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Sample records for intra-and intergenic recombination

  1. Recombination drives evolution of the Clostridium difficile 16S-23S rRNA intergenic spacer region.

    Science.gov (United States)

    Janezic, Sandra; Indra, Alexander; Rattei, Thomas; Weinmaier, Thomas; Rupnik, Maja

    2014-01-01

    PCR-ribotyping, a typing method based on size variation in 16S-23S rRNA intergenic spacer region (ISR), has been used widely for molecular epidemiological investigations of C. difficile infections. In the present study, we describe the sequence diversity of ISRs from 43 C. difficile strains, representing different PCR-ribotypes and suggest homologous recombination as a possible mechanism driving the evolution of 16S-23S rRNA ISRs. ISRs of 45 different lengths (ranging from 185 bp to 564 bp) were found among 458 ISRs. All ISRs could be described with one of the 22 different structural groups defined by the presence or absence of different sequence modules; tRNAAla genes and different combinations of spacers of different lengths (33 bp, 53 bp or 20 bp) and 9 bp direct repeats separating the spacers. The ISR structural group, in most cases, coincided with the sequence length. ISRs that were of the same lengths had also very similar nucleotide sequence, suggesting that ISRs were not suitable for discriminating between different strains based only on the ISR sequence. Despite large variations in the length, the alignment of ISR sequences, based on the primary sequence and secondary structure information, revealed many conserved regions which were mainly involved in maturation of pre-rRNA. Phylogenetic analysis of the ISR alignment yielded strong evidence for intra- and inter-homologous recombination which could be one of the mechanisms driving the evolution of C. difficile 16S-23S ISRs. The modular structure of the ISR, the high sequence similarities of ISRs of the same sizes and the presence of homologous recombination also suggest that different copies of C. difficile 16S-23S rRNA ISR are evolving in concert.

  2. Recombination drives evolution of the Clostridium difficile 16S-23S rRNA intergenic spacer region.

    Directory of Open Access Journals (Sweden)

    Sandra Janezic

    Full Text Available PCR-ribotyping, a typing method based on size variation in 16S-23S rRNA intergenic spacer region (ISR, has been used widely for molecular epidemiological investigations of C. difficile infections. In the present study, we describe the sequence diversity of ISRs from 43 C. difficile strains, representing different PCR-ribotypes and suggest homologous recombination as a possible mechanism driving the evolution of 16S-23S rRNA ISRs. ISRs of 45 different lengths (ranging from 185 bp to 564 bp were found among 458 ISRs. All ISRs could be described with one of the 22 different structural groups defined by the presence or absence of different sequence modules; tRNAAla genes and different combinations of spacers of different lengths (33 bp, 53 bp or 20 bp and 9 bp direct repeats separating the spacers. The ISR structural group, in most cases, coincided with the sequence length. ISRs that were of the same lengths had also very similar nucleotide sequence, suggesting that ISRs were not suitable for discriminating between different strains based only on the ISR sequence. Despite large variations in the length, the alignment of ISR sequences, based on the primary sequence and secondary structure information, revealed many conserved regions which were mainly involved in maturation of pre-rRNA. Phylogenetic analysis of the ISR alignment yielded strong evidence for intra- and inter-homologous recombination which could be one of the mechanisms driving the evolution of C. difficile 16S-23S ISRs. The modular structure of the ISR, the high sequence similarities of ISRs of the same sizes and the presence of homologous recombination also suggest that different copies of C. difficile 16S-23S rRNA ISR are evolving in concert.

  3. BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features.

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    Matthew Wohlgemuth Blair

    Full Text Available Highly polymorphic markers such as simple sequence repeats (SSRs or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES from non-contigged, non-overlapping bacterial artificial clones (BACs in common bean (Phaseolus vulgaris L.. These so called "singleton" BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

  4. The Intergenic Recombinant HLA-B*46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands

    DEFF Research Database (Denmark)

    Hilton, Hugo G.; McMurtrey, Curtis P.; Han, Alex S.

    2017-01-01

    HLA-B*46:01 was formed by an intergenic mini-conversion, between HLA-B*15:01 and HLA-C*01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA...

  5. Characterization of MHC class I in a long-distance migrant shorebird suggests multiple transcribed genes and intergenic recombination.

    Science.gov (United States)

    Buehler, Deborah M; Verkuil, Yvonne I; Tavares, Erika S; Baker, Allan J

    2013-03-01

    The major histocompatibility complex (MHC) includes highly polymorphic gene families encoding proteins crucial to the vertebrate acquired immune system. Classical MHC class I (MHCI) genes code for molecules expressed on the surfaces of most nucleated cells and are associated with defense against intracellular pathogens, such as viruses. These genes have been studied in a few wild bird species, but have not been studied in long-distance migrating shorebirds. Red Knots Calidris canutus are medium-sized, monogamous sandpipers with migratory routes that span the globe. Understanding how such long-distance migrants protect themselves from disease has gained new relevance since the emergence of avian-borne diseases, including intracellular pathogens recognized by MHCI molecules, such as avian influenza. In this study, we characterized MHCI genes in knots and found 36 alleles in eight individuals and evidence for six putatively functional and expressed MHCI genes in a single bird. We also found evidence for recombination and for positive selection at putative peptide binding sites in exons 2 and 3. These results suggest surprisingly high MHC diversity in knots, given their demographic history. This may be a result of selection from diverse pathogens encountered by shorebirds throughout their annual migrations.

  6. A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae.

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    Lisa Sanguinetti

    Full Text Available Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.

  7. Effects of the rad52 gene on recombination in Saccharomyces cerevisiae. [Comparison of. gamma. -, uv-induced meiotic and spontaneous mitotic recombination

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, S.; Prakash, L.; Burke, W.; Montelone, B.A.

    1979-01-01

    Effects of the rad52 mutation in Saccharomyces cerevisiae on meiotic, ..gamma..-ray-induced, uv-induced, and spontaneous mitotic recombination were studied. The rad52/rad52 diploids undergo premeiotic DNA synthesis; sporulation occurs but inviable spores are produced. Intra- and intergenic recombination during meiosis were examined in cells transferred from sporulation medium to vegetative medium at different time intervals. No intragenic recombination was observed at the hisl-1/hisl-315 and trp5-2/trp5-48 heteroalleles. Gene-centromere recombination was also not observed in rad52/rad52 diploids. No ..gamma..-ray-induced intragenic mitotic recombination is seen in rad52/rad52 diploids and uv-induced intragenic recombination is greatly reduced. However, spontaneous mitotic recombination is not similarly affected. The RAD52 gene thus functions in recombination in meiosis and in ..gamma..-ray and uv-induced mitotic recombination but not in spontaneous mitotic recombination.

  8. Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5' Untranslated Region.

    Science.gov (United States)

    Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

    2015-01-01

    Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species' C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5' untranslated region (5' UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5' UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5' UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5' UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5' UTR. By contrast to the recombination of the cVDPV with the 5' UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5' UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages.

  9. Determination of recombination in Mycoplasma hominis

    DEFF Research Database (Denmark)

    Jacobsen, Iben Søgaard; Boesen, Thomas; Mygind, Tina

    2002-01-01

    indicating the presence of recombination. In order to test for intergenic recombination, phylogenetic trees were reconstructed for each of the genes but no well-supported bifurcating phylogenetic trees could be obtained. The genes were tested for intragenic recombination using the correlation between linkage...

  10. Genetic Analysis of Meiotic Recombination in Schizosaccharomyces pombe

    OpenAIRE

    Smith, Gerald R.

    2009-01-01

    The fission yeast Schizosaccharomyces pombe is well-suited for studying meiotic recombination. Methods are described here for culturing S. pombe and for genetic assays of intragenic recombination (gene conversion), intergenic recombination (crossing-over), and spore viability. Both random spore and tetrad analyses are described.

  11. Intergenic and intragenic conjugal transfer of multiple antibiotic ...

    African Journals Online (AJOL)

    intragenic) in combination with sulphamethoxazole-trimethoprim (SXT), streptomycin and erythromycin as a self transposable tetracycline element. In intergenic transfer, conjugation frequency was more than intragenic transfer. Frequencies of ...

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

    African Journals Online (AJOL)

    Two microsporidian isolates extracted from infected tasar silkworms (Antheraea mylitta) collected from forest area in Deoghar district, Jharkhand, India were subjected to PCR amplification using intergenic spacer (IGS) region and small subunit rRNA (SSU-rRNA) gene specific primers followed by cloning and sequencing.

  13. Plant viral intergenic DNA sequence repeats with transcription enhancing activity

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    Cazzonelli Christopher I

    2005-02-01

    Full Text Available Abstract Background The geminivirus and nanovirus families of DNA plant viruses have proved to be a fertile source of viral genomic sequences, clearly demonstrated by the large number of sequence entries within public DNA sequence databases. Due to considerable conservation in genome organization, these viruses contain easily identifiable intergenic regions that have been found to contain multiple DNA sequence elements important to viral replication and gene regulation. As a first step in a broad screen of geminivirus and nanovirus intergenic sequences for DNA segments important in controlling viral gene expression, we have 'mined' a large set of viral intergenic regions for transcriptional enhancers. Viral sequences that are found to act as enhancers of transcription in plants are likely to contribute to viral gene activity during infection. Results DNA sequences from the intergenic regions of 29 geminiviruses or nanoviruses were scanned for repeated sequence elements to be tested for transcription enhancing activity. 105 elements were identified and placed immediately upstream from a minimal plant-functional promoter fused to an intron-containing luciferase reporter gene. Transient luciferase activity was measured within Agrobacteria-infused Nicotiana tobacum leaf tissue. Of the 105 elements tested, 14 were found to reproducibly elevate reporter gene activity (>25% increase over that from the minimal promoter-reporter construct, p Conclusion Biological significance for the active DNA elements identified is supported by repeated isolation of a previously defined viral element (CLE, and the finding that two of three viral enhancer elements examined were markedly enriched within both geminivirus sequences and within Arabidopsis promoter regions. These data provide a useful starting point for virologists interested in undertaking more detailed analysis of geminiviral promoter function.

  14. Isolation and characterization of an unusual repeated sequence from the ribosomal intergenic spacer of the crucifer Sisymbrium irio.

    Science.gov (United States)

    Grellet, F; Delcasso-Tremousaygue, D; Delseny, M

    1989-06-01

    A recombinant plasmid containing a 433 base pair (bp) Bam HI fragment from Sisymbrium irio genomic DNA was isolated and characterized. This fragment was shown to be a ribosomal intergenic spacer (IGS) sequence which is reiterated up to six times in the IGS and extends close to the 5' end of the 18S rRNA gene. The nucleotide sequence of the cloned element is composed of 10-11 40 bp blocks that are probably derived from a common ancestor. The presence of a similar sequence can be detected in the DNA of another Sisymbrium species and in Matthiola incana. Homology was also found with the last 43 nucleotides of the radish IGS 3' end, suggesting that there is possibly a common ancestral nucleotide motif in cruciferous IGS sequences. The cloned element hybridises to RNA transcripts, indicating that the S. irio IGS repetitive sequence is at least partially transcribed during the pre-rRNA transcription process.

  15. Pathoadaptation of a Human Pathogen Through Non-Coding Intergenic Mutations

    DEFF Research Database (Denmark)

    Khademi, Seyed Mohammad Hossein

    of opportunistic pathogen Pseudomonas aeruginosa in long-term chronic airway infections of Cystic fibrosis (CF) patients. Using sequenced genomes of P. aeruginosa isolated from this setting, 88 intergenic regions under positive selection for adaptive mutations within and across isolates of different P. aeruginosa......Most knowledge gained from evolutionary studies of bacteria in natural and experimental settings center around contribution of intragenic mutations on bacterial evolution. While cases of adaptive intergenic mutations have sometimes been reported or explored, none of these studies consider...... intergenic mutations in broader context as key players in evolutionary adaptation of bacteria. The focus of this thesis has been to provide novel insights on contributions of non-coding intergenic mutations in natural evolution of bacteria. The model system used for these investigations is adaptation...

  16. Evidence for Introduction Bottleneck and Extensive Inter-Gene Pool (Mesoamerica x Andes) Hybridization in the European Common Bean (Phaseolus vulgaris L.) Germplasm

    Science.gov (United States)

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

    2013-01-01

    Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from “pure” accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with “pure” accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed. PMID:24098412

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

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    Tania Gioia

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

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

    Science.gov (United States)

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

    2013-01-01

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

  19. Genetic Recombination

    Science.gov (United States)

    Whitehouse, H. L. K.

    1973-01-01

    Discusses the mechanisms of genetic recombination with particular emphasis on the study of the fungus Sordaria brevicollis. The study of recombination is facilitated by the use of mutants of this fungus in which the color of the ascospores is affected. (JR)

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

    African Journals Online (AJOL)

    Several studies are being made to get high productive wheats throughout the world because they provide the most of human energy and protein needs. In this study, 11 wheat species of Triticum and. Aegilops were investigated. One of the intergenic regions of cpDNA was studied. This region was amplified with PCR and ...

  1. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

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    Monjane Adérito L

    2011-12-01

    Full Text Available Abstract Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae, the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots

  2. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution.

    Science.gov (United States)

    Monjane, Adérito L; van der Walt, Eric; Varsani, Arvind; Rybicki, Edward P; Martin, Darren P

    2011-12-02

    Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV

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

    Science.gov (United States)

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

    2017-03-01

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

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

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    Augix Guohua Xu

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

  5. Associating disease-related genetic variants in intergenic regions to the genes they impact

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    Geoff Macintyre

    2014-10-01

    Full Text Available We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.

  6. Novel insights in the genomic organization and hotspots of recombination in the human KIR locus through analysis of intergenic regions

    NARCIS (Netherlands)

    Vendelbosch, S.; de Boer, M.; van Leeuwen, K.; Pourfarzad, F.; Geissler, J.; van den Berg, T. K.; Kuijpers, T. W.

    2015-01-01

    The Killer Immunoglobulin-like Receptor (KIR) proteins constitute a family of highly homologous surface receptors involved in the regulation of the innate cytotoxicity of natural killer (NK) cells. Within the human genome, 17 KIR genes are present, many of which show large variation across the

  7. Characterization of MHC class I in a long-distance migrant shorebird suggests multiple transcribed genes and intergenic recombination

    NARCIS (Netherlands)

    Buehler, Deborah M.; Verkuil, Yvonne I.; Tavares, Erika S.; Baker, Allan J.

    The major histocompatibility complex (MHC) includes highly polymorphic gene families encoding proteins crucial to the vertebrate acquired immune system. Classical MHC class I (MHCI) genes code for molecules expressed on the surfaces of most nucleated cells and are associated with defense against

  8. Recombination in feline immunodeficiency virus from feral and companion domestic cats

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    Rodrigo Allen G

    2008-06-01

    Full Text Available Abstract Background Recombination is a relatively common phenomenon in retroviruses. We investigated recombination in Feline Immunodeficiency Virus from naturally-infected New Zealand domestic cats (Felis catus by sequencing regions of the gag, pol and env genes. Results The occurrence of intragenic recombination was highest in env, with evidence of recombination in 6.4% (n = 156 of all cats. A further recombinant was identified in each of the gag (n = 48 and pol (n = 91 genes. Comparisons of phylogenetic trees across genes identified cases of incongruence, indicating intergenic recombination. Three (7.7%, n = 39 of these incongruencies were found to be significantly different using the Shimodaira-Hasegawa test. Surprisingly, our phylogenies from the gag and pol genes showed that no New Zealand sequences group with reference subtype C sequences within intrasubtype pairwise distances. Indeed, we find one and two distinct unknown subtype groups in gag and pol, respectively. These observations cause us to speculate that these New Zealand FIV strains have undergone several recombination events between subtype A parent strains and undefined unknown subtype strains, similar to the evolutionary history hypothesised for HIV-1 "subtype E". Endpoint dilution sequencing was used to confirm the consensus sequences of the putative recombinants and unknown subtype groups, providing evidence for the authenticity of these sequences. Endpoint dilution sequencing also resulted in the identification of a dual infection event in the env gene. In addition, an intrahost recombination event between variants of the same subtype in the pol gene was established. This is the first known example of naturally-occurring recombination in a cat with infection of the parent strains. Conclusion Evidence of intragenic recombination in the gag, pol and env regions, and complex intergenic recombination, of FIV from naturally-infected domestic cats in New Zealand was found. Strains

  9. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

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    Blencowe Benjamin J

    2005-08-01

    Full Text Available Abstract Background Systematic identification and functional characterization of novel types of noncoding (ncRNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs typically do not possess sequence features such as splicing or translation signals, or long open reading frames. Recent "tiling" microarray studies have reported that a surprisingly larger proportion of mammalian genomes is transcribed than was previously anticipated. However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known. Results To systematically search for functional ncRNAs, we designed microarrays to detect 3,478 intergenic and intronic sequences that are conserved between the human, mouse, and rat genomes, and that score highly by other criteria that characterize ncRNAs. We probed these arrays with total RNA isolated from 16 wild-type mouse tissues. Among 55 candidates for highly-expressed novel ncRNAs tested by northern blotting, eight were confirmed as small, highly-and ubiquitously-expressed RNAs in mouse. Of the eight, five were also detected in rat tissues, but none were detected at appreciable levels in human tissues or cultured cells. Conclusion Since the sequence and expression of most known coding transcripts and functional ncRNAs is conserved between human and mouse, the lack of northern-detectable expression in human cells and tissues of the novel mouse and rat ncRNAs that we identified suggests that they are not functional or possibly have rodent-specific functions. Our results confirm that relatively little of the intergenic sequence conserved between human, mouse and rat is transcribed at high levels in mammalian tissues, possibly suggesting a limited role for transcribed intergenic and intronic sequences as independent functional elements.

  10. Transcriptional regulation of an evolutionary conserved intergenic region of CDT2-INTS7.

    Directory of Open Access Journals (Sweden)

    Hiroki Nakagawa

    2008-01-01

    Full Text Available In the mammalian genome, a substantial number of gene pairs (approximately 10% are arranged head-to-head on opposite strands within 1,000 base pairs, and separated by a bidirectional promoter(s that generally drives the co-expression of both genes and results in functional coupling. The significance of unique genomic configuration remains elusive.Here we report on the identification of an intergenic region of non-homologous genes, CDT2, a regulator of DNA replication, and an integrator complex subunit 7 (INTS7, an interactor of the largest subunit of RNA polymerase II. The CDT2-INTS7 intergenic region is 246 and 245 base pairs long in human and mouse respectively and is evolutionary well-conserved among several mammalian species. By measuring the luciferase activity in A549 cells, the intergenic human sequence was shown to be able to drive the reporter gene expression in either direction and notably, among transcription factors E2F, E2F1 approximately E2F4, but not E2F5 and E2F6, this sequence clearly up-regulated the reporter gene expression exclusively in the direction of the CDT2 gene. In contrast, B-Myb, c-Myb, and p53 down-regulated the reporter gene expression in the transcriptional direction of the INTS7 gene. Overexpression of E2F1 by adenoviral-mediated gene transfer resulted in an increased CDT2, but not INTS7, mRNA level. Real-time polymerase transcription (RT-PCR analyses of the expression pattern for CDT2 and INTS7 mRNA in human adult and fetal tissues and cell lines revealed that transcription of these two genes are asymmetrically regulated. Moreover, the abundance of mRNA between mouse and rat tissues was similar, but these patterns were quite different from the results obtained from human tissues.These findings add a unique example and help to understand the mechanistic insights into the regulation of gene expression through an evolutionary conserved intergenic region of the mammalian genome.

  11. The High Degree of Sequence Plasticity of the Arenavirus Noncoding Intergenic Region (IGR) Enables the Use of a Nonviral Universal Synthetic IGR To Attenuate Arenaviruses.

    Science.gov (United States)

    Iwasaki, Masaharu; Cubitt, Beatrice; Sullivan, Brian M; de la Torre, Juan C

    2016-01-06

    Hemorrhagic fever arenaviruses (HFAs) pose important public health problems in regions where they are endemic. Concerns about human-pathogenic arenaviruses are exacerbated because of the lack of FDA-licensed arenavirus vaccines and because current antiarenaviral therapy is limited to an off-label use of ribavirin that is only partially effective. We have recently shown that the noncoding intergenic region (IGR) present in each arenavirus genome segment, the S and L segments (S-IGR and L-IGR, respectively), plays important roles in the control of virus protein expression and that this knowledge could be harnessed for the development of live-attenuated vaccine strains to combat HFAs. In this study, we further investigated the sequence plasticity of the arenavirus IGR. We demonstrate that recombinants of the prototypic arenavirus lymphocytic choriomeningitis virus (rLCMVs), whose S-IGRs were replaced by the S-IGR of Lassa virus (LASV) or an entirely nonviral S-IGR-like sequence (Ssyn), are viable, indicating that the function of S-IGR tolerates a high degree of sequence plasticity. In addition, rLCMVs whose L-IGRs were replaced by Ssyn or S-IGRs of the very distantly related reptarenavirus Golden Gate virus (GGV) were viable and severely attenuated in vivo but able to elicit protective immunity against a lethal challenge with wild-type LCMV. Our findings indicate that replacement of L-IGR by a nonviral Ssyn could serve as a universal molecular determinant of arenavirus attenuation. Hemorrhagic fever arenaviruses (HFAs) cause high rates of morbidity and mortality and pose important public health problems in regions where they are endemic. Implementation of live-attenuated vaccines (LAVs) will represent a major step to combat HFAs. Here we document that the arenavirus noncoding intergenic region (IGR) has a high degree of plasticity compatible with virus viability. This observation led us to generate recombinant LCMVs containing nonviral synthetic IGRs. These r

  12. The intergenic spacer region of the rDNA in Haplopappus gracilis (Nutt.) Gray.

    Science.gov (United States)

    Ruffini Castiglione, M; Gelati, M T; Cremonini, R; Frediani, M

    2013-06-01

    In this paper, we provide further information on the genome organisation of Haplopappus gracilis, one of the six angiosperms showing the lowest chromosome number, i.e. 2n = 4, by determining the nucleotide sequence of the intergenic spacer region of the ribosomal RNA genes and its cytological localization on metaphase chromosomes. DNA sequence analysis reveals the occurring of a product of 4,382 bp in length, characterised by the presence of four blocks of different repeated sequences. Our analysis also evidenced putative promoter regions with three transcription initiation sites for polymerase I, as previously reported in Artemisia absinthium, belonging to the same Asteraceae family. A fluorescent in situ hybridization with the intergenic spacer probe indicates the presence of rDNA genes only in the satellited chromosomes of H. gracilis; besides, differences in the signal intensity between homologous chromosomes were frequently observed, thus suggesting for these chromosome sites the presence of a variable number of rDNA gene copies, even if a divergent chromatin organisation in corresponding regions cannot be ruled out.

  13. Effects of Mutagen-Sensitive Mus Mutations on Spontaneous Mitotic Recombination in Aspergillus

    OpenAIRE

    Zhao, P.; Kafer, E.

    1992-01-01

    Methyl methane-sulfonate (MMS)-sensitive, radiation-induced mutants of Aspergillus were shown to define nine new DNA repair genes, musK to musS. To test mus mutations for effects on mitotic recombination, intergenic crossing over was assayed between color markers and their centromeres, and intragenic recombination between two distinguishable adE alleles. Of eight mutants analyzed, four showed significant deviations from mus(+) controls in both tests. Two mutations, musK and musL, reduced reco...

  14. Variation of 16S-23S rRNA intergenic spacer regions (ISRs) in Acinetobacter baylyi (strain B2) isolated from activated sludge.

    Science.gov (United States)

    Carr, Emma L; Gürtler, Volker; Seviour, Robert J

    2004-08-01

    To determine the variability of the 16S-23S rRNA intergenic spacer region (ISR) of the newly described Acinetobacter baylyi, 88 clones containing ISR amplicons were screened and 14 chosen for further analysis. Two different sized 16S-23S rRNA ISRs were distinguished comprising five variable and four conserved nucleotide blocks. The major regions of heterogeneity between the different sized ISRs were due to blocks of substitutions with unique secondary structures interspersed with nucleotide substitutions, rather than differences caused by presence or absence of tRNA genes, which is often the case. Recombination events causing shuffling of nucleotide blocks are considered the most likely explanation for the mosaic structure observed between the different copies of the ISR. Single base differences present in the long ISR (LISR) were then exploited in attempts to detect possible heterogeneity between rrn copies in Acinetobacter baylyi but variability was not detected by RFLP analysis of LISR-specific PCR products. These primers were shown to be highly specific for 3 Acinetobacter baylyi strains based on LISR sequence homogeneity.

  15. Teaching Statistics: Creating an Intersection for Intra and Interdisciplinarity

    Science.gov (United States)

    Savard, Annie; Manuel, Dominic

    2016-01-01

    Statistics is taught in mathematics courses in all school levels. We suggest that using rich tasks in statistics can develop statistical reasoning and create both intra and interdisciplinary links in students. In this paper, we present three case studies where middle school mathematics teachers used different tasks in lessons on pie charts. We…

  16. Intra- and interspecies virus transfer in Aspergilli via protoplast fusion

    NARCIS (Netherlands)

    van Diepeningen, A D; Debets, A J; Hoekstra, R F

    1998-01-01

    Intra- and interspecies transfer of dsRNA viruses between black Aspergilli and Aspergillus nidulans strains has been investigated using protoplast fusion. We found interspecies transfer of virus in all combinations of black Aspergillus and A. nidulans strains and vice versa. Using the same

  17. Goal orientation, intra- and interpersonal relations in competitive sport

    African Journals Online (AJOL)

    The standardised TEOSQ (Task and Ego Orientation in Sport Questionnaire) of Duda (1989) and intra- and interpersonal relations scale of Minnaar (1997) were administered to 112 male and female South African competitive sport participants between the ages of 17 and 25 years. The results of the study confirmed the ...

  18. Intra- and inter- correlative responses among fruits physical traits ...

    African Journals Online (AJOL)

    Intra- and inter- correlative responses among fruits physical traits, seedling growth parameters and fruit and nut proximate qualities of the Nigerian shea nut tree ... Results indicated that the first three PCA axes retained explained 96.3% of total variability among seedling provenances, revealing that leaf area, seedling girth, ...

  19. Sequence organization of the Acanthamoeba rRNA intergenic spacer: identification of transcriptional enhancers.

    Science.gov (United States)

    Yang, Q; Zwick, M G; Paule, M R

    1994-01-01

    The primary sequence of the entire 2330 bp intergenic spacer of the A.castellanii ribosomal RNA gene was determined. Repeated sequence elements averaging 140 bp were identified and found to bind a protein required for optimum initiation at the core promoter. These repeated elements were shown to stimulate rRNA transcription by RNA polymerase I in vitro. The repeats inhibited transcription when placed in trans, and stimulated transcription when in cis, in either orientation, but only when upstream of the core promoter. Thus, these repeated elements have characteristics similar to polymerase I enhancers found in higher eukaryotes. The number of rRNA repeats in Acanthamoeba cells was determined to be 24 per haploid genome, the lowest number so far identified in any eukaryote. However, because Acanthamoeba is polyploid, each cell contains approximately 600 rRNA genes. Images PMID:7984432

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

    Directory of Open Access Journals (Sweden)

    Karin Jacobs

    2010-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Zhiqiang Hao

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

  2. Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands.

    Science.gov (United States)

    Tong, Chao; Chen, Qiaoling; Zhao, Lili; Ma, Junfei; Ibeagha-Awemu, Eveline M; Zhao, Xin

    2017-06-19

    Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified. By comparison to the NONCODE2016 database and a domestic-animal long noncoding RNA database (ALDB), 112 novel lincRNAs were revealed in bovine mammary glands. Many lincRNAs were found to be located in quantitative trait loci (QTL). In particular, 36 lincRNAs were found in 172 milk related QTLs, whereas one lincRNA was within clinical mastitis QTL region. In addition, targeted genes for 10 lincRNAs with the highest fragments per kilobase of transcript per million fragments mapped (FPKM) were predicted by LncTar for forecasting potential biological functions of these lincRNAs. Further analyses indicate involvement of lincRNAs in several biological functions and different pathways. Our study has provided a panoramic view of lincRNAs in bovine mammary glands and suggested their involvement in many biological functions including susceptibility to clinical mastitis as well as milk quality and production. This integrative annotation of mammary gland lincRNAs broadens and deepens our understanding of bovine mammary gland biology.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    , the stop codon usage of the upstream gene changes to accommodate the overlap between the SD sequence and the stop codon. CONCLUSION: The SD presence makes the intergenic lengths from 5 to 8 bps less frequent and causes an adaptation of the stop codon usage. Our results introduce new elements...

  4. Intra- and inter-examiner reproducibility of manual probing depth

    OpenAIRE

    Andrade,Roberto; Espinoza,Manuel; Gómez,Elena Maria; Rolando Espinoza,José; Cruz,Elizabeth

    2012-01-01

    The periodontal probe remains the best clinical diagnostic tool for the collection of information regarding the health status and the attachment level of periodontal tissues. The aim of this study was to evaluate intra- and inter-examiner reproducibility of probing depth (PD) measurements made with a manual probe. With the approval of an Ethics Committee, 20 individuals without periodontal disease were selected if they presented at least 6 teeth per quadrant. Using a Williams periodontal prob...

  5. Effects of mutagen-sensitive mus mutations on spontaneous mitotic recombination in Aspergillus.

    Science.gov (United States)

    Zhao, P; Kafer, E

    1992-04-01

    Methyl methane-sulfonate (MMS)-sensitive, radiation-induced mutants of Aspergillus were shown to define nine new DNA repair genes, musK to musS. To test mus mutations for effects on mitotic recombination, intergenic crossing over was assayed between color markers and their centromeres, and intragenic recombination between two distinguishable adE alleles. Of eight mutants analyzed, four showed significant deviations from mus+ controls in both tests. Two mutations, musK and musL, reduced recombination, while musN and musQ caused increases. In contrast, musO diploids produced significantly higher levels only for intragenic recombination. Effects were relatively small, but averages between hypo- and hyperrec mus differed 15-20-fold. In musL diploids, most of the rare color segregants resulted from mitotic malsegregation rather than intergenic crossing over. This indicates that the musL gene product is required for recombination and that DNA lesions lead to chromosome loss when it is deficient. In addition, analysis of the genotypes of intragenic (ad+) recombinants showed that the musL mutation specifically reduced single allele conversion but increased complex conversion types (especially recombinants homozygous for ad+). Similar analysis revealed differences between the effects of two hyperrec mutations; musN apparently caused high levels solely of mitotic crossing over, while musQ increased various conversion types but not reciprocal crossovers. These results suggest that mitotic gene conversion and crossing over, while generally associated, are affected differentially in some of the mus strains of Aspergillus nidulans.

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

    Directory of Open Access Journals (Sweden)

    Jessica A Lehoczky

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

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

    Science.gov (United States)

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

    2013-08-01

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

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

    Science.gov (United States)

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

    2015-01-01

    To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of ‘breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes. PMID:26521696

  9. Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication.

    Science.gov (United States)

    Wang, Yun-Mei; Xu, Hai-Bo; Wang, Ming-Shan; Otecko, Newton Otieno; Ye, Ling-Qun; Wu, Dong-Dong; Zhang, Ya-Ping

    2017-08-15

    Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes. Our study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals.

  10. Long intergenic non-coding RNA TUG1 is overexpressed in urothelial carcinoma of the bladder.

    Science.gov (United States)

    Han, Yonghua; Liu, Yuchen; Gui, Yaoting; Cai, Zhiming

    2013-04-01

    Long intergenic non-coding RNAs (lincRNAs) are a class of non-coding RNAs that regulate gene expression via chromatin reprogramming. Taurine Up-regulated Gene 1 (TUG1) is a lincRNA that is associated with chromatin-modifying complexes and plays roles in gene regulation. In this study, we determined the expression patterns of TUG1 and the cell proliferation inhibition and apoptosis induced by silencing TUG1 in urothelial carcinoma of the bladder. The expression levels of TUG1 were determined using Real-Time qPCR in a total of 44 patients with bladder urothelial carcinomas. Bladder urothelial carcinoma T24 and 5637 cells were transfected with TUG1 siRNA or negative control siRNA. Cell proliferation was evaluated using MTT assay. Apoptosis was determined using ELISA assay. TUG1 was up-regulated in bladder urothelial carcinoma compared to paired normal urothelium. High TUG1 expression levels were associated with high grade and stage carcinomas. Cell proliferation inhibition and apoptosis induction were observed in TUG1 siRNA-transfected bladder urothelial carcinoma T24 and 5637 cells. Our data suggest that lincRNA TUG1 is emerging as a novel player in the disease state of bladder urothelial carcinoma. TUG1 may have potential roles as a biomarker and/or a therapeutic target in bladder urothelial carcinoma. Copyright © 2012 Wiley Periodicals, Inc.

  11. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  12. Tracing Method with Intra and Inter Protocols Correlation

    Directory of Open Access Journals (Sweden)

    Marin Mangri

    2009-05-01

    Full Text Available MEGACO or H.248 is a protocol enabling acentralized Softswitch (or MGC to control MGsbetween Voice over Packet (VoP networks andtraditional ones. To analyze much deeper the realimplementations it is useful to use a tracing systemwith intra and inter protocols correlation. For thisreason in the case of MEGACO-H.248 it is necessaryto find the appropriate method of correlation with allprotocols involved. Starting from Rel4 a separation ofCP (Control Plane and UP (User Plane managementwithin the networks appears. MEGACO protocol playsan important role in the migration to the new releasesor from monolithic platform to a network withdistributed components.

  13. A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages

    OpenAIRE

    Garmire, Lana X.; Garmire, David G.; Huang, Wendy; Yao, Joyee; Glass, Christopher K.; Subramaniam, Shankar

    2011-01-01

    Identification of diffuse signals from the chromatin immunoprecipitation and high-throughput massively parallel sequencing (ChIP-Seq) technology poses significant computational challenges, and there are few methods currently available. We present a novel global clustering approach to enrich diffuse CHIP-Seq signals of RNA polymerase II and histone 3 lysine 4 trimethylation (H3K4Me3) and apply it to identify putative long intergenic non-coding RNAs (lincRNAs) in macrophage cells. Our global cl...

  14. The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination.

    Science.gov (United States)

    Devault, Alain; Bañuls, Anne-Laure

    2008-10-24

    PSA (promastigote surface antigen) is one of the major classes of membrane proteins present at the surface of the parasitic protozoan Leishmania. While it harbours leucine rich repeats, which are suggestive of its involvement in parasite-to-host physical interactions, its exact role is largely unknown. Furthermore, the extent of diversity of this gene family, both in copy number and sequence has not been established. From the newly available complete genome sequences of L. major, L. infantum and L. braziliensis, we have established the complete list of PSA genes, based on the conservation of specific domain architecture. The latter includes an array of leucine rich repeats of unique signature flanked by conserved cysteine-rich domains. All PSA genes code either for secreted or membrane-anchored surface proteins. Besides the few previously identified PSA genes, which are shown here to be part of a relatively large subclass of PSA genes located on chromosome 12, this study identifies seven other PSA subtypes. The latter, whose genes lie on chromosomes 5, 9, 21 and 31 in all three species, form single gene (two genes in one instance) subfamilies, which phylogenetically cluster as highly related orthologs. On the other hand, genes found on chromosome 12 generally show high diversification, as reflected in greater sequence divergence between species, and in an extended set of divergent paralogs. Moreover, we show that the latter genes are submitted to strong positive selection. We also provide evidence that evolution of these genes is driven by intra- and intergenic recombination, thereby modulating the number of LRRs in protein and generating chimeric genes. PSA is a Leishmania family of membrane-bound or secreted proteins, whose main signature consists in a specific LRR sequence. All PSA genes found in the genomes of three sequenced Leishmania species unambiguously distribute into eight subfamilies of orthologs. Seven of these are evolving relatively slowly and could

  15. The promastigote surface antigen gene family of the Leishmania parasite: differential evolution by positive selection and recombination

    Directory of Open Access Journals (Sweden)

    Bañuls Anne-Laure

    2008-10-01

    Full Text Available Abstract Background PSA (promastigote surface antigen is one of the major classes of membrane proteins present at the surface of the parasitic protozoan Leishmania. While it harbours leucine rich repeats, which are suggestive of its involvement in parasite-to-host physical interactions, its exact role is largely unknown. Furthermore, the extent of diversity of this gene family, both in copy number and sequence has not been established. Results From the newly available complete genome sequences of L. major, L. infantum and L. braziliensis, we have established the complete list of PSA genes, based on the conservation of specific domain architecture. The latter includes an array of leucine rich repeats of unique signature flanked by conserved cysteine-rich domains. All PSA genes code either for secreted or membrane-anchored surface proteins. Besides the few previously identified PSA genes, which are shown here to be part of a relatively large subclass of PSA genes located on chromosome 12, this study identifies seven other PSA subtypes. The latter, whose genes lie on chromosomes 5, 9, 21 and 31 in all three species, form single gene (two genes in one instance subfamilies, which phylogenetically cluster as highly related orthologs. On the other hand, genes found on chromosome 12 generally show high diversification, as reflected in greater sequence divergence between species, and in an extended set of divergent paralogs. Moreover, we show that the latter genes are submitted to strong positive selection. We also provide evidence that evolution of these genes is driven by intra- and intergenic recombination, thereby modulating the number of LRRs in protein and generating chimeric genes. Conclusion PSA is a Leishmania family of membrane-bound or secreted proteins, whose main signature consists in a specific LRR sequence. All PSA genes found in the genomes of three sequenced Leishmania species unambiguously distribute into eight subfamilies of orthologs

  16. Glomus jugulare tumor with intra- and extracranial extension

    International Nuclear Information System (INIS)

    Morisako, Toshitaka; Goya, Tomokazu; Wakisaka, Shinichiro; Kinoshita, Kazuo

    1987-01-01

    A case of glomus jugulare tumor with intra- and extracranial extension is described. The patient was a 63-year-old woman who complained of gait and memory disturbances. On admission neurological examination revealed recent memory disturbance, left deafness, left XI, XIIth cranial nerve palsies, and slight ataxic gait. Roentgenogram of the skull showed an enlarged left jugular foramen with bone erosion. Plain X-ray computerized tomography scan (X-CT) indicated obstructive hydrocephalus and X-CT with contrast enhancement revealed a mass lesion in the left posterior cranial fossa extending through enlarged left jugular foramen to the extracranial space toward the level of C 2 . Cerebral angiography demonstrated a large mass with blood supply from branches of left external carotid and vertebral arteries. The tumor stain was not remarkable. Left internal jugular vein was completely obstructed at the level of the second cervical vertebral body. Magnetic resonance imaging (MRI) clearly showed the tumor extending from the anterolateral portion to the second cervical vertebral body through the enlarged jugular foramen to the posterior cranial fossa. Brain stem and cerebellar hemisphere which were markedly compressed by the mass were clearly visualized. At first a ventriculo-peritoneal shunt was made and four weeks later subtotal removal of the tumor was undertaken. Histopathology of tumor specimen showed typical glomus jugulare tumor. MRI was considered to be very useful for the diagnosis and treatment of the glomus jugulare tumor with intra- and extracranial extension. (author)

  17. The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions.

    Science.gov (United States)

    Oliveira, Graziele Pereira; Lima, Maurício Teixeira; Arantes, Thalita Souza; Assis, Felipe Lopes; Rodrigues, Rodrigo Araújo Lima; da Fonseca, Flávio Guimarães; Bonjardim, Cláudio Antônio; Kroon, Erna Geessien; Colson, Philippe; La Scola, Bernard; Abrahão, Jônatas Santos

    2017-11-01

    Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba , its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses. IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the

  18. Analysis of a ribosomal DNA intergenic spacer region from the yellow fever mosquito, Aedes aegypti.

    Science.gov (United States)

    Wu, C C; Fallon, A M

    1998-02-01

    We have sequenced the 1.8 kb intergenic spacer (IGS) region from an Aedes aegypti ribosomal DNA repeat and have identified conserved functional motifs shared with the related mosquito, Aedes albopictus. Despite the shorter length and greater homogeneity of the Ae. aegypti IGS region, the sequences of two potential RNA polymerase I core promoters and closely associated terminator elements were highly conserved. Primer extension analysis indicated that the predominant transcription initiation site in the Ae. aegypti rDNA repeat unit region lay at or near the A residue at nucleotide position 1003 in the 'upstream' RNA polymerase I promoter. This observation was supported by the higher sequence identity between the upstream promoters in Ae. aegypti and Ae. albopictus, relative to the downstream promoters. In contrast to strong similarities among proximal regulatory elements, the Ae. aegypti IGS sequence upstream of the transcription initiation site lacked the ordered array of contiguous approximately 200 nucleotide subrepeats previously found in the IGS of Ae. albopictus. In Ae. aegypti, only 4 approximately 50 nucleotide R subrepeats separated by unique sequences, followed by 2 approximately 50 nucleotide E subrepeats, occurred upstream of the transcription initiation site. Despite their differences in size and sequence, however, the four Ae. aegypti R subrepeats shared an internal structural organization that included a conserved core with 'spacer' promoters and recombinogenic elements similar to those in the longer Ae. albopictus subrepeats. These observations provide an important basis for further characterization of transcription specificity among mosquito RNA polymerase I promoters and associated regulatory elements, and contribute towards the eventual use of these elements in transgenic applications.

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

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

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

  20. The music of trees: the intergenerative tie between primary care and public health.

    Science.gov (United States)

    Whitehouse, Peter

    2016-01-01

    Stories help us frame and understand complex ideas and challenges. Metaphors are particularly powerful linguistic devices that guide and extend our thinking by bridging conceptual domains, for example to consider the brain as a digital computer. Trees are widely used as metaphors for broad concepts like evolution, history, society, and even life itself, i.e. 'the tree of life'. Tree-like diagrams of roots and branches are used to demonstrate historical and cultural relationships, for example, between different species or different languages. In this paper, we describe a theatrical character called a tree doctor which is a living metaphor. A human being, namely the author, lectures, acts or dances as a tree and offers lessons to Homo Sapiens about 'holistic' ideas of health. The character teaches us to not only see the value of our relationships to trees, but the importance of seeing forests as well the individual trees. The metaphorical statement that we should not 'miss the forest for the trees' means we should learn to think of health embedded in systems and communities. In medicine, we too often focus on individual molecules, pharmaceuticals, or even patients and miss the bigger picture of public and environmental health. In a time of great ecological system change, the tree doctor points to broad ethical responsibility for each other and future generations of humans and other living creatures. The character embraces arts and particularly music as a powerful way of infusing purpose and improving the qualities of our lives together, especially as we age. The tree doctor knows the value of intergenerational relationships. But it also points to intergenerative innovations across many cultural domains, disciplines and professions. The tree doctor supports primary care and empowers the value of intergenerational relationships, art and music in the recommendations doctors make to patients to improve their health and well-being.

  1. Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell.

    Science.gov (United States)

    Tang, Xing; Hou, Mei; Ding, Yang; Li, Zhaohui; Ren, Lichen; Gao, Ge

    2013-01-01

    While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these novel regulators but also shed light on their functionalities. Based on multiple RNA-Seq datasets, we systematically identified 300 human embryonic stem cell lincRNAs (hES lincRNAs). Of which, one forth (78 out of 300) hES lincRNAs were further identified to be biasedly expressed in human ES cells. Functional analysis showed that they were preferentially involved in several early-development related biological processes. Comparative genomics analysis further suggested that around half of the identified hES lincRNAs were conserved in mouse. To facilitate further investigation of these hES lincRNAs, we constructed an online portal for biologists to access all their sequences and annotations interactively. In addition to navigation through a genome browse interface, users can also locate lincRNAs through an advanced query interface based on both keywords and expression profiles, and analyze results through multiple tools. By integrating multiple RNA-Seq datasets, we systematically characterized and annotated 300 hES lincRNAs. A full functional web portal is available freely at http://scbrowse.cbi.pku.edu.cn. As the first global profiling and annotating of human embryonic stem cell lincRNAs, this work aims to provide a valuable resource for both experimental biologists and bioinformaticians.

  2. Optical investigation of intra- and extra-cellular dynamics

    DEFF Research Database (Denmark)

    Leijnse, Natascha

    In this thesis we investigated intra- and extra-cellular dynamics with the help of optical tweezers and confocal imaging. Firstly, we measured in vivo diffusion inside endothelial cells by tracking lipid granules and compared the results to in vitro diffusion of polystyrene beads in wormlike......, investigations of force generation by living cells embedded in 3D matrices, conducted in Alexander Dunn's lab at Stanford University, are described in the last chapter....... micelles. Furthermore, we studied F-actin dynamics in, and curvature sensing of, a receptor and its ligand on artificially pulled membrane tethers. Force measurements between a cell and an approaching optically trapped bead were conducted in order to probe the endothelial cell's glycocalyx. Finally...

  3. Intra and interpersonal determinants for relapse in drug addicts

    Directory of Open Access Journals (Sweden)

    Aline Cristina Zerwes Ferreira

    2016-03-01

    Full Text Available A descriptive qualitative research conducted with 20 drug addicts during treatment at a Center of Psychosocial Attention for Alcohol and other Drugs, aimed to identify intra and interpersonal determinants of relapse perceived by the drug addict. The data were collected through semi-structured interviews, submitted to Content Analysis, and organized into categories following predictive determinants for relapse. The relapse occurred by intrapersonal determinants, as self-efficacy expressed by self-confidence in interrupting the drug consumption; the result expectation by anticipation of pleasurable drug effects; the motivation by the absence of volition to interrupt the consumption; coping with the difficulty to confront daily problems; negative and positive emotional states; and craving. Interpersonal determinants expressed by social support were related to the influence of thirds. The identification of these determinants during treatment to favor relapse prevention and effective rehabilitation.

  4. Transetherification on Polyols by Intra- and Intermolecular Nucleophilic Substitutions

    Science.gov (United States)

    Muraoka, Takahiro; Adachi, Kota; Chowdhury, Rainy; Kinbara, Kazushi

    2014-01-01

    Transetherification on polyols involving intra- and intermolecular nucleophilic substitutions is reported. Di- or trialkoxide formation of propane-1,3-diol or 2-(hydroxymethyl)propane-1,3-diol derivatives by NaH triggers the reaction via oxetanes formation, where the order to add NaH and a polyol significantly influences the yields of products. It was demonstrated that the protective group on the pentaerythritol skeleton is apparently transferred to the hydrophilic and hydrophobic chain molecules bearing a leaving group in one-step, and a protective group conversion from tosyl to benzyl was successful using a benzyl-appending triol to afford a desired product in 67% yield. PMID:24663293

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

    Directory of Open Access Journals (Sweden)

    Jianqin Li

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-07

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

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

    Directory of Open Access Journals (Sweden)

    Tran Duc

    2010-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Zoghbi Huda Y

    2001-10-01

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

  9. Recombinant clotting factors.

    Science.gov (United States)

    Pipe, Steven W

    2008-05-01

    The recombinant era for haemophilia began in the early 1980s with the cloning and subsequent expression of functional proteins for both factors VIII and IX. Efficient production of recombinant clotting factors in mammalian cell culture systems required overcoming significant challenges due to the complex post-translational modifications that were integral to their pro-coagulant function. The quick development and commercialization of recombinant clotting factors was, in part, facilitated by the catastrophic impact of viral contamination of plasma-derived clotting factor concentrates at the time. Since their transition into the clinic, the recombinant versions of both factor VIII and IX have proven to be remarkable facsimiles of their plasma-derived counterparts. The broad adoption of recombinant therapy throughout the developed world has significantly increased the supply of clotting factor concentrates and helped advance aggressive therapeutic interventions such as prophylaxis. The development of recombinant VIIa was a further advance bringing a recombinant option to haemophilia patients with inhibitors. Recombinant DNA technology remains the platform to address ongoing challenges in haemophilia care such as reducing the costs of therapy, increasing the availability to the developing world, and improving the functional properties of these proteins. In turn, the ongoing development of new recombinant clotting factor concentrates is providing alternatives for patients with other inherited bleeding disorders.

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

    Directory of Open Access Journals (Sweden)

    Bose Mridula

    2010-04-01

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

  11. Recombinant gene expression protocols

    National Research Council Canada - National Science Library

    Tuan, Rocky S

    1997-01-01

    .... A fundamental requirement for successful recombinant gene expression is the design of the cloning vector and the choice of the host organism for expression. Recombinant Gene Expression Protocols grows out of the need for a laboratory manual that provides the reader the background and rationale, as well as the practical protocols for the preparation of...

  12. Intra- and intergenerational discounting in the climate game

    Science.gov (United States)

    Jacquet, Jennifer; Hagel, Kristin; Hauert, Christoph; Marotzke, Jochem; Röhl, Torsten; Milinski, Manfred

    2013-12-01

    The difficulty of avoiding dangerous climate change arises from a tension between group and self-interest and is exacerbated by climate change's intergenerational nature. The present generation bears the costs of cooperation, whereas future generations accrue the benefits if present cooperation succeeds, or suffer if present cooperation fails. Although temporal discounting has long been known to matter in making individual choices, the extent of temporal discounting is poorly understood in a group setting. We represent the effect of both intra- and intergenerational discounting through a collective-risk group experiment framed around climate change. Participants could choose to cooperate or to risk losing an additional endowment with a high probability. The rewards of defection were immediate, whereas the rewards of cooperation were delayed by one day, delayed by seven weeks (intragenerational discounting), or delayed by several decades and spread over a much larger number of potential beneficiaries (intergenerational discounting). We find that intergenerational discounting leads to a marked decrease in cooperation; all groups failed to reach the collective target. Intragenerational discounting was weaker by comparison. Our results experimentally confirm that international negotiations to mitigate climate change are unlikely to succeed if individual countries' short-term gains can arise only from defection.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  14. Proteins mediating intra- and intercellular transport of lipids and lipid-modified proteins

    NARCIS (Netherlands)

    Neumann, S.

    2008-01-01

    Proteins mediating intra- and intercellular transport of lipids and lipid-modified proteins In this thesis, I studied the intra- and intercellular transport of lipidic molecules, in particular glycosphingolipids and lipid-modified proteins. The first part focuses on the intracellular transport of

  15. Hadron correlations from recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-01-01

    Quark recombination is a successful model to describe the hadronization of a deconfined quark gluon plasma. Jet-like dihadron correlations measured at RHIC provide a challenge for this picture. We discuss how correlations between hadrons can arise from correlations between partons before hadronization. An enhancement of correlations through the recombination process, similar to the enhancement of elliptic flow is found. Hot spots from completely or partially quenched jets are a likely source of such parton correlations.

  16. Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata

    Directory of Open Access Journals (Sweden)

    Kiwoung Yang

    2015-12-01

    Full Text Available Ribosomal DNA (rDNA of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS. The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2, and the intergenic spacer 45S-IGS (25S-18S. This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F1s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies variation of the 45S IGS in B. oleracea.

  17. Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata.

    Science.gov (United States)

    Yang, Kiwoung; Robin, Arif Hasan Khan; Yi, Go-Eun; Lee, Jonghoon; Chung, Mi-Young; Yang, Tae-Jin; Nou, Ill-Sup

    2015-12-03

    Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F₁s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea.

  18. Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L..

    Directory of Open Access Journals (Sweden)

    Morad M Mokhtar

    Full Text Available The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6% were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4% were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars.

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

    NARCIS (Netherlands)

    Oliveira, de V.M.; Manfio, G.P.; Coutinho, H.L.D.; Keijzer-Wolters, A.C.; Elsas, van J.D.

    2006-01-01

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

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

    NARCIS (Netherlands)

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

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

  1. Regulation of Meiotic Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Gregory p. Copenhaver

    2011-11-09

    Meiotic recombination results in the heritable rearrangement of DNA, primarily through reciprocal exchange between homologous chromosome or gene conversion. In plants these events are critical for ensuring proper chromosome segregation, facilitating DNA repair and providing a basis for genetic diversity. Understanding this fundamental biological mechanism will directly facilitate trait mapping, conventional plant breeding, and development of genetic engineering techniques that will help support the responsible production and conversion of renewable resources for fuels, chemicals, and the conservation of energy (1-3). Substantial progress has been made in understanding the basal recombination machinery, much of which is conserved in organisms as diverse as yeast, plants and mammals (4, 5). Significantly less is known about the factors that regulate how often and where that basal machinery acts on higher eukaryotic chromosomes. One important mechanism for regulating the frequency and distribution of meiotic recombination is crossover interference - or the ability of one recombination event to influence nearby events. The MUS81 gene is thought to play an important role in regulating the influence of interference on crossing over. The immediate goals of this project are to use reverse genetics to identify mutants in two putative MUS81 homologs in the model plant Arabidopsis thaliana, characterize those mutants and initiate a novel forward genetic screen for additional regulators of meiotic recombination. The long-term goal of the project is to understand how meiotic recombination is regulated in higher eukaryotes with an emphasis on the molecular basis of crossover interference. The ability to monitor recombination in all four meiotic products (tetrad analysis) has been a powerful tool in the arsenal of yeast geneticists. Previously, the qrt mutant of Arabidopsis, which causes the four pollen products of male meiosis to remain attached, was developed as a facile system

  2. Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer.

    Science.gov (United States)

    Dahmane, Narimane; Libante, Virginie; Charron-Bourgoin, Florence; Guédon, Eric; Guédon, Gérard; Leblond-Bourget, Nathalie; Payot, Sophie

    2017-07-01

    -modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius Closely related ICEs were also detected in silico in other Streptococcus species ( S. pneumoniae and S. parasanguinis ), thus indicating that diffusion of ICE St3 -related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present. Copyright © 2017 American Society for Microbiology.

  3. The effect of L-NAME on intra- and inter-nephron synchronization

    DEFF Research Database (Denmark)

    Sosnovtseva, Olga; Pavlov, A. N.; Pavlova, O. N.

    2009-01-01

    Kidney autoregulation involves complicated intra- and inter-nephron synchronization phenomena among oscillatory modes produced, respectively, by the tubuloglomerular feedback (TGF) mechanism and by the myogenic regulation of the afferent arteriolar blood flow. The present study aims at examining ...

  4. Gateway Recombinational Cloning.

    Science.gov (United States)

    Reece-Hoyes, John S; Walhout, Albertha J M

    2018-01-02

    The Gateway recombinatorial cloning system was developed for cloning multiple DNA fragments in parallel (e.g., in 96-well formats) in a standardized manner using the same enzymes. Gateway cloning is based on the highly specific integration and excision reactions of bacteriophage λ into and out of the Escherichia coli genome. Because the sites of recombination (" att " sites) are much longer (25-242 bp) than restriction sites, they are extremely unlikely to occur by chance in DNA fragments. Therefore, the same recombination enzyme can be used to robustly clone many different fragments of variable size in parallel reactions. © 2018 Cold Spring Harbor Laboratory Press.

  5. Recombinant renewable polyclonal antibodies.

    Science.gov (United States)

    Ferrara, Fortunato; D'Angelo, Sara; Gaiotto, Tiziano; Naranjo, Leslie; Tian, Hongzhao; Gräslund, Susanne; Dobrovetsky, Elena; Hraber, Peter; Lund-Johansen, Fridtjof; Saragozza, Silvia; Sblattero, Daniele; Kiss, Csaba; Bradbury, Andrew R M

    2015-01-01

    Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.

  6. Infectious mutants of cassava latent virus generated in vivo from intact recombinant DNA clones containing single copies of the genome.

    Science.gov (United States)

    Stanley, J; Townsend, R

    1986-08-11

    Intact recombinant DNAs containing single copies of either component of the cassava latent virus genome can elicit infection when mechanically inoculated to host plants in the presence of the appropriate second component. Characterisation of infectious mutant progeny viruses, by analysis of virus-specific supercoiled DNA intermediates, indicates that most if not all of the cloning vector has been deleted, achieved at least in some cases by intermolecular recombination in vivo between DNAs 1 and 2. Significant rearrangements within the intergenic region of DNA 2, predominantly external to the common region, can be tolerated without loss of infectivity suggesting a somewhat passive role in virus multiplication for the sequences in question. Although packaging constraints might impose limits on the amount of DNA within geminate particles, isolation of an infectious coat protein mutant defective in virion production suggests that packaging is not essential for systemic spread of the viral DNA.

  7. PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants

    Directory of Open Access Journals (Sweden)

    Lucas Maciel Vieira

    2017-03-01

    Full Text Available Non-coding RNAs (ncRNAs constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs, which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM. We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane (Saccharum spp. and in maize (Zea mays. From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms.

  8. Large Intergenic Non-coding RNA-RoR Inhibits Aerobic Glycolysis of Glioblastoma Cells via Akt Pathway.

    Science.gov (United States)

    Li, Yong; He, Zhi-Cheng; Liu, Qing; Zhou, Kai; Shi, Yu; Yao, Xiao-Hong; Zhang, Xia; Kung, Hsiang-Fu; Ping, Yi-Fang; Bian, Xiu-Wu

    2018-01-01

    Reprogramming energy metabolism is a hallmark of malignant tumors, including glioblastoma (GBM). Aerobic glycolysis is often utilized by tumor cells to maintain survival and proliferation. However, the underlying mechanisms of aerobic glycolysis in GBM remain elusive. Herein, we demonstrated that large intergenic non-coding RNA-RoR (LincRNA-RoR) functioned as a critical suppressor to inhibit the aerobic glycolysis and viability of GBM cells. We found that LincRNA-RoR was markedly reduced in GBM tissues compared with adjacent non-tumor tissues from 10 cases of GBM patients. Consistently, LincRNA-RoR expression in GBM cells was significantly lower than that in normal glial cells. The aerobic glycolysis of GBM cells, as determined by the measurement of glucose uptake and lactate production, was impaired by LincRNA-RoR overexpression. Mechanistically, LincRNA-RoR inhibited the expression of Rictor, the key component of mTORC2 (mammalian target of rapamycin complex 2), to suppress the activity of Akt pathway and impair the expression of glycolytic effectors, including Glut1, HK2, PKM2 and LDHA. Finally, enforced expression of LincRNA-RoR reduced the proliferation of GBM cells in vitro , restrained tumor growth in vivo, and repressed the expression of glycolytic molecules in GBM xenografts. Collectively, our results underscore LincRNA-RoR as a new suppressor of GBM aerobic glycolysis with therapeutic potential.

  9. Large intergenic non-coding RNA-ROR reverses gemcitabine-induced autophagy and apoptosis in breast cancer cells.

    Science.gov (United States)

    Chen, Yao-Min; Liu, Yu; Wei, Hai-Yan; Lv, Ke-Zhen; Fu, Pei-Fen

    2016-09-13

    The purpose of this study was to elucidate the potential role of long intergenic non-protein coding RNA, regulator of reprogramming (linc-ROR) in gemcitabine (Gem)-induced autophagy and apoptosis in breast cancer cells. MDA-MB-231 cells were treated with short hairpin RNA (shRNA) to knockdown Linc-ROR expression in the presence of Gem. Gem treatment alone decreased cell survival and increased both apoptosis and autophagy. Gem treatment also increased the expression of LC3-II, Beclin 1, NOTCH1 and Bcl-2, but decreased expression of p62 and p53. Untreated MDA-MB-231 cell lines strongly expressed linc-ROR, but linc-ROR knockdown decreased cell viability and expression of p62 and p53 while increasing apoptosis. Linc-ROR knockdown also increased LC3-II/β-actin, Beclin 1, NOTCH1, and Bcl-2 expression, as well as the number of autophagic vesicles in MDA-MB-231 cells. Linc-ROR negatively regulated miR-34a expression by inhibiting histone H3 acetylation in the miR-34a promoter. We conclude that linc-ROR suppresses Gem-induced autophagy and apoptosis in breast cancer cells by silencing miR-34a expression.

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

    Science.gov (United States)

    Wang, Chao; Dong, Dong; Wang, Guangce; Zhang, Baoyu; Peng, Guang; Xu, Pu; Tang, Xiaorong

    2009-09-01

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

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

    Directory of Open Access Journals (Sweden)

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

    2013-07-01

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

  12. Evaluation of automated ribosomal intergenic spacer analysis for bacterial fingerprinting of rumen microbiome compared to pyrosequencing technology.

    Science.gov (United States)

    Jami, Elie; Shterzer, Naama; Mizrahi, Itzhak

    2014-01-22

    The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA), an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data.

  13. Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology

    Directory of Open Access Journals (Sweden)

    Elie Jami

    2014-01-01

    Full Text Available The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA, an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Travers Ching

    2016-05-01

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

  16. A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response.

    Science.gov (United States)

    Melo, C A; Léveillé, N; Rooijers, K; Wijchers, P J; Geeven, G; Tal, A; Melo, S A; de Laat, W; Agami, R

    2016-08-18

    Genome-wide chromatin studies identified the tumor suppressor p53 as both a promoter and an enhancer-binding transcription factor. As an enhancer factor, p53 can induce local production of enhancer RNAs, as well as transcriptional activation of distal neighboring genes. Beyond the regulation of protein-coding genes, p53 has the capacity to regulate long intergenic noncoding RNA molecules (lincRNAs); however, their importance to the p53 tumor suppressive function remains poorly characterized. Here, we identified and characterized a novel p53-bound intronic enhancer that controls the expression of its host, the lincRNA00475 (linc-475). We demonstrate the requirement of linc-475 for the proper induction of a p53-dependent cell cycle inhibitory response. We further confirm the functional importance of linc-475 in the maintenance of CDKN1A/p21 levels, a cell cycle inhibitor and a major p53 target gene, following p53 activation. Interestingly, loss of linc-475 reduced the binding of both p53 and RNA polymerase II (RNAPII) to the promoter of p21, attenuating its transcription rate following p53 activation. Altogether, our data suggest a direct role of p53-bound enhancer domains in the activation of lincRNAs required for an efficient p53 transcriptional response.

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

    Science.gov (United States)

    Zoolkifli, Nurliyana Wan; Mutalib, Sahilah Abd

    2013-11-01

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

  18. Large Intergenic Non-coding RNA-RoR Inhibits Aerobic Glycolysis of Glioblastoma Cells via Akt Pathway

    Science.gov (United States)

    Li, Yong; He, Zhi-Cheng; Liu, Qing; Zhou, Kai; Shi, Yu; Yao, Xiao-Hong; Zhang, Xia; Kung, Hsiang-Fu; Ping, Yi-Fang; Bian, Xiu-Wu

    2018-01-01

    Reprogramming energy metabolism is a hallmark of malignant tumors, including glioblastoma (GBM). Aerobic glycolysis is often utilized by tumor cells to maintain survival and proliferation. However, the underlying mechanisms of aerobic glycolysis in GBM remain elusive. Herein, we demonstrated that large intergenic non-coding RNA-RoR (LincRNA-RoR) functioned as a critical suppressor to inhibit the aerobic glycolysis and viability of GBM cells. We found that LincRNA-RoR was markedly reduced in GBM tissues compared with adjacent non-tumor tissues from 10 cases of GBM patients. Consistently, LincRNA-RoR expression in GBM cells was significantly lower than that in normal glial cells. The aerobic glycolysis of GBM cells, as determined by the measurement of glucose uptake and lactate production, was impaired by LincRNA-RoR overexpression. Mechanistically, LincRNA-RoR inhibited the expression of Rictor, the key component of mTORC2 (mammalian target of rapamycin complex 2), to suppress the activity of Akt pathway and impair the expression of glycolytic effectors, including Glut1, HK2, PKM2 and LDHA. Finally, enforced expression of LincRNA-RoR reduced the proliferation of GBM cells in vitro, restrained tumor growth in vivo, and repressed the expression of glycolytic molecules in GBM xenografts. Collectively, our results underscore LincRNA-RoR as a new suppressor of GBM aerobic glycolysis with therapeutic potential. PMID:29581766

  19. Comparison of pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR and biochemical tests to characterize Lactococcus garvieae.

    Science.gov (United States)

    Ture, M; Altinok, I; Capkin, E

    2015-01-01

    Biochemical test, pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) were used to compare 42 strains of Lactococcus garvieae isolated from different regions of Turkey, Italy, France and Spain. Twenty biotypes of L. garvieae were formed based on 54 biochemical tests. ERIC-PCR of genomic DNA from different L. garvieae strains resulted in amplification of multiple fragments of DNA in sizes ranging between 200 and 5000 bp with various band intensities. After cutting DNA with ApaI restriction enzyme and running on the PFGE, 11–22 resolvable bands ranging from 2 to 194 kb were observed. Turkish isolates were grouped into two clusters, and only A58 (Italy) strain was connected with Turkish isolates. Similarities between Turkish, Spanish, Italian and French isolates were Turkey, first lactococcosis occurred in Mugla, and then, it has been spread all over the country. Based on ERIC-PCR, Spanish and Italian strains of L. garvieae were related to Mugla strains. Therefore, after comparing PFGE profiles, ERIC-PCR profiles and phenotypic characteristics of 42 strains of L. garvieae, there were no relationships found between these three typing methods. PFGE method was more discriminative than the other methods. © 2014 John Wiley & Sons Ltd.

  20. Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection.

    Science.gov (United States)

    Kwenda, Stanford; Birch, Paul R J; Moleleki, Lucy N

    2016-08-11

    Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

  1. Search Region of Origin Honey Bee A. mellifera in Indonesia Region Using Mitochondrial DNA intergenic cox1/cox2

    Directory of Open Access Journals (Sweden)

    Mohamad Rusdi Hidayat

    2011-12-01

    Full Text Available Apis mellifera is a favourite honey bee for the beekeepers throughout many countries. This species comprise of 24 subspecies. Based on phylogeography and morphometric evidences, these subspecies have been grouped into four lineage; namely the African (A, Western and Northern Europe (M, Southeastern Europe (C, and Near Eastern (O. Apis mellifera have been imported to Indonesia since 1972, and mostly from Australia. However, until recently there are no data about the A. mellifera subspecies and the origin. Therefore the objective of this research is to determine the lineage of A. mellifera in Indonesia based on mtDNA intergenic region between cox1/cox2 genes. In this region there are two DNA fragments, P and Q fragnant, that can be used to determine the A. mellifera lineage. The methodology used consist of samples collection, DNA isolation, DNA amplification, DNA restriction using DraI enzyme, DNA sequencing, and DNA alignment using Clustal X and MEGA spftwares. DNA fragment amplified by using E2 and H1 primer revealed a 863 bp. Digestion of the region with the DraI restriction enzyme revealed one haplotype, which consist of five DNA fragments. Based on DNA sequences and DNA alignment, A. mellifera in Indonesia was homologue with the C lineage. Its subspecies is A. m. ligustica that lived natively in Italy, they were imported to Indonesia from Australia

  2. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  3. Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

    Science.gov (United States)

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

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

  4. Nonradiative recombination in semiconductors

    CERN Document Server

    Abakumov, VN; Yassievich, IN

    1991-01-01

    In recent years, great progress has been made in the understandingof recombination processes controlling the number of excessfree carriers in semiconductors under nonequilibrium conditions. As a result, it is now possible to give a comprehensivetheoretical description of these processes. The authors haveselected a number of experimental results which elucidate theunderlying physical problems and enable a test of theoreticalmodels. The following topics are dealt with: phenomenological theory ofrecombination, theoretical models of shallow and deep localizedstates, cascade model of carrier captu

  5. Molecular Characterization of QX-Like and Variant Infectious Bronchitis Virus Strains in Malaysia Based on Partial Genomic Sequences Comprising the S-3a/3b-E-M-Intergenic Region-5a/5b-N Gene Order.

    Science.gov (United States)

    Khanh, N P; Tan, S W; Yeap, S K; Satharasinghe, D A; Hair-Bejo, M; Bich, T N; Omar, A R

    2017-12-01

    Infectious bronchitis virus (IBV) is one of the major poultry pathogens of global importance. However, the prevalence of IBV strains in Malaysia is poorly characterized. The partial genomic sequences (6.8 kb) comprising the S-3a/3b-E-M-intergenic region-5a/5b-N gene order of 11 Malaysian IBVs isolated in 2014 and 2015 were sequenced using next-generation sequencing technology. Phylogenetic and pairwise sequence comparison analysis showed that the isolated IBVs are divided into two groups. Group 1 (IBS124/2015, IBS125/2015, IBS126/2015, IBS130/2015, IBS131/2015, IBS138/2015, and IBS142/2015) shared 90%-95% nucleotide and deduced amino acid similarities to the QX-like strain. Among these isolates, IBS142/2015 is the first IBV detected in Sarawak state located in East Malaysia (Borneo Island). Meanwhile, IBV isolates in Group 2 (IBS037A/2015, IBS037B/2015, IBS051/2015, and IBS180/2015) were 91.62% and 89.09% identical to Malaysian variant strain MH5365/95 (EU086600) at nucleotide and amino acid levels, respectively. In addition, all studied IBVs were distinctly separate from Massachusetts (70%-72% amino acid similarity) and European strains including 793/B, Italy-02, and D274 (68%-73% amino acid similarity). Viruses in Group 1 have the insertion of three amino acids at positions 23, 121, and 122 of the S1 protein and recombinant events detected at nucleotide position 4354-5864, with major parental sequence derived from QX-like (CK-CH-IBYZ-2011) and a minor parental sequence derived from Massachusetts vaccine strain (H120). This study demonstrated coexistence of the IBV Malaysian variant strain along with the QX-like strain in Malaysia.

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Directory of Open Access Journals (Sweden)

    MacKenzie Alasdair

    2009-12-01

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

  8. Direct Employment of Skilled Labour by Foreign Owned Subsidiaries and the Development of Autonomy and Intra and Inter Organizational Relationships

    DEFF Research Database (Denmark)

    Gammelgaard, Jens; McDonald, Frank; Tüselmann, Heinz-Josef

    2006-01-01

    This paper develops a conceptual framework on the strategic development of subsidiaries and the direct employment of skilled labour. The framework is based on autonomy, and intra and inters organizational relationships. The conceptual model outlines the conditions that are likely to lead to too...... much, or too little, autonomy and intra and inter organizational relationships. This model is then used to develop propositions on the links between autonomy and intra and inter organizational relationships and direct employment of skilled labour....

  9. Detection and analysis of circulating large intergenic non‐coding RNA regulator of reprogramming in plasma for breast cancer

    Science.gov (United States)

    Zhang, Kaijiong; Luo, Zhenglian; Zhang, Yi; Wang, Yuzhi; Cui, Meng; Liu, Lian

    2017-01-01

    Background Previous studies have indicated that large intergenic non‐coding RNA regulator of reprogramming (lincRNA‐ROR) plays an important role in regulating tumor carcinogenesis and metastasis; however, whether circulating lincRNA‐ROR could function as a potential biomarker for breast cancer (BC) diagnosis and monitoring is unknown. This study was conducted to investigate circulating lincRNA‐ROR in plasma as a potential biomarker for BC diagnosis and monitoring. Methods We performed reverse transcription‐quantitative‐PCR to examine lincRNA‐ROR expression levels in cell lines, 24 pairs of BC tissue samples, and 94 plasma samples from BC patients. Potential correlations between plasma lincRNA‐ROR levels and clinicopathological characteristics were analyzed. A receiver operating characteristic curve was calculated to evaluate the diagnostic values for BC. Pearson correlation analysis of lincRNA‐ROR in plasma samples and the corresponding tissues of the same patients was performed to explore tumor monitoring values. Results LincRNA‐ROR expression was significantly increased in BC cell lines, tissues, and plasma (all P ROR levels were associated with estrogen receptors (P = 0.042) and lymph node metastasis (P = 0.046). The area under the receiver operating characteristic curve of plasma lincRNA‐ROR was 0.844 (sensitivity 80.0%, specificity 56.7%), which was higher than carcinoembryonic and carbohydrate antigen 15‐3 values. Moreover, plasma lincRNA‐ROR levels were decreased in postoperative compared to preoperative samples (P ROR levels moderately correlated with the corresponding tissue level in the same patients (r2 = 0.638, P ROR may be a potential biomarker for BC diagnosis and a dynamic monitor. PMID:29090518

  10. Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs

    Directory of Open Access Journals (Sweden)

    Cheng Zou

    2018-03-01

    Full Text Available Intramuscular fat (IMF content is an important trait that can affect pork quality. Previous studies have identified many genes that can regulate IMF. Long intergenic non-coding RNAs (lincRNAs are emerging as key regulators in various biological processes. However, lincRNAs related to IMF in pig are largely unknown, and the mechanisms by which they regulate IMF are yet to be elucidated. Here we reconstructed 105,687 transcripts and identified 1,032 lincRNAs in pig longissimus dorsi muscle (LDM of four stages with different IMF contents based on published RNA-seq. These lincRNAs show typical characteristics such as shorter length and lower expression compared with protein-coding genes. Combined with methylation data, we found that both the promoter and genebody methylation of lincRNAs can negatively regulate lincRNA expression. We found that lincRNAs exhibit high correlation with their protein-coding neighbors in expression. Co-expression network analysis resulted in eight stage-specific modules, gene ontology and pathway analysis of them suggested that some lincRNAs were involved in IMF-related processes, such as fatty acid metabolism and peroxisome proliferator-activated receptor signaling pathway. Furthermore, we identified hub lincRNAs and found six of them may play important roles in IMF development. This work detailed some lincRNAs which may affect of IMF development in pig, and facilitated future research on these lincRNAs and molecular assisted breeding for pig.

  11. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  12. Endotracheal temperature and humidity measurements in laryngectomized patients: intra- and inter-patient variability

    NARCIS (Netherlands)

    Scheenstra, R.J.; Muller, S.H.; Vincent, A.; Sinaasappel, M.; Zuur, J.K.; Hilgers, F.J.M.

    2009-01-01

    This study assesses intra- and inter-patient variability in endotracheal climate (temperature and humidity) and effects of heat and moister exchangers (HME) in 16 laryngectomized individuals, measured repeatedly (N = 47). Inhalation Breath Length (IBL) was 1.35 s without HME and 1.05 s with HME (P <

  13. Endotracheal temperature and humidity measurements in laryngectomized patients: intra- and inter-patient variability

    NARCIS (Netherlands)

    Scheenstra, R. J.; Muller, S. H.; Vincent, A.; Sinaasappel, M.; Zuur, J. K.; Hilgers, Frans J. M.

    2009-01-01

    This study assesses intra- and inter-patient variability in endotracheal climate (temperature and humidity) and effects of heat and moister exchangers (HME) in 16 laryngectomized individuals, measured repeatedly (N = 47). Inhalation Breath Length (IBL) was 1.35 s without HME and 1.05 s with HME (P

  14. The Leech method for diagnosing constipation: intra- and interobserver variability and accuracy

    NARCIS (Netherlands)

    de Lorijn, Fleur; van Rijn, Rick R.; Heijmans, Jarom; Reitsma, Johannes B.; Voskuijl, Wieger P.; Henneman, Onno D. F.; Taminiau, Jan A.; Benninga, Marc A.

    2006-01-01

    BACKGROUND: The data concerning the value of a plain abdominal radiograph in childhood constipation are inconsistent. Recently, positive results have been reported of a new radiographic scoring system, "the Leech method", for assessing faecal loading. OBJECTIVE: To assess intra- and interobserver

  15. Detection of antigen in sera of patients with invasive aspergillosis : Intra- and interlaboratory reproducibility

    NARCIS (Netherlands)

    Verweij, PE; Erjavec, Z; Sluiters, W; Goessens, W; Rozenberg-Arska, M; Debets-Ossenkopp, YJ; Guiot, HFL; Meis, JFGM

    The intra-and interlaboratory reproducibilities of a commercial sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of Aspergillus galactomannan in serum (Platelia Aspergillus; Sanofi Diagnostics Pasteur, Marnes-La-Coquette, France) were evaluated in six laboratories of university

  16. Intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injuries.

    Science.gov (United States)

    Wangensteen, Arnlaug; Tol, Johannes L; Roemer, Frank W; Bahr, Roald; Dijkstra, H Paul; Crema, Michel D; Farooq, Abdulaziz; Guermazi, Ali

    2017-04-01

    To assess and compare the intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injury. Male athletes (n=40) with clinical diagnosis of acute hamstring injury and MRI ≤5days were selected from a prospective cohort. Two radiologists independently evaluated the MRIs using standardised scoring form including the modified Peetrons grading system, the Chan acute muscle strain injury classification and the British Athletics Muscle Injury Classification. Intra-and interrater reliability was assessed with linear weighted kappa (κ) or unweighted Cohen's κ and percentage agreement was calculated. We observed 'substantial' to 'almost perfect' intra- (κ range 0.65-1.00) and interrater reliability (κ range 0.77-1.00) with percentage agreement 83-100% and 88-100%, respectively, for severity gradings, overall anatomical sites and overall classifications for the three MRI systems. We observed substantial variability (κ range -0.05 to 1.00) for subcategories within the Chan classification and the British Athletics Muscle Injury Classification, however, the prevalence of positive scorings was low for some subcategories. The modified Peetrons grading system, overall Chan classification and overall British Athletics Muscle Injury Classification demonstrated 'substantial' to 'almost perfect' intra- and interrater reliability when scored by experienced radiologists. The intra- and interrater reliability for the anatomical subcategories within the classifications remains unclear. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Usefulness of MRI and its limitation in the diagnosis of intra- and extraforaminal nerve root compression

    Energy Technology Data Exchange (ETDEWEB)

    Kunogi, Junichi; Hasue, Mitsuo; Hamanaka, Ikki; Kaneoka, Tsuneharu; Shinko, Yuichiro (Japan Red Cross Central Hospital, Tokyo (Japan))

    1992-04-01

    To determine the diagnostic value of MRI for intra- and extraforaminal nerve root compression, parasagittal images, available in a total of 86 patients with lumbar degenerative disease, were reviewed in retrospect. Twenty surgical patients had intra- and extraforaminal nerve root compression, and the other 66 patients without this condition were served as controls. Intra- and extraforaminal nerve root compression was frequently associated with obstruction or constriction of the intervertebral foramina. MRI is considered useful for detecting the presence and constriction of the intervertebral foramina. MRI had a higher false positive rate in the elderly and patients with spondylolisthesis or multiple intervertebral degeneration. In detecting the site of compression lesions, including herniation of the intervertebral foramina, horizontal, coronal, and oblique coronal images were helpful. To increase the sensitivity of MRI in intra- and extraforaminal nerve root compression, it should be recommended that the form and constriction of the intervertebral foramina be determined on parasagittal images, findings on parasagittal images be compared with those on horizontal images, and MRI be combined with coronal and oblique coronal images, and the other imaging diagnostic methods, such as radiculomyelography and CT. (N.K.).

  18. Usefulness of MRI and its limitation in the diagnosis of intra- and extraforaminal nerve root compression

    International Nuclear Information System (INIS)

    Kunogi, Junichi; Hasue, Mitsuo; Hamanaka, Ikki; Kaneoka, Tsuneharu; Shinko, Yuichiro

    1992-01-01

    To determine the diagnostic value of MRI for intra- and extraforaminal nerve root compression, parasagittal images, available in a total of 86 patients with lumbar degenerative disease, were reviewed in retrospect. Twenty surgical patients had intra- and extraforaminal nerve root compression, and the other 66 patients without this condition were served as controls. Intra- and extraforaminal nerve root compression was frequently associated with obstruction or constriction of the intervertebral foramina. MRI is considered useful for detecting the presence and constriction of the intervertebral foramina. MRI had a higher false positive rate in the elderly and patients with spondylolisthesis or multiple intervertebral degeneration. In detecting the site of compression lesions, including herniation of the intervertebral foramina, horizontal, coronal, and oblique coronal images were helpful. To increase the sensitivity of MRI in intra- and extraforaminal nerve root compression, it should be recommended that the form and constriction of the intervertebral foramina be determined on parasagittal images, findings on parasagittal images be compared with those on horizontal images, and MRI be combined with coronal and oblique coronal images, and the other imaging diagnostic methods, such as radiculomyelography and CT. (N.K.)

  19. Intra- and Inter-Examiner Reliability in Angular Measurements of the Knee with a Smartphone Application

    Directory of Open Access Journals (Sweden)

    Derhon Viviane

    2017-06-01

    Full Text Available Purpose. Goniometric smartphone applications to measure joint angles offer greater practicality and accessibility, which makes them potential alternatives to a conventional goniometer. The aim of the present study was to evaluate the intra- and inter-examiner reliability in measuring the angles of the range of motion of the knee with the use of the ROM© goniometric smartphone application.

  20. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

    Directory of Open Access Journals (Sweden)

    Mark D Stenglein

    2015-05-01

    Full Text Available Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L and small (S genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on

  1. Cell biology of mitotic recombination

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2015-01-01

    Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules...... as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics...

  2. Thymic measurements in pathologically proven normal thymus and thymic hyperplasia: Intra- and interobserver variability

    Science.gov (United States)

    Araki, Tetsuro; Sholl, Lynette M.; Gerbaudo, Victor H.; Hatabu, Hiroto; Nishino, Mizuki

    2014-01-01

    Objective: Determine the intra- and interobserver variability of thymic measurements on computed tomography (CT) in patients with pathological diagnosis of thymic hyperplasia or normal thymus. Materials and Methods: Thirty-three patients with pathological diagnosis of thymic hyperplasia (n=25) or normal thymus (n=8) who had identifiable thymus gland on CT were retrospectively studied. Two radiologists independently measured thymic size and CT attenuation. Concordance correlation coefficients (CCCs) and Bland-Altman plots were used to assess intra- and interobserver agreements. Results: The intra- and interobserver agreements of thymic diameters and the lobe length were moderate, with CCCs ranging 0.73-0.89 and 0.72-0.81, respectively. Higher agreement was noted among patients whose measurements were performed on the same CT image in two independent measurements, with intraobserver CCC ≥0.95 for diameters and length. After providing readers with an instruction for consistent selection of CT image for measurements, the intra- and interobserver agreement improved, resulting in CCCs ranging 0.81-0.92 and 0.77-0.85 for diameters and length, respectively. Thymic lobe thickness had the least agreement. CT attenuation measurements were highly reproducible, with CCCs ranging 0.88-0.97. In patients with thymic CT attenuation >30HU, the attenuation measurements were more reproducible with narrower 95% limits of agreement. Conclusion: Thymic size measurements had moderate to high intra- and interobserver agreement, when the instruction for consistent selection of images were provided to the readers. CT attenuation was highly reproducible, with higher reproducibility for thymic glands with >30HU. Awareness of thymic measurement variability is necessary when interpreting measured values of normal thymus and thymic pathology on CT. PMID:24809315

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

    Directory of Open Access Journals (Sweden)

    Stanton Lawrence W

    2008-04-01

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

  4. Paenibacillus larvae 16S-23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization.

    Science.gov (United States)

    Dingman, Douglas W

    2012-07-01

    Paenibacillus larvae is the causative agent of American foulbrood in honey bee (Apis mellifera) larvae. PCR amplification of the 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions, and agarose gel electrophoresis of the amplified DNA, was performed using genomic DNA collected from 134 P. larvae strains isolated in Connecticut, six Northern Regional Research Laboratory stock strains, four strains isolated in Argentina, and one strain isolated in Chile. Following electrophoresis of amplified DNA, all isolates exhibited a common migratory profile (i.e., ITS-PCR fingerprint pattern) of six DNA bands. This profile represented a unique ITS-PCR DNA fingerprint that was useful as a fast, simple, and accurate procedure for identification of P. larvae. Digestion of ITS-PCR amplified DNA, using mung bean nuclease prior to electrophoresis, characterized only three of the six electrophoresis bands as homoduplex DNA and indicating three true ITS regions. These three ITS regions, DNA migratory band sizes of 915, 1010, and 1474 bp, signify a minimum of three types of rrn operons within P. larvae. DNA sequence analysis of ITS region DNA, using P. larvae NRRL B-3553, identified the 3' terminal nucleotides of the 16S rRNA gene, 5' terminal nucleotides of the 23S rRNA gene, and the complete DNA sequences of the 5S rRNA, tRNA(ala), and tRNA(ile) genes. Gene organization within the three rrn operon types was 16S-23S, 16S-tRNA(ala)-23S, and l6S-5S-tRNA(ile)-tRNA(ala)-23S and these operons were named rrnA, rrnF, and rrnG, respectively. The 23S rRNA gene was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to be present as seven copies. This was suggestive of seven rrn operon copies within the P. larvae genome. Investigation of the 16S-23S rDNA regions of this bacterium has aided the development of a diagnostic procedure and has helped genomic mapping investigations via characterization of the ITS regions. Copyright © 2012 Elsevier Inc

  5. CETP TaqIB genotype modifies the association between alcohol and coronary heart disease: the INTERGENE case-control study.

    Science.gov (United States)

    Mehlig, Kirsten; Strandhagen, Elisabeth; Svensson, Per-Arne; Rosengren, Annika; Torén, Kjell; Thelle, Dag S; Lissner, Lauren

    2014-11-01

    Alcohol consumption at moderate levels has been associated with decreased risk of coronary heart disease (CHD). However, the cardio-protective effect of alcohol may be restricted to subjects with a particular genotype of the cholesteryl ester transfer protein (CETP) polymorphism. There is evidence for this from one study in men, but the finding has not been confirmed since. The present study specifically re-examines the potential modification of the association between alcohol consumption and CHD by the CETP TaqIB (rs708272) polymorphism in a sample including both men and women. The INTERGENE case-control study consists of 618 patients with CHD and 2921 control subjects, of whom 19% were homozygous for the CETP TaqIB B2 allele. Alcohol consumption was categorized into sex-specific tertiles of ethanol intake, with non-drinkers constituting a separate category. Logistic regression was used to determine the association between CHD with genotype, ethanol intake, and their interaction. Participants with intermediate ethanol intake (2nd tertile) had lower risk of CHD than those with low ethanol intake (odds ratio [OR] = 0.65; 95% confidence interval [CI] 0.50-0.85). The strongest protective association was seen in the CETP TaqIB B2 homozygotes for intermediate vs. low ethanol intake (odds ratio OR = 0.21; 95% CI 0.10-0.44). The interaction between ethanol intake and genotype was statistically significant (p = 0.008), and of similar size in men and women though significant only in men (p = 0.01). The effect modification could not be explained by differences in lifestyle, socioeconomics, or alcohol-related biological variables such as HDL-cholesterol. Our study is the first to replicate previous findings of an effect modification in men. It gives only suggestive results for women, possibly due to the small number of female cases (n = 165). The prevented fraction for the favorable combination of genotype and alcohol consumption is about 6%, a value suggesting that the

  6. Intra- and Extra-Familial Child Molestation as Pathways Building on Parental and Relational Deficits and Personality Disorders

    NARCIS (Netherlands)

    Bogaerts, Stefan; Buschman, J.; Kunst, M. J. J.; Winkel, F. W.

    This article addresses the intra- and extra-familial pathways of child molestation. The data presented show preliminary evidence that the difference between the intra- and extra-familial routes can be explained by schizoid and avoidant (intra-familial) and antisocial and passive-aggressive

  7. Investigation of respiration induced intra- and inter-fractional tumour motion using a standard Cone Beam CT

    DEFF Research Database (Denmark)

    Gottlieb, Karina Lindberg; Hansen, Christian R; Hansen, Olfred

    2010-01-01

    To investigate whether a standard Cone beam CT (CBCT) scan can be used to determined the intra- and inter-fractional tumour motion for lung tumours that have infiltrated the mediastinum.......To investigate whether a standard Cone beam CT (CBCT) scan can be used to determined the intra- and inter-fractional tumour motion for lung tumours that have infiltrated the mediastinum....

  8. Hadron Correlations and Parton Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fries, R.J. [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)]. E-mail: rjfries@comp.tamu.edu

    2007-02-15

    Parton recombination has been found to be an extremely useful model to understand hadron production at the Relativistic Heavy Ion Collider. It is particularly important to explore its connections with hard processes. This article reviews some of the aspects of the quark recombination model and places particular emphasis on hadron correlations.

  9. The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

    CERN Document Server

    Lukashov, Sergey; Pravilov, Anatoly

    2018-01-01

    This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

  10. Intra- and inter-observer agreement and reliability of bone mineral density measurements around acetabular cup

    DEFF Research Database (Denmark)

    Mussmann, Bo Redder; Overgaard, Soren; Torfing, Trine

    2017-01-01

    with single-energy CT (SECT) and DECT in cemented and cementless cups.Material and Methods: Twenty-four acetabular cups inserted in porcine hip specimens were scanned with SECT and DECT. Bone density was measured in a three-dimensional volume adjacent to the cup. Double measurements were performed.......Results: BMD derived from SECT was approximately four times higher than that of DECT. In both scan modes, intraclass correlation coefficient (ICC) was >0.90 with no differences between repeated measurements, except for uncemented cups where a statistically significant difference of 11 mg/cm3 was found...... with DECT. DECT showed narrower limits of agreement than SECT. Inter-observer analysis showed small differences.Conclusion: BMD can be estimated with high intra- and inter-observer reliability with SECT and DECT around acetabular cups using custom software. The intra- and inter-observer agreement of DECT...

  11. Intra- and interfraction breathing variations during curative radiotherapy for lung cancer

    DEFF Research Database (Denmark)

    Juhler Nøttrup, Trine; Korreman, Stine Sofia; Pedersen, Anders Navrsted

    2007-01-01

    BACKGROUND AND PURPOSE: This study aimed at quantifying the breathing variations among lung cancer patients over full courses of fractionated radiotherapy. The intention was to relate these variations to the margins assigned to lung tumours, to account for respiratory motion, in fractionated...... radiotherapy. MATERIALS AND METHODS: Eleven lung cancer patients were included in the study. The patients' chest wall motions were monitored as a surrogate measure for breathing motion during each fraction of radiotherapy by use of an external optical marker. The exhale level variations were evaluated...... with respect to exhale points and fraction-baseline, defined for intra- and interfraction variations respectively. The breathing amplitude was evaluated as breathing cycle amplitudes and fraction-max-amplitudes defined for intra- and interfraction breathing, respectively. RESULTS: The breathing variations over...

  12. The relation between intra- and interpersonal factors and food consumption level among Iranian adolescent girls

    OpenAIRE

    Kazemi, Ashraf; Zahraei, Nafisehsadat Nekuei; Nazarian, Naser

    2016-01-01

    Background: Poor nutrition habits in adolescent girls endanger their health and are followed by serious systemic diseases in adulthood and negative effects on their reproductive health. To design health promotion programs, understanding of the intra- and interpersonal associated factors with treatment is essential, and this was the aim of this study. Materials and Methods: This cross-sectional study was conducted on 193 adolescent girls of age 11-15 years. Random cluster selection was used fo...

  13. Intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injuries

    International Nuclear Information System (INIS)

    Wangensteen, Arnlaug; Tol, Johannes L.; Roemer, Frank W.; Bahr, Roald; Dijkstra, H. Paul; Crema, Michel D.; Farooq, Abdulaziz; Guermazi, Ali

    2017-01-01

    Highlights: • Three different MRI grading and classification systems for acute hamstring injuries are overall reliable. • Reliability for the subcategories within these MRI grading and classification systems remains, however, unclear. - Abstract: Objective: To assess and compare the intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injury. Methods: Male athletes (n = 40) with clinical diagnosis of acute hamstring injury and MRI ≤5 days were selected from a prospective cohort. Two radiologists independently evaluated the MRIs using standardised scoring form including the modified Peetrons grading system, the Chan acute muscle strain injury classification and the British Athletics Muscle Injury Classification. Intra-and interrater reliability was assessed with linear weighted kappa (κ) or unweighted Cohen's κ and percentage agreement was calculated. Results: We observed ‘substantial’ to ‘almost perfect’ intra- (κ range 0.65–1.00) and interrater reliability (κ range 0.77–1.00) with percentage agreement 83–100% and 88–100%, respectively, for severity gradings, overall anatomical sites and overall classifications for the three MRI systems. We observed substantial variability (κ range −0.05 to 1.00) for subcategories within the Chan classification and the British Athletics Muscle Injury Classification, however, the prevalence of positive scorings was low for some subcategories. Conclusions: The modified Peetrons grading system, overall Chan classification and overall British Athletics Muscle Injury Classification demonstrated ‘substantial' to ‘almost perfect' intra- and interrater reliability when scored by experienced radiologists. The intra- and interrater reliability for the anatomical subcategories within the classifications remains unclear.

  14. Intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injuries

    Energy Technology Data Exchange (ETDEWEB)

    Wangensteen, Arnlaug, E-mail: arnlaug.wangensteen@nih.no [Aspetar, Orthopaedic and Sports Medicine Hospital, Doha (Qatar); Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo (Norway); Tol, Johannes L., E-mail: johannes.tol@aspetar.com [Aspetar, Orthopaedic and Sports Medicine Hospital, Doha (Qatar); Amsterdam Center for Evidence Sports Medicine, Academic Medical Center (Netherlands); The Sports Physician Group, OLVG, Amsterdam (Netherlands); Roemer, Frank W. [Quantitative Imaging Center, Department of Radiology, Boston University School of Medicine, Boston, MA (United States); Department of Radiology, University of Erlangen-Nuremberg, Erlangen (Germany); Bahr, Roald [Aspetar, Orthopaedic and Sports Medicine Hospital, Doha (Qatar); Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo (Norway); Dijkstra, H. Paul [Aspetar, Orthopaedic and Sports Medicine Hospital, Doha (Qatar); Crema, Michel D. [Quantitative Imaging Center, Department of Radiology, Boston University School of Medicine, Boston, MA (United States); Department of Radiology, Saint-Antoine Hospital, University Paris VI, Paris (France); Farooq, Abdulaziz [Aspetar, Orthopaedic and Sports Medicine Hospital, Doha (Qatar); Guermazi, Ali [Quantitative Imaging Center, Department of Radiology, Boston University School of Medicine, Boston, MA (United States)

    2017-04-15

    Highlights: • Three different MRI grading and classification systems for acute hamstring injuries are overall reliable. • Reliability for the subcategories within these MRI grading and classification systems remains, however, unclear. - Abstract: Objective: To assess and compare the intra- and interrater reliability of three different MRI grading and classification systems after acute hamstring injury. Methods: Male athletes (n = 40) with clinical diagnosis of acute hamstring injury and MRI ≤5 days were selected from a prospective cohort. Two radiologists independently evaluated the MRIs using standardised scoring form including the modified Peetrons grading system, the Chan acute muscle strain injury classification and the British Athletics Muscle Injury Classification. Intra-and interrater reliability was assessed with linear weighted kappa (κ) or unweighted Cohen's κ and percentage agreement was calculated. Results: We observed ‘substantial’ to ‘almost perfect’ intra- (κ range 0.65–1.00) and interrater reliability (κ range 0.77–1.00) with percentage agreement 83–100% and 88–100%, respectively, for severity gradings, overall anatomical sites and overall classifications for the three MRI systems. We observed substantial variability (κ range −0.05 to 1.00) for subcategories within the Chan classification and the British Athletics Muscle Injury Classification, however, the prevalence of positive scorings was low for some subcategories. Conclusions: The modified Peetrons grading system, overall Chan classification and overall British Athletics Muscle Injury Classification demonstrated ‘substantial' to ‘almost perfect' intra- and interrater reliability when scored by experienced radiologists. The intra- and interrater reliability for the anatomical subcategories within the classifications remains unclear.

  15. Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses.

    Science.gov (United States)

    Gell, Gyöngyvér; Sebestyén, Endre; Balázs, Ervin

    2015-02-01

    Recombination among RNA viruses is a natural phenomenon that appears to have played a significant role in the species development and the evolution of many strains. It also has particular significance for the risk assessment of plants which have been genetically modified for disease resistance by incorporating viral sequences into their genomes. However, the exact recombination events taking place in viral genomes are not investigated in detail for many virus groups. In this analysis, different single-stranded positive-sense RNA potyviruses were compared using various in silico recombination detection methods and new recombination events in the Sugarcane mosaic virus (SCMV) subgroup were detected. For an extended in silico recombination analysis, two of the analyzed Maize dwarf mosaic virus full-length genomes were sequenced additionally during this work. These results strengthen the evidence that recombination is a major driving force in virus evolution, and the emergence of new virus variants in the SCMV subgroup, paired with mutations, could generate viruses with altered biological properties. The intra- and interspecific homolog recombinations seem to be a general trait in this virus group, causing little or no changes to the amino acid of the progenies. However, we found a few breakpoints between the members of SCMV subgroup and the weed-infecting distant relatives, but only a few methods of the RDP3 package predicted these events with low significance level.

  16. A Bacillus megaterium System for the Production of Recombinant Proteins and Protein Complexes.

    Science.gov (United States)

    Biedendieck, Rebekka

    2016-01-01

    For many years the Gram-positive bacterium Bacillus megaterium has been used for the production and secretion of recombinant proteins. For this purpose it was systematically optimized. Plasmids with different inducible promoter systems, with different compatible origins, with small tags for protein purification and with various specific signals for protein secretion were combined with genetically improved host strains. Finally, the development of appropriate cultivation conditions for the production strains established this organism as a bacterial cell factory even for large proteins. Along with the overproduction of individual proteins the organism is now also used for the simultaneous coproduction of up to 14 recombinant proteins, multiple subsequently interacting or forming protein complexes. Some of these recombinant strains are successfully used for bioconversion or the biosynthesis of valuable components including vitamins. The titers in the g per liter scale for the intra- and extracellular recombinant protein production prove the high potential of B. megaterium for industrial applications. It is currently further enhanced for the production of recombinant proteins and multi-subunit protein complexes using directed genetic engineering approaches based on transcriptome, proteome, metabolome and fluxome data.

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

    DEFF Research Database (Denmark)

    Wyszynski, Asaf; Hong, Chi-chen; Lam, Kristin

    2016-01-01

    gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα......-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings...... in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10(-19)) and identify 13 additional linked...

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

    Science.gov (United States)

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

    2014-05-01

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

  19. Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes.

    Science.gov (United States)

    Zhu, Luchang; Olsen, Randall J; Horstmann, Nicola; Shelburne, Samuel A; Fan, Jia; Hu, Ye; Musser, James M

    2016-07-01

    Variable-number tandem-repeat (VNTR) polymorphisms are ubiquitous in bacteria. However, only a small fraction of them has been functionally studied. Here, we report an intergenic VNTR polymorphism that confers an altered level of toxin production and increased virulence in Streptococcus pyogenes The nature of the polymorphism is a one-unit deletion in a three-tandem-repeat locus upstream of the rocA gene encoding a sensor kinase. S. pyogenes strains with this type of polymorphism cause human infection and produce significantly larger amounts of the secreted cytotoxins S. pyogenes NADase (SPN) and streptolysin O (SLO). Using isogenic mutant strains, we demonstrate that deleting one or more units of the tandem repeats abolished RocA production, reduced CovR phosphorylation, derepressed multiple CovR-regulated virulence factors (such as SPN and SLO), and increased virulence in a mouse model of necrotizing fasciitis. The phenotypic effect of the VNTR polymorphism was nearly the same as that of inactivating the rocA gene. In summary, we identified and characterized an intergenic VNTR polymorphism in S. pyogenes that affects toxin production and virulence. These new findings enhance understanding of rocA biology and the function of VNTR polymorphisms in S. pyogenes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Intra- and extra-familial child molestation as pathways building on parental and relational deficits and personality disorders.

    Science.gov (United States)

    Bogaerts, S; Buschman, J; Kunst, M J J; Winkel, F W

    2010-08-01

    This article addresses the intra- and extra-familial pathways of child molestation. The data presented show preliminary evidence that the difference between the intra- and extra-familial routes can be explained by schizoid and avoidant (intra-familial) and antisocial and passive-aggressive (extra-familial) personality structures. This study also reveals that the amount of warmth and autonomy received during childhood is associated with both intra- and extra-familial child-molesting behaviour. These findings contribute to a further explanation of this deviant sexual conduct and to the development and differentiation of the treatment of child molesters.

  1. Controlled Release from Recombinant Polymers

    Science.gov (United States)

    Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

    2014-01-01

    Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed. PMID:24956486

  2. Hydrogen recombiner development at AECL

    International Nuclear Information System (INIS)

    Dewit, W.A.; Koroll, G.W.; Loesel Sitar, J.; Graham, W.R.C.

    1997-01-01

    Catalytic recombiners have been developed at AECL for the purpose of hydrogen removal in post-accident nuclear containment buildings. The recombiners are based on a particular catalyst designed by AECL which has extraordinary resistance to fouling from water and water vapour and a large thermodynamic range of operation. The catalysts were developed, originally, for the purpose of heavy water manufacturing by way of a catalytic exchange process. Application of these catalyst materials in recombiners for containment applications began in the late 1980's. The first application was a passive recombiner, qualified for use in control of radiolytic hydrogen in the headspace of a pool-type experimental reactor of AECL design in 1988. The passive, or natural convection recombiner concept has continued development to commercial stage for application in power reactor containments. This paper reviews the AECL recombiner development, describes the current model and shows results from tests of full-scale recombiners in the Large Scale Vented Combustion Test Facility at AECL-WL. The AECL recombiner is designed for compactness and ease of engineering into containment. The design is a simple, open-ended rectangular enclosure with catalyst elements arranged inside to promote optimum convective flow driven by heat of recombination at the catalyst surface. Self start, as evidenced by catalyst heating and initiation of flow, is achieved in less than 1% hydrogen, with available oxygen, at room temperature and 100% relative humidity. This low temperature start-up in condensing atmospheres is viewed as the most challenging condition for wet-proofing effectiveness. Cold start-up is a vital performance requirement in containments, such as CANDU, where engineered air-cooling systems are operating and where long-term hydrogen control is required, after containment atmospheres have cooled. Once started, the removal capacity scales linearly with the inlet cross-section area and the partial

  3. Review of Parton Recombination Models

    International Nuclear Information System (INIS)

    Bass, Steffen A

    2006-01-01

    Parton recombination models have been very successful in explaining data taken at RHIC on hadron spectra and emission patterns in Au+Au collisions at transverse momenta above 2 GeV/c, which have exhibited features which could not be understood in the framework of basic perturbative QCD. In this article I will review the current status on recombination models and outline which future challenges need to be addressed by this class of models

  4. Recombinant snake venom prothrombin activators

    OpenAIRE

    L?vgren, Ann

    2012-01-01

    Three prothrombin activators; ecarin, which was originally isolated from the venom of the saw-scaled viper Echis carinatus, trocarin from the rough-scaled snake Tropidechis carinatus, and oscutarin from the Taipan snake Oxyuranus scutellatus, were expressed in mammalian cells with the purpose to obtain recombinant prothrombin activators that could be used to convert prothrombin to thrombin. We have previously reported that recombinant ecarin can efficiently generate thrombin without the need ...

  5. Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences.

    Science.gov (United States)

    Pilla, Giulia; McVicker, Gareth; Tang, Christoph M

    2017-09-01

    Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.

  6. Intergenic sequence between Arabidopsis caseinolytic protease B-cytoplasmic/heat shock protein100 and choline kinase genes functions as a heat-inducible bidirectional promoter.

    Science.gov (United States)

    Mishra, Ratnesh Chandra; Grover, Anil

    2014-11-01

    In Arabidopsis (Arabidopsis thaliana), the At1g74310 locus encodes for caseinolytic protease B-cytoplasmic (ClpB-C)/heat shock protein100 protein (AtClpB-C), which is critical for the acquisition of thermotolerance, and At1g74320 encodes for choline kinase (AtCK2) that catalyzes the first reaction in the Kennedy pathway for phosphatidylcholine biosynthesis. Previous work has established that the knockout mutants of these genes display heat-sensitive phenotypes. While analyzing the AtClpB-C promoter and upstream genomic regions in this study, we noted that AtClpB-C and AtCK2 genes are head-to-head oriented on chromosome 1 of the Arabidopsis genome. Expression analysis showed that transcripts of these genes are rapidly induced in response to heat stress treatment. In stably transformed Arabidopsis plants harboring this intergenic sequence between head-to-head oriented green fluorescent protein and β-glucuronidase reporter genes, both transcripts and proteins of the two reporters were up-regulated upon heat stress. Four heat shock elements were noted in the intergenic region by in silico analysis. In the homozygous transfer DNA insertion mutant Salk_014505, 4,393-bp transfer DNA is inserted at position -517 upstream of ATG of the AtClpB-C gene. As a result, AtCk2 loses proximity to three of the four heat shock elements in the mutant line. Heat-inducible expression of the AtCK2 transcript was completely lost, whereas the expression of AtClpB-C was not affected in the mutant plants. Our results suggest that the 1,329-bp intergenic fragment functions as a heat-inducible bidirectional promoter and the region governing the heat inducibility is possibly shared between the two genes. We propose a model in which AtClpB-C shares its regulatory region with heat-induced choline kinase, which has a possible role in heat signaling. © 2014 American Society of Plant Biologists. All Rights Reserved.

  7. Intra and inter-rater reliability study of pelvic floor muscle dynamometric measurements

    Directory of Open Access Journals (Sweden)

    Natalia M. Martinho

    2015-04-01

    Full Text Available OBJECTIVE: The aim of this study was to evaluate the intra and inter-rater reliability of pelvic floor muscle (PFM dynamometric measurements for maximum and average strengths, as well as endurance. METHOD: A convenience sample of 18 nulliparous women, without any urogynecological complaints, aged between 19 and 31 (mean age of 25.4±3.9 participated in this study. They were evaluated using a pelvic floor dynamometer based on load cell technology. The dynamometric evaluations were repeated in three successive sessions: two on the same day with a rest period of 30 minutes between them, and the third on the following day. All participants were evaluated twice in each session; first by examiner 1 followed by examiner 2. The vaginal dynamometry data were analyzed using three parameters: maximum strength, average strength, and endurance. The Intraclass Correlation Coefficient (ICC was applied to estimate the PFM dynamometric measurement reliability, considering a good level as being above 0.75. RESULTS: The intra and inter-raters' analyses showed good reliability for maximum strength (ICCintra-rater1=0.96, ICCintra-rater2=0.95, and ICCinter-rater=0.96, average strength (ICCintra-rater1=0.96, ICCintra-rater2=0.94, and ICCinter-rater=0.97, and endurance (ICCintra-rater1=0.88, ICCintra-rater2=0.86, and ICCinter-rater=0.92 dynamometric measurements. CONCLUSIONS: The PFM dynamometric measurements showed good intra- and inter-rater reliability for maximum strength, average strength and endurance, which demonstrates that this is a reliable device that can be used in clinical practice.

  8. Intra and inter-examiner reliability of the subacromial impingement index

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Carlos Eduardo Sala; Ferreira, Felipe Varella; Carvalho Sposito, Guilherme de; Nogueira-Barbosa, Marcello Henrique; Oliveira, Anamaria Siriani de [University of Sao Paulo, Ribeirao Preto School of Medicine, Ribeirao Preto, SP (Brazil)

    2010-01-15

    The present study aimed to assess the reliability of intra and inter-examiner subacromial impingement index (SII) measures obtained from radiographs. Thirty-six individuals were enrolled and divided into two groups: control group, composed of 18 volunteers in good general health without shoulder problems, and a group of 18 patients with subacromial impingement syndrome (SIS). Radiographic images were taken with the dominant upper limb in neutral rotation, while the volunteers held their arm at 90 of abduction in the frontal plane. The beam of radiation at 30 craniocaudal inclination was used to provide an antero-posterior image view. Three blinded examiners each performed three measurements from the subacromial space (SS) and the anatomical neck of the humerus (NH). The SII was calculated as the ratio of the SS and the NH measures. The mean values of SII were compared using t-tests. The intra-class correlation coefficient (ICC) was used to assess intra- and inter-examiner reliability of the measures. The mean values of SII were greater for the control group (0.12) than for the SIS group (0.08; p = 0.0071). SII measurements showed excellent intra (0.96-0.99) and inter-examiner reliability (0.94) for both the control and SIS group. The results of this study show the potential use of the SII; a greater mean value for the control group compared to the SIS group and excellent reliability for intra- and inter-examiner measurement. Validation studies of the index should be conducted to correlate the index with clinical findings from subacromial impingement syndrome. (orig.)

  9. Decreased intra- and inter- salience network functional connectivity is related to trait anxiety in adolescents

    Directory of Open Access Journals (Sweden)

    Haiyang eGeng

    2016-01-01

    Full Text Available Objective: Adolescence is a critical period for the vulnerability of anxiety. Imaging studies focusing on adolescents’ susceptibility to anxiety suggest that the different development trajectories between the limbic system and the executive control system may play important roles in this phenomenon. However, few studies have explored the brain basis of this susceptibility from the perspective of functional networks. The salience network(SN)consists of a series of key limbic and prefrontal regions that are engaged in the development of anxiety, such as the amygdala, anterior insula (AI and dorsal anterior cingulate cortex (dACC. Intra- and inter- network connections in this system play essential roles in bottom-up attention and top-down regulation of anxiety, nevertheless, little is known about whether the SN-centered connections are associated with trait anxiety (i.e., susceptibility to anxiety in adolescents. Method: Here, we applied resting-state functional magnetic resonance imaging (fMRI to explore the relationship between intra- and inter- network functional connectivity (FC of the SN and trait anxiety in adolescents using the amygdala, AI and dACC as the regions of interest (ROI. Results: We found that trait anxiety levels were inversely associated with both characteristic AI-dACC FC in the SN and distributed inter-network FC between the SN and multiple functional systems, which included the default mode network and the executive control network. Conclusions: Our results indicate that weaker intra- and inter- network FC of the SN was linked to higher trait anxiety among adolescents, and it may underlie altered salience processing and cognitive regulation.

  10. Intra- and interfraction breathing variations during curative radiotherapy for lung cancer

    International Nuclear Information System (INIS)

    Juhler Nottrup, Trine; Korreman, Stine Sofia; Pedersen, Anders Navrsted; Aarup, Lasse Rye; Nystroem, Hakan; Olsen, Mikael; Specht, Lena

    2007-01-01

    Background and purpose: This study aimed at quantifying the breathing variations among lung cancer patients over full courses of fractionated radiotherapy. The intention was to relate these variations to the margins assigned to lung tumours, to account for respiratory motion, in fractionated radiotherapy. Materials and methods: Eleven lung cancer patients were included in the study. The patients' chest wall motions were monitored as a surrogate measure for breathing motion during each fraction of radiotherapy by use of an external optical marker. The exhale level variations were evaluated with respect to exhale points and fraction-baseline, defined for intra- and interfraction variations respectively. The breathing amplitude was evaluated as breathing cycle amplitudes and fraction-max-amplitudes defined for intra- and interfraction breathing, respectively. Results: The breathing variations over a full treatment course, including both intra- and interfraction variations, were 15.2 mm (median over the patient population), range 5.5-26.7 mm, with the variations in exhale level as the major contributing factor. The median interfraction span in exhale level was 14.8 mm, whereas the median fraction-max-amplitude was 6.1 mm (median of patient individual SD 1.4). The median intrafraction span in exhale level was 1.6 mm, and the median breathing cycle amplitude was 4.0 mm (median of patient individual SD 1.4). Conclusions: The variations in externally measured exhale levels are larger than variations in breathing amplitude. The interfraction variations in exhale level are in general are up to 10 times larger than intrafraction variations. Margins to account for respiratory motion cannot safely be based on one planning session, especially not if relying on measuring external marker motion. Margins for lung tumours should include interfraction variations in breathing

  11. Intra- and interobserver reliability of the Eaton classification for trapeziometacarpal arthritis: a systematic review.

    Science.gov (United States)

    Berger, Aaron J; Momeni, Arash; Ladd, Amy L

    2014-04-01

    Trapeziometacarpal, or thumb carpometacarpal (CMC), arthritis is a common problem with a variety of treatment options. Although widely used, the Eaton radiographic staging system for CMC arthritis is of questionable clinical utility, as disease severity does not predictably correlate with symptoms or treatment recommendations. A possible reason for this is that the classification itself may not be reliable, but the literature on this has not, to our knowledge, been systematically reviewed. We therefore performed a systematic review to determine the intra- and interobserver reliability of the Eaton staging system. We systematically reviewed English-language studies published between 1973 and 2013 to assess the degree of intra- and interobserver reliability of the Eaton classification for determining the stage of trapeziometacarpal joint arthritis and pantrapezial arthritis based on plain radiographic imaging. Search engines included: PubMed, Scopus(®), and CINAHL. Four studies, which included a total of 163 patients, met our inclusion criteria and were evaluated. The level of evidence of the studies included in this analysis was determined using the Oxford Centre for Evidence Based Medicine Levels of Evidence Classification by two independent observers. A limited number of studies have been performed to assess intra- and interobserver reliability of the Eaton classification system. The four studies included were determined to be Level 3b. These studies collectively indicate that the Eaton classification demonstrates poor to fair interobserver reliability (kappa values: 0.11-0.56) and fair to moderate intraobserver reliability (kappa values: 0.54-0.657). Review of the literature demonstrates that radiographs assist in the assessment of CMC joint disease, but there is not a reliable system for classification of disease severity. Currently, diagnosis and treatment of thumb CMC arthritis are based on the surgeon's qualitative assessment combining history, physical

  12. Mn∕Ca intra- and inter-test variability in the benthic foraminifer Ammonia tepida

    Directory of Open Access Journals (Sweden)

    J. Petersen

    2018-01-01

    Full Text Available The adaptation of some benthic foraminiferal species to low-oxygen conditions provides the prospect of using the chemical composition of their tests as proxies for bottom water oxygenation. Manganese may be particularly suitable as such a geochemical proxy because this redox element is soluble in reduced form (Mn2+ and hence can be incorporated into benthic foraminiferal tests under low-oxygen conditions. Therefore, intra- and inter-test differences in foraminiferal Mn∕Ca ratios may hold important information about short-term variability in pore water Mn2+ concentrations and sediment redox conditions. Here, we studied Mn∕Ca intra- and inter-test variability in living individuals of the shallow infaunal foraminifer Ammonia tepida sampled in Lake Grevelingen (the Netherlands in three different months of 2012. The deeper parts of this lake are characterized by seasonal hypoxia/anoxia with associated shifts in microbial activity and sediment geochemistry, leading to seasonal Mn2+ accumulation in the pore water. Earlier laboratory experiments with similar seawater Mn2+ concentrations as encountered in the pore waters of Lake Grevelingen suggest that intra-test variability due to ontogenetic trends (i.e. size-related effects and/or other vital effects occurring during calcification in A. tepida (11–25 % relative SD, RSD is responsible for part of the observed variability in Mn∕Ca. Our present results show that the seasonally highly dynamic environmental conditions in the study area lead to a strongly increased Mn∕Ca intra- and inter-test variability (average of 45 % RSD. Within single specimens, both increasing and decreasing trends in Mn∕Ca ratios with size are observed. Our results suggest that the variability in successive single-chamber Mn∕Ca ratios reflects the temporal variability in pore water Mn2+. Additionally, active or passive migration of the foraminifera in the surface sediment may explain part of the observed Mn

  13. Intra and inter-examiner reliability of the subacromial impingement index

    International Nuclear Information System (INIS)

    Ramos, Carlos Eduardo Sala; Ferreira, Felipe Varella; Carvalho Sposito, Guilherme de; Nogueira-Barbosa, Marcello Henrique; Oliveira, Anamaria Siriani de

    2010-01-01

    The present study aimed to assess the reliability of intra and inter-examiner subacromial impingement index (SII) measures obtained from radiographs. Thirty-six individuals were enrolled and divided into two groups: control group, composed of 18 volunteers in good general health without shoulder problems, and a group of 18 patients with subacromial impingement syndrome (SIS). Radiographic images were taken with the dominant upper limb in neutral rotation, while the volunteers held their arm at 90 of abduction in the frontal plane. The beam of radiation at 30 craniocaudal inclination was used to provide an antero-posterior image view. Three blinded examiners each performed three measurements from the subacromial space (SS) and the anatomical neck of the humerus (NH). The SII was calculated as the ratio of the SS and the NH measures. The mean values of SII were compared using t-tests. The intra-class correlation coefficient (ICC) was used to assess intra- and inter-examiner reliability of the measures. The mean values of SII were greater for the control group (0.12) than for the SIS group (0.08; p = 0.0071). SII measurements showed excellent intra (0.96-0.99) and inter-examiner reliability (0.94) for both the control and SIS group. The results of this study show the potential use of the SII; a greater mean value for the control group compared to the SIS group and excellent reliability for intra- and inter-examiner measurement. Validation studies of the index should be conducted to correlate the index with clinical findings from subacromial impingement syndrome. (orig.)

  14. Mn/Ca intra- and inter-test variability in the benthic foraminifer Ammonia tepida

    Science.gov (United States)

    Petersen, Jassin; Barras, Christine; Bézos, Antoine; La, Carole; de Nooijer, Lennart J.; Meysman, Filip J. R.; Mouret, Aurélia; Slomp, Caroline P.; Jorissen, Frans J.

    2018-01-01

    The adaptation of some benthic foraminiferal species to low-oxygen conditions provides the prospect of using the chemical composition of their tests as proxies for bottom water oxygenation. Manganese may be particularly suitable as such a geochemical proxy because this redox element is soluble in reduced form (Mn2+) and hence can be incorporated into benthic foraminiferal tests under low-oxygen conditions. Therefore, intra- and inter-test differences in foraminiferal Mn/Ca ratios may hold important information about short-term variability in pore water Mn2+ concentrations and sediment redox conditions. Here, we studied Mn/Ca intra- and inter-test variability in living individuals of the shallow infaunal foraminifer Ammonia tepida sampled in Lake Grevelingen (the Netherlands) in three different months of 2012. The deeper parts of this lake are characterized by seasonal hypoxia/anoxia with associated shifts in microbial activity and sediment geochemistry, leading to seasonal Mn2+ accumulation in the pore water. Earlier laboratory experiments with similar seawater Mn2+ concentrations as encountered in the pore waters of Lake Grevelingen suggest that intra-test variability due to ontogenetic trends (i.e. size-related effects) and/or other vital effects occurring during calcification in A. tepida (11-25 % relative SD, RSD) is responsible for part of the observed variability in Mn/Ca. Our present results show that the seasonally highly dynamic environmental conditions in the study area lead to a strongly increased Mn/Ca intra- and inter-test variability (average of 45 % RSD). Within single specimens, both increasing and decreasing trends in Mn/Ca ratios with size are observed. Our results suggest that the variability in successive single-chamber Mn/Ca ratios reflects the temporal variability in pore water Mn2+. Additionally, active or passive migration of the foraminifera in the surface sediment may explain part of the observed Mn/Ca variability.

  15. Intra and extracellular nuclease production by Aspergillus niger and Aspergillus nidulans

    Directory of Open Access Journals (Sweden)

    Ferreira Adlane V. B.

    1998-01-01

    Full Text Available Intra and extracellular nuclease production by strains of Aspergillus niger and Aspergillus nidulans was estimated using a modified DNAse test agar and cell-free extract assays. Differences in the production of nucleases by A. niger and A. nidulans were observed. These observations suggest that the DNAse test agar can be helpful for a quick screening for some types of nucleases in filamentous fungi. The assays using cell-free extracts can also be useful for initial characterization of other types of nucleases.

  16. COMPETITION AND FACILITATION EFFECTS OF DIFFERENTIAL INTRA-AND INTER-ROW WEED MANAGEMENT IN SUGARCANE

    OpenAIRE

    Martin , J; Chabalier , M; Letourmy , P; Chopart , J.-L; Arhiman , E; Marion , D

    2013-01-01

    International audience; Differential intra-and inter-row weed management can be a mean to reduce herbicide use in sugarcane. In 2011, a field experiment was conducted in La Reunion Island to assess inter-row weed competition. Four inter-row weed competition treatments for a duration of one (T1), two (T2), three (T3) and four (T4) months after planting were compared in a randomized complete block design with 5 replicates; treatment plots were paired with non-weeded inter-row control plots. All...

  17. Recovery of Moraxella ovis from the bovine respiratory tract and differentiation of Moraxella species by tDNA-intergenic spacer PCR.

    Science.gov (United States)

    Catry, Boudewijn; Boyen, Filip; Baele, Margo; Dewulf, Jeroen; de Kruif, Aart; Vaneechoutte, Mario; Haesebrouck, Freddy; Decostere, Annemie

    2007-03-10

    The purpose of the present study was to identify Moraxella (M.)--like organisms recovered from calves suffering from respiratory disease down to species level by means of tDNA-intergenic spacer length polymorphism analysis (tDNA-PCR), and to perform antimicrobial susceptibility testing of these isolates using an agar dilution technique. A total of 16 isolates originating from 12 unrelated occasions were identified as Moraxella ovis, and tDNA fingerprinting showed clear delineation from other Moraxella species. The minimal inhibitory concentrations (in microg/mL) for 90% of the investigated isolates were combination trimethoprim-sulfonamides; 4 for erythromycin; 8 for tilmicosin; 1 for florfenicol and 0.125 for enrofloxacin.

  18. Genomic relationships of Actinobacillus pleuropneumoniae serotype 2 strains evaluated by ribotyping, sequence analysis of ribosomal intergenic regions, and pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Fussing, V.

    1998-01-01

    The aim of the present study was to examine the genomic relationship among 112 Actinobacillus pleuropneumoniae serotype 2 strains obtained throughout Europe and North America. HindIII ribotyping of the strains resulted in five ribotypes of high similarity (87-98%). Sequence analysis of the riboso......The aim of the present study was to examine the genomic relationship among 112 Actinobacillus pleuropneumoniae serotype 2 strains obtained throughout Europe and North America. HindIII ribotyping of the strains resulted in five ribotypes of high similarity (87-98%). Sequence analysis...... of the ribosomal intergenic region of strains representing each ribotype and each country showed no differences. A common ribotype was further characterized by PFGE of 12 strains representing all countries. The resultant five PFGE patterns of European strains showed a similarity of more than 91%, to which the two...

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

    Directory of Open Access Journals (Sweden)

    J Stephen Dumler

    2016-09-01

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

  20. beta-Cyclodextrin derivatives as carriers to enhance the antiviral activity of an antisense oligonucleotide directed toward a coronavirus intergenic consensus sequence.

    Science.gov (United States)

    Abdou, S; Collomb, J; Sallas, F; Marsura, A; Finance, C

    1997-01-01

    The ability of cyclodextrins to enhance the antiviral activity of a phosphodiester oligodeoxynucleotide has been investigated. A 18-mer oligodeoxynucleotide complementary to the initiation region of the mRNA coding for the spike protein and containing the intergenic consensus sequence of an enteric coronavirus has been tested for antiviral action against virus growth in human adenocarcinoma cells. The phosphodiester oligodeoxynucleotide only showed a limited effect on virus growth rate (from 12 to 34% viral inhibition in cells treated with 7.5 to 25 microM oligodeoxynucleotide, respectively, at a multiplicity of infection of 0.1 infectious particle per cell). In the same conditions, the phosphorothioate analogue exhibited stronger antiviral activity, the inhibition increased from 56 to 90%. The inhibitory effect of this analogue was antisense and sequence-specific. Northern blot analysis showed that the sequence-dependent mechanism of action appears to be the inhibition of mRNA transcription. We conclude that the coronavirus intergenic consensus sequence is a good target for an antisense oligonucleotide antiviral action. The properties of the phosphodiester oligonucleotide was improved after its complexation with cyclodextrins. The most important increase of the antiviral activity (90% inhibition) was obtained with only 7.5 microM oligonucleotide complexed to a cyclodextrin derivative, 6-deoxy-6-S-beta-D-galactopyranosyl-6-thio-cyclomalto-heptaose+ ++ in a molar ratio of 1:100. These studies suggest that the use of cyclodextrin derivatives as carrier for phosphodiester oligonucleotides delivery may be an effective method for increasing the therapeutic potential of these compounds in viral infections.

  1. Elevated expression of long intergenic non-coding RNA HOTAIR in a basal-like variant of MCF-7 breast cancer cells

    Science.gov (United States)

    Zhuang, Yan; Nguyen, Hong T.; Burow, Matthew E.; Zhuo, Ying; El-Dahr, Samir S.; Yao, Xiao; Cao, Subing; Flemington, Erik K.; Nephew, Kenneth P.; Fang, Fang; Collins-Burow, Bridgette; Rhodes, Lyndsay V.; Yu, Qiang; Jayawickramarajah, Janarthanan; Shan, Bin

    2015-01-01

    Epigenetic regulation of gene expression is critical to phenotypic maintenance and transition of human breast cancer cells. HOX antisense intergenic RNA (HOTAIR) is a long intergenic non-coding RNA that epigenetically represses gene expression via recruitment of enhancer of zeste homolog 2 (EZH2), a histone methyltransferase. Elevated expression of HOTAIR promotes progression of breast cancer. In the current study we examined the expression and function of HOTAIR in MCF-7-TNR cells, a derivative of the luminal-like breast cancer cell line MCF-7 that acquired resistance to TNF-α-induced cell death. The expression of HOTAIR, markers of the luminal-like and basal-like subtypes, and growth were compared between MCF-7 and MCF-7-TNR cells. These variables were further assessed upon inhibition of HOTAIR, EZH2, p38 MAPK, and SRC kinase in MCF-7-TNR cells. When compared with MCF-7 cells, MCF-7-TNR cells exhibited an increase in the expression of HOTAIR, which correlated with characteristics of a luminal-like to basal-like transition as evidenced by dysregulated gene expression and accelerated growth. MCF-7-TNR cells exhibited reduced suppressive histone H3 lysine27 trimethylation on the HOTAIR promoter. Inhibition of HOTAIR and EZH2 attenuated the luminal-like to basal-like transition in terms of gene expression and growth in MCF-7-TNR cells. Inhibition of p38 and SRC diminished HOTAIR expression and the basal-like phenotype in MCF-7-TNR cells. HOTAIR was robustly expressed in the native basal-like breast cancer cells and inhibition of HOTAIR reduced the basal-like gene expression and growth. Our findings suggest HOTAIR-mediated regulation of gene expression and growth associated with the basal-like phenotype of breast cancer cells. PMID:25328122

  2. Brain intra- and extracellular sodium concentration in multiple sclerosis: a 7 T MRI study.

    Science.gov (United States)

    Petracca, Maria; Vancea, Roxana O; Fleysher, Lazar; Jonkman, Laura E; Oesingmann, Niels; Inglese, Matilde

    2016-03-01

    Intra-axonal accumulation of sodium ions is one of the key mechanisms of delayed neuro-axonal degeneration that contributes to disability accrual in multiple sclerosis. In vivo sodium magnetic resonance imaging studies have demonstrated an increase of brain total sodium concentration in patients with multiple sclerosis, especially in patients with greater disability. However, total sodium concentration is a weighted average of intra- and extra-cellular sodium concentration whose changes reflect different tissue pathophysiological processes. The in vivo, non-invasive measurement of intracellular sodium concentration is quite challenging and the few applications in patients with neurological diseases are limited to case reports and qualitative assessments. In the present study we provide first evidence of the feasibility of triple quantum filtered (23)Na magnetic resonance imaging at 7 T, and provide in vivo quantification of global and regional brain intra- and extra-cellular sodium concentration in 19 relapsing-remitting multiple sclerosis patients and 17 heathy controls. Global grey matter and white matter total sodium concentration (respectively P brain regional level, clusters of increased total sodium concentration and intracellular sodium concentration and decreased intracellular sodium volume fraction were found in several cortical, subcortical and white matter regions when patients were compared with healthy controls (P Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. The Leech method for diagnosing constipation: intra- and interobserver variability and accuracy

    International Nuclear Information System (INIS)

    Lorijn, Fleur de; Voskuijl, Wieger P.; Taminiau, Jan A.; Benninga, Marc A.; Rijn, Rick R. van; Henneman, Onno D.F.; Heijmans, Jarom; Reitsma, Johannes B.

    2006-01-01

    The data concerning the value of a plain abdominal radiograph in childhood constipation are inconsistent. Recently, positive results have been reported of a new radiographic scoring system, ''the Leech method'', for assessing faecal loading. To assess intra- and interobserver variability and determine diagnostic accuracy of the Leech method in identifying children with functional constipation (FC). A total of 89 children (median age 9.8 years) with functional gastrointestinal disorders were included in the study. Based on clinical parameters, 52 fulfilled the criteria for FC, six fulfilled the criteria for functional abdominal pain (FAP), and 31 for functional non-retentive faecal incontinence (FNRFI); the latter two groups provided the controls. To assess intra- and interobserver variability of the Leech method three scorers scored the same abdominal radiograph twice. A Leech score of 9 or more was considered as suggestive of constipation. ROC analysis was used to determine the diagnostic accuracy of the Leech method in separating patients with FC from control patients. Significant intraobserver variability was found between two scorers (P=0.005 and P<0.0001), whereas there was no systematic difference between the two scores of the other scorer (P=0.89). The scores between scorers differed systematically and displayed large variability. The area under the ROC curve was 0.68 (95% CI 0.58-0.80), indicating poor diagnostic accuracy. The Leech scoring method for assessing faecal loading on a plain abdominal radiograph is of limited value in the diagnosis of FC in children. (orig.)

  4. Effects of intra- and interspecific competition on the sensitivity of aquatic macroinvertebrates to carbendazim.

    Science.gov (United States)

    Del Arco, Ana Isabel; Parra, Gema; Rico, Andreu; Van den Brink, Paul J

    2015-10-01

    The Ecological Risk Assessment of pesticides and other potentially toxic chemicals is generally based on toxicity data obtained from single-species laboratory experiments. In the field, however, contaminant effects are ubiquitously co-occurring with ecological interactions such as species competition and predation, which might influence the sensitivity of the individuals exposed to toxicants. The present experimental study investigated how intra- and interspecific competition influence the response of sensitive aquatic organisms to a pesticide. For this, the effects of the fungicide carbendazim were assessed on the mortality and growth of the snail Bithynia tentaculata and the crustacean Gammarus pulex under different levels of intraspecific and interspecific competition for a food resource. Interspecific competition was created by adding individuals of Radix peregra and Asellus aquaticus, respectively. The interaction of competition and carbendazim exposure significantly influenced B. tentaculata growth, however, combined effects on survival and immobility were considered transient and were less easily demonstrated. Positive influence of competition on G. pulex survival was observed under low-medium carbendazim concentrations and under medium-high density pressures, being partly related to cannibalistic and predation compensatory mechanisms, enhanced under food limiting conditions. This study shows that intra- and interspecific competition pressure may influence the response of sensitive aquatic organisms in a more complex way (positive, non-significant and negative effects were observed) than just increasing the sensitivity of the studied species, as has generally been hypothesized. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Intra- and interobserver variability in interpretation of DMSA scans using a set of standardized criteria

    International Nuclear Information System (INIS)

    Patel, K.; Charron, M.; Hoberman, A.; Brown, M.L.; Rogers, K.D.

    1993-01-01

    A set of criteria was developed to standardize assessment of DMSA renal scintigraphy which were performed to evaluate children for acute pyelonephritis and renal scarring. This study was undertaken to assess intra-and interobserver vriability in the interpretation of DMSA renal scintigraphy using these criteria. Renal contours and parenchyma were assessed in three zones. Contours were assessed as normal or abnormal and parenchymal defects were evaluated in terms of character, shape and degree in three regions (upper and lower pole and midzone). Two nuclear medicine physicians blindly reviewed 57 DMSA scintigraphy on two occasions each. Disagreement of each observer's evaluation of the same scintigraphy on two different occasions was described as intraobserver variability, and the comparison between readings by each of the two observers was described as interobserver variability. High levels of intra- (95.9% and 90.6% respectively, p<0.05) and interobserver agreement (84.4%, p<0.05) were demonstrated. There were minor differences in inconsistencies between the two kidneys of different kidney zones. We conclude that standardization of criteria resulted in higher intra- and interobserver consistency in interpretation of DMSA scintigraphy. (orig.)

  6. Intra- and Interobserver Reliability of Three Classification Systems for Hallux Rigidus.

    Science.gov (United States)

    Dillard, Sarita; Schilero, Christina; Chiang, Sharon; Pham, Peter

    2018-04-18

    There are over ten classification systems currently used in the staging of hallux rigidus. This results in confusion and inconsistency with radiographic interpretation and treatment. The reliability of hallux rigidus classification systems has not yet been tested. The purpose of this study was to evaluate intra- and interobserver reliability using three commonly used classifications for hallux rigidus. Twenty-one plain radiograph sets were presented to ten ACFAS board-certified foot and ankle surgeons. Each physician classified each radiograph based on clinical experience and knowledge according to the Regnauld, Roukis, and Hattrup and Johnson classification systems. The two-way mixed single-measure consistency intraclass correlation was used to calculate intra- and interrater reliability. The intrarater reliability of individual sets for the Roukis and Hattrup and Johnson classification systems was "fair to good" (Roukis, 0.62±0.19; Hattrup and Johnson, 0.62±0.28), whereas the intrarater reliability of individual sets for the Regnauld system bordered between "fair to good" and "poor" (0.43±0.24). The interrater reliability of the mean classification was "excellent" for all three classification systems. Conclusions Reliable and reproducible classification systems are essential for treatment and prognostic implications in hallux rigidus. In our study, Roukis classification system had the best intrarater reliability. Although there are various classification systems for hallux rigidus, our results indicate that all three of these classification systems show reliability and reproducibility.

  7. In vivo importance of homologous recombination DNA repair for mouse neural stem and progenitor cells.

    Directory of Open Access Journals (Sweden)

    Laure Rousseau

    Full Text Available We characterized the in vivo importance of the homologous recombination factor RAD54 for the developing mouse brain cortex in normal conditions or after ionizing radiation exposure. Contrary to numerous homologous recombination genes, Rad54 disruption did not impact the cortical development without exogenous stress, but it dramatically enhanced the radiation sensitivity of neural stem and progenitor cells. This resulted in the death of all cells irradiated during S or G2, whereas the viability of cells irradiated in G1 or G0 was not affected by Rad54 disruption. Apoptosis occurred after long arrests at intra-S and G2/M checkpoints. This concerned every type of neural stem and progenitor cells, showing that the importance of Rad54 for radiation response was linked to the cell cycle phase at the time of irradiation and not to the differentiation state. In the developing brain, RAD54-dependent homologous recombination appeared absolutely required for the repair of damages induced by ionizing radiation during S and G2 phases, but not for the repair of endogenous damages in normal conditions. Altogether our data support the existence of RAD54-dependent and -independent homologous recombination pathways.

  8. Electric hydrogen recombiner special tests

    International Nuclear Information System (INIS)

    Wilson, J.F.

    1975-12-01

    Westinghouse has produced an electric hydrogen recombiner to control hydrogen levels in reactor containments following a postulated loss-of-coolant accident. The recombiner underwent extensive testing for NRC qualification (see WCAP 7709-L and Supplements 1, 2, 3, 4). As a result, WCAP 7709-L and Supplements 1, 2, 3, and 4 have been accepted by the NRC for reference in applications not committed to IEEE-323-1974. Supplement 5 and the next supplement will demonstrate conformance to IEEE-323-1974. This supplement describes additional tests, beyond those necessary to qualify the system, which will be referenced in supplement 6. Each test has demonstrated a considerable margin of safety over required performance. Concurrently, the test results increased the fund of technical information on the electric hydrogen recombiner

  9. The effect of a single recombination event

    DEFF Research Database (Denmark)

    Schierup, Mikkel Heide; Jensen, Thomas Mailund; Wiuf, Carsten

    We investigate the variance in how visible a single recombination event is in a SNP data set as a function of the type of recombination event and its age. Data is simulated under the coalescent with recombination and inference is by the popular composite likelihood methods. The major determinant...... of the effect of a recombination event is the genealogical type of the event and whether SNP variation is present that can reveal the genealogical consequences of the recombination event. Recombination events that only change some branch lengths in the genealogy have a very small, but detectable, effect....... The more lineages left when the recombination event occurs, the larger effect it has, implying that it is mainly young recombination events that we detect when estimating the rate. If the population is growing, though, more lineages are present back in time and relatively more ancient recombination events...

  10. Enhancers located in heavy chain regulatory region (hs3a, hs1,2, hs3b, and hs4) are dispensable for diversity of VDJ recombination.

    Science.gov (United States)

    Rouaud, Pauline; Vincent-Fabert, Christelle; Fiancette, Remi; Cogné, Michel; Pinaud, Eric; Denizot, Yves

    2012-03-09

    V(D)J recombination occurs during the antigen-independent early steps of B-cell ontogeny. Multiple IgH cis-regulatory elements control B-cell ontogeny. IGCR1 (intergenic control region 1), the DQ52 promoter/enhancer, and the intronic Emu enhancer, all three located upstream of Cmu, have important roles during V(D)J recombination, whereas there is no clue about a role of the IgH regulatory region (RR) encompassing the four transcriptional enhancers hs3a, hs1,2, hs3b, and hs4 during these early stages. To clarify the role of the RR in V(D)J recombination, we totally deleted it in the mouse genome. Here, we show that V(D)J recombination is unaffected by the complete absence of the IgH RR, highlighting that this region only orchestrates IgH locus activity during the late stages of B-cell differentiation. In contrast, the earliest antigen-independent steps of B-cell ontogeny would be under the control of only the upstream Cmu elements of the locus.

  11. Enhancers Located in Heavy Chain Regulatory Region (hs3a, hs1,2, hs3b, and hs4) Are Dispensable for Diversity of VDJ Recombination*

    Science.gov (United States)

    Rouaud, Pauline; Vincent-Fabert, Christelle; Fiancette, Remi; Cogné, Michel; Pinaud, Eric; Denizot, Yves

    2012-01-01

    V(D)J recombination occurs during the antigen-independent early steps of B-cell ontogeny. Multiple IgH cis-regulatory elements control B-cell ontogeny. IGCR1 (intergenic control region 1), the DQ52 promoter/enhancer, and the intronic Emu enhancer, all three located upstream of Cmu, have important roles during V(D)J recombination, whereas there is no clue about a role of the IgH regulatory region (RR) encompassing the four transcriptional enhancers hs3a, hs1,2, hs3b, and hs4 during these early stages. To clarify the role of the RR in V(D)J recombination, we totally deleted it in the mouse genome. Here, we show that V(D)J recombination is unaffected by the complete absence of the IgH RR, highlighting that this region only orchestrates IgH locus activity during the late stages of B-cell differentiation. In contrast, the earliest antigen-independent steps of B-cell ontogeny would be under the control of only the upstream Cmu elements of the locus. PMID:22270371

  12. Effect of merging levels of locomotion scores for dairy cows on intra- and interrater reliability and agreement.

    Science.gov (United States)

    Schlageter-Tello, Andrés; Bokkers, Eddie A M; Groot Koerkamp, Peter W G; Van Hertem, Tom; Viazzi, Stefano; Romanini, Carlos E B; Halachmi, Ilan; Bahr, Claudia; Berckmans, Daniël; Lokhorst, Kees

    2014-09-01

    Locomotion scores are used for lameness detection in dairy cows. In research, locomotion scores with 5 levels are used most often. Analysis of scores, however, is done after transformation of the original 5-level scale into a 4-, 3-, or 2-level scale to improve reliability and agreement. The objective of this study was to evaluate different ways of merging levels to optimize resolution, reliability, and agreement of locomotion scores for dairy cows. Locomotion scoring was done by using a 5-level scale and 10 experienced raters in 2 different scoring sessions from videos from 58 cows. Intra- and interrater reliability and agreement were calculated as weighted kappa coefficient (κw) and percentage of agreement (PA), respectively. Overall intra- and interrater reliability and agreement and specific intra- and interrater agreement were determined for the 5-level scale and after transformation into 4-, 3-, and 2-level scales by merging different combinations of adjacent levels. Intrarater reliability (κw) ranged from 0.63 to 0.86, whereas intrarater agreement (PA) ranged from 60.3 to 82.8% for the 5-level scale. Interrater κw=0.28 to 0.84 and interrater PA=22.6 to 81.8% for the 5-level scale. The specific intrarater agreement was 76.4% for locomotion level 1, 68.5% for level 2, 65% for level 3, 77.2% for level 4, and 80% for level 5. Specific interrater agreement was 64.7% for locomotion level 1, 57.5% for level 2, 50.8% for level 3, 60% for level 4, and 45.2% for level 5. Specific intra- and interrater agreement suggested that levels 2 and 3 were more difficult to score consistently compared with other levels in the 5-level scale. The acceptance threshold for overall intra- and interrater reliability (κw and κ ≥0.6) and agreement (PA ≥75%) and specific intra- and interrater agreement (≥75% for all levels within locomotion score) was exceeded only for the 2-level scale when the 5 levels were merged as (12)(345) or (123)(45). In conclusion, when locomotion

  13. Improving recombinant protein purification yield

    Science.gov (United States)

    Production of adequate amounts of recombinant proteins is essential for antibody production, biochemical activity study, and structural determination during the post-genomic era. It’s technologically challenging and a limiting factor for tung oil research because analytical reagents such as high qua...

  14. A recombinant protein expression system

    African Journals Online (AJOL)

    Aghomotsegin

    2015-06-23

    Jun 23, 2015 ... Serum free cultivation of Leishmania is cost-effective and improves large scale production of well- defined parasite material. Moreover, the production of recombinant pharmaceutical proteins requires cultivation of the host in a culture medium free of animal materials, so several culture media for.

  15. Production and recombination of gluons

    International Nuclear Information System (INIS)

    Temiraliev, A.T.

    2006-01-01

    Full text: Nonlinear Markov process of parton production has been considered. The Kolmogorov equation is applied for the evolution equation based on the approximation of independent gluons production in every decay act. We introduced a 'crossing' parameter and used the combination relations to obtain nonlinear recombination equation for the evolution of gluon structure function. (author)

  16. Recombination in hepatitis C virus.

    Science.gov (United States)

    González-Candelas, Fernando; López-Labrador, F Xavier; Bracho, María Alma

    2011-10-01

    Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus.

  17. How to assess intra- and inter-observer agreement with quantitative PET using variance component analysis

    DEFF Research Database (Denmark)

    Gerke, Oke; Vilstrup, Mie Holm; Segtnan, Eivind Antonsen

    2016-01-01

    BACKGROUND: Quantitative measurement procedures need to be accurate and precise to justify their clinical use. Precision reflects deviation of groups of measurement from another, often expressed as proportions of agreement, standard errors of measurement, coefficients of variation, or the Bland...... relation to Bland-Altman plots. Here, we present this approach for assessment of intra- and inter-observer variation with PET/CT exemplified with data from two clinical studies. METHODS: In study 1, 30 patients were scanned pre-operatively for the assessment of ovarian cancer, and their scans were assessed...... (THG) in study 2. RESULTS: In study 1, we found a RC of 2.46 equalling half the width of the Bland-Altman limits of agreement. In study 2, the RC for identical conditions (same scanner, patient, time point, and observer) was 2392; allowing for different scanners increased the RC to 2543. Inter...

  18. Intra- and interobserver agreement in the diagnosis of malocclusion in sleep-disordered breathing.

    Science.gov (United States)

    Carvalho, Fernando Rodrigues; Lentini-Oliveira, Débora Aparecida; Carvalho, Graziele Maria Missiano; Singer, Julio Motta; Prado, Lucila Bizari Fernandes; Prado, Gilmar Fernandes; Carvalho, Luciane Bizari Coin

    2014-02-01

    Sleep-disordered breathing (SDB) is often related to malocclusion, and dentists should be able to recognize occlusal changes that may be associated with the development, onset, or persistence of SDB. Although clinical examination is routinely used by specialists in orthodontics and functional jaw orthopedics, differences in diagnosis are very common. Two observers, both dentists specializing in functional jaw orthopedics, examined 56 children aged 7 to 9 years. Intra- and interobserver agreement in identification of functional orthopedic and orthodontic conditions were assessed. Intraobserver agreement was strong for all variables. Interobserver agreement was also strong, except for the variable overbite, which showed good agreement. Diagnostic criteria provide an opportunity for dentists to recognize dental malocclusions that may be associated with sleep-disordered breathing.

  19. Dynamics of Moment Neuronal Networks with Intra- and Inter-Interactions

    Directory of Open Access Journals (Sweden)

    Xuyan Xiang

    2015-01-01

    Full Text Available A framework of moment neuronal networks with intra- and inter-interactions is presented. It is to show how the spontaneous activity is propagated across the homogeneous and heterogeneous network. The input-output firing relationship and the stability are first explored for a homogeneous network. For heterogeneous network without the constraint of the correlation coefficients between neurons, a more sophisticated dynamics is then explored. With random interactions, the network gets easily synchronized. However, desynchronization is produced by a lateral interaction such as Mexico hat function. It is the external intralayer input unit that offers a more sophisticated and unexpected dynamics over the predecessors. Hence, the work further opens up the possibility of carrying out a stochastic computation in neuronal networks.

  20. Effects of time-delay in a model of intra- and inter-personal motor coordination

    Science.gov (United States)

    Słowiński, Piotr; Tsaneva-Atanasova, Krasimira; Krauskopf, Bernd

    2016-11-01

    Motor coordination is an important feature of intra- and inter-personal interactions, and several scenarios — from finger tapping to human-computer interfaces — have been investigated experimentally. In the 1980s, Haken, Kelso and Bunz formulated a coupled nonlinear two-oscillator model, which has been shown to describe many observed aspects of coordination tasks. We present here a bifurcation study of this model, where we consider a delay in the coupling. The delay is shown to have a significant effect on the observed dynamics. In particular, we find a much larger degree of bistablility between in-phase and anti-phase oscillations in the presence of a frequency detuning.

  1. Intra- and interobserver agreement in the diagnosis of malocclusion in sleep-disordered breathing

    Directory of Open Access Journals (Sweden)

    Fernando Rodrigues Carvalho

    2014-02-01

    Full Text Available Sleep-disordered breathing (SDB is often related to malocclusion, and dentists should be able to recognize occlusal changes that may be associated with the development, onset, or persistence of SDB. Although clinical examination is routinely used by specialists in orthodontics and functional jaw orthopedics, differences in diagnosis are very common. Method : Two observers, both dentists specializing in functional jaw orthopedics, examined 56 children aged 7 to 9 years. Intra- and interobserver agreement in identification of functional orthopedic and orthodontic conditions were assessed. Results : Intraobserver agreement was strong for all variables. Interobserver agreement was also strong, except for the variable overbite, which showed good agreement. Conclusion : Diagnostic criteria provide an opportunity for dentists to recognize dental malocclusions that may be associated with sleep-disordered breathing.

  2. The effect of intra- and interregional labour mobility on plant performance in Denmark

    DEFF Research Database (Denmark)

    Timmermans, Bram; Boschma, Ron

    2014-01-01

    This article investigates the impact of labour mobility on plant performance in Denmark. Our study shows that the effect of labour mobility can only be assessed when one accounts for the type of skills that flow into the plant and the degree to which these match the existing skills at the plant...... level. As expected, we found that the inflow of skills that are related to skills in the plant impacts positively on plant productivity growth, while inflows of skills that are similar to the plant skills have a negative effect. We used a sophisticated indicator of revealed relatedness that measures...... the degree of skill relatedness between sectors on the basis of the intensity of labour flows between sectors. Intra-regional mobility of skilled labour had a negative effect on plant performance, but the impacts of intra- and inter-regional mobility depended on the type of skills that flow into the plant....

  3. Empathy and Prosocial Behaviours. Insights from Intra- and Inter-species Interactions

    Directory of Open Access Journals (Sweden)

    Maria elide Vanutelli

    2015-04-01

    Full Text Available It has been suggested that “sharing the same body” between the observer and the observed subject allows for a direct form of understanding and emotional attuning by a process of simulation. Then, what happens when we don’t share the same body? The aim of the present paper is to review available evidence of intra- and inter-species empathic and prosocial behaviours, with respect to within-human, within-animals and cross-specifies interactions. Similarities and differences will be evaluated using a comparative perspective, and some possible moral and ethical implications for human-animal interactions will be discussed. According to Charles Darwin’s work, the perceived differences between human and animal empathy could be more quantitative than qualitative, suggesting a common affective core which allows both categories to mirror and tune to conspecifics’ feelings, where in the case of humans it can be integrated with more complex cognitive processes.

  4. Live recombinant BHV/BRSV vaccine

    NARCIS (Netherlands)

    Keil, G.M.; Rijsewijk, F.A.M.

    1998-01-01

    The present invention refers to synthetic Bovine Respiratory Syncytium virus genes. Also the invention relates to live attenuated Bovine Herpesvirus recombinants carrying such synthetic genes. Furthermore, the invention relates to vaccines based on these live attenuated recombinants, for the

  5. Hadron production at RHIC: recombination of quarks

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-01-01

    We discuss quark recombination applied to the hadronization of a quark gluon plasma. It has been shown that the quark recombination model can explain essential features of hadron production measured in high energy heavy ion collisions.

  6. The Leech method for diagnosing constipation: intra- and interobserver variability and accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Lorijn, Fleur de; Voskuijl, Wieger P.; Taminiau, Jan A.; Benninga, Marc A. [Emma Children' s Hospital, Department of Paediatric Gastroenterology and Nutrition, Amsterdam (Netherlands); Rijn, Rick R. van; Henneman, Onno D.F. [Academic Medical Centre, Department of Radiology, Amsterdam (Netherlands); Heijmans, Jarom [Emma Children' s Hospital, Department of Paediatric Gastroenterology and Nutrition, Amsterdam (Netherlands); Academic Medical Centre, Department of Radiology, Amsterdam (Netherlands); Reitsma, Johannes B. [Academic Medical Centre, Department of Clinical Epidemiology and Biostatistics, Amsterdam (Netherlands)

    2006-01-01

    The data concerning the value of a plain abdominal radiograph in childhood constipation are inconsistent. Recently, positive results have been reported of a new radiographic scoring system, ''the Leech method'', for assessing faecal loading. To assess intra- and interobserver variability and determine diagnostic accuracy of the Leech method in identifying children with functional constipation (FC). A total of 89 children (median age 9.8 years) with functional gastrointestinal disorders were included in the study. Based on clinical parameters, 52 fulfilled the criteria for FC, six fulfilled the criteria for functional abdominal pain (FAP), and 31 for functional non-retentive faecal incontinence (FNRFI); the latter two groups provided the controls. To assess intra- and interobserver variability of the Leech method three scorers scored the same abdominal radiograph twice. A Leech score of 9 or more was considered as suggestive of constipation. ROC analysis was used to determine the diagnostic accuracy of the Leech method in separating patients with FC from control patients. Significant intraobserver variability was found between two scorers (P=0.005 and P<0.0001), whereas there was no systematic difference between the two scores of the other scorer (P=0.89). The scores between scorers differed systematically and displayed large variability. The area under the ROC curve was 0.68 (95% CI 0.58-0.80), indicating poor diagnostic accuracy. The Leech scoring method for assessing faecal loading on a plain abdominal radiograph is of limited value in the diagnosis of FC in children. (orig.)

  7. Intra- and Intersession Repeatability of an Optical Quality and Intraocular Scattering Measurement System in Children.

    Directory of Open Access Journals (Sweden)

    Mi Tian

    Full Text Available To evaluate intra- and intersession repeatability of objective optical quality and intraocular scattering measurements with a double-pass system in children.Forty-two eyes of 42 children were included in the study. An optical quality analysis system (OQAS was used to measure optical quality parameters, including modulation transfer function cutoff frequency (MTFcutoff, Strehl ratio (SR, OQAS values (OV at 3 different contrasts and objective scatter index (OSI. Three measurement sessions with 10-min intervals were operated by the same technician, and in each session four consecutive measurements were obtained.Mean values for MTFcutoff, SR and OSI were 46.85 ± 7.45cpd, 0.27 ± 0.06 and 0.34 ± 0.22 respectively. 1 The intraclass correlation coefficients were ranged from 0.89 to 0.97 and coefficients of variation from 0.06 to 0.16 for all the parameters in the first session; the relative repeatability were 11.1% (MTFcutoff, 22.5% (SR, 10.9% (OV100%, 16.6% (OV2%, 22.4% (OV9% and 56.3% (OSI. Similar results were found in the second and third sessions. 2 Bland-Altman analysis showed that narrow 95% confidence intervals (compared between the first and second sessions ranged from -5.42 to 5.28 (MTFcutoff, -0.05 to 0.07 (SR, -0.18 to 0.18 (OV100%, -0.26 to 0.29 (OV20%, -0.33 to 0.39 (OV9% and -0.11 to 0.09 (OSI; the comparison between any two of the three sessions showed similar results.Measurements of optical quality and intraocular scattering in children by the double-pass system showed good intra- and intersession repeatability. Retinal image quality is high and intraocular scattering is low in children.

  8. Fitness of Streptococcus pneumoniae fluoroquinolone-resistant strains with topoisomerase IV recombinant genes.

    Science.gov (United States)

    Balsalobre, Luz; de la Campa, Adela G

    2008-03-01

    The low prevalence of ciprofloxacin-resistant (Cp r) Streptococcus pneumoniae isolates carrying recombinant topoisomerase IV genes could be attributed to a fitness cost imposed by the horizontal transfer, which often implies the acquisition of larger-than-normal parE-parC intergenic regions. A study of the transcription of these genes and of the fitness cost for 24 isogenic Cp r strains was performed. Six first-level transformants were obtained either with PCR products containing the parC quinolone resistance-determining regions (QRDRs) of S. pneumoniae Cp r mutants with point mutations or with a PCR product that includes parE-QRDR-ant-parC-QRDR from a Cp r Streptococcus mitis isolate. The latter yielded two strains, T6 and T11, carrying parC-QRDR and parE-QRDR-ant-parC-QRDR, respectively. These first-level transformants were used as recipients in further transformations with the gyrA-QRDR PCR products to obtain 18 second-level transformants. In addition, strain Tr7 (which contains the GyrA E85K change) was used. Reverse transcription-PCR experiments showed that parE and parC were cotranscribed in R6, T6, and T11; and a single promoter located upstream of parE was identified in R6 by primer extension. The fitness of the transformants was estimated by pairwise competition with R6 in both one-cycle and two-cycle experiments. In the one-cycle experiments, most strains carrying the GyrA E85K change showed a fitness cost; the exception was recombinant T14. In the two-cycle experiments, a fitness cost was observed in most first-level transformants carrying the ParC changes S79F, S79Y, and D83Y and the GyrA E85K change; the exceptions were recombinants T6 and T11. The results suggest that there is no impediment due to a fitness cost for the spread of recombinant Cp r S. pneumoniae isolates, since some recombinants (T6, T11, and T14) exhibited an ability to compensate for the cost.

  9. High efficiency recombineering in lactic acid bacteria

    OpenAIRE

    van Pijkeren, Jan-Peter; Britton, Robert A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lact...

  10. Population inversion in recombining hydrogen plasma

    International Nuclear Information System (INIS)

    Furukane, Utaro; Yokota, Toshiaki; Oda, Toshiatsu.

    1978-11-01

    The collisional-radiative model is applied to a recombining hydrogen plasma in order to investigate the plasma condition in which the population inversion between the energy levels of hydrogen can be generated. The population inversion is expected in a plasma where the three body recombination has a large contribution to the recombining processes and the effective recombination rate is beyond a certain value for a given electron density and temperature. Calculated results are presented in figures and tables. (author)

  11. Cloning, purification and characterization of recombinant silkworm ...

    African Journals Online (AJOL)

    The recombinant His-tagged BmAK protein was expressed in soluble form in Escherichia coli Rosetta and purified by metal chelating affinity chromatography. The amino acid sequence of recombinant protein was confirmed by mass spectroscopic analysis and the enzyme activity assay that indicated the recombinant ...

  12. Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

    Directory of Open Access Journals (Sweden)

    Patenge Nadja

    2012-10-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49, employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases. Results We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5′ rapid amplification of cDNA ends-PCR (RACE-PCR analysis. Conclusions In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of s

  13. Sequence characterization of cotton leaf curl virus from Rajasthan: phylogenetic relationship with other members of geminiviruses and detection of recombination.

    Science.gov (United States)

    Kumar, A; Kumar, J; Khan, J A

    2010-04-01

    Diseased cotton plants showing typical leaf curl symptoms were collected from experimental plot of Agriculture Research Station-Sriganganagar, Rajasthan. Complete DNA-A component from samples taken from two areas were amplified through rolling circle amplification (RCA) using templiphi kit (GE Healthcare) and characterized. DNA-A of one isolate consists of 2751 nucleotides and second isolate of 2759 nucleotide. Both sequences comprised six ORF's. Genome organization of DNA-A of one isolate shows high sequence similarity with other characterized local begomovirus isolates of Rajasthan, while other isolate shows high sequence similarity with CLCuV reported from Pakistan. The maximum similarity of first isolate, CLCuV-SG01, shows highest sequence identity with Cotton leaf curl Abohar (Rajasthan) virus, and second isolate, CLCuV-SG02, shows highest sequence identity with cotton leaf curl virus from Pakistan. Both isolates showed 85% similarities with each other. The sequence data revealed probable infiltration of some strains of Cotton leaf curl virus from Pakistan to India, or co-existence of different isolates under similar geographical conditions. While CLCuV-SG01 shows highest nt sequence similarity with CLCuV Rajasthan (Abohar), nt identity of V1 ORF (encoding coat protein) of SG01 shows the highest nt identity (100%) with CLCuV Multan (Bhatinda) and Abohar virus while AC1 region also showed difference. Complete nucleotide sequence of SG01 shows only 86% similarity with CLCuV Multan virus. Similarity search revealed significant difference in AV1 and AC1 regions with respect to DNA-A suggesting an evolutionary history of recombination. Computer based analysis, recombination detection Program (RDP) supports the recombination hypothesis, indicated that recombination with other begomoviruses had taken place within V1 ORF and AC1 ORF of CLCuV-SG01 and AC1 ORF of CLCuV-SG02 and also in noncoding intergenic region (IR).

  14. Mechanisms of sister chromatid recombination

    International Nuclear Information System (INIS)

    Nakai, Sayaka; Machida, Isamu; Tsuji, Satsuki

    1985-01-01

    Studies using T948 as a model system have been carried out aimed at elucidating the mechanism of sister chromatid recombination (SCR). Characterization of U.V. light- and x-ray-induced SCR, the relationiship between SCR induction and DNA repair using rad mutations, and the relationship between SCR induction and the time of cell division using cdc mutations are presented. It has been supposed that SCR is induced at the phase of S-G 2 following DNA replication, that postreplication break of DNA strands is strongly involved in the induction of SCR, and that induction type of SCR, i.e., conversion type or recombination type, is dependent upon the type of molecular damage of DNA. (Namekawa, K.)

  15. Heterogeneity in recombinant protein production

    DEFF Research Database (Denmark)

    Schalén, Martin; Johanson, Ted; Lundin, Luisa

    2012-01-01

    contribute to make a population in a fermenter heterogeneous, resulting in cell-to-cell variation in physiological parameters of the microbial culture. Our study aims at investigating how population heterogeneity and recombinant protein production is affected by environmental gradients in bioreactors....... For this purpose, a Saccharomyces cerevisiae strain, that functions as a protein production reporter, has been developed. A heterologous protein has been tagged with a fluorescent protein providing a way to measure the amount of heterologous protein produced by the cells on single cell level. Gradients...... are simulated in small bioreactors and the population heterogeneity can be visualised by analysing single cells with flow cytometry. This can give new insights to cell physiology and recombinant protein production at the industrial scale....

  16. Workshop on Radio Recombination Lines

    CERN Document Server

    1980-01-01

    Since their first detection 15 years ago, radio recombination lines from several elements have been observed in a wide variety of objects including HII regions, planetary nebulae, molecular clouds, the diffuse interstellar medium, and recently, other galaxies. The observations span almost the entire range from 0.1 to 100 GHz, and employ both single­ djsh and aperture synthesis techniques. The theory of radio recombination lines has also advanced strongly, to the point where it is perhaps one of the best-understood in astro­ physics. In a parallel development, it has become possible over the last decade to study these same highly-excited atoms in the laboratory; this work provides further confirmation of the theoretical framework. However there has been continuing controversy over the astrophysical interpre­ tation of radio recombination line observations, especially regarding the role of stimulated emission. A workshop was held in Ottawa on 24-25 August, 1979, bringing together many of the active scientist...

  17. Nondisjunction of chromosome 15: Origin and recombination

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, W.P.; Bernasconi, F.; Schinzel, A.A.; Mutirangura, A.; Ledbetter, D.H. (Baylor College of Medicine, Houston, TX (United States)); Langlois, S. (Univ. of Britisch Columbia, Vancouver (Canada)); Morris, M.A.; Malcolm, S.

    1993-09-01

    Thirty-two cases of uniparental disomy (UPD), ascertained from Prader-Willi syndrome patients (N=27) and Angelman syndrome patients (N-5), are used to investigate the pattern of recombination associated with nondisjunction of chromosome 15. In addition, the meiotic stage of nondisjunction is inferred by using markers mapping near the centromere. Two basic approaches to the analysis of recombination in specific pairwise intervals along the chromosome. This method shows a significant reduction in recombination for two of five intervals examined. Second, the observed frequency of each recombinant class (i.e., zero, one, two, three, or more observable crossovers) is compared with expected values. This is useful for testing whether the reduction in recombination can be attributed solely to a proportion of cases with no recombination at all (because of asynapsis), with the remaining groups showing normal recombination (or even excess recombination), or whether recombination is uniformly reduced. Analysis of maternal UPD(15) data shows a slight reduction in the multiple-recombinant classes, with a corresponding increase in both the zero- and one-recombinant classes over expected values. The majority, more than 82%, of the extra chromosomes in maternal UPD(15) cases are due to meiotic I nondisjunction events. In contrast, more paternal UPD(15) cases so far examined appear to have a postzygotic origin of the extra paternal chromosome. 33 refs., 1 fig., 7 tabs.

  18. Consequences of recombination on traditional phylogenetic analysis

    DEFF Research Database (Denmark)

    Schierup, M H; Hein, J

    2000-01-01

    We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mt......DNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination....... With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may...

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

    International Nuclear Information System (INIS)

    El Khoury, A.; Atoui, A.; Lebrihi, A.; Rizk, T.; Lteif, R.; Kallassy, M.

    2011-01-01

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

  20. Unique organization of the 16S-23S intergenic spacer regions of strains of Acinetobacter baylyi provides a means for its identification from other Acinetobacter species.

    Science.gov (United States)

    Maslunka, Christopher; Gürtler, Volker; Carr, Emma L; Seviour, Robert J

    2008-06-01

    This paper extends an earlier report on rrn operon characteristics in members of the genus Acinetobacter. It describes a systematic approach towards developing and validating a protocol for elucidating how the intergenic spacer regions (ISR) in Acinetobacter baylyi strains are organized and allows the numbers of long and short ISRs to be determined. Experimental data confirmed the in silico predictions based on available A. baylyi rrn sequence data. All were shown to possess three long ISRs and 4 short ISRs, differing in most cases in length by about 90nt. However, the ISR arrangement in A. baylyi strain 93A2 was different. Although it also possessed 4 SISRs and three LISRs, their length difference was less (39nt) which was confirmed from its ISR sequence data. Primer sets for PCR identification of A. baylyi could then be determined. Applying the same approach to other species of Acinetobacter showed none shared the same ISR organization as A. baylyi. Its value in typing members of this genus is discussed.

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

    Science.gov (United States)

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

    2013-01-01

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

  2. Technical note: use of transfer RNA-intergenic spacer PCR combined with capillary electrophoresis to identify coagulase-negative Staphylococcus species originating from bovine milk and teat apices.

    Science.gov (United States)

    Supré, K; De Vliegher, S; Sampimon, O C; Zadoks, R N; Vaneechoutte, M; Baele, M; De Graef, E; Piepers, S; Haesebrouck, F

    2009-07-01

    Coagulase-negative staphylococci (CNS) are the most frequently isolated bacteria in milk samples from cows with and without mastitis. Elucidating their relevance in bovine udder health is hampered because identification at the species level, if done at all, used to be performed based on phenotypic features. To provide a rapid, cheap, and easy-to-use genotypic technique that can be used to identify CNS species from milk and teat apices from cows, the performance of transfer RNA-intergenic spacer PCR (tDNA-PCR) in combination with capillary electrophoresis was evaluated. After updating the tDNA library with CNS reference strains, 288 field isolates were identified with tDNA-PCR and gene sequencing, and the latter was used as the reference method. The field isolates were divided in 2 groups of 144. Isolates of the first group were identified with tDNA-PCR with a typeability of 81.9% and an accuracy of 94.1%. Peak patterns of these isolates were then added to the tDNA library with species identity as determined by DNA sequencing. The second group was identified with the updated tDNA library, resulting in 91.0% typeability and 99.2% accuracy. This study showed that the updated tDNA-PCR in combination with capillary electrophoresis was almost as accurate as gene sequencing but faster and cheaper (only $3 per isolate), and is a useful tool in observational studies concerning the epidemiology of bovine CNS species.

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

    Science.gov (United States)

    de Oliveira, Valéria Maia; Manfio, Gilson Paulo; da Costa Coutinho, Heitor Luiz; Keijzer-Wolters, Anneke Christina; van Elsas, Jan Dirk

    2006-03-01

    A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was followed by specific amplification of (1) sequences affiliated with Rhizobium leguminosarum "sensu lato" and (2) R. tropici. Using analysis of the amplified sequences in clone libraries obtained on the basis of soil DNA, this two-sided method was shown to be very specific for rhizobial subpopulations in soil. It was then further validated as a direct fingerprinting tool of the target rhizobia based on denaturing gradient gel electrophoresis (DGGE). The PCR-DGGE approach was applied to soils from fields in Brazil cultivated with common bean (Phaseolus vulgaris) under conventional or no-tillage practices. The community fingerprints obtained allowed the direct analysis of the respective rhizobial community structures in soil samples from the two contrasting agricultural practices. Data obtained with both primer sets revealed clustering of the community structures of the target rhizobial types along treatment. Moreover, the DGGE profiles obtained with the R. tropici primer set indicated that the abundance and diversity of these organisms were favoured under NT practices. These results suggest that the R. leguminosarum-as well as R. tropici-targeted IGS-based nested PCR and DGGE are useful tools for monitoring the effect of agricultural practices on these and related rhizobial subpopulations in soils.

  4. Analysis of intergenic spacer transcripts suggests ‘read-around’ transcription of the extrachromosomal circular rDNA in Euglena gracilis

    Science.gov (United States)

    Greenwood, Spencer J.; Schnare, Murray N.; Cook, James R.; Gray, Michael W.

    2001-01-01

    We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3′-end of the large subunit ribosomal RNA (rRNA) gene from the 5′-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A′ and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A′ that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of ‘read-around’ transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination. PMID:11353089

  5. Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells*

    Science.gov (United States)

    Zheng, Peng; Xiong, Qian; Wu, Ying; Chen, Ying; Chen, Zhuo; Fleming, Joy; Gao, Ding; Bi, Lijun; Ge, Feng

    2015-01-01

    Long noncoding RNAs (lncRNAs), which have emerged in recent years as a new and crucial layer of gene regulators, regulate various biological processes such as carcinogenesis and metastasis. HOTAIR (Hox transcript antisense intergenic RNA), a lncRNA overexpressed in most human cancers, has been shown to be an oncogenic lncRNA. Here, we explored the role of HOTAIR in HeLa cells and searched for proteins regulated by HOTAIR. To understand the mechanism of action of HOTAIR from a systems perspective, we employed a quantitative proteomic strategy to systematically identify potential targets of HOTAIR. The expression of 170 proteins was significantly dys-regulated after inhibition of HOTAIR, implying that they could be potential targets of HOTAIR. Analysis of this data at the systems level revealed major changes in proteins involved in diverse cellular components, including the cytoskeleton and the respiratory chain. Further functional studies on vimentin (VIM), a key protein involved in the cytoskeleton, revealed that HOTAIR exerts its effects on migration and invasion of HeLa cells, at least in part, through the regulation of VIM expression. Inhibition of HOTAIR leads to mitochondrial dysfunction and ultrastructural alterations, suggesting a novel role of HOTAIR in maintaining mitochondrial function in cancer cells. Our results provide novel insights into the mechanisms underlying the function of HOTAIR in cancer cells. We expect that the methods used in this study will become an integral part of functional studies of lncRNAs. PMID:25762744

  6. Long Intergenic Noncoding RNA 00511 Acts as an Oncogene in Non–small-cell Lung Cancer by Binding to EZH2 and Suppressing p57

    Directory of Open Access Journals (Sweden)

    Cheng-Cao Sun

    2016-01-01

    Full Text Available Long noncoding RNAs (lncRNAs play crucial roles in carcinogenesis. However, the function and mechanism of lncRNAs in human non–small-cell lung cancer (NSCLC are still remaining largely unknown. Long intergenic noncoding RNA 00511 (LINC00511 has been found to be upregulated and acts as an oncogene in breast cancer, but little is known about its expression pattern, biological function and underlying mechanism in NSCLC. Herein, we identified LINC00511 as an oncogenic lncRNA by driving tumorigenesis in NSCLC. We found LINC00511 was upregulated and associated with oncogenesis, tumor size, metastasis, and poor prognosis in NSCLC. Moreover, LINC00511 affected cell proliferation, invasiveness, metastasis, and apoptosis in multiple NSCLC cell lines. Mechanistically, LINC00511 bound histone methyltransferase enhancer of zeste homolog 2 ((EZH2, the catalytic subunit of the polycomb repressive complex 2 (PRC2, a highly conserved protein complex that regulates gene expression by methylating lysine 27 on histone H3, and acted as a modular scaffold of EZH2/PRC2 complexes, coordinated their localization, and specified the histone modification pattern on the target genes, including p57, and consequently altered NSCLC cell biology. Thus, LINC00511 is mechanistically, functionally, and clinically oncogenic in NSCLC. Targeting LINC00511 and its pathway may be meaningful for treating patients with NSCLC.

  7. East African cassava mosaic Zanzibar virus - a recombinant begomovirus species with a mild phenotype.

    Science.gov (United States)

    Maruthi, M N; Seal, S; Colvin, J; Briddon, R W; Bull, S E

    2004-12-01

    Cassava plants exhibiting mild symptoms of cassava mosaic disease (CMD) were collected from Unguja island, Zanzibar. Cuttings grown from these plants in the glasshouse produced similar symptoms, which were milder than those caused by other known cassava mosaic geminiviruses (CMGs). The whitefly vector, Bemisia tabaci (Gennadius), transmitted the putative virus to 27.7% (n = 18) of target plants. Total DNA extracted from diseased leaves did not yield diagnostic PCR-bands using virus-specific primers to known CMGs. Degenerate primers, however, produced a diagnostic band indicating the presence of a begomovirus. Full-length DNA-A (2785 nucleotides) and DNA-B (2763 nucleotides) components were subsequently PCR-amplified, cloned and sequenced. Phylogenetic analyses of DNA-A and -B sequences showed that they were most similar to strains of East African cassava mosaic virus from Tanzania and Uganda at 83% and 86% nucleotide identities, respectively. The number and arrangement of open reading frames were similar to those of bipartite begomoviruses from the Old World. DNA-A was predicted to have recombined in the intergenic region (IR), AC1 and AC4 genes, and DNA-B in the IR. A maximum nucleotide identity of 83% in the DNA-A component with other sequenced begomoviruses, together with different biological properties allows this virus to be recognised as belonging to a new species named East African cassava mosaic Zanzibar virus (EACMZV).

  8. MRT diagnosis of intra- and paraspinal abscesses; Kernspintomographische Diagnostik intra- und paraspinaler Abszesse

    Energy Technology Data Exchange (ETDEWEB)

    Lanfermann, H. [Inst. und Poliklinik fuer Radiologische Diagnostik, Univ. Koeln (Germany); Heindel, W. [Inst. und Poliklinik fuer Radiologische Diagnostik, Univ. Koeln (Germany); Gierenz, M. [Inst. und Poliklinik fuer Radiologische Diagnostik, Univ. Koeln (Germany); Haupt, W.F. [Klinik und Poliklinik fuer Neurologie, Univ. Koeln (Germany); Hildebrandt, G. [Klinik und Poliklinik fuer Neurochirurgie, Univ. Koeln (Germany); Lackner, K. [Inst. und Poliklinik fuer Radiologische Diagnostik, Univ. Koeln (Germany)

    1996-07-01

    Analysis of the MRT signals and their extent from intra- and paraspinal abscesses with reference to predisposing factors, their causes and localisation. The histories and MRT findings in 34 Patients with intra- and paraspinal abscesses were evaluated retrospectively. Most of the patients (24/34) were older than 50 years. A second peak was below 30 years. 27/34 patients had some underlying disease which predisposed to infection, e.g., diabetes mellitus. The most common causal organisms were Staph. aureus (53%) and streptococci (15%). In 23/34 cases (68%), the abscesses were in the thoraco-lumbar or lumbar region, while only 6/34 occurred in the upper two-thirds of the thoracic spine and only 5/34 in the cervical region. In only 8/34 was the abscess confined to two vertebral lengths; in the remaining patients it was much more extensive. Intraspinal abscesses were about twice as large as the vertebral components and 1.5 times greater than paravertebral abscesses. The age of the abscesses could be estimated approximately from the signals. Contrast enhanced MRT permits detailed analysis of the compartments and exact estimation of the extent of the lesions and permits accurate monitoring of treatment. (orig.) [Deutsch] MR-tomographische Analyse des Signal- und Ausbreitungsverhaltens intra- und paraspinaler Abszesse unter Beruecksichtigung praedisponierender Faktoren, des Erregerspektrums und der Lokalisation. Die Krankengeschichten und MRT von 34 Patienten mit intra- und paraspinalen Abszessen wurden retrospektiv ausgewertet. Die Mehrzahl der Patienten (24/34) war aelter als 50 Jahre. Ein zweiter Altersgipfel lag bei unter 30 Jahren. 27/34 Patienten litten an Grunderkrankungen, die Infektionen beguenstigen, wie zum Beispiel Diabetes mellitus. Die haeufigsten Erreger waren Staphylococcus aureus (53%) und Streptokokken (15%). Die Abszesse waren in 23/34 Faellen (68%) im thorakolumbalen Uebergang und lumbal lokalisiert, waehrend die oberen zwei Drittel der BWS nur bei 6

  9. Evaluation of intra- and inter-fraction movement of the cervix during intensity modulated radiation therapy

    International Nuclear Information System (INIS)

    Haripotepornkul, Nora H.; Nath, Sameer K.; Scanderbeg, Daniel; Saenz, Cheryl; Yashar, Catheryn M.

    2011-01-01

    Background and purpose: To assess the degree of intra- and inter-fraction cervical motion throughout a course of intensity modulated radiation therapy (IMRT) for cervical cancer patients. Materials and methods: A retrospective study of 10 women with stage 1B1-3B cervical cancer diagnosed from September 2007 to July 2008 was conducted. All patients were treated with chemoradiation using IMRT followed by intracavitary brachytherapy. Pretreatment, patients had 2 seeds placed at a depth of 10 mm into the cervix. On-Board Imaging (OBI) was used to obtain anterior/posterior (AP) and lateral X-rays before and after each treatment. OBI images were rigidly aligned to baseline digitally reconstructed radiographs (DRRs), and movement of cervical seeds was determined in the lateral, vertical, and AP directions. Mean differences in cervical seed position and standard error of the mean (SEM) were calculated. Results: A total of 922 images were reviewed, with approximately 90 images per patient. The mean intra-fractional movement in cervical seed position in the lateral, vertical, and AP directions were 1.6 mm (SD ± 2.0), 2.6 mm (SD ± 2.4), and 2.9 mm (SD ± 2.7), respectively, with a range from 0 to 15 mm for each direction. The mean inter-fractional movement in the lateral, vertical, and AP directions were 1.9 mm (SD ± 1.9), 4.1 mm (SD ± 3.2), and 4.2 mm (SD ± 3.5), respectively, with a range from 0 to 18 mm for each direction. Conclusions: This is the first study to assess intra- and inter-fractional movement of the cervix using daily imaging before and after each fraction. Within and between radiation treatments, cervical motion averages approximately 3 mm in any given direction. However, maximal movement of the cervix can be as far as 18 mm from baseline. This wide range of motion needs to be accounted for when generating planning treatment volumes.

  10. Intra- and multicenter reproducibility of pulsed, continuous and pseudo-continuous arterial spin labeling methods for measuring cerebral perfusion

    NARCIS (Netherlands)

    Gevers, Sanna; van Osch, Matthias J.; Bokkers, Reinoud P. H.; Kies, Dennis A.; Teeuwisse, Wouter M.; Majoie, Charles B.; Hendrikse, Jeroen; Nederveen, Aart J.

    2011-01-01

    Intra- and multicenter reproducibility of currently used arterial spin labeling (ASL) methods were assessed at three imaging centers in the Netherlands, equipped with Philips 3TMR scanners. Six healthy participants were scanned twice at each site. The imaging protocol consisted of continuous ASL

  11. Intra- and inter-observer variation in histological criteria used in age at death determination based on femoral cortical bone

    DEFF Research Database (Denmark)

    Lynnerup, N; Thomsen, J L; Frohlich, B

    1998-01-01

    elements as observed on photographic images of cortical bone, in order to assess intra- and inter-observer error. Overall, substantial error was present at the level of identifying and counting secondary osteons, osteon fragments and Haversian canals. Only secondary osteons can be reliably identified...

  12. Intra- and Interexaminer Variability of Two Separate Video Head Impulse Test Systems Assessing All Six Semicircular Canals

    DEFF Research Database (Denmark)

    Abrahamsen, Emil Riis; Christensen, Ann-Eva; Hougaard, Dan Dupont

    2018-01-01

    OBJECTIVE: To evaluate intra- and interexaminer variability of the video Head Impulse Test (v-HIT) when assessing all six semicircular canals (SCCs) of two separate v-HIT systems. STUDY DESIGN: Prospective study. SETTING: Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hos...

  13. Effects of intra- and interspecific competition on diet, growth and behaviour of Labeo calbasu (Hamilton) and Cirrhinus cirrhosus (Bloch)

    NARCIS (Netherlands)

    Rahman, M.M.; Verdegem, M.C.J.

    2010-01-01

    Effects of intra- and interspecific competition on diet, growth, grazing, swimming, resting and social behaviour of two carps calbasu (Labeo calbasu) and mrigal (Cirrhinus cirrhosus) were examined in single and mixed species treatments. Three treatments (tanks with 4 L. calbasu, 4 C. cirrhosus or 2

  14. High intra- and inter-rater chance variation of the movement assessment battery for children 2, ageband 2.

    Science.gov (United States)

    Holm, Inger; Tveter, Anne Therese; Aulie, Vibeke Smith; Stuge, Britt

    2013-02-01

    The aim of the present study was to evaluate the intra- and inter-tester reliability of the movement assessment battery for children-second edition (MABC-2), ageband 2. We wanted to analyze the collected data, with adequate statistical methods, to provide relevant recommendations for physical therapists who are interpreting changes in the context of daily clinical practice. Forty-five healthy children, 23 girls and 22 boys with a mean age of 8.7±0.7 years, participated in the study, the inter-tester procedures were performed the same day and the intra-tester procedures within a one to two week interval. The statistical methods used were intra-class correlation coefficient (ICC), standard error of measurement (SEM), and smallest detectable change (SDC). The children had no failed items during the tests. The ICC values ranged from 0.23 to 0.76. The items "treading lace" and "one-board balance" showed the highest measurement errors both for the intra- and inter-rater reliability. The SDC(90%) values were 9.7 and 18.5 for the intra- and inter-rater reliability, respectively. The present study showed high intra- and inter-rater chance variation MABC-2, ageband 2. A change of more than ±9.7 and ±18.5 on the total test score (TTS) should be required to state (with a 90% confidence) that a real change in a single individual has occurred, for intra- and inter-rater testing, respectively. These findings may indicate that the MABC-2 might be more suitable for diagnostic or clinical decision making purposes, than for evaluation of change over time. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Deep vein thrombosis of the upper extremity: intra- and interobserver study of digital subtraction venography

    Energy Technology Data Exchange (ETDEWEB)

    Baarslag, Henk J.; Delden, Otto M. van; Bakker, Ad J.; Reekers, Jim A. [Department of Radiology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam (Netherlands); Beek, Edwin J.R. van [Department of Radiology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam (Netherlands); Section of Academic Radiology, Floor C, Royal Hallamshire Hospital, Glossop Road, Sheffield S10 2JF (United Kingdom); Tijssen, Jan G.P. [Department of Cardiology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam (Netherlands)

    2003-02-01

    Our objective was to assess the inter-observer and intra-observer agreement in the interpretation of digital subtraction venography (DSV) in patients with suspected deep vein thrombosis of the upper extremity (DVTUE). Prospectively, 62 consecutive DSV studies in 54 patients with clinically suspected DVTUE were included. Hard copies were presented without demographic data or original report. All venograms were read twice, at 3-month intervals, by an interventional vascular radiologist (observer 1) and an experienced general radiologist (observer 2). Consensus reading took place in the presence of a third experienced interventional radiologist. Inter-observer and intra-observer agreement were assessed using kappa statistics. Initial reading in 62 venograms showed an inter-observer agreement of 71% (kappa 0.48). The inter-observer agreement of the second reading was 83% (kappa 0.71). The agreement with the consensus report ranged from 76 to 94%. The intra-observer agreement for the first and second observer was 94% (kappa 0.89) and 76% (kappa 0.56), respectively (p<0.01). Digital subtraction venography has moderate to excellent intra- and inter-observer agreement, suggesting that digital subtraction venography is reliable for the diagnosis of DVTUE. (orig.)

  16. Intra-and interobserver reproducibility of shear wave elastography for evaluation of the breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Min Ji [Dept. of Radiology, Gil Hospital, Gachon University of Medicine and Science, Incheon (Korea, Republic of); Kim, Hak Hee [Dept. of Radiology, and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

    2017-03-15

    To evaluate reproducibility of shear wave elastography (SWE) for breast lesions within and between observers and compare the reproducibility of SWE features. For intraobserver reproducibility, 225 masses with 208 patients were included; and two consecutive SWE images were acquired by each observer. For interobserver reproducibility, SWE images of the same mass were obtained by another observer before surgery in 40 patients. Intraclass correlation coefficients (ICC) were used to determine intra- and interobserver reproducibility. Intraobserver reliability for mean elasticity (Emean) and maximum elasticity (Emax) were excellent (ICC = 0.803, 0.799). ICC for SWE ratio and minimum elasticity (Emin) were fair to good (ICC = 0.703, 0.539). Emean showed excellent ICC regardless of histopathologic type and tumor size. Emax, SWE ratio and Emin represented excellent or fair to good reproducibility based on histopathologic type and tumor size. In interobserver study, ICC for Emean, Emax and SWE ratio were excellent. Emean, Emax and SWE ratio represented excellent ICC irrespective of histopathologic type. ICC for Emean was excellent regardless of tumor size. SWE ratio and Emax showed fair to good interobserver reproducibility based on tumor size. Emin represented poor interobserver reliability. Emean in SWE was highly reproducible within and between observers.

  17. Intra and interobserver variability of renal allograft ultrasound volume and resistive index measurements

    International Nuclear Information System (INIS)

    Mancini, Marcello; Liuzzi, Raffaele; Daniele, Stefania; Raffio, Teresa; Salvatore, Marco; Sabbatini, Massimo; Cianciaruso, Bruno; Ferrara, Liberato Aldo

    2005-01-01

    Purpose: Aim of the presents study was to evaluate the repeatability and reproducibility of the Doppler Resistive Index (R.I.) and the Ultrasound renal volume measurement in renal transplants. Materials and methods: Twenty -six consecutive patients (18 men, 8 women) mean age of 42,8±12,4 years (M±SD)(range 22-65 years) were studied twice by each of two trained sonographers using a color Doppler ultrasound scanner. Twelve of them had a normal allograft function (defined as stable serum creatinine levels ≤123,76 μmol/L), whilst the remaining 14 had decreased allograft function (serum creatinine 132.6-265.2 μmol/L). Results were given as mean of 6 measurements performed at upper, middle and lower pole of the kidney. Intra- and interobserver variability was assessed by the repeatability coefficient and coefficient of variation (CV). Results: Regarding Resistive Index measurement, repeatability coefficient was between 0.04 and 0.06 and the coefficient of variation was [it

  18. Doppler ultrasonography in living donor liver transplantation recipients: Intra- and post-operative vascular complications.

    Science.gov (United States)

    Abdelaziz, Omar; Attia, Hussein

    2016-07-21

    Living-donor liver transplantation has provided a solution to the severe lack of cadaver grafts for the replacement of liver afflicted with end-stage cirrhosis, fulminant disease, or inborn errors of metabolism. Vascular complications remain the most serious complications and a common cause for graft failure after hepatic transplantation. Doppler ultrasound remains the primary radiological imaging modality for the diagnosis of such complications. This article presents a brief review of intra- and post-operative living donor liver transplantation anatomy and a synopsis of the role of ultrasonography and color Doppler in evaluating the graft vascular haemodynamics both during surgery and post-operatively in accurately defining the early vascular complications. Intra-operative ultrasonography of the liver graft provides the surgeon with useful real-time diagnostic and staging information that may result in an alteration in the planned surgical approach and corrections of surgical complications during the procedure of vascular anastomoses. The relevant intra-operative anatomy and the spectrum of normal and abnormal findings are described. Ultrasonography and color Doppler also provides the clinicians and surgeons early post-operative potential developmental complications that may occur during hospital stay. Early detection and thus early problem solving can make the difference between graft survival and failure.

  19. Measurement of transplanted pancreatic volume using computed tomography: reliability by intra- and inter-observer variability

    Energy Technology Data Exchange (ETDEWEB)

    Lundqvist, Eva; Segelsjoe, Monica; Magnusson, Anders [Uppsala Univ., Dept. of Radiology, Oncology and Radiation Science, Section of Radiology, Uppsala (Sweden)], E-mail: eva.lundqvist.8954@student.uu.se; Andersson, Anna; Biglarnia, Ali-Reza [Dept. of Surgical Sciences, Section of Transplantation Surgery, Uppsala Univ. Hospital, Uppsala (Sweden)

    2012-11-15

    Background Unlike other solid organ transplants, pancreas allografts can undergo a substantial decrease in baseline volume after transplantation. This phenomenon has not been well characterized, as there are insufficient data on reliable and reproducible volume assessments. We hypothesized that characterization of pancreatic volume by means of computed tomography (CT) could be a useful method for clinical follow-up in pancreas transplant patients. Purpose To evaluate the feasibility and reliability of pancreatic volume assessment using CT scan in transplanted patients. Material and Methods CT examinations were performed on 21 consecutive patients undergoing pancreas transplantation. Volume measurements were carried out by two observers tracing the pancreatic contours in all slices. The observers performed the measurements twice for each patient. Differences in volume measurement were used to evaluate intra- and inter-observer variability. Results The intra-observer variability for the pancreatic volume measurements of Observers 1 and 2 was found to be in almost perfect agreement, with an intraclass correlation coefficient (ICC) of 0.90 (0.77-0.96) and 0.99 (0.98-1.0), respectively. Regarding inter-observer validity, the ICCs for the first and second measurements were 0.90 (range, 0.77-0.96) and 0.95 (range, 0.85-0.98), respectively. Conclusion CT volumetry is a reliable and reproducible method for measurement of transplanted pancreatic volume.

  20. Proteomic insights into intra- and intercellular plant-bacteria symbiotic association during root nodule formation

    Directory of Open Access Journals (Sweden)

    Afshin eSalavati

    2013-02-01

    Full Text Available Over the last several decades, there have been a large number of studies done on the all aspects of legumes and bacteria which participate in nitrogen-fixing symbiosis. The analysis of legume-bacteria interaction is not just a matter of numerical complexity in terms of variants of gene products that can arise from a single gene. Bacteria regulate their quorum-sensing genes to enhance their ability to induce conjugation of plasmids and symbiotic islands, and various protein secretion mechanisms; that can stimulate a collection of chain reactions including species-specific combinations of plant-secretion isoflavonoids, complicated calcium signaling pathways and autoregulation of nodulation mechanisms. Quorum-sensing systems are introduced by the intra- and intercellular organization of gene products lead to protein–protein interactions or targeting of proteins to specific cellular structures. In this study, an attempt has been made to review significant contributions related to nodule formation and development and their impacts on cell proteome for better understanding of plant-bacterium interaction mechanism at protein level. This review would not only provide new insights into the plant-bacteria symbiosis response mechanisms but would also highlights the importance of studying changes in protein abundance inside and outside of cells in response to symbiosis. Furthermore, the application to agriculture programe of plant-bacteria interaction will be discussed.

  1. Genetic evidence for intra- and interspecific slavery in honey ants (genus Myrmecocystus).

    Science.gov (United States)

    Kronauer, D J C; Gadau, J; Hölldobler, B

    2003-04-22

    The New World honey ant species Myrmecocystus mimicus is well known for its highly stereotyped territorial tournaments, and for the raids on conspecific nests that can lead to intraspecific slavery. Our results from mitochondrial and nuclear markers show that the raided brood emerges in the raiding colony and is subsequently incorporated into the colony's worker force. We also found enslaved conspecifics in a second honey ant species, M. depilis, the sister taxon of M. mimicus, which occurs in sympatry with M. mimicus at the study site. Colonies of this species furthermore contained raided M. mimicus workers. Both species have an effective mating frequency that is not significantly different from 1. This study provides genetic evidence for facultative intra- and interspecific slavery in the genus Myrmecocystus. Slavery in ants has evolved repeatedly and supposedly by different means. We propose that, in honey ants, secondary contact between two closely related species that both exhibit intraspecific slavery gave rise to an early form of facultative interspecific slavery.

  2. Intra and Inter-Individual Differences in Social Intelligence of Portuguese Students

    Directory of Open Access Journals (Sweden)

    Joana Carneiro Pinto

    2015-08-01

    Full Text Available Social intelligence is a favorable condition for career decision-making and development. The social intelligence indices of Portuguese students in school years prior to a career transition are characterized and intra and interindividual differences are analyzed. Participants were 1095 students (552, 50.4% women with a mean age of 14.78 years (SD = 1.86, in the 8th (542, 49.5%, 10th (295, 26.9% and 11th (258, 23.6% grades. The Cognitive Test of Social Intelligence (PCIS was administered at two moments, six months apart. Results indicate that the 8th grade obtained higher average scores in Problem Solving, Motivation and Self-confidence (time 1, while the 10th grade obtained better results in Problem Solving, Motivation and Familiarity (time 2. Between the assessment moments, all school years register an increase in Problem Solving and Self-confidence in social situations. These results constitute favorable psychological conditions for the promotion of ethical questioning in career guidance interventions.

  3. Internet Search Alters Intra- and Inter-regional Synchronization in the Temporal Gyrus.

    Science.gov (United States)

    Liu, Xiaoyue; Lin, Xiao; Zheng, Ming; Hu, Yanbo; Wang, Yifan; Wang, Lingxiao; Du, Xiaoxia; Dong, Guangheng

    2018-01-01

    Internet search changed the way we store and recall information and possibly altered our brain functions. Previous studies suggested that Internet search facilitates the information-acquisition process. However, this process may cause individuals to lose the ability to store and recollect specific contents. Despite the numerous behavioral studies conducted in this field, little is known about the neural mechanisms underlying Internet searches. The present study explores potential brain activity changes induced by Internet search. The whole paradigm includes three phases, namely, pre-resting state fMRI (rs-fMRI) scan, 6-day Internet search training, and post rs-fMRI scan. We detected the functional integrations induced by Internet search training by comparing post- with pre-scan. Regional homogeneity (ReHo) and functional connectivity (FC) were used to detect intra- and interregional synchronized activity in 42 university students. Compared with pre-scan, post-scan showed decreased ReHo in the temporal gyrus, the middle frontal gyrus, and the postcentral gyrus. Further seed-based FC analysis showed that the temporal gyrus exhibited decreased FC in the parahippocampal cortex and the temporal gyrus after training. Based on the features of current task and functions exhibited by these brain regions, results indicate that short-term Internet search training changed the brain regional activities involved in memory retrieval. In general, this study provides evidence that supports the idea that Internet search can affect our brain functions.

  4. Intra- and interhemispheric variations of diffusivity in subcortical white matter in normal human brain

    Energy Technology Data Exchange (ETDEWEB)

    Yoshiura, Takashi; Noguchi, Tomoyuki; Hiwatashi, Akio; Togao, Osamu; Yamashita, Koji; Nagao, Eiki; Kamano, Hironori; Honda, Hiroshi [Kyushu University, Department of Clinical Radiology, Graduate School of Medical Sciences, Fukuoka (Japan)

    2010-01-15

    Our purpose was to reveal potential regional variations in water molecular diffusivity within each cerebral hemisphere and across the right and left hemispheres. Diffusion-weighted images of 44 healthy right-handed adult male subjects were obtained using a diffusion tensor imaging sequence. Mean diffusivity (MD) values in subcortical white matter (WM) within 39 regions in each hemisphere were measured using an automated method. Intrahemispheric comparisons of MDs in subcortical WM were performed among six brain regions (frontal, parietal, occipital and temporal lobes and pre- and postcentral gyri). Interhemispheric comparisons of MDs were performed between the right and left counterparts of the 39 regions. In both hemispheres, diffusivity in the precentral gyrus was lower than those in other regions, while diffusivity in the parietal lobe was higher than others. MD asymmetry in which the left was lower than the right was found in the parietal lobe, middle occipital gyrus, and medial and orbital aspects of the frontal lobe. The converse asymmetry was revealed in the frontal operculum, supplementary motor cortex, temporal lobe, limbic cortices, precuneus and cuneus. Our results revealed significant intra- and interhemispheric regional variations in MD in subcortical WM, which may be related to different densities of axons and myelin sheaths. (orig.)

  5. Laryngeal tumor volume measurements determined with CT: a study on intra- and interobserver variability

    International Nuclear Information System (INIS)

    Hermans, Robert; Feron, Michel; Bellon, Erwin; Dupont, Patrick; Van den Bogaert, Walter; Baert, Albert L.

    1998-01-01

    Purpose: To investigate the intra- and interobserver variability of computed tomography-based volume measurements of laryngeal tumors. Methods and Materials: The volume of 13 laryngeal tumors was repeatedly measured by five independent observers in four different sessions, using the summation-of-areas technique. Mean tumor volume and its standard deviation were calculated for each tumor. Statistical analysis was done with analysis of variance, Spearman rank correlation, and linear regression. Results: Both the effect of the observers (p < 0.0001) and the effect of the session (p < 0.01) on tumor volume was statistically significant. Interobserver variability was the most important component of total variability (89.3%). A significant rank correlation was found between mean volume and standard deviation (p < 0.01); the relationship between mean tumor volume and standard deviation can be described using linear regression [standard deviation = 0.28 volume + 0.35 (R = 0.79)]. Conclusion: Total variability in the computed tomography-based measurement of laryngeal tumor volume can be reduced by having the measurements done by a single trained observer

  6. Longitudinal intra- and inter-individual variability in young swimmers' performance and determinant competition factors

    Directory of Open Access Journals (Sweden)

    Jorge Estrela Morais

    2014-09-01

    Full Text Available The main purpose of this study was to follow-up the intra- and inter-individual variability of young swimmers' performance and determinant factors over two competitive seasons. Thirty young swimmers (14 boys: 12.33±0.65 years-old; 16 girls: 11.15±0.55 years-old were followed-up throughout two consecutive seasons (seven evaluation moments. Performance (100m freestyle, anthropometric, kinematic, hydrodynamic and efficiency features were evaluated. A gender and skill-level effect was observed. Boys improved in a higher amount (% comparing to girls. Overall, swimmers in skill-level 2 (both genders presented a higher intra-individual variability. Performance and anthropometrics showed a significant inter-individual variability in most moments, but hydrodynamics, kinematics and efficiency did not. Within each skill-level hydrodynamics, kinematics and efficiency were the variables that showed a high inter-individual variability. As a gender and skill-level effect was noticed in an age-group of young swimmers, coaches and practitioners should put the focus in specific and customized training plans for each skill-level of swimmers.

  7. INTRA- AND INTER-OBSERVER AGREEMENT IN THE AO AND GARNAVOS SYSTEMS FOR DIAPHYSEAL HUMERUS FRACTURE.

    Science.gov (United States)

    Meriqui, Roberto; Masuda, Rodrigo Yuzo; Utino, Artur Yudi; Pierami, Rafael; Matsunaga, Fábio Teruo; Tamaoki, Marcel Jun Sugawara

    2017-01-01

    The objective of this study was to compare inter- and intra-observer agreement using the Garnavos and AO/ASIF systems for classifying humeral diaphysis fractures . Eighty X-ray images taken of humeral diaphysis fractures in adult patients (age≥18 years) between January 2013 and September 2015 in the Radiology Department of Hospital São Paulo were selected for subsequent classification by five orthopedic surgeons with differing levels of experience. The images were examined at two different times and reproducibility analysis was evaluated using Fleiss' kappa to verify intra- and inter-observer agreement . High-level agreement was observed for both classification systems, but particularly for the AO/ASIF classification. Inter-observer evaluation yielded excellent levels of agreement for both classifications, but principally for the Garnavos classification . Good or excellent inter- and intra-observer agreement was seen for both the AO/ASIF and Garnavos classification systems. However, intra-observer agreement was higher for the AO/ASIF system and inter-observer agreement was higher for the Garnavos classification. Level of Evidence II, Diagnostic Studies - Investigating a Diagnostic Examination.

  8. Measurement of transplanted pancreatic volume using computed tomography: reliability by intra- and inter-observer variability

    International Nuclear Information System (INIS)

    Lundqvist, Eva; Segelsjoe, Monica; Magnusson, Anders; Andersson, Anna; Biglarnia, Ali-Reza

    2012-01-01

    Background Unlike other solid organ transplants, pancreas allografts can undergo a substantial decrease in baseline volume after transplantation. This phenomenon has not been well characterized, as there are insufficient data on reliable and reproducible volume assessments. We hypothesized that characterization of pancreatic volume by means of computed tomography (CT) could be a useful method for clinical follow-up in pancreas transplant patients. Purpose To evaluate the feasibility and reliability of pancreatic volume assessment using CT scan in transplanted patients. Material and Methods CT examinations were performed on 21 consecutive patients undergoing pancreas transplantation. Volume measurements were carried out by two observers tracing the pancreatic contours in all slices. The observers performed the measurements twice for each patient. Differences in volume measurement were used to evaluate intra- and inter-observer variability. Results The intra-observer variability for the pancreatic volume measurements of Observers 1 and 2 was found to be in almost perfect agreement, with an intraclass correlation coefficient (ICC) of 0.90 (0.77-0.96) and 0.99 (0.98-1.0), respectively. Regarding inter-observer validity, the ICCs for the first and second measurements were 0.90 (range, 0.77-0.96) and 0.95 (range, 0.85-0.98), respectively. Conclusion CT volumetry is a reliable and reproducible method for measurement of transplanted pancreatic volume

  9. Noninvasive, optoacoustic detection and characterization of intra- and extracranial hematomas and cerebral hypoxia

    Science.gov (United States)

    Petrov, Andrey; Prough, Donald S.; Petrov, Yuriy; Petrov, Irene Y.; Robertson, Claudia S.; Asokan, Vasantha; Agbor, Adaeze; Esenaliev, Rinat O.

    2015-03-01

    Early diagnosis of intracranial hematomas is necessary to improve outcome in patients with traumatic brain injury (TBI). CT and MRI can diagnose intracranial hematomas, but cannot be used until the patient arrives at a major healthcare facility, resulting in delayed diagnosis. Near infrared spectroscopy may suggest the presence of unilateral intracranial hematomas, but provides minimal information on hematoma type and location due to limitations associated with strong light scattering. We have used optoacoustics (which combines high endogenous optical contrast with the resolution of ultrasound) to diagnose hematomas and monitor cerebral oxygenation. We performed animal and clinical studies on detection and characterization of hematomas and on monitoring cerebral hypoxia by probing the superior sagittal sinus (SSS). Recently, we built a medical grade, multi-wavelength, OPO-based optoacoustic system tunable in the near infrared spectral range. We developed new patient interfaces for noninvasive, transcranial measurements in the transmission mode in the presence of dense hair and used it in patients with TBI. The optoacoustic system was capable of detecting and characterizing intra- and extracranial hematomas. SSS blood oxygenation was measured as well with the new interface. The obtained results indicate that the optoacoustic system in the transmission mode provides detection and characterization of hematomas in TBI patients, as well as cerebral venous blood oxygenation monitoring. The transmission mode approach can be used for optoacoustic brain imaging, tomography, and mapping in humans.

  10. VOC emissions influence intra- and interspecific interactions among stored-product Coleoptera in paddy rice.

    Science.gov (United States)

    Giunti, Giulia; Palmeri, Vincenzo; Algeri, Giuseppe Massimo; Campolo, Orlando

    2018-02-01

    Olfaction is a pivotal sense for insects and granivorous pests may exploit grain volatiles for food selection. Tribolium confusum, is a secondary pest of stored cereals that benefits from primary pests' infestation, as other secondary feeders, triggering competition. This study aimed to evaluate the preferences of T. confusum females toward different-infested paddy rice, highlighting the impact of intra- and interspecific competition. Tribolium confusum showed positive chemotaxis toward rice infested by larvae of a primary pest (Sitophilus zeamais), but not for grain attacked by adults alone. Furthermore, kernels concurrently infested by a primary (S. zeamais) and a secondary pest (T. confusum or Cryptolestes ferrugineus) were evaluated in Y-tube bioassays, highlighting that both food-sources were innately attractive for T. confusum females. Moreover, females positively oriented toward rice infested by conspecifics, while they avoided grain infested by C. ferrugineus, averting an extremely competitive habitat. Behavioural responses of T. confusum females and volatile emissions of different-infested rice highlighted the occurrence of plant-mediated interactions among insects from the same trophic guild. Seventy volatiles were identified and significant differences among the tested food-sources were recorded, emphasizing the presence of 6 putative attractants and 6 repellents, which may be useful biocontrol tools.

  11. Intra- and Interspecific Competition Between Western Flower Thrips and Sweetpotato Whitefly

    Science.gov (United States)

    Wu, Qing-Jun; Hou, Wen-Jie; Li, Fei; Xu, Bao-Yun; Xie, Wen; Wang, Shao-Li; Zhang, You-Jun

    2014-01-01

    Abstract The western flower thrips, Frankliniella occidentalis (Pergande), and the sweetpotato whitefly, Bemisia tabaci (Gennadius), are both invasive insect pests and are present in most of the same agricultural crops without a clear dominance of either species. Here, intra- and interspecific competition in B. tabaci and F. occidentalis was determined under controlled experiments. The results showed that intraspecific competition was distinct in F. occidentalis and that the co-occurrence of B. tabaci had a strong effect on F. occidentalis , resulting in a decrease in oviposition. Significant intraspecific competition was found in B. tabaci , and the coexistence of F. occidentalis had limited effect on the oviposition of B. tabaci . In a selective host plant preference experiment, both F. occidentalis and B. tabaci preferred eggplants most, followed by cucumbers and tomatoes. On cucumber plants, B. tabaci was predominant, whereas on eggplant and tomato plants, F. occidentalis and B. tabaci exhibited comparative competitive abilities during the initial stage. However, over time, higher numbers of B. tabaci than that of F. occidentalis were found on the two host plants. Our in vitro and potted plant experiments indicate that B. tabaci is competitively superior to F. occidentalis , which might help to explain their differential distribution patterns in China. PMID:25480973

  12. Intergenic and external transcribed spacers of ribosomal RNA genes in lizard-infecting Leishmania: molecular structure and phylogenetic relationship to mammal-infecting Leishmania in the subgenus Leishmania (Leishmania

    Directory of Open Access Journals (Sweden)

    Orlando Tereza C

    2002-01-01

    Full Text Available To establish the relationships of the lizard- and mammal-infecting Leishmania, we characterized the intergenic spacer region of ribosomal RNA genes from L. tarentolae and L. hoogstraali. The organization of these regions is similar to those of other eukaryotes. The intergenic spacer region was approximately 4 kb in L. tarentolae and 5.5 kb in L. hoogstraali. The size difference was due to a greater number of 63-bp repetitive elements in the latter species. This region also contained another element, repeated twice, that had an inverted octanucleotide with the potential to form a stem-loop structure that could be involved in transcription termination or processing events. The ribosomal RNA gene localization showed a distinct pattern with one chromosomal band (2.2 Mb for L. tarentolae and two (1.5 and 1.3 Mb for L. hoogstraali. The study also showed sequence differences in the external transcribed region that could be used to distinguish lizard Leishmania from the mammalian Leishmania. The intergenic spacer region structure features found among Leishmania species indicated that lizard and mammalian Leishmania are closely related and support the inclusion of lizard-infecting species into the subgenus Sauroleishmania proposed by Saf'janova in 1982.

  13. Vaccine platform recombinant measles virus.

    Science.gov (United States)

    Mühlebach, Michael D

    2017-10-01

    The classic development of vaccines is lengthy, tedious, and may not necessarily be successful as demonstrated by the case of HIV. This is especially a problem for emerging pathogens that are newly introduced into the human population and carry the inherent risk of pandemic spread in a naïve population. For such situations, a considerable number of different platform technologies are under development. These are also under development for pathogens, where directly derived vaccines are regarded as too complicated or even dangerous due to the induction of inefficient or unwanted immune responses causing considerable side-effects as for dengue virus. Among platform technologies are plasmid-based DNA vaccines, RNA replicons, single-round infectious vector particles, or replicating vaccine-based vectors encoding (a) critical antigen(s) of the target pathogens. Among the latter, recombinant measles viruses derived from vaccine strains have been tested. Measles vaccines are among the most effective and safest life-attenuated vaccines known. Therefore, the development of Schwarz-, Moraten-, or AIK-C-strain derived recombinant vaccines against a wide range of mostly viral, but also bacterial pathogens was quite straightforward. These vaccines generally induce powerful humoral and cellular immune responses in appropriate animal models, i.e., transgenic mice or non-human primates. Also in the recent first clinical phase I trial, the results have been quite encouraging. The trial indicated the expected safety and efficacy also in human patients, interestingly independent from the level of prevalent anti-measles immunity before the trial. Thereby, recombinant measles vaccines expressing additional antigens are a promising platform for future vaccines.

  14. CRMAGE: CRISPR Optimized MAGE Recombineering

    DEFF Research Database (Denmark)

    Ronda, Carlotta; Pedersen, Lasse Ebdrup; Sommer, Morten Otto Alexander

    2016-01-01

    A bottleneck in metabolic engineering and systems biology approaches is the lack of efficient genome engineering technologies. Here, we combine CRISPR/Cas9 and λ Red recombineering based MAGE technology (CRMAGE) to create a highly efficient and fast method for genome engineering of Escherichia coli...... that are assembled by a USER-cloning approach enabling quick and cost efficient gRNA replacement. CRMAGE furthermore utilizes CRISPR/Cas9 for efficient plasmid curing, thereby enabling multiple engineering rounds per day. To facilitate the design process, a web-based tool was developed to predict both the λ Red...

  15. Atomic excitation and recombination in external fields

    International Nuclear Information System (INIS)

    Nayfeh, M.H.; Clark, C.W.

    1985-01-01

    This volume offers a timely look at Rydberg states of atoms in external fields and dielectronic recombination. Each topic provides authoritative coverage, presents a fresh account of a flourishing field of current atomic physics and introduces new opportunities for discovery and development. Topics considered include electron-atom scattering in external fields; observations of regular and irregular motion as exemplified by the quadratic zeeman effect and other systems; Rydberg atoms in external fields and the Coulomb geometry; crossed-field effects in the absorption spectrum of lithium in a magnetic field; precise studies of static electric field ionization; widths and shapes of stark resonances in sodium above the saddle point; studies of electric field effects and barium autoionizing resonances; autoionization and dielectronic recombination in plasma electric microfields; dielectronic recombination measurements on multicharged ions; merged beam studies of dielectronic recombination; Rydberg atoms and dielectronic recombination in astrophysics; and observations on dielectronic recombination

  16. Recombinant vaccines: experimental and applied aspects

    DEFF Research Database (Denmark)

    Lorenzen, Niels

    1999-01-01

    in induction of a protective immune response may become vital. The few recombinant vaccines licensd so far, despite much research during the last decade, illustrate that this is not a straightforward matter. However, as vaccine technology as well as our knowledge of the fish immune system is steadily improved......, these fields will open up a number of interesting research objectives of mutual benefit. Recent aspects of recombinant protein vaccines, live recombinant vaccines and DNA vaccines are discussed....

  17. Quantum mechanical theory of collisional recombination rates

    International Nuclear Information System (INIS)

    Miller, W.H.

    1995-01-01

    Quantum mechanical expressions for the pressure-dependent recombination rate (within the strong collision assumption) are presented which have a very similar form to those developed recently for rate constants of chemical reactions: eqs. 11 and 12 express the recombination rate in terms of a flux autocorrelation function, and eqs. 14-16 in terms of a cumulative recombination probability. The qualitative behavior of these functions is illustrated by several pedagogical examples. 24 refs., 1 fig

  18. Recombination chambers for BNCT dosimetry

    International Nuclear Information System (INIS)

    Tulik, Piotr

    2006-01-01

    Parallel plate recombination ionization chambers are known as the detectors which can be used for determination of gamma and high-LET dose components and for characterization of radiation quality of mixed radiation fields. Specially designed chambers can operate correctly even at dose rates of therapeutic beams. In this work the investigations were extended to a set of cylindrical chambers including a TE chamber and three graphite chambers filled with different gases - CO 2 , N 2 and 10 BF 3 , in order to determine the thermal neutrons, 14 N capture, gamma, and fast neutron dose components. The separation of the dose components is based on differences of the shape of the saturation curve, in dependence on LET spectrum of the investigated radiation. The measurements using all the chambers and a parallel plate recombination chamber were performed in a reactor beam of NRI Rez (Czech Republic). The gamma component was determined with accuracy of about 5%, while the variations of its value could be monitored with accuracy of about 0.5%. Relative changes of the beam components could be detected with accuracy of about 5% using the parallel plate chamber. The use of the chambers filled with different gases considerably improved the resolution of the method. (author)

  19. Rapid purification of recombinant histones.

    Science.gov (United States)

    Klinker, Henrike; Haas, Caroline; Harrer, Nadine; Becker, Peter B; Mueller-Planitz, Felix

    2014-01-01

    The development of methods to assemble nucleosomes from recombinant histones decades ago has transformed chromatin research. Nevertheless, nucleosome reconstitution remains time consuming to this day, not least because the four individual histones must be purified first. Here, we present a streamlined purification protocol of recombinant histones from bacteria. We termed this method "rapid histone purification" (RHP) as it circumvents isolation of inclusion bodies and thereby cuts out the most time-consuming step of traditional purification protocols. Instead of inclusion body isolation, whole cell extracts are prepared under strongly denaturing conditions that directly solubilize inclusion bodies. By ion exchange chromatography, the histones are purified from the extracts. The protocol has been successfully applied to all four canonical Drosophila and human histones. RHP histones and histones that were purified from isolated inclusion bodies had similar purities. The different purification strategies also did not impact the quality of octamers reconstituted from these histones. We expect that the RHP protocol can be readily applied to the purification of canonical histones from other species as well as the numerous histone variants.

  20. The Red Queen theory of recombination hotspots.

    Science.gov (United States)

    Ubeda, F; Wilkins, J F

    2011-03-01

    Recombination hotspots are small chromosomal regions, where meiotic crossover events happen with high frequency. Recombination is initiated by a double-strand break (DSB) that requires the intervention of the molecular repair mechanism. The DSB repair mechanism may result in the exchange of homologous chromosomes (crossover) and the conversion of the allelic sequence that breaks into the one that does not break (biased gene conversion). Biased gene conversion results in a transmission advantage for the allele that does not break, thus preventing recombination and rendering recombination hotspots transient. How is it possible that recombination hotspots persist over evolutionary time (maintaining the average chromosomal crossover rate) when they are self-destructive? This fundamental question is known as the recombination hotspot paradox and has attracted much attention in recent years. Yet, that attention has not translated into a fully satisfactory answer. No existing model adequately explains all aspects of the recombination hotspot paradox. Here, we formulate an intragenomic conflict model resulting in Red Queen dynamics that fully accounts for all empirical observations regarding the molecular mechanisms of recombination hotspots, the nonrandom targeting of the recombination machinery to hotspots and the evolutionary dynamics of hotspot turnover. © 2010 The Authors. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology.

  1. Genotypic characterization of Escherichia coli O157:H7 isolates from different sources in the North-West Province, South Africa, using enterobacterial repetitive intergenic consensus PCR analysis.

    Science.gov (United States)

    Ateba, Collins Njie; Mbewe, Moses

    2014-05-30

    In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli) O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v) agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003) and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA) and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I-VIII) were identified. Overall, the remarkable similarities (72% to 91%) between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa.

  2. Genotypic Characterization of Escherichia coli O157:H7 Isolates from Different Sources in the North-West Province, South Africa, Using Enterobacterial Repetitive Intergenic Consensus PCR Analysis

    Directory of Open Access Journals (Sweden)

    Collins Njie Ateba

    2014-05-01

    Full Text Available In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC polymerase chain reaction (PCR typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003 and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I–VIII were identified. Overall, the remarkable similarities (72% to 91% between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa.

  3. Large intergenic non-coding RNA-ROR as a potential biomarker for the diagnosis and dynamic monitoring of breast cancer.

    Science.gov (United States)

    Zhao, Tianhe; Wu, Lichun; Li, Xinyang; Dai, Huangmei; Zhang, Zunzhen

    2017-08-23

    Recent study has revealed that large intergenic non-coding RNA-ROR (linc-ROR) is aberrantly expressed in a number of cancers including breast cancer. However, whether circulating linc-ROR in plasma could be used for breast cancer diagnosis and dynamic monitoring is not clear. The objective of this study is to determine if plasma linc-ROR could be applied as a biomarker for the diagnosis and dynamic monitoring of breast cancer. We tested the expression levels of linc-ROR in 24 pairs of tissue samples and 96 plasma samples from breast cancer patients by quantitative real time-polymerase chain reaction (qRT-PCR), and analyzed the correlation between plasma linc-ROR levels and clinico-pathological characteristics. Receiver operating characteristic (ROC) curve was used to assess the diagnostic power of plasma linc-ROR, carcinoembryonic antigen (CEA) and carbohydrate antigen (CA)153 for breast cancer. Furthermore, we explored the monitoring values of plasma linc-ROR for breast cancer by analyzing the preoperative and postoperative plasma linc-ROR levels of the same patients. The expression levels of linc-ROR were significantly higher in breast cancer tissues and plasma than the levels in the control (PROR expression levels in plasma were correlated with lymph node metastasis (PROR was 0.758 (sensitivity 80.0%; specificity 73.3%), which was higher than CEA and CA153 values from the same patients obtained. Combination of the linc-ROR with the conventional biomarkers might produce better diagnostic ability. Additionally, the linc-ROR expression levels of plasma in postoperative patients were lower than those in preoperative patients (PROR may be a potential biomarker for the diagnosis and dynamic monitoring of breast cancer.

  4. Trypanosoma cruzi I genotypes in different geographic regions and transmission cycles based on a microsatellite motif of the intergenic spacer of spliced leader genes✯

    Science.gov (United States)

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

    2011-01-01

    The intergenic region of spliced-leader (SL-IR) genes from 105 Trypanosoma cruzi I (Tc I) infected biological samples, culture isolates and stocks from 11 endemic countries, from Argentina to the USA were characterised, allowing identification of 76 genotypes with 54 polymorphic sites from 123 aligned sequences. On the basis of the microsatellite motif proposed by Herrera et al. (2007) to define four haplotypes in Colombia, we could classify these genotypes into four distinct Tc I SL-IR groups, three corresponding to the former haplotypes Ia (11 genotypes), Ib (11 genotypes) and Id (35 genotypes); and one novel group, Ie (19 genotypes). Genotypes harboring the Tc Ic motif were not detected in our study. Tc Ia was associated with domestic cycles in southern and northern South America and sylvatic cycles in Central and North America. Tc Ib was found in all transmission cycles from Colombia. Tc Id was identified in all transmission cycles from Argentina and Colombia, including Chagas cardiomyopathy patients, sylvatic Brazilian samples and human cases from French Guiana, Panama and Venezuela. Tc Ie gathered five samples from domestic Triatoma infestans from northern Argentina, nine samples from wild Mepraia spinolai and Mepraia gajardoi and two chagasic patients from Chile and one from a Bolivian patient with chagasic reactivation. Mixed infections by Tc Ia + Tc Id, Tc Ia + Tc Ie and Tc Id + Tc Ie were detected in vector faeces and isolates from human and vector samples. In addition, Tc Ia and Tc Id were identified in different tissues from a heart transplanted Chagas cardiomyopathy patient with reactivation, denoting histotropism. Trypanosoma cruzi I SL-IR genotypes from parasites infecting Triatoma gerstaeckeri and Didelphis virginiana from USA, T. infestans from Paraguay, Rhodnius nasutus and Rhodnius neglectus from Brazil and M. spinolai and M. gajardoi from Chile are to our knowledge described for the first time. PMID:20670628

  5. CHIR99021 promotes self-renewal of mouse embryonic stem cells by modulation of protein-encoding gene and long intergenic non-coding RNA expression

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yongyan [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Ai, Zhiying [Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); College of Life Sciences, Northwest A and F University, Yangling 712100, Shaanxi (China); Yao, Kezhen [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Cao, Lixia; Du, Juan; Shi, Xiaoyan [Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); College of Life Sciences, Northwest A and F University, Yangling 712100, Shaanxi (China); Guo, Zekun, E-mail: gzk@nwsuaf.edu.cn [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China); Zhang, Yong, E-mail: zhylab@hotmail.com [College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi (China); Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi (China)

    2013-10-15

    Embryonic stem cells (ESCs) can proliferate indefinitely in vitro and differentiate into cells of all three germ layers. These unique properties make them exceptionally valuable for drug discovery and regenerative medicine. However, the practical application of ESCs is limited because it is difficult to derive and culture ESCs. It has been demonstrated that CHIR99021 (CHIR) promotes self-renewal and enhances the derivation efficiency of mouse (m)ESCs. However, the downstream targets of CHIR are not fully understood. In this study, we identified CHIR-regulated genes in mESCs using microarray analysis. Our microarray data demonstrated that CHIR not only influenced the Wnt/β-catenin pathway by stabilizing β-catenin, but also modulated several other pluripotency-related signaling pathways such as TGF-β, Notch and MAPK signaling pathways. More detailed analysis demonstrated that CHIR inhibited Nodal signaling, while activating bone morphogenetic protein signaling in mESCs. In addition, we found that pluripotency-maintaining transcription factors were up-regulated by CHIR, while several developmental-related genes were down-regulated. Furthermore, we found that CHIR altered the expression of epigenetic regulatory genes and long intergenic non-coding RNAs. Quantitative real-time PCR results were consistent with microarray data, suggesting that CHIR alters the expression pattern of protein-encoding genes (especially transcription factors), epigenetic regulatory genes and non-coding RNAs to establish a relatively stable pluripotency-maintaining network. - Highlights: • Combined use of CHIR with LIF promotes self-renewal of J1 mESCs. • CHIR-regulated genes are involved in multiple pathways. • CHIR inhibits Nodal signaling and promotes Bmp4 expression to activate BMP signaling. • Expression of epigenetic regulatory genes and lincRNAs is altered by CHIR.

  6. Methylation pattern of the intergenic spacer of rRNA genes in excised cotyledons of Cucurbita pepo L. (Zucchini) after hormone treatment

    International Nuclear Information System (INIS)

    Ananiev, E.; Abdulova, G.; Grozdanov, P.; Karagyozov, L.

    2003-01-01

    High molecular mass genomic DNA was isolated from excised marrow cotyledons (Cucurbita pepo L. zucchini) treated with 6-benzyladenine (BA) of methyl ester of jasmonic acid (MeJA) for 24 h in darkness. DNA purified from contaminating polysaccharides with Celite column was completely digested with the restriction enzyme Eco RI and the changes in the methylation pattern of the intergenic spacer (IGS) of r RNA genes were studied after subsequent digestion with the couple of restriction enzymes-isoschizomers MSP I and Hpa II by the method of 'indirect end labelling'. As rDNA units probe a cloned 32 P-labelled Eco RI 2.1 kb fragment spanning in the most part of 18S r RNA gene from flax rDNA was used. Results showed heavy methylation of the rRNA genes. As judged from the almost total lack of digestion with HPA II, there were no methylation free regions in repeated rDNA units or little if any were observed. A hypo methylated Hps II site was detected near the promoter region in some of the repeats. Digestion with Msp I affected nearly 50% of the repeating units. The Msp digestion fragments of the 6.2 kb Eco RI fragment of r DNA were few in number and large in size (0.5 - 2.5 kb). This suggested that in addition with -CpG- sequences, methylation in -CpNpG- might not be random. Methylation pattern in IGS was not changed upon treatment of the cotyledons in vivo with BA and MeJA. Thus, previously observed hormone-mediated effects on the eactivity of rRNA gene expression were not accompanied by any significant changes of the methylation pattern in IGS. (authors)

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

    Science.gov (United States)

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

    2015-09-04

    Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses. This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

  8. Molecular Typing of Papillomatous Digital Dermatitis-Associated Treponema Isolates Based on Analysis of 16S-23S Ribosomal DNA Intergenic Spacer Regions

    Science.gov (United States)

    Stamm, L. V.; Bergen, H. L.; Walker, R. L.

    2002-01-01

    Papillomatous digital dermatitis (PDD), an emerging infectious disease of cattle, is characterized by painful, ulcerative foot lesions. The detection of high numbers of invasive spirochetes in PDD lesions suggests an important role for these organisms in the pathogenesis of PDD. PDD-associated spirochetes have phenotypic characteristics consistent with members of the genus Treponema. Partial 16S ribosomal DNA (rDNA) sequence analysis of clonal isolates from California cattle showed that they comprise three phylotypes which cluster closely with human-associated Treponema spp. of the oral cavity (T. denticola and T. medium/T. vincentii) or genital area (T. phagedenis). The goal of our study was to apply 16S-23S rDNA intergenic spacer region (ISR) sequence analysis to the molecular typing of U.S. PDD-associated Treponema isolates. This methodology has potentially greater discriminatory power for differentiation of closely related bacteria than 16S rDNA analysis. We PCR amplified, cloned, and sequenced the ISRs from six California PDD-associated Treponema isolates and, for comparative purposes, one strain each of T. denticola, T. medium, T. vincentii, and T. phagedenis. Two ISRs that varied in length and composition were present in all the PDD-associated Treponema isolates and in T. denticola, T. medium, and T. phagedenis. ISR1 contained a tRNAAla gene, while ISR2 contained a tRNAIle gene. Only a single ISR (ISR1) was identified in T. vincentii. Comparative analyses of the ISR1 and ISR2 sequences indicated that the California PDD-associated Treponema isolates comprised three phylotypes, in agreement with the results of 16S rDNA analysis. PCR amplification of the 16S-tRNAIle region of ISR2 permitted rapid phylotyping of California and Iowa PDD-associated Treponema isolates based on product length polymorphisms. PMID:12202594

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

    Directory of Open Access Journals (Sweden)

    Su Ying-Juan

    2011-04-01

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

  10. The relation between intra- and interpersonal factors and food consumption level among Iranian adolescent girls.

    Science.gov (United States)

    Kazemi, Ashraf; Zahraei, Nafisehsadat Nekuei; Nazarian, Naser

    2016-01-01

    Poor nutrition habits in adolescent girls endanger their health and are followed by serious systemic diseases in adulthood and negative effects on their reproductive health. To design health promotion programs, understanding of the intra- and interpersonal associated factors with treatment is essential, and this was the aim of this study. This cross-sectional study was conducted on 193 adolescent girls of age 11-15 years. Random cluster selection was used for sample selection. Food group consumption pattern was assessed by food frequency questionnaire. Also, perceived susceptibility/severity and nutritional attitude as intrapersonal factors and social support as interpersonal factor were assessed. The relationship between food group consumption level and nutritional attitude and perceived treat (susceptibility/severity) as intrapersonal factors and perceived social support as interpersonal factor were assessed by linear multiple regression and analysis of variance (ANOVA). Results showed that the level of sweetmeat food consumption was related to perceived social support (P = 0.03) and nutritional attitude (P = 0.01) negatively. In addition, an inverse and significant association was found between the level of junk food intake and informational perceived social support (P = 0.004). The association between the level of fast food intake and the perceived parental social support for preparation of healthy food was negatively significant (P = 0.03). Breakfast consumption was related to nutritional attitude (P = 0.03), social support (P = 0.03), and perceived severity (P = 0.045). Results revealed that perceived social support and nutritional attitude are the important and related factors in dietary intake among girls, and promotion of social support and modification of nutritional attitude may lead to healthy nutritional behaviors among them.

  11. Takbir Mursal Procession at Brambang Village : A Review of Intra and Extra Aesthetic of Lantern Arts

    Directory of Open Access Journals (Sweden)

    Nur Rokhmat

    2016-01-01

    Full Text Available People at Brambang village, Karangawen subdistrict, Demak regency in Central Java province, have a procession tradition called takbiran.  It is a procession which has been conducted for years at the end of Ramadan, the eve of Eid. This Takbiran procession in which the villagers of Brambang carrying lanterns called "Takbeer Mursal". In the procession, it is echoed with the name of Allah "Allahu Akbar, Allahu Akbar, Allahu Akbar, laa-ilaha-illallaahu wallaahu Akbar.-walillaahil-hamd Allahu Akbar". Artwork lanterns carried in this procession is interesting to study especially its intra and extra aesthetic value. The study employed a qualitative approach. The shapes and themes of the lanterns are very diverse, and they express something creative, aesthetic, and symbolic. Diversity of forms and themes of the lantern in takbir mursal classified as follows; theme associated with the idea of responding to the technology; the shape of the building, and modern equipment of transportation. They are forms relating to the animals; birds, land animals, reptiles, insects, and animals living in the water. Some mythological animal forms are namely Burok (winged horse, dragons, winged lizards, Nyi Blorong. While themes related to imaginary creatures or monsters are namely Satan, Jin, Gandarwa, and giants. In addition, there are also the art of doll-shaped lanterns displayed such as Doraemon, mascot ball, and teletabis. Lantern’s shape, is generally structurally integrated elements such as a harmonious, balanced and proportionate and rhythmic having aesthetic value. Symbolic meaning contained in the works of art lanterns generally convey a message of religious values, education, and social criticism.

  12. The relation between intra- and interpersonal factors and food consumption level among Iranian adolescent girls

    Directory of Open Access Journals (Sweden)

    Ashraf Kazemi

    2016-01-01

    Full Text Available Background: Poor nutrition habits in adolescent girls endanger their health and are followed by serious systemic diseases in adulthood and negative effects on their reproductive health. To design health promotion programs, understanding of the intra- and interpersonal associated factors with treatment is essential, and this was the aim of this study. Materials and Methods: This cross-sectional study was conducted on 193 adolescent girls of age 11-15 years. Random cluster selection was used for sample selection. Food group consumption pattern was assessed by food frequency questionnaire. Also, perceived susceptibility/severity and nutritional attitude as intrapersonal factors and social support as interpersonal factor were assessed. The relationship between food group consumption level and nutritional attitude and perceived treat (susceptibility/severity as intrapersonal factors and perceived social support as interpersonal factor were assessed by linear multiple regression and analysis of variance (ANOVA. Results: Results showed that the level of sweetmeat food consumption was related to perceived social support (P = 0.03 and nutritional attitude (P = 0.01 negatively. In addition, an inverse and significant association was found between the level of junk food intake and informational perceived social support (P = 0.004. The association between the level of fast food intake and the perceived parental social support for preparation of healthy food was negatively significant (P = 0.03. Breakfast consumption was related to nutritional attitude (P = 0.03, social support (P = 0.03, and perceived severity (P = 0.045. Conclusions: Results revealed that perceived social support and nutritional attitude are the important and related factors in dietary intake among girls, and promotion of social support and modification of nutritional attitude may lead to healthy nutritional behaviors among them.

  13. Different intra- and interspecific facilitation mechanisms between two Mediterranean trees under a climate change scenario.

    Science.gov (United States)

    Gimeno, Teresa E; Escudero, Adrián; Valladares, Fernando

    2015-01-01

    In harsh environments facilitation alleviates biotic and abiotic constraints on tree recruitment. Under ongoing drier climate change, we expect facilitation to increase as a driver of coexistence. However, this might not hold under extreme abiotic stress and when the outcome depends on the interaction with other drivers such as altered herbivore pressure due to land use change. We performed a field water-manipulation experiment to quantify the importance of facilitation in two coexisting Mediterranean trees (dominant Juniperus thurifera and coexisting Quercus ilex subsp. ballota) under a climate change scenario. Shifts in canopy dominance favouring Q. ilex could be based on the extension of heterospecific facilitation to the detriment of conspecific alleviation. We found that saplings of both species transplanted under the canopy of nurse trees had greater survival probability, growth and photochemical efficiency. Intra- and interspecific facilitation mechanisms differed: alleviation of abiotic stress benefited both species during summer and J. thurifera during winter, whereas browsing protection was relevant only for Q. ilex. Facilitation was greater under the dry treatment only for Q. ilex, which partially agreed with the predictions of the stress gradient hypothesis. We conclude that present rainfall availability limits neither J. thurifera nor Q. ilex establishment. Nevertheless, under current global change scenarios, imposing increasing abiotic stress together with altered herbivore browsing, nurse trees could differentially facilitate the establishment of Q. ilex due to species-specific traits, i.e. palatability; drought, heat and cold tolerance, underlying species differences in the facilitation mechanisms and eventually triggering a change from pure juniper woodlands to mixed formations.

  14. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate.

    Science.gov (United States)

    Lin, Yin C; Benner, Christopher; Mansson, Robert; Heinz, Sven; Miyazaki, Kazuko; Miyazaki, Masaki; Chandra, Vivek; Bossen, Claudia; Glass, Christopher K; Murre, Cornelis

    2012-12-01

    The genome is folded into domains located in compartments that are either transcriptionally inert or transcriptionally permissive. Here we used genome-wide strategies to characterize domains during B cell development. Structured interaction matrix analysis showed that occupancy by the architectural protein CTCF was associated mainly with intradomain interactions, whereas sites bound by the histone acetyltransferase p300 or the transcription factors E2A or PU.1 were associated with intra- and interdomain interactions that are developmentally regulated. We identified a spectrum of genes that switched nuclear location during early B cell development. In progenitor cells, the transcriptionally inactive locus encoding early B cell factor (Ebf1) was sequestered at the nuclear lamina, which thereby preserved their multipotency. After development into the pro-B cell stage, Ebf1 and other genes switched compartments to establish new intra- and interdomain interactions associated with a B lineage-specific transcription signature.

  15. Intra- and Trans-Generational Costs of Reduced Female Body Size Caused by Food Limitation Early in Life in Mites

    OpenAIRE

    Walzer, Andreas; Schausberger, Peter

    2013-01-01

    Background Food limitation early in life may be compensated for by developmental plasticity resulting in accelerated development enhancing survival at the expense of small adult body size. However and especially for females in non-matching maternal and offspring environments, being smaller than the standard may incur considerable intra- and trans-generational costs. Methodology/Principal Findings Here, we evaluated the costs of small female body size induced by food limitation early in life i...

  16. Hepatic arginase activity in intra- and extrauterine larvae of the ovoviviparous salamander. Salamandra salamandra (L.) (Amphibia, Urodela).

    Science.gov (United States)

    Schindelmeiser, J; Schindelmeiser, I; Greven, H

    1983-01-01

    The hepatic arginase activity of Salamandra salamandra was determined at three different stages of intra- and extrauterine larval development and at fully metamorphosed juveniles. The highest enzymatic activity was found in intrauterine larvae in November, the lowest in intrauterine larvae in June of the following year. These data can be correlated with the ureotelism of intrauterine larvae previously described and are discussed with respect to the metabolism of larval and juvenile fire salamanders.

  17. The influence of intra- and inter-annual meteorological variability on dengue transmission: a multi-level modeling analysis

    Science.gov (United States)

    Wen, Tzai-Hung; Chen, Tzu-Hsin

    2017-04-01

    Dengue fever is one of potentially life-threatening mosquito-borne diseases and IPCC Fifth Assessment Report (AR5) has confirmed that dengue incidence is sensitive to the critical weather conditions, such as effects of temperature. However, previous literature focused on the effects of monthly or weekly average temperature or accumulative precipitation on dengue incidence. The influence of intra- and inter-annual meteorological variability on dengue outbreak is under investigated. The purpose of the study focuses on measuring the effect of the intra- and inter-annual variations of temperature and precipitation on dengue outbreaks. We developed the indices of intra-annual temperature variability are maximum continuity, intermittent, and accumulation of most suitable temperature (MST) for dengue vectors; and also the indices of intra-annual precipitation variability, including the measure of continuity of wetness or dryness during a pre-epidemic period; and rainfall intensity during an epidemic period. We used multi-level modeling to investigate the intra- and inter-annual meteorological variations on dengue outbreaks in southern Taiwan from 1998-2015. Our results indicate that accumulation and maximum continuity of MST are more significant than average temperature on dengue outbreaks. The effect of continuity of wetness during the pre-epidemic period is significantly more positive on promoting dengue outbreaks than the rainfall effect during the epidemic period. Meanwhile, extremely high or low rainfall density during an epidemic period do not promote the spread of dengue epidemics. Our study differentiates the effects of intra- and inter-annual meteorological variations on dengue outbreaks and also provides policy implications for further dengue control under the threats of climate change. Keywords: dengue fever, meteorological variations, multi-level model

  18. Predictive risk factors for intra- and postoperative complications in 526 laparoscopic sigmoid resections due to recurrent diverticulitis: a multivariate analysis.

    Science.gov (United States)

    Kirchhoff, Philipp; Matz, Daniel; Dincler, Selim; Buchmann, Peter

    2011-03-01

    Laparoscopic sigmoid resection is a feasible and frequent operation for patients who suffer from recurrent diverticulitis. There is still an ongoing debate about the optimal timing for surgery in patients who suffer from recurrent diverticulitis episodes. In elective situations the complication rate for this procedure is moderate, but there are patients at high risk for perioperative complications. The few identified risk factors so far refer to open surgery. Data for the elective laparoscopic approach is rare. The objective of this study was to identify potential predictive risk factors for intra- and postoperative complications in patients who underwent laparoscopic sigmoid resection due to diverticular disease. Uni- and multivariate analyses of a prospectively gathered database (1993-2006) were performed on a consecutive series of 526 patients who underwent laparoscopic sigmoid resection due to recurrent diverticulitis in a single institution. Patients were assessed for demographic data, operative indications, and intra- and postoperative complications. Altogether, we analyzed 17 potential risk factors to identify significant influence on the intra- and postoperative outcome, including timing of surgery. Statistical analysis of specific medical and surgical complications revealed anemia, previous myocardial infarction, heart failure, experience of the surgeon, and male gender, as independent predictive risk factors for postoperative complications. Patients older than age 75 years was the only independent risk factor for intraoperative complications in a multiple logistic regression model. Early elective surgery led to increased conversion rate but did not influence the postoperative complication rate. This large, single-center study provides first evidence of the significance of specific predictive risk factors for intra- and postoperative complications in laparoscopic sigmoid resection for diverticular disease.

  19. Intra and interobserver concordance of the AO classification system for fractures of the long bones in the pediatric population.

    Science.gov (United States)

    Utino, Artur Yudi; de Alencar, Douglas Rene; Fernadez Maringolo, Leonardo; Negrão, Julia Machado; Blumetti, Francesco Camara; Dobashi, Eiffel Tsuyoshi

    2015-01-01

    The AO classification for fractures of the long bones in the pediatric population was developed and validated in 2006. However, the complexity of this system has limited its use in clinical practice and few studies in the literature have evaluated its reproducibility and applicability. The present study had the objective of determining the intra and interobserver agreement using the pediatric AO system, among physicians with different levels of experience. After making the sample calculation, 108 consecutive radiographs on long-bone fractures in patients aged 0-16 years, coming from the digital files of the quaternary-level hospital, were selected. The radiographs were classified by five examiners with different levels of experience after prior explanations about the system. A chart containing images from the classification was made available for consultation. The evaluations were made at two different times by each observer. The Fleiss kappa index was used to ascertain the intra and interobserver agreement. Intraobserver agreement that was at least substantial was obtained for all the items of the classification and it reached excellent levels for all observers in relation to five of the seven items considered. The interobserver evaluation presented excellent levels of agreement in two items, substantial in two items, moderate to substantial in one item and poor to moderate in one item. No influence from the observer's experience was observed with regard to obtaining higher or lower levels of agreement, either in the intraobserver or in the interobserver evaluation. In this study, the intra and interobserver agreement was considered to be good or excellent for the pediatric AO classification system, for the parameters of bone, segment, paired bone, subsegment, standard and deviation. However, the intra and interobserver agreement was statistically unsatisfactory for the parameter of severity/side of avulsion. The levels of agreement obtained did not depend on the

  20. Intra- and inter-observer reliability of MRI examination of intervertebral disc abnormalities in patients with cervical myelopathy

    Energy Technology Data Exchange (ETDEWEB)

    Braga-Baiak, Andresa [Center for Excellence in Surgical Outcomes, Duke University Medical Center, Durham, NC (United States); Post-graduation Program, Department of Radiology, University of Sao Paulo (Brazil); Shah, Anand [Center for Excellence in Surgical Outcomes, Duke University Medical Center, Durham, NC (United States); Pietrobon, Ricardo [Center for Excellence in Surgical Outcomes, Duke University Medical Center, Durham, NC (United States); Department of Surgery, Duke University Medical Center, Durham, NC (United States); Braga, Larissa [Center for Excellence in Surgical Outcomes, Duke University Medical Center, Durham, NC (United States); University of Nebraska Medical Center, Lincoln NE (United States); Neto, Arnolfo Carvalho [Clinica DAPI, Curitiba (Brazil); Section of Diagnostic Radiology, Department of Internal Medicine, Universidade Federal do Parana (Brazil); Cook, Chad [Center for Excellence in Surgical Outcomes, Duke University Medical Center, Durham, NC (United States); Division of Physical Therapy, Duke University Medical Center, Durham, NC (United States)], E-mail: chad.cook@duke.edu

    2008-01-15

    Purpose: Intervertebral cervical disc herniation (CDH) is a relatively common disorder that can coexist with degenerative changes to worsen cervicogenic myelopathy. Despite the frequent disc abnormalities found in asymptomatic populations, magnetic resonance imaging (MRI) is considered excellent at detecting cervical spine myelopathy (CSM) associated with disc abnormality. The objective of this study was to investigate the intra- and inter-observer reliability of MRI detection of CSM in subjects who also had co-existing intervertebral disc abnormalities. Materials and methods: Seven experienced radiologists reviewed twice the MRI of 10 patients with clinically and/or imaging determined myelopathy. MRI assessment was performed individually, with and without operational guidelines. A Fleiss Kappa statistic was used to evaluate the intra- and inter-observer agreement. Results: The study found high intra-observer percent agreement but relatively low Kappa values on selected variables. Inter-observer reliability was also low and neither observation was improved with operational guidelines. We believe that those low values may be associated with the base rate problem of Kappa. Conclusion: In conclusion, this study demonstrated high intra-observer percent agreement in MR examination for intervertebral disc abnormalities in patients with underlying cervical myelopathy, but differing levels of intra- and inter-observer Kappa agreement among seven radiologists.

  1. Intra and interrater reliability of spinal sagittal curves and mobility using pocket goniometer IncliMed® in healthy subjects.

    Science.gov (United States)

    Alderighi, Marzia; Ferrari, Raffaello; Maghini, Irene; Del Felice, Alessandra; Masiero, Stefano

    2016-11-21

    Radiographic examination is the gold standard to evaluate spine curves, but ionising radiations limit routine use. Non-invasive methods, such as skin-surface goniometer (IncliMed®) should be used instead. To evaluate intra- and interrater reliability to assess sagittal curves and mobility of the spine with IncliMed®. a reliability study on agonistic football players. Thoracic kyphosis, lumbar lordosis and mobility of the spine were assessed by IncliMed®. Measurements were repeated twice by each examiner during the same session with between-rater blinding. Intrarater and interrater reliability were measured by Intraclass Correlation Coefficient (ICC), 95% Confidence Interval (CI 95%) and Standard Error of Measurement (SEM). Thirty-four healthy female football players (19.17 ± 4.52 years) were enrolled. Statistical results showed high intrarater (0.805-0.923) and interrater (0.701-0.886) reliability (ICC > 0.8). The obtained intra- and interrater SEM were low, with overall absolute intrarater values between 1.39° and 2.76° and overall interrater values between 1.71° and 4.25°. IncliMed® provides high intra- and interrater reliability in healthy subjects, with limited Standard Error of Measurement. These results encourage its use in clinical practice and scientific research.

  2. Fundamental Studies of Recombinant Hydrogenases

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Michael W. [Univ. of Georgia, Athens, GA (United States)

    2014-01-25

    This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.

  3. Electronic recombination in some physics problems

    International Nuclear Information System (INIS)

    Guzman, O.

    1988-01-01

    This work is related to calculations of electronic recombination rates, as a function of electronic density, electronic temperature, and ion nuclear charge. Recombination times can be calculated and compared to cooling time, in cooling processes of ion beans by electrons from storage rings. (A.C.A.S.) [pt

  4. Electron-ion recombination at low energy

    International Nuclear Information System (INIS)

    Andersen, L.H.

    1993-01-01

    The work is based on results obtained with a merged-beams experiment. A beam of electronics with a well characterized density and energy distribution was merged with a fast, monoenergetic ion beam. Results have been obtained for radiative recombination and dielectronic recombination at low relative energies (0 to ∼70eV). The obtained energy resolution was improved by about a factor of 30. High vacuum technology was used to suppress interactions with electrons from the environments. The velocity distribution of the electron beam was determined. State-selective dielectronic-recombination measurements were performable. Recombination processes were studied. The theoretical background for radiative recombination and Kramers' theory are reviewed. The quantum mechanical result and its relation to the semiclassical theory is discussed. Radiative recombination was also measured with several different non-bare ions, and the applicability of the semiclassical theory to non-bare ions was investigated. The use of an effective charge is discussed. For dielectronic recombination, the standard theoretical approach in the isolated resonance and independent-processes approximation is debated. The applicability of this method was tested. The theory was able to reproduce most of the experimental data except when the recombination process was sensitive to couplings between different electronic configurations. The influence of external perturbing electrostatic fields is discussed. (AB) (31 refs.)

  5. Recombinant human endostatin reduces hypertrophic scar ...

    African Journals Online (AJOL)

    Background: Recombinant human endostatin (Endostar) has been widely used to suppress angiogenesis in carcinoma patients. ... Cite as: Wang P, Jiang L-Z, Xue B. Recombinant human endostatin reduces hypertrophic scar formation in rabbit ear model through ... wounds on the tail of each ear were discarded because.

  6. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces...

  7. Generation of Modified Pestiviruses by Targeted Recombination

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Friis, Martin Barfred; Risager, Peter Christian

    involves targeted modification of viral cDNA genomes, cloned within BACs, by Red/ET recombination-mediated mutagenesis in E.coli DH10B cells. Using recombination-mediated mutagenesis for the targeted design, the work can be expedited and focused in principal on any sequence within the viral genome...

  8. Molecular requirements for radiation-activated recombination

    International Nuclear Information System (INIS)

    Stevens, Craig W.; Zeng Ming; Stamato, Thomas; Cerniglia, George

    1997-01-01

    Purpose/Objective: The major stumbling block to successful gene therapy today is poor gene transfer. We hypothesized that ionizing radiation might activate cellular recombination, and so improve stable gene transfer. We further hypothesized that known DNA-damage-repair proteins might also be important in radiation-activated recombination. Materials and Methods: The effect of irradiation on stable gene transfer efficiency was determined in human (A549 and 39F) and rodent (NIH/3T3) cell lines. Continuous low dose rate and multiple radiation fractions were also tested. Nuclear extracts were made and the effect of irradiation on inter-plasmid recombination/ligation determined. Multiple DNA damage-repair deficient cell lines were tested for radiation-activated recombination. Results: A significant radiation dose-dependent improvement in stable plasmid transfection (by as much as 1300 fold) is demonstrated in neoplastic and primary cells. An improvement in transient plasmid transfection is also seen, with as much as 85% of cells transiently expressing b-galactosidase (20-50 fold improvement). Stable transfection is only improved for linearized or nicked plasmids. Cells have improved gene transfer for at least 96 hours after irradiation. Both fractionated and continuous low dose rate irradiation are effective at improving stable gene transfer in mammalian cells, thus making relatively high radiation dose delivery clinically feasible. Inter-plasmid recombination is radiation dose dependent in nuclear extract assays, and the type of overhang (3', 5' or blunt end) significantly affects recombination efficiency and the type of product. The most common end-joining activity involves filling-in of the overhang followed by blunt end ligation. Adenovirus is a linear, double stranded DNA virus. We demonstrate that adenoviral infection efficiency is increased by irradiation. The duration of transgene expression is lengthened because the virus integrates with high efficiency (∼10

  9. Effects of UV radiation on genetic recombination

    International Nuclear Information System (INIS)

    Vlahovic, K.; Zahradka, D.; Petranovic, M.; Petranovic, D.

    1996-01-01

    We have used the model consisting of Escherichia coli cells and l phage to study the effects of UV radiation on genetic recombination. We found two radiation induced processes that reduce or inhibit genetic recombination. One such process leads to the inability of prophage to excise itself from the irradiated bacterial chromosome by the site-specific recombination. The other process was shown to inhibit a type of general recombination by which the prophage transfers one of its genetic markers to the infecting homologous phage. Loss of the prophage ability to take part in both site-specific and general recombination was shown to develop in recB + but not in recB cells. From this we infer that the loss of prophage recombinogenicity in irradiated cells is a consequence of one process in which RecBCD enzyme (the product of recB, recC and recD genes) plays an essential role. (author)

  10. RNAi and heterochromatin repress centromeric meiotic recombination

    DEFF Research Database (Denmark)

    Ellermeier, Chad; Higuchi, Emily C; Phadnis, Naina

    2010-01-01

    to genetic disabilities, including birth defects. The basis by which centromeric meiotic recombination is repressed has been largely unknown. We report here that, in fission yeast, RNAi functions and Clr4-Rik1 (histone H3 lysine 9 methyltransferase) are required for repression of centromeric recombination....... Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between...... types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis....

  11. Trunk mutational events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma.

    Science.gov (United States)

    Torrecilla, Sara; Sia, Daniela; Harrington, Andrew N; Zhang, Zhongyang; Cabellos, Laia; Cornella, Helena; Moeini, Agrin; Camprecios, Genis; Leow, Wei-Qiang; Fiel, Maria Isabel; Hao, Ke; Bassaganyas, Laia; Mahajan, Milind; Thung, Swan N; Villanueva, Augusto; Florman, Sander; Schwartz, Myron E; Llovet, Josep M

    2017-12-01

    According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in hepatocellular carcinoma (HCC) and study their intra- and inter-tumor distribution in advanced lesions. A total of 151 samples representing the multistep process of hepatocarcinogenesis were analyzed by targeted-sequencing and a single nucleotide polymorphism array. Genes altered in early lesions (31 dysplastic nodules [DNs] and 38 small HCCs [sHCC]) were defined as trunk. Their distribution was explored in: a) different regions of large tumors (43 regions, 21 tumors), and b) different nodules of the same patient (39 tumors, 17 patients). Multinodular lesions were classified as intrahepatic metastases (IMs) or synchronous tumors based on chromosomal aberrations. TERT promoter mutations (10.5%) and broad copy-number aberrations in chromosomes 1 and 8 (3-7%) were identified as trunk gatekeepers in DNs and were maintained in sHCCs. Trunk drivers identified in sHCCs included TP53 (23%) and CTNNB1 (11%) mutations, and focal amplifications or deletions in known drivers (6%). Overall, TERT, TP53 and CTNNB1 mutations were the most frequent trunk events and at least one was present in 51% of sHCCs. Around 90% of mutations in these genes were ubiquitous among different regions of large tumors. In multinodular HCCs, 35% of patients harbored IMs; 85% of mutations in TERT, TP53 and/or CTNNB1 were retained in primary and metastatic tumors. Trunk events in early stages (TERT, TP53, CTNNB1 mutations) were ubiquitous across different regions of the same tumor and between primary and metastatic nodules in >85% of cases. This concept supports the knowledge that single biopsies would suffice to capture trunk mutations in HCC. Trunk alterations arise at early stages of cancer and are shared among all malignant cells of the tumor. In order to identify trunk alterations

  12. Containment air circulation for optimal hydrogen recombination

    International Nuclear Information System (INIS)

    Spinks, N.; Krause, M.

    1997-01-01

    An accepted first-line defense for hydrogen mitigation is to design for the hydrogen to be rapidly mixed with the containment atmosphere and diluted to below flammability concentrations. Then, as hydrogen continues to be produced in the longer term, recombiners can be used to remove hydrogen: recombiners can be located in forced-air ducts or passive recombiners can be distributed within containment and the heat of recombination used to promote local air circulation. However, this principle does not eliminate the possibility of high hydrogen concentrations at locations removed from the recombiners. An improvement on this strategy is to arrange for a specific, buoyancy-driven, overall circulation of the containment atmosphere such that the recombiners can be located within the recirculation flow, immediately downstream of the hydrogen source. This would make the mixing process more predictable and solve the mass-transfer problem associated with distributed recombiners. Ideally, the recombiners would be located just above the hydrogen source so that the heat of recombination would assist the overall circulation. In this way, the hydrogen would be removed as close as possible to the source, thereby minimizing the amount of hydrogen immediately downstream of the source and reducing the hydrogen concentration to acceptable levels at other locations. Such a strategy requires the containment volume to be divided into an upflow path, past the hydrogen source and the recombiner, and a downflow path to complete the circuit. The flow could be generated actively using fans or passively using buoyancy forces arising from the difference in density of gases in the upfiow and downflow paths; the gases in the downflow path being cooled at an elevated heat sink. (author)

  13. The recombinational anatomy of a mouse chromosome.

    Directory of Open Access Journals (Sweden)

    Kenneth Paigen

    2008-07-01

    Full Text Available Among mammals, genetic recombination occurs at highly delimited sites known as recombination hotspots. They are typically 1-2 kb long and vary as much as a 1,000-fold or more in recombination activity. Although much is known about the molecular details of the recombination process itself, the factors determining the location and relative activity of hotspots are poorly understood. To further our understanding, we have collected and mapped the locations of 5,472 crossover events along mouse Chromosome 1 arising in 6,028 meioses of male and female reciprocal F1 hybrids of C57BL/6J and CAST/EiJ mice. Crossovers were mapped to a minimum resolution of 225 kb, and those in the telomere-proximal 24.7 Mb were further mapped to resolve individual hotspots. Recombination rates were evolutionarily conserved on a regional scale, but not at the local level. There was a clear negative-exponential relationship between the relative activity and abundance of hotspot activity classes, such that a small number of the most active hotspots account for the majority of recombination. Females had 1.2x higher overall recombination than males did, although the sex ratio showed considerable regional variation. Locally, entirely sex-specific hotspots were rare. The initiation of recombination at the most active hotspot was regulated independently on the two parental chromatids, and analysis of reciprocal crosses indicated that parental imprinting has subtle effects on recombination rates. It appears that the regulation of mammalian recombination is a complex, dynamic process involving multiple factors reflecting species, sex, individual variation within species, and the properties of individual hotspots.

  14. Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex

    Directory of Open Access Journals (Sweden)

    Mouton Laurence

    2012-01-01

    Full Text Available Abstract Background Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism, making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera, in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology. Results Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers. Conclusions This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the

  15. Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases.

    Science.gov (United States)

    Zhang, Hanrui; Xue, Chenyi; Wang, Ying; Shi, Jianting; Zhang, Xuan; Li, Wenjun; Nunez, Sara; Foulkes, Andrea S; Lin, Jennie; Hinkle, Christine C; Yang, Wenli; Morrisey, Edward E; Rader, Daniel J; Li, Mingyao; Reilly, Muredach P

    2017-11-13

    Sustained and dysfunctional macrophage activation promotes inflammatory cardiometabolic disorders, but the role of long intergenic noncoding RNA (lincRNA) in human macrophage activation and cardiometabolic disorders is poorly defined. Through transcriptomics, bioinformatics, and selective functional studies, we sought to elucidate the lincRNA landscape of human macrophages. We used deep RNA sequencing to assemble the lincRNA transcriptome of human monocyte-derived macrophages at rest and following stimulation with lipopolysaccharide and IFN-γ (interferon γ) for M1 activation and IL-4 (interleukin 4) for M2 activation. Through de novo assembly, we identified 2766 macrophage lincRNAs, including 861 that were previously unannotated. The majority (≈85%) was nonsyntenic or was syntenic but not annotated as expressed in mouse. Many macrophage lincRNAs demonstrated tissue-enriched transcription patterns (21.5%) and enhancer-like chromatin signatures (60.9%). Macrophage activation, particularly to the M1 phenotype, markedly altered the lincRNA expression profiles, revealing 96 lincRNAs differentially expressed, suggesting potential roles in regulating macrophage inflammatory functions. A subset of lincRNAs overlapped genomewide association study loci for cardiometabolic disorders. MacORIS (macrophage-enriched obesity-associated lincRNA serving as a repressor of IFN-γ signaling), a macrophage-enriched lincRNA not expressed in mouse macrophages, harbors variants associated with central obesity. Knockdown of MacORIS , which is located in the cytoplasm, enhanced IFN-γ-induced JAK2 (Janus kinase 2) and STAT1 (signal transducer and activator of transcription 1) phosphorylation in THP-1 macrophages, suggesting a potential role as a repressor of IFN-γ signaling. Induced pluripotent stem cell-derived macrophages recapitulated the lincRNA transcriptome of human monocyte-derived macrophages and provided a high-fidelity model with which to study lincRNAs in human macrophage

  16. Overexpression of long intergenic noncoding RNA LINC00312 inhibits the invasion and migration of thyroid cancer cells by down-regulating microRNA-197-3p.

    Science.gov (United States)

    Liu, Kai; Huang, Wen; Yan, Dan-Qing; Luo, Qing; Min, Xiang

    2017-08-31

    The study evaluated the ability of long intergenic noncoding RNA LINC00312 (LINC00312) to influence the proliferation, invasion, and migration of thyroid cancer (TC) cells by regulating miRNA-197-3p. TC tissues and adjacent normal tissues were collected from 211 TC patients. K1 (papillary TC), SW579 (squamous TC), and 8505C (anaplastic TC) cell lines were assigned into a blank, negative control (NC), LINC00312 overexpression, miR-197-3p inhibitors, and LINC00312 overexpression + miR-197-3p mimics group. The expression of LINC00312, miR-197-3p , and p120 were measured using quantitative real-time PCR (qRT-PCR) and Western blotting. Cell proliferation was assessed via CCK8 assay, cell invasion through the scratch test, and cell migration via Transwell assay. In comparison with adjacent normal tissues, the expression of LINC00312 is down-regulated and the expression of miR-197-3p is up-regulated in TC tissues. The dual luciferase reporter gene assay confirmed that P120 is a target of miR-197-3p The expression of LINC00312 and p120 was higher in the LINC00312 overexpression group than in the blank and NV groups. However, the expression of miR-197-3p was lower in the LINC00312 overexpression group than in the blank and NC groups. The miR-197-3p inhibitors group had a higher expression of miR-197-3p , but a lower expression of p120 than the blank and NC groups. The LINC00312 overexpression and miR-197-3p inhibitor groups had reduced cell proliferation, invasion and migration than the blank and NC groups. These results indicate that a LINC00312 overexpression inhibits the proliferation, invasion, and migration of TC cells and that this can be achieved by down-regulating miR-197-3p . © 2017 The Author(s).

  17. Maternal oral origin of Fusobacterium nucleatum in adverse pregnancy outcomes as determined using the 16S-23S rRNA gene intergenic transcribed spacer region.

    Science.gov (United States)

    Gonzales-Marin, Cecilia; Spratt, David A; Allaker, Robert P

    2013-01-01

    Fusobacterium nucleatum, a common Gram-negative anaerobe prevalent in the oral cavity, possesses the ability to colonize the amniotic cavity and the fetus. However, F. nucleatum may also be part of the vaginal microbiota from where it could reach the amniotic tissues. Due to the heterogeneity of F. nucleatum, consisting of five subspecies, analysis at the subspecies/strain level is desirable to determine its precise origin. The aims of this study were: (i) to evaluate the use of the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region as a tool to differentiate subspecies of F. nucleatum, and (ii) to design a simplified technique based on the ITS to determine the origin of F. nucleatum strains associated with adverse pregnancy outcomes. Amplified fragments of the 16S-23S rRNA gene ITS region corresponding to the five subspecies of F. nucleatum were subjected to cloning and sequencing to characterize the different ribosomal operons of the subspecies. Distinctive length and sequence patterns with potential to be used for identification of the subspecies/strain were identified. These were used to evaluate the origin of F. nucleatum identified in neonatal gastric aspirates (swallowed amniotic fluid) by sequence comparisons with the respective oral and vaginal maternal samples. A simplified technique using a strain-specific primer in a more sensitive nested PCR was subsequently developed to analyse ten paired neonatal-maternal samples. Analysing the variable fragment of the ITS region allowed the identification of F. nucleatum subsp. polymorphum from an oral origin as potentially being involved in neonatal infections. Using a strain-specific primer, the F. nucleatum subsp. polymorphum strain was detected in both neonatal gastric aspirates and maternal oral samples in cases of preterm birth from mothers presenting with localized periodontal pockets. Interestingly, the same strain was not present in the vaginal sample of any case investigated. The 16S-23S r

  18. Reciprocality of Recombination Events That Rearrange the Chromosome

    OpenAIRE

    Mahan, M. J.; Roth, J. R.

    1988-01-01

    We describe a genetic system for studying the reciprocality of chromosomal recombination; all substrates and recombination functions involved are provided exclusively by the bacterial chromosome. The genetic system allows the recovery of both recombinant products from a single recombination event. The system was used to demonstrate the full reciprocality of three different types of recombination events: (1) intrachromosomal recombination between direct repeats, causing deletions; (2) intrachr...

  19. Intra- and inter-observer variability in ultrasonographical measurements of the uterus and ovaries in healthy, non-pregnant queens.

    Science.gov (United States)

    Gatel, Laure; Gory, Guillaume; Chalvet-Monfray, Karine; Saunders, Jimmy H; Rault, Delphine N

    2016-02-01

    We aimed to (1) evaluate how frequently the uterus and ovaries of healthy, non-pregnant queens are visible; (2) describe their appearance; (3) take their measurements; and (4) determine intra- and inter-observer variabilities in their measurements. We hypothesised that, using a high-frequency linear probe, the uterus and ovaries could be ultrasonographically visualised during any period of the sexual cycle and with any level of operator expertise. Eight queens were enrolled in the study and the ultrasonographical appearance of their uterus and ovaries assessed with a high-frequency linear probe of 15-19 MHz. The diameter of the uterine horns, body and cervix in transverse and longitudinal sections, and the length of the ovaries were recorded. Three observers of different expertise level participated in the study, and the differences between the separate measurements made per queen were evaluated. The ovaries and the entire uterus were visualised in every queen. The ovaries were ovoid structures with submillimetric follicles during anoestrus and additional larger follicles depending on the stage of the cycle. An ovarian pattern suggesting cortex and medulla was observed in half the cases. In the uterus, the serosa was a thin hyperechoic outer rim, and layering was observed in half the cases. The cervix was difficult to identify. The intra- and inter-observer variabilities in the uterine horns and the ovaries were minimal (coefficient of variation [CV] 1.4-4.1%) compared with the differences within the queens (CV 10.9-43.4%). The longitudinal and transverse measurements of the horns and the uterine body were the same. The ovaries and uterine horns in queens are accessible ultrasonographically at any stage of their cycle, and can be measured with low intra- and inter-observer variabilities. © ISFM and AAFP 2015.

  20. Intra- and extra-familial adverse childhood experiences and a history of childhood psychosomatic disorders among Japanese university students.

    Science.gov (United States)

    Masuda, Akinori; Yamanaka, Takao; Hirakawa, Tadatoshi; Koga, Yasuyuki; Minomo, Ryosuke; Munemoto, Takao; Tei, Chuwa

    2007-04-02

    Japan has been witnessing a considerable increase in the number of children with psychosomatic disorders. The purpose of this study is to examine the relationship between the risk of psychosomatic disorder in adolescents and intra- and extra-familial adverse childhood experiences (ACEs). A retrospective cohort study of 1592 Japanese university students (52% male, mean age 19.9 years) who completed a survey about intra- and extra-familial ACEs and the incidence of childhood psychosomatic disorders. Intra-familial ACEs included domestic violence, physical violence, emotional abuse, illness in household, parental divorce, no parental affection, and dysfunctional family. Extra-familial ACEs included physical violence or negative recognition by teachers, being bullied in elementary or junior high school, or sexual violence. The frequency of psychosomatic disorders among the respondents was 14.8%. Among the 7 intra-familial ACEs, emotional abuse (relative risk, RR = 1.9) and illness in household (RR = 1.7) increased the risk of psychosomatic disorders. Estimates of the relative risk for the 5 extra-familial ACEs were statistically significant and ranged from 1.5 for being bullied in elementary school or physical violence from teachers to 2.4. Students who had 3 or more intra-familial ACEs and 2 or more extra-familial ACEs had a 3.0 relative risk for psychosomatic disorder. These results suggest that intra- and extra-familial ACEs are associated with the development of psychosomatic disorders. Therefore, sufficient evaluation of ACEs should be performed in adolescent patients with psychosomatic disorder.

  1. Intra- and interobserver analysis in the morphological assessment of early stage embryos during an IVF procedure: a multicentre study

    Directory of Open Access Journals (Sweden)

    Devroe Johanna

    2011-09-01

    Full Text Available Abstract Background Quality control programs are necessary to maintain good clinical practice. Embryo grading has been described as one of the external quality assurance schemes. Although the evaluation of embryos is based on the assessment of morphological characteristics, considerable intra- and inter-observer variability has been described. In this multicentre study, the variability in the embryo evaluation has been evaluated using morphological characteristics on day 1, day 2 and day 3 of embryo development. Methods Five embryologists of four different IVF centers participated in this study. Multilevel images of embryos were presented on a website at different time points to evaluate intra-and inter-observer agreement in the assessment of embryo morphology. The embryos were evaluated on day 1, day 2 and day 3 of their development and each embryologist had to decide if the embryo had to be transferred, cryopreserved or discarded. Results Both intra-observer agreement and inter-observer agreement were good to excellent for the position of the pronuclei on day 1, the number of blastomeres on day 2 and day 3 and the clinical decision (transfer, cryopreservation, discard. For all other characteristics (size of pronuclei, presence of cytoplasomic halo, degree of fragmentation and size of blastomeres the intra- and inter-observer agreement was moderate to very poor. Conclusions Mono- or multicentre quality control on embryo scoring by morphological assessment can easily be performed through the design of a simple website. In the future the website design can be adapted to generate statistical feedback upon scoring and can even include a training module.

  2. Intra- and extra-familial adverse childhood experiences and a history of childhood psychosomatic disorders among Japanese university students

    Directory of Open Access Journals (Sweden)

    Munemoto Takao

    2007-04-01

    Full Text Available Abstract Background Japan has been witnessing a considerable increase in the number of children with psychosomatic disorders. The purpose of this study is to examine the relationship between the risk of psychosomatic disorder in adolescents and intra- and extra-familial adverse childhood experiences (ACEs. Methods A retrospective cohort study of 1592 Japanese university students (52% male, mean age 19.9 years who completed a survey about intra- and extra-familial ACEs and the incidence of childhood psychosomatic disorders. Intra-familial ACEs included domestic violence, physical violence, emotional abuse, illness in household, parental divorce, no parental affection, and dysfunctional family. Extra-familial ACEs included physical violence or negative recognition by teachers, being bullied in elementary or junior high school, or sexual violence. Results The frequency of psychosomatic disorders among the respondents was 14.8%. Among the 7 intra-familial ACEs, emotional abuse (relative risk, RR = 1.9 and illness in household (RR = 1.7 increased the risk of psychosomatic disorders. Estimates of the relative risk for the 5 extra-familial ACEs were statistically significant and ranged from 1.5 for being bullied in elementary school or physical violence from teachers to 2.4. Students who had 3 or more intra-familial ACEs and 2 or more extra-familial ACEs had a 3.0 relative risk for psychosomatic disorder. Conclusion These results suggest that intra- and extra-familial ACEs are associated with the development of psychosomatic disorders. Therefore, sufficient evaluation of ACEs should be performed in adolescent patients with psychosomatic disorder.

  3. Intra- and interobserver reliability of gray scale/dynamic range evaluation of ultrasonography using a standardized phantom

    International Nuclear Information System (INIS)

    Lee, Song; Choi, Joon Il; Park, Michael Yong; Yeo, Dong Myung; Byun, Jae Young; Jung, Seung Eun; Rha, Sung Eun; Oh, Soon Nam; Lee, Young Joon

    2014-01-01

    To evaluate intra- and interobserver reliability of the gray scale/dynamic range of the phantom image evaluation of ultrasonography using a standardized phantom, and to assess the effect of interactive education on the reliability. Three radiologists (a resident, and two board-certified radiologists with 2 and 7 years of experience in evaluating ultrasound phantom images) performed the gray scale/dynamic range test for an ultrasound machine using a standardized phantom. They scored the number of visible cylindrical structures of varying degrees of brightness and made a pass or fail decision. First, they scored 49 phantom images twice from a 2010 survey with limited knowledge of phantom images. After this, the radiologists underwent two hours of interactive education for the phantom images and scored another 91 phantom images from a 2011 survey twice. Intra- and interobserver reliability before and after the interactive education session were analyzed using K analyses. Before education, the K-value for intraobserver reliability for the radiologist with 7 years of experience, 2 years of experience, and the resident was 0.386, 0.469, and 0.465, respectively. After education, the K-values were improved (0.823, 0.611, and 0.711, respectively). For interobserver reliability, the K-value was also better after the education for the 3 participants (0.067, 0.002, and 0.547 before education; 0.635, 0.667, and 0.616 after education, respectively). The intra- and interobserver reliability of the gray scale/dynamic range was fair to substantial. Interactive education can improve reliability. For more reliable results, double- checking of phantom images by multiple reviewers is recommended.

  4. Intra- and Interobserver Reliability of the Cobb Angle-Vertebral Rotation Angle-Spinous Process Angle for Adolescent Idiopathic Scoliosis.

    Science.gov (United States)

    Chan, Amanda C Y; Morrison, Devlin G; Nguyen, Duc V; Hill, Douglas L; Parent, Eric; Lou, Edmond H M

    2014-05-01

    A reliability analysis of Cobb angle, vertebral rotation (VR), and spinous process angle (SPA) measurements in adolescent idiopathic scoliosis. To determine the intra- and interobserver reliability of semi-automated digital radiograph measurements. Cobb angle measurements on posteroanterior radiographs are commonly used to determine the severity of scoliosis. Vertebral rotation helps assess scoliosis 3-dimensionally and has a role in predicting curve progression. Recent studies have shown that the spinous process angle is a useful parameter in assessing scoliosis when using ultrasound imaging. Because the reliability of SPA measurements on radiographs has yet to be determined, it is important to compare the reliability of these 3 parameters (Cobb angle, VR, and SPA) using a computer assisted semi-automated method. Sixty posteroanterior radiographs of patients with adolescent idiopathic scoliosis were obtained and measured twice by 3 observers who were blinded to their previous measurements, using an in-house developed program. Measurements were obtained using a semi-automated method to minimize variability resulting from observer reliability. The intra- and interobserver reliabilities were analyzed using intra-class correlation coefficients (ICCs) as well as Bland-Altman's bias and limits of agreement. Over 350 (intra) and 90 (inter) sets of curves with an average Cobb angle of 26° ± 9° (range, 10° to 44°) were compared for each parameter. Intra-observer reliabilities for each parameter were excellent (ICC [2,1] , .82; 1.00), with mean absolute differences under 3° between most measurements. Interobserver reliability (ICC [2,1] , .72; .95) was mostly good to excellent, with mean absolute differences ranging from 2.0° to 5.6°. Both the intra- and interobserver assessment of the Cobb, VR, and SPA from the semi-automated measurements had clinically acceptable reliability ranges and may be considered for clinical implementation. Additional studies will be

  5. Invariant Measures of Genetic Recombination Processes

    Science.gov (United States)

    Akopyan, Arseniy V.; Pirogov, Sergey A.; Rybko, Aleksandr N.

    2015-07-01

    We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory.

  6. Ultramicroscopic observation of recombinant adenoassociated virus ...

    African Journals Online (AJOL)

    Ultramicroscopic observation of recombinant adenoassociated virus type 2 on the surface of formvarcarbon coated copper grids under different relative humidity and incubation time using negative stain transmission electron microscopy.

  7. Recombinant Human Papillomavirus (HPV) Bivalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) bivalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  8. Recombinant Human Papillomavirus (HPV) Nonavalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) nonavalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  9. Recombinant Human Papillomavirus (HPV) Quadrivalent Vaccine

    Science.gov (United States)

    This page contains brief information about recombinant human papillomavirus (HPV) quadrivalent vaccine and a collection of links to more information about the use of this vaccine, research results, and ongoing clinical trials.

  10. Recombinant vaccines: experimental and applied aspects

    DEFF Research Database (Denmark)

    Lorenzen, Niels

    1999-01-01

    Development of vaccines for aquaculture fish represent an important applied functional aspect of fish immunology research. Particularly in the case of recombinant vaccines, where a single antigen is usually expected to induce immunity to a specific pathogen, knowledge of mechanisms involved...... in induction of a protective immune response may become vital. The few recombinant vaccines licensd so far, despite much research during the last decade, illustrate that this is not a straightforward matter. However, as vaccine technology as well as our knowledge of the fish immune system is steadily improved......, these fields will open up a number of interesting research objectives of mutual benefit. Recent aspects of recombinant protein vaccines, live recombinant vaccines and DNA vaccines are discussed....

  11. Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.

    Science.gov (United States)

    Wang, Jun; Keightley, Peter D; Halligan, Daniel L

    2007-12-01

    Interspecies divergence of orthologous transposable element remnants is often assumed to be simply due to genetic drift of neutral mutations that occurred after the divergence of the species. However, divergence may also be affected by other factors, such as variation in the mutation rate, ancestral polymorphisms, or selection. Here we attempt to determine the impact of these forces on divergence of three classes of sites that are often assumed to be selectively unconstrained (INE-1 TE remnants, sites within short introns, and fourfold degenerate sites) in two different pairwise comparisons of Drosophila (D. melanogaster vs. D. simulans and D. simulans vs. D. sechellia). We find that divergence of these three classes of sites is strongly influenced by the recombination environment in which they are located, and this is especially true for the closer D. simulans vs. D. sechellia comparison. We suggest that this is mainly a result of the contribution of ancestral polymorphisms in different recombination regions. We also find that intergenic INE-1 elements are significantly more diverged than intronic INE-1 in both pairwise comparisons, implying the presence of either negative selection or lower mutation rates in introns. Furthermore, we show that substitution rates in INE-1 elements are not associated with the length of the noncoding sequence in which they are located, suggesting that reduced divergence in long noncoding sequences is not due to reduced mutation rates in these regions. Finally, we show that GC content for each site within INE-1 sequences has evolved toward an equilibrium value (approximately 33%) since insertion.

  12. Recombinant aequorin and recombinant semi-synthetic aequorins. Cellular Ca2+ ion indicators.

    OpenAIRE

    Shimomura, O; Inouye, S; Musicki, B; Kishi, Y

    1990-01-01

    Properties of a recombinant aequorin were investigated in comparison with those of natural aequorin. In chromatographic behaviour the recombinant aequorin did not match any of ten isoaequorins tested, although it was very similar to aequorin J. Its sensitivity to Ca2+ was found to be higher than that of any isoaequorin except aequorin D. The recombinant aequorin exhibited no toxicity when tested in various kinds of cells, even where samples of natural aequorin had been found to be toxic. Prop...

  13. Live recombinant BHV/BRSV vaccine

    OpenAIRE

    Keil, G.M.; Rijsewijk, F.A.M.

    1998-01-01

    The present invention refers to synthetic Bovine Respiratory Syncytium virus genes. Also the invention relates to live attenuated Bovine Herpesvirus recombinants carrying such synthetic genes. Furthermore, the invention relates to vaccines based on these live attenuated recombinants, for the protection of cattle against both Bovine herpesvirus infection and against Bovine Respiratory Syncytium virus infection. Also the invention relates to methods for the preparation of such live attenuated r...

  14. Recombination-deficient mutant of Streptococcus faecalis

    International Nuclear Information System (INIS)

    Yagi, Y.; Clewell, D.B.

    1980-01-01

    An ultraviolet radiation-sensitive derivative of Streptococcus faecalis strain JH2-2 was isolated and found to be deficient in recombination, using a plasmid-plasmid recombination system. The strain was sensitive to chemical agents which interact with deoxyribonucleic acid and also underwent deoxyribonucleic acid degradation after ultraviolet irradiation. Thus, the mutant has properties similar to those of recA strains of Escherichia coli

  15. Hadron correlations from recombination and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2005-04-01

    We review the formalism of quark recombination applied to the hadronization of a quark-gluon plasma. Evidence in favour of the quark recombination model is outlined. Recent work on parton correlations, leading to detectable correlations between hadrons, is discussed. Hot spots from completely quenched jets are a likely source of such correlations which appear to be jet like. It will be discussed how such a picture compares with measurement of associated hadron yields at RHIC.

  16. Intra and Inter Specific Profiling of Pakistani Quercus Species Growing in The Hilly Areas of District Dir Khyber Pakhtunkhwa

    International Nuclear Information System (INIS)

    Nisar, M.; Wadood, S. F.; Iqbal, A.; Nausheen, A.

    2016-01-01

    The intra and inter genetic diversity among 20 genotypes of Pakistani Quercus species viz., ten genotypes of Q. incana, eight Q. baloot and two Q. dilatata were analyzed using morphological characterization and proteomic profiling. A total of 14 morphological traits were scored for estimation of genetic diversity through descriptive statistics, traits similarity index and cluster plotting. Similarly, seven loci (bands) were detected in the collected germplasm of Quercus sp. Intra species locus contribution to genetic diversity (LCGD) was 42.9 percent in Q. baloot and 14.2 percent in Q. incana. Similarly, inter species LCGD was 71.43 percent in the collected germplasm. Out of seven loci, locus-1, 5 and 6 showed polymorphic in Q. baloot and locus 6 in Q. incana. Importantly, locus 3 and 4 was monomorphic in all collected lines and marked as generic specific locus for Quercus (sp.). SDS-PAGE profiling based on one-way cluster plotting successfully resolved the three species into separate clusters. The present data reflect that though the Quercus sp. showing intra and Inter species genetic diversity, but maintained species specific identity in the area regardless of environmental fluctuation. (author)

  17. Intra- and multicenter reproducibility of pulsed, continuous and pseudo-continuous arterial spin labeling methods for measuring cerebral perfusion.

    Science.gov (United States)

    Gevers, Sanna; van Osch, Matthias J; Bokkers, Reinoud P H; Kies, Dennis A; Teeuwisse, Wouter M; Majoie, Charles B; Hendrikse, Jeroen; Nederveen, Aart J

    2011-08-01

    Intra- and multicenter reproducibility of currently used arterial spin labeling (ASL) methods were assessed at three imaging centers in the Netherlands, equipped with Philips 3TMR scanners. Six healthy participants were scanned twice at each site. The imaging protocol consisted of continuous ASL (CASL), pseudo-continuous ASL (p-CASL) with and without background suppression, pulsed ASL (PASL) with single and multiple inversion times (TIs), and selective ASL for segmentation. Reproducibility was expressed in terms of the coefficient of repeatability and the repeatability index. Voxelwise analysis of variance was performed, yielding brain maps that reflected regional variability. Intra- and multicenter reproducibility were comparable for all methods, except for single TI PASL, with better intracenter reproducibility (F-test of equality of two variances, Pfeeding arteries within sessions and in gray matter between sessions. On the basis of the results of this study, one could consider the use of reference values in clinical routine, with whole-brain p-CASL perfusion varying <20% over repeated measurements within the same individuals considered to be normal. Knowledge on regional variability allows for the use of perfusion-weighted images in the assessment of local cerebral pathology.

  18. [Extramucosal pylorotomy via the umbilical route under general anesthesia and para-umbilical cord: evaluation of intra- and postoperative analgesia].

    Science.gov (United States)

    Courrèges, P; Poddevin, F; Lecoutre, D

    1998-01-01

    To assess both intra- and postoperative analgesia in infants undergoing extramucosal pylorotomy via a circumumbilical incision under general anaesthesia with neither opioid nor muscle relaxant, associated with a paraumbilical block. Open prospective study covering a 1-year period. The study included 32 infants (age = 1.1 +/- 0.7 months, body weight = 4,427 +/- 876 g). General anaesthesia was induced with either thiopentone or halothane and, after tracheal intubation, maintained with halothane in a N2O-O2 50 vol% mixture. Para-umbilical block was obtained using 0.5 mL.kg-1 of 1% lidocaine with epinephrine. Pain was assessed using time course of respiratory rate, heart rate and mean arterial pressure. A change of more than 20% in one of these variables was considered as criterion for poor analgesia. Intraoperative analgesia was adequate in all patients but one, 3 minutes after incision. Surgical conditions were considered as being good or satisfactory in 76% and 24% of cases, respectively. Postoperative analgesia, assessed 1 and 6 hours after completion of surgery, was convenient in 90% of infants, the end of the action of the local anaesthetic resulting in a poor analgesia at the 6th hour in four of them. Provided a short bevel needle is used and basic safety rules of local anaesthesia are followed, the para-umbilical block provides adequate intra and postoperative analgesia in infants undergoing extramucosal pylorotomy via circumumbilical route.

  19. Generalized Confidence Intervals for Intra- and Inter-subject Coefficients of Variation in Linear Mixed-effects Models.

    Science.gov (United States)

    Forkman, Johannes

    2017-06-15

    Linear mixed-effects models are linear models with several variance components. Models with a single random-effects factor have two variance components: the random-effects variance, i. e., the inter-subject variance, and the residual error variance, i. e., the intra-subject variance. In many applications, it is practice to report variance components as coefficients of variation. The intra- and inter-subject coefficients of variation are the square roots of the corresponding variances divided by the mean. This article proposes methods for computing confidence intervals for intra- and inter-subject coefficients of variation using generalized pivotal quantities. The methods are illustrated through two examples. In the first example, precision is assessed within and between runs in a bioanalytical method validation. In the second example, variation is estimated within and between main plots in an agricultural split-plot experiment. Coverage of generalized confidence intervals is investigated through simulation and shown to be close to the nominal value.

  20. Computerized system to measure interproximal alveolar bone levels in epidemiologic, radiographic investigations. II. Intra- and inter-examinar variation study

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, F.R.; Frithiof, L.; Soeder, P.Oe.; Hellden, L.; Lavstedt, S.; Salonen, L.

    1988-01-01

    The study was aimed at analyzing intra- and inter-examiner variations in computerized measurement and in non-measurability of alveolar bone level in a cross-sectional, epidemiologic material. At each interproximal tooth surface, alveolar bone height in percentage of root length (B/R) and tooth length (B/T) were determined twice by one examiner and once by a second examiner from X5-magnified periapical radiographs. The overall intra- and inter-examiner variations in measurement were 2.85% and 3.84% of root length and 1.97% and 2.82% of tooth length, respectively. The varations were different for different tooth groups and for different degrees of severity of marginal periodontitis. The overall proportions on non-measurable tooth surfaces varied with examiner from 32% to 39% and from 43% to 48% of the available interproximal tooth surfaces for B/R and B/T, respectively. With regard to the level of reliability, the computerized method reported is appropriate to cross-sectional, epidemiologic investigations from radiographs.

  1. Recombination of electrons with an anisotropic velocity distribution. Continuation of recombination continuum to series lines

    International Nuclear Information System (INIS)

    Fujimoto, Takashi; Imaida, Takashi

    1998-01-01

    For ions in recombination with electrons with directional motion, the recombination continuum to a J = 0 state is π polarized, and this polarization characteristic should continue across the ionization threshold down to the series lines. A Monte Carlo calculation has been performed for electron collisions on a classical atom in excited states. No evidence is found to support the above conclusion. (author)

  2. Spontaneous radiative recombination and nonradiative Auger recombination in quantum-confined heterostructures

    International Nuclear Information System (INIS)

    Asryan, L V

    2005-01-01

    General approach is described to the rates, fluxes and current densities associated with spontaneous radiative and nonradiative Auger recombinations in heterostructure lasers with different types of a quantum-confined active region (quantum wells, quantum wires, and quantum dots). The proper way of defining the spontaneous radiative and Auger recombination coefficients and their dimensionality are discussed. It is shown that only in a quantum dot, true time constants can be introduced for spontaneous radiative and nonradiative Auger recombinations, which are independent of the injection level. Closed-form elegant expressions are presented for the radiative recombination coefficient as an explicit function of temperature and parameters in bulk and quantum-confined structures. These expressions clearly demonstrate inappropriateness of the common practice of deriving the recombination coefficients in low-dimensional heterostructures from the bulk values. (lasers)

  3. Graded Recombination Layers for Multijunction Photovoltaics

    KAUST Repository

    Koleilat, Ghada I.

    2012-06-13

    Multijunction devices consist of a stack of semiconductor junctions having bandgaps tuned across a broad spectrum. In solar cells this concept is used to increase the efficiency of photovoltaic harvesting, while light emitters and detectors use it to achieve multicolor and spectrally tunable behavior. In series-connected current-matched multijunction devices, the recombination layers must allow the hole current from one cell to recombine, with high efficiency and low voltage loss, with the electron current from the next cell. We recently reported a tandem solar cell in which the recombination layer was implemented using a progression of n-type oxides whose doping densities and work functions serve to connect, with negligible resistive loss at solar current densities, the constituent cells. Here we present the generalized conditions for design of efficient graded recombination layer solar devices. We report the number of interlayers and the requirements on work function and doping of each interlayer, to bridge an work function difference as high as 1.6 eV. We also find solutions that minimize the doping required of the interlayers in order to minimize optical absorption due to free carriers in the graded recombination layer (GRL). We demonstrate a family of new GRL designs experimentally and highlight the benefits of the progression of dopings and work functions in the interlayers. © 2012 American Chemical Society.

  4. Evaluating performance of a user-trained MR lung tumor autocontouring algorithm in the context of intra- and interobserver variations.

    Science.gov (United States)

    Yip, Eugene; Yun, Jihyun; Gabos, Zsolt; Baker, Sarah; Yee, Don; Wachowicz, Keith; Rathee, Satyapal; Fallone, B Gino

    2018-01-01

    Real-time tracking of lung tumors using magnetic resonance imaging (MRI) has been proposed as a potential strategy to mitigate the ill-effects of breathing motion in radiation therapy. Several autocontouring methods have been evaluated against a "gold standard" of a single human expert user. However, contours drawn by experts have inherent intra- and interobserver variations. In this study, we aim to evaluate our user-trained autocontouring algorithm with manually drawn contours from multiple expert users, and to contextualize the accuracy of these autocontours within intra- and interobserver variations. Six nonsmall cell lung cancer patients were recruited, with institutional ethics approval. Patients were imaged with a clinical 3 T Philips MR scanner using a dynamic 2D balanced SSFP sequence under free breathing. Three radiation oncology experts, each in two separate sessions, contoured 130 dynamic images for each patient. For autocontouring, the first 30 images were used for algorithm training, and the remaining 100 images were autocontoured and evaluated. Autocontours were compared against manual contours in terms of Dice's coefficient (DC) and Hausdorff distances (d H ). Intra- and interobserver variations of the manual contours were also evaluated. When compared with the manual contours of the expert user who trained it, the algorithm generates autocontours whose evaluation metrics (same session: DC = 0.90(0.03), d H  = 3.8(1.6) mm; different session DC = 0.88(0.04), d H  = 4.3(1.5) mm) are similar to or better than intraobserver variations (DC = 0.88(0.04), and d H  = 4.3(1.7) mm) between two sessions. The algorithm's autocontours are also compared to the manual contours from different expert users with evaluation metrics (DC = 0.87(0.04), d H  = 4.8(1.7) mm) similar to interobserver variations (DC = 0.87(0.04), d H  = 4.7(1.6) mm). Our autocontouring algorithm delineates tumor contours (algorithm may be a key component of the real

  5. Constraints from jet calculus on quark recombination

    International Nuclear Information System (INIS)

    Jones, L.M.; Lassila, K.E.; Willen, D.

    1979-01-01

    Within the QCD jet calculus formalism, we deduce an equation describing recombination of quarks and antiquarks into mesons within a quark or gluon jet. This equation relates the recombination function R(x 1 ,x 2 ,x) used in current literature to the fragmentation function for producing that same meson out of the parton initiating the jet. We submit currently used recombination functions to our consistency test, taking as input mainly the u-quark fragmentation data into π + mesons, but also s-quark fragmentation into K - mesons. The constraint is well satisfied at large Q 2 for large moments. Our results depend on one parameter, Q 0 2 , the constraint equation being satisfied for small values of this parameter

  6. Recombinant human erythropoietin in sports: a review

    Directory of Open Access Journals (Sweden)

    Rafael Maia de Almeida Bento

    2003-06-01

    Full Text Available Erythropoietin is an endogenous hormone of glicoproteic nature secreted by the kidneys and is the main regulator of the erythropoiesis. An alteration in its production generates a disturbance in the plasmatic concentration giving rise to several types of pathologies related to the hematopoietic system. The recombinant forms of erythropoietin have indiscriminately been used by athletes, mainly in endurance sports, by increasing the erythrocytes concentration, generating a better delivery of oxygen to the muscle tissue. The administration of recombinant erythropoietin was prohibited by the International Olympic Committee and its use considered as doping. This review has the intention to describe the physical, biological and pharmacokinetic properties of the endogenous erythropoietin, as well as its recombinant form, describing also its use in sports and the process of searching methodologies for its detection in doping control.

  7. Traumatic Arteriovenous Fistula of the Scalp in the Left Temporoparietal Region with Intra- and Extracranial Blood Supply

    Directory of Open Access Journals (Sweden)

    Feng Zheng

    2016-01-01

    Full Text Available Traumatic AVF of the scalp is a rare abnormal vascular disease. It is defined as a communication between the high flow arterial system and the low flow venous network, which directly connects the arterial feeding vessels of the scalp and the draining veins without an intervening capillary bed. The superficial temporal artery (STA was involved in 90% of the cases, and 71% of the patients only had one dominant feeding STA. Here, we report the case of a rare large traumatic arteriovenous fistula (AVF of the scalp that is fed by intra- and extracranial blood supply. The clinical and radiological features are presented, and the possible pathogenesis and surgical technique are discussed.

  8. Intra- and Extra-abdominal Actinomycosis Mimicking Urachal Tumor in an Intrauterine Device Carrier: A Case Report

    Directory of Open Access Journals (Sweden)

    Hsi-Lin Hsiao

    2008-01-01

    Full Text Available Actinomycosis is a rare, chronic suppurative infection caused by the Gram-positive anaerobic filamentous bacterium, Actinomyces Israeli. In most cases, the diagnosis is made postoperatively because of its unusual clinical presentation. Abdominal actinomycosis is the second most common site of the disease and may mimic abdominal cancer, inflammatory bowel disease or diverticulitis. The abdominal-pelvic form of this disease mostly results from the prolonged use of an intrauterine device. We report a rare case of combined intra- and extra-abdominal actinomycosis mimicking urachal tumor that was diagnosed by computed tomography, which presented as two tender abdominal palpable masses following long-term intrauterine device use. The disease was confirmed by postoperative histopathologic examination, which revealed sulfur granules microscopically, and was successfully treated by complete surgical resection following a period of appropriate antibiotic treatment.

  9. A recombinant rabies virus expressing luciferase.

    Science.gov (United States)

    Liang, H; Tan, Y; Dun, C; Guo, X

    2010-01-01

    A recombinant Rabies virus (RV) expressing firefly luciferase (rRV-luc) was generated by an improved reverse genetics system. Its biological properties were compared with those of the parental RV. The rRV-luc grew in BHK-21 cells similarly to RV, but its virulence for mice was weaker as shown by the lower infectious titers in brain. Rising infectious titers of rRV-luc during its passaging in BHK-21 cells indicated a virus adaptation, while the luciferase (luc) expression was stable. These results suggest that the recombinant RV carrying luc gene might prove a useful tool for further analysis of pathogenesis of RV in small animal models.

  10. Thermal recombination: Beyond the valence quark approximation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, B. [Department of Physics, Duke University, Durham, NC 27708 (United States); Fries, R.J. [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)]. E-mail: fries@physics.umn.edu; Bass, S.A. [Department of Physics, Duke University, Durham, NC 27708 (United States); RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2005-07-07

    Quark counting rules derived from recombination models agree well with data on hadron production at intermediate transverse momenta in relativistic heavy-ion collisions. They convey a simple picture of hadrons consisting only of valence quarks. We discuss the inclusion of higher Fock states that add sea quarks and gluons to the hadron structure. We show that, when recombination occurs from a thermal medium, hadron spectra remain unaffected by the inclusion of higher Fock states. However, the quark number scaling for elliptic flow is somewhat affected. We discuss the implications for our understanding of data from the Relativistic Heavy Ion Collider.

  11. Theoretical models for recombination in expanding gas

    International Nuclear Information System (INIS)

    Avron, Y.; Kahane, S.

    1978-09-01

    In laser isotope separation of atomic uranium, one is confronted with the theoretical problem of estimating the concentration of thermally ionized uranium atoms. To investigate this problem theoretical models for recombination in an expanding gas and in the absence of local thermal equilibrium have been constructed. The expansion of the gas is described by soluble models of the hydrodynamic equation, and the recombination by rate equations. General results for the freezing effect for the suitable ranges of the gas parameters are obtained. The impossibility of thermal equilibrium in expanding two-component systems is proven

  12. Intra- and trans-generational costs of reduced female body size caused by food limitation early in life in mites.

    Science.gov (United States)

    Walzer, Andreas; Schausberger, Peter

    2013-01-01

    Food limitation early in life may be compensated for by developmental plasticity resulting in accelerated development enhancing survival at the expense of small adult body size. However and especially for females in non-matching maternal and offspring environments, being smaller than the standard may incur considerable intra- and trans-generational costs. Here, we evaluated the costs of small female body size induced by food limitation early in life in the sexually size-dimorphic predatory mite Phytoseiulus persimilis. Females are larger than males. These predators are adapted to exploit ephemeral spider mite prey patches. The intra- and trans-generational effects of small maternal body size manifested in lower maternal survival probabilities, decreased attractiveness for males, and a reduced number and size of eggs compared to standard-sized females. The trans-generational effects of small maternal body size were sex-specific with small mothers producing small daughters but standard-sized sons. Small female body size apparently intensified the well-known costs of sexual activity because mortality of small but not standard-sized females mainly occurred shortly after mating. The disadvantages of small females in mating and egg production may be generally explained by size-associated morphological and physiological constraints. Additionally, size-assortative mate preferences of standard-sized mates may have rendered small females disproportionally unattractive mating partners. We argue that the sex-specific trans-generational effects were due to sexual size dimorphism - females are the larger sex and thus more strongly affected by maternal stress than the smaller males - and to sexually selected lower plasticity of male body size.

  13. Intra- and trans-generational costs of reduced female body size caused by food limitation early in life in mites.

    Directory of Open Access Journals (Sweden)

    Andreas Walzer

    Full Text Available Food limitation early in life may be compensated for by developmental plasticity resulting in accelerated development enhancing survival at the expense of small adult body size. However and especially for females in non-matching maternal and offspring environments, being smaller than the standard may incur considerable intra- and trans-generational costs.Here, we evaluated the costs of small female body size induced by food limitation early in life in the sexually size-dimorphic predatory mite Phytoseiulus persimilis. Females are larger than males. These predators are adapted to exploit ephemeral spider mite prey patches. The intra- and trans-generational effects of small maternal body size manifested in lower maternal survival probabilities, decreased attractiveness for males, and a reduced number and size of eggs compared to standard-sized females. The trans-generational effects of small maternal body size were sex-specific with small mothers producing small daughters but standard-sized sons.Small female body size apparently intensified the well-known costs of sexual activity because mortality of small but not standard-sized females mainly occurred shortly after mating. The disadvantages of small females in mating and egg production may be generally explained by size-associated morphological and physiological constraints. Additionally, size-assortative mate preferences of standard-sized mates may have rendered small females disproportionally unattractive mating partners. We argue that the sex-specific trans-generational effects were due to sexual size dimorphism - females are the larger sex and thus more strongly affected by maternal stress than the smaller males - and to sexually selected lower plasticity of male body size.

  14. Intra- and Inter-Rater Reliability of Bioimpedance in the Evaluation of Lymphedema Secondary to Treatment of Breast Cancer.

    Science.gov (United States)

    Ferro, Ana Paula; Ferreira, Vânia Tie Koga; Rezende, Monique Silva; de Souza, Thamires Rodrigues; Almeida, Ana Maria de; Guirro, Rinaldo Roberto de Jesus; Guirro, Elaine Caldeira de Oliveira

    2017-12-18

    The objective of the study was to evaluate the intra- and inter-rater reliability of bioimpedance in determining upper limb volume in women with lymphedema resulting from breast cancer treatment, as well as its correlation with the upper limb volume calculated by circumferential measurement. A blind cross-sectional study was performed in which 27 women (62.59 ± 10.50 years) were evaluated with upper limb lymphedema secondary to breast cancer treatment. Two examiners performed assessments in the same volunteers independently and twice, with an interval of 1 week between assessments. The collections were performed by the direct tetrapolar multifrequency segmental bioimpedance and by the circumference of the upper limb homolateral to the breast cancer. The results of the circumference showed that the homolateral limb had lymphedema. The intra- and inter-rater analysis showed excellent reliability with intraclass correlation coefficient (ICC) values ranging from 0.954 to 0.999 for the amount of liquid and excellent reliability with ICC values ranging from 0.852 to 0.999 for the electrical impedance of the upper limb with lymphedema. The correlation was strong and negative (p < 0.05) between intracellular, extracellular, and total water when associated with electrical impedance and moderate and positive (p < 0.05) when associated with upper limb volume for all frequencies. The correlations between upper limb volume and water quantities were moderate and positive (p < 0.05). The results indicate that bioimpedance is a reliable method for the evaluation of lymphedema, and the volume of the homolateral upper limb is associated with the amount of water in women with lymphedema secondary to the treatment of breast cancer.

  15. Three-dimensional Mass Measurement of Subsolid Pulmonary Nodules on Chest CT: Intra and Inter-observer Variability

    Directory of Open Access Journals (Sweden)

    Huiting LIU

    2015-05-01

    Full Text Available Background and objective Subsolid pulmonary nodules tend to exhibit considerably slower growth rates than solid lesions, nevertheless, higher malignancy probability. The diagnosis of indeterminate nodules largely depends on the growth evaluation during follow-up. The growth can manifested as an increase in size or the appearance and/or subsequent increase of solid components. The mass reflect the product of volume and density and can be more sensitive in growth evaluation. However, the repeatability needs a further validation. The purpose of this study is to assess the intra and inter-observer variability of mass measurement for subsolid nodules. Methods 80 subsolid nodules in 44 patients were retrospectively enrolled. Both the volume and mass were measured by two radiologists using blind method independently. Intra-observer and inter-observer variability were analyzed and compared by Bland-Altman method intra-class correlation test and Wilcoxon test. Results Software achieved satisfied segmentation for 92.5% nodules. Of them, 35% underwent manual modification. The 95% limits of agreement for intra-observer variability were -11.5%-10.4% for mass and -8.4%-8.8% for volume. The 95% limits of agreement for inter-observer variability were -17.4%-19.3% for mass and -17.9%-19.4% for volume.The intra-class correlation foefficients between volume and mass measument was 0.95 and 0.93 (both P<0.001 and no significant differences (P=0.78, 0.09 was found for intra- and inter-observer variability. Manual modification of the segmentation caused the worse mass measurement repeatability in spite of the reader satisfaction. Conclusion The repeatability of mass measurement has no significant difference with that of volume measurement and may act as a reliable method in the follow-up of subsolid nodules.

  16. Anomalous Abundances in Gaseous Nebulae From Recombination and Collisional Lines: Improved Photoionization and Recombination Studies

    Science.gov (United States)

    Pradhan, Anil Kumar; Nahar, S. N.; Eissner, W. B.; Montenegro, M.

    2011-01-01

    A perplexing anomaly arises in the determination of abundances of common elements in gaseous nebulae, as derived from collisionally excited lines (CEL) as opposed to those from Recombination Lines (RCL). The "abundance discrepancy factors" can range from a factor of 2 to an order of magnitude or more. That has led to quite different interpretation of the physical structure and processes in gaseous nebulae, such as temperature fluctuations across the object, or metal-rich concentrations leading to a dual-abundnace scenario. We show that the problem may lie in inaccuracies in photoionization and recombination models neglecting low-energy resonance phenomena due to fine structure. Whereas the atomic physics of electron impact excitation of forbidden lines is well understood, and accurate collision strengths have long been available, that is not generally the case for electron-ion recombination cross sections. A major problem is the inclusion of relativisitic effects as it pertains to the existence of very low-energy fine structure resonances in photoionization cross sections. We carry out new relativistic calculations for photoionization and recombination cross sections using a recently extended version of the Breit-Pauli R-matrix codes, and the unified electron-ion recombination method that subsumes both the radiative and the dielectronic recombination (RR and DR) processes in an ab initio and self-consistent manner. We find that near-thresold resonances manifest themselves within fine structure levels of the ground state of ions, enhancing low-temperature recombination rate coefficients at 1000-10,000 K. The resulting enahncement in level-specific and total recombination rate coefficients should therefore lead to reduced abundances derived from RCL, and in accordance with those from CEL. We present results for photoionization of O II into, and recombination from, O III. Theoretical cross sections are benchmarked against high-resolution measurements from synchrotron

  17. Low DNA Sequence Diversity of the Intergenic Spacer 1 Region in the Human Skin Commensal Fungi Malassezia sympodialis and M. dermatis Isolated from Patients with Malassezia-Associated Skin Diseases and Healthy Subjects.

    Science.gov (United States)

    Cho, Otomi; Sugita, Takashi

    2016-12-01

    As DNA sequences of the intergenic spacer (IGS) region in the rRNA gene show remarkable intraspecies diversity compared with the small subunit, large subunit, and internal transcribed spacer region, the IGS region has been used as an epidemiological tool in studies on Malassezia globosa and M. restricta, which are responsible for the exacerbation of atopic dermatitis (AD) and seborrheic dermatitis (SD). However, the IGS regions of M. sympodialis and M. dermatis obtained from the skin of patients with AD and SD, as well as healthy subjects, lacked sequence diversity. Of the 105 M. sympodialis strains and the 40 M. dermatis strains, the sequences of 103 (98.1 %) and 39 (97.5 %), respectively, were identical. Thus, given the lack of intraspecies diversity in the IGS regions of M. sympodialis and M. dermatis, studies of the diversity of these species should be performed using appropriate genes and not the IGS.

  18. H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3.

    Directory of Open Access Journals (Sweden)

    Richárd Bártfai

    Full Text Available Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however, the epigenetic component of gene expression in P. falciparum is poorly understood. Dynamic or stable association of epigenetic marks with genomic features provides important clues about their function and helps to understand how histone variants/modifications are used for indexing the Plasmodium epigenome. We describe a novel, linear amplification method for next-generation sequencing (NGS that allows unbiased analysis of the extremely AT-rich Plasmodium genome. We used this method for high resolution, genome-wide analysis of a histone H2A variant, H2A.Z and two histone H3 marks throughout parasite intraerythrocytic development. Unlike in other organisms, H2A.Z is a constant, ubiquitous feature of euchromatic intergenic regions throughout the intraerythrocytic cycle. The almost perfect colocalisation of H2A.Z with H3K9ac and H3K4me3 suggests that these marks are preferentially deposited on H2A.Z-containing nucleosomes. By performing RNA-seq on 8 time-points, we show that acetylation of H3K9 at promoter regions correlates very well with the transcriptional status whereas H3K4me3 appears to have stage-specific regulation, being low at early stages, peaking at trophozoite stage, but does not closely follow changes in gene expression. Our improved NGS library preparation procedure provides a foundation to exploit the malaria epigenome in detail. Furthermore, our findings place H2A.Z at the cradle of P. falciparum epigenetic regulation by stably defining intergenic regions and providing a platform for dynamic assembly of epigenetic and other transcription related complexes.

  19. An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis thaliana Is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

    Science.gov (United States)

    Banerjee, Joydeep; Sahoo, Dipak Kumar; Dey, Nrisingha; Houtz, Robert L.; Maiti, Indu Bhushan

    2013-01-01

    On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications. PMID:24260266

  20. An intergenic region shared by At4g35985 and At4g35987 in Arabidopsis thaliana is a tissue specific and stress inducible bidirectional promoter analyzed in transgenic arabidopsis and tobacco plants.

    Directory of Open Access Journals (Sweden)

    Joydeep Banerjee

    Full Text Available On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985 are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85 showed stronger expression (about 3.5 fold compared to the At4g35987 promoter (P87. The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.

  1. Algae-based oral recombinant vaccines

    Directory of Open Access Journals (Sweden)

    Elizabeth A Specht

    2014-02-01

    Full Text Available Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for molecular pharming in food crops has waned in the last decade due to difficulty in developing transgenic crop plants and concerns of contaminating the food supply. Microalgae are poised to become the next candidate in recombinant subunit vaccine production, and they present several advantages over terrestrial crop plant-based platforms including scalable and contained growth, rapid transformation, easily obtained stable cell lines, and consistent transgene expression levels. Algae have been shown to accumulate and properly fold several vaccine antigens, and efforts are underway to create recombinant algal fusion proteins that can enhance antigenicity for effective orally-delivered vaccines. These approaches have the potential to revolutionize the way subunit vaccines are made and delivered – from costly parenteral administration of purified protein, to an inexpensive oral algae tablet with effective mucosal and system immune reactivity.

  2. Mismatch Repair during Homologous and Homeologous Recombination

    Science.gov (United States)

    Spies, Maria; Fishel, Richard

    2015-01-01

    Homologous recombination (HR) and mismatch repair (MMR) are inextricably linked. HR pairs homologous chromosomes before meiosis I and is ultimately responsible for generating genetic diversity during sexual reproduction. HR is initiated in meiosis by numerous programmed DNA double-strand breaks (DSBs; several hundred in mammals). A characteristic feature of HR is the exchange of DNA strands, which results in the formation of heteroduplex DNA. Mismatched nucleotides arise in heteroduplex DNA because the participating parental chromosomes contain nonidentical sequences. These mismatched nucleotides may be processed by MMR, resulting in nonreciprocal exchange of genetic information (gene conversion). MMR and HR also play prominent roles in mitotic cells during genome duplication; MMR rectifies polymerase misincorporation errors, whereas HR contributes to replication fork maintenance, as well as the repair of spontaneous DSBs and genotoxic lesions that affect both DNA strands. MMR suppresses HR when the heteroduplex DNA contains excessive mismatched nucleotides, termed homeologous recombination. The regulation of homeologous recombination by MMR ensures the accuracy of DSB repair and significantly contributes to species barriers during sexual reproduction. This review discusses the history, genetics, biochemistry, biophysics, and the current state of studies on the role of MMR in homologous and homeologous recombination from bacteria to humans. PMID:25731766

  3. Affinity purification of recombinant human plasminogen activator ...

    African Journals Online (AJOL)

    Purpose: To develop processes for effective isolation and purification of recombinant human plasminogen activator (rhPA) from transgenic rabbit milk. Methods: Immunoaffinity chromatography was selected and improved by a special polyol-responsive monoclonal antibody (PR-mAb). Alteplase was used as immunogen ...

  4. Recombinant Poliovirus circulation among healthy children ...

    African Journals Online (AJOL)

    In order to assess the level of polio virus with natural recombinant genome and wild polio virus circulating in the environment of healthy children aged 0 to 5 years in Abidjan, 130 polio viruses made up of 26 polio type 1, 55 type 2 and 49 type 3 were identified by neutralisation test with monoclonal antibodies and restriction ...

  5. RECOMBINANT HUMAN INTERLEUKIN-3 IN CLINICAL ONCOLOGY

    NARCIS (Netherlands)

    DEVRIES, EGE; VANGAMEREN, MM; WILLEMSE, PHB

    Interleukin 3 (IL-3) is a multipotent hematopoietic growth factor which became available as a recombinant (rh) growth factor for use in the clinic a few years ago. In dose-finding studies, this hematopoietic growth factor has been evaluated without and after standard chemotherapy. Stimulatory

  6. Carbon source feeding strategies for recombinant protein ...

    African Journals Online (AJOL)

    Pichia pastoris and Pichia methanolica have been used as expression systems for the production of recombinant protein. The main problems of the production are the slow hierarchic consumption of ethanol and acetate which cause toxicity problems due to methanol accumulation when this surpasses 0.5 gl-1. In some ...

  7. Recombinant human activated protein C (Xigris)

    NARCIS (Netherlands)

    Levi, M. [=Marcel M.; de Jonge, E.; van der Poll, T.

    2002-01-01

    An impaired function of the protein C pathway plays a central role in the pathogenesis of sepsis. Administration of human recombinant activated protein C (Xigris) may restore the dysfunctional anticoagulant mechanism and prevent amplification and propagation of thrombin generation and formation of

  8. Asthma and Therapeutics: Recombinant Therapies in Asthma

    Directory of Open Access Journals (Sweden)

    Cockcroft Donald W

    2005-03-01

    Full Text Available Abstract Numerous recombinant therapies are being investigated for the treatment of asthma. This report reviews the current status of several of these novel agents. Anti-immunoglobulin (IgE (omalizumab, Xolair markedly inhibits all aspects of the allergen challenge in subjects who have reduction of free serum IgE to undetectable levels. Several clinical studies in atopic asthma have demonstrated benefit by improved symptoms and lung function and a reduction in corticosteroid requirements. Early use in atopic asthmatics may be even more effective. Several approaches target interleukin (IL-4. Soluble IL-4 receptor has been shown to effectively replace inhaled corticosteroid; further studies are under way. Recombinant anti-IL-5 and recombinant IL-12 inhibit blood and sputum eosinophils and allergen-induced eosinophilia without any effect on airway responsiveness, allergen-induced airway responses, or allergen-induced airway hyperresponsiveness. Efalizumab, a recombinant antibody that inhibits lymphocyte trafficking, is effective in psoriasis. A bronchoprovocation study showed a reduction in allergen-induced late asthmatic response and allergen-induced eosinophilia, which suggests that it should be effective in clinical asthma. These exciting novel therapies provide not only promise of new therapies for asthma but also valuable tools for investigation of asthma mechanisms.

  9. Expression of recombinant Streptokinase from local Egyptian ...

    African Journals Online (AJOL)

    Jane

    2011-08-17

    Aug 17, 2011 ... DISCUSSION. Isolation and identification of Streptococcus sp. In this study, SK isolated from local Streptococcus sp. SalMarEg was efficiently produced in a recombinant bioactive form. It is worthy to mention that the binding of plasminogen by pathogenic Group C streptococci isolated from human, horses, ...

  10. Expression of recombinant Streptokinase from local Egyptian ...

    African Journals Online (AJOL)

    We reported for the first time the expression of a recombinant SK from a local Streptococcus strain. When produced on industrial scale this r-SK may substantially contribute to reducing the costs of thrombolytic therapy in developing countries. In this study, a highly purified r-SK from Streptococcus sp. isolated from Egyptian ...

  11. CATALYTIC RECOMBINER FOR A NUCLEAR REACTOR

    Science.gov (United States)

    King, L.D.P.

    1960-07-01

    A hydrogen-oxygen recombiner is described for use with water-boiler type reactors. The catalyst used is the wellknown platinized alumina, and the novelty lies in the structural arrangement used to prevent flashback through the gas input system. The recombiner is cylindrical, the gases at the input end being deflected by a baffle plate through a first flashback shield of steel shot into an annular passage adjacent to and extending the full length of the housing. Below the baffle plate the gases flow first through an outer annular array of alumina pellets which serve as a second flashback shield, a means of distributing the flowing gases evenly and as a means of reducing radiation losses to the walls. Thereafter the gases flow inio the centrally disposed catalyst bed where recombination is effected. The steam and uncombined gases flow into a centrally disposed cylindrical passage inside the catalyst bod and thereafter out through the exit port. A high rate of recombination is effected.

  12. Expression and characterization of recombinant human serum ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... Key words: C-peptide, human serum albumin, recombinant fusion protein, Pichia pastoris, bioactivity, biological half-time. ... lines were purchased from Cell bank of Chinese academy of sciences (Shanghai, China). .... agarose electrophoresis and DNA sequencing (data was not shown). Expression and ...

  13. Therapeutic implications of recombinant human erythropoietin in ...

    African Journals Online (AJOL)

    AJB SERVER

    2006-12-29

    Dec 29, 2006 ... The introduction of recombinant human erythropoietin (RHUEPO) has revolutionised the treatment strategies for patients suffering with anaemia of chronic renal disease and chronic heart failure. Clinical studies and several observational evidences have demonstrated that RHUEPO is also useful in various.

  14. Recombinant Supercharged Polypeptides Restore and Improve Biolubrication

    NARCIS (Netherlands)

    Veeregowda, Deepak H.; Kolbe, Anke; van der Mei, Henny C.; Busscher, Henk J.; Herrmann, Andreas; Sharma, Prashant K.

    2013-01-01

    Recombinant supercharged polypeptides (SUPs) with low cytotoxicity are developed and applied to rejuvenate the lubrication of naturally occurring salivary conditioning films (SCFs). SUPs with 72 positive charges adsorbed and rigidified the SCFs and recruited mucins to form a hydrated layer. These

  15. Algae-based oral recombinant vaccines

    Science.gov (United States)

    Specht, Elizabeth A.; Mayfield, Stephen P.

    2014-01-01

    Recombinant subunit vaccines are some of the safest and most effective vaccines available, but their high cost and the requirement of advanced medical infrastructure for administration make them impractical for many developing world diseases. Plant-based vaccines have shifted that paradigm by paving the way for recombinant vaccine production at agricultural scale using an edible host. However, enthusiasm for “molecular pharming” in food crops has waned in the last decade due to difficulty in developing transgenic crop plants and concerns of contaminating the food supply. Microalgae could be poised to become the next candidate in recombinant subunit vaccine production, as they present several advantages over terrestrial crop plant-based platforms including scalable and contained growth, rapid transformation, easily obtained stable cell lines, and consistent transgene expression levels. Algae have been shown to accumulate and properly fold several vaccine antigens, and efforts are underway to create recombinant algal fusion proteins that can enhance antigenicity for effective orally delivered vaccines. These approaches have the potential to revolutionize the way subunit vaccines are made and delivered – from costly parenteral administration of purified protein, to an inexpensive oral algae tablet with effective mucosal and systemic immune reactivity. PMID:24596570

  16. Catalytic hydrogen recombination for nuclear containments

    International Nuclear Information System (INIS)

    Koroll, G.W.; Lau, D.W.P.; Dewit, W.A.; Graham, W.R.C.

    1994-01-01

    Catalytic recombiners appear to be a credible option for hydrogen mitigation in nuclear containments. The passive operation, versatility and ease of back fitting are appealing for existing stations and new designs. Recently, a generation of wet-proofed catalyst materials have been developed at AECL which are highly specific to H 2 -O 2 , are active at ambient temperatures and are being evaluated for containment applications. Two types of catalytic recombiners were evaluated for hydrogen removal in containments based on the AECL catalyst. The first is a catalytic combustor for application in existing air streams such as provided by fans or ventilation systems. The second is an autocatalytic recombiner which uses the enthalpy of reaction to produce natural convective flow over the catalyst elements. Intermediate-scale results obtained in 6 m 3 and 10 m 3 spherical and cylindrical vessels are given to demonstrate self-starting limits, operating limits, removal capacity, scaling parameters, flow resistance, mixing behaviour in the vicinity of an operating recombiner and sensitivity to poisoning, fouling and radiation. (author). 13 refs., 10 figs

  17. Theory of dielectronic recombination and plasma effects

    International Nuclear Information System (INIS)

    Yukap Hahn

    2000-01-01

    Current status of the various theoretical approaches to calculation of dielectronic recombination rates is summarized, with emphasis on the available data base and on the plasma effects of both the plasma ion (and external) fields and plasma electron collisional effects which seriously affect the rates and complicate compilation of data. (author)

  18. Ultramicroscopic observation of recombinant adenoassociated virus ...

    African Journals Online (AJOL)

    The purpose of this investigation was to compare the effects of different relative humidity (RH) on the microcosmic conformation of the recombinant AAV-2 virion at 22°C. rAAV-2 virions prepared on copper grid were placed in a high, middle or low RH cabinet and incubated for 72, 48 and 24 h, respectively. The rAAV-2 ...

  19. Expression and characterization of recombinant ecarin.

    NARCIS (Netherlands)

    Jonebring, A.; Lange, U.; Bucha, E.; Deinum, J.; Elg, M.; Lovgren, A.

    2012-01-01

    The snake venom protease ecarin from Echis carinatus was expressed in stable transfected CHO-S cells grown in animal component free cell culture medium. Recombinant ecarin (r-ecarin) was secreted from the suspension adapted Chinese Hamster Ovary (CHO-S) host cells as a pro-protein and activation to

  20. Radiative recombination of excitons in amorphous semiconductors

    International Nuclear Information System (INIS)

    Singh, Jai

    2005-01-01

    A theory for calculating the radiative lifetime of excitons in amorphous semiconductors is presented. Four possibilities of excitonic radiative recombination are considered and the corresponding rates are derived at thermal equilibrium. The radiative lifetime is calculated from the inverse of the maximum rate for all the four possibilities. Results agree very well with experiments

  1. Correlations in the Parton Recombination Model

    Energy Technology Data Exchange (ETDEWEB)

    Bass, S.A. [Department of Physics, Duke University, Durham, NC 27708-0305 (United States); RIKEN BNL Research Center, Brookhaven Nat. Lab., Upton, NY 11973 (United States); Fries, R.J. [School of Physics and Astronomy, Univ. of Minnesota, Minneapolis, MN 55455 (United States); Mueller, B. [Department of Physics, Duke University, Durham, NC 27708-0305 (United States)

    2006-08-07

    We describe how parton recombination can address the recent measurement of dynamical jet-like two particle correlations. In addition we discuss the possible effect realistic light-cone wave-functions including higher Fock-states may have on the well-known elliptic flow valence-quark number scaling law.

  2. Production, purification and characterization of two recombinant ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-17

    Jun 17, 2008 ... Two recombinant DNA-derived variants of ovine growth hormone were produced, purified, characterized and compared with the authentic pituitary derived GH. The variants oGH3 and oGH5 were isolated by differential centrifugation method and were purified after refolding by ion-exchange.

  3. Gas recombination assembly for electrochemical cells

    Science.gov (United States)

    Levy, Isaac; Charkey, Allen

    1989-01-01

    An assembly for recombining gases generated in electrochemical cells wherein a catalyst strip is enveloped within a hydrophobic, gas-porous film which, in turn, is encased between gas-porous, metallic layers. The sandwich construction of metallic layers and film is formed into a spiral with a tab for connection to the cell.

  4. Improving recombinant protein solubility in Escherichia coli ...

    African Journals Online (AJOL)

    user

    2010-11-22

    Nov 22, 2010 ... capable of improving solubility ratio of human lysozyme. All these studies show that while this approach has been very successful for a large number of unrelated sub- strates, there is no guarantee that chaperones co- overproduction will improve the folding of a recombinant protein. For the first time in this ...

  5. Recombination times in germanium under high pressure

    International Nuclear Information System (INIS)

    Kuyt, J.H.

    1975-01-01

    The influence of pressure on a well defined recombination process was studied. The centres were introduced by γirradiation and the lifetime determined by the decay time of photoconductivity. An optical pressure vessel is described which allows for a hydrostatic variation of 3000 bars. The diffusion constant and lifetime measurements are presented and analysed. (V.J.C.)

  6. Virus efficacy of recombined Autographa californica M ...

    African Journals Online (AJOL)

    Ectropis obliqua is a major tea pest and chitin synthase (CHS) plays a key role in the pest growth and development. A 192 bp conserved domain from E. obliqua CHS gene was cloned and it was used to construct recombined Autographa californica M nucleopolyhedrovirus (AcMNPV) with double-stranded RNA interference ...

  7. Purification of human recombinant granulocyte colony stimulating ...

    African Journals Online (AJOL)

    In Escherichia coli, recombinant proteins were produced either as three dimensionally folded forms or as unfolded forms, inclusion body (IB). The formation of IB was a frequent consequence of high-level protein production and inadequacy of folding agents namely chaperones in the cytoplasm. The structure of the protein in ...

  8. A molecular recombination map of Antirrhinum majus

    Directory of Open Access Journals (Sweden)

    Hudson Andrew

    2010-12-01

    Full Text Available Abstract Background Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot Antirrhinum majus is the result of a cross with Antirrhinum molle, limiting its usefulness within A. majus. Results We created a molecular linkage map of A. majus based on segregation of markers in the F2 population of two inbred lab strains of A. majus. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the A. majus karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size. Conclusions The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the IDLE MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of A. majus.

  9. Extrachromosomal recombination substrates recapitulate beyond 12/23 restricted VDJ recombination in nonlymphoid cells.

    Science.gov (United States)

    Jung, David; Bassing, Craig H; Fugmann, Sebastian D; Cheng, Hwei-Ling; Schatz, David G; Alt, Frederick W

    2003-01-01

    V(D)J recombination occurs efficiently only between gene segments flanked by recombination signals (RSs) containing 12 and 23 base pair spacers (the 12/23 rule). A further limitation "beyond the 12/23 rule" (B12/23) exists at the TCRbeta locus and ensures Dbeta usage. Herein, we show that extrachromosomal V(D)J recombination substrates recapitulate B12/23 restriction in nonlymphoid cells. We further demonstrate that the Vbeta coding flank, the 12-RS heptamer/nonamer, and the 23-RS spacer each can significantly influence B12/23 restriction. Finally, purified core RAG1 and RAG2 proteins (together with HMG2) also reproduce B12/23 restriction in a cell-free system. Our findings indicate that B12/23 restriction of V(D)J recombination is cemented at the level of interactions between the RAG proteins and TCRbeta RS sequences.

  10. In vivo production of recombinant proteins using occluded recombinant AcMNPV-derived baculovirus vectors.

    Science.gov (United States)

    Guijarro-Pardo, Eva; Gómez-Sebastián, Silvia; Escribano, José M

    2017-12-01

    Trichoplusia ni insect larvae infected with vectors derived from the Autographa californica multiple nucleopolyhedrovirus (AcMNPV), are an excellent alternative to insect cells cultured in conventional bioreactors to produce recombinant proteins because productivity and cost-efficiency reasons. However, there is still a lot of work to do to reduce the manual procedures commonly required in this production platform that limit its scalability. To increase the scalability of this platform technology, a current bottleneck to be circumvented in the future is the need of injection for the inoculation of larvae with polyhedrin negative baculovirus vectors (Polh-) because of the lack of oral infectivity of these viruses, which are commonly used for production in insect cell cultures. In this work we have developed a straightforward alternative to obtain orally infective vectors derived from AcMNPV and expressing recombinant proteins that can be administered to the insect larvae (Trichoplusia ni) by feeding, formulated in the insect diet. The approach developed was based on the use of a recombinant polyhedrin protein expressed by a recombinant vector (Polh+), able to co-occlude any recombinant Polh- baculovirus vector expressing a recombinant protein. A second alternative was developed by the generation of a dual vector co-expressing the recombinant polyhedrin protein and the foreign gene of interest to obtain the occluded viruses. Additionally, by the incorporation of a reporter gene into the helper Polh+ vector, it was possible the follow-up visualization of the co-occluded viruses infection in insect larvae and will help to homogenize infection conditions. By using these methodologies, the production of recombinant proteins in per os infected larvae, without manual infection procedures, was very similar in yield to that obtained by manual injection of recombinant Polh- AcMNPV-based vectors expressing the same proteins. However, further analyses will be required for a

  11. High recombination rate in natural populations of Plasmodium falciparum

    NARCIS (Netherlands)

    Conway, D. J.; Roper, C.; Oduola, A. M.; Arnot, D. E.; Kremsner, P. G.; Grobusch, M. P.; Curtis, C. F.; Greenwood, B. M.

    1999-01-01

    Malaria parasites are sexually reproducing protozoa, although the extent of effective meiotic recombination in natural populations has been debated. If meiotic recombination occurs frequently, compared with point mutation and mitotic rearrangement, linkage disequilibrium between polymorphic sites is

  12. Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination.

    Directory of Open Access Journals (Sweden)

    Joseph A Ross

    2011-07-01

    Full Text Available The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.

  13. RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant

    Directory of Open Access Journals (Sweden)

    Chia-Chi Lin

    2017-12-01

    Full Text Available Background/Purpose: Hepatitis delta virus (HDV is the only animal RNA virus that has an unbranched rod-like genome with ribozyme activity. It replicates in the nucleus by host RNA polymerase via a rolling circle mechanism. Similar to many RNA viruses encoding their own RNA-dependent RNA polymerases, homologous recombination of HDV occurs in mixed-genotype infections and in cultured cells cotransfected with two HDV sequences, as demonstrated by molecular analyses. Methods: Among 237 published complete genomic sequences, 34 sequences were reported from the small and isolated Miyako Island, Japan, and belonged to the Asia-specific genotypes, HDV-2 and HDV-4 (the majority of them belonged to the known Miyako Island-specific subgroup, HDV-4M. We investigated the presence of naturally occurring HDV recombinant in Miyako Island using phylogenetic and recombination analyses. Results: We identified a two-switch HDV-4/4M intersubtype recombinant with an unbranched rod-like RNA genome. Conclusion: Our data suggest that RNA recombination plays an important role in the rapid evolution of HDV, allowing the production of new HDV strains with correct genomic structures. Keywords: hepatitis delta virus, RNA recombination

  14. Genetic analysis of japonica x indica recombinant inbred lines and ...

    African Journals Online (AJOL)

    Genetic analysis of japonica x indica recombinant inbred lines and characterization of major fragrance gene by microsatellite markers. ... At some SSR loci, new/recombinant alleles were observed, which indicate the active recombination between genomes of two rice varieties and can be used for linkage mapping once ...

  15. Regulation of homologous recombination at telomeres in budding yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2010-01-01

    Homologous recombination is suppressed at normal length telomere sequences. In contrast, telomere recombination is allowed when telomeres erode in the absence of telomerase activity or as a consequence of nucleolytic degradation or incomplete replication. Here, we review the mechanisms...... that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae....

  16. Recombinant zoster (shingles) vaccine, RZV - what you need to know

    Science.gov (United States)

    ... year in the United States get shingles. Shingles vaccine (recombinant) Recombinant shingles vaccine was approved by FDA in 2017 for the ... life-threatening allergic reaction after a dose of recombinant shingles vaccine, or has a severe allergy to any component ...

  17. Bimolecular recombination in ambipolar organic field effect transistors

    NARCIS (Netherlands)

    Charrier, D.S.H.; Vries, T. de; Mathijssen, S.G.J.; Geluk, E.-J.; Smits, E.C.P.; Kemerink, M.; Janssen, R.A.J.

    2009-01-01

    In ambipolar organic field effect transistors (OFET) the shape of the channel potential is intimately related to the recombination zone width W, and hence to the electron–hole recombination strength. Experimentally, the recombination profile can be assessed by scanning Kelvin probe microscopy

  18. Anti-proliferative activity of recombinant melittin expressed in ...

    African Journals Online (AJOL)

    Recombinant melittin was then successfully expressed in Escherichia coli. The activity of affinity-purified recombinant melittin was determined in human leukemic U937 cells. Results show that the recombinant melittin had the same anti-proliferative activity in human leukemic U937 cells in vitro as natural one. This shows the ...

  19. Translational and rotational intra- and inter-fractional errors in patient and target position during a short course of frameless stereotactic body radiotherapy

    DEFF Research Database (Denmark)

    Josipovic, Mirjana; Persson, Gitte Fredberg; Logadottir, Ashildur

    2012-01-01

    Implementation of cone beam computed tomography (CBCT) in frameless stereotactic body radiotherapy (SBRT) of lung tumours enables setup correction based on tumour position. The aim of this study was to compare setup accuracy with daily soft tissue matching to bony anatomy matching and evaluate...... intra- and inter-fractional translational and rotational errors in patient and target positions....

  20. Intra- and inter-grader agreement in grading of coverage of panretinal photocoagulation by ultra-wide field color fundus images

    DEFF Research Database (Denmark)

    Torp, Thomas Lee; Jakobsen, Ditte Borup; Grauslund, Jakob

    on 20 UWF color fundus images in patients treated for PDR was quantified by two independent graders (grader A and B), and intra- and inter-grader association (Kappa) were calculated. In each retinal quadrant, OPTOS UWF color fundus images (Optomap, Optos PLC., Dunfermline, Scotland, UK) were used...

  1. Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and inter-laboratory testing, life stage, and species - SETAC Abstract

    Science.gov (United States)

    We developed a toxicity database for unionid mussels to examine the extent of intra- and inter-laboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the two life stages; and the variation in sensitiv...

  2. Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and inter-laboratory testing, life stage, and species

    Science.gov (United States)

    The authors developed a toxicity database for unionid mussels to examine the extent of intra- and interlaboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the 2 life stages; and the variation in se...

  3. Intra- and Inter-Rater Reliability of the Rate of Force Development of Hip Abductor Muscles Measured by Hand-Held Dynamometer

    Science.gov (United States)

    Takeda, Kazuya; Tanabe, Shigeo; Koyama, Soichiro; Nagai, Tomoko; Sakurai, Hiroaki; Kanada, Yoshikiyo; Shomoto, Koji

    2018-01-01

    The aim of this study was to clarify the intra- and inter-rater reliability of the rate of force development in hip abductor muscle force measurements using a hand-held dynamometer. Thirty healthy adults were separately assessed by two independent raters on two separate days. Rate of force development was calculated from the slope of the…

  4. The intra- and interrater reliability of the action research arm test: a practical test of upper extremity function in patients with stroke

    NARCIS (Netherlands)

    van der Lee, J. H.; de Groot, V.; Beckerman, H.; Wagenaar, R. C.; Lankhorst, G. J.; Bouter, L. M.

    2001-01-01

    To determine the intra- and interrater reliability of the Action Research Arm (ARA) test, to assess its ability to detect a minimal clinically important difference (MCID) of 5.7 points, and to identify less reliable test items. Intrarater reliability of the sum scores and of individual items was

  5. Rapid NMR-scale purification of15N,13C isotope-labeled recombinant human STIM1 coiled coil fragments.

    Science.gov (United States)

    Rathner, Petr; Stadlbauer, Michael; Romanin, Christoph; Fahrner, Marc; Derler, Isabella; Müller, Norbert

    2018-02-01

    We report a new NMR-scale purification procedure for two recombinant wild type fragments of the stromal interaction molecule 1 (STIM1). This protein acts as a calcium sensor in the endoplasmic reticulum (ER) and extends into the cytosol accumulating at ER - plasma membrane (PM) junctions upon calcium store depletion ultimately leading to activation of the Orai/CRAC channel. The functionally relevant cytosolic part of STIM1 consists of three coiled coil domains, which are mainly involved in intra- and inter-molecular homomeric interactions as well as coupling to and gating of CRAC channels. The optimized one-step rapid purification procedure for two 15 N, 13 C isotope-labeled cytosolic coiled coil fragments, which avoids the problems of previous approaches. The high yields of soluble well folded 15 N, 13 C isotope-labeled cytosolic coiled coil fragments followed by detergent screening provide for initial NMR characterization of these domains. The longer 30.5 kDa fragment represents the largest STIM1 wild type fragment that has been recombinantly prepared and characterized in solution without need for mutation or refolding. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    Directory of Open Access Journals (Sweden)

    Kumaran Narayanan

    2011-01-01

    Full Text Available Gene expression from bacterial artificial chromosome (BAC clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

  7. Dissipative Stern-Gerlach recombination experiment

    International Nuclear Information System (INIS)

    Oliveira, Thiago R. de; Caldeira, A. O.

    2006-01-01

    The possibility of obtaining the initial pure state in a usual Stern-Gerlach experiment through the recombination of the two emerging beams is investigated. We have extended the previous work of Englert, Schwinger, and Scully [Found Phys. 18, 1045 (1988)] including the fluctuations of the magnetic field generated by a properly chosen magnet. As a result we obtained an attenuation factor to the possible revival of coherence when the beams are perfectly recombined. When the source of the magnetic field is a superconducting quantum interference device (SQUID) the attenuation factor can be controlled by external circuits and the spin decoherence directly measured. For the proposed SQUID with dimensions in the scale of microns the attenuation factor has been shown unimportant when compared with the interaction time of the spin with the magnet

  8. Charge exchange recombination x-ray laser

    International Nuclear Information System (INIS)

    Kawachi, Tetsuya; Namba, Shinichi; Kado, Masataka; Tanaka, Momoko; Hasegawa, Noboru; Nagashima, Keisuke; Kato, Yoshiaki

    2001-01-01

    A recombining plasma x-ray laser using charge exchange recombination (CXR) is proposed. Fully stripped carbon ions collide with neutral He atoms and become excited hydrogenlike carbon ions, in which the excited levels with n=3 or 4 are mainly populated. We calculate the gain coefficients of the Balmer α and the Lyman β line of the hydrogenlike carbon ions by the use of a collisional-radiative model in which the CXR process is included. The calculated result shows that substantial gain can be generated for the Lyman β and Balmer α lines and that the gain of the Balmer α line can be strongly enhanced by the effect of CXR. We also report a preliminary experiment of this scheme. (author)

  9. Thermostable exoshells fold and stabilize recombinant proteins.

    Science.gov (United States)

    Deshpande, Siddharth; Masurkar, Nihar D; Girish, Vallerinteavide Mavelli; Desai, Malan; Chakraborty, Goutam; Chan, Juliana M; Drum, Chester L

    2017-11-13

    The expression and stabilization of recombinant proteins is fundamental to basic and applied biology. Here we have engineered a thermostable protein nanoparticle (tES) to improve both expression and stabilization of recombinant proteins using this technology. tES provides steric accommodation and charge complementation to green fluorescent protein (GFPuv), horseradish peroxidase (HRPc), and Renilla luciferase (rLuc), improving the yields of functional in vitro folding by ~100-fold. Encapsulated enzymes retain the ability to metabolize small-molecule substrates, presumably via four 4.5-nm pores present in the tES shell. GFPuv exhibits no spectral shifts in fluorescence compared to a nonencapsulated control. Thermolabile proteins internalized by tES are resistant to thermal, organic, chaotropic, and proteolytic denaturation and can be released from the tES assembly with mild pH titration followed by proteolysis.

  10. CFD Analysis of Passive Autocatalytic Recombiner

    Directory of Open Access Journals (Sweden)

    B. Gera

    2011-01-01

    Full Text Available In water-cooled nuclear power reactors, significant quantities of hydrogen could be produced following a postulated loss-of-coolant accident (LOCA along with nonavailability of emergency core cooling system (ECCS. Passive autocatalytic recombiners (PAR are implemented in the containment of water-cooled power reactors to mitigate the risk of hydrogen combustion. In the presence of hydrogen with available oxygen, a catalytic reaction occurs spontaneously at the catalyst surfaces below conventional ignition concentration limits and temperature and even in presence of steam. Heat of reaction produces natural convection flow through the enclosure and promotes mixing in the containment. For the assessment of the PAR performance in terms of maximum temperature of catalyst surface and outlet hydrogen concentration an in-house 3D CFD model has been developed. The code has been used to study the mechanism of catalytic recombination and has been tested for two literature-quoted experiments.

  11. Multiple Exponential Recombination for Differential Evolution.

    Science.gov (United States)

    Xin Qiu; Kay Chen Tan; Jian-Xin Xu

    2017-04-01

    Differential evolution (DE) is a popular population-based metaheuristic approach for solving numerical optimization problems. In recent years, considerable research has been devoted to the development of new mutation strategies and parameter adaptation mechanisms. However, as one of the basic algorithmic components of DE, the crossover operation has not been sufficiently examined in existing works. Most of the main DE variants solely employ traditional binomial recombination, which has intrinsic limitations in handling dependent subsets of variables. To fill this research niche, we propose a multiple exponential recombination that inherits all the main advantages of existing crossover operators while possessing a stronger ability in managing dependent variables. Multiple segments of the involved solutions will be exchanged during the proposed operator. The properties of the new scheme are examined both theoretically and empirically. Experimental results demonstrate the robustness of the proposed operator in solving problems with unknown variable interrelations.

  12. Recombination clumping factor during cosmic reionization

    International Nuclear Information System (INIS)

    Kaurov, Alexander A.; Gnedin, Nickolay Y.

    2014-01-01

    We discuss the role of recombinations in the intergalactic medium, and the related concept of the clumping factor, during cosmic reionization. The clumping factor is, in general, a local quantity that depends on both the local overdensity and the scale below which the baryon density field can be assumed smooth. That scale, called the filtering scale, depends on over-density and local thermal history. We present a method for building a self-consistent analytical model of inhomogeneous reionization, assuming the linear growth rate of the density fluctuation, which simultaneously accounts for these effects. We show that taking into account the local clumping factor introduces significant corrections to the total recombination rate, compared to the model with a globally uniform clumping factor.

  13. Regulation of Homologous Recombination by SUMOylation

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina

    , deletions, and genome rearrangements that can lead to cell death or cancer in humans. The post-translational modification by SUMO (small ubiquitinlike modifier) has proven to be an important regulator of HR and genome integrity, but the molecular mechanisms responsible for these roles are still unclear......Double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions challenging genome integrity. The DNA damage response (DDR) promotes fast and effective detection and repair of the damaged DNA, leading to cell cycle arrest through checkpoint activation and the recruitment of repair...... factors such as the homologous recombination (HR) machinery. HR constitutes the main DSB repair pathway in Saccharomyces cerevisiae and despite being largely considered an error-free process and essential for genome stability, uncontrolled recombination can lead to loss of heterozygosity, translocations...

  14. Intra- and inter-community variation in leaf water repellency along a 4000 m elevation transect in the Peruvian Andes

    Science.gov (United States)

    Goldsmith, G. R.; Doughty, C.; Bentley, L. P.; Shenkin, A.; Castro-Ccoscco, R. M.; Salinas, N.; Malhi, Y.

    2014-12-01

    Leaf water repellency is a measure of the hydrophobicity, or wettability, of leaf surfaces. At the scale of the plant, leaf water repellency can affect gas exchange, nutrient exchange, and pathogen growth. At the scale of the ecosystem, it can affect canopy water storage, throughfall, and evaporation. To date, very few studies have measured intra- and inter- community variation in leaf water repellency of tropical forest ecosystems. In the context of a broad survey of plant functional traits, we measured leaf water repellency in nine forest plots occurring across a 4000 m elevation gradient in the eastern Andes of Peru. Observed angles of incidence (63 ± 13°) indicate high leaf wettability, with no significant difference between sun and shade leaves. In contrast with previous research along elevation gradients, we find no strong evidence for variation across sites, but rather find high variation within a given site. Finally, we find that leaf water repellency may be predicted using sunlit leaf spectra with a low RMSE (<25% of the mean), indicating that future research on leaf water repellency could be carried out using high resolution hyperspectral remote sensing. As the climate of tropical ecosystems changes, the resultant changes in leaf water repellency will impact plants, communities and ecosystems. Our results inform our understanding of where and to what extent these impacts are most likely to occur.

  15. Intra- and Inter-Individual Differences in Adolescent Depressive Mood: the Role of Relationships with Parents and Friends.

    Science.gov (United States)

    Zhang, Shiyu; Baams, Laura; van de Bongardt, Daphne; Dubas, Judith Semon

    2018-05-01

    Utilizing four waves of data from 1126 secondary school Dutch adolescents (Mage = 13.95 at the first wave; 53% boys), the current study examined the interplay between parent-adolescent and friend-adolescent relationship quality (satisfaction and conflict) in relation to adolescents' depressive mood. Using multilevel analyses, the interacting effects of parent/friend relationship quality on depressive mood were tested at both the intra- and inter-individual level. Analyses at the intra-individual level investigated whether individual depressive mood fluctuated along with changes in their social relationships regardless of one's general level of depressive mood; and analyses at the inter-individual level examined whether the average differences in depressive mood between adolescents were associated with different qualities of social relationships. We interpreted the patterns of interactions between parent and friend relationships using four theoretical models: the reinforcement, toxic friends, compensation, and additive model. The results demonstrate the covariation of parent- and friend- relationship quality with adolescents' depressive mood, and highlight that parent and peer effects are not independent from each other-affirming the compensation and additive models at the intra-individual and the reinforcement and additive models at the inter-individual level. The findings highlight the robustness of the protective effects of parent and peer support and the deleterious effects of conflictual relationships for adolescent mental health. The results have implications for both the theoretical and practical design of (preventive) interventions aimed at decreasing adolescents' depressive mood.

  16. MR Imaging of Intra- and Periarticular Cyst-Like Lesions of the Knee Joint in Workers with Occupational Kneeling

    DEFF Research Database (Denmark)

    Rytter, Søren; Jensen, Lilli Kirkeskov; Bonde, Jens Peter

    2012-01-01

    Objective. To determine the risk of intra- and periarticular cyst-like lesions of the knee joint in occupational kneeling. Methods. Magnetic resonance imaging of both knees (n = 282) was conducted in 92 male floor layers and 49 male graphic designers (referents), with a mean age of 55.6 years...... injuries, and knee-straining sports. Results. Floor layers had a significantly higher prevalence of cyst-like lesions in the posterior part of the knee joint compared to graphic designers (OR 2.70, 95% CI 1.50-4.84). Floor layers also had a higher prevalence of fluid collections in the popliteus tendon...... recess (OR 2.17, 95% CI 0.99-4.77) and large cystic lesions of the popliteus muscle (OR 3.83, 95% CI 0.78-18.89). The prevalence of cystic lesions in the anterior part of the knee joint was low among floor layers (8.7%) and there was no significant difference between the two trade groups (P = 0...

  17. Intra- and interobserver error of the Greulich-Pyle method as used on a Danish forensic sample

    DEFF Research Database (Denmark)

    Lynnerup, N; Belard, E; Buch-Olsen, K

    2008-01-01

    The Section of Forensic Medicine at the University of Copenhagen performs age evaluations of the living at the request of the police. The established procedure in these cases involves: (1) a physical examination; (2) an odontological examination based on evaluation of an orthopantomogram and intr......The Section of Forensic Medicine at the University of Copenhagen performs age evaluations of the living at the request of the police. The established procedure in these cases involves: (1) a physical examination; (2) an odontological examination based on evaluation of an orthopantomogram...... of the age estimations by carpal X-rays and odontological age estimation. We retrieved 159 cases from the years 2000-2002 (inclusive). The intra- and interobserver errors are overall small. We found full agreement in 126/159 cases, and this was between experienced users and novices. Overall, the mean...... that atlas-based techniques are obsolete and ought to be replaced by other methods. Specifically, the GPA test sample consisted of American "white" children "above average in economic and educational status", leading to the question as to how comparable subjects being scored by the GPA method today...

  18. Periorbital biometric measurements using ImageJ software: Standardisation of technique and assessment of intra- and interobserver variability

    Directory of Open Access Journals (Sweden)

    R Rajyalakshmi

    2017-01-01

    Full Text Available Purpose: To assess the reliability and repeatability of periorbital biometric measurements using ImageJ software and to assess if the horizontal visible iris diameter (HVID serves as a reliable scale for facial measurements. Methods: This study was a prospective, single-blind, comparative study. Two clinicians performed 12 periorbital measurements on 100 standardised face photographs. Each individual’s HVID was determined by Orbscan IIz and used as a scale for measurements using ImageJ software. All measurements were repeated using the ‘average’ HVID of the study population as a measurement scale. Intraclass correlation coefficient (ICC and Pearson product-moment coefficient were used as statistical tests to analyse the data. Results: The range of ICC for intra- and interobserver variability was 0.79–0.99 and 0.86–0.99, respectively. Test-retest reliability ranged from 0.66–1.0 to 0.77–0.98, respectively. When average HVID of the study population was used as scale, ICC ranged from 0.83 to 0.99, and the test-retest reliability ranged from 0.83 to 0.96 and the measurements correlated well with recordings done with individual Orbscan HVID measurements. Conclusion: Periorbital biometric measurements using ImageJ software are reproducible and repeatable. Average HVID of the population as measured by Orbscan is a reliable scale for facial measurements.

  19. Intra- and inter-individual variation in flight direction in a migratory butterfly co-vary with individual mobility.

    Science.gov (United States)

    Larranaga, Nicolas; Baguette, Michel; Calvez, Olivier; Trochet, Audrey; Ducatez, Simon; Legrand, Delphine

    2013-08-15

    Flight direction is a major component of an animal's migratory success. However, few studies have focused on variation in flight direction both between and within individuals, which is likely to be correlated with other traits implied in migration processes. We report patterns of intra- and inter-individual variation in flight direction in the large white butterfly Pieris brassicae. The presence of inter-individual variation in flight direction for individuals tested in the same conditions suggests that this trait is inherited in P. brassicae and we propose that a rapid loss of migratory skills may exist in the absence of selection for migration. The magnitude of intra-individual variation was negatively correlated to two surrogates of the potential for migration: mobility and wing length. Highly mobile and longed-winged individuals within the same family were found to fly in similar directions, whereas less mobile and short-winged individuals displayed divergent flight direction compared with the average direction of their kin. There was also a negative correlation between the variance to the mean flight direction of a family and its average mobility, but no correlation with wing length. We discuss these issues in terms of the evolution of traits potentially implied in both migration and dispersal in P. brassicae.

  20. Sexual Abuse Within Employment Settings: A Comparison of Work-Related, Intra- and Extra-Familial Child Molesters.

    Science.gov (United States)

    Falkenbach, Diana M; Foehse, Antonia; Jeglic, Elizabeth; Calkins, Cynthia; Raymaekers, Linsey

    2017-06-01

    Child sexual abuse (CSA) is a serious problem not only in the community but also in institutional settings such as youth-serving organizations, churches, and schools. Although research has started to examine the problem of abuse in institutional settings, there remains a dearth of information about the nature and context of CSA in different employment settings, including those that do not specifically cater to children. In addition, research on the similarities and differences between perpetrators who work with children and other sex offenders is scarce. As such, the present study compared offenders on variables relating to financial/employment lifestyle stability, risk/dangerousness level, abuse opportunity, and victim selection. Data revealed that child abusers who worked with children tended to be better educated, were less likely to be married, had fewer nonsexual convictions, and were more likely to abuse male post-pubescent children compared with intra- and extra-familial offenders who did not work with children. Implications for future research, prevention of CSA, and clinical practice are discussed.

  1. Recombinant cells and organisms having persistent nonstandard amino acid dependence and methods of making them

    Science.gov (United States)

    Church, George M.; Mandell, Daniel J.; Lajoie, Marc J.

    2017-12-05

    Recombinant cells and recombinant organisms persistently expressing nonstandard amino acids (NSAAs) are provided. Methods of making recombinant cells and recombinant organisms dependent on persistently expressing NSAAs for survival are also provided. These methods may be used to make safe recombinant cells and recombinant organisms and/or to provide a selective pressure to maintain one or more reassigned codon functions in recombinant cells and recombinant organisms.

  2. Expression, purification and characterization of recombinant ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... aggregation activity analysis, we found that the anti-thrombin activity of the fusion protein did not change comparing with the ... the recombinant protein r-HV into the expression vector pPIC9K and pPIC9K1 and pPIC9K2 were ..... coagulation proteases (Dodt et al., 1984; Seemmuller et al., 1986). Hirudin is a ...

  3. DSMC Modeling of Flows with Recombination Reactions

    Science.gov (United States)

    2017-06-23

    Reactions S. Gimelshein, I. Wysong Air Force Research Laboratory (AFMC) AFRL/RQRC 10 E. Saturn Blvd. Edwards AFB, CA 93524-7680 Air Force Research...dimensional flows, modeling is usually con- ducted for Knudsen numbers Kn > 0.001, where the impact of recombination reactions is almost always minor, so...prac- tical applicability of the DSMC method. These methods have already been tested for reacting air flows.20 Today, modeling of gas flows at

  4. Modelling of procecces in catalytic recombiners

    International Nuclear Information System (INIS)

    Boehm, J.

    2007-01-01

    In order to achieve a high degree of safety in nuclear power plants and prevent possible accident scenarios, their consequences are calculated and analysed with numeric codes. One of the most important part of nuclear safety research of hazardous incidents are development and validation of these numeric models, which are implemented into accident codes. The severe hydrogen release during a core meltdown is one of the considered scenario of performed accident analyses. One of the most important measure for the elimination of the hydrogen is catalytic recombiners. Converting the hydrogen with the atmospheric oxygen to water vapor in an exothermic reaction will prevent possible detonation of the hydrogen/air atmosphere. Within the dissertation the recombiner simulation REKO-DIREKT was developed and validated by an extensive experimental database. The performance of recombiners with regard to the conversion of the hydrogen and the temperature development is modelled. The REKO-DIREKT program is unique and has made significant revolution in research of hydrogen safety. For the first time it has been possible to show the performance of the recombiner so great in detail by using REKO-DIREKT. In the future engineers of nuclear power plants will have opportunity to have precise forecasts about the process of the possible accidents with hydrogen release. Also with presence of water vapor or with oxygen depletion which are included in the model. The major discussion of the hydrogen ignition at hot catalyst steel plates can be evaluated in the future with REKO-DIREKT more reliably than the existing used models. (orig.)

  5. Cultivating Insect Cells To Produce Recombinant Proteins

    Science.gov (United States)

    Spaulding, Glenn; Goodwin, Thomas; Prewett, Tacey; Andrews, Angela; Francis, Karen; O'Connor, Kim

    1996-01-01

    Method of producing recombinant proteins involves growth of insect cells in nutrient solution in cylindrical bioreactor rotating about cylindrical axis, oriented horizontally and infecting cells with viruses into which genes of selected type cloned. Genes in question those encoding production of desired proteins. Horizontal rotating bioreactor preferred for use in method, denoted by acronym "HARV", described in "High-Aspect-Ratio Rotating Cell-Culture Vessel" (MSC-21662).

  6. Ancestries of a recombining diploid population.

    Science.gov (United States)

    Sainudiin, R; Thatte, B; Véber, A

    2016-01-01

    We derive the exact one-step transition probabilities of the number of lineages that are ancestral to a random sample from the current generation of a bi-parental population that is evolving under the discrete Wright-Fisher model with n diploid individuals. Our model allows for a per-generation recombination probability of r . When r = 1, our model is equivalent to Chang's (Adv Appl Probab 31:1002-1038, 1999) model for the karyotic pedigree. When r = 0, our model is equivalent to Kingman's (Stoch Process Appl 13:235-248, 1982) discrete coalescent model for the cytoplasmic tree or sub-karyotic tree containing a DNA locus that is free of intra-locus recombination. When 0 r r . Thus, our family of models indexed by r ∈ [0, 1] connects Kingman's discrete coalescent to Chang's pedigree in a continuous way as r goes from 0 to 1. For large populations, we also study three properties of the ancestral process corresponding to a given r ∈ (0, 1): the time Tn to a most recent common ancestor (MRCA) of the population, the time Un at which all individuals are either common ancestors of all present day individuals or ancestral to none of them, and the fraction of individuals that are common ancestors at time Un. These results generalize the three main results of Chang's (Adv Appl Probab 31:1002-1038, 1999). When we appropriately rescale time and recombination probability by the population size, our model leads to the continuous time Markov chain called the ancestral recombination graph of Hudson (Theor Popul Biol 23:183-201, 1983) and Griffiths (The two-locus ancestral graph, Institute of Mathematical Statistics 100-117, 1991).

  7. Dissociation of recombinant prion autocatalysis from infectivity

    OpenAIRE

    Noble, Geoffrey P; Supattapone, Surachai

    2015-01-01

    Within the mammalian prion field, the existence of recombinant prion protein (PrP) conformers with self-replicating (ie. autocatalytic) activity in vitro but little to no infectious activity in vivo challenges a key prediction of the protein-only hypothesis of prion replication – that autocatalytic PrP conformers should be infectious. To understand this dissociation of autocatalysis from infectivity, we recently performed a structural and functional comparison between a highly infectious and ...

  8. Development of Mycoplasma hyopneumoniae Recombinant Vaccines.

    Science.gov (United States)

    Marchioro, Silvana Beutinger; Simionatto, Simone; Dellagostin, Odir

    2016-01-01

    Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia (EP), a disease that affects swine production worldwide. Vaccination is the most cost-effective strategy for the control and prevention of the disease. Research using genome-based approach has the potential to elucidate the biology and pathogenesis of M. hyopneumoniae and contribute to the development of more effective vaccines. Here, we describe the protocol for developing M. hyopneumoniae recombinant vaccines using reverse vaccinology approaches.

  9. Kinetic studies of ion - recombination in gases

    Energy Technology Data Exchange (ETDEWEB)

    Caulfield, K.J.; Bhave, R.N.; Cooper, R. [Melbourne Univ., Parkville, VIC (Australia). Dept. of Chemistry

    1996-12-31

    Full text: Subsequent to primary ionisation/excitation and dissociation events in irradiated systems, the medium relaxes by various secondary processes which may also be precursors to lasting chemical and physical changes in the system. Pulse radiolysis techniques can be successfully utilised to directly observe such processes so that kinetic parameters may be determined to subsequently accurately model these processes in irradiated systems. Time resolved microwave absorption techniques on a Febetron 706 pulsed electron beam system have been used to study ion recombination in simple gas systems. The microwave absorption method relies on the mobility of charged species within the system and effectively measures an ac-conductivity of the irradiated medium. The technique has a time resolution of about one nanosecond. The decay of conductivity in irradiated gases over the pressure range 50 to 1500 torr has been measured on time scales from 10 nanoseconds to 10 microseconds. Bulk gas pressure and ion densities were such that measurements yielded recombination coefficients for dimeric rare gas cations with thermal electrons. The recombination rate constant, {alpha}{sub T}, is shown to be both independent and dependent on the total pressure in the system ({alpha}{sub T} = {alpha}{sub 2} + {alpha}{sub 3} [M]; {alpha}{sub T} has values up to approx 10{sup +14} L. M{sup -1} s{sup -1} ). Total recombination coefficients {alpha}{sub T} have been measured for the noble gases helium, neon, argon, krypton and xenon. Measurements have also been made for the simple diatomic molecules nitrogen and hydrogen. All the systems studied, except for argon, show both two and three body processes occurring. The three body or assisted process requires the thermalisation of electrons in the neighborhood of the positive ion prior capture. The two body effect is thought to be a radiative or dissociative process. The mechanistic implications of the pulse radiolysis results will be discussed in

  10. Recent advances in DNA repair and recombination.

    Science.gov (United States)

    Iwanejko, L A; Jones, N J

    1998-09-11

    The subjects of the talks at this 1-day DNA Repair Network meeting, held at City University, London on December 15, 1997, encompassed a range of topics and reflected some of the current areas of research in the United Kingdom. Topics included DNA double-strand break repair, V(D)J recombination, DNA ligases, the RecQ family of helicases and Bloom's syndrome, UVB and immunosuppression, the repair of oxidative damage and mismatch repair mechanisms.

  11. Dissociative recombination of small molecular ions

    International Nuclear Information System (INIS)

    Mul, P.M.

    1981-01-01

    In this thesis an analysis is given of merged electron-ion beam experiment and work on dissociative recombination of molecular ions and electrons is described. Chapter II covers a brief introduction of the theory of dissociative recombination. In chapter III, a description is given of the merged electron-ion beam experiment and a method is described which allows the determination of the mean angle between the electron and ion trajectories in a merged electron-ion beam experiment. In chapter IV a paper on the three dominant atmospheric diatomic ions NO + , O 2 + and N 2 + is presented and in chapter V the dissociative recombination for N 2 H + and N 2 D + is discussed. In chapter VI two papers on the polyatomic ions of the carbon-containing molecular ions are presented, and in chapter VII a letter with some results of the work presented in more detail in the chapters IV, V and VI is presented. The magnitude and the energy dependence of the cross-section measured by the merged beam technique and by other techniques is compared and discussed. (Auth.)

  12. Heavy-ion cooling and radiative recombination

    International Nuclear Information System (INIS)

    Beyer, H.F.

    1988-09-01

    There is presently a large number of ion storage rings under construction which will use electron cooling for increasing the phase-space density of the stored ions in order to gain luminosity and resolution advantages for a variety of experiments. In this review a more general introduction to the electron-cooling technique is given. The atomic-physics aspects of electron-ion interactions at low relative velocity are identified. One of the most important processes is electron-ion radiative recombination because it can have strong implications on the operation of a storage ring employing electron cooling. Estimates are given of the ion-beam lifetime, as limited by recombination losses, as a function of electron density and temperature and for all values of the atomic number Z of the ions. The use of recombination processes in the electron cooler for atomic spectroscopy of few-electron heavy ions is discussed along with their implication on diagnostics of electron cooling. (orig.)

  13. Recombination-dependent concatemeric viral DNA replication.

    Science.gov (United States)

    Lo Piano, Ambra; Martínez-Jiménez, María I; Zecchi, Lisa; Ayora, Silvia

    2011-09-01

    The initiation of viral double stranded (ds) DNA replication involves proteins that recruit and load the replisome at the replication origin (ori). Any block in replication fork progression or a programmed barrier may act as a factor for ori-independent remodelling and assembly of a new replisome at the stalled fork. Then replication initiation becomes dependent on recombination proteins, a process called recombination-dependent replication (RDR). RDR, which is recognized as being important for replication restart and stability in all living organisms, plays an essential role in the replication cycle of many dsDNA viruses. The SPP1 virus, which infects Bacillus subtilis cells, serves as a paradigm to understand the links between replication and recombination in circular dsDNA viruses. SPP1-encoded initiator and replisome assembly proteins control the onset of viral replication and direct the recruitment of host-encoded replisomal components at viral oriL. SPP1 uses replication fork reactivation to switch from ori-dependent θ-type (circle-to-circle) replication to σ-type RDR. Replication fork arrest leads to a double strand break that is processed by viral-encoded factors to generate a D-loop into which a new replisome is assembled, leading to σ-type viral replication. SPP1 RDR proteins are compared with similar proteins encoded by other viruses and their possible in vivo roles are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. CFD modeling of passive autocatalytic recombiners*

    Directory of Open Access Journals (Sweden)

    Orszulik Magdalena

    2015-06-01

    Full Text Available This study deals with numerical modeling of passive autocatalytic hydrogen recombiners (PARs. Such devices are installed within containments of many nuclear reactors in order to remove hydrogen and convert it to steam. The main purpose of this work is to develop a numerical model of passive autocatalytic recombiner (PAR using the commercial computational fluid dynamics (CFD software ANSYS-FLUENT and tuning the model using experimental results. The REKO 3 experiment was used for this purpose. Experiment was made in the Institute for Safety Research and Reactor Technology in Julich (Germany. It has been performed for different hydrogen concentrations, different flow rates, the presence of steam, and different initial temperatures of the inlet mixture. The model of this experimental recombiner was elaborated within the framework of this work. The influence of mesh, gas thermal conductivity coefficient, mass diffusivity coefficients, and turbulence model was investigated. The best results with a good agreement with REKO 3 data were received for k-ɛ model of turbulence, gas thermal conductivity dependent on the temperature and mass diffusivity coefficients taken from CHEMKIN program. The validated model of the PAR was next implemented into simple two-dimensional simulations of hydrogen behavior within a subcompartment of a containment building.

  15. Antagonistic experimental coevolution with a parasite increases host recombination frequency

    Directory of Open Access Journals (Sweden)

    Kerstes Niels AG

    2012-02-01

    Full Text Available Abstract Background One of the big remaining challenges in evolutionary biology is to understand the evolution and maintenance of meiotic recombination. As recombination breaks down successful genotypes, it should be selected for only under very limited conditions. Yet, recombination is very common and phylogenetically widespread. The Red Queen Hypothesis is one of the most prominent hypotheses for the adaptive value of recombination and sexual reproduction. The Red Queen Hypothesis predicts an advantage of recombination for hosts that are coevolving with their parasites. We tested predictions of the hypothesis with experimental coevolution using the red flour beetle, Tribolium castaneum, and its microsporidian parasite, Nosema whitei. Results By measuring recombination directly in the individuals under selection, we found that recombination in the host population was increased after 11 generations of coevolution. Detailed insights into genotypic and phenotypic changes occurring during the coevolution experiment furthermore helped us to reconstruct the coevolutionary dynamics that were associated with this increase in recombination frequency. As coevolved lines maintained higher genetic diversity than control lines, and because there was no evidence for heterozygote advantage or for a plastic response of recombination to infection, the observed increase in recombination most likely represented an adaptive host response under Red Queen dynamics. Conclusions This study provides direct, experimental evidence for an increase in recombination frequency under host-parasite coevolution in an obligatory outcrossing species. Combined with earlier results, the Red Queen process is the most likely explanation for this observation.

  16. Monitoring homologous recombination in rice (Oryza sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhuanying; Tang Li [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Li Meiru [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Chen Lei; Xu Jie [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Wu Goujiang [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Li Hongqing, E-mail: hqli@scnu.edu.cn [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China)

    2010-09-10

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10{sup -5} recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  17. FASEB Summer Research Conference. Genetic Recombination and Chromosome Rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    Jinks-Robertson, Sue

    2002-02-01

    The 2001 meeting entitled ''Genetic Recombination and Genome Rearrangements'' was held July 21-26 in Snowmass, Colorado. The goal of the meeting was to bring together scientists using diverse approaches to study all aspects of genetic recombination. This goal was achieved by integrating talks covering the genetics, biochemistry and structural biology of homologous recombination, site-specific recombination, and nonhomologous recombination. The format of the meeting consisted of a keynote address on the opening evening, two formal plenary sessions on each of the four full meeting days, a single afternoon workshop consisting of short talks chosen from among submitted abstracts, and afternoon poster sessions on each of the four full meeting days. The eight plenary session were entitled: (1) Recombination Mechanisms, (2) Prokaryotic Recombination, (3) Repair and Recombination, (4) Site-specific Recombination and Transposition, (5) Eukaryotic Recombination I, (6) Genome Rearrangements, (7) Meiosis, and (8) Eukaryotic Recombination II. Each session included a mix of genetic, biochemical and structural talks; talks were limited to 20 minutes, followed by 10 minutes of very lively, general discussion. Much of the data presented in the plenary sessions was unpublished, thus providing attendees with the most up-to-date knowledge of this rapidly-moving field.

  18. V(D)J recombination frequency is affected by the sequence interposed between a pair of recombination signals: sequence comparison reveals a putative recombinational enhancer element

    DEFF Research Database (Denmark)

    Roch, F A; Hobi, R; Berchtold, M W

    1997-01-01

    this activity suggests that the effect is no mediated through attachment of the recombination substrate to a nuclear matrix-associated recombination complex but through cis-activation. The presence of a 26 bp A-T-rich sequence motif in the 5' and 3' MARs of Emu and in all of the other upregulating fragments....... These we prepared by interposing between the recombination signal sequences (RSS) of the plasmid pBlueRec various fragments, including Emu, possibly affecting V(D)J recombination. Our work shows that sequences inserted between RSS 23 and RSS 12, with distances from their proximal ends of 26 and 284 bp...

  19. Mechanisms and factors that influence high frequency retroviral recombination

    DEFF Research Database (Denmark)

    Delviks-Frankenberry, Krista; Galli, Andrea; Nikolaitchik, Olga

    2011-01-01

    With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse...... transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity...... of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment...

  20. Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference.

    Science.gov (United States)

    Segura, Joana; Ferretti, Luca; Ramos-Onsins, Sebastián; Capilla, Laia; Farré, Marta; Reis, Fernanda; Oliver-Bonet, Maria; Fernández-Bellón, Hugo; Garcia, Francisca; Garcia-Caldés, Montserrat; Robinson, Terence J; Ruiz-Herrera, Aurora

    2013-11-22

    Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.

  1. [Gene fusion of egfp & kan and recombinant plasmid construction by red mediated in vivo homologous recombination].

    Science.gov (United States)

    Wu, Yang; Li, Shan-Hu; Shi, Qing-Guo; Liu, Dang-Sheng; Zhou, Jian-Guang

    2007-07-01

    Recombineering, a new genetic engineering technology based on high efficiency in vivo homologous recombination, can be used in target DNA knock-in, knock-out and gene cloning. In the process of gene subcloning mediated by Recombineering technique, high-quality target DNA fragments were difficult to obtain using in vitro overlapping PCR,therefore the efficiency of in vivo homologous recombination was severely interrupted. To solve this problem, some technology improvements have been established based on the principle of Red recombinases. The PCR DNA fragments of egfp and kan genes with complementary sequences on the end of each fragment were co-introduced into a pcDNA3.1 vector and Red recombinases containing E. coli DY331 host cells by electroporation. A recombinant plasmid pcDNA3.1-egfp-kan was screened directly by antibiotic marker. The positive rates can reach to 45%. The EGFP gene expression of pcDNA3.1-egfp-kan can be observed by transient transfection of 293 eukaryotic cells.

  2. Mobility dependent recombination models for organic solar cells

    Science.gov (United States)

    Wagenpfahl, Alexander

    2017-09-01

    Modern solar cell technologies are driven by the effort to enhance power conversion efficiencies. A main mechanism limiting power conversion efficiencies is charge carrier recombination which is a direct function of the encounter probability of both recombination partners. In inorganic solar cells with rather high charge carrier mobilities, charge carrier recombination is often dominated by energetic states which subsequently trap both recombination partners for recombination. Free charge carriers move fast enough for Coulomb attraction to be irrelevant for the encounter probability. Thus, charge carrier recombination is independent of charge carrier mobilities. In organic semiconductors charge carrier mobilities are much lower. Therefore, electrons and holes have more time react to mutual Coulomb-forces. This results in the strong charge carrier mobility dependencies of the observed charge carrier recombination rates. In 1903 Paul Langevin published a fundamental model to describe the recombination of ions in gas-phase or aqueous solutions, known today as Langevin recombination. During the last decades this model was used to interpret and model recombination in organic semiconductors. However, certain experiments especially with bulk-heterojunction solar cells reveal much lower recombination rates than predicted by Langevin. In search of an explanation, many material and device properties such as morphology and energetic properties have been examined in order to extend the validity of the Langevin model. A key argument for most of these extended models is, that electron and hole must find each other at a mutual spatial location. This encounter may be limited for instance by trapping of charges in trap states, by selective electrodes separating electrons and holes, or simply by the morphology of the involved semiconductors, making it impossible for electrons and holes to recombine at high rates. In this review, we discuss the development of mobility limited

  3. Modeling and measuring intracellular fluxes of secreted recombinant protein in Pichia pastoris with a novel 34S labeling procedure

    Directory of Open Access Journals (Sweden)

    Hann Stephan

    2011-06-01

    Full Text Available Abstract Background The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein formation, degradation and secretion defines the major bottleneck of the production system. Because these parameters are different for unlimited growth (shake flask and carbon-limited growth (bioreactor conditions, they should be determined under "production like" conditions. Thus labeling procedures must be compatible with minimal production media and the usage of bioreactors. The inorganic and non-radioactive 34S labeled sodium sulfate meets both demands. Results We used a novel labeling method with the stable sulfur isotope 34S, administered as sodium sulfate, which is performed during chemostat culivations. The intra- and extracellular sulfur 32 to 34 ratios of purified recombinant protein, the antibody fragment Fab3H6, are measured by HPLC-ICP-MS. The kinetic model described here is necessary to calculate the kinetic parameters from sulfur ratios of consecutive samples as well as for sensitivity analysis. From the total amount of protein produced intracellularly (143.1 μg g-1 h-1 protein per yeast dry mass and time about 58% are degraded within the cell, 35% are secreted to the exterior and 7% are inherited to the daughter cells. Conclusions A novel 34S labeling procedure that enables in vivo quantification of intracellular fluxes of recombinant protein under "production like" conditions is described. Subsequent sensitivity analysis of the fluxes by using MATLAB, indicate the most promising approaches for strain improvement towards increased secretion.

  4. Multiple barriers to recombination between divergent HIV-1 variants revealed by a dual-marker recombination assay

    DEFF Research Database (Denmark)

    Nikolaitchik, Olga A; Galli, Andrea; Moore, Michael D

    2011-01-01

    Recombination is a major force for generating human immunodeficiency virus type 1 (HIV-1) diversity and produces numerous recombinants circulating in the human population. We previously established a cell-based system using green fluorescent protein gene (gfp) as a reporter to study the mechanisms...... between variants from different groups is further reduced compared with green fluorescent protein, indicating that sequence divergence interferes with recombination efficiency in the gag gene. Compared with identical sequences, we estimate that recombination rates are reduced by 3-fold and by 10- to 13...... of HIV-1 recombination. We now report an improved system capable of detecting recombination using authentic viral sequences. Frameshift mutations were introduced into the gag gene so that parental viruses do not express full-length Gag; however, recombination can generate a progeny virus that expresses...

  5. Recombinant pinoresinol/lariciresinol reductase, recombinant dirigent protein, and methods of use

    Science.gov (United States)

    Lewis, Norman G.; Davin, Laurence B.; Dinkova-Kostova, Albena T.; Fujita, Masayuki; Gang, David R.; Sarkanen, Simo; Ford, Joshua D.

    2001-04-03

    Dirigent proteins and pinoresinol/lariciresinol reductases have been isolated, together with cDNAs encoding dirigent proteins and pinoresinol/lariciresinol reductases. Accordingly, isolated DNA sequences are provided which code for the expression of dirigent proteins and pinoresinol/lariciresinol reductases. In other aspects, replicable recombinant cloning vehicles are provided which code for dirigent proteins or pinoresinol/lariciresinol reductases or for a base sequence sufficiently complementary to at least a portion of dirigent protein or pinoresinol/lariciresinol reductase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding dirigent protein or pinoresinol/lariciresinol reductase. Thus, systems and methods are provided for the recombinant expression of dirigent proteins and/or pinoresinol/lariciresinol reductases.

  6. Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution.

    Directory of Open Access Journals (Sweden)

    Catherine J Pink

    Full Text Available In mammals sequences that are either late replicating or highly recombining have high rates of evolution at putatively neutral sites. As early replicating domains and highly recombining domains both tend to be GC rich we a priori expect these two variables to covary. If so, the relative contribution of either of these variables to the local neutral substitution rate might have been wrongly estimated owing to covariance with the other. Against our expectations, we find that sex-averaged recombination rates show little or no correlation with replication timing, suggesting that they are independent determinants of substitution rates. However, this result masks significant sex-specific complexity: late replicating domains tend to have high recombination rates in females but low recombination rates in males. That these trends are antagonistic explains why sex-averaged recombination is not correlated with replication timing. This unexpected result has several important implications. First, although both male and female recombination rates covary significantly with intronic substitution rates, the magnitude of this correlation is moderately underestimated for male recombination and slightly overestimated for female recombination, owing to covariance with replicating timing. Second, the result could explain why male recombination is strongly correlated with GC content but female recombination is not. If to explain the correlation between GC content and replication timing we suppose that late replication forces reduced GC content, then GC promotion by biased gene conversion during female recombination is partly countered by the antagonistic effect of later replicating sequence tending increase AT content. Indeed, the strength of the correlation between female recombination rate and local GC content is more than doubled by control for replication timing. Our results underpin the need to consider sex-specific recombination rates and potential covariates in

  7. Late Replicating Domains Are Highly Recombining in Females but Have Low Male Recombination Rates: Implications for Isochore Evolution

    Science.gov (United States)

    Pink, Catherine J.; Hurst, Laurence D.

    2011-01-01

    In mammals sequences that are either late replicating or highly recombining have high rates of evolution at putatively neutral sites. As early replicating domains and highly recombining domains both tend to be GC rich we a priori expect these two variables to covary. If so, the relative contribution of either of these variables to the local neutral substitution rate might have been wrongly estimated owing to covariance with the other. Against our expectations, we find that sex-averaged recombination rates show little or no correlation with replication timing, suggesting that they are independent determinants of substitution rates. However, this result masks significant sex-specific complexity: late replicating domains tend to have high recombination rates in females but low recombination rates in males. That these trends are antagonistic explains why sex-averaged recombination is not correlated with replication timing. This unexpected result has several important implications. First, although both male and female recombination rates covary significantly with intronic substitution rates, the magnitude of this correlation is moderately underestimated for male recombination and slightly overestimated for female recombination, owing to covariance with replicating timing. Second, the result could explain why male recombination is strongly correlated with GC content but female recombination is not. If to explain the correlation between GC content and replication timing we suppose that late replication forces reduced GC content, then GC promotion by biased gene conversion during female recombination is partly countered by the antagonistic effect of later replicating sequence tending increase AT content. Indeed, the strength of the correlation between female recombination rate and local GC content is more than doubled by control for replication timing. Our results underpin the need to consider sex-specific recombination rates and potential covariates in analysis of GC

  8. Poliovirus Polymerase Leu420 Facilitates RNA Recombination and Ribavirin Resistance.

    Science.gov (United States)

    Kempf, Brian J; Peersen, Olve B; Barton, David J

    2016-10-01

    RNA recombination is important in the formation of picornavirus species groups and the ongoing evolution of viruses within species groups. In this study, we examined the structure and function of poliovirus polymerase, 3D(pol), as it relates to RNA recombination. Recombination occurs when nascent RNA products exchange one viral RNA template for another during RNA replication. Because recombination is a natural aspect of picornavirus replication, we hypothesized that some features of 3D(pol) may exist, in part, to facilitate RNA recombination. Furthermore, we reasoned that alanine substitution mutations that disrupt 3D(pol)-RNA interactions within the polymerase elongation complex might increase and/or decrease the magnitudes of recombination. We found that an L420A mutation in 3D(pol) decreased the frequency of RNA recombination, whereas alanine substitutions at other sites in 3D(pol) increased the frequency of recombination. The 3D(pol) Leu420 side chain interacts with a ribose in the nascent RNA product 3 nucleotides from the active site of the polymerase. Notably, the L420A mutation that reduced recombination also rendered the virus more susceptible to inhibition by ribavirin, coincident with the accumulation of ribavirin-induced G→A and C→U mutations in viral RNA. We conclude that 3D(pol) Leu420 is critically important for RNA recombination and that RNA recombination contributes to ribavirin resistance. Recombination contributes to the formation of picornavirus species groups and the emergence of circulating vaccine-derived polioviruses (cVDPVs). The recombinant viruses that arise in nature are occasionally more fit than either parental strain, especially when the two partners in recombination are closely related, i.e., members of characteristic species groups, such as enterovirus species groups A to H or rhinovirus species groups A to C. Our study shows that RNA recombination requires conserved features of the viral polymerase. Furthermore, a polymerase

  9. How to assess intra- and inter-observer agreement with quantitative PET using variance component analysis: a proposal for standardisation.

    Science.gov (United States)

    Gerke, Oke; Vilstrup, Mie Holm; Segtnan, Eivind Antonsen; Halekoh, Ulrich; Høilund-Carlsen, Poul Flemming

    2016-09-21

    Quantitative measurement procedures need to be accurate and precise to justify their clinical use. Precision reflects deviation of groups of measurement from another, often expressed as proportions of agreement, standard errors of measurement, coefficients of variation, or the Bland-Altman plot. We suggest variance component analysis (VCA) to estimate the influence of errors due to single elements of a PET scan (scanner, time point, observer, etc.) to express the composite uncertainty of repeated measurements and obtain relevant repeatability coefficients (RCs) which have a unique relation to Bland-Altman plots. Here, we present this approach for assessment of intra- and inter-observer variation with PET/CT exemplified with data from two clinical studies. In study 1, 30 patients were scanned pre-operatively for the assessment of ovarian cancer, and their scans were assessed twice by the same observer to study intra-observer agreement. In study 2, 14 patients with glioma were scanned up to five times. Resulting 49 scans were assessed by three observers to examine inter-observer agreement. Outcome variables were SUVmax in study 1 and cerebral total hemispheric glycolysis (THG) in study 2. In study 1, we found a RC of 2.46 equalling half the width of the Bland-Altman limits of agreement. In study 2, the RC for identical conditions (same scanner, patient, time point, and observer) was 2392; allowing for different scanners increased the RC to 2543. Inter-observer differences were negligible compared to differences owing to other factors; between observer 1 and 2: -10 (95 % CI: -352 to 332) and between observer 1 vs 3: 28 (95 % CI: -313 to 370). VCA is an appealing approach for weighing different sources of variation against each other, summarised as RCs. The involved linear mixed effects models require carefully considered sample sizes to account for the challenge of sufficiently accurately estimating variance components.

  10. Distribution of ischemic infarction and stenosis of intra- and extracranial arteries in young Chinese patients with ischemic stroke.

    Science.gov (United States)

    Ojha, Rajeev; Huang, Dongya; An, Hedi; Liu, Rong; Du, Cui; Shen, Nan; Tu, Zhilan; Li, Ying

    2015-11-23

    The distribution of cerebral ischemic infarction and stenosis in ischemic stroke may vary with age-group, race and gender. This study was conducted to understand the risk factors and characteristics of cerebral infarction and stenosis of vessels in young Chinese patients with ischemic stroke. This was a retrospective study, from January 2007 to July 2012, of 123 patients ≤50 years diagnosed with acute ischemic stroke. Patient characteristics were compared according to sex (98 males and 25 females) and age group (51 patients were ≤45 years and 72 patients were 46-50 years). Characteristics of acute ischemic infarction were studied by diffusion weighted imaging. Stenosis of intra- and extracranial arteries was diagnosed by duplex sonography, head magnetic resonance angiography (MRA) or cervical MRA. Common risk factors were hypertension (72.4 %), dyslipidemia (55.3 %), smoking (54.4 %) and diabetes (33.3 %). Lacunar Infarction was most common in our patients (41.5 %). Partial anterior circulation infarction was predominant in females (52.0 vs 32.7 %; P = 0.073) and posterior circulation infarction in males (19.8 vs 4 %; P = 0.073). Multiple brain infarctions were found in 38 patients (30.9 %). Small artery atherosclerosis was found in 54 patients (43.9 %), with higher prevalence in patients of the 46-50 years age-group. Intracranial stenosis was more common than extracranial stenosis, and middle cerebral artery stenosis was most prevalent (27.3 %). Stenosis in the anterior circulation was more frequent than in the posterior circulation (P young patients, hypertension, smoking, dyslipidemia and diabetes were common risk factors. Intracranial stenosis was most common. The middle cerebral artery was highly vulnerable.

  11. Fate of phosphorus fractions in an adsorptive-filter subject to intra- and inter-event runoff phenomena.

    Science.gov (United States)

    Berretta, Christian; Sansalone, John

    2012-07-30

    In-situ filtration of phosphorus (P) and particulate matter (PM) transported in runoff is increasingly implemented for urban source areas. While monitoring of filter response is commonly based on an event mean of total phosphorus (TP), this study examines the fate of specific P fractions through intra- and inter-event phenomena. This continuous filter monitoring program includes 15 wet weather loadings and the dry weather periods between these events. Aqueous P adsorption and PM-bound P (suspended, settleable and sediment) filtration phenomena are examined for runoff events from a landscaped carpark with biogenic loads in Gainesville (GNV), FL. Filter response is compared to a similar aluminum oxide Al-Ox modified media filter subject to anthropogenic loads from an urban paved source area in Baton Rouge (BTR), LA. Results for the GNV filter indicate that while intra-event settleable, sediment and dissolved P fractions are controlled by the filter, the suspended P fraction remained relatively mobile compared to the other P fractions. P adsorption is primarily influenced by intra-event flow rates, contact times, runoff volume, pH and by the inter-event chemistry of runoff stored in the filter. P effluent partitioning is dominated by the suspended PM as a consequence of effective adsorption by the filter. Inter-event phenomena generate decreasing redox with commensurate increases in alkalinity, conductivity as well as dissolved P as a consequence of re-partitioning. Dissolved P fate suggests that filters should be designed and managed to remain aerobic between wet weather events. For effective separation of suspended P and PM fractions by passive filters with low driving head, sustainability of performance, including head loss {<3 kPa}, requires upstream volumetric attenuation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Intra- and interpersonal emotion regulation and adjustment symptoms in couples: The role of co-brooding and co-reappraisal

    Directory of Open Access Journals (Sweden)

    Andrea B. Horn

    2016-10-01

    Full Text Available Abstract Background Adult emotion regulation is not only occurring within the person but includes strategies that happen in social interactions and that are framed as co-regulating. The current study investigates the role of the interpersonal emotion regulation strategies of co-reappraisal and co-brooding in couples for adjustment disorder symptoms as the disorder will be outlined in the International Classification of Diseases-11 (ICD-11. Methods Couples registered together in an online questionnaire study reporting whether or not they are adjusting to a major stressor that is psychologically challenging to them. In total, one hundred and forty-six participants (N = 73 male; N = 73 female reported having experienced a major stressor in the last 12 months and were thus be identified as at risk for adjustment disorder. Those individuals at risk were assessed for adjustment disorder and depressive symptoms; intra- and interpersonal emotion regulation (co-/brooding, co-/reappraisal were assessed not only in the individual at risk but also in the romantic partner. Results Regression-based dyadic analyses revealed that above and beyond intrapersonal emotion regulation, interpersonal co-brooding and for the female participants also co-reappraisal were significantly associated with symptoms of adjustment disorder and depression, standardized betas varied between .24 and .36, suggesting medium effect sizes. An association with the female partner’s tendency to reappraise with fewer symptoms in the male partner at risk for adjustment disorder could also be observed. Conclusions Co-brooding and co-reappraisal represent emotion regulation strategies that happen in social interaction and seem to play a relevant role in the context of adjustment disorders above and beyond the commonly assessed intrapersonal emotion regulation strategies.

  13. Intra- and inter-observer reliability of the application of the cellulite severity scale to a Spanish female population.

    Science.gov (United States)

    De La Casa Almeida, M; Suarez Serrano, C; Jiménez Rejano, J J; Chillón Martínez, R; Medrano Sánchez, E M; Rebollo Roldán, J

    2013-06-01

    'Hexsel, dal'Forno and Hexsel Cellulite Severity Scale' (CSS) was developed to evaluate cellulite with an objective and easy to apply tool. Objective  Study CSS intra- and inter-observer reliability in a Spanish female population by evaluating patients' cellulite through photographs of their overall gluteofemoral zone as opposed to its creators who distinguished between buttocks and thigh. Cellulite Severity Scale was applied to 27 women, evaluating gluteofemoral cellulite, differentiating between left and right. Evaluations were made by three expert examiners each at three times with a 1-week separation. Variables were the five CSS dimensions (number of evident depressions; depth of depressions; morphological appearance of skin surface alterations; grade of laxity, flaccidity, or sagging skin; and the Nürnberger and Müller classification scale), and the overall CSS score. Cronbach's alpha, intra-class correlation and item total correlation were analysed. Cronbach's alpha values were 0.951 (right) and 0.944 (left). In the intra-observer reliability analysis, intra-class correlation coefficient ranged from 0.993 to 0.999 (P Cellulite Severity Scale has excellent reliability and internal consistency when used to evaluate cellulite on the buttocks and back of the thighs considered together. Nevertheless, the dimension grade of laxity, flaccidity or sagging skin does not contribute positively to the final consistency of the scale. This dimension needs to be analysed in greater depth in future studies. © 2012 The Authors. Journal of the European Academy of Dermatology and Venereology © 2012 European Academy of Dermatology and Venereology.

  14. Intra- and postoperative parathyroid hormone-kinetics do not advocate for autotransplantation of discolored parathyroid glands during thyroidectomy.

    Science.gov (United States)

    Promberger, Regina; Ott, Johannes; Kober, Friedrich; Mikola, Barbara; Karik, Michael; Freissmuth, Michael; Hermann, Michael

    2010-12-01

    Thyroidectomy continues to pose the risk of typical complications, including postoperative hypocalcemia and permanent hypoparathyroidism. The strategic decision on how to preserve parathyroid hormone (PTH) secretion relies on assessing the viability of the parathyroid glands (PGs). The aim of this study was to assess parathyroid discoloration as an indicator for loss of parathyroid function. The prospective study included 29 patients (24 women, 5 men; age 53.2 ± 13.0 years) who underwent near-total or total thyroidectomy. An intra- and postoperative PTH and calcium monitoring was performed. The intraoperative situs of the PGs was documented by a study protocol. The patients were grouped in three categories: group A, 12 patients with four visualized and normally colored PGs; group B, 13 patients with four visualized and three or four discolored PGs; group C, 4 patients who had undergone autotransplantation of two PGs. Compared to group A, groups B and C showed sharper intraoperative PTH declines. PTH values recovered more quickly in group B than in group C. However, no significant differences in PTH kinetics were found in the general linear model for repeated measures (p = 0.132). However, a significantly higher incidence of protracted hypocalcemia-related symptoms for more than 14 postoperative days was found for group C (50.0%) than for groups A (0%) and B (0%; p = 0.011). None of the patients developed permanent hypoparathyroidism. The function of discolored PGs is only transiently impaired and recovers within a short time after surgery. Our observations do not support autotransplantation as a generally applicable first-line intervention for discolored PGs in the absence of other criteria for autotransplantation.

  15. [Three-dimensional Mass Measurement of Subsolid Pulmonary Nodules on Chest CT: Intra and Inter-observer Variability].

    Science.gov (United States)

    Liu, Huiting; Wang, Ying; Feng, Lei; Yu, Tielian

    2015-05-01

    Subsolid pulmonary nodules tend to exhibit considerably slower growth rates than solid lesions, nevertheless, higher malignancy probability. The diagnosis of indeterminate nodules largely depends on the growth evaluation during follow-up. The growth can manifested as an increase in size or the appearance and/or subsequent increase of solid components. The mass reflect the product of volume and density and can be more sensitive in growth evaluation. However, the repeatability needs a further validation. The purpose of this study is to assess the intra and inter-observer variability of mass measurement for subsolid nodules. 80 subsolid nodules in 44 patients were retrospectively enrolled. Both the volume and mass were measured by two radiologists using blind method independently. Intra-observer and inter-observer variability were analyzed and compared by Bland-Altman method intra-class correlation test and Wilcoxon test. Software achieved satisfied segmentation for 92.5% nodules. Of them, 35% underwent manual modification. The 95% limits of agreement for intra-observer variability were -11.5%-10.4% for mass and -8.4%-8.8% for volume. The 95% limits of agreement for inter-observer variability were -17.4%-19.3% for mass and -17.9%-19.4% for volume.The intra-class correlation foefficients between volume and mass measument was 0.95 and 0.93 (both Psegmentation caused the worse mass measurement repeatability in spite of the reader satisfaction. The repeatability of mass measurement has no significant difference with that of volume measurement and may act as a reliable method in the follow-up of subsolid nodules.

  16. Intra- and inter-rater reliability of movement and palpation tests in patients with neck pain: A systematic review.

    Science.gov (United States)

    Jonsson, Anders; Rasmussen-Barr, Eva

    2018-03-01

    Neck pain is common and often becomes chronic. Various clinical tests of the cervical spine are used to direct and evaluate treatment. This systematic review aimed to identify studies examining the intra- and/or interrater reliability of tests used in clinical examination of patients with neck pain. A database search up to April 2016 was conducted in PubMed, CINAHL, and AMED. The Quality Appraisal of Reliability Studies Checklist (QAREL) was used to assess risk of bias. Eleven studies were included, comprising tests of active and passive movement and pain evaluating participants with ongoing neck pain. One study was assessed with a low risk of bias, three with medium risk, while the rest were assessed with high risk of bias. The results showed differing reliabilities for the included tests ranging from poor to almost perfect. In conclusion, active movement and pain for pain or mobility overall presented acceptable to very good reliability (Kappa >0.40); while passive intervertebral tests had lower Kappa values, suggesting poor reliability. It may be a coincidence that the studies indicating very good reliability tended to be of higher quality (low to moderate risk of bias), while studies finding poor reliability tended to be of lower quality (high risk of bias). Regardless, the current recommendation from this review would suggest the clinical use of tests with acceptable reliability and avoiding the use of tests that have been shown to not be reliable. Finally, it is critical that all future reliability studies are of higher quality with low risk of bias.

  17. Recombination: the good, the bad and the variable.

    Science.gov (United States)

    Stapley, Jessica; Feulner, Philine G D; Johnston, Susan E; Santure, Anna W; Smadja, Carole M

    2017-12-19

    Recombination, the process by which DNA strands are broken and repaired, producing new combinations of alleles, occurs in nearly all multicellular organisms and has important implications for many evolutionary processes. The effects of recombination can be good , as it can facilitate adaptation, but also bad when it breaks apart beneficial combinations of alleles, and recombination is highly variable between taxa, species, individuals and across the genome. Understanding how and why recombination rate varies is a major challenge in biology. Most theoretical and empirical work has been devoted to understanding the role of recombination in the evolution of sex-comparing between sexual and asexual species or populations. How recombination rate evolves and what impact this has on evolutionary processes within sexually reproducing organisms has received much less attention. This Theme Issue focusses on how and why recombination rate varies in sexual species, and aims to coalesce knowledge of the molecular mechanisms governing recombination with our understanding of the evolutionary processes driving variation in recombination within and between species. By integrating these fields, we can identify important knowledge gaps and areas for future research, and pave the way for a more comprehensive understanding of how and why recombination rate varies. © 2017 The Authors.

  18. Creating Porcine Biomedical Models Through Recombineering

    Directory of Open Access Journals (Sweden)

    Lawrence B. Schook

    2006-03-01

    Full Text Available Recent advances in genomics provide genetic information from humans and other mammals (mouse, rat, dog and primates traditionally used as models as well as new candidates (pigs and cattle. In addition, linked enabling technologies, such as transgenesis and animal cloning, provide innovative ways to design and perform experiments to dissect complex biological systems. Exploitation of genomic information overcomes the traditional need to choose naturally occurring models. Thus, investigators can utilize emerging genomic knowledge and tools to create relevant animal models. This approach is referred to as reverse genetics. In contrast to ‘forward genetics’, in which gene(s responsible for a particular phenotype are identified by positional cloning (phenotype to genotype, the ‘reverse genetics’ approach determines the function of a gene and predicts the phenotype of a cell, tissue, or organism (genotype to phenotype. The convergence of classical and reverse genetics, along with genomics, provides a working definition of a ‘genetic model’ organism (3. The recent construction of phenotypic maps defining quantitative trait loci (QTL in various domesticated species provides insights into how allelic variations contribute to phenotypic diversity. Targeted chromosomal regions are characterized by the construction of bacterial artificial chromosome (BAC contigs to isolate and characterize genes contributing towards phenotypic variation. Recombineering provides a powerful methodology to harvest genetic information responsible for phenotype. Linking recombineering with gene-targeted homologous recombination, coupled with nuclear transfer (NT technology can provide ‘clones’ of genetically modified animals.

  19. Recombinational DNA repair and human disease

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Larry H.; Schild, David

    2002-11-30

    We review the genes and proteins related to the homologous recombinational repair (HRR) pathway that are implicated in cancer through either genetic disorders that predispose to cancer through chromosome instability or the occurrence of somatic mutations that contribute to carcinogenesis. Ataxia telangiectasia (AT), Nijmegen breakage syndrome (NBS), and an ataxia-like disorder (ATLD), are chromosome instability disorders that are defective in the ataxia telangiectasia mutated (ATM), NBS, and Mre11 genes, respectively. These genes are critical in maintaining cellular resistance to ionizing radiation (IR), which kills largely by the production of double-strand breaks (DSBs). Bloom syndrome involves a defect in the BLM helicase, which seems to play a role in restarting DNA replication forks that are blocked at lesions, thereby promoting chromosome stability. The Werner syndrome gene (WRN) helicase, another member of the RecQ family like BLM, has very recently been found to help mediate homologous recombination. Fanconi anemia (FA) is a genetically complex chromosomal instability disorder involving seven or more genes, one of which is BRCA2. FA may be at least partially caused by the aberrant production of reactive oxidative species. The breast cancer-associated BRCA1 and BRCA2 proteins are strongly implicated in HRR; BRCA2 associates with Rad51 and appears to regulate its activity. We discuss in detail the phenotypes of the various mutant cell lines and the signaling pathways mediated by the ATM kinase. ATM's phosphorylation targets can be grouped into oxidative stress-mediated transcriptional changes, cell cycle checkpoints, and recombinational repair. We present the DNA damage response pathways by using the DSB as the prototype lesion, whose incorrect repair can initiate and augment karyotypic abnormalities.

  20. The identification of two Trypanosoma cruzi I genotypes from domestic and sylvatic transmission cycles in Colombia based on a single polymerase chain reaction amplification of the spliced-leader intergenic region

    Directory of Open Access Journals (Sweden)

    Lina Marcela Villa

    2013-11-01

    Full Text Available A single polymerase chain reaction (PCR reaction targeting the spliced-leader intergenic region of Trypanosoma cruzi I was standardised by amplifying a 231 bp fragment in domestic (TcIDOM strains or clones and 450 and 550 bp fragments in sylvatic strains or clones. This reaction was validated using 44 blind coded samples and 184 non-coded T. cruzi I clones isolated from sylvatic triatomines and the correspondence between the amplified fragments and their domestic or sylvatic origin was determined. Six of the nine strains isolated from acute cases suspected of oral infection had the sylvatic T. cruzi I profile. These results confirmed that the sylvatic T. cruzi I genotype is linked to cases of oral Chagas disease in Colombia. We therefore propose the use of this novel PCR reaction in strains or clones previously characterised as T. cruzi I to distinguish TcIDOMfrom sylvatic genotypes in studies of transmission dynamics, including the verification of population selection within hosts or detection of the frequency of mixed infections by both T. cruzi I genotypes in Colombia.

  1. A recombinant wheat serpin with inhibitory activity

    DEFF Research Database (Denmark)

    Rasmussen, Søren K; Dahl, Søren Weis; Nørgård, Anette

    1996-01-01

    , equipped with a histidine affinity tag at the N-terminus and expressed in Escherichia coli BL(21) DE3 pLysS. Recombinant WSZ1 from the soluble fraction was partially purified on Ni-NTA agarose and MonoQ columns and shown to form SDS-stable complexes with sc-chymotrypsin. Southern blots and amino acid...... sequencing indicated that only few serpins are encoded by wheat, but at least three distinct genes are expressed in the grain. Cleavage experiments on a chymotrypsin column suggested a Gln-Gln reactive site bond not previously observed in inhibitory serpins....

  2. Dissociative recombination of molecular ions H2+

    International Nuclear Information System (INIS)

    Abarenov, A.V.; Marchenko, V.S.

    1989-01-01

    The total cross sections of dissociation and dissociative recombination of slow electrons and molecular ions H 2 + have been calculated in terms of the quasiclassical and dipole approximations. In the calculations allowance was made for the quantum nature of vibrational motion of heavy particles and presence of autoionization of divergence states of the H 2 (Σ u , nl) molecules. It is shown that the H 2 + ion dissociation cross sections are dominant in increase of the electron energy in the ε >or approx. 2-3 eV region for H 2 + (v) ion distribution over the vibrational levels characteristic for the beam experiments. 15 refs.; 5 figs

  3. Population inversion in a stationary recombining plasma

    International Nuclear Information System (INIS)

    Otsuka, M.

    1980-01-01

    Population inversion, which occurs in a recombining plasma when a stationary He plasma is brought into contact with a neutral gas, is examined. With hydrogen as a contact gas, noticeable inversion between low-lying levels of H as been found. The overpopulation density is of the order of 10 8 cm -3 , which is much higher then that (approx. =10 5 cm -3 ) obtained previously with He as a contact gas. Relations between these experimental results and the conditions for population inversion are discussed with the CR model

  4. An introduction to recombination and linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mcpeek, M.S. [Univ. of Chicago, IL (United States)

    1996-12-31

    With a garden as his laboratory, Mendel was able to discern basic probabilistic laws of heredity. Although it first appeared as a baffling exception to one of Mendel`s principles, the phenomenon of variable linkage between characters was soon recognized to be a powerful tool in the process of chromosome mapping and location of genes of interest. In this introduction, we first describe Mendel`s work and the subsequent discovery of linkage. Next we describe the apparent cause of variable linkage, namely recombination, and we introduce linkage analysis. 33 refs., 1 fig., 2 tabs.

  5. Nanobodies and recombinant binders in cell biology

    Science.gov (United States)

    Helma, Jonas; Cardoso, M. Cristina; Muyldermans, Serge

    2015-01-01

    Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes. PMID:26056137

  6. Hydrogen recombiner catalyst test supporting data

    Energy Technology Data Exchange (ETDEWEB)

    Britton, M.D.

    1995-01-19

    This is a data package supporting the Hydrogen Recombiner Catalyst Performance and Carbon Monoxide Sorption Capacity Test Report, WHC-SD-WM-TRP-211, Rev 0. This report contains 10 appendices which consist of the following: Mass spectrometer analysis reports: HRC samples 93-001 through 93-157; Gas spectrometry analysis reports: HRC samples 93-141 through 93-658; Mass spectrometer procedure PNL-MA-299 ALO-284; Alternate analytical method for ammonia and water vapor; Sample log sheets; Job Safety analysis; Certificate of mixture analysis for feed gases; Flow controller calibration check; Westinghouse Standards Laboratory report on Bois flow calibrator; and Sorption capacity test data, tables, and graphs.

  7. Recombinant DNA. Rifkin's regulatory revivalism runs riot.

    Science.gov (United States)

    David, P

    Jeremy Rifkin, activist opponent of genetic engineering, has adopted tactics of litigation, persuasion, and confrontation in his campaign to halt genetic experimentation. The Recombinant DNA Advisory Committee of the National Institutes of Health has often been the target of his criticism, most recently for its failure to prepare an environmental risk assessment for some DNA tests it approved. Rifkin has won support for his position from religious organizations in the United States, and in June 1983 persuaded an ecumenical group of religious leaders to ask Congress to ban genetic experiments that would affect the human germ line.

  8. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets.

    Directory of Open Access Journals (Sweden)

    Carol M Anderson

    Full Text Available In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-crossovers. The mechanisms underlying meiotic recombination remain elusive, largely because of the difficulty of analyzing large numbers of recombination events by traditional genetic methods. These traditional methods are increasingly being superseded by high-throughput techniques capable of surveying meiotic recombination on a genome-wide basis. Next-generation sequencing or microarray hybridization is used to genotype thousands of polymorphic markers in the progeny of hybrid yeast strains. New computational tools are needed to perform this genotyping and to find and analyze recombination events. We have developed a suite of programs, ReCombine, for using short sequence reads from next-generation sequencing experiments to genotype yeast meiotic progeny. Upon genotyping, the program CrossOver, a component of ReCombine, then detects recombination products and classifies them into categories based on the features found at each location and their distribution among the various chromatids. CrossOver is also capable of analyzing segregation data from microarray experiments or other sources. This package of programs is designed to allow even researchers without computational expertise to use high-throughput, whole-genome methods to study the molecular mechanisms of meiotic recombination.

  9. Growing Region Segmentation Software (GRES) for quantitative magnetic resonance imaging of multiple sclerosis: intra- and inter-observer agreement variability: a comparison with manual contouring method

    International Nuclear Information System (INIS)

    Parodi, Roberto C.; Sardanelli, Francesco; Renzetti, Paolo; Rosso, Elisabetta; Losacco, Caterina; Ferrari, Alessandra; Levrero, Fabrizio; Pilot, Alberto; Inglese, Matilde; Mancardi, Giovanni L.

    2002-01-01

    Lesion area measurement in multiple sclerosis (MS) is one of the key points in evaluating the natural history and in monitoring the efficacy of treatments. This study was performed to check the intra- and inter-observer agreement variability of a locally developed Growing Region Segmentation Software (GRES), comparing them to those obtained using manual contouring (MC). From routine 1.5-T MRI study of clinically definite multiple sclerosis patients, 36 lesions seen on proton-density-weighted images (PDWI) and 36 enhancing lesion on Gd-DTPA-BMA-enhanced T1-weighted images (Gd-T1WI) were randomly chosen and were evaluated by three observers. The mean range of lesion size was 9.9-536.0 mm 2 on PDWI and 3.6-57.2 mm 2 on Gd-T1WI. The median intra- and inter-observer agreement were, respectively, 97.1 and 90.0% using GRES on PDWI, 81.0 and 70.0% using MC on PDWI, 88.8 and 80.0% using GRES on Gd-T1WI, and 85.8 and 70.0% using MC on Gd-T1WI. The intra- and inter-observer agreements were significantly greater for GRES compared with MC (P<0.0001 and P=0.0023, respectively) for PDWI, while no difference was found between GRES an MC for Gd-T1WI. The intra-observer variability for GRES was significantly lower on both PDWI (P=0.0001) and Gd-T1WI (P=0.0067), whereas for MC the same result was found only for PDWI (P=0.0147). These data indicate that GRES reduces both the intra- and the inter-observer variability in assessing the area of MS lesions on PDWI and may prove useful in multicentre studies. (orig.)

  10. New Techniques for Cartilage Magnetic Resonance Imaging Relaxation Time Analysis: Texture Analysis of Flattened Cartilage and Localized Intra- and Inter-subject Comparisons

    OpenAIRE

    Carballido-Gamio, Julio; Link, Thomas M.; Majumdar, Sharmila

    2008-01-01

    MR relaxation time measurements of knee cartilage have shown potential to characterize knee osteoarthritis (OA). In this work, techniques that allow localized intra- and inter-subject comparisons of cartilage relaxation times, as well as cartilage flattening for texture analysis parallel and perpendicular to the natural cartilage layers, are presented. The localized comparisons are based on the registration of bone structures and the assignment of relaxation time feature vectors to each point...

  11. Sites involved in intra- and interdomain allostery associated with the activation of factor VIIa pinpointed by hydrogen-deuterium exchange and electron transfer dissociation mass spectrometry

    DEFF Research Database (Denmark)

    Song, Hongjian; Olsen, Ole H; Persson, Egon

    2014-01-01

    Factor VIIa (FVIIa) is a trypsin-like protease which plays an important role in initiating blood coagulation. Very limited structural information is available for the free, inactive form of FVIIa that circulates in the blood prior to vascular injury and the molecular details of its activity...... signal extends to the EGF1 domain in the light chain of FVIIa, underscoring a remarkable intra- and interdomain allosteric regulation of this trypsin-like protease....

  12. Metal binding proteins, recombinant host cells and methods

    Science.gov (United States)

    Summers, Anne O.; Caguiat, Jonathan J.

    2004-06-15

    The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

  13. Expression and purification of recombinant hemoglobin in Escherichia coli

    DEFF Research Database (Denmark)

    Natarajan, Chandrasekhar; Jiang, Xiaoben; Fago, Angela

    2011-01-01

    BACKGROUND: Recombinant DNA technologies have played a pivotal role in the elucidation of structure-function relationships in hemoglobin (Hb) and other globin proteins. Here we describe the development of a plasmid expression system to synthesize recombinant Hbs in Escherichia coli, and we describe...... a protocol for expressing Hbs with low intrinsic solubilities. Since the alpha- and beta-chain Hbs of different species span a broad range of solubilities, experimental protocols that have been optimized for expressing recombinant human HbA may often prove unsuitable for the recombinant expression......-translational modifications. CONCLUSION/SIGNIFICANCE: Our protocol should prove useful for the experimental study of recombinant Hbs in many non-human animals. One of the chief advantages of our protocol is that we can express soluble recombinant Hb without co-expressing molecular chaperones, and without the need...

  14. Test tube systems with cutting/recombination operations

    Energy Technology Data Exchange (ETDEWEB)

    Freund, R. [Technische Universitaet Wien (Austria); Csuhaj-Varju, E. [Computer and Automation Institute, Budapest (Hungary); Wachtler, F. [Universitaet Wien (Austria)

    1996-12-31

    We introduce test tube systems based on operations that are closely related to the splicing operations, i.e. we consider the operations of cutting a string at a specific site into two pieces with marking them at the cut ends and of recombining two strings with specifically marked endings. Whereas in the splicing of two strings these strings are cut at specific sites and the cut pieces are recombined immediately in a crosswise way, in CR(cutting/recombination)-schemes cutting can happen independently from recombining the cut pieces. Test tube systems based on these operations of cutting and recombination turn out to have maximal generative power even if only very restricted types of input filters for the test tubes are used for the redistribution of the contents of the test tubes after a period of cuttings and recombinations in the test tubes. 10 refs.

  15. Two is better than one: The effects of strategic cooperation on intra- and inter-brain connectivity by fNIRS.

    Directory of Open Access Journals (Sweden)

    Michela Balconi

    Full Text Available Inter-brain synchronization during joint actions is a core question in social neuroscience, and the differential contribution of intra- and inter-brain functional connectivity has yet to be clarified along with the role of psychological variables such as perceived self-efficacy. The cognitive performance and the neural activation underlying the execution of joint actions were recorded by functional Near-Infrared imaging during a synchronicity game. An 8-channel array of optodes was positioned over the frontal and prefrontal regions. During the task, the dyads received reinforcing feedback that was experimentally manipulated to induce adoption of common strategies. Intra- and inter-brain connectivity indices were computed along with an inter-brain/intra-brain connectivity index (ConIndex. Finally, correlation analyses were run to assess the relationship between behavioral and physiological levels. The results showed that the external feedback could modulate participant responses in both behavioral and neural components. After the reinforcing manipulation, there were faster response times and increased inter-brain connectivity, and ConIndex emerged primarily over the dorsolateral prefrontal cortex. Additionally, the presence of significant correlations between response times and inter-brain connectivity revealed that only the "two-players connection" may guarantee an efficient performance. The present study provides a significant contribution to the identification of intra- and inter-brain functional connectivity when social reinforcement is provided.

  16. Bimanual Capacity of Children With Cerebral Palsy: Intra- and Interrater Reliability of a Revised Edition of the Bimanual Fine Motor Function Classification.

    Science.gov (United States)

    Elvrum, Ann-Kristin G; Beckung, Eva; Sæther, Rannei; Lydersen, Stian; Vik, Torstein; Himmelmann, Kate

    2017-08-01

    To develop a revised edition of the Bimanual Fine Motor Function (BFMF 2), as a classification of fine motor capacity in children with cerebral palsy (CP), and establish intra- and interrater reliability of this edition. The content of the original BFMF was discussed by an expert panel, resulting in a revised edition comprising the original description of the classification levels, but in addition including figures with specific explanatory text. Four professionals classified fine motor function of 79 children (3-17 years; 45 boys) who represented all subtypes of CP and Manual Ability Classification levels (I-V). Intra- and inter-rater reliability was assessed using overall intra-class correlation coefficient (ICC), and Cohen's quadratic weighted kappa. The overall ICC was 0.86. Cohen's weighted kappa indicated high intra-rater (к w : >0.90) and inter-rater (к w : >0.85) reliability. The revised BFMF 2 had high intra- and interrater reliability. The classification levels could be determined from short video recordings (classification of fine motor capacity both in research and in clinical practice.

  17. Replication and recombination factors contributing to recombination-dependent bypass of DNA lesions by template switch.

    Directory of Open Access Journals (Sweden)

    Fabio Vanoli

    2010-11-01

    Full Text Available Damage tolerance mechanisms mediating damage-bypass and gap-filling are crucial for genome integrity. A major damage tolerance pathway involves recombination and is referred to as template switch. Template switch intermediates were visualized by 2D gel electrophoresis in the proximity of replication forks as X-shaped structures involving sister chromatid junctions. The homologous recombination factor Rad51 is required for the formation/stabilization of these intermediates, but its mode of action remains to be investigated. By using a combination of genetic and physical approaches, we show that the homologous recombination factors Rad55 and Rad57, but not Rad59, are required for the formation of template switch intermediates. The replication-proficient but recombination-defective rfa1-t11 mutant is normal in triggering a checkpoint response following DNA damage but is impaired in X-structure formation. The Exo1 nuclease also has stimulatory roles in this process. The checkpoint kinase, Rad53, is required for X-molecule formation and phosphorylates Rad55 robustly in response to DNA damage. Although Rad55 phosphorylation is thought to activate recombinational repair under conditions of genotoxic stress, we find that Rad55 phosphomutants do not affect the efficiency of X-molecule formation. We also examined the DNA polymerase implicated in the DNA synthesis step of template switch. Deficiencies in translesion synthesis polymerases do not affect X-molecule formation, whereas DNA polymerase δ, required also for bulk DNA synthesis, plays an important role. Our data indicate that a subset of homologous recombination factors, together with DNA polymerase δ, promote the formation of template switch intermediates that are then preferentially dissolved by the action of the Sgs1 helicase in association with the Top3 topoisomerase rather than resolved by Holliday Junction nucleases. Our results allow us to propose the choreography through which different

  18. Homologous recombination-mediated cloning and manipulation of genomic DNA regions using Gateway and recombineering systems.

    Science.gov (United States)

    Rozwadowski, Kevin; Yang, Wen; Kagale, Sateesh

    2008-11-17

    Employing genomic DNA clones to characterise gene attributes has several advantages over the use of cDNA clones, including the presence of native transcription and translation regulatory sequences as well as a representation of the complete repertoire of potential splice variants encoded by the gene. However, working with genomic DNA clones has traditionally been tedious due to their large size relative to cDNA clones and the presence, absence or position of particular restriction enzyme sites that may complicate conventional in vitro cloning procedures. To enable efficient cloning and manipulation of genomic DNA fragments for the purposes of gene expression and reporter-gene studies we have combined aspects of the Gateway system and a bacteriophage-based homologous recombination (i.e. recombineering) system. To apply the method for characterising plant genes we developed novel Gateway and plant transformation vectors that are of small size and incorporate selectable markers which enable efficient identification of recombinant clones. We demonstrate that the genomic coding region of a gene can be directly cloned into a Gateway Entry vector by recombineering enabling its subsequent transfer to Gateway Expression vectors. We also demonstrate how the coding and regulatory regions of a gene can be directly cloned into a plant transformation vector by recombineering. This construct was then rapidly converted into a novel Gateway Expression vector incorporating cognate 5' and 3' regulatory regions by using recombineering to replace the intervening coding region with the Gateway Destination cassette. Such expression vectors can be applied to characterise gene regulatory regions through development of reporter-gene fusions, using the Gateway Entry clones of GUS and GFP described here, or for ectopic expression of a coding region cloned into a Gateway Entry vector. We exemplify the utility of this approach with the Arabidopsis PAP85 gene and demonstrate that the expression

  19. The estimation of recombination rates from population genetic data

    OpenAIRE

    2007-01-01

    Genetic recombination is an important process that generates new combinations of genes on which natural selection can operate. As such, an understanding of recombination in the human genome will provide insight into the evolutionary processes that have shaped our genetic history. The aim of this thesis is to use samples of population genetic data to explore the patterns of variation in the rate of recombination in the human genome. To do this I introduce a novel means of estimating recombinat...

  20. Modified Fragmentation Function from Quark Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Majumder, A.; Wang, Enke; Wang, Xin-Nian

    2005-07-26

    Within the framework of the constituent quark model, it isshown that the single hadron fragmentation function of a parton can beexpressed as a convolution of shower diquark or triquark distributionfunction and quark recombination probability, if the interference betweenamplitudes of quark recombination with different momenta is neglected.Therecombination probability is determined by the hadron's wavefunction inthe constituent quark model. The shower diquark or triquark distributionfunctions of a fragmenting jet are defined in terms of overlappingmatrices of constituent quarks and parton field operators. They aresimilar in form to dihadron or trihadron fragmentation functions in termsof parton operator and hadron states. Extending the formalism to thefield theory at finite temperature, we automatically derive contributionsto the effective single hadron fragmentation function from therecombination of shower and thermal constituent quarks. Suchcontributions involve single or diquark distribution functions which inturn can be related to diquark or triquark distribution functions via sumrules. We also derive QCD evolution equations for quark distributionfunctions that in turn determine the evolution of the effective jetfragmentation functions in a thermal medium.

  1. Sweetness characterization of recombinant human lysozyme.

    Science.gov (United States)

    Matano, Mami; Nakajima, Kana; Kashiwagi, Yutaka; Udaka, Shigezo; Maehashi, Kenji

    2015-10-01

    Lysozyme, a bacteriolytic enzyme, is widely distributed in nature and is a component of the innate immune system. It is established that chicken egg lysozyme elicits sweetness. However, the sweetness of human milk lysozyme, which is vital for combating microbial infections of the gastrointestinal tract of breast-fed infants, has not been characterized. This study aimed to assess the elicitation of sweetness using recombinant mammalian lysozymes expressed in Pichia pastoris. Recombinant human lysozyme (h-LZ) and other mammalian lysozymes of mouse, dog, cat and bovine milk elicited similar sweetness as determined using a sensory test, whereas bovine stomach lysozyme (bs-LZ) did not. Assays of cell cultures showed that h-LZ activated the human sweet taste receptor hT1R2/hT1R3, whereas bs-LZ did not. Point mutations confirmed that the sweetness of h-LZ was independent of enzyme activity and substrate-binding sites, although acidic amino acid residues of bs-LZ played a significant role in diminishing sweetness. Therefore, we conclude that elicitation of sweetness is a ubiquitous function among all lysozymes including mammalian lysozymes. These findings may provide novel insights into the biological implications of T1R2/T1R3-activation by mammalian lysozyme in the oral cavity and gastrointestinal tract. However, the function of lysozyme within species lacking the functional sweet taste receptor gene, such as cat, is currently unknown. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Simulation and Optimisation of CLIC's recombination complex

    CERN Document Server

    Costa, Raul; Barroso, Manuel

    In this thesis we present the first Placet2 recombination simulations of the drive beam recombination complex (DBRC) design for the compact linear collider (CLIC). We start by presenting a review of the CLIC project and the DBRC’s role and design within it. We then discuss some of the core principles of beam dynamics and how tracking codes like Placet2 implement them. We follow that by presenting the design issues raised by our simulations and our proposed strategy to address them, key among which is a previously unknown parabolic dependency of the longitudinal position to the momentum (T 566 ), which threat- ens the efficiency of the power extraction structures. Through iterative opti- misation of the design, we eliminated this aberration both in the delay loop and in combiner ring 1. We also found the beam’s horizontal emittance to be significantly over the design budget (150 μm) and attempted to meet that budget, reaching 157 μm. In order to obtain this emittance value, an update to the combiner ring...

  3. The landscape of recombination in African Americans

    Science.gov (United States)

    Hinch, Anjali G.; Tandon, Arti; Patterson, Nick; Song, Yunli; Rohland, Nadin; Palmer, Cameron D.; Chen, Gary K.; Wang, Kai; Buxbaum, Sarah G.; Akylbekova, Meggie; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Bock, Cathryn H.; Boerwinkle, Eric; Cai, Qiuyin; Caporaso, Neil; Casey, Graham; Cupples, L. Adrienne; Deming, Sandra L.; Diver, W. Ryan; Divers, Jasmin; Fornage, Myriam; Gillanders, Elizabeth M.; Glessner, Joseph; Harris, Curtis C.; Hu, Jennifer J.; Ingles, Sue A.; Isaacs, Williams; John, Esther M.; Kao, W. H. Linda; Keating, Brendan; Kittles, Rick A.; Kolonel, Laurence N.; Larkin, Emma; Le Marchand, Loic; McNeill, Lorna H.; Millikan, Robert C.; Murphy, Adam; Musani, Solomon; Neslund-Dudas, Christine; Nyante, Sarah; Papanicolaou, George J.; Press, Michael F.; Psaty, Bruce M.; Reiner, Alex P.; Rich, Stephen S.; Rodriguez-Gil, Jorge L.; Rotter, Jerome I.; Rybicki, Benjamin A.; Schwartz, Ann G.; Signorello, Lisa B.; Spitz, Margaret; Strom, Sara S.; Thun, Michael J.; Tucker, Margaret A.; Wang, Zhaoming; Wiencke, John K.; Witte, John S.; Wrensch, Margaret; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A.; Zheng, Wei; Ziegler, Regina G.; Zhu, Xiaofeng; Redline, Susan; Hirschhorn, Joel N.; Henderson, Brian E.; Taylor, Herman A.; Price, Alkes L.; Hakonarson, Hakon; Chanock, Stephen J.; Haiman, Christopher A.; Wilson, James G.; Reich, David; Myers, Simon R.

    2011-01-01

    Recombination, together with mutation, is the ultimate source of genetic variation in populations. We leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing-over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P<10−245). We identify a 17 base pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of African-enriched alleles of PRDM9. PMID:21775986

  4. Recombinant protein scaffolds for tissue engineering

    International Nuclear Information System (INIS)

    Werkmeister, Jerome A; Ramshaw, John A M

    2012-01-01

    New biological materials for tissue engineering are now being developed using common genetic engineering capabilities to clone and express a variety of genetic elements that allow cost-effective purification and scaffold fabrication from these recombinant proteins, peptides or from chimeric combinations of these. The field is limitless as long as the gene sequences are known. The utility is dependent on the ease, product yield and adaptability of these protein products to the biomedical field. The development of recombinant proteins as scaffolds, while still an emerging technology with respect to commercial products, is scientifically superior to current use of natural materials or synthetic polymer scaffolds, in terms of designing specific structures with desired degrees of biological complexities and motifs. In the field of tissue engineering, next generation scaffolds will be the key to directing appropriate tissue regeneration. The initial period of biodegradable synthetic scaffolds that provided shape and mechanical integrity, but no biological information, is phasing out. The era of protein scaffolds offers distinct advantages, particularly with the combination of powerful tools of molecular biology. These include, for example, the production of human proteins of uniform quality that are free of infectious agents and the ability to make suitable quantities of proteins that are found in low quantity or are hard to isolate from tissue. For the particular needs of tissue engineering scaffolds, fibrous proteins like collagens, elastin, silks and combinations of these offer further advantages of natural well-defined structural scaffolds as well as endless possibilities of controlling functionality by genetic manipulation. (topical review)

  5. The intra- and inter-rater reliability of five clinical muscle performance tests in patients with and without neck pain

    Science.gov (United States)

    2013-01-01

    = 0.19-0.25). Conclusions Intra- and inter-rater reliability ranged from moderate to almost perfect agreement with the exception of a new test (neck extensor test), which ranged from slight to moderate agreement. The significant variability observed suggests that tests like the neck extensor test and the neck flexor muscle endurance test performed in a 45°-upright position are too unstable to be used when evaluating neck muscle performance. PMID:24299621

  6. Clinical effect of laparoscopic reoperation combined with choledochoscope in treatment of intra- and extrahepatic bile duct stones: analysis of 35 cases

    Directory of Open Access Journals (Sweden)

    WU Liming

    2013-07-01

    Full Text Available ObjectiveTo investigate the feasibility and safety of laparoscopic reoperation combined with choledochoscope in the treatment of intra- and extrahepatic bile duct stones. MethodsThe 35 patients with intra- and extrahepatic bile duct stones who underwent laparoscopic bile duct reoperation from January 2008 to May 2012 were selected as a laparoscopic treatment group; 50 patients with recurrent intra- and extrahepatic bile duct stones who underwent open surgery in the same period were selected as an open surgery group. The t-test was used to compare the two groups in terms of off-bed activity early after operation, recovery of intestinal function, and length of hospital stay; the chi-square test was used to compare the incision infection rate between the two groups. ResultsAmong the 35 cases of intra- and extrahepatic bile duct stones, 32 completed laparoscopic surgery, 2 had the procedure converted to open surgery due to severe adhesion, and 1 had the procedure converted to open surgery due to subcutaneous emphysema. In the laparoscopic treatment group, the mean operative time of laparoscopic bile duct reoperation was 148 min (range, 105-200 min; there were no bleeding and bile leak in the perioperative period. All patients underwent T-tube drainage; postoperative peritoneal drainage was performed for 2-5 d; the mean length of hospital stay after operation was 5-8 d. No case of incision infection occurred in the laparoscopic treatment group. The laparoscopic treatment group had a significantly better outcome than the open surgery group in terms of time to off-bed activity early after operation, time to recovery of intestinal function, length of hospital stay after operation, and incision infection rate (P<0.05. In the laparoscopic treatment group, 3 cases had retained bile duct stones, and the stones were taken out through the sinus tract using a fiber choledochoscope at 2 months after operation. All cases were followed up for 6-24 months after

  7. Evidence of recombination in intrapatient populations of hepatitis C virus.

    Science.gov (United States)

    Sentandreu, Vicente; Jiménez-Hernández, Nuria; Torres-Puente, Manuela; Bracho, María Alma; Valero, Ana; Gosalbes, María José; Ortega, Enrique; Moya, Andrés; González-Candelas, Fernando

    2008-09-18

    Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient. Given the important implications of recombination for RNA virus evolution, our aim in this study has been to assess the existence and eventually the frequency of intragenic recombination on HCV. For this, we retrospectively have analyzed two regions of the HCV genome (NS5A and E1-E2) in samples from two different groups: (i) patients infected only with HCV (either treated with interferon plus ribavirin or treatment naïve), and (ii) HCV-HIV co-infected patients (with and without treatment against HIV). The complete data set comprised 17712 sequences from 136 serum samples derived from 111 patients. Recombination analyses were performed using 6 different methods implemented in the program RDP3. Recombination events were considered when detected by at least 3 of the 6 methods used and were identified in 10.7% of the amplified samples, distributed throughout all the groups described and the two genomic regions studied. The resulting recombination events were further verified by detailed phylogenetic analyses. The complete experimental procedure was applied to an artificial mixture of relatively closely viral populations and the ensuing analyses failed to reveal artifactual recombination. From these results we conclude that recombination should be considered as a potentially

  8. Omenn Syndrome and DNA recombination defects.

    Science.gov (United States)

    Yachie, Akihiro

    2017-01-01

    Mutations in the RAG1/RAG2 genes are associated with a broad spectrum of clinical phenotypes, ranging from severe combined immunodeficiency to various autoimmune diseases. The diversity of the clinical symptoms is determined not only by the residual RAG recombinase enzyme activity as determined by the mutations, but also by multiple environmental factors and, in rare cases, by second site mutations within the RAG1/RAG2 genes. The residual recombinase activity is responsible for the oligoclonal expansion of autoreactive T cells. Omenn syndrome is the result of intense Th2 type inflammation involving the skin and multiple other organs triggered by these T cells. In this review, the molecular pathology of diseases caused by RAG1/RAG2 mutations, in particular Omenn syndrome, will be discussed. Furthermore, abnormalities in other molecules involved in V(D)J recombination will be discussed in relation to Omenn-like syndrome.

  9. Classification of Recombinant Biologics in the EU

    DEFF Research Database (Denmark)

    Klein, Kevin; De Bruin, Marie L; Broekmans, Andre W

    2015-01-01

    BACKGROUND AND OBJECTIVE: Biological medicinal products (biologics) are subject to specific pharmacovigilance requirements to ensure that biologics are identifiable by brand name and batch number in adverse drug reaction (ADR) reports. Since Member States collect ADR data at the national level...... before the data is aggregated at the European Union (EU) level, it is important that an unambiguous understanding of which medicinal products belong to the biological product category exists. This study aimed to identify the level of consistency between Member States regarding the classification...... of biologics by national authorities responsible for ADR reporting. METHODS: A sample list of recombinant biologics from the European Medicines Agency database of European Public Assessment Reports was created to analyze five Member States (Belgium, the Netherlands, Spain, Sweden, and the UK) according...

  10. Scavenging and recombination kinetics in radiation chemistry.

    Science.gov (United States)

    Al-Samra, Eyad H; Green, Nicholas J B

    2017-08-02

    This work describes stochastic models developed to study the competition between radical scavenging and recombination for simple model systems typical of radiation chemistry, where the reactive particles are tightly clustered and reactions are assumed fully diffusion limited. Three models are developed: a Monte Carlo random flights model with a periodic boundary condition for scavengers, Monte Carlo simulations in which the scavenging rate is calculated from the Smoluchowski theory for diffusion-limited reactions and a modification of the independent reaction times method where the scavengers close to the spur are explicitly included and the scavengers further away are treated as a continuum. The results indicate that the Smoluchowski theory makes a systematic overestimate of the scavenging rate when such competition is present. A correction for the Smoluchowski rate constant is suggested, an analytical justification is presented and it is tested against the simulations, and shown to be a substantial improvement.

  11. Recombinant expression of backbone-cyclized polypeptides.

    Science.gov (United States)

    Borra, Radhika; Camarero, Julio A

    2013-09-01

    Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities. Copyright © 2013 Wiley Periodicals, Inc.

  12. Soluble variants of human recombinant glutaminyl cyclase.

    Directory of Open Access Journals (Sweden)

    Cristiana Castaldo

    Full Text Available Recombinant human Glutaminyl Cyclase expressed in E. coli is produced as inclusion bodies. Lack of glycosylation is the main origin of its accumulation in insoluble aggregates. Mutation of single isolated hydrophobic amino acids into negative amino acids was not able to circumvent inclusion bodies formation. On the contrary, substitution with carboxyl-terminal residues of two or three aromatic residues belonging to extended hydrophobic patches on the protein surface provided soluble but still active forms of the protein. These mutants could be expressed in isotopically enriched forms for NMR studies and the maximal attainable concentration was sufficient for the acquisition of (1H-(15N HSQC spectra that represent the starting point for future drug development projects targeting Alzheimer's disease.

  13. MSD Recombination Method in Statistical Machine Translation

    Science.gov (United States)

    Gros, Jerneja Žganec

    2008-11-01

    Freely available tools and language resources were used to build the VoiceTRAN statistical machine translation (SMT) system. Various configuration variations of the system are presented and evaluated. The VoiceTRAN SMT system outperformed the baseline conventional rule-based MT system in all English-Slovenian in-domain test setups. To further increase the generalization capability of the translation model for lower-coverage out-of-domain test sentences, an "MSD-recombination" approach was proposed. This approach not only allows a better exploitation of conventional translation models, but also performs well in the more demanding translation direction; that is, into a highly inflectional language. Using this approach in the out-of-domain setup of the English-Slovenian JRC-ACQUIS task, we have achieved significant improvements in translation quality.

  14. Guiding recombinant antivenom development by omics technologies

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard

    2017-01-01

    , endogenous animal proteins with toxin-neutralizing capabilities, and recombinant monoclonal antibodies. Harnessing either of these approaches, antivenom development may benefit from an in-depth understanding of venom compositions and the medical importance of individual venom toxins. Focus is thus also...... directed towards the different omics technologies (particularly venomics, antivenomics, and toxicovenomics) that are being used to uncover novel animal toxins, shed light on venom complexity, and provide directions for how to determine the medical relevance of individual toxins within whole venoms. Finally......In this review, the different approaches that have been employed with the aim of developing novel antivenoms against animal envenomings are presented and discussed. Reported efforts have focused on the use of innovative immunization strategies, small molecule inhibitors against enzymatic toxins...

  15. Recombinant Brucella abortus gene expressing immunogenic protein

    Energy Technology Data Exchange (ETDEWEB)

    Mayfield, J.E.; Tabatabai, L.B.

    1991-06-11

    This patent describes a synthetic recombinant DNA molecule containing a DNA sequence. It comprises a gene of Brucella abortus encoding an immunogenic protein having a molecular weight of approximately 31,000 daltons as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis under denaturing conditions, the protein having an isoelectric point around 4.9, and containing a twenty-five amino acid sequence from its amino terminal end consisting of Gln-Ala-Pro-Thr-Phe-Phe-Arg-Ile-Gly-Thr-Gly-Gly-Thr-Ala-Gly-Thr-Tyr-Tyr-Pro-Ile-Gly-Gly-Leu-Ile-Ala, wherein Gln, Ala, Pro, Thr, Phe, Arg, Ile, Gly, Tyr, and Leu, respectively, represent glutamine, alanine, proline, threonine, phenylalanine, arginine, isolecuine, glycine, tyrosine, and leucine.

  16. Initiation of Meiotic Recombination in Mammals

    Directory of Open Access Journals (Sweden)

    Rajeev Kumar

    2010-12-01

    Full Text Available Meiotic recombination is initiated by the induction of programmed DNA double strand breaks (DSBs. DSB repair promotes homologous interactions and pairing and leads to the formation of crossovers (COs, which are required for the proper reductional segregation at the first meiotic division. In mammals, several hundred DSBs are generated at the beginning of meiotic prophase by the catalytic activity of SPO11. Currently it is not well understood how the frequency and timing of DSB formation and their localization are regulated. Several approaches in humans and mice have provided an extensive description of the localization of initiation events based on CO mapping, leading to the identification and characterization of preferred sites (hotspots of initiation. This review presents the current knowledge about the proteins known to be involved in this process, the sites where initiation takes place, and the factors that control hotspot localization.

  17. Functional, Responsive Materials Assembled from Recombinant Oleosin

    Science.gov (United States)

    Hammer, Daniel

    Biological cells are surrounded by a plasma membrane made primarily of phospholipids that form a bilayer. This membrane is permselective and compartmentalizes the cell. A simple form of artificial cell is the vesicle, in which a phospholipid bilayer membrane surrounds an aqueous solution. However, there is no a priori reason why a membrane needs to be made of phospholipids. It could be made of any surfactant that forms a bilayer. We have assembled membranes and other structures from the recombinant plant protein oleosin. The ability to assemble from a recombinant protein means that every molecule is identical, we have complete control over the sequence, and hence can build in designer functionality with high fidelity, including adhesion and enzymatic activity. Such incorporation is trivial using the tools of molecular biology. We find that while many variants of oleosin make membranes, others make micelles and sheets. We show how the type of supramolecular structure can be altered by the conditions of solvent, such as ionic strength, and the architecture of the surfactant itself. We show that protease cleavable domains can be incorporated within oleosin, and be engineered to protect other functional domains such as adhesive motifs, to make responsive materials whose activity and shape depend on the action of proteases. We will also present the idea of making ``Franken''-oleosins, where large domains of native oleosin are replaced with domains from other functional proteins, to make hybrids conferred by the donor protein. Thus, we can view oleosin as a template upon which a vast array of designer functionalities can be imparted..

  18. Dynamic protein assemblies in homologous recombination with single DNA molecules

    NARCIS (Netherlands)

    van der Heijden, A.H.

    2007-01-01

    What happens when your DNA breaks? This thesis describes experimental work on the single-molecule level focusing on the interaction between DNA and DNA-repair proteins, in particular bacterial RecA and human Rad51, involved in homologous recombination. Homologous recombination and its central event

  19. Improved means and methods for expressing recombinant proteins

    NARCIS (Netherlands)

    Poolman, Berend; Martinez Linares, Daniel; Gul, Nadia

    2014-01-01

    The invention relates to the field of genetic engineering and the production of recombinant proteins in microbial host cells. Provided is a method for enhanced expression of a recombinant protein of interest in a microbial host cell, comprising providing a microbial host cell wherein the function of

  20. The pharmacology of recombinant hirudin, a new anticoagulant

    African Journals Online (AJOL)

    1990-09-01

    Sep 1, 1990 ... The pharmacology of recombinant hirudin, a new anticoagulant. B. H. MEYER, H. G. LUUS, F. O. MULLER, P. N. BADENHORST, H.-J. ROTHIG. Summary. A new anticoagulant, recombinant hirudin, was given to hea"hy volunteers (5 per test dose) in single .intravenous doses of 0,01, 0,02, 0,04, 0,07 and 0 ...

  1. Dielectronic recombination measurements using the Electron Beam Ion Trap

    International Nuclear Information System (INIS)

    Knapp, D.A.

    1991-01-01

    We have used the Electron Beam Ion Trap at LLNL to study dielectronic recombination in highly charged ions. Our technique is unique because we observe the x-rays from dielectronic recombination at the same time we see x-rays from all other electron-ion interactions. We have recently taken high-resolution, state-selective data that resolves individual resonances

  2. Activity of recombinant factor VIIa under different conditions in vitro

    DEFF Research Database (Denmark)

    Bladbjerg, Else-Marie; Jespersen, Jørgen

    2008-01-01

    Recombinant activated factor VII (NovoSeven; Novo Nordisk A/S, Måløv, Denmark) is an effective drug for treatment of bleeding in patients with haemophilia A or B and inhibitors. Little is known about physiological conditions influencing the efficacy of recombinant activated factor VII. We...

  3. Collision and recombination driven instabilities in variable charged ...

    Indian Academy of Sciences (India)

    neglected in comparison to the effect due to the recombination for estimating the dust-acoustic instability; later the other report shows that the recombination effect is negligible in the presence of dust-neutral collisions. In line of this present situation our investigation revealed that the recom- bination is more important than ...

  4. Recombinant HT.sub.m4 gene, protein and assays

    Science.gov (United States)

    Lim, Bing; Adra, Chaker N.; Lelias, Jean-Michel

    1996-01-01

    The invention relates to a recombinant DNA molecule which encodes a HT.sub.m4 protein, a transformed host cell which has been stably transfected with a DNA molecule which encodes a HT.sub.m4 protein and a recombinant HT.sub.m4 protein. The invention also relates to a method for detecting the presence of a hereditary atopy.

  5. Mitochondrial recombination increases with age in Podospora anserina

    NARCIS (Netherlands)

    van Diepeningen, Anne D; Goedbloed, Daniël J; Slakhorst, S Marijke; Koopmanschap, A Bertha; Maas, Marc F P M; Hoekstra, Rolf F; Debets, Alfons J M

    With uniparental inheritance of mitochondria, there seems little reason for homologous recombination in mitochondria, but the machinery for mitochondrial recombination is quite well-conserved in many eukaryote species. In fungi and yeasts heteroplasmons may be formed when strains fuse and transfer

  6. Effect of dielectronic recombination on the charge-state distribution ...

    Indian Academy of Sciences (India)

    either neglecting dielectronic recombination [6] or later is taken to be proportional to radiative recombination [7]. Since the theoretically calculated population density of an ionic charge state depends on the rate coefficients used, it is interesting to investigate their effect on the charge-state distribution and spectral line ...

  7. Measurements of EEDF in recombination dominated afterglow plasma

    Science.gov (United States)

    Plasil, R.; Korolov, I.; Kotrik, T.; Varju, J.; Dohnal, P.; Donko, Z.; Bano, G.; Glosik, J.

    2009-11-01

    Electron energy distribution functions (EEDF) have been measured in decaying plasma in Flowing Afterglow Langmuir Probe (FALP) experiment. The measurements have been carried out in diffusion and recombination governed plasmas used for studies of recombination of KrD+ and H3+ ions.

  8. Measurements of EEDF in recombination dominated afterglow plasma

    Energy Technology Data Exchange (ETDEWEB)

    Plasil, R; Korolov, I; Kotrik, T; Varju, J; Dohnal, P; Glosik, J [Charles University, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Prague (Czech Republic); Donko, Z; Bano, G, E-mail: radek.plasil@mff.cuni.c [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, Budapest (Hungary)

    2009-11-15

    Electron energy distribution functions (EEDF) have been measured in decaying plasma in Flowing Afterglow Langmuir Probe (FALP) experiment. The measurements have been carried out in diffusion and recombination governed plasmas used for studies of recombination of KrD{sup +} and H{sub 3}{sup +} ions.

  9. Measurements of EEDF in recombination dominated afterglow plasma

    International Nuclear Information System (INIS)

    Plasil, R; Korolov, I; Kotrik, T; Varju, J; Dohnal, P; Glosik, J; Donko, Z; Bano, G

    2009-01-01

    Electron energy distribution functions (EEDF) have been measured in decaying plasma in Flowing Afterglow Langmuir Probe (FALP) experiment. The measurements have been carried out in diffusion and recombination governed plasmas used for studies of recombination of KrD + and H 3 + ions.

  10. Recombinant-activated factor VII in the paediatric cardiac surgery ...

    African Journals Online (AJOL)

    Recombinant-activated factor VII in the paediatric cardiac surgery: Single unit experience. V Agarwal, KE Okonta, PS Lal. Abstract. Background: The control of excessive bleeding after paediatric cardiac surgery can be challenging. This may make the use of recombinant-activated factor VII (rFVIIa) in preventing this ...

  11. Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus

    Directory of Open Access Journals (Sweden)

    Mark W. Jackwood

    2011-09-01

    Full Text Available Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.

  12. Collision and recombination driven instabilities in variable charged ...

    Indian Academy of Sciences (India)

    The dust-acoustic instability driven by recombination of electrons and ions on the surface of charged and variably-charged dust grains as well as by collisions in dusty plasmas with significant pressure of background neutrals have been theoretically investigated. The recombination driven instability is shown to be dominant ...

  13. Co-solute assistance in refolding of recombinant proteins | Gerami ...

    African Journals Online (AJOL)

    Prokaryotic expression system is the most widely used host for the production of recombinant proteins but inclusion body formation is a major bottleneck in the production of recombinant proteins in prokaryotic cells, especially in Escherichia coli. In vitro refolding of inclusion body into the the proteins with native ...

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

    Science.gov (United States)

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

    2012-12-01

    Coagulase-negative staphylococci (CNS) are the most commonly isolated bacteria from goat milk, but they have often been identified with phenotypic methods, which may have resulted in misclassification. The aims of this paper were to assess the amount of misclassification of a phenotypic test for identifying CNS species from goat milk compared with transfer RNA intergenic spacer PCR (tDNA-PCR) followed by capillary electrophoresis, and to apply the tDNA-PCR technique on different capillary electrophoresis equipment. Milk samples were collected from 416 does in 5 Californian dairy goat herds on 3 occasions during lactation. In total, 219 CNS isolates were identified at the species level with tDNA-PCR and subjected to the API 20 Staph identification test kit (API Staph; bioMérieux, Durham, NC). If the same species was isolated multiple times from the same udder gland, only the first isolate was used for further analyses, resulting in 115 unique CNS isolates. According to the tDNA-PCR test, the most prevalent CNS species were Staphylococcus epidermidis, Staphylococcus caprae, and Staphylococcus simulans. Typeability with API staph was low (72%). Although the API Staph test was capable of identifying the majority of Staph. epidermidis and Staph. caprae isolates, sensitivity for identification of Staph. simulans was low. The true positive fraction was high for the 3 most prevalent species. It was concluded that the overall performance of API Staph in differentiating CNS species from goat milk was moderate to low, mainly because of the low typeability, and that genotypic methods such as tDNA-PCR are preferred. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  15. A study on the hydrogen recombination rates of catalytic recombiners and deliberate ignition

    International Nuclear Information System (INIS)

    Fineschi, F.; Bazzichi, M.; Carcassi, M.

    1994-01-01

    A study is being carried out by the Department of Nuclear and Mechanical Constructions (DCMN) at the University of Pisa on catalytic recombiners and on deliberately induced weak deflagration. The recombination rates of different types of catalytic devices were obtained from a thorough analysis of published experimental data. The main parameter that affects the effectiveness of these devices seems to be the molar density of the deficiency reactant rather than its volumetric concentration. The recombination rate of weak deflagrations in vented compartments has been assessed with experimental tests carried out in a small scale glass vessel. Through a computerized system of analysis of video recordings of the deflagrations, the flame surface and the burned gas volume were obtained as functions of time. Although approximations are inevitable, the method adopted to identify the position of the flame during propagation is more reliable than other non-visual methods (thermocouples and ion-probes). It can only easily be applied to vented weak deflagrations, i.e. when the hydrogen concentration is far from stoichiometric conditions and near to flammability limits, because the pressurization has to be limited due to the low mechanical resistance of the glass. The values of flame surface and burned gas volume were used as inputs for a computer code to calculate the recombining rate, the burning velocity and the pressure transient in the experimental test. The code is being validated with a methodology principally based on a comparison of the measurements of pressure with the calculated values. The research gave some very interesting results on a small scale which should in the future be compared with large scale data

  16. The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate

    Directory of Open Access Journals (Sweden)

    Wissing Josef

    2010-04-01

    Full Text Available Abstract Background The filamentous fungus Aspergillus niger is well-known as a producer of primary metabolites and extracellular proteins. For example, glucoamylase is the most efficiently secreted protein of Aspergillus niger, thus the homologous glucoamylase (glaA promoter as well as the glaA signal sequence are widely used for heterologous protein production. Xylose is known to strongly repress glaA expression while maltose is a potent inducer of glaA promoter controlled genes. For a more profound understanding of A. niger physiology, a comprehensive analysis of the intra- and extracellular proteome of Aspergillus niger AB1.13 growing on defined medium with xylose or maltose as carbon substrate was carried out using 2-D gel electrophoresis/Maldi-ToF and nano-HPLC MS/MS. Results The intracellular proteome of A. niger growing either on xylose or maltose in well-aerated controlled bioreactor cultures revealed striking similarities. In both cultures the most abundant intracellular protein was the TCA cycle enzyme malate-dehydrogenase. Moreover, the glycolytic enzymes fructose-bis-phosphate aldolase and glyceraldehyde-3-phosphate-dehydrogenase and the flavohemoglobin FhbA were identified as major proteins in both cultures. On the other hand, enzymes involved in the removal of reactive oxygen species, such as superoxide dismutase and peroxiredoxin, were present at elevated levels in the culture growing on maltose but only in minor amounts in the xylose culture. The composition of the extracellular proteome differed considerably depending on the carbon substrate. In the secretome of the xylose-grown culture, a variety of plant cell wall degrading enzymes were identified, mostly under the control of the xylanolytic transcriptional activator XlnR, with xylanase B and ferulic acid esterase as the most abundant ones. The secretome of the maltose-grown culture did not contain xylanolytic enzymes, instead high levels of catalases were found and

  17. Optimal recombination in genetic algorithms for flowshop scheduling problems

    Science.gov (United States)

    Kovalenko, Julia

    2016-10-01

    The optimal recombination problem consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We prove NP-hardness of the optimal recombination for various variants of the flowshop scheduling problem with makespan criterion and criterion of maximum lateness. An algorithm for solving the optimal recombination problem for permutation flowshop problems is built, using enumeration of prefect matchings in a special bipartite graph. The algorithm is adopted for the classical flowshop scheduling problem and for the no-wait flowshop problem. It is shown that the optimal recombination problem for the permutation flowshop scheduling problem is solvable in polynomial time for almost all pairs of parent solutions as the number of jobs tends to infinity.

  18. Recombinant expression systems: the obstacle to helminth vaccines?

    Science.gov (United States)

    Geldhof, Peter; De Maere, Veerle; Vercruysse, Jozef; Claerebout, Edwin

    2007-11-01

    The need for alternative ways to control helminth parasites has in recent years led to a boost in vaccination experiments with recombinant antigens. Despite the use of different expression systems, only a few recombinants induced high levels of protection against helminths. This is often attributed to the limitations of the current expression systems. Therefore, the need for new systems that can modify and glycosylate the expressed antigens has been advocated. However, analysis of over 100 published vaccine trials with recombinant helminth antigens indicates that it is often not known whether the native parasite antigen itself can induce protection or, if it does, which epitopes are important. This information is vital for a well-thought-out strategy for recombinant production. So, in addition to testing more expression systems, it should be considered that prior evaluation and characterization of the native antigens might help the development of recombinant vaccines against helminths in the long term.

  19. Recombination Rate Evolution and the Origin of Species.

    Science.gov (United States)

    Ortiz-Barrientos, Daniel; Engelstädter, Jan; Rieseberg, Loren H

    2016-03-01

    A recipe for dissolving incipient species into a continuum of phenotypes is to recombine their genetic material. Therefore, students of speciation have become increasingly interested in the mechanisms by which recombination between locally adapted lineages is reduced. Evidence abounds that chromosomal rearrangements, via their suppression of recombination during meiosis in hybrids, play a major role in adaptation and speciation. By contrast, genic modifiers of recombination rates have been largely ignored in studies of speciation. We show how both types of reduction in recombination rates facilitate divergence in the face of gene flow, including the early stages of adaptive divergence, the persistence of species after secondary contact, and reinforcement. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Sex recombination, and reproductive fitness: an experimental study using Paramecium

    Energy Technology Data Exchange (ETDEWEB)

    Nyberg, D.

    1982-08-01

    The effect of sex and recombination on reproductive fitness are measured using five wild stocks of Paramecium primaurelia. Among the wild stocks there were highly significant differences in growth rates. No hybrid had as low a fitness as the least fit parental stock. Recombination produced genotypes of higher fitness than those of either parent only in the cross between the two stocks of lowest fitness. The increase in variance of fitness as a result of recombination was almost exclusively attributable to the generation lines with low fitness. The fitness consequences of sexuality and mate choice were stock specific; some individuals leaving the most descendants by inbreeding, others by outcrossing. For most crosses the short-term advantage of sex, if any, accrue from the fusion of different gametes (hybrid vigor) and not from recombination. Since the homozygous genotype with the highest fitnes left the most progeny by inbreeding (no recombination), the persistence of conjugation in P. primaurelia is paradoxical. (JMT)

  1. Charge carrier recombination dynamics in perovskite and polymer solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Paulke, Andreas; Kniepert, Juliane; Kurpiers, Jona; Wolff, Christian M.; Schön, Natalie; Brenner, Thomas J. K.; Neher, Dieter [Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476, Potsdam (Germany); Stranks, Samuel D. [Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Snaith, Henry J. [Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom)

    2016-03-14

    Time-delayed collection field experiments are applied to planar organometal halide perovskite (CH{sub 3}NH{sub 3}PbI{sub 3}) based solar cells to investigate charge carrier recombination in a fully working solar cell at the nanosecond to microsecond time scale. Recombination of mobile (extractable) charges is shown to follow second-order recombination dynamics for all fluences and time scales tested. Most importantly, the bimolecular recombination coefficient is found to be time-dependent, with an initial value of ca. 10{sup −9} cm{sup 3}/s and a progressive reduction within the first tens of nanoseconds. Comparison to the prototypical organic bulk heterojunction device PTB7:PC{sub 71}BM yields important differences with regard to the mechanism and time scale of free carrier recombination.

  2. Looking for the optimal rate of recombination for evolutionary dynamics

    Science.gov (United States)

    Saakian, David B.

    2018-01-01

    We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.

  3. Expression and purification of recombinant hemoglobin in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Chandrasekhar Natarajan

    Full Text Available Recombinant DNA technologies have played a pivotal role in the elucidation of structure-function relationships in hemoglobin (Hb and other globin proteins. Here we describe the development of a plasmid expression system to synthesize recombinant Hbs in Escherichia coli, and we describe a protocol for expressing Hbs with low intrinsic solubilities. Since the α- and β-chain Hbs of different species span a broad range of solubilities, experimental protocols that have been optimized for expressing recombinant human HbA may often prove unsuitable for the recombinant expression of wildtype and mutant Hbs of other species.As a test case for our expression system, we produced recombinant Hbs of the deer mouse (Peromyscus maniculatus, a species that has been the subject of research on mechanisms of Hb adaptation to hypoxia. By experimentally assessing the combined effects of induction temperature, induction time and E. coli expression strain on the solubility of recombinant deer mouse Hbs, we identified combinations of expression conditions that greatly enhanced the yield of recombinant protein and which also increased the efficiency of post-translational modifications.Our protocol should prove useful for the experimental study of recombinant Hbs in many non-human animals. One of the chief advantages of our protocol is that we can express soluble recombinant Hb without co-expressing molecular chaperones, and without the need for additional reconstitution or heme-incorporation steps. Moreover, our plasmid construct contains a combination of unique restriction sites that allows us to produce recombinant Hbs with different α- and β-chain subunit combinations by means of cassette mutagenesis.

  4. Expression and purification of recombinant hemoglobin in Escherichia coli.

    Science.gov (United States)

    Natarajan, Chandrasekhar; Jiang, Xiaoben; Fago, Angela; Weber, Roy E; Moriyama, Hideaki; Storz, Jay F

    2011-01-01

    Recombinant DNA technologies have played a pivotal role in the elucidation of structure-function relationships in hemoglobin (Hb) and other globin proteins. Here we describe the development of a plasmid expression system to synthesize recombinant Hbs in Escherichia coli, and we describe a protocol for expressing Hbs with low intrinsic solubilities. Since the α- and β-chain Hbs of different species span a broad range of solubilities, experimental protocols that have been optimized for expressing recombinant human HbA may often prove unsuitable for the recombinant expression of wildtype and mutant Hbs of other species. As a test case for our expression system, we produced recombinant Hbs of the deer mouse (Peromyscus maniculatus), a species that has been the subject of research on mechanisms of Hb adaptation to hypoxia. By experimentally assessing the combined effects of induction temperature, induction time and E. coli expression strain on the solubility of recombinant deer mouse Hbs, we identified combinations of expression conditions that greatly enhanced the yield of recombinant protein and which also increased the efficiency of post-translational modifications. Our protocol should prove useful for the experimental study of recombinant Hbs in many non-human animals. One of the chief advantages of our protocol is that we can express soluble recombinant Hb without co-expressing molecular chaperones, and without the need for additional reconstitution or heme-incorporation steps. Moreover, our plasmid construct contains a combination of unique restriction sites that allows us to produce recombinant Hbs with different α- and β-chain subunit combinations by means of cassette mutagenesis.

  5. Recombination in Escherichia coli V. Genetic analysis of recombinants from crosses with recipients deficient in ATP-dependent exonuclease activity

    NARCIS (Netherlands)

    Haan, P.G. de; Hoekstra, W.P.M.; Verhoef, C.

    A genetic analysis of recombinants from crosses with recombination-deficient recipients, lacking the ATP-dependent exonuclease activity, demonstrated differences in the inheritance pattern of donor markers compared with a Rec+ recipient. In particular the donor markers proximal to the transfer

  6. Intra- and inter-rater reliability of maximum inspiratory pressure measured using a portable capsule-sensing pressure gauge device in healthy adults.

    Science.gov (United States)

    Jalan, Nikita S; Daftari, Sonam S; Retharekar, Seemi S; Rairikar, Savita A; Shyam, Ashok M; Sancheti, Parag K

    2015-01-01

    Measurement of maximum inspiratory pressure is the most prevalent method used in clinical practice to assess the strength of the inspiratory muscles. Although there are many devices available for the assessment of inspiratory muscle strength, there is a dearth of literature describing the reliability of devices that can be used in clinical patient assessment. The capsule-sensing pressure gauge (CSPG-V) is a new tool that measures the strength of inspiratory muscles; it is easy to use, noninvasive, inexpensive and lightweight. To test the intra- and inter-rater reliability of a CSPG-V device in healthy adults. A cross-sectional study involving 80 adult subjects with a mean (± SD) age of 22±3 years was performed. Using simple randomization, 40 individuals (20 male, 20 female) were used for intrarater and 40 (20 male, 20 female) were used for inter-rater reliability testing of the CSPG-V device. The subjects performed three inspiratory efforts, which were sustained for at least 3 s; the best of the three readings was used for intra- and inter-rater comparison. The intra- and inter-rater reliability were calculated using intraclass correlation coefficients (ICCs). The intrarater reliability ICC was 0.962 and the inter-rater reliability ICC was 0.922. Results of the present study suggest that maximum inspiratory pressure measured using a CSPG-V device has excellent intraand inter-rater reliability, and can be used as a diagnostic and prognostic tool in patients with respiratory muscle impairment.

  7. Vibration sensibility of the median nerve in a population with chronic whiplash associated disorder: Intra- and inter-rater reliability study.

    Science.gov (United States)

    Tyros, I; Soundy, A; Heneghan, N R

    2016-09-01

    Whiplash Associated Disorders (WAD) grade II are the most prevalent group of whiplash patients seen on a regular basis by musculoskeletal physiotherapists. Impairment of vibration sensibility may be an early indicator of nerve pathology and it has previously been demonstrated in individuals with chronic WAD symptoms utilising vibrameters. A less expensive option, such the tuning fork (TF) may assist with these measures, but research regarding its measurement properties is lacking. To investigate the intra- and inter-rater reliability of vibration sensibility of the median nerve in chronic WAD II (CWAD II). A double blinded, within day intra- and inter-rater reliability study was undertaken. A convenience sample of 26 individuals (8 males, 18 females, age mean 29.9 ± 10.0 years) with CWADII was recruited. WAD I, III & indications of neuropathic pain. Vibration attenuation times were recorded from skin innervated by the median nerve (thenar eminence). Descriptive statistics (mean scores) and reliability statistics [intraclass correlation coefficient (ICC2,1) and Bland and Altman limits of agreement] were undertaken with p = 0.05. Almost perfect intra-rater reliability (Intraclass Correlation Coefficiency (ICC): 0.972-0.955) and inter-rater reliability (ICC: 0.983) were identified. Confidence Intervals (CI) for inter-rater reliability were 95% CI: -1.461 to -0.056. Almost perfect reliability scores across intra- and inter-rater reliability were found. This provides evidence that, with a standardised testing protocol the TF can be a highly reliable means of vibration sensibility testing. Future studies assessing the validity of the TF in different WAD populations may provide further information about the usefulness of this protocol. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Comparative intra-and inter-specific sexual organ reciprocity in four distylous Primula species in the Himalaya-Hengduan Mountains.

    Science.gov (United States)

    Li, Hai-Dong; Ren, Zong-Xin; Zhou, Wei; Bernhardt, Peter; Zhao, Yan-Hui; Wu, Zhi-Kun; Li, De-Zhu; Wang, Hong

    2018-04-23

    Distyly is a mechanism promoting cross-pollination within a balanced polymorphism. Numerous studies show that the degree of inter-morph sexual organ reciprocity (SOR) within species relates to its pollen-mediated gene flow. Similarly, a lower inter-specific SOR should promote inter-specific isolation when congeners are sympatric, co-blooming, and share pollinators. In this comparative study, we address the significance of SOR at both intra- and inter-specific levels. Seventeen allopatric and eight sympatric populations representing four Primula species (P. anisodora, P. beesiana, P. bulleyana and P. poissonii) native to the Himalaya-Hengduan Mountains were measured for eight floral traits in both long- and short-styled morphs. GLMM and spatial overlap methods were used to compare intra- and inter-specific SOR. While floral morphology differed among four Primula species. SOR within species was generally higher than between species, but species pairs P. poissonii / P. anisodora and P. beesiana / P. bulleyana, the SOR was high at both intra- and inter-specific levels. We didn't detect a significant variation in intra-specific SOR or inter-specific SOR when compare allopatric vs. sympatric populations for all species studied. As intra-specific SOR increased, disassortative mating may be promoted. As inter-specific SOR decreased, inter-specific isolation between co-flowering species pairs also may increase. Hybridization between congeners occurred when inter-specific SOR increased in sympatric populations was confirmed in two species pairs, P. poissonii / P. anisodora and P. beesiana / P. bulleyana. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. Bio-equivalent doses of recombinant HCG and recombinant LH during ovarian stimulation result in similar oestradiol output

    DEFF Research Database (Denmark)

    Alsbjerg, Birgit; Elbaek, Helle Olesen; Laursen, Rita Jakubcionyte

    2017-01-01

    In nature, HCG is secreted by the implanting embryo from peri-implantation and onwards. In contrast, LH is mandatory for steroidogenesis and follicular development during the follicular phase, working in synergy with FSH. Moreover, LH is mandatory for the function of the corpus luteum. Although LH...... and HCG bind to the same receptor, significant molecular, structural and functional differences exist, inducing differences in bioactivity. This randomized controlled study compared the effect of recombinant FSH stimulation combined with daily either micro-dose recombinant HCG or recombinant LH...... oestradiol level in the HCG supplemented group was 8662 pmol/l versus 9203 pmol/l in the recombinant LH supplemented group; therefore, no significant difference was found. Moreover, no differences were observed in the number of oocytes retrieved or in the live birth rate. We conclude that recombinant HCG...

  10. Orchestrating Information Sharing among Intra- And Inter-Organisational Core Actors in a Large New Product Development Project - The Particular Role of The Project Manager

    DEFF Research Database (Denmark)

    Jepsen, Lisbeth Brøde

    The success of NPD projects of high-cost, engineering-intensive, and customized development products is largely dependent on information sharing with actors from customers regarding their specific requirements (Von Hippel, 1986). But information sharing is also necessary among actors from different...... expertise and critical information are integrated in a timely fashion into the development process (Edmondson and Nembhard, 2009). However, prior research has not simultaneously studied and addressed the differences in intra- and inter-organisational information sharing during the various phases of the NPD...

  11. Cold Spring Harbor symposia on quantitative biology: Volume 49, Recombination at the DNA level

    International Nuclear Information System (INIS)

    1984-01-01

    This volume contains full papers prepared by the participants to the 1984 Cold Springs Harbor Symposia on Quantitative Biology. This year's theme is entitled Recombination at the DNA level. The volume consists of 93 articles grouped into subject areas entitled chromosome mechanics, yeast systems, mammalian homologous recombination, transposons, mu, plant transposons/T4 recombination, topoisomerase, resolvase and gyrase, Escherichia coli general recombination, RecA, repair, leukaryotic enzymes, integration and excision of bacteriophage, site-specific recombination, and recombination in vitro

  12. Recombination properties of dislocations in GaN

    Science.gov (United States)

    Yakimov, Eugene B.; Polyakov, Alexander Y.; Lee, In-Hwan; Pearton, Stephen J.

    2018-04-01

    The recombination activity of threading dislocations in n-GaN with different dislocation densities and different doping levels was studied using electron beam induced current (EBIC). The recombination velocity on a dislocation, also known as the dislocation recombination strength, was calculated. The results suggest that dislocations in n-GaN giving contrast in EBIC are charged and surrounded by a space charge region, as evidenced by the observed dependence of dislocation recombination strength on dopant concentration. For moderate (below ˜108 cm-2) dislocation densities, these defects do not primarily determine the average diffusion length of nonequilibrium charge carriers, although locally, dislocations are efficient recombination sites. In general, it is observed that the effect of the growth method [standard metalorganic chemical vapor deposition (MOCVD), epitaxial lateral overgrowth versions of MOCVD, and hydride vapor phase epitaxy] on the recombination activity of dislocations is not very pronounced, although the average diffusion lengths can widely differ for various samples. The glide of basal plane dislocations at room temperature promoted by low energy electron irradiation does not significantly change the recombination properties of dislocations.

  13. Retroviral Vectors for Analysis of Viral Mutagenesis and Recombination

    Directory of Open Access Journals (Sweden)

    Jonathan M.O. Rawson

    2014-09-01

    Full Text Available Retrovirus population diversity within infected hosts is commonly high due in part to elevated rates of replication, mutation, and recombination. This high genetic diversity often complicates the development of effective diagnostics, vaccines, and antiviral drugs. This review highlights the diverse vectors and approaches that have been used to examine mutation and recombination in retroviruses. Retroviral vectors for these purposes can broadly be divided into two categories: those that utilize reporter genes as mutation or recombination targets and those that utilize viral genes as targets of mutation or recombination. Reporter gene vectors greatly facilitate the detection, quantification, and characterization of mutants and/or recombinants, but may not fully recapitulate the patterns of mutagenesis or recombination observed in native viral gene sequences. In contrast, the detection of mutations or recombination events directly in viral genes is more biologically relevant but also typically more challenging and inefficient. We will highlight the advantages and disadvantages of the various vectors and approaches used as well as propose ways in which they could be improved.

  14. Phylogenetic and recombination analysis of tomato spotted wilt virus.

    Directory of Open Access Journals (Sweden)

    Sen Lian

    Full Text Available Tomato spotted wilt virus (TSWV severely damages and reduces the yield of many economically important plants worldwide. In this study, we determined the whole-genome sequences of 10 TSWV isolates recently identified from various regions and hosts in Korea. Phylogenetic analysis of these 10 isolates as well as the three previously sequenced isolates indicated that the 13 Korean TSWV isolates could be divided into two groups reflecting either two different origins or divergences of Korean TSWV isolates. In addition, the complete nucleotide sequences for the 13 Korean TSWV isolates along with previously sequenced TSWV RNA segments from Korea and other countries were subjected to phylogenetic and recombination analysis. The phylogenetic analysis indicated that both the RNA L and RNA M segments of most Korean isolates might have originated in Western Europe and North America but that the RNA S segments for all Korean isolates might have originated in China and Japan. Recombination analysis identified a total of 12 recombination events among all isolates and segments and five recombination events among the 13 Korea isolates; among the five recombinants from Korea, three contained the whole RNA L segment, suggesting reassortment rather than recombination. Our analyses provide evidence that both recombination and reassortment have contributed to the molecular diversity of TSWV.

  15. Data Mining for Expressivity of Recombinant Protein Expression

    Science.gov (United States)

    Kira, Satoshi; Isoai, Atsushi; Yamamura, Masayuki

    We analyzed the expressivity of recombinant proteins by using data mining methods. The expression technique of recombinant protein is a key step towards elucidating the functions of genes discovered through genomic sequence projects. We have studied the productive efficiency of recombinant proteins in fission yeast, Schizosaccharomyces pombe (S.pombe), by mining the expression results. We gathered 57 proteins whose expression levels were known roughly in the host. Correlation analysis, principal component analysis and decision tree analysis were applied to these expression data. Analysis featuring codon usage and amino acid composition clarified that the amino acid composition affected to the expression levels of a recombinant protein strongly than the effect of codon usage. Furthermore, analysis of amino acid composition showed that protein solubility and the metabolism cost of amino acids correlated with a protein expressivity. Codon usage was often interesting in the field of recombinant expressions. However, our analysis found the weak correlation codon features with expressivities. These results indicated that ready-made indices of codon bias were irrelevant ones for modeling the expressivities of recombinant proteins. Our data driven approach was an easy and powerful method to improve recombinant protein expression, and this approach should be concentrated attention with the huge amount of expression data accumulating through the post-genome era.

  16. Experimental study of para- and ortho-H3+ recombination

    International Nuclear Information System (INIS)

    Plasil, R; Varju, J; Hejduk, M; Dohnal, P; KotrIk, T; Glosik, J

    2011-01-01

    Recombination of H 3 + with electrons is a key process for many plasmatic environments. Recent experiments on storage ring devices used ion sources producing H 3 + with enhanced populations of H 3 + ions in the para nuclear spin configuration to shed light on the theoretically predicted faster recombination of para states. Although increased recombination rates were observed, no in situ characterization of recombining ions was performed. We present a state selective recombination study of para- and ortho-H 3 + ions with electrons at 77 K in afterglow plasma in a He/Ar/H 2 gas-mixture. Both spin configurations of H 3 + have been observed in situ with a near infrared cavity ring down spectrometer (NIR-CRDS) using the two lowest energy levels of H 3 + . Using hydrogen with an enhanced population of H 2 molecules in para states allowed us to influence the [para-H 3 + ]/[ortho-H 3 + ] ratio in the discharge and in the afterglow. We observed an increase in the measured effective recombination rate coefficients with the increase of the fraction of para-H 3 + . Measurements with different fractions of para-H 3 + at otherwise identical conditions allowed us to determine the binary recombination rate coefficients for pure para-H 3 + p α bin (77 K) = (2.0±0.4)x10 -7 cm 3 s -1 and pure ortho-H 3 + o α bin (77 K) = (4±3)x10 -8 cm 3 s -1 .

  17. Triplet formation in the ion recombination in irradiated liquids

    International Nuclear Information System (INIS)

    Bartczak, W.M.; Tachiya, M.; Hummel, A.

    1990-01-01

    The formation of singlet and triplet excited stages in the ion recombination in groups of oppositely charged ions (or positive ions and electrons) in nonpolar liquids, as occurs in the tracks of high energy electrons, is considered. Theoretical studies on triplet formation in groups of ion pairs have thus far concentrated on the case where recombination of the negative ions with any of the positive ions in the group is equally probable (random recombination). In this paper the probability for geminate recombination (electron and parent positive ion) vs cross-recombination (an electron with a positive ion other than its parent ion) in multiple ion pair groups is calculated by computer simulation and the effect of the initial spatial configuration of the charged species is investigated. It is also shown explicitly that the probability for singlet formation as a result of cross recombination is equal to 1/4, when spin relaxation by magnetic interaction with the medium and by exchange interaction can be neglected. The effect of the preferential recombination on the singlet formation probability is illustrated and recent experimental results on singlet to triplet ratios are discussed. (author)

  18. Evaluation of somatic embryos of alfalfa for recombinant protein expression.

    Science.gov (United States)

    Fu, Guohua; Grbic, Vojislava; Ma, Shengwu; Tian, Lining

    2015-02-01

    Somatic embryos of alfalfa can accumulate higher levels of recombinant proteins comparing to vegetative organs. Somatic embryos may be explored as a new system for new protein production for plants. Plants have been explored via genetic engineering as an inexpensive system for recombinant protein production. However, protein expression levels in vegetative tissues have been low, which limits the commercial utilization of plant expression systems. Somatic embryos resemble zygotic embryos in many aspects and may accumulate higher levels of proteins as true seed. In this study, somatic embryo of alfalfa (Medicago sativa L.) was investigated for the expression of recombinant proteins. Three heterologous genes, including the standard scientific reporter uid that codes for β-glucuronidase and two genes of interest: ctb coding for cholera toxin B subunit (CTB), and hIL-13 coding for human interleukin 13, were independently introduced into alfalfa via Agrobacterium-mediated transformation. Somatic embryos were subsequently induced from transgenic plants carrying these genes. Somatic embryos accumulated approximately twofold more recombinant proteins than vegetative organs including roots, stems, and leaves. The recombinant proteins of CTB and hIL-13 accumulated up to 0.15 and 0.18 % of total soluble protein in alfalfa somatic embryos, respectively. The recombinant proteins expressed in somatic embryos also exhibited biological activities. As somatic embryos can be induced in many plant species and their production can be scaled up via different avenues, somatic embryos may be developed as an efficient expression system for recombinant protein production.

  19. Homologous plasmid recombination is elevated in immortally transformed cells.

    Science.gov (United States)

    Finn, G K; Kurz, B W; Cheng, R Z; Shmookler Reis, R J

    1989-09-01

    The levels of intramolecular plasmid recombination, following transfection of a plasmid substrate for homologous recombination into normal and immortally transformed cells, have been examined by two independent assays. In the first assay, recovered plasmid was tested for DNA rearrangements which regenerate a functional neomycin resistance gene from two overlapping fragments. Following transformation of bacteria, frequencies of recombinationlike events were determined from the ratio of neomycin-resistant (recombinant) colonies to ampicillin-resistant colonies (indicating total plasmid recovery). Such events, yielding predominantly deletions between the directly repeated sequences, were substantially more frequent in five immortal cell lines than in any of three normal diploid cell strains tested. Effects of plasmid replication or interaction with T antigen and of bacterially mediated rejoining of linear molecules generated in mammalian cells were excluded by appropriate controls. The second assay used limited coamplification of a control segment of plasmid DNA, and of the predicted recombinant DNA region, primed by two sets of flanking oligonucleotides. Each amplified band was quantitated by reference to a near-linear standard curve generated concurrently, and recombination frequencies were determined from the ratio of recombinant/control DNA regions. The results confirmed that recombinant DNA structures were generated within human cells at direct repeats in the transfected plasmid and were markedly more abundant in an immortal cell line than in the diploid normal cells from which that line was derived.

  20. Analysis of intermolecular RNA-RNA recombination by rubella virus

    International Nuclear Information System (INIS)

    Adams, Sandra D.; Tzeng, W.-P.; Chen, M.-H.; Frey, Teryl K.

    2003-01-01

    To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating