKI' (PLANET-C) was successfully launched at 06:58:22JST on May 21, by H-IIA F17. After the separation from H-IIA, the telemetry from AKATSUKI was normally detected by DSN Goldstone station (10:00JST) and the solar cell paddles' expansion was confirmed. AKATSUKI was put into the 3-axis stabilized mode in the initial operation from Uchinoura station and the critical operation was finished at 20:00JST on the same day. AKATSUKI will arrive at Venus on Dec 7, 2010. From the orbit around Venus, it will take pictures of the distribution of clouds and minor gas components at different wavelength by 4 cameras. These data will be analyzed to study the meteorology on Venus, especially the mechanism of the super-rotation of Venusian atmosphere which is still the top mystery of the Venus science. Simultaneous observation with ESA's Venus Express is highly expected to study the Venusian atmosphere. We will present the present status of AKATSUKI after the Venus orbit insertion with the latest results from the cameras.

  3. Measure Lines

    ERIC Educational Resources Information Center

    Crissman, Sally

    2011-01-01

    One tool for enhancing students' work with data in the science classroom is the measure line. As a coteacher and curriculum developer for The Inquiry Project, the author has seen how measure lines--a number line in which the numbers refer to units of measure--help students not only represent data but also analyze it in ways that generate…

  4. Vector-hexamer PCR isolation of all insert ends from a YAC contig of the mouse Igh locus.

    PubMed

    Herring, C D; Chevillard, C; Johnston, S L; Wettstein, P J; Riblet, R

    1998-06-01

    We have developed a simple PCR strategy, termed vector-hexamer PCR, that is unique in its ability to easily recover every insert end from large insert clones in YAC and BAC vectors. We used this method to amplify and isolate all insert ends from a YAC contig covering the mouse Igh locus. Seventy-seven ends were amplified and sequenced from 36 YAC clones from four libraries in the pYAC4 vector. Unexpectedly, 40% of the insert ends of these YACs were LINE1 repeats. Nonrepetitive ends were suitable for use as probes on Southern blots of digested YACs to identify overlaps and construct a contig. The same strategy was used successfully to amplify insert ends from YACs in the pRML vector from the Whitehead Institute/MIT-820 mouse YAC library and from BACs in pBeloBAC11. The simplicity of this technique and its ability to isolate every end from large insert clones are of great utility in genomic investigation. [The nucleotide sequence data reported in this paper are accessible in GenBank under accession nos. B07512-B07598.] PMID:9647641

  5. VectorHexamer PCR Isolation of All Insert Ends from a YAC Contig of the Mouse Igh?Locus

    PubMed Central

    Herring, Christopher D.; Chevillard, Christophe; Johnston, Sean L.; Wettstein, Peter J.; Riblet, Roy

    1998-01-01

    We have developed a simple PCR strategy, termed vectorhexamer PCR, that is unique in its ability to easily recover every insert end from large insert clones in YAC and BAC vectors. We used this method to amplify and isolate all insert ends from a YAC contig covering the mouse Igh locus. Seventy-seven ends were amplified and sequenced from 36 YAC clones from four libraries in the pYAC4 vector. Unexpectedly, 40% of the insert ends of these YACs were LINE1 repeats. Nonrepetitive ends were suitable for use as probes on Southern blots of digested YACs to identify overlaps and construct a contig. The same strategy was used successfully to amplify insert ends from YACs in the pRML vector from the Whitehead Institute/MIT-820 mouse YAC library and from BACs in pBeloBAC11. The simplicity of this technique and its ability to isolate every end from large insert clones are of great utility in genomic investigation. [The nucleotide sequence data reported in this paper are accessible in GenBank under accession nos. B07512B07598.] PMID:9647641

  6. Identification of the lacZ insertion site and beta-galactosidase expression in transgenic chickens.

    PubMed

    Mozdziak, Paul E; Wu, Qian; Bradford, Jennifer M; Pardue, Samuel L; Borwornpinyo, Suparerk; Giamario, Carol; Petitte, James N

    2006-04-01

    The quail:chick chimera system is a classical research model in developmental biology. An improvement over the quail:chick chimera system would be a line of transgenic chickens expressing a reporter gene. Transgenic chickens carrying lacZ and expressing bacterial beta-galactosidase have been generated, but complete characterization of the insertion event and characterization of beta-galactosidase expression have not previously been available. The genomic sequences flanking the retroviral insertion site have now been identified by using inverse polymerase chain reaction (PCR), homozygous individuals have been identified by using PCR-based genotyping, and beta-galactosidase expression has been evaluated by using Western analysis and histochemistry. Based upon the current draft of the chicken genome, the viral insertion carrying the lacZ gene has been located on chromosome 11 within the predicted gene for neurotactin/fractalkine (CX3CL1); neurotactin mRNA expression appears to be missing from the brain of homozygous individuals. When Generation 2 (G2) lacZ-positive individuals were inter-mated, they generated 361 G3 progeny; 82 were homozyous for lacZ (22.7%), 97 were wild-type non-transgenic (26.9%), and 182 (50.4%) were hemizygous for lacZ. Western analysis revealed the highest expression in the muscle and liver. With the identification of homozygous birds, the line of chickens is now designated NCSU-Blue1. PMID:16408197

  7. Upregulations of metallothionein gene expressions and tolerance to heavy metal toxicity by three dimensional cultivation of HepG2 cells on VECELL 3-D inserts.

    PubMed

    Kubo, Takashi; Kuroda, Yukie; Horiuchi, Shinichiro; Kim, Su-Ryang; Sekino, Yuko; Ishida, Seiichi

    2016-02-01

    The VECELL 3-D insert is a new culture scaffold consisting of collagen-coated ePTFE (expanded polytetrafluoroethylene) mesh. We analyzed the effects of VECELL 3-D inserts on the functionality of HepG2, a human hepatocellular carcinoma cell line. HepG2 cells cultured on VECELL 3-D inserts maintained a round shape, while those cultured on a standard culture plate or collagen-coated cell culture plate showed a flattened and cubic epithelial-like shape. HepG2 cells cultured on VECELL 3-D inserts had showed upregulated expression of metallothionein genes and in turn a higher tolerance to toxicity induced by heavy metals. These results suggest that HepG2 cell functions were changed by the cell morphology that is induced by culturing on a VECELL 3-D insert. PMID:26763402

  8. Everyman's Guide to Bacterial Insertion Sequences.

    PubMed

    Siguier, Patricia; Gourbeyre, Edith; Varani, Alessandro; Ton-Hoang, Bao; Chandler, Mick

    2015-04-01

    The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers. PMID:26104715

  9. Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage.

    PubMed

    Chen, Jian-Min; Chuzhanova, Nadia; Stenson, Peter D; Férec, Claude; Cooper, David N

    2005-02-01

    Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and approximately 10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all >or=276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene. PMID:15643617

  10. 41 CFR 50-201.3 - Insertion of stipulations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Insertion of stipulations. 50-201.3 Section 50-201.3 Public Contracts and Property Management Other Provisions Relating to Public Contracts PUBLIC CONTRACTS, DEPARTMENT OF LABOR 201-GENERAL REGULATIONS § 50-201.3 Insertion...

  11. Load beam unit replaceable inserts for dry coal extrusion pumps

    DOEpatents

    Saunders, Timothy; Brady, John D.

    2012-11-13

    A track assembly for a particulate material extrusion pump according to an exemplary aspect of the present disclosure includes a link assembly with a roller bearing. An insert mounted to a load beam located such that the roller bearing contacts the insert.

  12. Combined plasma and thermal hollow cathode insert model

    NASA Technical Reports Server (NTRS)

    Katz, Ira; Polk, James E.; Mikellides, Ionnis G.; Goebel, Dan m.; Hornbeck, Sarah E.

    2005-01-01

    In this paper, we present the first results from a Hollow Cathode Thermal (HCThermal) model that uses the spatially distributed plasma fluxes calculated by the InsertRegion of an Orificed Cathode (IROrCa2D) code as the heat source to predict the hollow cathode and insert temperatures.

  13. Endoscopic Achilles tenodesis: a surgical alternative for chronic insertional tendinopathy.

    PubMed

    Maquirriain, Javier

    2007-07-01

    This report describes an endoscopic approach for visualization and repair of heel structures potentially involved in patients presenting chronic calcaneal tendon insertion pain. Tendon-bone junction separation allows enthesis debridement. Tenodesis with a knotless absorbable anchor completes this minimally invasive surgical procedure for chronic insertional Achilles tendinopathy. PMID:17053930

  14. Cruciate retaining and cruciate substituting ultra-congruent insert.

    PubMed

    Mazzucchelli, Luca; Deledda, Davide; Rosso, Federica; Ratto, Nicola; Bruzzone, Matteo; Bonasia, Davide Edoardo; Rossi, Roberto

    2016-01-01

    The posterior cruciate ligament (PCL) conservation and the polyethylene insert constraint in total knee arthroplasty (TKA) are still debated. The PCL is one of the primary stabilizers of the joint, but cruciate retaining (CR) implants have the disadvantage of a difficult balancing of the PCL. Postero-stabilized (PS) implants were introduced to reduce this problem. However, also the PS implants have some disadvantages, due to the cam-mechanism, such as high risk of cam-mechanism polyethylene wear. To minimize the polyethylene wear of the cam-mechanism and the bone sacrifice due to the intercondylar box, different types of inserts were developed, trying to increase the implant conformity and to reduce stresses on the bone-implant interface. In this scenario ultra-congruent (UC) inserts were developed. Those inserts are characterized by a high anterior wall and a deep-dished plate. This conformation should guarantee a good stability without the posterior cam. Few studies on both kinematic and clinical outcomes of UC inserts are available. Clinical and radiological outcomes, as well as kinematic data are similar between UC mobile bearing (MB) and standard PS MB inserts at short to mid-term follow-up. In this manuscript biomechanics and clinical outcomes of UC inserts will be described, and they will be compared to standard PS or CR inserts. PMID:26855938

  15. Cruciate retaining and cruciate substituting ultra-congruent insert

    PubMed Central

    Deledda, Davide; Rosso, Federica; Ratto, Nicola; Bruzzone, Matteo; Bonasia, Davide Edoardo; Rossi, Roberto

    2016-01-01

    The posterior cruciate ligament (PCL) conservation and the polyethylene insert constraint in total knee arthroplasty (TKA) are still debated. The PCL is one of the primary stabilizers of the joint, but cruciate retaining (CR) implants have the disadvantage of a difficult balancing of the PCL. Postero-stabilized (PS) implants were introduced to reduce this problem. However, also the PS implants have some disadvantages, due to the cam-mechanism, such as high risk of cam-mechanism polyethylene wear. To minimize the polyethylene wear of the cam-mechanism and the bone sacrifice due to the intercondylar box, different types of inserts were developed, trying to increase the implant conformity and to reduce stresses on the bone-implant interface. In this scenario ultra-congruent (UC) inserts were developed. Those inserts are characterized by a high anterior wall and a deep-dished plate. This conformation should guarantee a good stability without the posterior cam. Few studies on both kinematic and clinical outcomes of UC inserts are available. Clinical and radiological outcomes, as well as kinematic data are similar between UC mobile bearing (MB) and standard PS MB inserts at short to mid-term follow-up. In this manuscript biomechanics and clinical outcomes of UC inserts will be described, and they will be compared to standard PS or CR inserts. PMID:26855938

  16. Measurement of Vein Diameter for Peripherally Inserted Central Catheter (PICC) Insertion: An Observational Study.

    PubMed

    Sharp, Rebecca; Cummings, Melita; Childs, Jessie; Fielder, Andrea; Mikocka-Walus, Antonina; Grech, Carol; Esterman, Adrian

    2015-01-01

    Choosing an appropriately sized vein reduces the risk of venous thromboembolism associated with peripherally inserted central catheters. This observational study described the diameters of the brachial, basilic, and cephalic veins and determined the effect of patient factors on vein size. Ultrasound was used to measure the veins of 176 participants. Vein diameter was similar in both arms regardless of hand dominance and side. Patient factors-including greater age, height, and weight, as well as male gender-were associated with increased vein diameter. The basilic vein tended to have the largest diameter statistically. However, this was the case in only 55% of patients. PMID:26339941

  17. Z-2 Threaded Insert Design and Testing Abstract

    NASA Technical Reports Server (NTRS)

    Rhodes, RIchard; Graziosi, Dave; Jones, Bobby; Ferl, Jinny; Scarborough, Steve; Sweeney, Mitch

    2016-01-01

    The Z-2 Prototype Planetary Extravehicular Space Suit Assembly is a continuation of NASA's Z series of spacesuits. The Z-2 is another step in the NASA's technology development roadmap leading to human exploration of the Martian surface. To meet a more challenging set of requirements than previous suit systems standard design features, such as threaded inserts, have been re-analyzed and improved. NASA's Z-2 prototype space suit contains several components fabricated from an advanced hybrid composite laminate consisting of IM10 carbon fiber and fiber glass. One requirement NASA levied on the suit composites was the ability to have removable, replaceable helicoil inserts to which other suit components would be fastened. An approach utilizing bonded in inserts with helicoils inside of them was implemented. The design of the interface flanges of the composites allowed some of the inserts to be a "T" style insert that was installed through the entire thickness of the laminate. The flange portion of the insert provides a mechanical lock as a redundancy to the adhesive aiding in the pullout load that the insert can withstand. In some locations it was not possible to utilize at "T" style insert and a blind insert was used instead. These inserts rely completely on the bond strength of the adhesive to resist pullout. It was determined during the design of the suit that the inserts did not need to withstand loads induced from pressure cycling but instead tension induced from torqueing the screws to bolt on hardware which creates a much higher stress on them. Bolt tension is determined by dividing the torque on the screw by a k value multiplied by the thread diameter of the bolt. The k value is a factor that accounts for friction in the system. A common value used for k for a non-lubricated screw is 0.2. The k value can go down by as much as 0.1 if the screw is lubricated which means for the same torque, a much larger tension could be placed on the bolt and insert. This paper summarizes testing that was performed to determine a k value for helicoil inserts in the Z2 suit and how the insert design was modified to resist a higher pull out tension.

  18. Detection for processing history of seam insertion and contrast enhancement

    NASA Astrophysics Data System (ADS)

    Li, Jianwei; Zhao, Yao; Ni, Rongrong

    2014-11-01

    With the development of manipulations techniques of digital images, digital image forensic technology is becoming more and more necessary. However, the determination of processing history of multi-operation is still a challenge problem. In this paper, we improve the traditional seam insertion algorithm, and propose corresponding detection method. Then an algorithm that focuses on detecting the processing history of seam insertion and contrast enhancement is proposed, which can be widely used in practical image forgery. Based on comprehensive analysis, we have discovered the inherent relationship between seam insertion and contrast enhancement. Different orders of processing make different impacts on images. By using the newly proposed algorithm, both contrast enhancement followed by seam insertion and seam insertion followed by contrast enhancement can be detected correctly. Plenty of experiments have been implemented to prove the accuracy.

  19. Method for improving the durability of ion insertion materials

    DOEpatents

    Lee, Se-Hee; Tracy, C. Edwin; Cheong, Hyeonsik M.

    2002-01-01

    The invention provides a method of protecting an ion insertion material from the degradative effects of a liquid or gel-type electrolyte material by disposing a protective, solid ion conducting, electrically insulating, layer between the ion insertion layer and the liquid or gel-type electrolyte material. The invention further provides liquid or gel-type electrochemical cells having improved durability having a pair of electrodes, a pair of ion insertion layers sandwiched between the pair of electrodes, a pair of solid ion conducting layers sandwiched between the ion insertion layers, and a liquid or gel-type electrolyte material disposed between the solid ion conducting layers, where the solid ion conducting layer minimizes or prevents degradation of the faces of the ion insertion materials facing the liquid or gel-type electrolyte material. Electrochemical cells of this invention having increased durability include secondary lithium batteries and electrochromic devices.

  20. Gas turbine nozzle vane insert and methods of installation

    DOEpatents

    Miller, William John (Simpsonville, SC); Predmore, Daniel Ross (Clifton Park, NY); Placko, James Michael (West Chester, OH)

    2002-01-01

    A pair of hollow elongated insert bodies are disposed in one or more of the nozzle vane cavities of a nozzle stage of a gas turbine. Each insert body has an outer wall portion with apertures for impingement-cooling of nozzle wall portions in registration with the outer wall portion. The insert bodies are installed into the cavity separately and spreaders flex the bodies toward and to engage standoffs against wall portions of the nozzle whereby the designed impingement gap between the outer wall portions of the insert bodies and the nozzle wall portions is achieved. The spreaders are secured to the inner wall portions of the insert bodies and the bodies are secured to one another and to the nozzle vane by welding or brazing.

  1. Functional Genomics of Rice Pollen and Seed Development by Genome-wide Transcript Profiling and Ds Insertion Mutagenesis

    PubMed Central

    Jiang, Shu-Ye; Ramachandran, Srinivasan

    2011-01-01

    Rice pollen and seed development are directly related to grain yield. To further improve rice yield, it is important for us to functionally annotate the genes controlling pollen/seed development and to use them for rice breeding. Here we first carried out a genome-wide expression analysis with an emphasis on genes being involved in rice pollen and seed development. Based on the transcript profiling, we have identified and functionally classified 82 highly expressed pollen-specific, 12 developing seed-specific and 19 germinating seed-specific genes. We then presented the utilization of the maize transposon Dissociation (Ds) insertion lines for functional genomics of rice pollen and seed development and as alternative germplasm resources for rice breeding. We have established a two-element Activator/Dissociation (Ac/Ds) gene trap tagging system and generated around 20,000 Ds insertion lines. We have subjected these lines for screens to obtain high and low yield Ds insertion lines. Some interesting lines have been obtained with higher yield or male sterility. Flanking Sequence Tags (FSTs) analyses showed that these Ds-tagged genes encoded various proteins including transcription factors, transport proteins, unknown functional proteins and so on. They exhibited diversified expression patterns. Our results suggested that rice could be improved not only by introducing foreign genes but also by knocking out its endogenous genes. This finding might provide a new way for rice breeder to further improve rice varieties. PMID:21209789

  2. Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure

    PubMed Central

    Neogi, Ujjwal; RAO, Shwetha D; BONTELL, Irene; VERHEYEN, Jens; RAO, Vasudev R; GORE, Sagar C; SONI, Neelesh; SHET, Anita; SCHÜLTER, Eugen; EKSTRAND, Maria L.; WONDWOSSEN, Amogne; KAISER, Rolf; MADHUSUDHAN, Mallur S.; PRASAD, Vinayaka R; SONNERBORG, Anders

    2014-01-01

    A novel tetra-peptide insertion was identified in Gag-p6 ALIX-binding region which is appears in protease inhibitor (PI) failure Indian HIV-1C sequences (Odds Ratio 17.1, p<0.001) but naturally present in half of untreated Ethiopian sequences. The insertion will probably restore the ALIX mediated virus release pathway, which is lacking in HIV-1C. The clinical importance of such insertion need to be evaluated in HIV-1C dominating regions were PI-drugs are being scaled up as second line treatment options. PMID:25102091

  3. The genomic landscape of polymorphic human nuclear mitochondrial insertions.

    PubMed

    Dayama, Gargi; Emery, Sarah B; Kidd, Jeffrey M; Mills, Ryan E

    2014-11-10

    The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon that has been previously limited to the study of static reference genomes. The recent advancement of high throughput sequencing has enabled an expanded exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) within human populations. We have developed an approach to discover and genotype novel Numt insertions using whole genome, paired-end sequencing data. We have applied this method to a thousand individuals in 20 populations from the 1000 Genomes Project and other datasets and identified 141 new sites of Numt insertions, extending our current knowledge of existing NumtS by almost 20%. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases that differ in some respects from previous studies on older, fixed NumtS in the reference genome. We determined the complete inserted sequence for a subset of these events and have identified a number of nearly full-length mitochondrial genome insertions into nuclear chromosomes. We further define their age and origin of insertion and present an analysis of their potential impact to ongoing studies of mitochondrial heteroplasmy and disease. PMID:25348406

  4. The genomic landscape of polymorphic human nuclear mitochondrial insertions

    PubMed Central

    Dayama, Gargi; Emery, Sarah B.; Kidd, Jeffrey M.; Mills, Ryan E.

    2014-01-01

    The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon that has been previously limited to the study of static reference genomes. The recent advancement of high throughput sequencing has enabled an expanded exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) within human populations. We have developed an approach to discover and genotype novel Numt insertions using whole genome, paired-end sequencing data. We have applied this method to a thousand individuals in 20 populations from the 1000 Genomes Project and other datasets and identified 141 new sites of Numt insertions, extending our current knowledge of existing NumtS by almost 20%. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases that differ in some respects from previous studies on older, fixed NumtS in the reference genome. We determined the complete inserted sequence for a subset of these events and have identified a number of nearly full-length mitochondrial genome insertions into nuclear chromosomes. We further define their age and origin of insertion and present an analysis of their potential impact to ongoing studies of mitochondrial heteroplasmy and disease. PMID:25348406

  5. Genomic Loci of the Porphyromonas gingivalis Insertion Element IS1126

    PubMed Central

    Dong, Hong; Chen, Tsute; Dewhirst, Floyd E.; Fleischmann, Robert D.; Fraser, Claire M.; Duncan, Margaret J.

    1999-01-01

    The Porphyromonas gingivalis genome contains multiple copies of insertion element IS1126. When chromosomal DNA digests of different strains were probed with IS1126, between 25 and 35 hybridizing fragments per genome were detected, depending on the strain. Unrelated strains had very different restriction fragment length polymorphism (RFLP) patterns. When different laboratory copies of a specific strain were examined, the IS1126 RFLP patterns were very similar but small differences were observed, indicating that element-associated changes had occurred during laboratory passage. Within the next year, genome sequencing, assembly, and annotation for P. gingivalis W83 will be completed. Because repetitive elements complicate the assembly of randomly sequenced DNA fragments, we isolated and sequenced the flanking regions of IS1126 copies in strain W83. We also isolated and sequenced the flanking regions of IS1126 copies in strain ATCC 33277 in order to compare insertion sites in phylogenetically divergent strains. We identified 37 new sequences flanking IS1126 from strain ATCC 33277 and 30 from strain W83. The insertion element was found between genes except where it transposed into another insertion element. Examination of identifiable flanking genes or open reading frames indicated that the insertion sites were different in the two strains, except that both strains possess an insertion adjacent to the Lys-gingipain gene (J. P. Lewis and F. L. Macrina, Infect. Immun. 66:3035–3042, 1998). Most of the genes or sequences flanking IS1126 in ATCC 33277 were present in W83 but were contiguous and not insertion element associated. Thus, where genes were identified in both strains, their order was maintained, indicating that the two genomes are organized similarly, but the loci of IS1126 are different. In both strains, insertion element-associated duplicated target sites were lost from several copies of IS1126, providing evidence of homologous recombination between elements. Larger organizational differences between the genomes, such as deletions and inversions, may result from insertion element-mediated recombination events. PMID:10377121

  6. Industrial stator vane with sequential impingement cooling inserts

    DOEpatents

    Jones, Russell B; Fedock, John A; Goebel, Gloria E; Krueger, Judson J; Rawlings, Christopher K; Memmen, Robert L

    2013-08-06

    A turbine stator vane for an industrial engine, the vane having two impingement cooling inserts that produce a series of impingement cooling from the pressure side to the suction side of the vane walls. Each insert includes a spar with a row of alternating impingement cooling channels and return air channels extending in a radial direction. Impingement cooling plates cover the two sides of the insert and having rows of impingement cooling holes aligned with the impingement cooling channels and return air openings aligned with the return air channel.

  7. The effect of ventilation tube insertion or trans-tympanic silicone plug insertion on a patulous Eustachian tube.

    PubMed

    Endo, Shiori; Mizuta, Kunihiro; Takahashi, Goro; Nakanishi, Hiroshi; Yamatodani, Takashi; Misawa, Kiyoshi; Hosokawa, Seiji; Mineta, Hiroyuki

    2016-06-01

    Conclusions This study suggests that long-term ventilation tube insertion is the first-choice surgical treatment for a 'sniff-type' patulous Eustachian tube (PET). When treating a refractory PET, it is important to determine whether the patient had a habitual sniff. Objectives PET patients were divided into two groups: patients with a habitual sniff (sniff-type PET) and those without a habitual sniff (non-sniff-type PET). This study examined the effects of ventilation tube insertion or silicone plug insertion in each group. Methods Surgical procedures such as ventilation tube insertion or trans-tympanic silicone plug insertion were performed for these patients. Tubotympanoaero-dynamic graphy (TTAG) was also performed to determine the mechanisms underlying these treatments. Results There were 11 cases (17 ears) of sniff-type PET and 20 cases (27 ears) of non-sniff-type PET. An improvement in symptoms was found in 72.7% of the patients who underwent silicone plug insertion (66.7% for sniff-type PET and 74.1% for non-sniff-type PET) and in 90.9% of the patients who underwent ventilation tube insertion for sniff-type PET. In TTAG assessments, many sniff-type PET patients showed significant synchronous changes at high levels of pressure (over 40 daPa) in the external auditory meatus and nasopharynx when performing a slight Valsalva manoeuvre (below 200 daPa). PMID:26903085

  8. A possible aid in targeted insertion of large DNA elements by CRISPR/Cas in mouse zygotes.

    PubMed

    Nakao, Harumi; Harada, Takeshi; Nakao, Kazuki; Kiyonari, Hiroshi; Inoue, Kenichi; Furuta, Yasuhide; Aiba, Atsu

    2016-02-01

    The CRISPR/Cas system has rapidly emerged recently as a new tool for genome engineering, and is expected to allow for controlled manipulation of specific genomic elements in a variety of species. A number of recent studies have reported the use of CRISPR/Cas for gene disruption (knockout) or targeted insertion of foreign DNA elements (knock-in). Despite the ease of simple gene knockout and small insertions or nucleotide substitutions in mouse zygotes by the CRISPR/Cas system, targeted insertion of large DNA elements remains an apparent challenge. Here the generation of knock-in mice with successful targeted insertion of large donor DNA elements ranged from 3.0 to 7.1 kb at the ROSA26 locus using the CRISPR/Cas system was achieved. Multiple independent knock-in founder mice were obtained by injection of hCas9 mRNA/sgRNA/donor vector mixtures into the cytoplasm of C57BL/6N zygotes when the injected zygotes were treated with an inhibitor of actin polymerization, cytochalasin. Successful germ line transmission of three of these knock-in alleles was also confirmed. The results suggested that treatment of zygotes with actin polymerization inhibitors following microinjection could be a viable method to facilitate targeted insertion of large DNA elements by the CRISPR/Cas system, enabling targeted knock-in readily attainable in zygotes. genesis 54:65-77, 2016. © 2016 Wiley Periodicals, Inc. PMID:26713866

  9. Spontaneous Radiation Emission from Short, High Field Strength Insertion Devices

    SciTech Connect

    Geoffrey Krafft

    2005-09-15

    Since the earliest papers on undulaters were published, it has been known how to calculate the spontaneous emission spectrum from ''short'' undulaters when the magnetic field strength parameter is small compared to unity, or in ''single'' frequency sinusoidal undulaters where the magnetic field strength parameter is comparable to or larger than unity, but where the magnetic field amplitude is constant throughout the undulater. Fewer general results have been obtained in the case where the insertion device is both short, i.e., the magnetic field strength parameter changes appreciably throughout the insertion device, and the magnetic field strength is high enough that ponderomotive effects, radiation retardation, and harmonic generation are important physical phenomena. In this paper a general method is presented for calculating the radiation spectrum for short, high-field insertion devices. It is used to calculate the emission from some insertion device designs of recent interest.

  10. Insertion of nitriles into complexes of tantalum pentachloride with amines

    SciTech Connect

    Glushkova, M.A.; Chumaevskii, N.A.; Khmelevskaya, L.V.; Ershova, M.M.; Buslaev, Yu.A.

    1988-01-01

    Data from the study of the insertion of aceto-, propio-, and benzonitrile into complexes of TaCl/sub 5/ with diethyl- and triethylamine in CCl/sub 4/ solutions have been discussed. It has been established that the nature of the ligands, rather than the nitrile being inserted into the complex, has a significant influence on the composition of the final products. In contrast to the case of acetonitrile, the insertion of propionitrile and benzonitrile into a complex is observed already at room temperature. On the basis of spectroscopic data it has been postulated that the carbon tetrachloride employed as a solvent accelerates the insertion of nitriles and promotes their deprotonation in the presence of an aprotic amine.

  11. Ureteric access sheath aided insertion of resonance metal ureteric stent

    PubMed Central

    Winter, Matthew; Strahan, Stephen; Wines, Michael

    2014-01-01

    Ureteral obstruction caused by malignancy is a challenging and often complicated problem for urologists. We present a novel technique of ureteric access sheath aided insertion of a Resonance metal ureteric stent in the setting of a difficult obstruction. PMID:24879725

  12. Bougie insertion: A common practice with underestimated dangers

    PubMed Central

    Theodorou, D.; Doulami, G.; Larentzakis, A.; Almpanopoulos, K.; Stamou, K.; Zografos, G.; Menenakos, E.

    2011-01-01

    Introduction Esophageal perforation after bariatric operations is rare. We report two cases of esophageal perforation after bariatric operations indicating the dangers of a common practice – like insertion of esophageal tubes – and we describe our management of that complication. Presentation of case A 56 year old woman who underwent laparoscopic sleeve gastrectomy and a 41 year old woman who underwent laparoscopic adjustable gastric banding respectively. In both operations a bougie has been used and led to esophageal perforation. Discussion The insertion of bougie and especially of inflated bougie is a common practice. It is an invasive procedure that in most cases is performed by the anesthesiologist team. Conclusion Bougie insertion is an invasive procedure with risks and should always be attempted under direct supervision of surgical team or should be inserted by a surgeon. PMID:22288051

  13. Pressure molding of powdered materials improved by rubber mold insert

    NASA Technical Reports Server (NTRS)

    1964-01-01

    Pressure molding tungsten microspheres is accomplished by applying hydraulic pressure to a silicone rubber mold insert with several barrel shaped chambers which is placed in a steel die cavity. This technique eliminates castings containing shear fractures.

  14. 21 CFR 529.1940 - Progesterone intravaginal inserts.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... postpartum estrus in suckled beef cows; and for advancement of first pubertal estrus in replacement beef... postpartum. Do not use an insert more than once. To prevent the potential transmission of venereal...

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

    SciTech Connect

    Novick, G.E.; Gonzalez, T.; Garrison, J.; Novick, C.C.; Herrera, R.J.; Batzer, M.A.; Deininger, P.L.

    1992-12-04

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

  16. Treatment of Calcified Insertional Achilles Tendinopathy by the Posterior Midline Approach.

    PubMed

    Miao, Xu-Dong; Jiang, Hongfei; Wu, Yong-Ping; Tao, Hui-Min; Yang, Di-Sheng; Hu, Hang

    2016-01-01

    The present study investigated the clinical outcomes of the posterior midline approach in the treatment of 34 patients with significantly calcified insertional Achilles tendinopathy. The posterior midline approach was applied for the surgical treatment of 34 patients with chronic significantly calcified insertional Achilles tendinopathy after failed conservative treatment. Gastrocnemius recession was performed simultaneously for patients with gastrocnemius contracture. The Fowler-Philip angle and parallel pitch lines were measured before surgery, and the visual analog scale, Tegner score, and Victorian Institute of Sport tendon study group score were recorded before and after surgery. The mean follow-up period was 45.2 ± 17.7 (range 24 to 84) months. After surgery, the visual analog scale score had decreased notably, and the Tegner score and Victorian Institute of Sport tendon study group score had increased significantly. The posterior midline approach can achieve satisfactory outcomes in the treatment of significantly calcified insertional Achilles tendinopathy, and gastrocnemius recession (Strayer procedure) should be performed for patients with gastrocnemius contracture to improve the surgical outcome. PMID:26874831

  17. Shoe inserts and orthotics for sport and physical activities.

    PubMed

    Nigg, B M; Nurse, M A; Stefanyshyn, D J

    1999-07-01

    The purposes of this paper were to discuss the perceived benefits of inserts and orthotics for sport activities and to propose a new concept for inserts and orthotics. There is evidence that inserts or orthotics reduce or prevent movement-related injuries. However, there is limited knowledge about the specific functioning an orthotic or insert provides. The same orthotic or insert is often proposed for different problems. Changes in skeletal movement due to inserts or orthotics seem to be small and not systematic. Based on the results of a study using bone pins, one may question the idea that a major function of orthotics or inserts consists in aligning the skeleton. Impact cushioning with shoe inserts or orthotics is typically below 10%. Such small reductions might not be important for injury reduction. It has been suggested that changes in material properties might produce adjustments in the muscular response of the locomotor system. The foot has various sensors to detect input signals with subject specific thresholds. Subjects with similar sensitivity threshold levels seem to respond in their movement pattern in a similar way. Comfort is an important variable. From a biomechanical point of view, comfort may be related to fit, additional stabilizing muscle work, fatigue, and damping of soft tissue vibrations. Based on the presented evidence, the concept of minimizing muscle work is proposed when using orthotics or inserts. A force signal acts as an input variable on the shoe. The shoe sole acts as a first filter, the insert or orthotic as a second filter, the plantar surface of the foot as a third filter for the force input signal. The filtered information is transferred to the central nervous system that provides a subject specific dynamic response. The subject performs the movement for the task at hand. For a given movement task, the skeleton has a preferred path. If an intervention supports/counteracts the preferred movement path, muscle activity can/must be reduced/increased. Based on this concept, an optimal insert or orthotic would reduce muscle activity, feel comfortable, and should increase performance. PMID:10416543

  18. Innovation in training for totally implanted port insertion.

    PubMed

    Kelly, Linda J; Moss, Jon

    This article discusses the use of fresh frozen cadavers as an innovative way to teach the procedure of totally implanted port insertion. In an attempt to increase the number of competent medical and nursing practitioners able to insert these devices, workshops have been devised and delivered at a university clinical anatomy skills centre. This method of teaching has had positive feedback from practitioners. PMID:27145548

  19. Metal-Matrix Composite Parts With Metal Inserts

    NASA Technical Reports Server (NTRS)

    Majkowski, T.; Kashalikar, U.

    1995-01-01

    Developmental fabrication process produces metal-matrix composite (MMC) parts with integral metal inserts. With inserts, MMC parts readily joined to similar parts by use of brazing, welding, or mechanical fasteners. Process conceived to make strong, lightweight components of structures erected in outer space. Also useful on Earth, in such automotive parts as rocker arms, cylinder liners, and pistons. Potential industrial applications include parts subjected to high stresses at high temperatures, as in power-generation, mining, and oil-drilling equipment.

  20. Shared Decision Making and Office Insertion of Tympanostomy Tubes.

    PubMed

    Rosenfeld, Richard M

    2016-05-01

    Office insertion of tympanostomy tubes in young children without anesthesia is facilitated through shared decision making with families, including a candid discussion about anticipated pain (which is usually brief and transient) and how their child might react to being restrained. This commentary elaborates on the rationale for office tube insertion as an alternative to general anesthesia, including a clinical decision aid and suggestions for optimizing outcomes. PMID:27130946

  1. Impediments to rapid insertion of innovative displays and peripherals

    NASA Astrophysics Data System (ADS)

    Nicholson, Gail

    2012-06-01

    In order to optimize system performance and minimize cost for a system to fill capability gaps, an improvement to rapid insertion of innovative display and peripheral technology is required to take advantage of human-machine intersections. Current approaches to testing and integration impedes successful rapid insertion of innovative technology for new systems and incremental upgrades. Considerations to innovative displays and peripherals must occur further to the left of the lifecycle to be successful and key integration areas must be address for success.

  2. The ProDisc artificial disc: insertion technique.

    PubMed

    Aryan, Henry E; Acosta, Frank L; Ames, Christopher P

    2005-10-01

    The ProDisc artificial lumbar disc was designed for use in treatment of degenerative lumbar disease. The disc is implanted using an anterior approach to the lumbar spine with the assistance of intraoperative fluoroscopy. A variety of insertion instruments guide the surgeon through this process. The disc is implanted via an anterior approach, generally retroperitoneally but on occasion transperitoneally. The different approaches and insertion technique are described in this article. PMID:16326288

  3. MTR MAIN FLOOR. MEN DEMONSTRATE INSERTION OF DUMMY PLUG INTO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    MTR MAIN FLOOR. MEN DEMONSTRATE INSERTION OF DUMMY PLUG INTO AN MTR BEAM HOLE. ONE MAN CHECKS RADIATION LEVEL AT THE END OF THE UNIVERSAL COFFIN, WHILE ANOTHER USES TOOL TO INSERT PLUG INTO HOLE THROUGH COFFIN. MEN WEAR "ANTI-C" (ANTI-CONTAMINATION) CLOTHING. INL NEGATIVE NO. 6198. R.G. Larsen, Photographer, 6/27/1952 - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

  4. Deep electrode insertion and sound coding in cochlear implants.

    PubMed

    Hochmair, Ingeborg; Hochmair, Erwin; Nopp, Peter; Waller, Melissa; Jolly, Claude

    2015-04-01

    Present-day cochlear implants demonstrate remarkable speech understanding performance despite the use of non-optimized coding strategies concerning the transmission of tonal information. Most systems rely on place pitch information despite possibly large deviations from correct tonotopic placement of stimulation sites. Low frequency information is limited as well because of the constant pulse rate stimulation generally used and, being even more restrictive, of the limited insertion depth of the electrodes. This results in a compromised perception of music and tonal languages. Newly available flexible long straight electrodes permit deep insertion reaching the apical region with little or no insertion trauma. This article discusses the potential benefits of deep insertion which are obtained using pitch-locked temporal stimulation patterns. Besides the access to low frequency information, further advantages of deeply inserted long electrodes are the possibility to better approximate the correct tonotopic location of contacts, the coverage of a wider range of cochlear locations, and the somewhat reduced channel interaction due to the wider contact separation for a given number of channels. A newly developed set of strategies has been shown to improve speech understanding in noise and to enhance sound quality by providing a more "natural" impression, which especially becomes obvious when listening to music. The benefits of deep insertion should not, however, be compromised by structural damage during insertion. The small cross section and the high flexibility of the new electrodes can help to ensure less traumatic insertions as demonstrated by patients' hearing preservation rate. This article is part of a Special Issue entitled . PMID:25456089

  5. Production Recesses for Replaceable Cutting Inserts of Milling Tools

    NASA Astrophysics Data System (ADS)

    Kousal, Luk; Sadlek, Marek

    2014-12-01

    This article describes the production of recesses for replaceable cutting inserts of milling tools. The recess manufacture is exemplified on a D20 shanktype milling cutter with three replaceable cutting inserts. A new production technology and its operating cycle are demonstrated. A com-parison of the old and the new technologies shows the percentage saving of change cycles and used tools, including overall evaluation of the tech-nology.

  6. Beau's Lines

    MedlinePlus

    ... run parallel to the shape of the white, moon-shaped portion of the nail bed (lunula) seen ... much time has elapsed since the line was formed. Because fingernails grow at a rate of approximately ...

  7. Evaluation of a high resolution silicon PET insert module

    NASA Astrophysics Data System (ADS)

    Grkovski, Milan; Brzezinski, Karol; Cindro, Vladimir; Clinthorne, Neal H.; Kagan, Harris; Lacasta, Carlos; Mikuž, Marko; Solaz, Carles; Studen, Andrej; Weilhammer, Peter; Žontar, Dejan

    2015-07-01

    Conventional PET systems can be augmented with additional detectors placed in close proximity of the region of interest. We developed a high resolution PET insert module to evaluate the added benefit of such a combination. The insert module consists of two back-to-back 1 mm thick silicon sensors, each segmented into 1040 1 mm2 pads arranged in a 40 by 26 array. A set of 16 VATAGP7.1 ASICs and a custom assembled data acquisition board were used to read out the signal from the insert module. Data were acquired in slice (2D) geometry with a Jaszczak phantom (rod diameters of 1.2-4.8 mm) filled with 18F-FDG and the images were reconstructed with ML-EM method. Both data with full and limited angular coverage from the insert module were considered and three types of coincidence events were combined. The ratio of high-resolution data that substantially improves quality of the reconstructed image for the region near the surface of the insert module was estimated to be about 4%. Results from our previous studies suggest that such ratio could be achieved at a moderate technological expense by using an equivalent of two insert modules (an effective sensor thickness of 4 mm).

  8. Sensorless Motion Planning for Medical Needle Insertion in Deformable Tissues

    PubMed Central

    Alterovitz, Ron; Goldberg, Kenneth Y.; Pouliot, Jean; Hsu, I-Chow

    2009-01-01

    Minimally invasive medical procedures such as biopsies, anesthesia drug injections, and brachytherapy cancer treatments require inserting a needle to a specific target inside soft tissues. This is difficult because needle insertion displaces and deforms the surrounding soft tissues causing the target to move during the procedure. To facilitate physician training and preoperative planning for these procedures, we develop a needle insertion motion planning system based on an interactive simulation of needle insertion in deformable tissues and numerical optimization to reduce placement error. We describe a 2-D physically based, dynamic simulation of needle insertion that uses a finite-element model of deformable soft tissues and models needle cutting and frictional forces along the needle shaft. The simulation offers guarantees on simulation stability for mesh modications and achieves interactive, real-time performance on a standard PC. Using texture mapping, the simulation provides visualization comparable to ultrasound images that the physician would see during the procedure. We use the simulation as a component of a sensorless planning algorithm that uses numerical optimization to compute needle insertion offsets that compensate for tissue deformations. We apply the method to radioactive seed implantation during permanent seed prostate brachytherapy to minimize seed placement error. PMID:19126473

  9. Ureteral Stent Insertion in the Management of Renal Colic during Pregnancy

    PubMed Central

    Choi, Chang Il; Yu, Young Dong

    2016-01-01

    To determine an optimal invasive intervention for renal colic patients during pregnancy after conservative treatments have been found to be unhelpful. Among the available invasive interventions, we investigated the reliability of a ureteral stent insertion, which is considered the least invasive intervention during pregnancy. Between June 2006 and February 2015, a total of 826 pregnant patients came to the emergency room or urology outpatient department, and 39 of these patients had renal colic. The mean patient age was 30.49 years. In this retrospective cohort study, the charts of the patients were reviewed to collect data that included age, symptoms, the lateralities and locations of urolithiasis, trimester, pain following treatment and pregnancy complications. Based on ultrasonography diagnoses, 13 patients had urolithiasis, and 13 patients had hydronephrosis without definite echogenicity of the ureteral calculi. Conservative treatments were successful in 25 patients. Among these treatments, antibiotics were used in 15 patients, and the remaining patients received only hydration and analgesics without antibiotics. Several urological interventions were required in 14 patients. The most common intervention was ureteral stent insertion, which was performed in 13 patients to treat hydronephrosis or urolithiasis. The patients' pain was relieved following these interventions. Only one patient received percutaneous nephrostomy due to pyonephrosis. No pregnancy complications were noted. Ureteral stent insertion is regarded as a reliable and stable first-line urological intervention for pregnant patients with renal colic following conservative treatments. Ureteral stent insertion has been found to be equally effective and safe as percutaneous nephrostomy, which is associated with complications that include bleeding and dislocation, and the inconvenience of using external drainage system. PMID:27231677

  10. Design of Revolute Joints for In-Mold Assembly Using Insert Molding.

    PubMed

    Ananthanarayanan, Arvind; Ehrlich, Leicester; Desai, Jaydev P; Gupta, Satyandra K

    2011-12-01

    Creating highly articulated miniature structures requires assembling a large number of small parts. This is a very challenging task and increases cost of mechanical assemblies. Insert molding presents the possibility of creating a highly articulated structure in a single molding step. This can be accomplished by placing multiple metallic bearings in the mold and injecting plastic on top of them. In theory, this idea can generate a multi degree of freedom structures in just one processing step without requiring any post molding assembly operations. However, the polymer material has a tendency to shrink on top of the metal bearings and hence jam the joints. Hence, until now insert molding has not been used to create articulated structures. This paper presents a theoretical model for estimating the extent of joint jamming that occurs due to the shrinkage of the polymer on top of the metal bearings. The level of joint jamming is seen as the effective torque needed to overcome the friction in the revolute joints formed by insert molding. We then use this model to select the optimum design parameters which can be used to fabricate functional, highly articulating assemblies while meeting manufacturing constraints. Our analysis shows that the strength of weld-lines formed during the in-mold assembly process play a significant role in determining the minimum joint dimensions necessary for fabricating functional revolute joints. We have used the models and methods described in this paper to successfully fabricate the structure for a minimally invasive medical robot prototype with potential applications in neurosurgery. To the best of our knowledge, this is the first demonstration of building an articulated structure with multiple degrees of freedom using insert molding. PMID:23904746

  11. Study of Insertion Characteristics of Si Neural Probe with Sharpened Tip for Minimally Invasive Insertion to Brain

    NASA Astrophysics Data System (ADS)

    Lee, Sanghoon; Kanno, Soichiro; Kino, Hisashi; Tanaka, Tetsu

    2013-04-01

    We have fabricated various types of Si neural probe for in vivo and in vitro neuronal signal recordings by combining standard photolithography with a bulk micromachining process. To place the probe tip at target areas in the brain precisely, the mechanical properties of the Si neural probes with various tip shapes were carefully investigated under different insertion conditions to brain phantoms. As results, the minimum length and penetration force of the Si neural probe were determined from conditions where the Si neural probe began to penetrate the surface of the brain phantom. To control buckling of the Si neural probe, it is necessary to optimize the insertion rate in accordance with the conditions of the Si neural probe. Although the insertion forces of the Si neural probe with a sharpened tip were smaller than those of the Si neural probe with a normal tip, the effect of the probe tip shape became small with increased insertion speeds.

  12. Method of splice loss control during restoration of optical telecommunication lines

    NASA Astrophysics Data System (ADS)

    Burdin, Vladimir A.; Bourdine, Anton V.

    2001-10-01

    During fiber optic communication lines restoration often appear optical cable short insert joint quality control needs. It is problem to measure of short cable insert fiber splice losses on long-haul optical communication lines. This problem is caused by limits of dynamic range and resolution of optical time domain reflectometer (OTDR). We present overview of ways of short cable insert optical power losses control on long- haul optical communication lines. Theoretical and experimental proof some of this methods is considered. Numerical results are represented. A good agreement of theoretically predicted and experimental values is demonstrated.

  13. Gene Transfer and Genome-Wide Insertional Mutagenesis by Retroviral Transduction in Fish Stem Cells

    PubMed Central

    Liu, Qizhi; Wang, Yunzhi; Lin, Fan; Zhang, Lei; Li, Yan; Ge, Ruowen; Hong, Yunhan

    2015-01-01

    Retrovirus (RV) is efficient for gene transfer and integration in dividing cells of diverse organisms. RV provides a powerful tool for insertional mutagenesis (IM) to identify and functionally analyze genes essential for normal and pathological processes. Here we report RV-mediated gene transfer and genome-wide IM in fish stem cells from medaka and zebrafish. Three RVs were produced for fish cell transduction: rvLegfp and rvLcherry produce green fluorescent protein (GFP) and mCherry fluorescent protein respectively under control of human cytomegalovirus immediate early promoter upon any chromosomal integration, whereas rvGTgfp contains a splicing acceptor and expresses GFP only upon gene trapping (GT) via intronic in-frame integration and spliced to endogenous active genes. We show that rvLegfp and rvLcherry produce a transduction efficiency of 11~23% in medaka and zebrafish stem cell lines, which is as 30~67% efficient as the positive control in NIH/3T3. Upon co-infection with rvGTgfp and rvLcherry, GFP-positive cells were much fewer than Cherry-positive cells, consistent with rareness of productive gene trapping events versus random integration. Importantly, rvGTgfp infection in the medaka haploid embryonic stem (ES) cell line HX1 generated GTgfp insertion on all 24 chromosomes of the haploid genome. Similar to the mammalian haploid cells, these insertion events were presented predominantly in intergenic regions and introns but rarely in exons. RV-transduced HX1 retained the ES cell properties such as stable growth, embryoid body formation and pluripotency gene expression. Therefore, RV is proficient for gene transfer and IM in fish stem cells. Our results open new avenue for genome-wide IM in medaka haploid ES cells in culture. PMID:26029933

  14. P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila Melanogaster: Correlation of Physical and Cytogenetic Maps in Chromosomal Region 86e-87f

    PubMed Central

    Deak, P.; Omar, M. M.; Saunders, RDC.; Pal, M.; Komonyi, O.; Szidonya, J.; Maroy, P.; Zhang, Y.; Ashburner, M.; Benos, P.; Savakis, C.; Siden-Kiamos, I.; Louis, C.; Bolshakov, V. N.; Kafatos, F. C.; Madueno, E.; Modolell, J.; Glover, D. M.

    1997-01-01

    We have established a collection of 2460 lethal or semi-lethal mutant lines using a procedure thought to insert single P elements into vital genes on the third chromosome of Drosophila melanogaster. More than 1200 randomly selected lines were examined by in situ hybridization and 90% found to contain single insertions at sites that mark 89% of all lettered subdivisions of the Bridges' map. A set of chromosomal deficiencies that collectively uncover ~25% of the euchromatin of chromosome 3 reveal lethal mutations in 468 lines corresponding to 145 complementation groups. We undertook a detailed analysis of the cytogenetic interval 86E-87F and identified 87 P-element-induced mutations falling into 38 complementation groups, 16 of which correspond to previously known genes. Twenty-one of these 38 complementation groups have at least one allele that has a P-element insertion at a position consistent with the cytogenetics of the locus. We have rescued P elements and flanking chromosomal sequences from the 86E-87F region in 35 lines with either lethal or genetically silent P insertions, and used these as probes to identify cosmids and P1 clones from the Drosophila genome projects. This has tied together the physical and genetic maps and has linked 44 previously identified cosmid contigs into seven ``supercontigs'' that span the interval. STS data for sequences flanking one side of the P-element insertions in 49 lines has identified insertions in the αγ element at 87C, two known transposable elements, and the open reading frames of seven putative single copy genes. These correspond to five known genes in this interval, and two genes identified by the homology of their predicted products to known proteins from other organisms. PMID:9409831

  15. Possible Application of NbTi Artificial Pinning Centers Wire for Insertion Devices

    NASA Astrophysics Data System (ADS)

    Holubek, T.; Casalbuoni, S.; Gerstl, S.; Grau, A.; Jauregui, D. Saez de; KlŠser, M.; Schneider, Th.; Motowidlo, L.

    Superconductive insertion devices (IDs) allow higher fields for a given gap and period length compared to the classical permanent magnet IDs. This technological concept enables an increase in the brilliance and/or the photon energy. The workhorse for superconducting magnets are multifilament NbTi wires, which are nowadays also used for superconducting insertion devices. Even higher magnetic fields can be reached by using a conductor with enhanced critical current density.Here, we propose a possible application for superconducting undulators, wound with NbTi wire with artificial pinning centers, developed by SupraMagnetics, Inc. We report the critical current characteristic, Jc(B), of a short wire measured in a liquid helium bath, and the load-line of a racetrack coil, designed to simulate the field configuration on the conductor as in a superconducting undulator. Based on the measured load line, we report on the simulations of the magnetic field on axis and of the spectrum in a third generation light source of a possible undulator wound with a wire having similar properties to the measured one.

  16. Recombination of an intrachromosomal paracentric insertion of chromosome 3

    SciTech Connect

    Best, R.G.; Burnett, W.J.; Brock, J.K.

    1994-09-01

    Cytogenetic studies were initiated on a newborn female due to multiple congenital anomalies including microcephaly, clinodactyly, abnormal positioning of hands, left facial palsy, heart defect, sacral dimple, and facial dysmorphic features. Facial features were described as low set rotated ears, nystagmus, and a small, flattened nose. A structural rearrangement of the long arm of chromosome 3 was observed with a complex banding pattern. Study of parental chromosomes revealed a normal male pattern for the father, and an intrachromosomal insertion on the long arm of chromosome 3 for the mother described as 46,XX,dir ins(3)(q21q23q26.2). Further characterization of the proband`s structurally abnormal chromosome 3 revealed a karyotype best described as: 46,XX,rec(3),dupq23{r_arrow}q26.2::q21{r_arrow}q23,dir ins(3)(q21q23q26.2), which is a partial duplication of both the inserted segment as well as the intervening segment between the inserted segment and the insertion site. This would appear to be the result of a three-strand double cross-over within the insertion loop. Molecular cytogenetic studies are presently underway to further elucidate chromosome structure of the proband and her mother.

  17. GAPDH regulates cellular heme insertion into inducible nitric oxide synthase

    PubMed Central

    Chakravarti, Ritu; Aulak, Kulwant S.; Fox, Paul L.; Stuehr, Dennis J.

    2010-01-01

    Heme proteins play essential roles in biology, but little is known about heme transport inside mammalian cells or how heme is inserted into soluble proteins. We recently found that nitric oxide (NO) blocks cells from inserting heme into several proteins, including cytochrome P450s, hemoglobin, NO synthases, and catalase. This finding led us to explore the basis for NO inhibition and to identify cytosolic proteins that may be involved, using inducible NO synthase (iNOS) as a model target. Surprisingly, we found that GAPDH plays a key role. GAPDH was associated with iNOS in cells. Pure GAPDH bound tightly to heme or to iNOS in an NO-sensitive manner. GAPDH knockdown inhibited heme insertion into iNOS and a GAPDH mutant with defective heme binding acted as a dominant negative inhibitor of iNOS heme insertion. Exposing cells to NO either from a chemical donor or by iNOS induction caused GAPDH to become S-nitrosylated at Cys152. Expressing a GAPDH C152S mutant in cells or providing a drug to selectively block GAPDH S-nitrosylation both made heme insertion into iNOS resistant to the NO inhibition. We propose that GAPDH delivers heme to iNOS through a process that is regulated by its S-nitrosylation. Our findings may uncover a fundamental step in intracellular heme trafficking, and reveal a mechanism whereby NO can govern the process. PMID:20921417

  18. Mechanisms of integral membrane protein insertion and folding

    PubMed Central

    2014-01-01

    The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, and the transport of solutes and signals across membranes. Nearly all MPs require translocons—often referred to as protein-conducting channels—for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of membrane protein insertion and the folding of polytopic membrane proteins in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure, it is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion. PMID:25277655

  19. Insertion of nanoparticles into polymer brush under variable solvent conditions.

    PubMed

    Egorov, S A

    2012-10-01

    In this work, two-dimensional lattice-based self-consistent field theory is used to study the free energy cost associated with the insertion of a nanoparticle into a polymer brush. The nanoparticle is modeled as a cylinder and the self-consistent field equations are formulated on a cylindrical lattice. The use of two-dimensional formalism makes it possible to take into account the distortion of the brush density profile due to the embedded nanoinclusion. The insertion free energy penalty is analyzed as a function of the particle size, the brush grafting density, and the solvent quality. In agreement with the earlier simulation work, we find that the insertion free energy cost increases both with the particle size and the brush grafting density and decreases with deteriorating solvent quality. For nanoparticles located deep inside the brush, the insertion free energy is shown to scale with either squared (good solvent) or cubed (poor solvent) monomer volume fraction profile, in agreement with the earlier theoretical results. For shallow nanoinclusions located close to the brush surface, the insertion free energy is shown to scale linearly with the monomer volume fraction profile under both good and theta solvent conditions, again in agreement with the earlier work. PMID:23039611

  20. Insertion of nanoparticles into polymer brush under variable solvent conditions

    NASA Astrophysics Data System (ADS)

    Egorov, S. A.

    2012-10-01

    In this work, two-dimensional lattice-based self-consistent field theory is used to study the free energy cost associated with the insertion of a nanoparticle into a polymer brush. The nanoparticle is modeled as a cylinder and the self-consistent field equations are formulated on a cylindrical lattice. The use of two-dimensional formalism makes it possible to take into account the distortion of the brush density profile due to the embedded nanoinclusion. The insertion free energy penalty is analyzed as a function of the particle size, the brush grafting density, and the solvent quality. In agreement with the earlier simulation work, we find that the insertion free energy cost increases both with the particle size and the brush grafting density and decreases with deteriorating solvent quality. For nanoparticles located deep inside the brush, the insertion free energy is shown to scale with either squared (good solvent) or cubed (poor solvent) monomer volume fraction profile, in agreement with the earlier theoretical results. For shallow nanoinclusions located close to the brush surface, the insertion free energy is shown to scale linearly with the monomer volume fraction profile under both good and theta solvent conditions, again in agreement with the earlier work.

  1. Mapping Insertions, Deletions and SNPs on Venter's Chromosomes

    PubMed Central

    Costantini, Maria; Bernardi, Giorgio

    2009-01-01

    Background The very recent availability of fully sequenced individual human genomes is a major revolution in biology which is certainly going to provide new insights into genetic diseases and genomic rearrangements. Results We mapped the insertions, deletions and SNPs (single nucleotide polymorphisms) that are present in Craig Venter's genome, more precisely on chromosomes 17 to 22, and compared them with the human reference genome hg17. Our results show that insertions and deletions are almost absent in L1 and generally scarce in L2 isochore families (GC-poor L1+L2 isochores represent slightly over half of the human genome), whereas they increase in GC-rich isochores, largely paralleling the densities of genes, retroviral integrations and Alu sequences. The distributions of insertions/deletions are in striking contrast with those of SNPs which exhibit almost the same density across all isochore families with, however, a trend for lower concentrations in gene-rich regions. Conclusions Our study strongly suggests that the distribution of insertions/deletions is due to the structure of chromatin which is mostly open in gene-rich, GC-rich isochores, and largely closed in gene-poor, GC-poor isochores. The different distributions of insertions/deletions and SNPs are clearly related to the two different responsible mechanisms, namely recombination and point mutations. PMID:19543403

  2. Customizable engineered blood vessels using 3D printed inserts.

    PubMed

    Pinnock, Cameron B; Meier, Elizabeth M; Joshi, Neeraj N; Wu, Bin; Lam, Mai T

    2016-04-15

    Current techniques for tissue engineering blood vessels are not customizable for vascular size variation and vessel wall thickness. These critical parameters vary widely between the different arteries in the human body, and the ability to engineer vessels of varying sizes could increase capabilities for disease modeling and treatment options. We present an innovative method for producing customizable, tissue engineered, self-organizing vascular constructs by replicating a major structural component of blood vessels - the smooth muscle layer, or tunica media. We utilize a unique system combining 3D printed plate inserts to control construct size and shape, and cell sheets supported by a temporary fibrin hydrogel to encourage cellular self-organization into a tubular form resembling a natural artery. To form the vascular construct, 3D printed inserts are adhered to tissue culture plates, fibrin hydrogel is deposited around the inserts, and human aortic smooth muscle cells are then seeded atop the fibrin hydrogel. The gel, aided by the innate contractile properties of the smooth muscle cells, aggregates towards the center post insert, creating a tissue ring of smooth muscle cells. These rings are then stacked into the final tubular construct. Our methodology is robust, easily repeatable and allows for customization of cellular composition, vessel wall thickness, and length of the vessel construct merely by varying the size of the 3D printed inserts. This platform has potential for facilitating more accurate modeling of vascular pathology, serving as a drug discovery tool, or for vessel repair in disease treatment. PMID:26732049

  3. Overview of insertion device controls at the Advanced Photon Source

    NASA Astrophysics Data System (ADS)

    Ramanathan, Mohan; Smith, Martin; Grimmer, John; Merritt, Michael

    2002-03-01

    The Advanced Photon Source (APS) is a third-generation synchrotron with major emphasis on insertion device (ID) sources. Currently, there are 25 sectors instrumented out of a possible 35 ID sources. Most of the insertion devices are undulators. Beamlines have been using the ID radiation at the APS for more than five years. The control system of choice at the APS is the experimental physics and industrial control system (EPICS) (http://www.aps.anl.gov/epics). Based on operational experience, the ID control system has been completely revamped. During user operations, the beamline user has complete control of the insertion device. Various interfaces, from RS-232 to EPICS channel access, have been provided for the users to control the IDs. The control system software has been designed to accommodate scanning of the insertion device synchronized to each user's beamline monochromator. The users have the option of operating the device in a tapered mode. The control software allows the users to control the undulators in energy space from the fundamental to the seventh harmonic. The design philosophy of the insertion device control system will be discussed. The implementation and operational experience will be presented in detail.

  4. Insertion of Totally Implantable Central Venous Access Devices by Surgeons

    PubMed Central

    An, Hyeonjun; Ryu, Chun-Geun; Jung, Eun-Joo; Kang, Hyun Jong; Paik, Jin Hee; Yang, Jung-Hyun

    2015-01-01

    Purpose The aim of this study is to evaluate the results for the insertion of totally implantable central venous access devices (TICVADs) by surgeons. Methods Total 397 patients, in whom TICVADs had been inserted for intravenous chemotherapy between September 2008 and June 2014, were pooled. This procedure was performed under local anesthesia in an operation room. The insertion site for the TICVAD was mainly in the right-side subclavian vein. In the case of breast cancer patients, the subclavian vein opposite the surgical site was used for insertion. Results The 397 patients included 73 males and 324 females. Primary malignant tumors were mainly colorectal and breast cancer. The mean operation time was 54 minutes (18-276 minutes). Operation-related complications occurred in 33 cases (8.3%). Early complications developed in 15 cases with catheter malposition and puncture failure. Late complications, which developed after 24 hours, included inflammation in 6 cases, skin necrosis in 6 cases, hematoma in 3 cases, port malfunction in 1 case, port migration in 1 case, and intractable pain at the port site in 1 case. Conclusion Insertion of a TICVAD under local anesthesia by a surgeon is a relatively safe procedure. Meticulous undermining of the skin and carefully managing the TICVAD could minimize complications. PMID:25960974

  5. Some physical and chemical indices of clique-inserted lattices

    NASA Astrophysics Data System (ADS)

    Zhang, Zuhe

    2013-10-01

    The operation of replacing every vertex of an r-regular lattice H by a complete graph of order r is called clique-insertion, and the resulting lattice is called the clique-inserted lattice of H. For any given r-regular lattice, applying this operation iteratively, an infinite family of r-regular lattices is generated. Some interesting lattices including the 3-12-12 lattice can be constructed this way. In this paper, we recall the relationship between the spectra of an r-regular lattice and that of its clique-inserted lattice, and investigate the graph energy and resistance distance statistics. As an application, the asymptotic energy per vertex and average resistance distance of the 3-12-12 and 3-6-24 lattices are computed. We also give formulae expressing the numbers of spanning trees and dimer coverings of the kth iterated clique-inserted lattices in terms of those of the original one. Moreover, we show that new families of expander graphs can be constructed from the known ones by clique-insertion.

  6. Sorting genomes by reciprocal translocations, insertions, and deletions.

    PubMed

    Qi, Xingqin; Li, Guojun; Li, Shuguang; Xu, Ying

    2010-01-01

    The problem of sorting by reciprocal translocations (abbreviated as SBT) arises from the field of comparative genomics, which is to find a shortest sequence of reciprocal translocations that transforms one genome Pi into another genome Gamma, with the restriction that Pi and Gamma contain the same genes. SBT has been proved to be polynomial-time solvable, and several polynomial algorithms have been developed. In this paper, we show how to extend Bergeron's SBT algorithm to include insertions and deletions, allowing to compare genomes containing different genes. In particular, if the gene set of Pi is a subset (or superset, respectively) of the gene set of Gamma, we present an approximation algorithm for transforming Pi into Gamma by reciprocal translocations and deletions (insertions, respectively), providing a sorting sequence with length at most OPT + 2, where OPT is the minimum number of translocations and deletions (insertions, respectively) needed to transform Pi into Gamma; if Pi and Gamma have different genes but not containing each other, we give a heuristic to transform Pi into Gamma by a shortest sequence of reciprocal translocations, insertions, and deletions, with bounds for the length of the sorting sequence it outputs. At a conceptual level, there is some similarity between our algorithm and the algorithm developed by El Mabrouk which is used to sort two chromosomes with different gene contents by reversals, insertions, and deletions. PMID:20431155

  7. Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis

    PubMed Central

    Danhorn, Thomas; Young, Curtis R; DeLong, Edward F

    2012-01-01

    The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary ‘next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world. PMID:22534608

  8. Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

    PubMed

    Danhorn, Thomas; Young, Curtis R; DeLong, Edward F

    2012-11-01

    The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world. PMID:22534608

  9. Tool Life Detecting System Using Damage Sensor-Integrated Insert

    NASA Astrophysics Data System (ADS)

    Sekiya, Katsuhiko; Yamane, Yasuo; Torimoto, Ayumu

    In-process tool life detecting system has been developed. In order to detect tool life, we monitored breakage of an electrical conductive thin film band of titanium nitride (TiN) on flank faces of a ceramic insert that was an insulation material. The conductive band was parallel to the cutting edge and was broken by fracture of the cutting edge or excessive tool wear. A coil and a capacitor were connected in series to the band on an insert to make a series resonance circuit in a tool holder for turning, or in an arbor for face milling. A detecting coil with high frequency oscillator was coupled to the coil in the holder/arbor electromagnetically. An electromagnetic induction between two coils was used to take the signal from the insert. The system developed in this study showed good stability against electric noises radiated from electrical devices of machine tools.

  10. Improved technique for insertion of intra-aortic balloon pump.

    PubMed

    Cutler, B S; Vander Salm, T J

    1980-06-01

    Polytetrafluoroethylene (PTFE, Gortex) grafts have several advantages over woven Dacron grafts for the insertion of intra-aortic balloons (IABP). Because of the smooth inner surface of the PTFE graft, an 8-mm graft may be used instead of the 10-mm minimum size with Dacron. The pliability of the PTFE graft makes it easier to sew with fine suture material, and its comformability permits a "blood tight" seal to be obtained with a single Dacron umbilical tape tie. We have used PTFE grafts for IABP insertion in 24 patients, with no infectious or thrombotic complications. This graft material seems to offer substantial technical advantages over woven Dacron for the insertion of IABP and subsequent arterial repair. PMID:7387373

  11. Gene Insertion Into Genomic Safe Harbors for Human Gene Therapy.

    PubMed

    Papapetrou, Eirini P; Schambach, Axel

    2016-04-12

    Genomic safe harbors (GSHs) are sites in the genome able to accommodate the integration of new genetic material in a manner that ensures that the newly inserted genetic elements: (i) function predictably and (ii) do not cause alterations of the host genome posing a risk to the host cell or organism. GSHs are thus ideal sites for transgene insertion whose use can empower functional genetics studies in basic research and therapeutic applications in human gene therapy. Currently, no fully validated GSHs exist in the human genome. Here, we review our formerly proposed GSH criteria and discuss additional considerations on extending these criteria, on strategies for the identification and validation of GSHs, as well as future prospects on GSH targeting for therapeutic applications. In view of recent advances in genome biology, gene targeting technologies, and regenerative medicine, gene insertion into GSHs can potentially catalyze nearly all applications in human gene therapy. PMID:26867951

  12. Electrochemical insertion of lithium into polyacrylonitrile-based disordered carbons

    SciTech Connect

    Jung, Y.; Suh, M.C.; Lee, S.I.; Shim, S.C.; Kwak, J.; Lee, H.; Kim, M.

    1997-12-01

    Electrochemical lithium insertion into polyacrylonitrile (PAN)-based disordered carbons was studied using the techniques of discharge/charge tests, cyclic voltammetry, and {sup 7}Li nuclear magnetic resonance (NMR) spectroscopy. The PAN-based carbons were prepared by vacuum pyrolysis of PAN at 500, 800, and 1,000 C. They showed charge capacities between 254 and 380 mAh/g in the first cycle. {sup 7}Li NMR spectra showed two kinds of lithium insertion sites in the PAN-based carbons: a reversible site where lithium is removed in the subsequent charge process and an irreversible site where lithium remains intact. The NMR results suggest that lithium in fully Li-inserted PAN-based carbons has an ionic character, and reversible site lithium resides between negatively charged carbon layers.

  13. Insertion of liquid crystal molecules into hydrocarbon monolayers

    SciTech Connect

    Popov, Piotr Mann, Elizabeth K.; Lacks, Daniel J.; Jákli, Antal

    2014-08-07

    Atomistic molecular dynamics simulations were carried out to investigate the molecular mechanisms of vertical surface alignment of liquid crystals. We study the insertion of nCB (4-Cyano-4{sup ′}-n-biphenyl) molecules with n = 0,…,6 into a bent-core liquid crystal monolayer that was recently found to provide good vertical alignment for liquid crystals. The results suggest a complex-free energy landscape for the liquid crystal within the layer. The preferred insertion direction of the nCB molecules (core or tail first) varies with n, which can be explained by entropic considerations. The role of the dipole moments was found to be negligible. As vertical alignment is the leading form of present day liquid crystal displays (LCD), these results will help guide improvement of the LCD technology, as well as lend insight into the more general problem of insertion of biological and other molecules into lipid and surfactant layers.

  14. Purification and characterization of YACs containing large inserts.

    PubMed

    Gemmill, R M; Bolin, R; Strauss, W M; Pavan, W

    2001-05-01

    This unit provides protocols for characterizing DNA segments cloned in YACs and for purifying YACs from yeast chromosomes. The first basic protocol describes Southern blotting and partial-digest restriction analysis of YACs. These methods are useful for determining the size and complexity of the cloned insert DNA, the presence and location of particular restriction sites or sequences, and even the species of origin of the insert DNA (indicated by hybridization to species-specific repetitive elements such as Alu repeats). The second basic protocol describes gel purification of YACs for use in procedures requiring pure YAC DNA, such as mammalian-cell transformation and subcloning into smaller insert vectors. The third basic protocol details characterizing and analyzing YACs: in vivo fragmentation via homologous recombination with specialized fragmentation vectors containing specific probe sequences or repetitive elements, followed by Southern blotting with YAC- and human-derived probes. PMID:18428294

  15. Synchronized monochromator and insertion device energy scans at SLS

    SciTech Connect

    Krempasky, J.; Flechsig, U.; Korhonen, T.; Zimoch, D.; Quitmann, Ch.; Nolting, F.

    2010-06-23

    Synchronous monochromator and insertion device energy scans were implemented at the Surfaces/Interfaces:Microscopy (SIM) beamline in order to provide the users fast X-ray magnetic dichroism studies (XMCD). A simple software control scheme is proposed based on a fast monochromator run-time energy readback which quickly updates the insertion device requested energy during an on-the-fly X-ray absorption scan (XAS). In this scheme the Plain Grating Monochromator (PGM) motion control, being much slower compared with the insertion device (APPLE-II type undulator), acts as a 'master' controlling the undulator 'slave' energy position. This master-slave software implementation exploits EPICS distributed device control over computer network and allows for a quasi-synchronous motion control combined with data acquisition needed for the XAS or XMCD experiment.

  16. African origin of human-specific polymorphic Alu insertions

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M. ); Stoneking, M. ); Bazan, H.; Kass, D.H.; Shaikh, T.H.; Scheer, W.D. ); Novick, G.E.; Herrera, R.J. ); Ioannou, P.A. )

    1994-12-06

    Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few [open quotes]master[close quotes] genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution. 45 refs., 2 figs., 1 tab.

  17. Spot welding of steel and aluminum using insert sheet

    SciTech Connect

    Oikawa, H.; Saito, T.; Yoshimura, T.

    1994-12-31

    Automobile industries have been increasingly interested in the use of aluminum and thus joining of steel and aluminum becomes of importance. The joining of the two types of metal raises a problem of brittle welds caused by the formation of intermetallic compounds. The authors solved the problem by using an insert sheet. This paper deals with the resistance spot welding of steel and aluminum sheets using insert sheets. The insert sheet used in the present development was a steel/aluminum clad sheet of the 0.8 mm thickness with 50% steel and 50% aluminum. The clad sheet was produced by warm rolling of steel and aluminum with a direct resistance heating process. Steel to be warm rolled was of EDDQ of the 0.4 mm thickness and aluminum was of JIS A1050 of 0.6 mm thickness. The mechanical properties of the insert clad sheets were in between those of the steel sheets and the aluminum sheets, while the clad sheets showed much better formability than the aluminum sheets. Resistance spot welding was conducted for 0.8 mm thick EDDQ steel sheets and 1.0 mm thick aluminum alloy (AL-5.5%Mg) sheets under the welding force of 1.96 kN, welding current ranging between 4.2 and 20.1 kA, and welding time from 0.5 to 10 cycles. The steel was spot welded to the steel side of the insert sheet while the aluminum was welded to the aluminum side. What the authors investigated were the applicable welding current range, nugget diameter, tensile shear strength, U-tension strength, and macro- and microstructures. In conclusion, steel sheets can be spot welded to aluminum sheets without difficulty by using clad sheets as insert materials while the strength level of the dissimilar metal spot welds is close to that of aluminum joints.

  18. Advanced photon source experience with vacuum chambers for insertion devices

    SciTech Connect

    Hartog, P.D.; Grimmer, J.; Xu, S.; Trakhtenberg, E.; Wiemerslage, G.

    1997-08-01

    During the last five years, a new approach to the design and fabrication of extruded aluminum vacuum chambers for insertion devices was developed at the Advanced Photon Source (APS). With this approach, three different versions of the vacuum chamber, with vertical apertures of 12 mm, 8 mm, and 5 mm, were manufactured and tested. Twenty chambers were installed into the APS vacuum system. All have operated with beam, and 16 have been coupled with insertion devices. Two different vacuum chambers with vertical apertures of 16 mm and 11 mm were developed for the BESSY-II storage ring and 3 of 16 mm chambers were manufactured.

  19. Metallocene Catalytic Insertion Polymerization of 1-Silene to Polycarbosilanes

    NASA Astrophysics Data System (ADS)

    Tian, Yuelong; Ge, Min; Zhang, Weigang; Lv, Xiaoxu; Yu, Shouquan

    2015-11-01

    Metallocene of zirconium were used as a catalyst for an insertion polymerization of 1-methylsilene directly into pre-ceramic precursor polyzirconocenecarbosilane (PZCS) during dechlorination of dichlorodimethylesilane by sodium, which exhibits high catalytic effectiveness with the maximum conversion ratio of polycarbosilane up to 91%. The average molecular weights of polymers synthesized are less than 1400, all with very narrow polymolecularities. The mechanism of catalytic polymerization was assumed to be similar to a coordination insertion polymerization of 1-olefins by metallocenes. The obtained PZCS show high ceramic yields with formation of composite ceramics of ZrC-SiC, which are novel polymeric precursors of ultra-high temperature ceramic (UHTC) fiber and composite.

  20. Insertion of lithium into electrochromic devices after completion

    SciTech Connect

    Berland, Brian Spencer; Lanning, Bruce Roy; Frey, Jonathan Mack; Barrett, Kathryn Suzanne; DuPont, Paul Damon; Schaller, Ronald William

    2015-12-22

    The present disclosure describes methods of inserting lithium into an electrochromic device after completion. In the disclosed methods, an ideal amount of lithium can be added post-fabrication to maximize or tailor the free lithium ion density of a layer or the coloration range of a device. Embodiments are directed towards a method to insert lithium into the main device layers of an electrochromic device as a post-processing step after the device has been manufactured. In an embodiment, the methods described are designed to maximize the coloration range while compensating for blind charge loss.

  1. Transposon-free insertions for insect genetic engineering.

    PubMed

    Dafa'alla, Tarig H; Condon, George C; Condon, Kirsty C; Phillips, Caroline E; Morrison, Neil I; Jin, Li; Epton, Matthew J; Fu, Guoliang; Alphey, Luke

    2006-07-01

    Methods involving the release of transgenic insects in the field hold great promise for controlling vector-borne diseases and agricultural pests. Insect transformation depends on nonautonomous transposable elements as gene vectors. The resulting insertions are stable in the absence of suitable transposase, however, such absence cannot always be guaranteed. We describe a method for post-integration elimination of all transposon sequences in the pest insect Medfly, Ceratitis capitata. The resulting insertions lack transposon sequences and are therefore impervious to transposase activity. PMID:16823373

  2. Tail-anchored membrane protein insertion into the endoplasmic reticulum

    PubMed Central

    Hegde, Ramanujan S.; Keenan, Robert J.

    2013-01-01

    Membrane proteins are inserted into the endoplasmic reticulum by two highly conserved parallel pathways. The well-studied co-translational pathway uses the signal recognition particle and its receptor for targeting, and the Sec61 translocon for membrane integration. A recently discovered post-translational pathway uses an entirely different set of factors involving transmembrane domain-selective cytosolic chaperones and an accompanying receptor at the endoplasmic reticulum. Elucidation of the structural and mechanistic basis of this post-translational membrane protein insertion pathway highlights general principles shared between the two pathways and key distinctions unique to each. PMID:22086371

  3. A modified trephining technique for the insertion of Jones tube.

    PubMed

    Henderson, P N

    1985-10-01

    The functional success of a Jones Pyrex tube depends on the accurate positioning of the tube. The modified trephining technique for the insertion of a Jones tube ensures accurate positioning by using a guide wire to maintain the selected position and direction of the tube while a 1.5-mm-diameter trephine cuts a cylindrical track around the guide wire, down which a straight Pyrex tube is threaded. The snug fit between the tube and the trephined track has minimized postoperative extrusion (5%) and migration (7%). This technique has been used to insert 93 tubes in 84 patients aged 7 to 83 years. PMID:3901989

  4. Method of modifying a volume mesh using sheet insertion

    DOEpatents

    Borden, Michael J.; Shepherd, Jason F.

    2006-08-29

    A method and machine-readable medium provide a technique to modify a hexahedral finite element volume mesh using dual generation and sheet insertion. After generating a dual of a volume stack (mesh), a predetermined algorithm may be followed to modify (refine) the volume mesh of hexahedral elements. The predetermined algorithm may include the steps of locating a sheet of hexahedral mesh elements, determining a plurality of hexahedral elements within the sheet to refine, shrinking the plurality of elements, and inserting a new sheet of hexahedral elements adjacently to modify the volume mesh. Additionally, another predetermined algorithm using mesh cutting may be followed to modify a volume mesh.

  5. Sequence and insertion sites of murine melanoma-associated retrovirus.

    PubMed

    Li, M; Huang, X; Zhu, Z; Gorelik, E

    1999-11-01

    We previously showed that B16 melanoma cells produce ecotropic melanoma-associated retrovirus (MelARV) which encodes a melanoma-associated antigen recognized by MM2-9B6 monoclonal antibody. The biological significance of MelARV in melanoma formation remains unknown. We found that infection of normal melanocytes with MelARV resulted in malignant transformation. It is likely that MelARV emerged from the defective Emv-2 provirus, a single copy of ecotropic provirus existing in the genome of C57BL/6 mice. In the present study, we cloned and sequenced the full-length MelARV genome and its insertion sites and we completed sequencing of the Emv-2 provirus. Our data show that MelARV has a typical full-length retroviral genome with high homology (98.54%) to Emv-2, indicating a close relationship between both viruses. MelARV probably emerged as a result of recombination between Emv-2 and an endogenous nonecotropic provirus. Some observed differences in the gag and pol regions of MelARV might account for the restoration of productivity and infectivity of a novel retrovirus that somatically emerged during melanoma formation. MelARV does not contain any oncogene and therefore might induce transformation by insertional mutagenesis. We sequenced two insertion sites of MelARV. The first insertion site represents the 3' coding region of the c-maf proto-oncogene at 67.0 centimorgans (cM) on chromosome 8. The c-maf proto-oncogene encodes a basic leucine zipper protein homologous to c-fos and c-jun. Insertion of MelARV in BL6 melanoma cells resulted in the up-regulation of c-maf. It is noteworthy that the Emv-2 provirus is also inserted into a noncoding region at 61.0 cM on the same chromosome 8. The second insertion site is the 3' noncoding region of the DNA polymerase gamma (PolG) gene on chromosome 7. The expression of PolG was not affected by the MelARV insertion. Further investigation of the biological significance of MelARV in melanoma formation is being undertaken. PMID:10516025

  6. A High-Throughput Arabidopsis Reverse Genetics System

    PubMed Central

    Sessions, Allen; Burke, Ellen; Presting, Gernot; Aux, George; McElver, John; Patton, David; Dietrich, Bob; Ho, Patrick; Bacwaden, Johana; Ko, Cynthia; Clarke, Joseph D.; Cotton, David; Bullis, David; Snell, Jennifer; Miguel, Trini; Hutchison, Don; Kimmerly, Bill; Mitzel, Theresa; Katagiri, Fumiaki; Glazebrook, Jane; Law, Marc; Goff, Stephen A.

    2002-01-01

    A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ?100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org. PMID:12468722

  7. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes.

    PubMed Central

    Spradling, A C; Stern, D; Beaton, A; Rhem, E J; Laverty, T; Mozden, N; Misra, S; Rubin, G M

    1999-01-01

    A fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking >920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing >250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring >85% of all Drosophila open reading frames under experimental control. PMID:10471706

  8. Resorbable polymeric inserts as a means of enhancing fixation of fractures of porotic bones. I. Stability of mechanical properties and viscoelasticity of the inserts aged in vitro.

    PubMed

    Mainil-Varlet, P; Cordey, J; Gogolewski, S

    1997-02-01

    A titanium screw-poly(L-lactide) medullary insert system intended for use in the fixation of porotic bone fractures was subjected to in vitro ageing at 37 degrees C and pH = 7.4 for up to 6 months. The pull-out force of the screw from the insert and the viscoelastic properties of the insert were measured. The pull-out force did not change up to 6 months of ageing, indicating that the polymeric insert provides a good purchase for the screws. The viscoelastic properties of the insert provides of bone and did not change substantially with temperatures up to 52 degrees C. This indicates that the medullary insert would maintain its properties in vivo even if the body temperature was increased. The molecular weight of the insert at 6 months was reduced by 60%, but the molecular weight reduction did not affect the mechanical properties of the insert. PMID:9068889

  9. A simple technique for insertion of PEJ via PEG.

    PubMed

    Bumpers, H L; Luchette, F A; Doerr, R J; Hoover, E L

    1994-02-01

    Percutaneous endoscopic jejunostomy provides good access for enteral nutrition in those patients at high risk for aspiration and poor tolerance of gastric feeding. Positioning the jejunostomy tube through the PEG tube and into the duodenum can be difficult and time consuming. We describe a simple method for gaining rapid control of the jejunal tube and its duodenal insertion. PMID:8165482

  10. Transposon insertion site profiling chip (TIP-chip)

    PubMed Central

    Wheelan, Sarah J.; Scheifele, Lisa Z.; Martínez-Murillo, Francisco; Irizarry, Rafael A.; Boeke, Jef D.

    2006-01-01

    Mobile elements are important components of our genomes, with diverse and significant effects on phenotype. Not only can transposons inactivate genes by direct disruption and shuffle the genome through recombination, they can also alter gene expression subtly or powerfully. Currently active transposons are highly polymorphic in host populations, including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast. For this reason, we wished to develop a simple genome-wide method for identifying all transposons in any given sample. We have designed a transposon insertion site profiling chip (TIP-chip), a microarray intended for use as a high-throughput technique for mapping transposon insertions. By selectively amplifying transposon flanking regions and hybridizing them to the array, we can locate all transposons present in a sample. We have tested the TIP-chip extensively to map Ty1 retrotransposon insertions in yeast and have achieved excellent results in two laboratory strains as well as in evolved Ty1 high-copy strains. We are able to identify all of the theoretically detectable transposons in the FY2 lab strain, with essentially no false positives. In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern. PMID:17101968

  11. Effects of Rotational Motion in Robotic Needle Insertion

    PubMed Central

    Ramezanpour, H.; Yousefi, H.; Rezaei, M.; Rostami, M.

    2015-01-01

    Background Robotic needle insertion in biological tissues has been known as one the most applicable procedures in sampling, robotic injection and different medical therapies and operations. Objective In this paper, we would like to investigate the effects of angular velocity in soft tissue insertion procedure by considering force-displacement diagram. Non-homogenous camel liver can be exploited as a tissue sample under standard compression test with Zwick/Roell device employing 1-D axial load-cell. Methods Effects of rotational motion were studied by running needle insertion experiments in 5, 50 and 200 mm/min in two types of with or without rotational velocity of 50, 150 and 300 rpm. On further steps with deeper penetrations, friction force of the insertion procedure in needle shaft was acquired by a definite thickness of the tissue. Results Designed mechanism of fixture for providing different frequencies of rotational motion is available in this work. Results for comparison of different force graphs were also provided. Conclusion Derived force-displacement graphs showed a significant difference between two procedures; however, tissue bleeding and disorganized micro-structure would be among unavoidable results. PMID:26688800

  12. Quench Module Insert Capabilities and Development Test Results

    NASA Technical Reports Server (NTRS)

    Carswell, B.; Crouch, M.; Farmer, J.; Breeding, S.; Rose, F.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Quench Module Insert is a directional solidification furnace, which will fly in the Materials Science Research Facility. The QMI provides high thermal gradient and quench capabilities for processing metals and alloys in microgravity. This paper will describe the capabilities and present of on-going analysis and development testing.

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

    PubMed

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

    2016-04-19

    Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that remain nearly intact, a subset of which is present as insertionally polymorphic loci that include approximately full-length (2-LTR) and solo-LTR alleles in addition to the unoccupied site. Several 2-LTR insertions have intact reading frames in some or all genes that are expressed as functional proteins. These properties reflect the activity of HERV-K and suggest the existence of additional unique loci within humans. We sought to determine the extent to which other polymorphic insertions are present in humans, using sequenced genomes from the 1000 Genomes Project and a subset of the Human Genome Diversity Project panel. We report analysis of a total of 36 nonreference polymorphic HERV-K proviruses, including 19 newly reported loci, with insertion frequencies ranging from <0.0005 to >0.75 that varied by population. Targeted screening of individual loci identified three new unfixed 2-LTR proviruses within our set, including an intact provirus present at Xq21.33 in some individuals, with the potential for retained infectivity. PMID:27001843

  14. Effects of lithium insertion on thermal conductivity of silicon nanowires

    SciTech Connect

    Xu, Wen; Zhang, Gang; Li, Baowen

    2015-04-27

    Recently, silicon nanowires (SiNWs) have been applied as high-performance Li battery anodes, since they can overcome the pulverization and mechanical fracture during lithiation. Although thermal stability is one of the most important parameters that determine safety of Li batteries, thermal conductivity of SiNWs with Li insertion remains unclear. In this letter, using molecular dynamics simulations, we study room temperature thermal conductivity of SiNWs with Li insertion. It is found that compared with the pristine SiNW, there is as much as 60% reduction in thermal conductivity with 10% concentration of inserted Li atoms, while under the same impurity concentration the reduction in thermal conductivity of the mass-disordered SiNW is only 30%. With lattice dynamics calculations and normal mode decomposition, it is revealed that the phonon lifetimes in SiNWs decrease greatly due to strong scattering of phonons by vibrational modes of Li atoms, especially for those high frequency phonons. The observed strong phonon scattering phenomenon in Li-inserted SiNWs is similar to the phonon rattling effect. Our study serves as an exploration of thermal properties of SiNWs as Li battery anodes or weakly coupled with impurity atoms.

  15. Stability analysis of chickpea large genomic DNA inserts in Agrobacterium.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Agrobacterium tumefaciens-mediated transformation of large DNA inserts directly into plants facilitates the transfer of gene clusters and flanking regulatory elements. It is recommended that the integrity of large genomic fragments in Agrobacterium be verified prior to plant transformation. In this ...

  16. Magnesium oxide inserts for the LECO Carbon Analyzer

    SciTech Connect

    Bagaasen, L.M.; Jensen, C.M.

    1991-01-16

    LECO carbon analysis of plutonium metal and plutonium oxide at the Rocky Flats Plant generates several hundred kilograms of high silica residues each year. The plutonium in these residues is difficult and expensive to recover using production dissolution processes. A magnesium oxide (MgO) insert has been developed that significantly lowers the plutonium recovery costs without adversely affecting accuracy of the carbon analysis.

  17. Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

    NASA Technical Reports Server (NTRS)

    Rodriquez-Gomez, D.; Darve, E.; Pohorille, A.

    2006-01-01

    Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

  18. Analysis of HIV-2 Vpx by modeling and insertional mutagenesis

    SciTech Connect

    Mahnke, Lisa A. . E-mail: lmahnke@im.wustl.edu; Belshan, Michael; Ratner, Lee . E-mail: lratner@im.wustl.edu

    2006-04-25

    Vpx facilitates HIV-2 nuclear localization by a poorly understood mechanism. We have compared Vpx to an NMR structure HIV-1 Vpr in a central helical domain and probed regions of Vpx by insertional mutagenesis. A predicted loop between helices two and three appears to be unique, overlapping with a known novel nuclear localization signal. Overall, Vpx was found to be surprisingly flexible, tolerating a series of large insertions. We found that insertion within the polyproline-containing C-terminus destabilizes nuclear localization, whereas mutating a second helix in the central domain disrupts viral packaging. Other insertional mutants in the predicted loop and in a linker region between the central domain and the C-terminus may be useful as sites of intramolecular tags as they could be packaged adequately and retained preintegration complex associated integration activity in a serum starvation assay. An unexpected result was found within a previously defined nuclear localization motif near aa 71. This mutant retained robust nuclear localization in a GFP fusion assay and was competent for preintegration complex associated nuclear import. In summary, we have modeled helical content in Vpx and assessed potential sites of intramolecular tags which may prove useful for protein-protein interactions studies.

  19. 31. Photocopy of map. Insert from Master Plan Notes Prepared ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. Photocopy of map. Insert from Master Plan Notes Prepared by Environmental Planning and Design, Pittsburgh, Pa. Original at Missouri Botanical Garden. 1972 MASTER PLAN 32. 'THE TREE,' SCULPTURE BY ALEXANDER CALDER, 1966 - Missouri Botanical Garden, 2345 Tower Grove Avenue, Saint Louis, Independent City, MO

  20. 21 CFR 310.515 - Patient package inserts for estrogens.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... patient package insert containing information concerning the drug's benefits and risks. An estrogen drug... information: (1) The name of the drug. (2) The name and place of business of the manufacturer, packer, or... Products, Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD 20993-0002....

  1. Observations on rotating needle insertions using a brachytherapy robot

    NASA Astrophysics Data System (ADS)

    Meltsner, M. A.; Ferrier, N. J.; Thomadsen, B. R.

    2007-09-01

    A robot designed for prostate brachytherapy implantations has the potential to greatly improve treatment success. Much of the research in robotic surgery focuses on measuring accuracy. However, there exist many factors that must be optimized before an analysis of needle placement accuracy can be determined. Some of these parameters include choice of the needle type, insertion velocity, usefulness of the rotating needle and rotation speed. These parameters may affect the force at which the needle interacts with the tissue. A reduction in force has been shown to decrease the compression of the prostate and potentially increase the accuracy of seed position. Rotating the needle as it is inserted may reduce frictional forces while increasing accuracy. However, needle rotations are considered to increase tissue damage due to the drilling nature of the insertion. We explore many of the factors involved in optimizing a brachytherapy robot, and the potential effects each parameter may have on the procedure. We also investigate the interaction of rotating needles in gel and suggest the rotate-cannula-only method of conical needle insertion to minimize any tissue damage while still maintaining the benefits of reduced force and increased accuracy.

  2. Effects of lithium insertion on thermal conductivity of silicon nanowires

    NASA Astrophysics Data System (ADS)

    Xu, Wen; Zhang, Gang; Li, Baowen

    2015-04-01

    Recently, silicon nanowires (SiNWs) have been applied as high-performance Li battery anodes, since they can overcome the pulverization and mechanical fracture during lithiation. Although thermal stability is one of the most important parameters that determine safety of Li batteries, thermal conductivity of SiNWs with Li insertion remains unclear. In this letter, using molecular dynamics simulations, we study room temperature thermal conductivity of SiNWs with Li insertion. It is found that compared with the pristine SiNW, there is as much as 60% reduction in thermal conductivity with 10% concentration of inserted Li atoms, while under the same impurity concentration the reduction in thermal conductivity of the mass-disordered SiNW is only 30%. With lattice dynamics calculations and normal mode decomposition, it is revealed that the phonon lifetimes in SiNWs decrease greatly due to strong scattering of phonons by vibrational modes of Li atoms, especially for those high frequency phonons. The observed strong phonon scattering phenomenon in Li-inserted SiNWs is similar to the phonon rattling effect. Our study serves as an exploration of thermal properties of SiNWs as Li battery anodes or weakly coupled with impurity atoms.

  3. 21 CFR 529.1940 - Progesterone intravaginal inserts.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 6 2012-04-01 2012-04-01 false Progesterone intravaginal inserts. 529.1940 Section 529.1940 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... periods greater than 7 days may result in reduced fertility. Dinoprost solution provided by No. 000009...

  4. 21 CFR 529.1940 - Progesterone intravaginal inserts.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 6 2013-04-01 2013-04-01 false Progesterone intravaginal inserts. 529.1940 Section 529.1940 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... periods greater than 7 days may result in reduced fertility. Dinoprost solution provided by No. 000009...

  5. 21 CFR 529.1940 - Progesterone intravaginal inserts.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 6 2014-04-01 2014-04-01 false Progesterone intravaginal inserts. 529.1940 Section 529.1940 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... may result in reduced fertility. Dinoprost solution provided by No. 054771 in § 510.600(c) of...

  6. 30. Photocopy of map. Insert, p. 138, Master Plan Report, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    30. Photocopy of map. Insert, p. 138, Master Plan Report, 1960, Vol. II. Layton, Layton and Rohrbach, General Planning and Resource Consultants. 1960 MASTER PLAN, SHOWING PROPOSED LOCATION OF LINNAEAN HOUSE - Missouri Botanical Garden, 2345 Tower Grove Avenue, Saint Louis, Independent City, MO

  7. PiggyBac Transgene Insertion Site GIZA Strain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetically modified New World screwworms were analyzed by inverse PCR and several sequences of genomic DNA flanking the transposon insertion sites were obtained. One transgenic strain, designated GIZA, exhibited the properties of a lethal genetic mutation. Classic genetic crosses of these insects r...

  8. Force modeling for needle insertion into soft tissue.

    PubMed

    Okamura, Allison M; Simone, Christina; O'Leary, Mark D

    2004-10-01

    The modeling of forces during needle insertion into soft tissue is important for accurate surgical simulation, preoperative planning, and intelligent robotic assistance for percutaneous therapies. We present a force model for needle insertion and experimental procedures for acquiring data from ex vivo tissue to populate that model. Data were collected from bovine livers using a one-degree-of-freedom robot equipped with a load cell and needle attachment. computed tomography imaging was used to segment the needle insertion process into phases identifying different relative velocities between the needle and tissue. The data were measured and modeled in three parts: 1) capsule stiffness, a nonlinear spring model; 2) friction, a modified Karnopp model; and 3) cutting, a constant for a given tissue. In addition, we characterized the effects of needle diameter and tip type on insertion force using a silicone rubber phantom. In comparison to triangular and diamond tips, a bevel tip causes more needle bending and is more easily affected by tissue density variations. Forces for larger diameter needles are higher due to increased cutting and friction forces. PMID:15490818

  9. Folding and insertion thermodynamics of the transmembrane WALP peptide.

    PubMed

    Bereau, Tristan; Bennett, W F Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-12-28

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum-in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence. PMID:26723612

  10. Folding and insertion thermodynamics of the transmembrane WALP peptide

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

    2015-12-01

    The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

  11. Type of Inserted Question and the Study-Posttest Delay.

    ERIC Educational Resources Information Center

    Andre, Thomas

    1990-01-01

    Two experiments with 254 and 76 undergraduates, respectively, investigated the hypothesis that there would be an effect of questions concerning application of concepts only when there was an interval between study and test. Results confirm the hypothesis regarding application questions inserted in text read by undergraduates. (TJH)

  12. Contrast-free endoscopic stent insertion in malignant biliary obstruction

    PubMed Central

    De Palma, Giovanni D; Lombardi, Giovanni; Rega, Maria; Simeoli, Immacolata; Masone, Stefania; Siciliano, Saverio; Maione, Francesco; Salvatori, Francesca; Balzano, Antonio; Persico, Giovanni

    2007-01-01

    AIM: To present a case series of MRCP-guided endoscopic biliary stent placement, performed entirely without contrast injection. METHODS: Contrast-free endoscopic biliary drainage was attempted in 20 patients with malignant obstruction, unsuitable for resection on the basis of tumor extent or medical illness. MRCP images were used to confirm the diagnosis of tumor, to exclude other biliary diseases and to demonstrate the stenoses as well as dilation of proximal liver segments. The procedure was carried out under conscious sedation. Patients were placed in the left lateral decubitus position. The endoscope was inserted, the papilla identified and cannulated by a papillotome. A guide wire was inserted and guided deeply into the biliary tree, above the stenosis, by fluoroscopy. A papillotomy approximately 1 cm. long was performed and the papillotome was exchanged with a guiding-catheter. A 10 Fr, Amsterdam-type plastic stent, 7 to 15 cm long, was finally inserted over the guide wire/guiding catheter by a pusher tube system. RESULTS: Successful stent insertion was achieved in all patients. There were no major complications. Successful drainage, with substantial reduction in bilirubin levels, was achieved in all patients. CONCLUSION: This new method of contrast-free endoscopic stenting in malignant biliary obstruction is a safe and effective method of palliation. However, a larger, randomized study comparing this new approach with the standard procedure is needed to confirm the findings of the present study. PMID:17663512

  13. External Tank (ET) Bipod Fitting Bolted Attachment Locking Insert Performance

    NASA Technical Reports Server (NTRS)

    Larsen, Curtis E.; Wilson, Tim R.; Elliott, Kenny B.; Raju, Ivatury S.; McManamen, John

    2008-01-01

    Following STS-107, the External Tank (ET) Project implemented corrective actions and configuration changes at the ET bipod fitting. Among the corrective actions, the existing bolt lock wire which provided resistance to potential bolt rotation was removed. The lock wire removal was because of concerns with creating voids during foam application and potential for lock wire to become debris. The bolts had been previously lubricated to facilitate assembly but, because of elimination of the lock wire, the ET Project wanted to enable the locking feature of the insert. Thus, the lubrication was removed from bolt threads and instead applied to the washer under the bolt head. Lubrication is necessary to maximize joint pre-load while remaining within the bolt torque specification. The locking feature is implemented by thread crimping in at four places in the insert. As the bolt is torqued into the insert the bolt threads its way past the crimped parts of the insert. This provides the locking of the bolt, as torque is required to loosen the joint after clamping.

  14. Insertion and deletion mutagenesis of the human cytomegalovirus genome

    SciTech Connect

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

    1987-10-01

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

  15. African origin of human-specific polymorphic Alu insertions.

    PubMed Central

    Batzer, M A; Stoneking, M; Alegria-Hartman, M; Bazan, H; Kass, D H; Shaikh, T H; Novick, G E; Ioannou, P A; Scheer, W D; Herrera, R J

    1994-01-01

    Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few "master" genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species; that is, not all chromosomes carry an Alu element at a particular locus. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay that uses primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution. Images PMID:7991620

  16. Cochlear implant insertion forces in microdissected human cochlea to evaluate a prototype array.

    PubMed

    Nguyen, Yann; Miroir, Mathieu; Kazmitcheff, Guillaume; Sutter, Jasmine; Bensidhoum, Morad; Ferrary, Evelyne; Sterkers, Olivier; Bozorg Grayeli, Alexis

    2012-01-01

    Cochlear implant array insertion forces are potentially related to cochlear trauma. We compared these forces between a standard (Digisonic SP; Neurelec, Vallauris, France) and an array prototype (Neurelec) with a smaller diameter. The arrays were inserted by a mechatronic tool in 23 dissected human cochlea specimens exposing the basilar membrane. The array progression under the basilar membrane was filmed together with dynamic force measurements. Insertion force profiles and depth of insertion were compared. The recordings showed lower insertion forces beyond 270° of insertion and deeper insertions with the thin prototype array. This will potentially allow larger cochlear coverage with less trauma. PMID:22653365

  17. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

    PubMed Central

    Mateo, Lidia; Ullastres, Anna; González, Josefa

    2014-01-01

    The increase in availability of whole genome sequences makes it possible to search for evidence of adaptation at an unprecedented scale. Despite recent progress, our understanding of the adaptive process is still very limited due to the difficulties in linking adaptive mutations to their phenotypic effects. In this study, we integrated different levels of biological information to pinpoint the ecologically relevant fitness effects and the underlying molecular and biochemical mechanisms of a putatively adaptive TE insertion in Drosophila melanogaster: the pogo transposon FBti0019627. We showed that other than being incorporated into Kmn1 transcript, FBti0019627 insertion also affects the polyadenylation signal choice of CG11699 gene. Consequently, only the short 3′UTR transcript of CG11699 gene is produced and the expression level of this gene is higher in flies with the insertion. Our results indicated that increased CG11699 expression leads to xenobiotic stress resistance through increased ALDH-III activity: flies with FBti0019627 insertion showed increased survival rate in response to benzaldehyde, a natural xenobiotic, and to carbofuran, a synthetic insecticide. Although differences in survival rate between flies with and without the insertion were not always significant, when they were, they were consistent with FBti0019627 mediating resistance to xenobiotics. Taken together, our results provide a plausible explanation for the increase in frequency of FBti0019627 in natural populations of D. melanogaster and add to the limited number of examples in which a natural genetic mutation has been linked to its ecologically relevant phenotype. Furthermore, the widespread distribution of TEs across the tree of life and conservation of stress response pathways across organisms make our results relevant not only for Drosophila, but for other organisms as well. PMID:25122208

  18. Inserting and removing levonorgestrel subdermal implants: an update.

    PubMed

    1994-11-01

    Risk factors for difficult removals of contraceptive implants are broken implants during removal, migration of implants, deeply embedded capsules, complication at insertion, and infection at the implant site at time of removal. Proper insertion and placement of the implants ease their removal. They should be inserted subdermally in a fan-like pattern all on the same plane just below the dermis. Clinicians should undergo training in insertion and removal of the implants. A modified insertion technique has been developed and studied. It uses a sharpened trocar to puncture the skin instead of using a scalpel to make a 4 mm incision. No significant differences between the modified technique and the original method exist. In addition to the Population Council or standard removal method, other modified removal techniques include the Pop-Out method, the Emory method, and the U technique. The Pop-Out method uses less anesthetic and a smaller incision and eliminates the need of hemostats when compared with the standard removal technique. Advantages are decreased pain, small incision, no tissue trauma, and no risk of fracture or implant damage. The Emory method uses more anesthetic, a larger incision (0.8-1 cm rather than 4 mm), and curved 5-inch Halstead mosquito forceps to dissect the subcutaneous tissues under the proximal ends of the capsules. Its advantages are increased ability to move forceps laterally and more deeply to locate difficult to find implants and shorter removal time. The U technique requires a 4-mm incision between and parallel to the third and fourth implants and uses a modified vas deferens holding forceps to grasp the implants from the side rather than at the tip. Advantages are snug grip of the implant with the modified instrument, lateral grasp of implants, and few broken implants. PMID:12288249

  19. Evaluation of the endodontic apical seal after post insertion by synchrotron radiation microtomography

    NASA Astrophysics Data System (ADS)

    Contardo, L.; De Luca, M.; Biasotto, M.; Longo, R.; Olivo, A.; Pani, S.; Di Lenarda, R.

    2005-08-01

    The commonly used methods for evaluating the endodontic apical seal, such as longitudinal and transversal section and diaphanization, show some operative difficulties and intrinsic limitation. This study suggests and describes a new method of analysis using a synchrotron radiation microtomography to analyse the root apex after post insertion, creating a three-dimensional image and analysing sections of the specimen every 5 μm. The study was performed at SYRMEP beam line at the Electra Synchrotron in Trieste using monochromatic X-rays of 32 KeV. Eleven monoradicular teeth were prepared using NiTi GT Rotary files instruments to an apical size 20 with conicity .06 and divided in four groups: in G1 ( n=4) and G2 ( n=2), the specimens were endodontically filled with guttapercha and a zinc-oxide sealer, in G3 ( n=3) and G4 ( n=2) guttapercha and a silicon-based sealer were used. An endodontic post was inserted in specimens of groups 1 and 3 following the manufacturer's instructions. Specimens were analysed using monochromatic X-rays of 32 KeV. A CCD detector with pixel dimension pf 5×5 μm 2 was used for the acquisition process. Seven hundred and twenty projections were performed over 180° range using a high-resolution rotator. The projections were reconstructed using standard algorithms for tomographic reconstruction. The apical infiltration was evaluated by verifying if black spots were detectable on the images. The specimens of groups 3 and 4 showed a better apical seal than the ones of groups 1 and 2. Post insertion, when a ZOE-based sealer is used, increases the apical gap even if it does not seem to be clinically relevant and sufficient to be a cause of endodontic failure. The new method for analysis appeared to be effective to detect small defects in endodontic obturation, analysing guttapercha-sealer and sealer-dentin interfaces.

  20. X-ray absorption spectroscopy of lithium insertion and de-insertion in copper birnessite nanoparticle electrodes.

    PubMed

    Pelliccione, Christopher J; Li, Yue Ru; Marschilok, Amy C; Takeuchi, Kenneth J; Takeuchi, Esther S

    2016-01-20

    The combination of ex situ X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) measurements on 2D layered copper birnessite cathode materials for lithium ion battery applications provides detailed insight into both bulk-crystalline and localized atomic structural changes resulting from electrochemically driven lithium insertion and de-insertion. Copper birnessite electrodes that had been galvanostatically discharged and charged were measured with XRD to determine the accompanying long-range crystalline structure changes, while Mn and Cu K-edge XAS measurements provided a detailed view of the Mn and Cu oxidation state changes along with variations of the local neighboring atom environments around the Mn and Cu centers. While not detectable with XRD spectra, through XAS measurements it was determined that the copper ions (Cu(2+)) are reduced to form amorphous nano-sized Cu metal, and can be oxidized back to Cu(2+). The reversible nature of the interconversion provides a rationale to the enhanced discharge capacity of copper birnessite relative to the analogous copper-free birnessite materials. The manganese oxide octahedra comprising the 2D layers in the original copper birnessite crystal structure disperse during lithium insertion, and revert back close to their original orientation after lithium de-insertion. During electrochemical oxidation or reduction the layered birnessite structure does not collapse, even though significant local disordering around Mn and Cu centers is directly observed. PMID:26735498

  1. Analysis of Primary Stability of Dental Implants Inserted in Different Substrates Using the Pullout Test and Insertion Torque

    PubMed Central

    Oliscovicz, Nathalia Ferraz; Shimano, Antnio Carlos; Marcantonio Junior, lcio; Lepri, Csar Penazzo; dos Reis, Andra Candido

    2013-01-01

    The aim of the study was to evaluate mechanical behavior of implants inserted in three substrates, by measuring the pullout strength and the relative stiffness. 32 implants (Master Porous-Conexao, cylindrical, external hexagon, and surface treatment) were divided into 4 groups (n = 8): pig rib bone, polyurethane Synbone, polyurethane Nacional 40 PCF, and pinus wood. Implants were installed with the exact distance of 5?mm of another implant. The insertion torque (Ncm) was quantified using the digital Kratos torque meter and the pullout test (N) was performed by an axial traction force toward the long axis of the implant (2?min/mm) through mount implant devices attached to a piece adapted to a load cell of 200?Kg of a universal testing machine (Emic DL10000). Data of insertion torque and maximum pullout force were submitted to one-way ANOVA and Bonferroni tests (? = 0.05). Polyurethane Nacional 40 PCF and pinus wood showed the highest values of insertion torque and pullout force, with significant statistical difference (P < 0.05) with other groups. The analysis showed stiffness materials with the highest values for primary stability. PMID:23431301

  2. Lesion insertion in the projection domain: Methods and initial results

    SciTech Connect

    Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia

    2015-12-15

    Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically acquired for the ACR phantom in terms of Hounsfield unit and high-contrast resolution. For the validation of the lesion realism, lesions of various types were successfully inserted, including well circumscribed and invasive lesions, homogeneous and heterogeneous lesions, high-contrast and low-contrast lesions, isolated and vessel-attached lesions, and small and large lesions. The two experienced radiologists who reviewed the original and inserted lesions could not identify the lesions that were inserted. The same lesion, when inserted into the projection domain and reconstructed with different parameters, demonstrated a parameter-dependent appearance. Conclusions: A framework has been developed for projection-domain insertion of lesions into commercial CT images, which can be potentially expanded to all geometries of CT scanners. Compared to conventional image-domain methods, the authors’ method reflected the impact of scan and reconstruction parameters on lesion appearance. Compared to prior projection-domain methods, the authors’ method has the potential to achieve higher anatomical complexity by employing clinical patient projections and real patient lesions.

  3. Subcloning Plus Insertion (SPI) - A Novel Recombineering Method for the Rapid Construction of Gene Targeting Vectors

    PubMed Central

    Reddy, Thimma R.; Kelsall, Emma J.; Fevat, Léna M.S.

    2015-01-01

    Gene targeting refers to the precise modification of a genetic locus using homologous recombination. The generation of novel cell lines and transgenic mouse models using this method necessitates the construction of a ‘targeting’ vector, which contains homologous DNA sequences to the target gene, and has for many years been a limiting step in the process. Vector construction can be performed in vivo in Escherichia coli cells using homologous recombination mediated by phage recombinases using a technique termed recombineering. Recombineering is the preferred technique to subclone the long homology sequences (>4kb) and various targeting elements including selection markers that are required to mediate efficient allelic exchange between a targeting vector and its cognate genomic locus. Typical recombineering protocols follow an iterative scheme of step-wise integration of the targeting elements and require intermediate purification and transformation steps. Here, we present a novel recombineering methodology of vector assembly using a multiplex approach. Plasmid gap repair is performed by the simultaneous capture of genomic sequence from mouse Bacterial Artificial Chromosome libraries and the insertion of dual bacterial and mammalian selection markers. This subcloning plus insertion method is highly efficient and yields a majority of correct recombinants. We present data for the construction of different types of conditional gene knockout, or knock-in, vectors and BAC reporter vectors that have been constructed using this method. SPI vector construction greatly extends the repertoire of the recombineering toolbox and provides a simple, rapid and cost-effective method of constructing these highly complex vectors. PMID:25590226

  4. Laser-induced defect insertion in DNA-linked 2D colloidal crystal array

    NASA Astrophysics Data System (ADS)

    Geiss, Erik; Kim, Sejong; Marcus, Harris L.; Papadimitrakopoulos, Fotios

    2009-02-01

    Insertion of vacancies at predetermined sites within the lattice of colloidal crystals is a prerequisite in order to realize high-quality, opaline-based photonic devices. In this contribution, we demonstrate a novel methodology to afford controlled insertion of vacancies within two-dimensional (2D) opaline arrays. These 2D opaline arrays have been substrate-anchored with the help of DNA hybridization. This provides a heat-sensitive ‘adhesive’ between substrate and microspheres within a surrounding aqueous medium that enables tuning the hybridization strength of DNA linker as well as a mechanism to facilitate the removal of unbound microspheres. Focusing a laser beam onto the substrate/microsphere interface induces a localized heating event that detaches the irradiated microspheres, leaving behind vacancies. By repeating this process, line vacancies were successfully obtained. The effects of salt concentration, laser power, light-absorbing dyes, DNA length and refractive-index mismatch were investigated and found to correlate with heat-induced microsphere release.

  5. Transgenic mouse model of hemifacial microsomia: Cloning and characterization of insertional mutation region on chromosome 10

    SciTech Connect

    Naora, Hiroyuki; Otani, Hiroki; Tanaka, Osamu

    1994-10-01

    The 643 transgenic mouse line carries an autosomal dominant insertional mutation that results in hemifacial microsomia (HFM), including microtia and/or abnormal biting. In this paper, we characterize the transgene integration site in transgenic mice and preintegration site of wildtype mice. The locus, designated Hfm (hemifacial microsomia-associated locus), was mapped to chromosome 10, B1-3, by chromosome in situ hybridization. We cloned the transgene insertion site from the transgenic DNA library. By using the 5{prime} and 3{prime} flanking sequences, the preintegration region was isolated. The analysis of these regions showed that a deletion of at least 23 kb DNA occurred in association with the transgene integration. Evolutionarily conserved regions were detected within and beside the deleted region. The result of mating between hemizygotes suggests that the phenotype of the homozygote is lethality in the prenatal period. These results suggests that the Hfm locus is necessary for prenatal development and that this strain is a useful animal model for investigating the genetic predisposition to HFM in humans.

  6. Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

    PubMed Central

    Girirajan, Santhosh; Chen, Lin; Graves, Tina; Marques-Bonet, Tomas; Ventura, Mario; Fronick, Catrina; Fulton, Lucinda; Rocchi, Mariano; Fulton, Robert S.; Wilson, Richard K.; Mardis, Elaine R.; Eichler, Evan E.

    2009-01-01

    The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), β-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human–NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution. PMID:19029537

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

    PubMed

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

    2015-10-01

    The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution. PMID:26174143

  8. NSCLC harboring EGFR exon-20 insertions after the regulatory C-helix of kinase domain responds poorly to known EGFR inhibitors.

    PubMed

    Yang, Mengmeng; Xu, Xiaoxi; Cai, Jie; Ning, Jinying; Wery, Jean Pierre; Li, Qi-Xiang

    2016-07-01

    Anecdote clinical observations hint that non-small cell lung cancer (NSCLC) with exon-20 insertions might respond poorly to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), contrasting to those with classic mutations. Lack of patient-derived experimental models has been a major hurdle for the discovery of new treatment for the diseases. We established two NSCLC-PDXs harboring two different exon-20 insertions, LU0387-adenocarcinoma (ADC) with a nine-base insertion at 2319 (H773-V774insNPH) and LU3075-squamous cell carcinoma (SCC) with a nine-base insertion at 2316 (P772-H773insDNP). Both insertions immediately follow the regulatory C-helix of the kinase domain. Contrary to the generally good responses to EGFR inhibitors observed in PDXs with classic mutations, both exon-20 insertions are largely resistant to cetuximab and TKIs in vivo, suggesting fundamental difference from the classic EGFR mutations, consistent with the poor response rate to TKI seen in anecdotal clinic reports. It is worth noting that although responses are generally poor, they differ between the two exon-20 mutants depending on the type of TKI. In vitro drug sensitivity assays using established primary cell lines from our two PDXs largely confirmed the in vivo data. Our data from patient-derived experimental models confirmed that exon-20 insertions in domain immediately following the C-helix confer poor response to all known EGFR inhibitors, and suggested that these models can be utilized to facilitate the discovery of new therapies targeting NSCLC harboring exon-20 insertions. PMID:26891175

  9. LINE retrotransposition and host DNA repair machinery

    PubMed Central

    Yamaguchi, Katsumi; Kajikawa, Masaki; Okada, Norihiro

    2015-01-01

    Long interspersed elements (LINEs), or non-long-terminal repeat (LTR) retrotransposons, are mobile genetic elements that exist in the genomic DNA of most eukaryotes, comprising a considerable portion of the host chromosomes. LINEs constitute endogenous mutagens that cause insertional mutations in host chromosomes and have a large impact on host genome evolution. Despite their importance, however, the molecular mechanism of LINE retrotransposition is not fully understood. Several studies suggest that host proteins that participate in the repair of DNA breaks modulate LINE retrotransposition. Recently, we provided evidence that there are 2 distinct pathways—annealing and direct—that join the 5′-end of LINEs to host chromosomal DNA. These pathways appear to be used distinctively by zebrafish LINEs and the human L1 in DT40 cells. In HeLa cells, only the annealing pathway appears to be used. This implies that different characteristics of the 2 LINEs and also host factors dictate which pathway is selected. Here, we discuss the 5′-end-joining pathways of LINE retrotransposition and propose that the pathways of LINE integration adopt certain host repair factors. PMID:26942045

  10. Disulfide Bond Bridge Insertion Turns Hydrophobic Anticancer Prodrugs into Self-Assembled Nanomedicines

    PubMed Central

    2015-01-01

    It is commonly observed that hydrophobic molecules alone cannot self-assemble into stable nanoparticles, requiring amphiphilic or ionic materials to support nanoparticle stability and function in vivo. We report herein newly self-assembled nanomedicines through entirely different mechanisms. We present proof-of-concept methodology and results in support of our hypothesis that disulfide-induced nanomedicines (DSINMs) are promoted and stabilized by the insertion of a single disulfide bond into hydrophobic molecules, in order to balance the competition between intermolecular forces involved in the self-assembly of nanomedicines. This hypothesis has been explored through diverse synthetic compounds, which include four first-line chemotherapy drugs (paclitaxel, doxorubicin, fluorouracil, and gemcitabine), two small-molecule natural products and their derivatives, as well as a fluorescent probe. Such an unprecedented and highly reproducible system has the potential to serve as a synthetic platform for a wide array of safe and effective therapeutic and diagnostic nanomedicine strategies. PMID:25188744

  11. New chicane magnet design for insertion device straights at the Advanced Light Source

    SciTech Connect

    Marks, Steve; Schlueter, Ross; Anderson, David; Gath, William; Jung, Jin-Young; Robin, David; Steier, Christoph; Stevens, Troy

    2001-12-10

    A chicane magnet incorporating counter-rotating permanent magnet pairs together with trim coils has been designed for use in the Advanced Light Source (ALS) straights in conjunction with two insertion devices. In particular, this design is being developed for use in the existing beam line (BL) 4 elliptically polarizing undulator (EPU) straight and in the BL11 EPU straight, currently under design and construction. The purpose of the chicane is to provide a fixed angular separation between two successive EPU photon fans, and to correct steering perturbations resulting from EPU polarization state changes. Polarization changes occur on the time scale of one second; associated steering corrections must be accomplished in less than a second. Hysteresis associated with conventional iron core electromagnets prevents fast steering correction to the required precision. This consideration motivated the iron-free design presented here.

  12. Influence of inserting a thin fullerene layer on pentacene organic thin-film transistor

    NASA Astrophysics Data System (ADS)

    Li, Yu-Chang; Lin, Yu-Ju; Wei, Chia-Yu; Chou, Dei-Wei; Tsao, Chun-Ho; Wang, Yeong-Her

    2012-03-01

    The performance of organic thin-film transistors (TFTs) with a pentacene/fullerene(C60)/pentacene (PCP) sandwich structure is presented. Using a 3.5 nm-thick C60 layer inserted between the pentacene films, the obtained hole mobility is improved by more than six times. By applying atomic force microscopy, x-ray diffraction, Raman spectrum, and transmission line method analysis, one can reasonably infer that the smoother surface of the pentacene film covered with thin C60 layer delays the phase transformation of the upper pentacene film, resulting in stronger intermolecular coupling and the reduction of channel resistance of the PCP TFTs from 3.03 to 1.72 MΩ, and, therefore, improving the device performance.

  13. Generation of an Enhancer-Trapping Vector for Insertional Mutagenesis in Zebrafish

    PubMed Central

    Liu, Chunyan; Song, Guili; Mao, Lin; Long, Yong; Li, Qing; Cui, Zongbin

    2015-01-01

    Enhancer trapping (ET) is a powerful approach to establish tissue- or cell-specific reporters and identify expression patterns of uncharacterized genes. Although a number of enhancer-trapping vectors have been developed and a large library of fish lines with distinct tissue- or cell-specific expression of reporter genes have been generated, the specificity and efficiency of trapping vectors need to be improved because of the bias interaction of minimal promoters with genomic enhancers. Accordingly, we generated an enhancer-trapping vector pTME that contains a minimal mouse metallothionein gene (mMTI) promoter upstream of EGFP reporter. In the first round of screening, twelve zebrafish lines that carry a single copy of ET cassettes were characterized to have tissue- or cell-specific EGFP expression. One of the highly conserved noncoding elements near an insertion site of trapping cassettes was characterized as an enhancer that can specifically regulate the expression of EGFP in cells of the central nervous system. In addition, the pTME vector contains a mutation-cassette that is able to effectively block the transcription of an endogenous gene in an ET line with ubiquitous EGFP expression. Thus, the pTME vector can be used as an alternative tool for both enhancer trapping and mutagenesis across a target genome. PMID:26436547

  14. A transposon insertion in FLOWERING LOCUS T is associated with delayed flowering in Brassica rapa.

    PubMed

    Zhang, Xueming; Meng, Lin; Liu, Bo; Hu, Yunyan; Cheng, Feng; Liang, Jianli; Aarts, Mark G M; Wang, Xiaowu; Wu, Jian

    2015-12-01

    Long days and vernalization accelerate the transition from vegetative growth to reproductive growth in Brassica rapa. Bolting before plants reach the harvesting stage is a serious problem in B. rapa vegetable crop cultivation. The genetic dissection of flowering time is important for breeding of premature bolting-resistant B. rapa crops. Using a recombinant inbred line (RIL) population, we twice detected two major quantitative trait loci (QTLs) for flowering time in two different growing seasons that were located on chromosomes A02 and A07, respectively. We hypothesized that an orthologue of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, named as BrFT2, was the candidate gene underlying the QTL localized to A07. A transposon insertion in the second intron of BrFT2 was detected in one of the parental lines, which was predicted to generate a loss-of-function allele. Transcription analysis revealed that the BrFT2 transcript was not present in the parental line that harbored the mutated allele. RILs carrying only the mutated BrFT2 allele showed delayed flowering regardless of growing seasons when compared to RILs carrying the wild-type BrFT2 allele. These data suggest that BrFT2 is involved in flowering time regulation in controlling flowering time in B. rapa. PMID:26706072

  15. Feasibility Study of Free-Hand Technique for Pedicle Screw Insertion at C7 without Fluoroscopy-Guidance

    PubMed Central

    Lee, Gun Woo; Kim, Ho-Joong; Yeom, Jin S.; Uh, Jae-Hyung; Park, Jong-Ho; Lee, Ji-Hoon; Kim, Dong-Wook

    2016-01-01

    Study Design Retrospective interventional study. Purpose To introduce a free-hand pedicle screw (PS) insertion technique without fluoroscopic guidance in the C7 vertebra and evaluate the procedure's feasibility and radiologic outcomes. Overview of Literature Although PS insertion at C7 has been recognized as a critical procedure in posterior cervical fusion surgery, conventional techniques for C7 PS have several limitations. Methods Thirty two patients (64 screws) who underwent PS insertion in C7 with the novel technique were included in this study. Postoperative clinical and radiological outcomes were evaluated. Special attention was paid to the presence of any problems in the screw position including cortical breaches of the PS and encroachment of the PS into the spinal canal or the vertebral foramen. This novel technique for PS insertion in C7 without fluoroscopy guidance had three key elements. First, the ideal PS entry point was chosen near the C6–7 facet joint using preoperative images. Second, the convergent angle distance was measured at axial computed tomography (CT) imaging, which defined the distance between the tip of C7 spinous process and the extended line passing through the pedicle axis from the ideal entry point. Third, the cranial-caudal angle distance was measured in sagittal CT images, which defined the distance between the tip of the C7 spinous process and the extended line passing through the pedicle axis. Results Cortical breach on postoperative CT images was observed in three screws. All violated only the lateral wall of the affected pedicle. The breached screws occurred in the initial five cases. Postoperative neurologic deterioration was not observed in any patient, regardless of cortical breaching. Conclusions The novel technique successfully allows for C7 PS to be placed and is associated with a low rate of cortical breach. PMID:26949456

  16. Insertional hypermutation in mineral oil-induced plasmacytomas

    PubMed Central

    Knittel, Gero; Metzner, Mirjam; Beck-Engeser, Gabriele; Kan, Ada; Ahrends, Tomasz; Eilat, Dan; Huppi, Konrad; Wabl, Matthias

    2014-01-01

    Unless stimulated by a chronic inflammatory agent such as mineral oil, plasma cell tumors are rare in young BALB/c mice. This raises the questions, What do inflammatory tissues provide to promote mutagenesis? and What is the nature of mutagenesis? We determined that mineral oil-induced plasmacytomas produce large amounts of endogenous retroelements—ecotropic and polytropic murine leukemia virus and intracisternal A-particles. Therefore, plasmacytoma formation might occur, in part, by de novo insertion of these retroelements, induced or helped by the inflammation. We recovered up to 10 de novo insertions in a single plasmacytoma, mostly in genes with common retroviral integration sites. Additional integrations accompany tumor evolution from a solid tumor through several generations in cell culture. The high frequency of de novo integrations into cancer genes suggests that endogenous retroelements are coresponsible for plasmacytoma formation and progression in BALB/c mice. PMID:24975032

  17. Biological insertion of computationally designed short transmembrane segments

    PubMed Central

    Baeza-Delgado, Carlos; von Heijne, Gunnar; Marti-Renom, Marc A.; Mingarro, Ismael

    2016-01-01

    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design. PMID:26987712

  18. CUDA accelerated simulation of needle insertions in deformable tissue

    NASA Astrophysics Data System (ADS)

    Patriciu, Alexandru

    2012-10-01

    This paper presents a stiff needle-deformable tissue interaction model. The model uses a mesh-less discretization of continuum; avoiding thus the expensive remeshing required by the finite element models. The proposed model can accommodate both linear and nonlinear material characteristics. The needle-deformable tissue interaction is modeled through fundamental boundaries. The forces applied by the needle on the tissue are divided in tangent forces and constraint forces. The constraint forces are adaptively computed such that the material is properly constrained by the needle. The implementation is accelerated using NVidia CUDA. We present detailed analysis of the execution timing in both serial and parallel case. The proposed needle insertion model was integrated in a custom software that loads DICOM images, generate the deformable model, and can simulate different insertion strategies.

  19. Malpositioned IUCD: the menace of postpartum IUCD insertion.

    PubMed

    Nigam, Aruna; Ahmad, Ayesha; Gupta, Neha; Kumari, Archana

    2015-01-01

    Use of a postpartum intrauterine contraceptive device (PPIUCD) is a highly effective, reversible and long-acting family planning method that can be initiated in the immediate postpartum period, especially in lactating women. PPIUCDs have been inserted in more than 65,000 women worldwide and the numbers are increasing with many countries introducing PPIUCDs as part of their family planning programme. As the numbers of PPIUCD insertions are increasing, we are getting wiser regarding complications of this procedure. One of the less-understood entities is a malpositioned PPIUCD, a situation where the IUCD is present inside the uterus but its placement is eccentric and a part or the whole of it may be embedded in the myometrium. It can present as lost strings or as a failure to remove the intrauterine device. We present a series of cases with malpositioned PPIUCDs and their management. PMID:26290564

  20. Tumor track seeding: A new complication of fiducial marker insertion

    PubMed Central

    Patel, Zeal; Retrouvey, Michele; Vingan, Harlan; Williams, Scott

    2015-01-01

    In the United States, lung cancer is the leading cause of cancer-related death. Candidates for tumor ablation using CyberKnife® require fiducial placement in or near the target tumor to achieve precision. Placing these reference points may lead to complications including pneumothorax and/or hemorrhage. We report a new complication: the appearance of metastatic foci along the track of the fiducial marker. Since the marker was inserted by traversing the original primary tumor, we hypothesize that malignant cells were seeded along the track. In light of this new complication, current techniques for the insertion of fiducial markers should consider a peripheral approach when possible to avoid tracking of malignant cells.

  1. Insertion devices for the Advanced Light Source at LBL

    SciTech Connect

    Hassenzahl, W.; Chin, J.; Halbach, K.; Hoyer, E.; Humphries, D.; Kincaid, B.; Savoy, R.

    1989-03-01

    The Advanced Light Source (ALS) at the Lawrence Berkeley Laboratory will be the first of the new generation of dedicated synchrotron light sources to be put into operation. Specially designed insertion devices will be required to realize the high brightness photon beams made possible by the low emittance of the electron beam. The complement of insertion devices on the ALS will include undulators with periods as short as 3.9 cm and one or more high field wigglers. The first device to be designed is a 5 m long, 5 cm period, hybrid undulator. The goal of very high brightness and high harmonic output imposes unusually tight tolerances on the magnetic field quality and thus on the mechanical structure. The design process, using a generic structure for all undulators, is described. 5 refs., 4 figs., 1 tab.

  2. Micro-optical insertion system for WDM transceiver

    NASA Astrophysics Data System (ADS)

    Bakala, Bretislav; Jerabek, Vitezslav; Mares, David; Prajzler, Vaclav

    2015-01-01

    The paper deals with the design of an micro-optical part of a WDM transceiver based on the circle volume holographic grating triplexer (VHGT) topology. The work is focused on detail description of the bidirectional micro-optical insertion system, especially on the coupling in the transmission direction of the WDM transceiver optical part. This micro-optical wavelength distribution system is imagine transmission system consisted of collimating cylindrical lenses set in the circle topology with the VHGT filter placed in the middle of the circle. The topology is described by ray matrices equations, calculated using analytic and numeric methods and optically measured. Considering simulation and measurement results of micro-optical insertion system the influence of these characteristics on ray path attenuation, diffraction efficiency and transceiver performance is estimated. The paper also discusses limits and conditions of the laser asymmetrical beam focus into the input/output optical fiber.

  3. Source insertion & location systems for the Borexino solar neutrino detector

    NASA Astrophysics Data System (ADS)

    Hardy, Steve; Joyce, Matt; Kidner, Steve; Vogelaar, Bruce; Back, Henning O.

    2008-11-01

    The Borexino solar neutrino detector is currently performing a real time measurement of the sub-MeVregion of the solar neutrino spectrum. In order to obtain the most accurate results, the detector mustundergo a careful calibration campaign. Monte Carlo simulations, as well as our recent data, haveshown that the main sources of systematic error are: fiducial volume determination, detector energyresponse as a function of event position, α, β, γ energy scales, and α/β discrimination efficiency. Inorder to reduce these uncertainties, systems have been developed to insert and locate radioactive andoptical sources both into the bulk volume of Borexino and into the buffer region. This poster willdescribe in detail the internal source insertion and location system as well as the external sourceinsertion system used to meet the aforementioned objectives.

  4. Phase transitions in insertion electrodes for lithium batteries

    SciTech Connect

    Thackeray, M. M.

    2000-02-02

    Phase transitions that occur during lithium insertion into layered and framework structures are discussed in the context of their application as positive and negative electrodes in lithium-ion batteries. The discussion is focused on the two-dimensional structures of graphite, LiNi{sub 1{minus}x}M{sub x}O{sub 2} (M = Co, Ti and Mg), and Li{sub 1.2}V{sub 3}O{sub 8}; examples of framework structures with a three-dimensional interstitial space for Li{sup +}-ion transport include the spinel oxides and intermetallic compounds with zinc-blende-type structures. The phase transitions are discussed in terms of their tolerance to lithium insertion and extraction and to the chemical stability of the electrodes in the cell environment.

  5. Enantioselective iron-catalysed O-H bond insertions

    NASA Astrophysics Data System (ADS)

    Zhu, Shou-Fei; Cai, Yan; Mao, Hong-Xiang; Xie, Jian-Hua; Zhou, Qi-Lin

    2010-07-01

    The ready availability, low price and environmentally benign character of iron mean that it is an ideal alternative to precious metals in catalysis. Recent growth in the number of iron-catalysed reactions reported reflects an increasing demand for sustainable chemistry. Only a limited number of chiral iron catalysts have been reported and these have, in general, proven less enantioselective than other transition-metal catalysts, thus limiting their appeal. Here, we report that iron complexes of spiro-bisoxazoline ligands are highly efficient catalysts for asymmetric O-H bond insertion reactions. These complexes catalyse insertions into the O-H bond of a wide variety of alcohols and even water, with exceptional enantioselectivities under mild reaction conditions. The selectivities surpass those obtained with other transition-metal catalysts. This study should inspire and encourage the use of iron instead of traditional precious metals in the development of greener catalysts for catalytic asymmetric synthesis.

  6. Flexibility in targeting and insertion during bacterial membrane protein biogenesis

    SciTech Connect

    Bloois, Edwin van; Hagen-Jongman, Corinne M. ten; Luirink, Joen

    2007-10-26

    The biogenesis of Escherichia coli inner membrane proteins (IMPs) is assisted by targeting and insertion factors such as the signal recognition particle (SRP), the Sec-translocon and YidC with translocation of (large) periplasmic domains energized by SecA and the proton motive force (pmf). The use of these factors and forces is probably primarily determined by specific structural features of an IMP. To analyze these features we have engineered a set of model IMPs based on endogenous E. coli IMPs known to follow distinct targeting and insertion pathways. The modified model IMPs were analyzed for altered routing using an in vivo protease mapping approach. The data suggest a facultative use of different combinations of factors.

  7. Convective heat transfer enhancement inside tubes using inserted helical coils

    NASA Astrophysics Data System (ADS)

    Ali, R. K.; Sharafeldeen, M. A.; Berbish, N. S.; Moawed, M. A.

    2016-01-01

    Convective heat transfer was experimentally investigated in tubes with helical coils inserts in turbulent flow regime within Reynolds number range of 14400 ≤ Re ≤ 42900. The present work aims to extend the experimental data available on wire coil inserts to cover wire diameter ratio from 0.044 to 0.133 and coil pitch ratio from 1 to 5. Uniform heat flux was applied to the external surface of the tube and air was selected as fluid. The effects of Reynolds number and wire diameter and coil pitch ratios on the Nusselt number and friction factor were studied. The enhancement efficiency and performance criteria ranges are of (46.9-82.6%) and (100.1-128%) within the investigated range of the different parameters, respectively. Correlations are obtained for the average Nusselt number and friction factor utilizing the present measurements within the investigated range of geometrical parameters and Re.

  8. Challenges for Insertion of Structural Nanomaterials in Aerospace Applications

    NASA Technical Reports Server (NTRS)

    Sochi, Emilie J.

    2012-01-01

    In the two decades since Iijima's report on carbon nanotubes (CNT), there has been great interest in realizing the benefits of mechanical properties observed at the nanoscale in large-scale structures. The weight savings possible due to dramatic improvements in mechanical properties relative to state-of-the-art material systems can be game changing for applications like aerospace vehicles. While there has been significant progress in commercial production of CNTs, major aerospace applications that take advantage of properties offered by this material have yet to be realized. This paper provides a perspective on the technical challenges and barriers for insertion of CNTs as an emerging material technology in aerospace applications and proposes approaches that may reduce the typical timeframe for technology maturation and insertion into aerospace structures.

  9. Metallocene Catalytic Insertion Polymerization of 1-Silene to Polycarbosilanes

    PubMed Central

    Tian, Yuelong; Ge, Min; Zhang, Weigang; Lv, Xiaoxu; Yu, Shouquan

    2015-01-01

    Metallocene of zirconium were used as a catalyst for an insertion polymerization of 1-methylsilene directly into pre-ceramic precursor polyzirconocenecarbosilane (PZCS) during dechlorination of dichlorodimethylesilane by sodium, which exhibits high catalytic effectiveness with the maximum conversion ratio of polycarbosilane up to 91%. The average molecular weights of polymers synthesized are less than 1400, all with very narrow polymolecularities. The mechanism of catalytic polymerization was assumed to be similar to a coordination insertion polymerization of 1-olefins by metallocenes. The obtained PZCS show high ceramic yields with formation of composite ceramics of ZrC-SiC, which are novel polymeric precursors of ultra-high temperature ceramic (UHTC) fiber and composite. PMID:26541636

  10. The first insertion devices at SSRL - some personal recollections

    SciTech Connect

    Winick, H.

    1995-02-01

    The author recounts his experiences with insertion devices at the Stanford Synchrotron Radiation Laboratory. His first experiences with wigglers occured at the Cambridge Electron Accelerator, and was carried over to SSRL with the proposal for a six pole electromagnetic wiggler. Most modern undulators, and many wigglers are now designed around permanent magnets, and the origin of this transition at SSRL was rather fortuitous and humorous. It reflects some of the personality characteristics of Klaus Halbach.

  11. Management of subcalcaneal pain and Achilles tendonitis with heel inserts

    PubMed Central

    Maclellan, G. E.; Vyvyan, Barbara

    1981-01-01

    Soft tissue symptoms in the leg due to sporting activity are commonly associated with the force of heel strike. Conventional training shoes compromise between comfort and performance; few models are suitably designed for both considerations. Using a visco-elastic polymer insert the symptoms of heel pain and Achilles tendonitis have been largely or completely abolished in a preliminary study. Imagesp117-ap117-bp117-cp118-a PMID:7272653

  12. Theoretical model for electrophilic oxygen atom insertion into hydrocarbons

    SciTech Connect

    Bach, R.D.; Su, M.D. ); Andres, J.L. Wayne State Univ., Detroit, MI ); McDouall, J.J.W. )

    1993-06-30

    A theoretical model suggesting the mechanistic pathway for the oxidation of saturated-alkanes to their corresponding alcohols and ketones is described. Water oxide (H[sub 2]O-O) is employed as a model singlet oxygen atom donor. Molecular orbital calculations with the 6-31G basis set at the MP2, QCISD, QCISD(T), CASSCF, and MRCI levels of theory suggest that oxygen insertion by water oxide occurs by the interaction of an electrophilic oxygen atom with a doubly occupied hydrocarbon fragment orbital. The electrophilic oxygen approaches the hydrocarbon along the axis of the atomic carbon p orbital comprising a [pi]-[sub CH(2)] or [pi]-[sub CHCH(3)] fragment orbital to form a carbon-oxygen [sigma] bond. A concerted hydrogen migration to an adjacent oxygen lone pair of electrons affords the alcohol insertion product in a stereoselective fashion with predictable stereochemistry. Subsequent oxidation of the alcohol to a ketone (or aldehyde) occurs in a similar fashion and has a lower activation barrier. The calculated (MP4/6-31G*//MP2/6-31G*) activation barriers for oxygen atom insertion into the C-H bonds of methane, ethane, propane, butane, isobutane, and methanol are 10.7, 8.2, 3.9, 4.8, 4.5, and 3.3 kcal/mol, respectively. We use ab initio molecular orbital calculations in support of a frontier MO theory that provides a unique rationale for both the stereospecificity and the stereoselectivity of insertion of electrophilic oxygen and related electrophiles into the carbon-hydrogen bond. 13 refs., 7 figs., 2 tabs.

  13. Accurate Insertion Loss Measurements of the Juno Patch Array Antennas

    NASA Technical Reports Server (NTRS)

    Chamberlain, Neil; Chen, Jacqueline; Hodges, Richard; Demas, John

    2010-01-01

    This paper describes two independent methods for estimating the insertion loss of patch array antennas that were developed for the Juno Microwave Radiometer instrument. One method is based principally on pattern measurements while the other method is based solely on network analyzer measurements. The methods are accurate to within 0.1 dB for the measured antennas and show good agreement (to within 0.1dB) of separate radiometric measurements.

  14. Bone metabolism induced by denture insertion in positron emission tomography.

    PubMed

    Suenaga, H; Chen, J; Yamaguchi, K; Sugazaki, M; Li, W; Swain, M; Li, Q; Sasaki, K

    2016-03-01

    18F-fluoride positron emission tomogra-phy (PET) can identify subtle functional variation prior to the major structural change detectable by X-ray. This study aims to investigate the mechanobiological bone reaction around the abutment tooth and in the residual ridge, induced by insertion of removable partial denture (RPD) within two different groups of patients: patients without denture experience (Group 1) and patients with denture experience before (Group 2), using 18F-fluoride PET imaging technique. 18F-fluoride PET/computerised tomography (CT) scan was performed to examine the bone metabolic change in mandible before and after the RPD treatment. Region of interests (ROIs) were placed in alveolar bone around abutment tooth and in residual bone beneath the RPD. Standardised uptake value (SUV), reflecting the accumulation of 18F-fluoride, was measured for each ROI. In all subjects of Group 1, SUVs after insertion were higher than before in both alveolar bone and residual bone, while there was less significant change in SUV in subjects of Group 2. This study demonstrated using longitudinal 18F-fluoride PET scans to effectively examine the bone metabolic change in mandible induced by occlusal loading after RPD insertion. Using this technique, within the six subjects in this study, it was shown that bone metabolism around abutment tooth and residual ridge increased after RPD insertion in case of first-time denture user, while there was no big change in the patient with experience of denture before. This study revealed the effectiveness of applying PET to evaluate bone metabolic activity as mechanobiolo-gical reaction. PMID:26431672

  15. Magnetic resonance urography in duplex kidney with ectopic ureteral insertion.

    PubMed

    Thambidorai, Conjeevaram Rajendrarao; Anuar, Zulfiqar

    2011-07-01

    This is a report on the use of magnetic resonance urography (MRU) in a 6-year-old girl who presented with urinary incontinence. She had a left duplex kidney with poorly functioning upper moiety and ectopic insertion of the dilated upper pole ureter. MRU has been shown to be superior to conventional imaging techniques in delineating poorly functioning moieties of duplex kidneys and ectopic ureters. PMID:21897576

  16. Laparoscopic insertion of gastric electrodes for electrical stimulation.

    PubMed

    Brody, Fred; Nam, Arthur; Drenon, Elizabeth; Ali, Aamir; Soffer, Edy

    2007-02-01

    Gastric electrical stimulation can provide symptomatic relief for patients with refractory gastroparesis. Traditionally, these wires are placed through a midline laparotomy. This paper describes and illustrates, in detail, the laparoscopic technique for successful implantation. Thirty-one consecutive patients from October 2003 to March 2005 underwent laparoscopic insertion of gastric stimulating wires for gastroparesis. Twenty-six patients were female. Four laparoscopic ports were used to insert a pair of electrodes. Anterior, cephalad retraction of the gastric wall is critical for accurate seromuscular placement of gastric leads. Intraoperative endoscopy was used to verify the seromuscular placement of the leads. Both leads were secured to a subcutaneous generator and electrical parameters were immediately established in the operating room. Patient demographics, operative details, and postoperative morbidities were recorded. All procedures were completed laparoscopically. The mean operative time was 114.4 +/- 20.9 minutes (range, 95-140). No perioperative mortality occurred. Two patients developed cellulitis at the generator site postoperatively and oral antibiotics were prescribed for one week postoperatively. No hardware was removed. Two patients had their generators repositioned due to pain at the pocket site. Gastric electrical stimulation is a novel treatment modality for patients with refractory gastroparesis and can be accomplished safely via laparoscopy. Laparoscopic insertion is successful even in patients with prior surgery and intact gastrointestinal tubes. Long-term follow-up and the current prospective multicenter trial continue to assess the efficacy of this treatment modality. PMID:17362169

  17. Characterization of Mycobacterium tuberculosis EsxA Membrane Insertion

    PubMed Central

    Ma, Yue; Keil, Verena; Sun, Jianjun

    2015-01-01

    EsxA (ESAT-6), an important virulence factor of Mycobacterium tuberculosis, plays an essential role in phagosome rupture and bacterial cytosolic translocation within host macrophages. Our previous study showed that EsxA exhibits a unique membrane-interacting activity that is not found in its ortholog from nonpathogenic Mycobacterium smegmatis. However, the molecular mechanism of EsxA membrane insertion remains unknown. In this study, we generated truncated EsxA proteins with deletions of the N- and/or C-terminal flexible arm. Using a fluorescence-based liposome leakage assay, we found that both the N- and C-terminal arms were required for membrane disruption. Moreover, we found that, upon acidification, EsxA converted into a more organized structure with increased α-helical content, which was evidenced by CD analysis and intrinsic tryptophan fluorescence. Finally, using an environmentally sensitive fluorescent dye, we obtained direct evidence that the central helix-turn-helix motif of EsxA inserted into the membranes and formed a membrane-spanning pore. A model of EsxA membrane insertion is proposed and discussed. PMID:25645924

  18. Localized control of the orbit in the RHIC insertions

    SciTech Connect

    Ohnuma, S.

    1992-08-01

    It is proposed here that, for RHIC92 insertions, we remove the corrector from Ql and the beam position monitor (BPM) from Q2 in order to alleviate difficulties associated with the physical layout of the quadrupole triplet (Ql-Q2-Q3). Furthermore, it is suggested that there should be both (horizontal and vertical) types of BPMs at each end of the free space between Q3 and Q4 and between Q7 and Q8 so that one can measure the direction of the closed orbit. With this model, a localized control of the beam position and angle at the interaction point (IP) with either four or six correctors has been investigated. Similarly, a control of the orbit within an insertion for minimizing the orbit displacements at seven (or eight) BPM locations with nine (or ten) correctors in each transverse direction has been studied. Examples are given for the beta at IP = 2m, 10m, 20m, and 200m. It is shown that the design value of the integrated field strength of 0.3 T-m for each corrector should be sufficient for the tasks considered here except for some cases with extreme parameter values. At the same time, it is emphasized that the overall correction of the closed orbit for the entire ring (arcs and insertions) should be re-examined for RHIC92 lattice with the proposed arrangement of correctors and BPMS.

  19. Retroviral gene insertion in breast milk mediated lymphomagenesis.

    PubMed

    Chakraborty, Joana; Okonta, Henry; Bagalb, Hussein; Lee, Soon Jin; Fink, Brian; Changanamkandat, Rajesh; Duggan, Joan

    2008-07-20

    We have demonstrated breast milk transmitted MoMuLV-ts1 retrovirus infection and subsequent lymphoma development in offspring of uninfected mothers suckled by infected surrogate mothers. Additionally, we have shown that the lymphoma development occurs as a result of viral gene integration into host genome. A total of 146 pups from Balb/C mice were divided into 5 groups; one control and 4 experimental. All offspring suckled from surrogate infected or control mothers, except one group of infected pups left with their biological mothers. Thirteen of 91 infected pups developed lymphoma. Inverse-PCR, DNA cloning, and quantitative real-time PCR (qRT-PCR) were used to study the virus integration sites (VIS) and alterations in gene expression. VIS were randomly distributed throughout the genome. The majority of insertion sites were found in chromosomes 10, 12 and 13. A total of 209 proviral genomic insertion sites were located with 52 intragenic and 157 intergenic sites. We have identified 29 target genes. Four genes including Tacc3, Aurka, Gfi1 and Ahi1 showed the maximum upregulation of mRNA expression. These four genes can be considered as candidate genes based on their association with cancer. Upregulation of these genes may be involved in this type of lymphoma development. This model provides an important opportunity to gain insight into the relationship of viral gene insertion into host genome and development of lymphoma via natural transmission route such as breast milk. PMID:18501945

  20. Effects of Tools Inserted through Snake-like Surgical Manipulators

    PubMed Central

    Murphy, Ryan J.; Otake, Yoshito; Wolfe, Kevin C.; Taylor, Russell H.; Armand, Mehran

    2015-01-01

    Snake-like manipulators with a large, open lumen can offer improved treatment alternatives for minimally- and less-invasive surgeries. In these procedures, surgeons use the manipulator to introduce and control flexible tools in the surgical environment. This paper describes a predictive algorithm for estimating manipulator configuration given tip position for nonconstant curvature, cable-driven manipulators using energy minimization. During experimental bending of the manipulator with and without a tool inserted in its lumen, images were recorded from an overhead camera in conjunction with actuation cable tension and length. To investigate the accuracy, the estimated manipulator configuration from the model and the ground-truth configuration measured from the image were compared. Additional analysis focused on the response differences for the manipulator with and without a tool inserted through the lumen. Results indicate that the energy minimization model predicts manipulator configuration with an error of 0.24 ± 0.22mm without tools in the lumen and 0.24 ± 0.19mm with tools in the lumen (no significant difference, p = 0.81). Moreover, tools did not introduce noticeable perturbations in the manipulator trajectory; however, there was an increase in requisite force required to reach a configuration. These results support the use of the proposed estimation method for calculating the shape of the manipulator with an tool inserted in its lumen when an accuracy range of at least 1mm is required. PMID:25571571

  1. A medical simulator for subcutaneous contraceptive implant insertion.

    PubMed

    Jardin, A; Pham, M T; Mallet, A; Redarce, T; Dupuis, O

    2008-11-01

    New contraceptive methods like the subcutaneous implant offers a new kind of comfort for women with an efficiency similar to the contraceptive pill. Unfortunately the few numbers of unintended pregnancies that have been reported are generally due to a bad insertion of the implant. In order to give more security to patients, we have designed, in close collaboration with physicians, a new kind of medical simulator. This paper focuses on a device dedicated to a specific subcutaneous implant but it is worth noting that this simulator is relatively generic since it will be used for other subcutaneous techniques or other implant instruments. This simulator can be used for two purposes: one for training novice physicians in the correct manipulation and the other for physician certification which will help determine if they are capable of inserting the implant in vivo. This paper describes the approach which has led to the design of this simulator. It describes its functionalities, its several components but also methods used to analyze the manipulation of the implant insertion inside the patient. Finally first experimental results are reported and discussed. The system used in this paper makes possible to carry out training in a constraint-free context and provides the first mean of visualizing a maneuver that, until now, has been performed blindly. PMID:18417413

  2. Catch basin inserts to reduce pollution from stormwater.

    PubMed

    Lau, S L; Khan, E; Stenstrom, M K

    2001-01-01

    Stormwater contamination represents the largest source of contaminants to many receiving waters in the United States, such as Santa Monica Bay in Los Angeles, California. Point sources to these same waters generally receive secondary or better treatment before they are released, and they are usually discharged through outfalls that diffuse the wastewater plume to prevent it from contacting the shoreline. Stormwaters receive no treatment and reach the receiving waters through a variety of ways, but most enter through catch basins or inserts to storm drains that terminate at the beach or in shallow coastal areas. Under these conditions, the stormwater discharge may have greater impact on the quality and utility of the receiving water than the treated wastewater discharges. One method of reducing pollution is to equip catch basins with an insert that can capture pollutants. A number of commercially available devices exist but few have been evaluated by independent parties in full-scale applications. A series of tests using bench and full-scale devices under both laboratory and field conditions were conducted to evaluate their ability to remove trash and debris, suspended solids and oil and grease in stormwaters. The results presented in the paper should provide a basis for future insert development and application. PMID:11724491

  3. Development of Needle Insertion Manipulator for Central Venous Catheterization

    NASA Astrophysics Data System (ADS)

    Kobayashi, Yo; Hong, Jaesung; Hamano, Ryutaro; Hashizume, Makoto; Okada, Kaoru; Fujie, Masakatsu G.

    Central venous catheterization is a procedure, which a doctor insert a catheter into the patient’s vein for transfusion. Since there are risks of bleeding from arterial puncture or pneumothorax from pleural puncture. Physicians are strictly required to make needle reach up into the vein and to stop the needle in the middle of vein. We proposed a robot system for assisting the venous puncture, which can relieve the difficulties in conventional procedure, and the risks of complication. This paper reports the design structuring and experimental results of needle insertion manipulator. First, we investigated the relationship between insertion force and angle into the vein. The results indicated that the judgment of perforation using the reaction force is possible in case where the needling angle is from 10 to 20 degree. The experiment to evaluate accuracy of the robot also revealed that it has beyond 0.5 mm accuracy. We also evaluated the positioning accuracy in the ultrasound images. The results displays that the accuracy is beyond 1.0 mm and it has enough for venous puncture. We also carried out the venous puncture experiment to the phantom and confirm our manipulator realized to make needle reach up into the vein.

  4. Thermodynamic study of benzocaine insertion into different lipid bilayers

    NASA Astrophysics Data System (ADS)

    Cascales, J. J. López; Costa, S. D. Oliveira; Porasso, R. D.

    2011-10-01

    Despite the general consensus concerning the role played by sodium channels in the molecular mechanism of local anesthetics, the potency of anaesthetic drugs also seems to be related with their solubility in lipid bilayers. In this respect, this work represents a thermodynamic study of benzocaine insertion into lipid bilayers of different compositions by means of molecular dynamics simulation. Thus, the free energy profiles associated with benzocaine insertion into symmetric lipid bilayers composed of different proportions of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine were studied. From the simulation results, a maximum in the free energy (ΔG) profile was measured in the region of the lipid/solution interface. This free energy barrier appears to be very much dependent on the lipid composition of the membrane. On the other hand, the minimum free energy (ΔG) within the bilayer remained almost independent of the lipid composition of the bilayer. By repeating the study at different temperatures, it was seen how the spontaneity of benzocaine insertion into the lipid bilayer is due to an increase in the entropy associated with the process.

  5. Enzymatic functionalization of a nanobody using protein insertion technology.

    PubMed

    Crasson, O; Rhazi, N; Jacquin, O; Freichels, A; Jérôme, C; Ruth, N; Galleni, M; Filée, P; Vandevenne, M

    2015-10-01

    Antibody-based products constitute one of the most attractive biological molecules for diagnostic, medical imagery and therapeutic purposes with very few side effects. Their development has become a major priority of biotech and pharmaceutical industries. Recently, a growing number of modified antibody-based products have emerged including fragments, multi-specific and conjugate antibodies. In this study, using protein engineering, we have functionalized the anti-hen egg-white lysozyme (HEWL) camelid VHH antibody fragment (cAb-Lys3), by insertion into a solvent-exposed loop of the Bacillus licheniformis β-lactamase BlaP. We showed that the generated hybrid protein conserved its enzymatic activity while the displayed nanobody retains its ability to inhibit HEWL with a nanomolar affinity range. Then, we successfully implemented the functionalized cAb-Lys3 in enzyme-linked immunosorbent assay, potentiometric biosensor and drug screening assays. The hybrid protein was also expressed on the surface of phage particles and, in this context, was able to interact specifically with HEWL while the β-lactamase activity was used to monitor phage interactions. Finally, using thrombin-cleavage sites surrounding the permissive insertion site in the β-lactamase, we reported an expression system in which the nanobody can be easily separated from its carrier protein. Altogether, our study shows that insertion into the BlaP β-lactamase constitutes a suitable technology to functionalize nanobodies and allows the creation of versatile tools that can be used in innovative biotechnological assays. PMID:25852149

  6. Optimising daytime deliveries when inducing labour using prostaglandin vaginal inserts

    PubMed Central

    Miller, Hugh; Goetzl, Laura; Wing, Deborah A.; Powers, Barbara; Rugarn, Olof

    2016-01-01

    Abstract Objective: To determine induction start time(s) that would maximise daytime deliveries when using prostaglandin vaginal inserts. Methods: Women enrolled into the Phase III trial, EXPEDITE (clinical trial registration: NCT01127581), had labour induced with either a misoprostol or dinoprostone vaginal insert (MVI or DVI). A secondary analysis was conducted to determine the optimal start times for induction by identifying the 12-h period with the highest proportion of deliveries by parity and treatment. Results: Optimal start times for achieving daytime deliveries when using MVI appear to be 19:00 in nulliparae and 23:00 in multiparae. Applying these start times, the median time of onset of active labour would be approximately 08:30 for both parities and the median time of delivery would be the following day at approximately 16:30 for nulliparae and 12:00 (midday) for multiparae. Optimal start times when using DVI appear to be 07:00 for nulliparae and 23:00 for multiparae. Using these start times, the median time of onset of active labour would be the following day at approximately 04:00 and 11:50, and the median time of delivery would be approximately 13:40 and 16:10, respectively. Conclusions: When optimising daytime deliveries, different times to initiate induction of labour may be appropriate depending on parity and the type of retrievable prostaglandin vaginal insert used. PMID:25758619

  7. Internal carotid artery rupture caused by carotid shunt insertion

    PubMed Central

    Illuminati, Giulio; Caliò, Francesco G.; Pizzardi, Giulia; Vietri, Francesco

    2015-01-01

    Introduction Shunting is a well-accepted method of maintaining cerebral perfusion during carotid endarterectomy (CEA). Nonetheless, shunt insertion may lead to complications including arterial dissection, embolization, and thrombosis. We present a complication of shunt insertion consisting of arterial wall rupture, not reported previously. Presentation of case A 78-year-old woman underwent CEA combined with coronary artery bypass grafting (CABG). At the time of shunt insertion an arterial rupture at the distal tip of the shunt was detected and was repaired via a small saphenous vein patch. Eversion CEA and subsequent CABG completed the procedure whose postoperative course was uneventful. Discussion Shunting during combined CEA-CABG may be advisable to assure cerebral protection from possible hypoperfusion due to potential hemodynamic instability of patients with severe coronary artery disease. Awareness and prompt management of possible shunt-related complications, including the newly reported one, may contribute to limiting their harmful effect. Conclusion Arterial wall rupture is a possible, previously not reported, shunt-related complication to be aware of when performing CEA. PMID:26255001

  8. Local Dispersion Insert: The {gamma}T knob for accelerators

    SciTech Connect

    Visnjic, V.

    1994-05-01

    The Local Dispersion Insert is a novel three-quadrupole cell which produces local dispersion and beta waves while leaving all other beam parameters unchanged. The obtained dispersion bump can be effectively used to control the transition energy and the so-called {gamma}T jump of an accelerator. Since the induced beta wave is local and the tune shift is zero, the Local Dispersion Insert is an extremely efficient cell, typically requiring only a small number of magnets in order to achieve a {gamma}T jump. Since the desired {gamma}T jump can be obtained by locally decreasing the dispersion, the well known problems which accompany the conventional {gamma}T jump schemes, like large maximal dispersion, transverse emittance growth etc. are absent. The paper contains three applications of the Local Dispersion Insert: the {gamma}T jump in the Main Injector, the {eta} adjustment in the Antiproton Debuncher (both at Fermi National Accelerator Laboratory), and the {gamma}T jump in the Relativistic Heavy Ion Collider at Brookhaven National Laboratory.

  9. A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation1[W][OA

    PubMed Central

    Pislariu, Catalina I.; D. Murray, Jeremy; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; A. Benedito, Vagner; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E.; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Chen, Rujin; Udvardi, Michael K.

    2012-01-01

    A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging. PMID:22679222

  10. Behavior of diphtheria toxin T domain containing substitutions that block normal membrane insertion at Pro345 and Leu307: control of deep membrane insertion and coupling between deep insertion of hydrophobic subdomains.

    PubMed

    Zhao, Gang; London, Erwin

    2005-03-22

    Diphtheria toxin T domain aids the translocation of toxin A chain across membranes. T domain has two hydrophobic layers/subdomains that can insert deeply into membranes: helices TH8 and 9, which form a transmembrane hairpin, and helices TH5-7, which form a nonclassical, nontransmembrane structure. Substitutions were made at Pro345, a residue located near the turn between TH8 and 9. P345 is critical for toxicity and pore formation by the T domain. Fluorescence methods showed that hairpin-disrupting Gly or Glu substitutions at 345 did not insert into lipid bilayers as deeply as the wild-type protein, and consistent with previous studies, these mutations reduced pore formation activity as assayed by a novel biotin-streptavidin-based influx assay. Introducing Pro at positions 347 or 353 not only failed to compensate for substitutions at P345, but also they further disrupted deep insertion and/or pore formation. Substitution of P345 with Asn, a residue that promotes helical hairpin formation almost as well as Pro, resulted in somewhat more normal insertion and pore formation than other substitutions. Importantly, a P345E substitution disrupted deep insertion of TH5-7. This suggests that TH8 and 9 and TH5-7 undergo some sort of coordinated insertion into the lipid bilayer and/or that the membrane-inserted T domain has a distinct tertiary structure in which TH5-7 interact with TH8 and 9 instead of consisting of noninteracting hydrophobic segments. Intriguingly, a L307R substitution in TH6, which disrupted deep insertion of TH7, had only a weak effect on pore formation and deep insertion of TH8 and 9. This suggests that the TH8 and 9 region can insert independently of TH5-7 to some degree and that TH8 and 9 insertion may occur early in T-domain insertion. PMID:15766279

  11. Tools for Targeted Genome Engineering of Established Drosophila Cell Lines

    PubMed Central

    Cherbas, Lucy; Hackney, Jennifer; Gong, Lei; Salzer, Claire; Mauser, Eric; Zhang, Dayu; Cherbas, Peter

    2015-01-01

    We describe an adaptation of φC31 integrase–mediated targeted cassette exchange for use in Drosophila cell lines. Single copies of an attP-bounded docking platform carrying a GFP-expression marker, with or without insulator elements flanking the attP sites, were inserted by P-element transformation into the Kc167 and Sg4 cell lines; each of the resulting docking-site lines carries a single mapped copy of one of the docking platforms. Vectors for targeted substitution contain a cloning cassette flanked by attB sites. Targeted substitution occurs by integrase-mediated substitution between the attP sites (integrated) and the attB sites (vector). We describe procedures for isolating cells carrying the substitutions and for eliminating the products of secondary off-target events. We demonstrate the technology by integrating a cassette containing a Cu2+-inducible mCherry marker, and we report the expression properties of those lines. When compared with clonal lines made by traditional transformation methods, which lead to the illegitimate insertion of tandem arrays, targeted insertion lines give more uniform expression, lower basal expression, and higher induction ratios. Targeted substitution, though intricate, affords results that should greatly improve comparative expression assays—a major emphasis of cell-based studies. PMID:26450921

  12. Tools for Targeted Genome Engineering of Established Drosophila Cell Lines.

    PubMed

    Cherbas, Lucy; Hackney, Jennifer; Gong, Lei; Salzer, Claire; Mauser, Eric; Zhang, Dayu; Cherbas, Peter

    2015-12-01

    We describe an adaptation of ?C31 integrase-mediated targeted cassette exchange for use in Drosophila cell lines. Single copies of an attP-bounded docking platform carrying a GFP-expression marker, with or without insulator elements flanking the attP sites, were inserted by P-element transformation into the Kc167 and Sg4 cell lines; each of the resulting docking-site lines carries a single mapped copy of one of the docking platforms. Vectors for targeted substitution contain a cloning cassette flanked by attB sites. Targeted substitution occurs by integrase-mediated substitution between the attP sites (integrated) and the attB sites (vector). We describe procedures for isolating cells carrying the substitutions and for eliminating the products of secondary off-target events. We demonstrate the technology by integrating a cassette containing a Cu(2+)-inducible mCherry marker, and we report the expression properties of those lines. When compared with clonal lines made by traditional transformation methods, which lead to the illegitimate insertion of tandem arrays, targeted insertion lines give more uniform expression, lower basal expression, and higher induction ratios. Targeted substitution, though intricate, affords results that should greatly improve comparative expression assays-a major emphasis of cell-based studies. PMID:26450921

  13. Stable transcription activities dependent on an orientation of Tam3 transposon insertions into Antirrhinum and yeast promoters occur only within chromatin.

    PubMed

    Uchiyama, Takako; Fujino, Kaien; Ogawa, Takashi; Wakatsuki, Akihito; Kishima, Yuji; Mikami, Tetsuo; Sano, Yoshio

    2009-11-01

    Transposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivea(recurrensTam3) (niv(rec)) and pallida(recurrensTam3) (pal(rec)), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the niv(rec) line produces pale red petals, whereas the pal(rec) line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the niv(rec) or pal(rec) alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In niv(rec), Tam3 is inserted in an orientation that results in the 3' end of Tam3 adjacent to the 5' region of the gene coding sequence. In contrast, the pal(rec) allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as niv(rec). The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin. PMID:19759347

  14. Method for reducing x-ray background signals from insertion device x-ray beam position monitors

    NASA Astrophysics Data System (ADS)

    Decker, Glenn; Singh, Om

    1999-11-01

    A method is described that provides a solution to the long-standing problem of stray radiation-induced signals on photoemission-based x-ray beam position monitors (BPMs) located on insertion device x-ray beam lines. The method involves the introduction of a chicane into the accelerator lattice that directs unwanted x radiation away from the photosensitive x-ray BPM blades. This technique has been implemented at the Advanced Photon Source, and experimental confirmation of the technique is provided.

  15. Investigation Of Plasma Discharges Within Maja-PF Device Operated With Tungsten Inserts In The Central Electrode

    SciTech Connect

    Malinowski, K.; Skladnik-Sadowska, E.; Jakubowski, L.; Sadowski, M. J.; Ladygina, M.

    2008-03-19

    The paper presents results of recent experimental studies with a MAJA-PF plasma-focus facility, as carried out for two different configurations of the end-plate of the central electrode. The main aim was to investigate an influence of the shape and material of the electrode end-plate on the formation and structure of the plasma column as well as to record and identify spectral lines of tungsten. The first version of the end-plate was made of Cu, while the second one had an insert made of a Cu-W alloy. Optical spectra were recorded by means of a Mechelle 900 spectrometer, operated with some delay in relation to a current peculiarity and with exposition times varied from 200 ns to 10 {mu}s. For shots with the Cu electrode spectral lines of deuterium (working gas) and carbon ions were recorded, but tungsten lines were not identified. It was estimated that the electron concentration changed from (8 divide 10)x10{sup 17} cm{sup -3} to about 2x10{sup 17} cm{sup -3} in 5 {mu}s after the current dip. In experiments with the second electrode version, among numerous spectral lines there were identified distinct WI and WII lines. Estimates of the tungsten ion concentration were impossible because of close positions of other lines. Diagrams of changes in the electron density are of importance for applications of DPM streams.

  16. Investigation Of Plasma Discharges Within Maja-PF Device Operated With Tungsten Inserts In The Central Electrode

    NASA Astrophysics Data System (ADS)

    Malinowski, K.; Skladnik-Sadowska, E.; Ladygina, M.; Jakubowski, L.; Sadowski, M. J.

    2008-03-01

    The paper presents results of recent experimental studies with a MAJA-PF plasma-focus facility, as carried out for two different configurations of the end-plate of the central electrode. The main aim was to investigate an influence of the shape and material of the electrode end-plate on the formation and structure of the plasma column as well as to record and identify spectral lines of tungsten. The first version of the end-plate was made of Cu, while the second one had an insert made of a Cu-W alloy. Optical spectra were recorded by means of a Mechelle®900 spectrometer, operated with some delay in relation to a current peculiarity and with exposition times varied from 200 ns to 10 μs. For shots with the Cu electrode spectral lines of deuterium (working gas) and carbon ions were recorded, but tungsten lines were not identified. It was estimated that the electron concentration changed from (8÷10)×1017 cm-3 to about 2×1017 cm-3 in 5 μs after the current dip. In experiments with the second electrode version, among numerous spectral lines there were identified distinct WI and WII lines. Estimates of the tungsten ion concentration were impossible because of close positions of other lines. Diagrams of changes in the electron density are of importance for applications of DPM streams.

  17. Efficient Merge and Insert Operations for Binary Heaps and Trees

    NASA Technical Reports Server (NTRS)

    Kuszmaul, Christopher Lee; Woo, Alex C. (Technical Monitor)

    2000-01-01

    Binary heaps and binary search trees merge efficiently. We introduce a new amortized analysis that allows us to prove the cost of merging either binary heaps or balanced binary trees is O(l), in the amortized sense. The standard set of other operations (create, insert, delete, extract minimum, in the case of binary heaps, and balanced binary trees, as well as a search operation for balanced binary trees) remain with a cost of O(log n). For binary heaps implemented as arrays, we show a new merge algorithm that has a single operation cost for merging two heaps, a and b, of O(absolute value of a + min(log absolute value of b log log absolute value of b. log absolute value of a log absolute value of b). This is an improvement over O(absolute value of a + log absolute value of a log absolute value of b). The cost of the new merge is so low that it can be used in a new structure which we call shadow heaps. to implement the insert operation to a tunable efficiency. Shadow heaps support the insert operation for simple priority queues in an amortized time of O(f(n)) and other operations in time O((log n log log n)/f (n)), where 1 less than or equal to f (n) less than or equal to log log n. More generally, the results here show that any data structure with operations that change its size by at most one, with the exception of a merge (aka meld) operation, can efficiently amortize the cost of the merge under conditions that are true for most implementations of binary heaps and search trees.

  18. Complications associated with different insertion techniques for Hickman catheters.

    PubMed

    Ahmed, Z; Mohyuddin, Z

    1998-02-01

    A dependable central venous access is an essential prerequisite for the delivery of care to the cancer patients. This has become easier since the introduction of indwelling central venous catheters. However, pancytopenia, often encountered in haematological malignancies, does influence the morbidity associated with these catheters. In this study the effects of two different placement techniques of Hickman catheters were evaluated. A total of 177 Hickman catheters were inserted in patients suffering from haematological malignancies. In 112 patients the catheters were placed percutaneously into subclavian veins without prior tunnelling; in the other 65 patients these were introduced, after having been tunnelled, into cephalic/external jugular veins by a cut-down technique. The catheters remained in use in each patient for between 18 and 253 days. Excessive bleeding and haematoma formation occurred in a significantly higher proportion of patients from the cut-down group (61% and 41%, respectively) compared to patients from the percutaneous group (8% and 0%, respectively). These in turn had a profound impact on the incidence of infective complications. Catheter exit site infection, tunnel infection and septicaemia were observed in 26%, 18%, and 41%, respectively, of the patients from the cut-down group, while in patients from the percutaneous group, skin exit site infection was noted only in 7% and septicaemia in 19% of patients. It was concluded that the placement technique of these catheters exerts a significant influence on the immediate as well as delayed complications. The results indicate that the insertion technique requiring minimal dissection is more beneficial. It is therefore recommended that percutaneous insertion without tunnelling should be the technique of choice for catheter placement. PMID:9616492

  19. The endogenous ecotropic murine retroviruses Emv-16 and Emv-17 are both capable of producing new proviral insertions in the mouse genome.

    PubMed

    Szabo, C; Kim, Y K; Mark, W H

    1993-09-01

    New germ line proviral insertions are acquired at a high frequency by the progeny of SWR/J-RF/J hybrid female mice that carry the endogenous ecotropic murine leukemia proviruses Emv-16 and Emv-17. The tight linkage of these RF/J strain proviral loci has prevented genetic segregation of the retroviral genomes. Hence, it is not known whether both of these proviruses are capable of giving rise to new proviral insertions. We have molecularly cloned Emv-16 and Emv-17 and have characterized them in vitro and in vivo. Restriction enzyme analysis of the recombinant clones revealed that the proviral genomes are very similar to each other and closely resemble the wild-type AKR virus. A comparison of the flanking cellular DNA suggests that the Emv-16 and Emv-17 loci did not arise by simple duplication of a viral insertion site within the RF/J genome but most likely are independent integration events. Both proviruses produce infectious virus when transfected into NIH 3T3 cells, indicating that they are nondefective retroviruses. Exogenous infection of SWR/J mice with either Emv-16 or Emv-17 leads to viremia in the host animals, and in both cases, progeny of viremic females acquire new proviral insertions. The ability of these retroviruses to generate novel retroviral integration sites in the mouse genome provides a simple method for inducing insertional mutations in mice. PMID:8394469

  20. Insertion mechanism and stability of boron nitride nanotubes in lipid bilayers.

    PubMed

    Thomas, Michael; Enciso, Marta; Hilder, Tamsyn A

    2015-04-16

    We provide insight into the interaction of boron nitride nanotubes (BNNTs) with cell membranes to better understand their improved biocompatibility compared to carbon nanotubes (CNTs). Contrary to CNTs, no computational studies exist investigating the insertion mechanism and stability of BNNTs in membranes. Our molecular dynamics simulations demonstrate that BNNTs are spontaneously attracted to lipid bilayers and are stable once inserted. They insert via a lipid-mediated, passive insertion mechanism. BNNTs demonstrate similar characteristics to more biocompatible functionalized CNTs. PMID:25800058

  1. Pediatric Enteric Feeding Techniques: Insertion, Maintenance, and Management of Problems

    SciTech Connect

    Nijs, Els L. F.; Cahill, Anne Marie

    2010-12-15

    Enteral feeding is considered a widespread, well-accepted means of delivering nutrition to adults and children who are unable to consume food by mouth or who need support in maintaining adequate nutrition for a variety of reasons, including acute and chronic disease states. Delivery of enteral feeding to nutritionally deprived patients may be achieved by several means. In this article, the indications and insertion of enteral access in children will be reviewed. In addition, common complications and management of problems will be discussed.

  2. Bone Scanning in the Adductor Insertion Avulsion Syndrome

    PubMed Central

    Mahajan, Madhuri Shimpi

    2013-01-01

    A thigh splint (adductor insertion avulsion syndrome) is a relatively uncommon diagnosis analogous to shin splints. This article reports a 19-year-old female patient NOT a regular athlete who presented with groin pain. Physical examination was non-specific; magnetic resonance imaging pelvis did not reveal any abnormality. Patient referred for whole body bone scan, especially to locate any abnormality in the spine. This study highlights the role of whole body bone scan in the evaluation of groin pain and importance of evaluation of whole lower extremity. PMID:25126001

  3. Modification of commercial force feedback hardware for needle insertion simulation.

    PubMed

    Coles, Timothy R; John, Nigel W; Sofia, Giuseppe; Gould, Derek A; Caldwell, Darwin G

    2011-01-01

    A SensAble Omni force feedback device has been modified to increase the face validity of a needle insertion simulation. The new end effector uses a real needle hub and shortened needle shaft in place of the Omni's pre-fitted pen shaped end effector. This modification facilitates correct procedural training through the simulation of co-located visual and haptic cues in an augmented reality approach to simulation. The development of the new end effector is described and a pictorial guide to its manufacture and the fitting process is provided. Initial results from face validation studies bode well for the fidelity of this low cost device. PMID:21335776

  4. Development and testing of the rack insertion device

    NASA Technical Reports Server (NTRS)

    Strickland, G. Scott

    1995-01-01

    Installing and removing experiment racks in a Space Station Logistics Module will become a repetitive operation at Kennedy Space Center (KSC) in the near future. A Rack Insertion Device (RID) consisting of an Extendible Boom, End Effector, and Positioning Base is being developed for the task. This paper discusses the key elements of the RlD's function and design. Prototype test results for the RlD's Extendible Boom and End Effector are presented. Also discussed are future end effectors that will further enhance the RlD's Space Station processing capability.

  5. A new gap separation mechanism for APS insertion devices.

    SciTech Connect

    Trakhtenberg, E. M.; Tcheskidov, V.; Den Hartog, P. K.; Deriy, B.; Erdmann, M.; Makarov, O.; Moog, E. R.

    1999-10-25

    A new gap separation mechanism for use with the standard Advanced Photon Source (APS) 3.3-cm-period undulator magnetic structures has been designed and built and the first system has been installed in the APS storage ring. The system allows a minimum magnetic gap of 10 mm for use with the APS 8-mm insertion device vacuum chambers. The mechanism is a bolted steel frame structure with a simple 4-motor mechanical drive train. The control system uses servomotors with incremental rotary encoders and virtual absolute linear encoders.

  6. ARTEMIS Lunar Orbit Insertion and Science Orbit Design Through 2013

    NASA Technical Reports Server (NTRS)

    Broschart, Stephen B.; Sweetser, Theodore H.; Angelopoulos, Vassilis; Folta, David; Woodard, Mark

    2015-01-01

    As of late-July 2011, the ARTEMIS mission is transferring two spacecraft from Lissajous orbits around Earth-Moon Lagrange Point #1 into highly-eccentric lunar science orbits. This paper presents the trajectory design for the transfer from Lissajous orbit to lunar orbit insertion, the period reduction maneuvers, and the science orbits through 2013. The design accommodates large perturbations from Earth's gravity and restrictive spacecraft capabilities to enable opportunities for a range of heliophysics and planetary science measurements. The process used to design the highly-eccentric ARTEMIS science orbits is outlined. The approach may inform the design of future planetary moon missions.

  7. Re-visiting the trans insertion model for complexin clamping.

    PubMed

    Krishnakumar, Shyam S; Li, Feng; Coleman, Jeff; Schauder, Curtis M; Kümmel, Daniel; Pincet, Frederic; Rothman, James E; Reinisch, Karin M

    2015-01-01

    We have previously proposed that complexin cross-links multiple pre-fusion SNARE complexes via a trans interaction to function as a clamp on SNARE-mediated neurotransmitter release. A recent NMR study was unable to detect the trans clamping interaction of complexin and therefore questioned the previous interpretation of the fluorescence resonance energy transfer and isothermal titration calorimetry data on which the trans clamping model was originally based. Here we present new biochemical data that underscore the validity of our previous interpretation and the continued relevancy of the trans insertion model for complexin clamping. PMID:25831964

  8. Fiber to polymer-waveguide coupling with low insertion loss

    NASA Astrophysics Data System (ADS)

    Rashidi, A.; Gharavi, R.; Gharavi, A.

    2015-04-01

    Low-loss coupling of optical fiber to a polymer waveguide was demonstrated using a V-groove on a silicon substrate. The waveguide was fabricated directly on the silicon substrate using a direct writing technique. The fiber was mounted in a V-groove on a SiO2-coated silicon substrate, and then the azo polymer was coated onto the substrate and cured at 200 °C. Finally a waveguide was ‘written’ precisely aligned with the fiber’s output tip. The insertion loss was measured to be about 1.1 dB.

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

    PubMed Central

    2011-01-01

    A method was developed to identify insertional mutants of Chlamydomonas reinhardtii disrupted for selected target genes. The approach relies on the generation of thousands of transformants followed by PCR-based screenings that allow for identification of strains harboring the introduced marker gene within specific genes of interest. Our results highlight the strengths and limitations of two independent screens that differed in the nature of the marker DNA used (PCR-amplified fragment containing the plasmid-free marker versus entire linearized plasmid with the marker) and in the strategies used to maintain and store transformants. PMID:21794168

  10. Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH) program

    NASA Technical Reports Server (NTRS)

    Fayette, Daniel F.; Speicher, Patricia; Stoklosa, Mark J.; Evans, Jillian V.; Evans, John W.; Gentile, Mike; Pagel, Chuck A.; Hakim, Edward

    1993-01-01

    A joint military-commercial effort to evaluate multichip module (MCM) structures is discussed. The program, Reliability Technology to Achieve Insertion of Advanced Packaging (RELTECH), has been designed to identify the failure mechanisms that are possible in MCM structures. The RELTECH test vehicles, technical assessment task, product evaluation plan, reliability modeling task, accelerated and environmental testing, and post-test physical analysis and failure analysis are described. The information obtained through RELTECH can be used to address standardization issues, through development of cost effective qualification and appropriate screening criteria, for inclusion into a commercial specification and the MIL-H-38534 general specification for hybrid microcircuits.

  11. Characterization and event specific-detection by quantitative real-time PCR of T25 maize insert.

    PubMed

    Collonnier, Cécile; Schattner, Alexandra; Berthier, Georges; Boyer, Francine; Coué-Philippe, Géraldine; Diolez, Annick; Duplan, Marie-Noëlle; Fernandez, Sophie; Kebdani, Naïma; Kobilinsky, André; Romaniuk, Marcel; de Beuckeleer, Marc; de Loose, Marc; Windels, Pieter; Bertheau, Yves

    2005-01-01

    T25 is one of the 4 maize transformation events from which commercial lines have so far been authorized in Europe. It was created by polyethylene glycol-mediated transformation using a construct bearing one copy of the synthetic pat gene associated with both promoter and terminator of the 35S ribosomal gene from cauliflower mosaic virus. In this article, we report the sequencing of the whole T25 insert and the characterization of its integration site by using a genome walking strategy. Our results confirmed that one intact copy of the initial construct had been integrated in the plant genome. They also revealed, at the 5' junction of the insert, the presence of a second truncated 35S promoter, probably resulting from rearrangements which may have occurred before or during integration of the plasmid DNA. The analysis of the junction fragments showed that the integration site of the insert presented high homologies with the Huck retrotransposon family. By using one primer annealing in the maize genome and the other in the 5' end of the integrated DNA, we developed a reliable event-specific detection system for T25 maize. To provide means to comply with the European regulation, a real-time PCR test was designed for specific quantitation of T25 event by using Taqman chemistry. PMID:15859082

  12. 21 CFR 872.3900 - Posterior artificial tooth with a metal insert.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Posterior artificial tooth with a metal insert... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3900 Posterior artificial tooth with a metal insert. (a) Identification. A posterior artificial tooth with a metal insert is...

  13. 21 CFR 872.3900 - Posterior artificial tooth with a metal insert.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Posterior artificial tooth with a metal insert... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3900 Posterior artificial tooth with a metal insert. (a) Identification. A posterior artificial tooth with a metal insert is...

  14. 21 CFR 872.3900 - Posterior artificial tooth with a metal insert.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Posterior artificial tooth with a metal insert... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3900 Posterior artificial tooth with a metal insert. (a) Identification. A posterior artificial tooth with a metal insert is...

  15. 21 CFR 872.3900 - Posterior artificial tooth with a metal insert.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Posterior artificial tooth with a metal insert... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3900 Posterior artificial tooth with a metal insert. (a) Identification. A posterior artificial tooth with a metal insert is...

  16. 21 CFR 872.3900 - Posterior artificial tooth with a metal insert.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Posterior artificial tooth with a metal insert... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Prosthetic Devices § 872.3900 Posterior artificial tooth with a metal insert. (a) Identification. A posterior artificial tooth with a metal insert is...

  17. Cholecystoduodenal fistula: A complication of inserted self-expandable metallic bilitary stents

    SciTech Connect

    Nishida, Hirotoshi; Inoue, Hiroki; Ueno, Kazuto; Nagata, Yukitaka; Kato, Takeshi; Miyazono, Nobuaki; Nakajo, Masayuki

    1998-05-15

    We encountered a case of hepatic hilar cholangiocarcinoma resulting in cholecystoduodenal fistula after insertion of self-expandable metallic biliary stents (EMBSs). To our knowledge, there has been no report of cholecystoduodenal fistula after insertion of EMBSs. This case suggests that immediate gallbladder decompression may be necessary if acute cholecystitis occurs after insertion of EMBSs.

  18. Cholecystoduodenal Fistula: A Complication of Inserted Self-Expandable Metallic Biliary Stents

    SciTech Connect

    Nishida, Hirotoshi; Inoue, Hiroki; Ueno, Kazuto; Nagata, Yukitaka; Kato, Takeshi; Miyazono, Nobuaki; Nakajo, Masayuki

    1998-05-15

    We encountered a case of hepatic hilar cholangiocarcinoma resulting in cholecystoduodenal fistula after insertion of self-expandable metallic biliary stents (EMBSs). To our knowledge, there has been no report of cholecystoduodenal fistula after insertion of EMBSs. This case suggests that immediate gallbladder decompression may be necessary if acute cholecystitis occurs after insertion of EMBSs.

  19. Insertable system for fast turnaround time microwave experiments in a dilution refrigerator

    NASA Astrophysics Data System (ADS)

    Ong, Florian R.; Orgiazzi, Jean-Luc; de Waard, Arlette; Frossati, Giorgio; Lupascu, Adrian

    2012-09-01

    Microwave experiments in dilution refrigerators are a central tool in the field of superconducting quantum circuits and other research areas. This type of experiments relied so far on attaching a device to the mixing chamber of a dilution refrigerator. The minimum turnaround time in this case is a few days as required by cooling down and warming up the entire refrigerator. We developed a new approach, in which a suitable sample holder is attached to a cold-insertable probe and brought in contact with transmission lines permanently mounted inside the cryostat. The total turnaround time is 8 h if the target temperature is 80 mK. The lowest attainable temperature is 30 mK. Our system can accommodate up to six transmission lines, with a measurement bandwidth tested from zero frequency to 12 GHz. This bandwidth is limited by low-pass components in the setup; we expect the intrinsic bandwidth to be at least 18 GHz. We present our setup, discuss the experimental procedure, and give examples of experiments enabled by this system. This new measurement method will have a major impact on systematic ultra-low temperature studies using microwave signals, including those requiring quantum coherence.

  20. Cervical cancer treatment with a locally insertable controlled release delivery system

    PubMed Central

    Keskar, Vandana; Mohanty, Prem S.; Gemeinhart, Ernest J.; Gemeinhart, Richard A.

    2006-01-01

    Local delivery of cancer chemotherapeutics enables sustained drug levels at the site of action thereby reducing systemic side effects. A novel insertable polymeric drug delivery system for cervical cancer treatment is presented. Cisplatin, the first line of therapy employed for cervical cancers, was incorporated in a poly(ethylene-co-vinyl acetate) (EVAc) device that is similar to those currently used for vaginal contraceptive delivery. Cisplatin crystals were uniformly dispersed in the polymeric system without undergoing significant dissolution in the polymer matrix. Cisplatin dissolution from the devices was biphasic, consistent with a matrix-type controlled-release system with an initial rapid release phase followed by a slower, linear release phase. Depending on the drug loading in the polymeric devices, the near-linear release phase varied in rate according both empirical, linear curve-fitting (0.38±0.15 μg/day to 46.9±10.0 μg/day) and diffusion analysis based upon diffusion through a porous structure (Dapp from 1.3±0.5×10−9 cm2/s to 5.8±0.3×10−12 cm2/s). The devices were tested for in vitro activity and found to be effective against both HPV positive and HPV negative cervical cancer cell lines. Preliminary studies indicate that this delivery system would be a good candidate for investigation as a choice of treatment in cervical cancers. PMID:17034891