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Sample records for actively transcribed regions

  1. DNA Methylation within Transcribed Regions

    PubMed Central

    To, Taiko K.; Saze, Hidetoshi; Kakutani, Tetsuji

    2015-01-01

    DNA methylation within transcribed genes is commonly found in diverse animals and plants. Here, we provide an overview of recent advances and the remaining mystery regarding intragenic DNA methylation. PMID:26143255

  2. The internal transcribed spacer region of belonolaimus (nemata: belonolaimidae).

    PubMed

    Cherry, T; Szalanski, A L; Todd, T C; Powers, T O

    1997-03-01

    Belonolaimus isolates from six U.S. states were compared by restriction endonuclease digestion of amplified first internal transcribed spacer region (ITS1) of the nuclear ribosomal genes. Seven restriction enzymes were selected for evaluation based on restriction sites inferred from the nucleotide sequence of a South Carolina Belonolaimus isolate. Amplified product size from individuals of each isolate was approximately 700 bp. All Midwestern isolates gave distinct restriction digestion patterns. Isolates identified morphologically as Belonolaimus longicaudatus from Florida, South Carolina, and Palm Springs, California, were identical for ITS1 restriction patterns. The correlation between ITS1 restriction patterns and the distribution of B. longicaudatus isolates suggest that the California isolate is a relatively recent introduction into the state.

  3. Transcribed DNA is preferentially located in the perichromatin region of mammalian cell nuclei

    SciTech Connect

    Niedojadlo, Janusz; Perret-Vivancos, Cecile; Kalland, Karl-Henning; Cmarko, Dusan; Cremer, Thomas; Driel, Roel van; Fakan, Stanislav

    2011-02-15

    The precise localization of transcribed DNA and resulting RNA is an important aspect of the functional architecture of the nucleus. To this end we have developed a novel in situ hybridization approach in combination with immunoelectron microscopy, using sense and anti-sense RNA probes that are derived from total cellular or cytoplasmic poly(A+) RNA. This new technology is much more gentle than classical in situ hybridization using DNA probes and shows excellent preservation of nuclear structure. Carried out on ultrathin sections of fixed and resin-embedded COS-7 cells, it revealed at high resolution the localization of the genes that code for the cellular mRNAs. Quantitative analysis shows that most transcribed DNA is concentrated in the perichromatin region, i.e. the interface between subchromosomal compact chromatin domains and the interchromatin space essentially devoid of DNA. The RNA that is produced is found mainly in the perichromatin region and the interchromatin space. These results imply that in the mammalian nucleus the chromatin fiber is folded so that active genes are predominantly present in the perichromatin region, which is the most prominent site of transcription.

  4. The structure of nucleosomal core particles within transcribed and repressed gene regions.

    PubMed Central

    Studitsky, V M; Belyavsky, A V; Melnikova, A F; Mirzabekov, A D

    1988-01-01

    The arrangement of histones along DNA in nucleosomal core particles within transcribed heat shock gene (hsp 70) region and repressed insertion within ribosomal genes of Drosophila was analysed by using protein-DNA crosslinking methods combined with hybridization tests. In addition, two-dimensional gel electrophoresis was employed to compare the overall nucleosomal shape and the nucleosomal DNA size. The arrangement of histones along DNA and general compactness of nucleosomes were shown to be rather similar in transcriptionally active and inactive genomic regions. On the other hand, nucleosomes within transcriptionally active chromatin are characterized by a larger size of nucleosomal DNA produced by micrococcal nuclease digestion and some peculiarity in electrophoretic mobility. Images PMID:3144704

  5. Phylogenetic analysis of Antrodia species and Antrodia camphorata inferred from internal transcribed spacer region.

    PubMed

    Chiu, Hua-Hsien

    2007-04-01

    The species of Antrodia are one of the difficult-to-classify and obscure groups of poroid Aphyllophorales based on morphological appearance. However, it is becoming increasingly important to reliably identify the entire suite of Antrodia camphorata strains and Antrodia species due to the potential pharmaceutical value of their biologically active ingredients. In this study, the internal transcribed spacer (ITS) region of the ribosomal RNA gene (rDNA) was sequenced and phylogenetically analyzed in a number of Antrodia fungal species and strains. ITS amplicons from the Antrodia species tested ranged in size from 543 to 610 bp; the size of the ITS of A. camphorata strains ranged from 592 to 596 bp. The overall sizes of ITS2 and 5.8S ribosomal RNA gene of all A. camphorata strains tested in this study were shown to be 217 and 158 bp, respectively. A phylogenetic analysis of ITS data generated, which included sequences of 11 A. camphorata strains and nine other Antrodia species, showed three clearly distinct groups. Group 1 includes A. camphorata, Antrodia salmonea, and Antrodia carbinca strains. Within Group 2, Antrodia sinuosa and Antrodia xantha were clustered together. Group 3 contained Antrodia albida, A. heteromorpha, A. serialis, and A. malicola. The observed sequence diversity among ITS alleles provided an effective tool for differentiating strains of A. camphorata, A. salmonea, A. xantha, A. sinuosa, or A. serialis. Polymorphisms arising within the ITS1-5.8S-ITS2 region can provide practical markers for establishing a foundation for the further expansion of an ITS sequence database of medically important fungi.

  6. Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

    PubMed Central

    2011-01-01

    Background Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of Oryza sativa japonica (rice) mitochondria, which was predicted to be approximately 490-kb long. Results Whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria. Conclusion The present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (Oryza sativa Mitochondrial rna Expression Server: OsMES) is publicly accessible at [http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search]. PMID:21627843

  7. Characterization of Dermanyssus gallinae (Acarina: Dermanissydae) by sequence analysis of the ribosomal internal transcribed spacer regions.

    PubMed

    Potenza, L; Cafiero, M A; Camarda, A; La Salandra, G; Cucchiarini, L; Dachà, M

    2009-10-01

    In the present work mites previously identified as Dermanyssus gallinae De Geer (Acari, Mesostigmata) using morphological keys were investigated by molecular tools. The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from mites were amplified and sequenced to examine the level of sequence variations and to explore the feasibility of using this region in the identification of this mite. Conserved primers located at the 3'end of 18S and at the 5'start of 28S rRNA genes were used first, and amplified fragments were sequenced. Sequence analyses showed no variation in 5.8S and ITS2 region while slight intraspecific variations involving substitutions as well as deletions concentrated in the ITS1 region. Based on the sequence analyses a nested PCR of the ITS2 region followed by RFLP analyses has been set up in the attempt to provide a rapid molecular diagnostic tool of D. gallinae.

  8. Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology.

    PubMed

    Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K P; Woo, Patrick C Y

    2015-10-22

    Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10-49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n=2), Pichia (Candida) norvegensis (n=2), Candida tropicalis (n=1) and Saccharomyces cerevisiae (n=1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.

  9. Determination of internal transcribed spacer regions (ITS) in Trichomonas vaginalis isolates and differentiation among Trichomonas species.

    PubMed

    Ibáñez-Escribano, Alexandra; Nogal-Ruiz, Juan José; Arán, Vicente J; Escario, José Antonio; Gómez-Barrio, Alicia; Alderete, J F

    2014-04-01

    The nucleotide sequence of the 5.8S rRNA gene and the flanked internal transcribed spacer (ITS) regions of six Trichomonas vaginalis isolates with different metronidazole sensitivity and geographic origin were genotyped. A multiple sequence alignment was performed with different sequences of other isolates available at the GenBank/EMBL/DDBJ databases, which revealed 5 different sequence patterns. Although a stable mutation in position 66 of the ITS1 (C66T) was observed in 26% (9/34) of the T. vaginalis sequences analyzed, there was 99.7% ITS nucleotide sequence identity among isolates for this sequence. The nucleotide sequence variation among other species of the genus Trichomonas ranged from 3.4% to 9.1%. Surprisingly, the % identity between T. vaginalis and Pentatrichomonas hominis was ~83%. There was >40% divergence in the ITS sequence between T. vaginalis and Tritrichomonas spp., including Tritrichomonas augusta, Tritrichomonas muris, and Tritrichomonas nonconforma and with Tetratrichomonas prowazeki. Dendrograms grouped the trichomonadid sequences in robust clades according to their genera. The absence of nucleotide divergence in the hypervariable ITS regions between T. vaginalis isolates suggests the early divergence of the parasite. Importantly, these data show this ITS1-5.8S rRNA-ITS2 region suitable for inter-species differentiation.

  10. 16S-23S rDNA internal transcribed spacer regions in four Proteus species.

    PubMed

    Cao, Boyang; Wang, Min; Liu, Lei; Zhou, Zhemin; Wen, Shaoping; Rozalski, Antoni; Wang, Lei

    2009-04-01

    Proteus is a Gram-negative, facultative anaerobic bacterium. In this study, 813 Proteus 16S-23S rDNA internal transcribed spacer (ITS) sequences were determined from 46 Proteus strains, including 388 ITS from 22 P. mirabilis strains, 211 ITS from 12 P. vulgaris strains, 169 ITS from 10 P. penneri strains, and 45 ITS from 2 P. myxofaciens strains. The Proteus strains carry mainly two types of ITS, ITS(Glu) (containing tRNA(Glu (UUC)) gene) and ITS(Ile+Ala) (containing tRNA(Ile (GAU)) and tRNA(Ala (UGC)) gene), and are in the forms of 28 variants with 25 genomic origins. The ITS sequences are a mosaic-like structure consisting of three conservative regions and two variable regions. The nucleotide identity of ITS subtypes in strains of the same species ranges from 96.2% to 100%. The divergence of Proteus ITS divergence was most likely due to intraspecies recombinations or horizontal transfers of sequence blocks. The phylogenetic relationship deduced from the second variable region of ITS sequences of the three facultative human pathogenic species P. mirabilis, P. vulgaris and P. penneri is similar with that based on 16S rDNA sequences, but has higher resolution to differentiate closely related P. vulgaris and P. penneri. This study is the first comprehensive study of ITS in four Proteus species and laid solid foundation for the development of high-throughput technology for quick and accurate identification of the important foodborne and nosocomial pathogens.

  11. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    PubMed Central

    Schoch, Conrad L.; Seifert, Keith A.; Huhndorf, Sabine; Robert, Vincent; Spouge, John L.; Levesque, C. André; Chen, Wen; Bolchacova, Elena; Voigt, Kerstin; Crous, Pedro W.; Miller, Andrew N.; Wingfield, Michael J.; Aime, M. Catherine; An, Kwang-Deuk; Bai, Feng-Yan; Barreto, Robert W.; Begerow, Dominik; Bergeron, Marie-Josée; Blackwell, Meredith; Boekhout, Teun; Bogale, Mesfin; Boonyuen, Nattawut; Burgaz, Ana R.; Buyck, Bart; Cai, Lei; Cai, Qing; Cardinali, G.; Chaverri, Priscila; Coppins, Brian J.; Crespo, Ana; Cubas, Paloma; Cummings, Craig; Damm, Ulrike; de Beer, Z. Wilhelm; de Hoog, G. Sybren; Del-Prado, Ruth; Dentinger, Bryn; Diéguez-Uribeondo, Javier; Divakar, Pradeep K.; Douglas, Brian; Dueñas, Margarita; Duong, Tuan A.; Eberhardt, Ursula; Edwards, Joan E.; Elshahed, Mostafa S.; Fliegerova, Katerina; Furtado, Manohar; García, Miguel A.; Ge, Zai-Wei; Griffith, Gareth W.; Griffiths, K.; Groenewald, Johannes Z.; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Guo, Liang-Dong; Hagen, Ferry; Hambleton, Sarah; Hamelin, Richard C.; Hansen, Karen; Harrold, Paul; Heller, Gregory; Herrera, Cesar; Hirayama, Kazuyuki; Hirooka, Yuuri; Ho, Hsiao-Man; Hoffmann, Kerstin; Hofstetter, Valérie; Högnabba, Filip; Hollingsworth, Peter M.; Hong, Seung-Beom; Hosaka, Kentaro; Houbraken, Jos; Hughes, Karen; Huhtinen, Seppo; Hyde, Kevin D.; James, Timothy; Johnson, Eric M.; Johnson, Joan E.; Johnston, Peter R.; Jones, E.B. Gareth; Kelly, Laura J.; Kirk, Paul M.; Knapp, Dániel G.; Kõljalg, Urmas; Kovács, Gábor M.; Kurtzman, Cletus P.; Landvik, Sara; Leavitt, Steven D.; Liggenstoffer, Audra S.; Liimatainen, Kare; Lombard, Lorenzo; Luangsa-ard, J. Jennifer; Lumbsch, H. Thorsten; Maganti, Harinad; Maharachchikumbura, Sajeewa S. N.; Martin, María P.; May, Tom W.; McTaggart, Alistair R.; Methven, Andrew S.; Meyer, Wieland; Moncalvo, Jean-Marc; Mongkolsamrit, Suchada; Nagy, László G.; Nilsson, R. Henrik; Niskanen, Tuula; Nyilasi, Ildikó; Okada, Gen; Okane, Izumi; Olariaga, Ibai; Otte, Jürgen; Papp, Tamás; Park, Duckchul; Petkovits, Tamás; Pino-Bodas, Raquel; Quaedvlieg, William; Raja, Huzefa A.; Redecker, Dirk; Rintoul, Tara L.; Ruibal, Constantino; Sarmiento-Ramírez, Jullie M.; Schmitt, Imke; Schüßler, Arthur; Shearer, Carol; Sotome, Kozue; Stefani, Franck O.P.; Stenroos, Soili; Stielow, Benjamin; Stockinger, Herbert; Suetrong, Satinee; Suh, Sung-Oui; Sung, Gi-Ho; Suzuki, Motofumi; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M. Teresa; Tretter, Eric; Untereiner, Wendy A.; Urbina, Hector; Vágvölgyi, Csaba; Vialle, Agathe; Vu, Thuy Duong; Walther, Grit; Wang, Qi-Ming; Wang, Yan; Weir, Bevan S.; Weiß, Michael; White, Merlin M.; Xu, Jianping; Yahr, Rebecca; Yang, Zhu L.; Yurkov, Andrey; Zamora, Juan-Carlos; Zhang, Ning; Zhuang, Wen-Ying; Schindel, David

    2012-01-01

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups. PMID:22454494

  12. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    NASA Astrophysics Data System (ADS)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  13. High-resolution profiling of novel transcribed regions during rat spermatogenesis.

    PubMed

    Chalmel, Frédéric; Lardenois, Aurélie; Evrard, Bertrand; Rolland, Antoine D; Sallou, Olivier; Dumargne, Marie-Charlotte; Coiffec, Isabelle; Collin, Olivier; Primig, Michael; Jégou, Bernard

    2014-07-01

    Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-encoding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in rat, using next-generation sequencing technology and highly enriched testicular cell populations. Among 20 424 high-confidence transcripts reconstructed, we defined a stringent set of 1419 long multi-exonic unannotated transcripts expressed in the testis (testis-expressed unannotated transcripts [TUTs]). TUTs were divided into 7 groups with different expression patterns. Most TUTs share many of the characteristics of vertebrate long noncoding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of noncoding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource for novel loci expressed during spermatogenesis that significantly contributes to rat genome annotation.

  14. Heterogeneity of the internal transcribed spacer region in Leishmania tropica isolates from southern Iran.

    PubMed

    Ghatee, Mohammad Amin; Sharifi, Iraj; Kuhls, Katrin; Kanannejad, Zahra; Harandi, Majid Fasihi; de Almeida, Marcos E; Hatam, Gholamreza; Mirhendi, Hossein

    2014-09-01

    Most of cutaneous leishmaniasis cases occur in only 7 countries, including Iran. Leishmania tropica is the main cause of anthroponotic cutaneous leishmaniasis in Iran. In order to study the heterogeneity and phylogeny of L. tropica in southern Iran, a total of 61 isolates were obtained from Bam district and the cities Kerman and Shiraz. The internal transcribed spacer (ITS) from the ribosomal DNA locus was amplified and then analysed by sequencing. Analysis of the ITS sequences showed four haplotypes in the isolates, including 3 haplotypes among the 58 isolates from the south eastern region, including Bam district and Kerman city, and 2 haplotypes among the 3 isolates from Shiraz city. The results showed a monophyletic structure for the south eastern population. In comparison to GenBank sequences of L. tropica from different countries, most of the southeast Iranian and Indian isolates are comprised in one cluster, while isolates from other countries and few other Iranian isolates group in a different cluster. Analysis of ITS sequences of south eastern L. tropica showed a homogeneous population which could be the basis for other molecular epidemiology studies using more discriminative markers and tracing possible changes in the population structure of L. tropica.

  15. Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions

    PubMed Central

    Leaw, Shiang Ning; Chang, Hsien Chang; Sun, Hsiao Fang; Barton, Richard; Bouchara, Jean-Philippe; Chang, Tsung Chain

    2006-01-01

    Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods. PMID:16517841

  16. Identification of Aspergillus Species Using Internal Transcribed Spacer Regions 1 and 2

    PubMed Central

    Henry, Travis; Iwen, Peter C.; Hinrichs, Steven H.

    2000-01-01

    Aspergillus species are the most frequent cause of invasive mold infections in immunocompromised patients. Although over 180 species are found within the genus, 3 species, Aspergillus flavus, A. fumigatus, and A. terreus, account for most cases of invasive aspergillosis (IA), with A. nidulans, A. niger, and A. ustus being rare causes of IA. The ability to distinguish between the various clinically relevant Aspergillus species may have diagnostic value, as certain species are associated with higher mortality and increased virulence and vary in their resistance to antifungal therapy. A method to identify Aspergillus at the species level and differentiate it from other true pathogenic and opportunistic molds was developed using the 18S and 28S rRNA genes for primer binding sites. The contiguous internal transcribed spacer (ITS) region, ITS 1–5.8S–ITS 2, from referenced strains and clinical isolates of aspergilli and other fungi were amplified, sequenced, and compared with non-reference strain sequences in GenBank. ITS amplicons from Aspergillus species ranged in size from 565 to 613 bp. Comparison of reference strains and GenBank sequences demonstrated that both ITS 1 and ITS 2 regions were needed for accurate identification of Aspergillus at the species level. Intraspecies variation among clinical isolates and reference strains was minimal. Sixteen other pathogenic molds demonstrated less than 89% similarity with Aspergillus ITS 1 and 2 sequences. A blind study of 11 clinical isolates was performed, and each was correctly identified. Clinical application of this approach may allow for earlier diagnosis and selection of effective antifungal agents for patients with IA. PMID:10747135

  17. Molecular analysis of fungal populations in patients with oral candidiasis using internal transcribed spacer region.

    PubMed

    Ieda, Shinsuke; Moriyama, Masafumi; Takeshita, Toru; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection.

  18. Molecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region

    PubMed Central

    Ieda, Shinsuke; Moriyama, Masafumi; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection. PMID:24979710

  19. Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons.

    PubMed

    Banday, Abdul Rouf; Baumgartner, Marybeth; Al Seesi, Sahar; Karunakaran, Devi Krishna Priya; Venkatesh, Aditya; Congdon, Sean; Lemoine, Christopher; Kilcollins, Ashley M; Mandoiu, Ion; Punzo, Claudio; Kanadia, Rahul N

    2014-01-01

    In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, in situ hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of Hist1h1b was higher embryonically, while that of Hist1h1c was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as "replication-dependent." Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.

  20. Phylogenetic analysis of cercospora and mycosphaerella based on the internal transcribed spacer region of ribosomal DNA.

    PubMed

    Goodwin, S B; Dunkle, L D; Zismann, V L

    2001-07-01

    ABSTRACT Most of the 3,000 named species in the genus Cercospora have no known sexual stage, although a Mycosphaerella teleomorph has been identified for a few. Mycosphaerella is an extremely large and important genus of plant pathogens, with more than 1,800 named species and at least 43 associated anamorph genera. The goal of this research was to perform a large-scale phylogenetic analysis to test hypotheses about the past evolutionary history of Cercospora and Mycosphaerella. Based on the phylogenetic analysis of internal transcribed spacer (ITS) sequence data (ITS1, 5.8S rRNA gene, ITS2), the genus Mycosphaerella is monophyletic. In contrast, many anamorph genera within Mycosphaerella were polyphyletic and were not useful for grouping species. One exception was Cercospora, which formed a highly supported monophyletic group. Most Cercospora species from cereal crops formed a subgroup within the main Cercospora cluster. Only species within the Cercospora cluster produced the toxin cercosporin, suggesting that the ability to produce this compound had a single evolutionary origin. Intraspecific variation for 25 taxa in the Mycosphaerella clade averaged 1.7 nucleotides (nts) in the ITS region. Thus, isolates with ITS sequences that differ by two or more nucleotides may be distinct species. ITS sequences of groups I and II of the gray leaf spot pathogen Cercospora zeae-maydis differed by 7 nts and clearly represent different species. There were 6.5 nt differences on average between the ITS sequences of the sorghum pathogen Cercospora sorghi and the maize pathogen Cercospora sorghi var. maydis, indicating that the latter is a separate species and not simply a variety of Cercospora sorghi. The large monophyletic Mycosphaerella cluster contained a number of anamorph genera with no known teleomorph associations. Therefore, the number of anamorph genera related to Mycosphaerella may be much larger than suspected previously.

  1. Molecular Systematics of Dictyostelids: 5.8S Ribosomal DNA and Internal Transcribed Spacer Region Analyses▿

    PubMed Central

    Romeralo, María; Escalante, Ricardo; Sastre, Leandro; Lado, Carlos

    2007-01-01

    The variability and adaptability of the amoebae from the class Dictyosteliomycetes greatly complicate their systematics. The nucleotide sequences of the ribosomal internal transcribed spacers and the 5.8S ribosomal DNA gene have been determined for 28 isolates, and their utility to discriminate between different species and genera has been shown. PMID:17056743

  2. Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells.

    PubMed

    Minsky, Neri; Shema, Efrat; Field, Yair; Schuster, Meromit; Segal, Eran; Oren, Moshe

    2008-04-01

    Histone modifications have emerged as important regulators of transcription. Histone H2B monoubiquitination has also been implicated in transcription; however, better understanding of the biological significance of this modification in mammalian cells has been hindered by the lack of suitable reagents, particularly antibodies capable of specifically recognizing ubiquitinated H2B (ubH2B). Here, we report the generation of anti-ubH2B monoclonal antibodies using a branched peptide as immunogen. These antibodies provide a powerful tool for exploring the biochemical functions of H2B monoubiquitination at both a genome-wide and gene-specific level. Application of these antibodies in high resolution chromatin immunoprecipitation (ChIP)-chip experiments in human cells, using tiling arrays, revealed preferential association of ubiquitinated H2B with the transcribed regions of highly expressed genes. Unlike dimethylated H3K4, ubH2B was not associated with distal promoter regions. Furthermore, experimental modulation of the transcriptional activity of the tumour suppressor p53 was accompanied by rapid changes in the H2B ubiquitination status of its p21 target gene, attesting to the dynamic nature of this process. It has recently been demonstrated that the apparent extent of gene expression often reflects elongation rather than initiation rates; thus, our findings suggest that H2B ubiquitination is intimately linked with global transcriptional elongation in mammalian cells.

  3. The anti-tumor drug bleomycin preferentially cleaves at the transcription start sites of actively transcribed genes in human cells.

    PubMed

    Murray, Vincent; Chen, Jon K; Galea, Anne M

    2014-04-01

    The genome-wide pattern of DNA cleavage at transcription start sites (TSSs) for the anti-tumor drug bleomycin was examined in human HeLa cells using next-generation DNA sequencing. It was found that actively transcribed genes were preferentially cleaved compared with non-transcribed genes. The 143,600 identified human TSSs were split into non-transcribed genes (82,596) and transcribed genes (61,004) for HeLa cells. These transcribed genes were further split into quintiles of 12,201 genes comprising the top 20, 20-40, 40-60, 60-80, and 80-100 % of expressed genes. The bleomycin cleavage pattern at highly transcribed gene TSSs was greatly enhanced compared with purified DNA and non-transcribed gene TSSs. The top 20 and 20-40 % quintiles had a very similar enhanced cleavage pattern, the 40-60 % quintile was intermediate, while the 60-80 and 80-100 % quintiles were close to the non-transcribed and purified DNA profiles. The pattern of bleomycin enhanced cleavage had peaks that were approximately 200 bp apart, and this indicated that bleomycin was identifying the presence of phased nucleosomes at TSSs. Hence bleomycin can be utilized to detect chromatin structures that are present at actively transcribed genes. In this study, for the first time, the pattern of DNA damage by a clinically utilized cancer chemotherapeutic agent was performed on a human genome-wide scale at the nucleotide level.

  4. Nucleotide sequence of the internal transcribed spacers and 5.8S region of ribosomal DNA in Pinus pinea L.

    PubMed

    Marrocco, R; Gelati, M T; Maggini, F

    1996-01-01

    The nucleotide sequence of the first internal transcribed spacer (ITS1) belonging to different ribosomal RNA genes from Pinus pinea are reported. The analyzed ITS1 can be distinguished on the basis of their length, being one 2631 bp and the other 271 bp long. Nucleotide comparison of these regions did not show appreciable sequence homology. The larger ITS1 contains five tandem arranged subrepeats with size ranging between 219 bp and 237 bp. The nucleotide sequence of the 5.8S and the ITS2 regions belonging to the larger ribosomal RNA gene are also reported.

  5. Identification of fungi based on the nucleotide sequence homology of their internal transcribed spacer 1 (ITS1) region.

    PubMed

    Narutaki, Shoji; Takatori, Kosuke; Nishimura, Hidekatsu; Terashima, Hiroshi; Sasaki, Tsuguo

    2002-01-01

    In this study, we examined the identification of fungi based on the sequence homology of the internal transcribed spacer 1 (ITS1) region. A newly designed primer pair could amplify the target region of all 42 strains tested. The PCR products were sequenced and the sequence homologies were searched by BLAST. It was demonstrated that this method is a reliable identification method at the genus or species level. At present, available databases are still insufficient to identify some fungi, but with the accumulation of further data in the ITS1 database, this method will be available for the identification of fungi.

  6. Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

    PubMed

    Chen, Wei-Hua; Lu, Guanting; Bork, Peer; Hu, Songnian; Lercher, Martin J

    2016-04-21

    Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides 'U' and 'C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides 'A' and 'G' at non-synonymous coding sites.

  7. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six DNA regions were evaluated in a multi-national, multi-laboratory consortium as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it...

  8. Sequence-specific binding of glucocorticoid receptor to MTV DNA at sites within and upstream of the transcribed region.

    PubMed

    Payvar, F; DeFranco, D; Firestone, G L; Edgar, B; Wrange, O; Okret, S; Gustafsson, J A; Yamamoto, K R

    1983-12-01

    Glucocorticoid receptor protein stimulates transcription initiation within murine mammary tumor virus (MTV) DNA sequences in vivo, and interacts selectively with MTV DNA in vitro. We mapped and compared five regions of MTV DNA that are bound specifically by purified receptor; one resides upstream of the transcription start site, and the others are distributed within transcribed sequences between 4 and 8 kb from the initiation site. Each region contains at least two strong binding sites for receptor, which itself appears to be a tetramer of 94,000 dalton hormone-binding subunits. Three of the five binding regions contain nine nuclease footprints that lack extensive homology, although a family of related octanucleotides can be discerned. Receptor interacts with the different regions with similar efficiencies, suggesting that receptor affinity for upstream and internal regions may differ by less than one order of magnitude. Moreover, each region appears to be bound independent of the others. A restriction fragment containing four footprint sequences from one of the regions has previously been shown to act in vivo as a receptor-dependent transcriptional enhancer element, implying that the binding sites detected in vitro may be biologically functional.

  9. Differentially transcribed regions of Haloferax volcanii genome depending on the medium salinity.

    PubMed Central

    Ferrer, C; Mojica, F J; Juez, G; Rodríguez-Valera, F

    1996-01-01

    To identify genomic regions involved in osmoregulation in the extremely halophilic archaeon Haloferax volcanii, we used a technique which involves hybridization of cDNAs obtained at different salinities against a cosmid library of the organism. Both low and high salt concentrations trigger differential expression; however, adaptation to low salinities seems to elicit a wider response. The presence of a large domain within the largest of the megaplasmids with a strong response to low salt concentrations is noteworthy. PMID:8550436

  10. Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

    PubMed Central

    2012-01-01

    Background Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. Results We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. Conclusions This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research. PMID:22929540

  11. Conservation in the first internal transcribed spacer (ITS1) region of Hematodinium perezi (genotype III) from Callinectes sapidus .

    PubMed

    Pagenkopp Lohan, Katrina M; Small, Hamish J; Shields, Jeffrey D; Place, Allen R; Reece, Kimberly S

    2013-03-13

    Hematodinium spp. infections have been reported from blue crabs Callinectes sapidus in high-salinity waters of the USA from New Jersey to Texas. Recently, H. perezi (genotype III) has been proposed as the parasite species and genotype infecting blue crabs from Virginia; however, it is unknown whether this same genotype is present in blue crabs from other locations. To address this question, we collected 317 blue crabs from Massachusetts, Virginia, Georgia, Florida, Louisiana, and Texas to test for the presence of H. perezi (III) using a specific PCR assay targeting the first internal transcribed spacer (ITS1) region of the ribosomal RNA gene complex. To examine the genetic variation within H. perezi (III), ITS1 region sequences from the parasite in blue crabs from multiple locations were compared to each other and to those of H. perezi (III) found in alternate hosts from Virginia. In total, 34 distinct ITS1 sequence variants of the parasite were identified from blue crabs alone, and 38 distinct variants were identified when alternate hosts were included. However, a single ITS1 sequence variant appeared in all geographic regions and hosts, and also in blue crabs sampled from a previous study. The high similarity among all the ITS1 region sequences examined (>98%) and the observation of a single variant found throughout a large geographic range, strongly suggests that a single species and genotype of Hematodinium, specifically H. perezi (III), infects blue crabs from Virginia to Texas and multiple alternate host species in Virginia.

  12. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.

    PubMed

    Lindner, Daniel L; Carlsen, Tor; Henrik Nilsson, R; Davey, Marie; Schumacher, Trond; Kauserud, Håvard

    2013-06-01

    The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3-5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.

  13. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

    PubMed Central

    Lindner, Daniel L; Carlsen, Tor; Henrik Nilsson, R; Davey, Marie; Schumacher, Trond; Kauserud, Håvard

    2013-01-01

    The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions. PMID:23789083

  14. Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

    PubMed Central

    Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying; Liu, Chang; Lv, Aiping; Deng, Youping; Larson-Rabin, Zachary; Wilkinson, Mike; Chen, Shilin

    2012-01-01

    Background Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. Methodology/Principal Findings In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. Conclusions Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification. PMID:22952830

  15. Evolution of the ribosomal RNA internal transcribed spacer one (ITS-1) in cichlid fishes of the Lake Victoria region.

    PubMed

    Booton, G C; Kaufman, L; Chandler, M; Oguto-Ohwayo, R; Duan, W; Fuerst, P A

    1999-03-01

    The nucleotide sequences of the first internal transcribed spacer (ITS-1) of the ribosomal RNA gene cluster have been determined for 11 species of closely related endemic cichlid fishes of the Lake Victoria region (LVR) and 6 related East African cichlids. The ITS-1 sequences confirmed independently derived basal phylogenies, but provide limited insight within this species flock. The line leading to Pseudocrenilabrus multicolor arose early, close to the divergence event that separated the tilapiine and haplochromine tribes of the "African Group" of the family Cichlidae. In this phylogeny, Astatoreochromis alluaudi and the riverine Astatotilapia burtoni are sister taxa, which together are a sister group to a monophyletic assemblage including both Lake Victoria and Lake Edward taxa. The ITS-1 data support the monophyly of haplochromine genera across lakes. Since Lake Victoria is believed to have been dry between 14, 500 and 12,400 BPE, the modern assemblage must have been derived from reinvasion by the products of earlier cladogenesis events. Thus, although the regional superflock is monophyletic, the haplochromines of Lake Victoria itself did not evolve in situ from a single ancestor.

  16. Sequence analysis of the internal transcribed spacer (ITS) region reveals a novel clade of Ichthyophonus sp. from rainbow trout

    USGS Publications Warehouse

    Rasmussen, C.; Purcell, M.K.; Gregg, J.L.; LaPatra, S.E.; Winton, J.R.; Hershberger, P.K.

    2010-01-01

    The mesomycetozoean parasite Ichthyophonus hoferi is most commonly associated with marine fish hosts but also occurs in some components of the freshwater rainbow trout Oncorhynchus mykiss aquaculture industry in Idaho, USA. It is not certain how the parasite was introduced into rainbow trout culture, but it might have been associated with the historical practice of feeding raw, ground common carp Cyprinus carpio that were caught by commercial fisherman. Here, we report a major genetic division between west coast freshwater and marine isolates of Ichthyophonus hoferi. Sequence differences were not detected in 2 regions of the highly conserved small subunit (18S) rDNA gene; however, nucleotide variation was seen in internal transcribed spacer loci (ITS1 and ITS2), both within and among the isolates. Intra-isolate variation ranged from 2.4 to 7.6 nucleotides over a region consisting of ~740 bp. Majority consensus sequences from marine/anadromous hosts differed in only 0 to 3 nucleotides (99.6 to 100% nucleotide identity), while those derived from freshwater rainbow trout had no nucleotide substitutions relative to each other. However, the consensus sequences between isolates from freshwater rainbow trout and those from marine/anadromous hosts differed in 13 to 16 nucleotides (97.8 to 98.2% nucleotide identity).

  17. Phylogenetics of Bonamia parasites based on small subunit and internal transcribed spacer region ribosomal DNA sequence data.

    PubMed

    Hill, Kristina M; Stokes, Nancy A; Webb, Stephen C; Hine, P Mike; Kroeck, Marina A; Moore, James D; Morley, Margaret S; Reece, Kimberly S; Burreson, Eugene M; Carnegie, Ryan B

    2014-07-24

    The genus Bonamia (Haplosporidia) includes economically significant oyster parasites. Described species were thought to have fairly circumscribed host and geographic ranges: B. ostreae infecting Ostrea edulis in Europe and North America, B. exitiosa infecting O. chilensis in New Zealand, and B. roughleyi infecting Saccostrea glomerata in Australia. The discovery of B. exitiosa-like parasites in new locations and the observation of a novel species, B. perspora, in non-commercial O. stentina altered this perception and prompted our wider evaluation of the global diversity of Bonamia parasites. Samples of 13 oyster species from 21 locations were screened for Bonamia spp. by PCR, and small subunit and internal transcribed spacer regions of Bonamia sp. ribosomal DNA were sequenced from PCR-positive individuals. Infections were confirmed histologically. Phylogenetic analyses using parsimony and Bayesian methods revealed one species, B. exitiosa, to be widely distributed, infecting 7 oyster species from Australia, New Zealand, Argentina, eastern and western USA, and Tunisia. More limited host and geographic distributions of B. ostreae and B. perspora were confirmed, but nothing genetically identifiable as B. roughleyi was found in Australia or elsewhere. Newly discovered diversity included a Bonamia sp. in Dendostrea sandvicensis from Hawaii, USA, that is basal to the other Bonamia species and a Bonamia sp. in O. edulis from Tomales Bay, California, USA, that is closely related to both B. exitiosa and the previously observed Bonamia sp. from O. chilensis in Chile.

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

    PubMed

    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.

  19. Internal transcribed spacer region sequence heterogeneity in Rhizopus microsporus: implications for molecular diagnosis in clinical microbiology laboratories.

    PubMed

    Woo, Patrick C Y; Leung, Shui-Yee; To, Kelvin K W; Chan, Jasper F W; Ngan, Antonio H Y; Cheng, Vincent C C; Lau, Susanna K P; Yuen, Kwok-Yung

    2010-01-01

    Although internal transcribed spacer region (ITS) sequence heterogeneity has been reported in a few fungal species, it has very rarely been reported in pathogenic fungi and has never been described in Mucorales, causes of the highly fatal mucormycosis. In a recent outbreak investigation of intestinal mucormycosis due to Rhizopus microsporus infection in patients with hematological malignancies, PCR of the ITS of four of the 28 R. microsporus strains, P11, P12, D3-1, and D4-1, showed thick bands at about 700 bp. Direct sequencing of the purified bands showed frequent double peaks along all of the sequence traces and occasional triple peaks for P12, D3-1, and D4-1. The thick bands of the four R. microsporus strains were purified and cloned. Sequencing of 10 clones for each strain revealed two different ITS sequences for P11 and three different ITS sequences for P12, D3-1, and D4-1. Variations in ITS sequence among the different ribosomal DNA (rDNA) operons in the same strain were observed in only ITS1 and ITS2 and not the 5.8S rDNA region. One copy of P11, P12, and D4-1, respectively, and one copy of P11, P12, D3-1, and D4-1, respectively, showed identical sequences. This represents the first evidence of ITS sequence heterogeneity in Mucorales. ITS sequence heterogeneity is an obstacle to molecular identification and genotyping of fungi in clinical microbiology laboratories. When thick bands and double peaks are observed during PCR sequencing of a gene target, such a strain should be sent to reference laboratories proficient in molecular technologies for further identification and/or genotyping.

  20. TSH stimulates 32P-labeling of thyroid nuclear HMG 14, a protein associated with actively transcribed chromatin

    SciTech Connect

    Cooper, E.; Palmer, R.J.; Spaulding, S.W.

    1982-04-01

    Thyroid slices were incubated with 32P with or without TSH. 32P-labeling of acid-soluble nuclear proteins was then examined by two-dimensional polyacrylamide gel electrophoresis and autoradiography. We found that TSH enhanced the labeling of the high mobility group protein HMG 14, a protein that is preferentially associated with actively transcribed chromatin. This observation suggests that changes in HMG 14 phosphorylation may be involved in mediating TSH-induced effects on the structure and function of active chromatin.

  1. Isolation and characterization of recombinant DNAs containing repeated elements of barley genome: identification of individual actively transcribed families of repeats

    SciTech Connect

    Prosnyak, M.I.; Kartel', N.A.; Ryskov, A.P.

    1986-05-01

    A bank of Escherichia coli clones containing fragments of barley nuclear DNA was obtained using plasmid pBR 322. Clones carrying repeated sequences of the plant genome were selected by means of colony and blot hybridization. Clones with actively transcribed sequences were selected by hybridization to complementary DNA synthesized by means of reverse transcription on a template of total barley poly(A)-containing RNA. Individual families of repeats, two of which contained transcriptionally active sequences of the barley genome, were identified by blot hybridization of recombinant plasmids containing labeled DNA fragments of the inserts of three different clones.

  2. Heat shock factor 1 binds to and transcribes satellite II and III sequences at several pericentromeric regions in heat-shocked cells

    SciTech Connect

    Eymery, Angeline; Souchier, Catherine; Vourc'h, Claire; Jolly, Caroline

    2010-07-01

    Cells respond to stress by activating the synthesis of heat shock proteins (HSPs) which protect the cells against the deleterious effects of stress. This mechanism is controlled by the heat shock factor 1 (HSF1). In parallel to HSP gene transcription, in human cells, HSF1 also binds to and transcribes satellite III repeated sequences present in numerous copies in the 9q12 pericentromeric region of chromosome 9. These HSF1 accumulation sites are termed nuclear stress bodies (nSBs). In tumor cells, however, the number of nSBs is higher than the number of 9q12 copies, suggesting the existence of other HSF1 targets. In this paper, we were interested in characterizing these other HSF1 binding sites. We show that HSF1 indeed binds to the pericentromeric region of 14 chromosomes, thereby directing the formation of 'secondary nSBs'. The appearance of secondary nSBs depends on the number of satellite sequences present in the target locus, and on the cellular amount of HSF1 protein. Moreover, secondary nSBs also correspond to transcription sites, thus demonstrating that heat shock induces a genome-wide transcription of satellite sequences. Finally, by analyzing published transcriptomic data, we show that the derepression of these large heterochromatic blocks does not significantly affect the transcription of neighboring genes.

  3. Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes

    SciTech Connect

    Venema, J.; van Hoffen, A.; Karcagi, V.; Natarajan, A.T.; van Zeeland, A.A.; Mullenders, L.H. )

    1991-08-01

    The authors have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5{prime} part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimers removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3{prime} part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells.

  4. Electrophoretic separation of a class of nucleosomes enriched in HMG 14 and 17 and actively transcribed globin genes.

    PubMed Central

    Albanese, I; Weintraub, H

    1980-01-01

    Monomer nucleosomes from chick erythrocytes can be fractionated according to their electrophoretic mobility in (comparatively) high salt acrylamide gels. We show that the fractionation is based predominantly on differences in charge. The monomer heterogeneity persists even when the nucleosomes are trimmed down to 145 bp with Exo III or when H1 and H5 are removed. The slowest migrating monomers are associated with HMG 14 and 17; however, we do not believe that these proteins are entirely responsible for the altered mobility since the nucleosome heterogeneity persists even after removal of HMG 14 and 17. The DNA associated with the HMG 14 and 17 containing nucleosomes is shown to be enriched in actively transcribed globin sequences. Images PMID:6448987

  5. Molecular genetics analysis for co-infection of Brugia malayi and Brugia pahangi in cat reservoirs based on internal transcribed spacer region 1.

    PubMed

    Areekit, Supatra; Khuchareontaworn, Sintawee; Kanjanavas, Pornpimon; Sriyapai, Thayat; Pakpitchareon, Arda; Khawsak, Paisarn; Chansiri, Kosum

    2009-01-01

    This study described the diagnosis of a mixed infection of Brugia malayi and Brugia pahangi in a single domestic cat using the internal transcribed spacer 1 (ITS1) region. Following polymerase chain reaction amplification of the ITS1 region, the 580 bp amplicon was cloned, and 29 white colonies were randomly selected for DNA sequencing and phylogenetic tree construction. A DNA parsimony tree generated two groups of Brugia spp with one group containing 6 clones corresponding to B. pahangi and the other 23 clones corresponding to B. malayi. This indicated that mixed infection of the two Brugia spp, B. pahangi and B. malayi, had occurred in a single host.

  6. Development of a Reverse Genetic System for Infectious Salmon Anemia Virus: Rescue of Recombinant Fluorescent Virus by Using Salmon Internal Transcribed Spacer Region 1 as a Novel Promoter

    PubMed Central

    Toro-Ascuy, Daniela; Tambley, Carolina; Beltran, Carolina; Mascayano, Carolina; Sandoval, Nicolas; Olivares, Eduardo; Medina, Rafael A.; Spencer, Eugenio

    2014-01-01

    Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report the development of a plasmid-based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). Salmon cells cotransfected with pSS-URG-based vectors expressing the eight viral RNA segments and four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, wild-type rISAV901_09 and rISAVrS6-NotI-HPR containing a NotI restriction site and rISAVS6/EGFP-HPR harboring the open reading frame of enhanced green fluorescent protein (EGFP), both within the highly polymorphic region (HPR) of segment 6. All rescued viruses showed replication activity and cytopathic effect in Atlantic salmon kidney-infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5 × 105 PFU/ml, similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and to develop a new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry. PMID:25480750

  7. Preferential repair of ionizing radiation-induced damage in the transcribed strand of an active human gene is defective in Cockayne syndrome

    SciTech Connect

    Leadon, S.A. ); Copper, P.K. )

    1993-11-15

    Cells from patients with Cockayne syndrome (CS), which are sensitive to killing by UV although overall damage removal appears normal, are specifically defective in repair of UV damage in actively transcribe genes. Because several CS strains display cross-sensitivity to killing by ionizing radiation, the authors examined whether ionizing radiation-induced damage in active genes is preferentially repaired by normal cells and whether the radiosensitivity of CS cells can be explained by a defect in this process. They found that ionizing radiation-induced damage was repaired more rapidly in the transcriptionally active metallothionein IIA (MTIIA) gene than in the inactive MTIIB gene or in the genome overall in normal cells as a result of faster repair on the transcribed strand of MTIIA. Cells of the radiosensitive CS strain CS1AN are completely defective in this strand-selective repair of ionizing radiation-induced damage, although their overall repair rate appears normal. CS3BE cells, which are intermediate in radiosensitivity, do exhibit more rapid repair of the transcribed strand but at a reduced rate compared to normal cells. Xeroderma pigmentosum complementation group A cells, which are hypersensitive to UV light because of a defect in the nucleotide excision repair pathway but do not show increased sensitivity to ionizing radiation, preferentially repair ionizing radiation-induced damage on the transcribed strand of MTIIA. Thus, the ability to rapidly repair ionizing radiation-induced damage in actively transcribing genes correlates with cell survival. The results extend the generality of preferential repair in active genes to include damage other than bulky lesions.

  8. Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region

    PubMed Central

    Sutton, Bruce D.; Steck, Gary J.; Norrbom, Allen L.; Rodriguez, Erick J.; Srivastava, Pratibha; Alvarado, Norma Nolazco; Colque, Fredy; Landa, Erick Yábar; Sánchez, Juan José Lagrava; Quisberth, Elizabeth; Peñaranda, Emilio Arévalo; Clavijo, P. A. Rodriguez; Alvarez-Baca, Jeniffer K.; Zapata, Tito Guevara; Ponce, Patricio

    2015-01-01

    Abstract The nuclear ribosomal internal transcribed spacer 1 (ITS1) was sequenced for Anastrepha fraterculus (Wiedemann, 1830) originating from 85 collections from the northern and central Andean countries of South America including Argentina (Tucumán), Bolivia, Perú, Ecuador, Colombia, and Venezuela. The ITS1 regions of additional specimens (17 collections) from Central America (México, Guatemala, Costa Rica, and Panamá), Brazil, Caribbean Colombia, and coastal Venezuela were sequenced and together with published sequences (Paraguay) provided context for interpretation. A total of six ITS1 sequence variants were recognized in the Andean region comprising four groups. Type I predominates in the southernmost range of Anastrepha fraterculus. Type II predominates in its northernmost range. In the central and northern Andes, the geographic distributions overlap and interdigitate with a strong elevational effect. A discussion of relationships between observed ITS1 types and morphometric types is included. PMID:26798259

  9. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions.

    PubMed

    Scorzetti, Gloria; Fell, J W; Fonseca, A; Statzell-Tallman, Adele

    2002-12-01

    Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.

  10. Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region.

    PubMed

    Sutton, Bruce D; Steck, Gary J; Norrbom, Allen L; Rodriguez, Erick J; Srivastava, Pratibha; Alvarado, Norma Nolazco; Colque, Fredy; Landa, Erick Yábar; Sánchez, Juan José Lagrava; Quisberth, Elizabeth; Peñaranda, Emilio Arévalo; Clavijo, P A Rodriguez; Alvarez-Baca, Jeniffer K; Zapata, Tito Guevara; Ponce, Patricio

    2015-01-01

    The nuclear ribosomal internal transcribed spacer 1 (ITS1) was sequenced for Anastrepha fraterculus (Wiedemann, 1830) originating from 85 collections from the northern and central Andean countries of South America including Argentina (Tucumán), Bolivia, Perú, Ecuador, Colombia, and Venezuela. The ITS1 regions of additional specimens (17 collections) from Central America (México, Guatemala, Costa Rica, and Panamá), Brazil, Caribbean Colombia, and coastal Venezuela were sequenced and together with published sequences (Paraguay) provided context for interpretation. A total of six ITS1 sequence variants were recognized in the Andean region comprising four groups. Type I predominates in the southernmost range of Anastrepha fraterculus. Type II predominates in its northernmost range. In the central and northern Andes, the geographic distributions overlap and interdigitate with a strong elevational effect. A discussion of relationships between observed ITS1 types and morphometric types is included.

  11. A new PCR primer for the identification of Paracoccidioides brasiliensis based on rRNA sequences coding the internal transcribed spacers (ITS) and 5 x 8S regions.

    PubMed

    Imai, T; Sano, A; Mikami, Y; Watanabe, K; Aoki, F H; Branchini, M L; Negroni, R; Nishimura, K; Miyaji, M

    2000-08-01

    Internal transcribed spacer (ITS) genes including the 5.8S ribosomal (r)RNA of Paracoccidioides brasiliensis were amplified and the DNA sequences were determined. Based on a comparison of the sequence information, a new polymerase chain reaction (PCR) primer pair was designed for specific amplification of DNA for P. brasiliensis. This primer pair amplified a 418-bp DNA sequence and was 100% successful in identifying 29 strains of P. brasiliensis (including the reference strains) isolated from the regions of Brazil, Costa Rica, Japan, Argentina or from different sources. The results of specificity tests of these primers to compare the fungus with those of Aspergillus fumigatus, Blastomyces dermatitidis, Candida albicans, Cryptococcus neoformans, Histoplasma capsulatum and Penicillium marneffei are also reported.

  12. Sequence variation of the ribosomal DNA second internal transcribed spacer region in two spatially-distinct populations of Amblyomma americanum (L.) (Acari: Ixodidae).

    PubMed

    Reichard, M V; Kocan, A A; Van Den Bussche, R A; Barker, R W; Wyckoff, J H; Ewing, S A

    2005-04-01

    Sequence analysis of the ribosomal DNA second internal transcribed spacer (ITS 2) region in 2 spatially distinct populations of Amblyomma americanum (L.) revealed intraspecific variation. Nucleotide sequences from multiple DNA extractions and several polymerase chain reaction amplifications of eggs from mixed-parentage samples from both populations of ticks revealed that 12 of 1,145 (1.0%) sites varied. Three of the 12 sites of variation were distinct between the 2 A. americanum populations, which corresponded to a rate of 0.26%. Phylogenetic analysis based on ITS 2 sequences provided strong support (i.e., bootstrap value of 80%) that wild A. americanum clustered into a distinguishable group separate from those derived from colony ticks.

  13. Intraspecific variation in Radopholus similis isolates assessed with restriction fragment length polymorphism and DNA sequencing of the internal transcribed spacer region of the ribosomal RNA cistron.

    PubMed

    Elbadri, Gamal A A; De Ley, Paul; Waeyenberge, Lieven; Vierstraete, Andy; Moens, Maurice; Vanfleteren, Jacques

    2002-02-01

    Restriction fragment length polymorphism and direct sequencing of the internal transcribed spacer rDNA region of 19 isolates of Radopholus similis yielded significant diversity, both among isolates and within some individuals. Restriction fragment length polymorphism with HaeIII, AluI and Tru9I yielded two sets of patterns. Digestion with RsaI revealed one or two supernumerary bands in single nematodes from five isolates, and sequencing confirmed microheterogeneity in four of these. Phylogenetic analysis grouped most isolates closely together, except for the five isolates with additional bands for RsaI. Our data reveal more population structure than previously found and lend further support to the synonymy of R. similis and 'Radopholus citrophilus'.

  14. The Nine Genes of the Nocardia lactamdurans Cephamycin Cluster Are Transcribed into Large mRNAs from Three Promoters, Two of Them Located in a Bidirectional Promoter Region

    PubMed Central

    Enguita, Francisco J.; Coque, Juan Jose R.; Liras, Paloma; Martin, Juan F.

    1998-01-01

    The nine biosynthesis genes of the Nocardia lactamdurans cephamycin cluster are expressed as three different mRNAs initiating at promoters latp, cefDp, and pcbABp, as shown by low-resolution S1 nuclease protection assays and Northern blotting analysis. Bidirectional expression occurred from divergent promoters (latp and cefDp) located in a 629-bp intergenic region that contains three heptameric direct repeats similar to those recognized by members of the SARP (Streptomyces antibiotic regulatory proteins) family. The lat gene is transcribed in a single monocistronic transcript initiating at latp. A second unusually long polycistronic mRNA (more than 16 kb) corresponding to six biosynthesis genes (pcbAB, pcbC, cmcI, cmcJ, cefF, and cmcH) started at pcbABp. A third polycistronic mRNA corresponding to the cefD and cefE genes started at cefDp. PMID:9765587

  15. Identification and Typing of Malassezia Species by Amplified Fragment Length Polymorphism and Sequence Analyses of the Internal Transcribed Spacer and Large-Subunit Regions of Ribosomal DNA

    PubMed Central

    Gupta, Aditya K.; Boekhout, Teun; Theelen, Bart; Summerbell, Richard; Batra, Roma

    2004-01-01

    Malassezia yeasts are associated with several dermatological disorders. The conventional identification of Malassezia species by phenotypic methods is complicated and time-consuming, and the results based on culture methods are difficult to interpret. A comparative molecular approach based on the use of three molecular techniques, namely, amplified fragment length polymorphism (AFLP) analysis, sequencing of the internal transcribed spacer, and sequencing of the D1 and D2 domains of the large-subunit ribosomal DNA region, was applied for the identification of Malassezia species. All species could be correctly identified by means of these methods. The results of AFLP analysis and sequencing were in complete agreement with each other. However, some discrepancies were noted when the molecular methods were compared with the phenotypic method of identification. Specific genotypes were distinguished within a collection of Malassezia furfur isolates from Canadian sources. AFLP analysis revealed significant geographical differences between the North American and European M. furfur strains. PMID:15365020

  16. Conservation in the first internal transcribed spacer region (ITS1) in Hematodinium species infecting crustacean hosts found in the UK and Newfoundland.

    PubMed

    Small, H J; Shields, J D; Moss, J A; Reece, K S

    2007-05-09

    Parasitic dinoflagellates in the genus Hematodinium infect a number of decapod crustaceans in waters off the UK, including the Norway lobster Nephrops norvegicus and the edible crab Cancer pagurus. This study investigated sequence variability in the first internal transcribed spacer (ITS1) region of the ribosomal RNA complex of Hematodinium spp. infecting N. norvegicus, C. pagurus, and Pagurus bernhardus from 4 locations in the UK and from the Hematodinium sp. infecting Chionoecetes opilio from the province of Newfoundland and Labrador, Canada. Phylogenetic analysis of the Hematodinium ITS1 sequences from N. norvegicus, C. pagurus, P. bernhardus and C. opilio suggest that these crustaceans are infected with the same species of Hematodinium. Length variability of the ITS1 region was observed (324 to 345 bp) and attributed to 4 variable microsatellite regions (CATG)n' (GCC)nTCCGC(TG)n' (TA)n' and (GAA)n(GGA)n within the sequenced ITS1 fragment. The observed variation may be due to co-infection of the host crustacean with several different strains of Hematodinium or differences among copies of ITS1 region within the genome of a single parasite cell. The Hematodinium ITS1 sequence from N. norvegicus, C. pagurus, P. bernhardus and C. opilio isolates was sufficiently conserved in primer binding regions targeted by previous molecular diagnostic assays; therefore, we suggest that this assay could be used to screen for Hematodinium infections in these crustacean hosts.

  17. Enhanced DNA repair of bleomycin-induced 3'-phosphoglycolate termini at the transcription start sites of actively transcribed genes in human cells.

    PubMed

    Murray, Vincent; Chen, Jon K; Galea, Anne M

    2014-11-01

    The anti-tumour agent, bleomycin, cleaves DNA to give 3'-phosphoglycolate and 5'-phosphate termini. The removal of 3'-phosphoglycolate to give 3'-OH ends is a very important step in the DNA repair of these lesions. In this study, next-generation DNA sequencing was utilised to investigate the repair of these 3'-phosphoglycolate termini at the transcription start sites (TSSs) of genes in HeLa cells. The 143,600 identified human TSSs in HeLa cells comprised 82,596 non-transcribed genes and 61,004 transcribed genes; and the transcribed genes were divided into quintiles of 12,201 genes comprising the top 20%, 20-40%, 40-60%, 60-80%, 80-100% of expressed genes. Repair of bleomycin-induced 3'-phosphoglycolate termini was enhanced at actively transcribed genes. The top 20% and 20-40% quintiles had a very similar level of enhanced repair, the 40-60% quintile was intermediate, while the 60-80% and 80-100% quintiles were close to the low level of enhancement found in non-transcribed genes. There were also interesting differences regarding bleomycin repair on the sense and antisense strands of DNA at TSSs. The sense strand had highly enhanced repair between 0 and 250bp relative to the TSS, while for the antisense strand highly enhanced repair was between 150 and 450bp. Repair of DNA damage is a major mechanism of resistance to anti-tumour drugs and this study provides an insight into this process in human tumour cells.

  18. Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

    PubMed

    Harpke, Doerte; Peterson, Angela

    2008-05-01

    The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

  19. Genetic diversity of Histoplasma capsulatum strains isolated from Argentina based on nucleotide sequence variations in the internal transcribed spacer regions of rDNA.

    PubMed

    Landaburu, Fernanda; Cuestas, María Luján; Rubio, Andrea; Elías, Nahuel Alejandro; Daneri, Gabriela Lopez; Veciño, Cecilia; Iovannitti, Cristina A; Mujica, María Teresa

    2014-05-01

    The internal transcribed spacer (ITS) regions of rDNA genes of 49 Histoplasma capsulatum (48 from clinical samples and one from soil) isolates were examined. Nucleotide sequence heterogeneity within this region was useful for phylogenetic classification of H. capsulatum and species identification. Thus, in 45 of 49 isolates we observed higher percentages of identity in the nucleotide sequences of ITS regions when the isolates studied herein were compared with those reported in our country in the South America B clade. Phylogenetic analyses of rDNA sequences corresponding to the 537 bp of the ITS region obtained from H. capsulatum isolates assigned South America type B clade (45 isolates), North America type 1 and Asia clade (2 isolates each one). H. capsulatum strains isolated from soil and from patients living in Argentina (45 of 49) clustered together with the H. capsulatum isolates of the South America B clade. The high level of genetic similarity among our isolates suggests that almost one genetic population is present in the microenvironment. Isolates described as H. capsulatum var. capsulatum or var. farciminosum (2 isolates) did not form a monophyletic group and were found in the Asia clade. Subsequent studies are needed to properly identify these isolates.

  20. Characterization of internal transcribed spacer (ITS1)-ITS2 region of ribosomal RNA gene from 25 species of Culicoides biting midges (Diptera: Ceratopogonidae) in Japan.

    PubMed

    Matsumoto, Y; Yanase, T; Tsuda, T; Noda, H

    2009-09-01

    We determined nucleotide sequences of the nuclear rDNA internal transcribed spacer (ITS)1-5.8S-ITS2a-2S-ITS2 region in 103 individuals of 25 Culicoides species (Diptera: Ceratopogonidae) from 11 locations in Japan. Ribosomal RNA genes, 5.8S and 2S rDNA, were highly conserved among the species with few variations. The ITS2a region showed length variation among species. Both ITS1 and ITS2 showed highly varied sequences among species. The noticeable indel regions among ITS1 sequences are present in some Culicoides species, separating species into two types having long or short ITS1 region. However, Culicoides cylindratus Kitaoka possesses both types of ITS1 in each individual; these results seem to indicate that the ITS1-long type was the prototype and the short type was produced through deletion in many Culicoides species. One species, belonging to subgenus Avaritia, possessed an Avaritia-specific sequence in ITS1 and phylogenetically formed a monophyletic group. Geographical genotypes in a species were not clear. Species-specific sequence features were observed, enabling molecular identification of Culicoides species.

  1. Coordinate regulation of two cytoplasmic RNA species transcribed from early region 2 of the adenovirus 2 genome.

    PubMed

    Goldenberg, C J; Rosenthal, R; Bhaduri, S; Raskas, H

    1981-06-01

    Early region 2 (E2) of the adenovirus 2 genome specifies a 72,000-dalton DNA-binding protein that is required for viral DNA replication. Electron microscopy studies have detected two major forms of 20S E2 mRNA, one species with a 5' leader from map position 75 and a second form having a leader from position 72 (Chow et al., J. Mol. Biol. 134:265-303, 1979). Only the species with a leader from position 75 was detected at early times; however, both forms were found at late times. We have analyzed the temporal regulation of E2 expression by documenting mRNA accumulation in the cytoplasm. Kinetic studies of pulse-labeled RNAs demonstrated a peak of E2 cytoplasmic RNa synthesis at 10 to 12 h, coinciding with the time of maximal synthesis of the 72,000-dalton DNA binding protein and viral DNA. To estimate the relative abundances of the two major E2 RNA species at various times during infection, total E2 cytoplasmic and polysomal 20S RNAs were isolated by hybridization-selection with specific DNA probes. The leader sequences in the selected RNAs were then quantitated by further RNA-DNA hybridization. We found that the elevated accumulation rate for E2 cytoplasmic RNA at late times reflected an increase in formation of both major species. Moreover, for all time points examined 66% of the mRNA species had a 5' end from map position 75, and 33% had a 5' terminus from position 72. Continuous labeling experiments provided evidence that both RNA forms have comparable half-lives. The results suggest that the two major species encoded by E2 are regulated in a coordinate fashion late in infection.

  2. Intraspecific variation and population structure of the German cockroach, Blattella germanica, revealed with RFLP analysis of the non-transcribed spacer region of ribosomal DNA.

    PubMed

    Mukha, D V; Kagramanova, A S; Lazebnaya, I V; Lazebnyi, O E; Vargo, E L; Schal, C

    2007-06-01

    Little information is available on genetic variation within and between populations of pest cockroaches. In this study, intraspecific HindIII polymorphism was investigated in the German cockroach, Blattella germanica (Linnaeus) (Dictyoptera, Blattaria: Blattellidae), using restriction fragment length polymorphisms (RFLP) of the non-transcribed spacer (NTS) region of ribosomal DNA (rDNA). Individual male insects were collected from infestations at three different pig farms. Each population was characterized by HindIII restriction fragment frequencies and haplotype (a particular X-chromosome pattern) frequencies. The inheritance of the X-chromosome HindIII rDNA patterns over 12 generations (3 years) follows Mendelian patterns, and the stability of this polymorphic marker indicates infrequent genetic recombination of variable sites. Although pairwise genetic distance measures were uncorrelated with geographical distance, the pattern of genetic differentiation of the three cockroach populations suggests that human-mediated transport of cockroaches is an important force in shaping the population genetic structure of cockroach infestations, at least at the regional scale of 10-100 km. Sequence variation in the ribosomal NTS is a useful marker, and RFLP of rDNA is a simple, robust and reproducible technique for differentiating recently diverged cockroach populations.

  3. Molecular characterization of the Indian poultry nodular tapeworm, Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) based on rDNA internal transcribed spacer 2 region.

    PubMed

    Ramnath; Jyrwa, D B; Dutta, A K; Das, B; Tandon, V

    2014-03-01

    The nodular tapeworm, Raillietina echinobothrida is a well studied avian gastrointestinal parasite of family Davaineidae (Cestoda: Cyclophyllidea). It is reported to be the largest in size and second most prevalent species infecting chicken in north-east India. In the present study, morphometrical methods coupled with the molecular analysis of the second internal transcribed spacer (ITS2) region of ribosomal DNA were employed for precise identification of the parasite. The annotated ITS2 region was found to be 446 bp long and further utilized to elucidate the phylogenetic relationships and its species-interrelationships at the molecular level. In phylogenetic analysis similar topology was observed among the trees obtained by distance-based neighbor-joining as well as character-based maximum parsimony tree building methods. The query sequence R. echinobothrida is well aligned and placed within the Davaineidae group, with all Raillietina species well separated from the other cyclophyllidean (taeniid and hymenolepid) cestodes, while Diphyllobothrium latum (Pseudophyllidea: Diphyllobothriidae) was rooted as an out-group. Sequence similarities indeed confirmed our hypothesis that Raillietina spp. are neighboring the position with other studied species of order Cyclophyllidea against the out-group order Pseudophyllidea. The present study strengthens the potential of ITS2 as a reliable marker for phylogenetic reconstructions.

  4. Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    ZARRIN, MAJID; GANJ, FARZANEH; FARAMARZI, SAMA

    2016-01-01

    The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species. PMID:27073635

  5. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  6. DNA fingerprinting of Paenibacillus popilliae and Paenibacillus lentimorbus using PCR-amplified 16S-23S rDNA intergenic transcribed spacer (ITS) regions.

    PubMed

    Dingman, Douglas W

    2009-01-01

    Failure to identify correctly the milky disease bacteria, Paenibacillus popilliae and Paenibacillus lentimorbus, has resulted in published research errors and commercial production problems. A DNA fingerprinting procedure, using PCR amplification of the 16S-23S rDNA intergenic transcribed spacer (ITS) regions, has been shown to easily and accurately identify isolates of milky disease bacteria. Using 34 P. popilliae and 15 P. lentimorbus strains, PCR amplification of different ITS regions produced three DNA fingerprints. For P. lentimorbus phylogenic group 2 strains and for all P. popilliae strains tested, electrophoresis of amplified DNA produced a migratory pattern (i.e., ITS-PCR fingerprint) exhibiting three DNA bands. P. lentimorbus group 1 strains also produced this ITS-PCR fingerprint. However, the fingerprint was phase-shifted toward larger DNA sizes. Alignment of the respective P. popilliae and P. lentimorbus group 1 ITS DNA sequences showed extensive homology, except for a 108bp insert in all P. lentimorbus ITS regions. This insert occurred at the same location relative to the 23S rDNA and accounted for the phase-shift difference in P. lentimorbus group 1 DNA fingerprints. At present, there is no explanation for this 108bp insert. The third ITS-PCR fingerprint, produced by P. lentimorbus group 3 strains, exhibited approximately eight DNA bands. Comparison of the three fingerprints of milky disease bacteria to the ITS-PCR fingerprints of other Paenibacillus species demonstrated uniqueness. ITS-PCR fingerprinting successfully identified eight unknown isolates as milky disease bacteria. Therefore, this procedure can serve as a standard protocol to identify P. popilliae and P. lentimorbus.

  7. Topoisomerase 1-dependent deletions initiated by incision at ribonucleotides are biased to the non-transcribed strand of a highly activated reporter

    PubMed Central

    Cho, Jang-Eun; Kim, Nayun; Jinks-Robertson, Sue

    2015-01-01

    DNA polymerases incorporate ribonucleoside monophosphates (rNMPs) into genomic DNA at a low level and such rNMPs are efficiently removed in an error-free manner by ribonuclease (RNase) H2. In the absence of RNase H2 in budding yeast, persistent rNMPs give rise to short deletions via a mutagenic process initiated by Topoisomerase 1 (Top1). We examined the activity of a 2-bp, rNMP-dependent deletion hotspot [the (TG)2 hotspot] when on the transcribed or non-transcribed strand (TS or NTS, respectively) of a reporter placed in both orientations near a strong origin of replication. Under low-transcription conditions, hotspot activity depended on whether the (TG)2 sequence was part of the newly synthesized leading or lagging strand of replication. In agreement with an earlier study, deletions occurred at a much higher rate when (TG)2 was on the nascent leading strand. Under high-transcription conditions, however, hotspot activity was not dependent on replication direction, but rather on whether the (TG)2 sequence was on the TS or NTS of the reporter. Deletion rates were several orders of magnitude higher when (TG)2 was on the NTS. These results highlight the complex interplay between replication and transcription in regulating Top1-dependent genetic instability. PMID:26271994

  8. A Real-Time PCR Method for Quantifying Viable Ascaris Eggs Using the First Internally Transcribed Spacer Region of Ribosomal DNA▿

    PubMed Central

    Pecson, Brian M.; Barrios, José Antonio; Johnson, David R.; Nelson, Kara L.

    2006-01-01

    Worldwide, 1.4 billion people are infected with the intestinal worm Ascaris lumbricoides. As a result, Ascaris eggs are commonly found in wastewater and sludges. The current microscopy method for detecting viable Ascaris eggs is time- and labor-intensive. The goal of this study was to develop a real-time quantitative PCR (qPCR) method to determine the levels of total and viable Ascaris eggs in laboratory solutions using the first internally transcribed spacer (ITS-1) region of ribosomal DNA (rDNA) and rRNA. ITS-1 rDNA levels were proportional to Ascaris egg cell numbers, increasing as eggs developed from single cells to mature larvae and ultimately reaching a constant level per egg. Treatments causing >99% inactivation (high heat, moderate heat, ammonia, and UV) eliminated this increase in ITS-1 rDNA levels and caused decreases that were dependent on the treatment type. By taking advantage of this difference in ITS-1 rDNA level between viable, larvated eggs and inactivated, single-celled eggs, qPCR results were used to develop inactivation profiles for the different treatments. No statistical difference from the standard microscopy method was found in 75% of the samples (12 of 16). ITS-1 rRNA was detected only in samples containing viable eggs, but the levels were more variable than rDNA levels and ITS-1 rRNA could not be used for quantification. The detection limit of the rDNA-based method was approximately one larvated egg or 90 single-celled eggs; the detection limit for the rRNA-based method was several orders of magnitude higher. The rDNA qPCR method is promising for both research and regulatory applications. PMID:17056687

  9. Delayed secondary glucocorticoid response elements. Unusual nucleotide motifs specify glucocorticoid receptor binding to transcribed regions of alpha 2u-globulin DNA.

    PubMed

    Chan, G C; Hess, P; Meenakshi, T; Carlstedt-Duke, J; Gustafsson, J A; Payvar, F

    1991-11-25

    Glucocorticoids stimulate the transcription of rat alpha 2u-globulin (RUG) genes. Because this induction occurs after a time lag of several hours and is blocked by inhibitors of protein synthesis, it exemplifies a delayed secondary response to steroid hormones. In this report, we show that a region of RUG-transcribed DNA (approximately +1800 to +2174) contains multiple footprint sites for glucocorticoid receptor that are, apparently, organized into at least three independent binding clusters. The DNA sequences bound by the receptor and the location of binding sites were determined. A family of sequences related to half-sites of the consensus primary glucocorticoid response element (GRE) is discernible at each cluster of sites. Compared to the consensus GRE, which contains two pseudo-palindromic hexanucleotides arranged in a tail-to-tail fashion and separated by three bases, the arrangements of hexanucleotides within this segment of RUG DNA are unusual and heterogeneous. Methylation interference of a binding cluster containing three receptor footprints demonstrates that certain guanines of the GRE-like hexanucleotides are essential for efficient receptor binding. A synthetic 29-base pair (bp) RUG element, containing one receptor footprint from this cluster, selectively binds the receptor. Within this 29-bp element, six nucleotides separate two directly repeated copies of GRE-like hexanucleotides. RUG DNA fragments containing all or part of the three binding clusters, including the 29-bp element, confer a delayed secondary hormone responsiveness upon a linked heterologous promoter and reporter gene in stably transfected cell lines. We speculate that the unusual DNA sequence motifs of the receptor-binding sites are crucial for the generation of certain delayed secondary responses.

  10. Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China.

    PubMed

    Li, F; Hu, T; Duan, N C; Li, W Y; Teng, Q; Li, H; Liu, W; Liu, Y; Cheng, T Y

    2016-01-01

    The present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5-72% for pcox1, 73.7-74.2% for pnad1 and 58-58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0-1.6% for pcox1, 0-1.9% for pnad1 and 0-1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1-12.5%, 13.3-17.7% and 8.5-18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

  11. Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species

    PubMed Central

    Chen, Sharon C.-A.; Wang, He; Zhang, Li; Fan, Xin; Xu, Zhi-Peng; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2–3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species. PMID:27105313

  12. Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The nuclear ribosomal internal transcribed spacer 1 (ITS1) was sequenced for Anastrepha fraterculus (Wiedemann, 1830) originating from 85 collections from the northern and central Andean countries of South America including Argentina (Tucumán), Bolivia, Perú, Ecuador, Colombia, and Venezuela. The IT...

  13. Evolution of the mouse H-2K region: a hot spot of mutation associated with genes transcribed in embryos and/or germ cells.

    PubMed

    Yeom, Y I; Abe, K; Artzt, K

    1992-03-01

    Active gene transcription is known to promote genetic change in neighboring DNA. We reasoned that the change would be readily heritable if transcription was occurring in germ cells or early embryonic cells before the germ cells are set aside. The H-2K region of the major histocompatibility complex (MHC) provides a good vehicle for testing this hypothesis because it is replete with such genes. We have compared the amount of polymorphism in 240 kb of DNA contiguous with H-2K and 150 kb of DNA flanking a homologous duplicated region in t-haplotypes and inbred strains. Using 90 probes and three restriction enzymes, we find a staggering difference in the amount of polymorphism in the H-2K region vs. the duplicated region (26% vs. 0%) of t-haplotypes. The disparity in the rate of divergence between the two regions indicates that the spatial distribution of genes and their expression pattern might be important factors in sequence evolution. Since t-haplotypes normally show extremely limited variability among themselves due to their recent divergence from a single ancestor, these results imply that the mutation rate in the H-2K region is unusually high. This is in apparent contradiction to the current view that the MHC loci have evolved at the same rate as other loci. The implications for the evolution of the H-2K gene are discussed.

  14. Assessment of preferential cleavage of an actively transcribed retroviral hybrid gene in murine cells by deoxyribonuclease I, bleomycin, neocarzinostatin, or ionizing radiation

    SciTech Connect

    Beckmann, R.P.; Agostino, M.J.; McHugh, M.M.; Sigmund, R.D.; Beerman, T.A.

    1987-08-25

    Preferential cleavage induced by bleomycin, neocarzinostatin, or ionizing radiation in a transcribed cellular gene was evaluated through comparisons with deoxyribonuclease I. The glucocorticoid-inducible LTL gene previously described served as the specific DNA target. A Southern blot analysis was used to specifically assess cleavage of the LTL gene in nuclei isolated from cells either treated or untreated with the synthetic glucocorticoid dexamethasone. Hypersensitivity of the gene to bleomycin or neocarzinostatin, which paralleled deoxyribonuclease I hypersensitivity, was evident only in nuclei isolated from dexamethasone-treated cells. Like deoxyribonuclease I, sites of dexamethasone-inducible drug hypersensitivity were coincident with the binding region for the glucocorticoid receptor found within the regulatory sequences of the LTL gene. In contrast, no hypersensitivity to ionizing radiation was evident. Although bleomycin and neocarzinostatin showed qualitatively similar preferences for the threshold LTL gene, quantitative evaluations of damage to total cellular DNA by filter elution showed that the relative specificity of bleomycin for the hypersensitive region was much less than that of either deoxyribonuclease I or neocarzinostatin.

  15. Transcriptionally active genome regions are preferred targets for retrovirus integration.

    PubMed Central

    Scherdin, U; Rhodes, K; Breindl, M

    1990-01-01

    We have analyzed the transcriptional activity of cellular target sequences for Moloney murine leukemia virus integration in mouse fibroblasts. At least five of the nine random, unselected integration target sequences studied showed direct evidence for transcriptional activity by hybridization to nuclear run-on transcripts prepared from uninfected cells. At least four of the sequences contained multiple recognition sites for several restriction enzymes that cut preferentially in CpG-rich islands, indicating integration into 5' or 3' ends or flanking regions of genes. Assuming that only a minor fraction (less than 20%) of the genome is transcribed in mammalian cells, we calculated the probability that this association of retroviral integration sites with transcribed sequences is due to chance to be very low (1.6 x 10(-2]. Thus, our results strongly suggest that transcriptionally active genome regions are preferred targets for retrovirus integration. Images PMID:2296087

  16. Active region seismology

    NASA Technical Reports Server (NTRS)

    Bogdan, Tom; Braun, D. C.

    1995-01-01

    Active region seismology is concerned with the determination and interpretation of the interaction of the solar acoustic oscillations with near-surface target structures, such as magnetic flux concentration, sunspots, and plage. Recent observations made with a high spatial resolution and a long temporal duration enabled measurements of the scattering matrix for sunspots and solar active regions to be carried out as a function of the mode properties. Based on this information, the amount of p-mode absorption, partial-wave phase shift, and mode mixing introduced by the sunspot, could be determined. In addition, the possibility of detecting the presence of completely submerged magnetic fields was raised, and new procedures for performing acoustic holography of the solar interior are being developed. The accumulating evidence points to the mode conversion of p-modes to various magneto-atmospheric waves within the magnetic flux concentration as being the unifying physical mechanism responsible for these diverse phenomena.

  17. dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes.

    PubMed

    Lloret-Llinares, Marta; Pérez-Lluch, Sílvia; Rossell, David; Morán, Tomás; Ponsa-Cobas, Joan; Auer, Herbert; Corominas, Montserrat; Azorín, Fernando

    2012-10-01

    H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol llo(ser5) form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.

  18. Genotyping of Pneumocystis jirovecii isolates from Chinese HIV-infected patients based on nucleotide sequence variations in the internal transcribed spacer regions of rRNA genes.

    PubMed

    Li, Kai; He, Ai; Cai, Wei Ping; Tang, Xiao Ping; Zheng, Xiao Ying; Li, Zhuo Ya; Zhan, Xi Mei

    2013-01-01

    Genetic diversity of Pneumocystis jirovecii isolates based on internal transcribed spacer (ITS) of the nuclear rRNA locus has previously been reported. The information about ITS genotype and epidemiology of this organism in Chinese human immunodeficiency virus-infected patients has not been available. In this study, 12 bronchoalveolar lavage fluid specimens obtained from HIV-infected patients were analyzed by PCR followed by cloning, sequencing and typing. Three ITS1 genotypes (E, B and 'H') and four ITS2 genotypes (b, g, i and r) as previously reported were identified, the most common of which were E, b and i. Five ITS haplotypes (Eg, Eb, Bi, Er and 'H'r) and 19 new combination types were also identified with the most common types being Eg (four of 12 patients, 10 of 60 clones), Eb (three of 12 patients, 11 of 60 clones) and Bi (three of 12 patients, 10 of 60 clones). Nine patients were found to be co-infected with more than one ITS genotype of P. jirovecii. The prevalence of ITS genotypes in HIV patients from one Chinese hospital did not seem to be significantly different when compared to reports from other countries.

  19. Primers ITS1, ITS2 and ITS4 detect the intraspecies variability in the internal transcribed spacers and 5.8S rRNA gene region in clinical isolates of fungi.

    PubMed

    Korabecná, M; Liska, V; Fajfrlík, K

    2003-01-01

    Restriction fragment length polymorphism analysis of the 5.8S rRNA gene and the internal transcribed spacers (ITS1 and ITS2) was used for examination of 66 isolates belonging to 19 species. Intraspecies variability was found in the examined region of 11 species (Candida albicans, C. catenulata, C. colliculosa, C. glabrata, C. kefyr, C. melinii, C. parapsilosis, C. guillermondii, C. solanii, C. tropicalis, Saccharomyces cerevisiae). Region of ITS-5.8S rDNA was amplified using the primers ITS1 and ITS4. The amplicons were digested by HaeIII, HinfI and CfoI. The recognized intraspecies variability was confirmed in the second step, in which the shorter fragments of this region were amplified using primers ITS1 and ITS2 and analyzed by capillary electrophoresis. Considerable intraspecific variability renders this method unsuitable for species identification, whereas it can be useful for epidemiological tracing of isolates.

  20. Seeing What They Meant: Transcribing as a Route To Noticing.

    ERIC Educational Resources Information Center

    Lynch, Tony

    2001-01-01

    Describes a reflective noticing activity in which pairs of adult learners of English for academic purposes transcribe their own performances of a routine classroom speaking task. Analysis of the process and product of these cycles of work suggest that collaborative transcribing and editing can encourage learners to focus on their form in output in…

  1. Nucleosomes are depleted at the VSG expression site transcribed by RNA polymerase I in African trypanosomes.

    PubMed

    Figueiredo, Luisa M; Cross, George A M

    2010-01-01

    In most eukaryotes, RNA polymerase I (Pol I) exclusively transcribes long arrays of identical rRNA genes (ribosomal DNA [rDNA]). African trypanosomes have the unique property of using Pol I to also transcribe the variant surface glycoprotein VSG genes. VSGs are important virulence factors because their switching allows trypanosomes to escape the host immune system, a mechanism known as antigenic variation. Only one VSG is transcribed at a time from one of 15 bloodstream-form expression sites (BESs). Although it is clear that switching among BESs does not involve DNA rearrangements and that regulation is probably epigenetic, it remains unknown why BESs are transcribed by Pol I and what roles are played by chromatin structure and histone modifications. Using chromatin immunoprecipitation, micrococcal nuclease digestion, and chromatin fractionation, we observed that there are fewer nucleosomes at the active BES and that these are irregularly spaced compared to silent BESs. rDNA coding regions are also depleted of nucleosomes, relative to the rDNA spacer. In contrast, genes transcribed by Pol II are organized in a more compact, regularly spaced, nucleosomal structure. These observations provide new insight on antigenic variation by showing that chromatin remodeling is an intrinsic feature of BES regulation.

  2. Regional Activities Division. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on library network activities in Canada, the Third World, Japan, Malaysia, Brazil, and Sweden which were presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "Canada: A Voluntary and Flexible Network," a review by Guy Sylvestre of the political, social, and economic structures…

  3. The Ancestral Gene for Transcribed, Low-Copy Repeats in the Prader-Willi/Angleman Region Encodes a Large Protein Implicated in Protein Trafficking that is Deficient in Mice with Neuromuscular and

    SciTech Connect

    Ji, Y.

    1999-01-01

    Transcribed, low-copy repeat elements are associated with the breakpoint regions of common deletions in Prader-Willi and Angelman syndromes. We report here the identification of the ancestral gene ( HERC2 ) and a family of duplicated, truncated copies that comprise these low-copy repeats. This gene encodes a highly conserved giant protein, HERC2, that is distantly related to p532 (HERC1), a guanine nucleotide exchange factor (GEF) implicated in vesicular trafficking. The mouse genome contains a single Herc2 locus, located in the jdf2 (juvenile development and fertility-2) interval of chromosome 7C. We have identified single nucleotide splice junction mutations in Herc2 in three independent N-ethyl-N-nitrosourea-induced jdf2 mutant alleles, each leading to exon skipping with premature termination of translation and/or deletion of conserved amino acids. Therefore, mutations in Herc2 lead to the neuromuscular secretory vesicle and sperm acrosome defects, other developmental abnormalities and juvenile lethality of jdf2 mice. Combined, these findings suggest that HERC2 is an important gene encoding a GEF involved in protein trafficking and degradation pathways in the cell.

  4. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    PubMed Central

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-01-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories. PMID:27074256

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

    PubMed

    Maslunka, Christopher; Gürtler, Volker; Seviour, Robert

    2015-02-01

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

  6. Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata.

    PubMed

    Sumida, Masayuki; Kato, Yoji; Kurabayashi, Atsushi

    2004-04-01

    The rDNA of eukaryotic organisms is transcribed as the 40S-45S rRNA precursor, and this precursor contains the following segments: 5' - ETS - 18S rRNA - ITS 1 - 5.8S rRNA - ITS 2 - 28S rRNA - 3'. In amphibians, the nucleotide sequences of the rRNA precursor have been completely determined in only two species of Xenopus. In the other amphibian species investigated so far, only the short nucleotide sequences of some rDNA fragments have been reported. We obtained a genomic clone containing the rDNA precursor from the Japanese pond frog Rana nigromaculata and analyzed its nucleotide sequence. The cloned genomic fragment was 4,806 bp long and included the 3'-terminus of 18S rRNA, ITS 1, 5.8S rRNA, ITS 2, and a long portion of 28S rRNA. A comparison of nucleotide sequences among Rana, the two species of Xenopus, and human revealed the following: (1) The 3'-terminus of 18S rRNA and the complete 5.8S rRNA were highly conserved among these four taxa. (2) The regions corresponding to the stem and loop of the secondary structure in 28S rRNA were conserved between Xenopus and Rana, but the rate of substitutions in the loop was higher than that in the stem. Many of the human loop regions had large insertions not seen in amphibians. (3) Two ITS regions had highly diverged sequences that made it difficult to compare the sequences not only between human and frogs, but also between Xenopus and Rana. (4) The short tracts in the ITS regions were strictly conserved between the two Xenopus species, and there was a corresponding sequence for Rana. Our data on the nucleotide sequence of the rRNA precursor from the Japanese pond frog Rana nigromaculata were used to examine the potential usefulness of the rRNA genes and ITS regions for evolutionary studies on frogs, because the rRNA precursor contains both highly conserved regions and rapidly evolving regions.

  7. Active Region Release Two CMEs

    NASA Video Gallery

    Solar material can be seen blowing off the sun in this video captured by NASA’s Solar Dynamics Observatory (SDO) on the night of Feb. 5, 2013. This active region on the sun sent out two coronal ...

  8. Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant–Associated Fungi

    PubMed Central

    Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

    2016-01-01

    The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant–associated fungi due to the similar homologies of sequences in primer–annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3′ end of the primer–binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant–associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant–associated fungi. PMID:27600711

  9. Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant-Associated Fungi.

    PubMed

    Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

    2016-09-29

    The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3' end of the primer-binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant-associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant-associated fungi.

  10. 16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria

    PubMed Central

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

    2016-01-01

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

  11. 16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria.

    PubMed

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

    2016-01-01

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

  12. Conservation and Purifying Selection of Transcribed Genes Located in a Rice Centromere[W

    PubMed Central

    Fan, Chuanzhu; Walling, Jason G.; Zhang, Jianwei; Hirsch, Cory D.; Jiang, Jiming; Wing, Rod A.

    2011-01-01

    Recombination is strongly suppressed in centromeric regions. In chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. Surprisingly, the centromere of chromosome8 (Cen8) of rice (Oryza sativa) contains several transcribed genes. However, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in Cen8. Sequencing of orthologous Cen8 regions from two additional Oryza species, Oryza glaberrima and Oryza brachyantha, which diverged from O. sativa 1 and 10 million years ago, respectively, revealed a set of seven transcribed Cen8 genes conserved across all three species. Chromatin immunoprecipitation analysis with the centromere-specific histone CENH3 confirmed that the sequenced orthologous regions are part of the functional centromere. All seven Cen8 genes have undergone purifying selection, representing a striking phenomenon of active gene survival within a recombination-free zone over a long evolutionary time. The coding sequences of the Cen8 genes showed sequence divergence and mutation rates that were significantly reduced from those of genes located on the chromosome arms. This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements. PMID:21856794

  13. SDO Sees Active Region Outbursts

    NASA Video Gallery

    This close up video by NASA’s Solar Dynamics Observatory shows an active region near the right-hand edge of the sun’s disk, which erupted with at least a dozen minor events over a 30-hour period fr...

  14. Distanced Data: Transcribing Other People's Research Tapes

    ERIC Educational Resources Information Center

    Tilley, Susan A.; Powick, Kelly D.

    2004-01-01

    In this article, we report on our qualitative study involving eight individuals hired to transcribe research tapes in university contexts. We consider issues of data analysis and data trustworthiness and the implications for both when transcription is assigned to someone other than the researcher. We explore the challenges transcribers faced…

  15. A quick transcribing technique for oral data

    USGS Publications Warehouse

    Schleicher, David

    1972-01-01

    Stenographic techniques offer a means for transcribing oral data accurately and efficiently. In one such application, during five Appolo lunar missions, a rough but helpful transcript was produced within minutes. Similarly, lectures, conferences, and audio tapes can be accurately transcribed as promptly as necessary. Computer programs for translating shorthand notes are being developed; they will increase both speed and accuracy of translation.

  16. Orientation-dependent influence of an intergenic enhancer on the promoter activity of the divergently transcribed mouse Shsp/alpha B-crystallin and Mkbp/HspB2 genes.

    PubMed

    Swamynathan, Shivalingappa K; Piatigorsky, Joram

    2002-12-20

    The mouse Shsp/alphaB-crystallin and Mkbp/HspB2 genes are closely linked and divergently transcribed. In this study, we have analyzed the contribution of the intergenic enhancer to Shsp/alphaB-crystallin and Mkbp/HspB2 promoter activity using dual-reporter vectors in transient transfection and transgenic mouse experiments. Deletion of the enhancer reduced Shsp/alphaB-crystallin promoter activity by 30- and 93-fold and Mkbp/HspB2 promoter activity by 6- and 10-fold in transiently transfected mouse lens alpha-TN4 and myoblast C2C12 cells, respectively. Surprisingly, inversion of the enhancer reduced Shsp/alphaB-crystallin promoter activity by 17-fold, but did not affect Mkbp/HspB2 promoter activity in the transfected cells. In contrast, enhancer activity was orientation-independent in combination with a heterologous promoter in transfected cells. Transgenic mouse experiments established the orientation dependence and Shsp/alphaB-crystallin promoter preference of the intergenic enhancer in its native context. The orientation dependence and preferential effect of the Shsp/alphaB-crystallin enhancer on the Shsp/alphaB-crystallin promoter provide an example of adaptive changes in gene regulation accompanying the functional diversification of duplicated genes during evolution.

  17. Decay of Solar Active Regions

    NASA Technical Reports Server (NTRS)

    Hathaway, David H.; Choudhary, Debi Prasad

    2005-01-01

    We examine the record of sunspot group areas observed over a period of 100 years to determine the rate of decay of solar active regions. We exclude observations of groups when they are more than 60deg in longitude from the central meridian and only include data when at least three days of observations are available following the date of maximum area for a spot group's disk passage. This leaves data for some 24,000 observations of active region decay. We find that the decay rate is a constant 20 microHem/day for spots smaller than about 200 microHem (about the size of a supergranule). This decay rate increases linearly to about 90 microHem/day for spots with areas of 1000 microHem. We find no evidence for significant variations in active region decay from one solar cycle to another. However, we do find that the decay rate is slower at lower latitudes. This gives a slower decay rate during the declining phase of sunspot cycles.

  18. Solar active region display system

    NASA Astrophysics Data System (ADS)

    Golightly, M.; Raben, V.; Weyland, M.

    2003-04-01

    The Solar Active Region Display System (SARDS) is a client-server application that automatically collects a wide range of solar data and displays it in a format easy for users to assimilate and interpret. Users can rapidly identify active regions of interest or concern from color-coded indicators that visually summarize each region's size, magnetic configuration, recent growth history, and recent flare and CME production. The active region information can be overlaid onto solar maps, multiple solar images, and solar difference images in orthographic, Mercator or cylindrical equidistant projections. Near real-time graphs display the GOES soft and hard x-ray flux, flare events, and daily F10.7 value as a function of time; color-coded indicators show current trends in soft x-ray flux, flare temperature, daily F10.7 flux, and x-ray flare occurrence. Through a separate window up to 4 real-time or static graphs can simultaneously display values of KP, AP, daily F10.7 flux, GOES soft and hard x-ray flux, GOES >10 and >100 MeV proton flux, and Thule neutron monitor count rate. Climatologic displays use color-valued cells to show F10.7 and AP values as a function of Carrington/Bartel's rotation sequences - this format allows users to detect recurrent patterns in solar and geomagnetic activity as well as variations in activity levels over multiple solar cycles. Users can customize many of the display and graph features; all displays can be printed or copied to the system's clipboard for "pasting" into other applications. The system obtains and stores space weather data and images from sources such as the NOAA Space Environment Center, NOAA National Geophysical Data Center, the joint ESA/NASA SOHO spacecraft, and the Kitt Peak National Solar Observatory, and can be extended to include other data series and image sources. Data and images retrieved from the system's database are converted to XML and transported from a central server using HTTP and SOAP protocols, allowing

  19. Evolution of active region outflows throughout an active region lifetime

    NASA Astrophysics Data System (ADS)

    Zangrilli, L.; Poletto, G.

    2016-10-01

    Context. We have shown previously that SOHO/UVCS data allow us to detect active region (AR) outflows at coronal altitudes higher than those reached by other instrumentation. These outflows are thought to be a component of the slow solar wind. Aims: Our purpose is to study the evolution of the outflows in the intermediate corona from AR 8100, from the time the AR first forms until it dissolves, after several transits at the solar limb. Methods: Data acquired by SOHO/UVCS at the time of the AR limb transits, at medium latitudes and at altitudes ranging from 1.5 to 2.3 R⊙, were used to infer the physical properties of the outflows through the AR evolution. To this end, we applied the Doppler dimming technique to UVCS spectra. These spectra include the H i Lyα line and the O vi doublet lines at 1031.9 and 1037.6 Å. Results: Plasma speeds and electron densities of the outflows were inferred over several rotations of the Sun. AR outflows are present in the newly born AR and persist throughout the entire AR life. Moreover, we found two types of outflows at different latitudes, both possibly originating in the same negative polarity area of the AR. We also analyzed the behavior of the Si xii 520 Å line along the UVCS slit in an attempt to reveal changes in the Si abundance when different regions are traversed. Although we found some evidence for a Si enrichment in the AR outflows, alternative interpretations are also plausible. Conclusions: Our results demonstrate that outflows from ARs are detectable in the intermediate corona throughout the whole AR lifetime. This confirms that outflows contribute to the slow wind.

  20. CME Productivity of Active Regions.

    NASA Astrophysics Data System (ADS)

    Liu, L.; Wang, Y.; Wang, J.; Shen, C.; Ye, P.; Zhang, Q.; Liu, R.; Wang, S.

    2015-12-01

    Solar active regions (ARs) are the major sources of two kinds of the most violent solar eruptions, namely flares and coronal mass ejections (CMEs). Although they are believed to be two phenomena in the same eruptive process, the productivity of them could be quiet different for various ARs. Why is an AR productive? And why is a flare-rich AR CME-poor? To answer these questions, we compared the recent super flare-rich but CME-poor AR 12192, with other four ARs; two were productive in both flares and CMEs and the other two were inert to produce any M-class or intenser flares or CMEs. By investigating the photospheric parameters based on the SDO/HMI vector magnetogram, we find the three productive ARs have larger magnetic flux, current and free magnetic energy than the inert ARs. Furthermore, the two ARs productive in both flares and CMEs contain higher current helicity, concentrating along both sides of the flaring neutral lines, indicating the presence of a seed magnetic structure( that is highly sheared or twisted) of a CME; they also have higher decay index in the low corona, showing weak constraint. The results suggest that productive ARs are always large and have strong current system and sufficient free energy to power flares, and more importantly whether or not a flare is accompanied by a CME is seemingly related to (1) if there is significant sheared or twisted core field serving as the seed of the CME and (2) if the constraint of the overlying arcades is weak enough. Moreover, some productive ARs may frequently produce more than one CME. How does this happen? We do a statistical investigation of waiting times of quasi-homologous CMEs ( CME ssuccessive originating from the same ARs within short intervals) from super ARs in solar cycle 23 to answer this question. The waiting times of quasi-homologous CMEs have a two-component distribution with a separation at about 18 hours, the first component peaks at 7 hours. The correlation analysis among CME waiting times

  1. The Main Sequence of Explosive Solar Active Regions: Comparison of Emerging and Mature Active Regions

    NASA Technical Reports Server (NTRS)

    Falconer, David; Moore, Ron

    2011-01-01

    For mature active regions, an active region s magnetic flux content determines the maximum free energy the active region can have. Most Large flares and CMEs occur in active regions that are near their free-energy limit. Active-region flare power radiated in the GOES 1-8 band increases steeply as the free-energy limit is approached. We infer that the free-energy limit is set by the rate of release of an active region s free magnetic energy by flares, CMEs and coronal heating balancing the maximum rate the Sun can put free energy into the active region s magnetic field. This balance of maximum power results in explosive active regions residing in a "mainsequence" in active-region (flux content, free energy content) phase space, which sequence is analogous to the main sequence of hydrogen-burning stars in (mass, luminosity) phase space.

  2. The Twist Limit for Bipolar Active Regions

    NASA Technical Reports Server (NTRS)

    Moore, Ron; Falconer, David; Gary, Allen

    2008-01-01

    We present new evidence that further supports the standard idea that active regions are emerged magnetic-flux-rope omega loops. When the axial magnetic twist of a cylindrical flux rope exceeds a critical amount, the flux rope becomes unstable to kinking, and the excess axial twist is converted into writhe twist by the kinking. This suggests that, if active regions are emerged omega loops, then (1) no active region should have magnetic twist much above the limit set by kinking, (2) active regions having twist near the limit should often arise from kinked omega loops, and (3) since active regions having large delta sunspots are outstandingly twisted, these arise from kinked omega loops and should have twist near the limit for kinking. From each of 36 vector magnetograms of bipolar active regions, we have measured (1) the total flux of the vertical field above 100 G, (2) the area covered by this flux, and (3) the net electric current that arches over the polarity inversion line. These three quantities yield an estimate of the axial magnetic twist in a simple model cylindrical flux rope that corresponds to the top of the active region s hypothetical omega loop prior to emergence. In all 36 cases, the estimated twist is below the critical limit for kinking. The 11 most twisted active regions (1) have estimated twist within a factor of approx.3 of the limit, and (2) include all of our 6 active regions having large delta sunspots. Thus, our observed twist limit for bipolar active regions is in good accord with active regions being emerged omega loops.

  3. Depth of origin of solar active regions

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1984-01-01

    Observations show that the individual bipolar magnetic regions on the sun remain confined during their decay phase, with much of the magnetic field pulling back under the surface, in reverse of the earlier emergence. This suggests that the magnetic field is held on a short rein by subsurface forces, for otherwise the region would decay entirely by dispersing across the face of the sun. With the simple assumption that the fields at the surface are controlled from well-defined anchor points at a depth h, it is possible to relate the length l of the bipolar region at the surface to the depth h, with h about equal to l. The observed dimensions l about equal to 100,000 km for normal active regions, and l about equal to 10,000 km for the ephemeral active regions, indicate comparable depths of origin. More detailed observational studies of the active regions may be expected to shed further light on the problem.

  4. Suppression of Active-Region CME Production by the Presence of Other Active Regions

    NASA Technical Reports Server (NTRS)

    Falconer, David; Moore, Ron; Barghouty, Abdulnasser; Khazanov, Igor

    2009-01-01

    From the SOHO mission s data base of MDI full-disk magnetograms spanning solar cycle 23, we have obtained a set of 40,000 magnetograms of 1,300 active regions, tracking each active region across the 30 degree central solar disk. Each active region magnetogram is cropped from the full-disk magnetogram by an automated code. The cadence is 96 minutes. From each active-region magnetogram, we have measured two whole-active-region magnetic quantities: (1) the magnetic size of the active region (the active region s total magnetic flux), and (2) a gauge of the active region s free magnetic energy (part of the free energy is released in the production of a flare and/or CME eruption). From NOAA Flare/CME catalogs, we have obtained the event (Flare/CME/SEP event) production history of each active region. Using all these data, we find that for each type of eruptive event, an active region s expected rate of event production increases as a power law of our gauge of active-region free magnetic energy. We have also found that, among active regions having nearly the same free energy, the rate of the CME production is less when there are many other active regions on the disk than when there are few or none, but there is no significant discernible suppression of the rate of flare production. This indicates that the presence of other active regions somehow tends to inhibit an active region s flare-producing magnetic explosions from becoming CMEs, contrary to the expectation from the breakout model for the production of CMEs.

  5. Active Region Emergence and Remote Flares

    NASA Astrophysics Data System (ADS)

    Fu, Yixing; Welsch, Brian T.

    2016-02-01

    We study the effect of new emerging solar active regions on the large-scale magnetic environment of existing regions. We first present a theoretical approach to quantify the "interaction energy" between new and pre-existing regions as the difference between i) the summed magnetic energies of their individual potential fields and ii) the energy of their superposed potential fields. We expect that this interaction energy can, depending upon the relative arrangements of newly emerged and pre-existing magnetic flux, indicate the existence of "topological" free magnetic energy in the global coronal field that is independent of any "internal" free magnetic energy due to coronal electric currents flowing within the newly emerged and pre-existing flux systems. We then examine the interaction energy in two well-studied cases of flux emergence, but find that the predicted energetic perturbation is relatively small compared to energies released in large solar flares. Next, we present an observational study of the influence of the emergence of new active regions on flare statistics in pre-existing active regions, using NOAA's Solar Region Summary and GOES flare databases. As part of an effort to precisely determine the emergence time of active regions in a large event sample, we find that emergence in about half of these regions exhibits a two-stage behavior, with an initial gradual phase followed by a more rapid phase. Regarding flaring, we find that the emergence of new regions is associated with a significant increase in the occurrence rate of X- and M-class flares in pre-existing regions. This effect tends to be more significant when pre-existing and new emerging active regions are closer. Given the relative weakness of the interaction energy, this effect suggests that perturbations in the large-scale magnetic field, such as topology changes invoked in the "breakout" model of coronal mass ejections, might play a significant role in the occurrence of some flares.

  6. Hinode Captures Images of Solar Active Region

    NASA Video Gallery

    In these images, Hinode's Solar Optical Telescope (SOT) zoomed in on AR 11263 on August 4, 2011, five days before the active region produced the largest flare of this cycle, an X6.9. We show images...

  7. Flare Size Distributions and Active Region Types

    NASA Astrophysics Data System (ADS)

    Bai, Taeil

    2007-05-01

    Size distributions of solar flares measured by various size indicators follow a power law with a negative index of about 1.8. On the basis of general appearance of power-law distributions, Lu and his collegues proposed an avalenche model. According to this model, the power-law index should be independent of active region size, but the cutoff size above which the size distribution steepens rapidly is expected to depend on the active region size. I have analyzed the size distribution of flares, using GOES soft X-ray observations for 2004 and 2005. For flares observed by GOES during these years, their locations are almost completely identified even for C-class flares. This enable us to study the dependence of size distribution on active region type. Comparing the power-law portion of size distributions below the high-end cutoff, I have found that the size distribution index depends on active region type. Flares from prolific active regions exhibit a flatter distribution, while flares from non-prolific active regions exhibit a steeper distribution. I plan to discuss a plausible mechanism for such behavior.

  8. Polar Field Reversals and Active Region Decay

    NASA Astrophysics Data System (ADS)

    Petrie, Gordon; Ettinger, Sophie

    2015-07-01

    We study the relationship between polar field reversals and decayed active region magnetic flux. Photospheric active region flux is dispersed by differential rotation and turbulent diffusion, and is transported poleward by meridional flows and diffusion. We summarize the published evidence from observation and modeling of the influence of meridional flow variations and decaying active region flux's spatial distribution, such as the Joy's law tilt angle. Using NSO Kitt Peak synoptic magnetograms covering cycles 21-24, we investigate in detail the relationship between the transport of decayed active region flux to high latitudes and changes in the polar field strength, including reversals in the magnetic polarity at the poles. By means of stack plots of low- and high-latitude slices of the synoptic magnetograms, the dispersal of flux from low to high latitudes is tracked, and the timing of this dispersal is compared to the polar field changes. In the most abrupt cases of polar field reversal, a few activity complexes (systems of active regions) are identified as the main cause. The poleward transport of large quantities of decayed trailing-polarity flux from these complexes is found to correlate well in time with the abrupt polar field changes. In each case, significant latitudinal displacements were found between the positive and negative flux centroids of the complexes, consistent with Joy's law bipole tilt with trailing-polarity flux located poleward of leading-polarity flux. The activity complexes of the cycle 21 and 22 maxima were larger and longer-lived than those of the cycle 23 and 24 maxima, and the poleward surges were stronger and more unipolar and the polar field changes larger and faster. The cycle 21 and 22 polar reversals were dominated by only a few long-lived complexes whereas the cycle 23 and 24 reversals were the cumulative effects of more numerous, shorter-lived regions. We conclude that sizes and lifetimes of activity complexes are key to

  9. The 17 GHz active region number

    SciTech Connect

    Selhorst, C. L.; Pacini, A. A.; Costa, J. E. R.; Giménez de Castro, C. G.; Valio, A.; Shibasaki, K.

    2014-08-01

    We report the statistics of the number of active regions (NAR) observed at 17 GHz with the Nobeyama Radioheliograph between 1992, near the maximum of cycle 22, and 2013, which also includes the maximum of cycle 24, and we compare with other activity indexes. We find that NAR minima are shorter than those of the sunspot number (SSN) and radio flux at 10.7 cm (F10.7). This shorter NAR minima could reflect the presence of active regions generated by faint magnetic fields or spotless regions, which were a considerable fraction of the counted active regions. The ratio between the solar radio indexes F10.7/NAR shows a similar reduction during the two minima analyzed, which contrasts with the increase of the ratio of both radio indexes in relation to the SSN during the minimum of cycle 23-24. These results indicate that the radio indexes are more sensitive to weaker magnetic fields than those necessary to form sunspots, of the order of 1500 G. The analysis of the monthly averages of the active region brightness temperatures shows that its long-term variation mimics the solar cycle; however, due to the gyro-resonance emission, a great number of intense spikes are observed in the maximum temperature study. The decrease in the number of these spikes is also evident during the current cycle 24, a consequence of the sunspot magnetic field weakening in the last few years.

  10. Fluxon Modeling of Active Region Evolution

    NASA Astrophysics Data System (ADS)

    Deforest, C. E.; Kankelborg, C. C.; Davey, A. R.; Rachmeler, L.

    2006-12-01

    We present current results and status on fluxon modeling of free energy buildup and release in active regions. Our publicly available code, FLUX, has the unique ability to track magnetic energy buildup with a truly constrained topology in evolving, nonlinear force-free conditions. Recent work includes validation of the model against Low &Lou force-free field solutions, initial evolution studies of idealized active regions, and inclusion of locally parameterized reconnection into the model. FLUX is uniquely able to simulate complete active regions in 3-D on a single workstation; we estimate that a parallelized fluxon model, together with computer vision code to ingest solar data, could run faster than real time on a cluster of \\textasciitilde 30 CPUs and hence provide a true predictive space weather model in the style of predictive simulations of terrestrial weather.

  11. The Magnetic Free Energy in Active Regions

    NASA Technical Reports Server (NTRS)

    Metcalf, Thomas R.; Mickey, Donald L.; LaBonte, Barry J.

    2001-01-01

    The magnetic field permeating the solar atmosphere governs much of the structure, morphology, brightness, and dynamics observed on the Sun. The magnetic field, especially in active regions, is thought to provide the power for energetic events in the solar corona, such as solar flares and Coronal Mass Ejections (CME) and is believed to energize the hot coronal plasma seen in extreme ultraviolet or X-rays. The question remains what specific aspect of the magnetic flux governs the observed variability. To directly understand the role of the magnetic field in energizing the solar corona, it is necessary to measure the free magnetic energy available in active regions. The grant now expiring has demonstrated a new and valuable technique for observing the magnetic free energy in active regions as a function of time.

  12. Active Region Segmentation Based on Stokes Asymmetries

    NASA Astrophysics Data System (ADS)

    Choi, Jieun; Harker-Lundberg, B.

    2011-01-01

    During the Stokes inversion process, we would ideally use a distinct model for each structure in an active region which addresses the differences in the physical conditions of these regions. While the Milne-Eddington model of the atmosphere---a frequently-used ideal model that assumes all local thermodynamic equilibrium (LTE) conditions are satisfied---is a sufficient approximation for the description of the solar photosphere, we almost always observe deviations from this model. It is thus of interest to devise a method to systematically and accurately identify the active regions based on their spectra, such that we could use a more sophisticated model catered to each structure in an active region during the actual Stokes inversion process. We present a classification scheme for different active region structures using Stokes asymmetries and line core depths as discriminators. The data used for this investigation were obtained from the Synoptic Optical Long-term Investigations of the Sun (SOLIS) facility using the Vector Spectromagnetograph (VSM), observed in a 3 A bandpass around Fe I 6302.5 A, from March 27, 2008 to March 29, 2008. This work is carried out through the National Solar Observatory Research Experiences for Undergraduate (REU) site program, which is co-funded by the Department of Defense in partnership with the National Science Foundation REU Program. The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation.

  13. Genetic diversity and phylogenetic analysis of Citrus (L) from north-east India as revealed by meiosis, and molecular analysis of internal transcribed spacer region of rDNA.

    PubMed

    Hynniewta, Marlykynti; Malik, Surendra Kumar; Rao, Satyawada Rama

    2014-12-01

    The north-eastern region of India is reported to be the center of origin and rich in diversity of Citrus (L.) species, where some wild and endangered species namely Citrus indica, Citrus macroptera, Citrus latipes, Citrus ichagensis and Citrus assamensis exist in their natural and undisturbed habitat. In order to have comprehensive information about the extent of genetic variability and the occurrence of cryptic genomic hybridity between and within various Citrus species, a combined approach involving morphological, cytogenetical and molecular approaches were adopted in the present study. Cytogenetic approaches are known to resolve taxonomic riddles in a more efficient manner, by clearly delineating taxa at species and sub species levels. Male meiotic studies revealed a gametic chromosome number of n = 9, without any evidence of numerical variations. Bivalents outnumbered all other types of associations in pollen mother cells (PMCs) analyzed at diplotene, diakinesis and metaphase I. Univalents were frequently encountered in nine species presently studied, though their presence appropriately did not influence the distributional pattern of the chromosomes at anaphases I and II. The molecular approaches for phylogenetic analysis based on sequence data related to ITS 1, ITS 2 and ITS 1 + 5.8 s + ITS 2 of rDNA using maximum parsimony method and Bayesian inference have thrown light on species inter-relationship and evolution of Citrus species confirming our cytogenetical interpretations. The three true basic species i.e. Citrus medica, Citrus maxima and Citrus reticulata with their unique status have been resolved into distinct clades with molecular approaches as well. C. indica which occupies a unique position in the phylogenetic ladder of the genus Citrus has been resolved as a distinct clade and almost behaving as an out-group. The presences of quadrivalents in C. indica also echo and support its unique position. From our study it is amply clear that C

  14. The putative imprinted locus D15S9 within the common deletion region for the Prader-Willi and Angelman syndromes encodes two overlapping mRNAs transcribed from opposite strands

    SciTech Connect

    Glenn, C.C.; Driscoll, D.J.; Saitoh, S.

    1994-09-01

    Prader-Willi syndrome is typically caused by a deletion of paternal 15q11-q13, or maternal uniparental disomy (UPD) of chromosome 15, while Angelman syndrome is caused by a maternal deletion or paternal UPD of the same region. Therefore, these two clinically distinct neurobehavioral syndromes result from differential expression of imprinted genes within 15q11-q13. A 3.1 kb cDNA, DN34, from the D15S9 locus within 15q11-q13 was isolated from a human fetal brain library. We showed previously that DN34 probe detects a DNA methylation imprint and therefore may represent a candidate imprinted gene. Isolation of genomic clones and DNA sequencing demonstrated that the gene segment encoding the partial cDNA DN34 was split by a 2 kb intron, but did not encode a substantial open reading frame (ORF). Preliminary analysis of expression by RT-PCR suggests that this gene is expressed in fetal but not in tested tissue types from the adult, and thus its imprinting status has not been possible to assess at present. Surprisingly, we found an ORF on the antisense strand of the DN34 cDNA. This ORF encodes a putative polypeptide of 505 amino acid residues containing a RING C{sub 3}HC{sub 4} zinc-finger motif and other features of nuclear proteins. Subsequent characterization of this gene, ZNF127, and a mouse homolog, demonstrated expression of 3.2 kb transcript from all tested fetal and adult tissues. Transcripts initiate from within a CpG-island, shown to be differentially methylated on parental alleles in the human. Interestingly, functional imprinting of the mouse homolog was subsequently demonstrated in an F{sub 1} cross by analyzing a VNTR polymorphism in the mRNA. The ZNF127 gene is intronless, has significant overlap with the DN34 gene on the antisense strand, and a 1 kb 3{prime} end within the 2 kb DN34 intron.

  15. ON THE FORMATION OF ACTIVE REGIONS

    SciTech Connect

    Stein, Robert F.; Nordlund, Ake E-mail: aake@nbi.dk

    2012-07-01

    Magnetoconvection can produce an active region without an initial coherent flux tube. A simulation was performed where a uniform, untwisted, horizontal magnetic field of 1 kG strength was advected into the bottom of a computational domain 48 Mm wide by 20 Mm deep. The up and down convective motions produce a hierarchy of magnetic loops with a wide range of scales, with smaller loops riding 'piggy-back' in a serpentine fashion on larger loops. When a large loop approaches the surface, it produces a small active region with a compact leading spot and more diffuse following spots.

  16. Polar Field Reversals and Active Region Decay

    NASA Astrophysics Data System (ADS)

    Petrie, Gordon; Ettinger, Sophie

    2015-04-01

    We study the relationship between polar field reversals and decayed active region magnetic flux. Photospheric active region flux is dispersed by differential rotation and turbulent diffusion, and is transported poleward by meridional flows and diffusion. Using NSO Kitt Peak synoptic magnetograms, we investigate in detail the relationship between the transport of decayed active region flux to high latitudes and changes in the polar field strength, including reversals in the magnetic polarity at the poles. By means of stack plots of low- and high-latitude slices of the synoptic magnetograms, the dispersal of flux from low to high latitudes is tracked, and the timing of this dispersal is compared to the polar field changes. In the most abrupt cases of polar field reversal, a few activity complexes (systems of active regions) are identified as the main cause. The poleward transport of large quantities of decayed lagging-polarity flux from these complexes is found to correlate well in time with the abrupt polar field changes. In each case, significant latitudinal displacements were found between the positive and negative flux centroids of the complexes, consistent with Joy's law bipole tilt with lagging-polarity flux located poleward of leading-polarity flux. This work is carried out through the National Solar Observatory Summer Research Assistantship (SRA) Program. The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation.

  17. Transcribed dark matter: meaning or myth?

    PubMed Central

    Ponting, Chris P.; Belgard, T. Grant

    2010-01-01

    Genomic tiling arrays, cDNA sequencing and, more recently, RNA-Seq have provided initial insights into the extent and depth of transcribed sequence across human and other genomes. These methods have led to greatly improved annotations of protein-coding genes, but have also identified transcription outside of annotated exons. One resultant issue that has aroused dispute is the balance of transcription of known exons against transcription outside of known exons. While non-genic ‘dark matter’ transcription was found by tiling arrays to be pervasive, it was seen to contribute only a small percentage of the polyadenylated transcriptome in some RNA-Seq experiments. This apparent contradiction has been compounded by a lack of clarity about what exactly constitutes a protein-coding gene. It remains unclear, for example, whether or not all transcripts that overlap on either strand within a genomic locus should be assigned to a single gene locus, including those that fail to share promoters, exons and splice junctions. The inability of tiling arrays and RNA-Seq to count transcripts, rather than exons or exon pairs, adds to these difficulties. While there is agreement that thousands of apparently non-coding loci are present outside of protein-coding genes in the human genome, there is vigorous debate of what constitutes evidence for their functionality. These issues will only be resolved upon the demonstration, or otherwise, that organismal or cellular phenotypes frequently result when non-coding RNA loci are disrupted. PMID:20798109

  18. Transcriptional activation by LR1 at the Eµ enhancer and switch region sites

    PubMed Central

    Hanakahi, L. A.; Maizels, Nancy

    2000-01-01

    LR1 is a B cell-specific, sequence-specific duplex DNA binding activity which is induced in B cells carrying out class switch recombination. Here we identify several properties of LR1 which enable it to function in transcriptional regulation. We show that LR1 contributes to transcriptional activation by the Eµ immunoglobulin heavy chain intron enhancer by binding to a site within the enhancer core. We further show that LR1 bends DNA upon binding. In addition, we show that LR1 is itself a bona fide transcriptional activator, as multimerized LR1 sites produce an element which can enhance transcription from a minimal promoter. In order for class switch recombination to occur, an activating signal must be transmitted via the Eµ core, and both S regions targeted for recombination must be actively transcribed. The properties of LR1 that we have identified suggest distinct potential functions of LR1 duplex DNA binding activity in class switch recombination. First, LR1 may contribute to recombinational activation by the Eµ core. Second, there are multiple potential LR1 duplex binding sites in each of the G-rich switch regions, and LR1 bound at contiguous sites may enhance recombination by stimulating transcription of the S regions. PMID:10908319

  19. A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes

    PubMed Central

    Diesch, Jeannine; Lesmana, Analia; Poortinga, Gretchen; Hein, Nadine; Lidgerwood, Grace; Cameron, Donald P.; Ellul, Jason; Goodall, Gregory J.; Wong, Lee H.; Dhillon, Amardeep S.; Hamdane, Nourdine; Rothblum, Lawrence I.; Pearson, Richard B.; Haviv, Izhak; Moss, Tom

    2015-01-01

    Mechanisms to coordinate programs of highly transcribed genes required for cellular homeostasis and growth are unclear. Upstream binding transcription factor (UBTF, also called UBF) is thought to function exclusively in RNA polymerase I (Pol I)-specific transcription of the ribosomal genes. Here, we report that the two isoforms of UBTF (UBTF1/2) are also enriched at highly expressed Pol II-transcribed genes throughout the mouse genome. Further analysis of UBTF1/2 DNA binding in immortalized human epithelial cells and their isogenically matched transformed counterparts reveals an additional repertoire of UBTF1/2-bound genes involved in the regulation of cell cycle checkpoints and DNA damage response. As proof of a functional role for UBTF1/2 in regulating Pol II transcription, we demonstrate that UBTF1/2 is required for recruiting Pol II to the highly transcribed histone gene clusters and for their optimal expression. Intriguingly, lack of UBTF1/2 does not affect chromatin marks or nucleosome density at histone genes. Instead, it results in increased accessibility of the histone promoters and transcribed regions to micrococcal nuclease, implicating UBTF1/2 in mediating DNA accessibility. Unexpectedly, UBTF2, which does not function in Pol I transcription, is sufficient to regulate histone gene expression in the absence of UBTF1. Moreover, depletion of UBTF1/2 and subsequent reduction in histone gene expression is associated with DNA damage and genomic instability independent of Pol I transcription. Thus, we have uncovered a novel role for UBTF1 and UBTF2 in maintaining genome stability through coordinating the expression of highly transcribed Pol I (UBTF1 activity) and Pol II genes (UBTF2 activity). PMID:25452314

  20. Silicon on insulator with active buried regions

    DOEpatents

    McCarthy, Anthony M.

    1996-01-01

    A method for forming patterned buried components, such as collectors, sources and drains, in silicon-on-insulator (SOI) devices. The method is carried out by epitaxially growing a suitable sequence of single or multiple etch stop layers ending with a thin silicon layer on a silicon substrate, masking the silicon such that the desired pattern is exposed, introducing dopant and activating in the thin silicon layer to form doped regions. Then, bonding the silicon layer to an insulator substrate, and removing the silicon substrate. The method additionally involves forming electrical contact regions in the thin silicon layer for the buried collectors.

  1. Silicon on insulator with active buried regions

    DOEpatents

    McCarthy, A.M.

    1998-06-02

    A method is disclosed for forming patterned buried components, such as collectors, sources and drains, in silicon-on-insulator (SOI) devices. The method is carried out by epitaxially growing a suitable sequence of single or multiple etch stop layers ending with a thin silicon layer on a silicon substrate, masking the silicon such that the desired pattern is exposed, introducing dopant and activating in the thin silicon layer to form doped regions. Then, bonding the silicon layer to an insulator substrate, and removing the silicon substrate. The method additionally involves forming electrical contact regions in the thin silicon layer for the buried collectors. 10 figs.

  2. Silicon on insulator with active buried regions

    DOEpatents

    McCarthy, A.M.

    1996-01-30

    A method is disclosed for forming patterned buried components, such as collectors, sources and drains, in silicon-on-insulator (SOI) devices. The method is carried out by epitaxially growing a suitable sequence of single or multiple etch stop layers ending with a thin silicon layer on a silicon substrate, masking the silicon such that the desired pattern is exposed, introducing dopant and activating in the thin silicon layer to form doped regions. Then, bonding the silicon layer to an insulator substrate, and removing the silicon substrate. The method additionally involves forming electrical contact regions in the thin silicon layer for the buried collectors. 10 figs.

  3. Silicon on insulator with active buried regions

    DOEpatents

    McCarthy, Anthony M.

    1998-06-02

    A method for forming patterned buried components, such as collectors, sources and drains, in silicon-on-insulator (SOI) devices. The method is carried out by epitaxially growing a suitable sequence of single or multiple etch stop layers ending with a thin silicon layer on a silicon substrate, masking the silicon such that the desired pattern is exposed, introducing dopant and activating in the thin silicon layer to form doped regions. Then, bonding the silicon layer to an insulator substrate, and removing the silicon substrate. The method additionally involves forming electrical contact regions in the thin silicon layer for the buried collectors.

  4. Magnetic helicity in emerging solar active regions

    SciTech Connect

    Liu, Y.; Hoeksema, J. T.; Bobra, M.; Hayashi, K.; Sun, X.; Schuck, P. W.

    2014-04-10

    Using vector magnetic field data from the Helioseismic and Magnetic Imager instrument aboard the Solar Dynamics Observatory, we study magnetic helicity injection into the corona in emerging active regions (ARs) and examine the hemispheric helicity rule. In every region studied, photospheric shearing motion contributes most of the helicity accumulated in the corona. In a sample of 28 emerging ARs, 17 follow the hemisphere rule (61% ± 18% at a 95% confidence interval). Magnetic helicity and twist in 25 ARs (89% ± 11%) have the same sign. The maximum magnetic twist, which depends on the size of an AR, is inferred in a sample of 23 emerging ARs with a bipolar magnetic field configuration.

  5. Supergranule Diffusion and Active Region Decay

    NASA Technical Reports Server (NTRS)

    Hathaway, David H.; Choudhary, Debi Prasad

    2004-01-01

    Models of the Sun's magnetic dynamo include turbulent diffusion to parameterize the effects of convective motions on the evolution of the Sun's magnetic field. Supergranules are known to dominate the evolution of the surface magnetic field structure as evidenced by the structure of both the active and quiet magnetic network. However, estimates for the dif hivity attributed to su perymules differ by an order of magnitude from about 100 km sup2/s to more than 1000 km sup2/s. We examine this question of the e i v i t y using three merent approaches. 1) We study the decay of more than 30,000 active regions by determining the rate of change in the sunspot area of each active region from day-to-day. 2) We study the decay of a single isolated active region near the time of solar minimum by examining the magnetic field evolution over five solar rotations fiom SOHOMDI magnetograms obtained at 96-minute intervals. 3) We study the characteristics of supergranules that influence the estimates of their diffusive properties - flow speeds and lifetimes as functions of size - fiom SOHO/MDI Dopplergrams.

  6. Patterns of helicity in solar active regions

    NASA Technical Reports Server (NTRS)

    Pevtsov, Alexei A.; Canfield, Richard C.; Metcalf, Thomas R.

    1994-01-01

    Using 46 vector magnetograms from the Stokes Polarimeter of Mees Solar Observatory (MSO), we studied patterns of local helicity in three diverse solar active regions. From these magnetograms we computed maps of the local helicity parameter alpha = J(sub z)/B(sub z). Although such maps are noisy, we found patterns at the level approximately 2 to 3 sigma(sub J(sub z)), which repeat in successive magnetograms for up to several days. Typically, the alpha maps of any given active region contain identifiable patches with both positive and negative values of alpha. Even within a single sunspot complex, several such alpha patches can often be seen. We followed 68 alpha patches that could be identified on at least two successive alpha maps. We found that the persistence fraction of such patches decrease exponentially, with a characteristic time approximately 27 hr.

  7. 7th International Workshop on the Identification of Transcribed Sequences. Beyond the Identification of Transcribed Sequences

    SciTech Connect

    Gardner, Kathleen

    1997-11-19

    The Seventh Annual Human Genome Conference: Beyond the Identification of Transcribed Sequences (BITS) was held November 16-19, 1997 at the Asilomar Conference Center in Monterey, California. The format for the meeting was a combination of oral presentations, group discussions and poster sessions. The original workshop was held to discuss methodologies for the identification of transcribed sequences in mammalian genomes. Over the years, the focus of the workshops has gradually shifted towards functional analysis, with the most dramatic change in emphasis at this meeting, as reflected in the modest change in the workshop title. Topics presented and discussed included: (1) large scale expression and mutational analysis in yeast, C. elegans, Drosophila and zebrafish, (2) comparative mapping of zebrafish, chicken and Fugu; (3) functional analysis in mouse using promoter traps, mutational analysis of biochemical pathways, and Cre/lox constructs; (4) construction of 5 foot end and complete cDNA libraries; (5) expression analysis in mammalian organisms by array screening and differential display; (6) genome organization as determined by detailed transcriptional mapping and genomic sequence analysis; (7) analysis of genomic sequence, including gene and regulatory sequence predictions, annotation of genomic sequence, development of expression databases and verification of sequence analysis predictions; and (8) structural/functional relationships as determined by RNA secondary structure analysis and evolutionary conservation of non-coding sequences.

  8. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

    PubMed Central

    Bonnet, Jacques; Wang, Chen-Yi; Baptista, Tiago; Vincent, Stéphane D.; Hsiao, Wei-Chun; Stierle, Matthieu; Kao, Cheng-Fu; Tora, László

    2014-01-01

    The SAGA (Spt–Ada–Gcn5 acetyltransferase) coactivator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. Changes in these modifications after inactivation of the corresponding enzyme revealed that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. In agreement with this broad distribution, we show that SAGA plays a critical role for RNA polymerase II recruitment at all expressed genes. In addition, through quantification of newly synthesized RNA, we demonstrated that SAGA inactivation induced a strong decrease of mRNA synthesis at all tested genes. Analysis of the SAGA deubiquitination activity further revealed that SAGA acts on the whole transcribed genome in a very fast manner, indicating a highly dynamic association of the complex with chromatin. Thus, our study uncovers a new function for SAGA as a bone fide cofactor for all RNA polymerase II transcription. PMID:25228644

  9. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

    PubMed Central

    Papantonis, Argyris; Kohro, Takahide; Baboo, Sabyasachi; Larkin, Joshua D; Deng, Binwei; Short, Patrick; Tsutsumi, Shuichi; Taylor, Stephen; Kanki, Yasuharu; Kobayashi, Mika; Li, Guoliang; Poh, Huay-Mei; Ruan, Xiaoan; Aburatani, Hiroyuki; Ruan, Yijun; Kodama, Tatsuhiko; Wada, Youichiro; Cook, Peter R

    2012-01-01

    Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete ‘NFκB factories'. Some factories further specialize in transcribing responsive genes encoding micro-RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories. PMID:23103767

  10. Analysis of Mammalian rDNA Internal Transcribed Spacers

    PubMed Central

    Coleman, Annette W.

    2013-01-01

    Nuclear rDNA Internal Transcribed Spacers, ITS1 and ITS2, are widely used for eukaryote phylogenetic studies from the ordinal level to the species level, and there is even a database for ITS2 sequences. However, ITS regions have been ignored in mammalian phylogenetic studies, and only a few rodent and ape sequences are represented in GenBank. The reasons for this dearth, and the remedies, are described here. We have recovered these sequences, mostly >1 kb in length, for 36 mammalian species. Sequence alignment and transcript folding comparisons reveal the rRNA transcript secondary structure. Mammalian ITS regions, though quite long, still fold into the recognizable secondary structure of other eukaryotes. The ITS2 in particular bears the four standard helix loops, and loops II and III have the hallmark characters universal to eukaryotes. Both sequence and insertions/deletions of transcript secondary structure helices observed here support the four superorder taxonomy of Placentalia. On the family level, major unique indels, neatly excising entire helices, will be useful when additional species are represented, resulting in significant further understanding of the details of mammalian evolutionary history. Furthermore, the identification of a highly conserved element of ITS1 common to warm-blooded vertebrates may aid in deciphering the complex mechanism of RNA transcript processing. This is the last major group of terrestrial vertebrates for which rRNA ITS secondary structure has been resolved. PMID:24260162

  11. Solar irradiance variations due to active regions

    SciTech Connect

    Oster, L.; Schatten, K.H.; Sofia, S.

    1982-05-15

    We have been able to reproduce the variations of the solar irradiance observed by ACRIM to an accuracy of better than +- 0.4 W m/sup -2/, assuming that during the 6 month observation period in 1980 the solar luminosity was constant. The improvement over previous attempts is primarily due to the inclusion of faculae. The reproduction scheme uses simple geometrical data on spot and facula areas, and conventional parameters for the respective fluxes and angular dependencies. The quality of reproduction is not very sensitive to most of the details of these parameters; nevertheless, there conventional parameters cannot be very different from their actual values in the solar atmosphere. It is interesting that the time average of the integrated excess emission (over directions) of the faculae cancels out the integrated deficit produced by the spots, within an accuracy of about 10%. If this behavior were maintained over longer periods of time, say, on the order of an activity cycle, active regions could be viewed as a kind of lighthouse where the energy deficit near the normal direction, associated with the spots, is primarily reemitted close to the tangential directions by the faculae. The currently available data suggest that energy ''storage'' associated with the redirection of flux near active regions on the Sun is comparable to the lifetime of the faculae.

  12. The evolution of active region loop plasma

    NASA Technical Reports Server (NTRS)

    Krall, K. R.; Antiochos, S. K.

    1980-01-01

    The adjustment of coronal active-region loops to changes in their heating rate is investigated numerically. The one-dimensional hydrodynamic equations are solved subject to boundary conditions in which heat flux-induced mass exchange between coronal and chromospheric components is allowed. The calculated evolution of physical parameters suggests that (1) mass supplied during chromospheric evaporation is much more effective in moderating coronal temperature excursions than when downward heat flux is dissipated by a static chromosphere, and (2) the method by which the chromosphere responds to changing coronal conditions can significantly influence coronal readjustment time scales. Observations are cited which illustrate the range of possible fluctuations in the heating rates.

  13. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    PubMed Central

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  14. Pederson Current Dissipation In Emerging Active Regions

    NASA Astrophysics Data System (ADS)

    Leake, James E.; Linton, M. G.

    2011-05-01

    Pederson current dissipation in emerging active regions. Certain regions of the solar atmosphere, such as the photosphere and chromosphere, as well as prominences, contain a significant amount of neutral atoms, and a complete description of the plasma requires including the effects of partial ionization. In the chromosphere the dissipation of Pederson currents is important for the evolution of emerging magnetic fields. Due to the relatively high number density in the chromosphere, the ion-neutral collision time-scale is much smaller than timescales associated with flux emergence. Hence we use a single-fluid approach to model the partially ionized plasma. Looking at both the emergence of large-scale sub-surface structures, and the emergence and reconnection of undulatory fields, we investigate the effect of Pederson current dissipation on the state of the emerging field, on magnetic reconnection and on dissipative heating of the atmosphere. Specifically we examine the effect of motions across fieldlines in the partially ionized regions, and how this can increase the free energy supplied to the corona by flux emergence. We also look at reconnection associated with flux emergence in the partially ionized atmosphere, and how this can account for observed small-scale brightenings (Ellerman Bombs).

  15. HEROES Observations of a Quiescent Active Region

    NASA Astrophysics Data System (ADS)

    Shih, A. Y.; Christe, S.; Gaskin, J.; Wilson-Hodge, C.

    2014-12-01

    Hard X-ray (HXR) observations of solar flares reveal the signatures of energetic electrons, and HXR images with high dynamic range and high sensitivity can distinguish between where electrons are accelerated and where they stop. Even in the non-flaring corona, high-sensitivity HXR measurements may be able to detect the presence of electron acceleration. The High Energy Replicated Optics to Explore the Sun (HEROES) balloon mission added the capability of solar observations to an existing astrophysics balloon payload, HERO, which used grazing-incidence optics for direct HXR imaging. HEROES measures HXR emission from ~20 to ~75 keV with an angular resolution of 33" HPD. HEROES launched on 2013 September 21 from Fort Sumner, New Mexico, and had a successful one-day flight. We present the detailed analysis of the 7-hour observation of AR 11850, which sets new upper limits on the HXR emission from a quiescent active region, with corresponding constraints on the numbers of tens of keV energetic electrons present. Using the imaging capability of HEROES, HXR upper limits are also obtained for the quiet Sun surrounding the active region. We also discuss what can be achieved with new and improved HXR instrumentation on balloons.

  16. Active region coronal loops - Structural and variability

    NASA Technical Reports Server (NTRS)

    Haisch, Bernhard M.; Strong, Keith T.; Harrison, Richard A.; Gary, G. A.

    1988-01-01

    X-ray images of a pair of active region loops are studied which show significant, short time-scale variability in the line fluxes of O VIII, Ne IX, and Mg XI and in the 3.5-11.5 keV soft X-ray bands. Vector magnetograms and high-resolution UV images were used to model the three-dimensional characteristics of the loops. X-ray light curves were generated spanning four consecutive orbits for both loops individually, and light curves of the loop tops and brightest points were also generated. The largest variations involve flux changes of up to several hundred percent on time scales of 10 minutes. No significant H-alpha flare activity is reported, and loop temperatures remain in the four to six million K range. The decay phases of the light curves indicate radiative cooling, inhibition of conduction, and some type of 'continued heating' due to ongoing, underlying activity at the microflare level.

  17. Active Region Transient Brightenings : EIT Versus SXT

    NASA Astrophysics Data System (ADS)

    Berghmans, D.; McKenzie, D.; Clette, F.

    1999-10-01

    On May 13, 1998, the Extreme-Ultraviolet Imaging Telescope (EIT, on board SOHO) has produced a unique image sequence operating in 'shutterless mode' (SOHO JOP 80). In JOP 80, EIT is the leading instrument, followed by several space born instruments (SXT, TRACE, MDI, CDS, SUMER), as well as two observatories on the ground (in La Palma and Sac Peak). The target of the campaign was a relatively small but rapidly evolving active region (AR 8218). For the EIT contribution, a 15 s cadence was achieved in the Fe XII bandpass at 195 deg by leaving EIT's shutter open for 1 hour and operating the CCD in frame transfer mode. We have started the analysis of the huge data set, by making an inventory of the transients observed in the EIT image sequence. These transients range from a B3.5 flare producing a large plasma flow along pre-existing loops, to smaller EUV brightenings of active region loops. In addition, a new class of weaker footpoint brightenings was discovered that produce wave-like disturbances propagating along quasi-open field lines (see the presentation by Eva Robbrecht at this workshop). In this paper we take the opportunity provided by JOP 80, to investigate the correspondence of the transient brightenings observed by EIT in this active region, with the ARTB previously observed by SXT and studied by Shimizu (1992). Within the simultaneous high cadence SOHO JOP 80 image sequences, both EIT and SXT accummulated a few tens of brightening events. At the time of the writing of this abstract, we can say that most of the SXT events have indeed 1 or more EIT counterparts. Typically the SXT events are somewhat bigger than the EIT events where the latter are ussualy located toward the point of origin of the SXT events. Whereas a few brightenings exist in one dataset without any trace in the other dataset (in both directions), we have additionally for a few brightenings in the SXT data, a corresponding EIT darkening as if the plasma is suddenly heated and dissappears from

  18. Dynamics and evolution of emerging active regions .

    NASA Astrophysics Data System (ADS)

    Battiato, V.; Billotta, S.; Contarino, L.; Romano, P.; Spadaro, D.; Zuccarello, F.

    In the framework of the study on active region emergence, we report the results obtained from the analysis of two ARs (NOAA 10050 and NOAA 10407), characterized by different lifetimes: recurrent the former and short-lived (7 days) the latter. The data used were acquired during two observational campaigns carried out at THEMIS telescope in IPM mode, coordinated with other instruments (IOACT, DOT, BBSO, MDI/SOHO, EIT/SOHO, TRACE). The results obtained have provided indications on the atmospheric layers where the first manifestations of the emerging AR are evidenced, on the rate of emergence of magnetic flux, on the upward velocity of AFS, on asymmetries in downward motions in the AFS legs.

  19. FIP bias in a sigmoidal active region

    NASA Astrophysics Data System (ADS)

    Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, Lidia; Green, L. M.; Steed, K.; Carlyle, J.

    2014-01-01

    We investigate first ionization potential (FIP) bias levels in an anemone active region (AR) - coronal hole (CH) complex using an abundance map derived from Hinode/EIS spectra. The detailed, spatially resolved abundance map has a large field of view covering 359'' × 485''. Plasma with high FIP bias, or coronal abundances, is concentrated at the footpoints of the AR loops whereas the surrounding CH has a low FIP bias, ~1, i.e. photospheric abundances. A channel of low FIP bias is located along the AR's main polarity inversion line containing a filament where ongoing flux cancellation is observed, indicating a bald patch magnetic topology characteristic of a sigmoid/flux rope configuration.

  20. EUV Observations of Active Region Dynamics

    NASA Astrophysics Data System (ADS)

    Deluca, E. E.; Cirtain, J. W.; del Zanna, G.; Mason, H. E.; Martens, P. C.; Schmelz, J.; Golub, L.

    2005-05-01

    Data collected during SoHO JOP 146, in collaboration with TRACE, is used to investigate the physical characteristics of coronal active region loops as a function of time and position along and across loop structures. These data include TRACE images in all three EUV passbands, and simultaneous CDS spectroscopic observations. Preliminary measurements of the loop temperature both along the loop half-length and loop cross-section are presented as a function of time. We will show the temperature and density profiles of several structures as a function of position, show changes in temperature and density with time and characterize the coronal background emission. Questions raised by these results will be greatly advanced with the high resolution spectra available from the EIS on Solar-B.

  1. Active region helicity evolution and related coronal mass ejection activity.

    NASA Astrophysics Data System (ADS)

    Green, L.; Mandrini, C.; van Driel-Gesztelyi, L.; Demoulin, P.

    The computation of magnetic helicity has become increasingly important in the studies of solar activity. Observations of helical structures in the solar atmosphere, and their subsequent ejection into the interplanetary medium, have resulted in considerable interest to find the link between the amount of helicity in the coronal magnetic field and the origin of coronal mass ejections (CMEs). This is reinforced by theory which shows magnetic helicity to be a well preserved quantity (Berger, 1984), and so with a continued injection into the corona an endless accumulation will occur. CMEs therefore provide a natural method to remove helicity from the corona. Recent works (DeVore, 2000, Chae, 2001, Chae et al., 2001, Demoulin et al., 2002, Green et al., 2002) have endeavoured to find the source of helicity in the corona to explain the observed CME activity in specific cases. The main candidates being differential rotation, shear motions or a transfer of helicity from below the photosphere into the corona. In order to establish a confident relation between CMEs and helicity, these works needs to be expanded to include CME source regions with different characteristics. A study of a very different active region will be presented and the relationship between helicity content and CME activity will be discussed in the framework of the previous studies.

  2. Molecular Identification of Two Strains of Phellinus sp. by Internal Transcribed Spacer Sequence Analysis

    PubMed Central

    2011-01-01

    Two species of cultivated Phellinus sp. were identified as P. baumii by internal transcribed spacer (ITS) sequence analysis. The fruit bodies of the examined strains were similar to those of naturally occurring strains, having a bracket-like form, yellow-to-orange color, and poroid hymenial surfaces. The DNA sequences of ITS region of both strains showed a homology of 99% with ITS1 to ITS2 sequences of P. (Inonotus) baumii strain PB0806. PMID:22783119

  3. Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III–transcribed genes in budding yeast

    PubMed Central

    Belagal, Praveen; Normand, Christophe; Shukla, Ashutosh; Wang, Renjie; Léger-Silvestre, Isabelle; Dez, Christophe; Bhargava, Purnima; Gadal, Olivier

    2016-01-01

    The association of RNA polymerase III (Pol III)–transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III–transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements—centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III–transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III–transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III–dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III–transcribed genes required active transcription. We conclude that the association of Pol III–transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization. PMID:27559135

  4. The Limit of Free Magnetic Energy in Active Regions

    NASA Technical Reports Server (NTRS)

    Moore, Ron; Falconer, David; Sterling, Alphonse

    2012-01-01

    By measuring from active-region magnetograms a proxy of the free energy in the active region fs magnetic field, it has been found previously that (1) there is an abrupt upper limit to the free energy the field can hold that increases with the amount of magnetic field in the active region, the active region fs magnetic flux content, and (2) the free energy is usually near its limit when the field explodes in a CME/flare eruption. That is, explosive active regions are concentrated in a main-sequence path bordering the free-energy ]limit line in (flux content, free-energy proxy) phase space. Here, from measurement of Marshall Space Flight Center vector magnetograms, we find the magnetic condition that underlies the free ]energy limit and the accompanying main sequence of explosive active regions. Using a suitable free ]energy proxy measured from vector magnetograms of 44 active regions, we find that (1) in active regions at and near their free ]energy limit, the ratio of magnetic-shear free energy to the non ]free magnetic energy the potential field would have is approximately 1 in the core field, the field rooted along the neutral line, and (2) this ratio is progressively less in active regions progressively farther below their free ]energy limit. This shows that most active regions in which this core-field energy ratio is much less than 1 cannot be triggered to explode; as this ratio approaches 1, most active regions become capable of exploding; and when this ratio is 1 or greater, most active regions are compelled to explode. From these results we surmise the magnetic condition that determines the free ]energy limit is the ratio of the free magnetic energy to the non-free energy the active region fs field would have were it completely relaxed to its potential ]field configuration, and that this ratio is approximately 1 at the free-energy limit and in the main sequence of explosive active regions.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-03-01

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

  7. Statistical Analysis of Acoustic Wave Parameters Near Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Rabello-Soares, M. Cristina; Bogart, Richard S.; Scherrer, Philip H.

    2016-08-01

    In order to quantify the influence of magnetic fields on acoustic mode parameters and flows in and around active regions, we analyze the differences in the parameters in magnetically quiet regions nearby an active region (which we call “nearby regions”), compared with those of quiet regions at the same disk locations for which there are no neighboring active regions. We also compare the mode parameters in active regions with those in comparably located quiet regions. Our analysis is based on ring-diagram analysis of all active regions observed by the Helioseismic and Magnetic Imager (HMI) during almost five years. We find that the frequency at which the mode amplitude changes from attenuation to amplification in the quiet nearby regions is around 4.2 mHz, in contrast to the active regions, for which it is about 5.1 mHz. This amplitude enhacement (the “acoustic halo effect”) is as large as that observed in the active regions, and has a very weak dependence on the wave propagation direction. The mode energy difference in nearby regions also changes from a deficit to an excess at around 4.2 mHz, but averages to zero over all modes. The frequency difference in nearby regions increases with increasing frequency until a point at which the frequency shifts turn over sharply, as in active regions. However, this turnover occurs around 4.9 mHz, which is significantly below the acoustic cutoff frequency. Inverting the horizontal flow parameters in the direction of the neigboring active regions, we find flows that are consistent with a model of the thermal energy flow being blocked directly below the active region.

  8. Training and Availability of Braille Transcribers in the United States.

    ERIC Educational Resources Information Center

    Corn, Anne L.; Wall, Robert S.

    2002-01-01

    A survey of Braille transcribers in 40 states found Braille production systems rely on volunteers and hence Braille transcription is not considered a bona fide career. The majority cited low funding and resources as obstacles to change. Issues of certification, training, availability, and definition are discussed, along with recommendations.…

  9. Technique for inferring sizes of stellar-active regions

    SciTech Connect

    Dobson-Hockey, A.K.; Radick, R.R.

    1986-01-01

    Inspection of spectroheliograms showing large, well-developed active regions generally show the sunspots to lead the associated plage, in the sense of the solar rotation. Measurements have been made from spectroheliograms of spot-plage offsets and compared with nearly contemporaneous integrated disk observations. Larger active regions generally show larger spot leads; however, information regarding active-region sizes and spot-plage offsets is not readily obtainable form stellar-type observations of the Sun.

  10. A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases

    PubMed Central

    Heberling, Tamra; Davis, Lisa; Gedeon, Jakub; Morgan, Charles; Gedeon, Tomáš

    2016-01-01

    In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases. PMID:27517607

  11. Tracked Active Region Patches for MDI and HMI

    NASA Astrophysics Data System (ADS)

    Turmon, Michael; Hoeksema, J. Todd; Bobra, Monica

    2014-06-01

    We describe tracked active-region patch data products that have been developed for HMI (HMI Active Region Patches, or HARPs) and for MDI (MDI Tracked Active Region Patches, or MDI TARPs). Both data products consist of tracked magnetic features on the scale of solar active regions. The now-released HARP data product covers 2010-present (>2000 regions to date). Like the HARPs, the MDI TARP data set is a catalog of active regions (ARs), indexed by a region ID number, analogous to a NOAA AR number, and time. The TARPs contain 6170 regions spanning 72000 images taken over 1996-2010, and will be availablein the MDI resident archive (RA).MDI TARPs are computed based on the 96-minute synoptic magnetograms and intensitygrams. As with the related HARP data product, the approximate threshold for significance is 100G. Use of both image types together allows faculae and sunspots to be separated out as sub-classes of activity, in addition to identifying the overall active region that they are in. After being identified in single images, the magnetically-active patches are grouped and tracked from image to image. Merges among growing active regions, as well as faint active regions hovering at the threshold of detection, are handled automatically. Regions are tracked from their inception until they decay within view, or transit off the visible disk. For each active region and for each time, a bitmap image is stored containing the precise outline of the active region. Also, metadata such as areas and integrated fluxes are stored for each AR and for each time. Because there is a cross-calibration between the HMI and MDI magnetograms (Liu et al. 2012), it is straightforward to use the same classification and tracking rules for the HMI HARPs and the MDI TARPs. We show results demonstrating region correspondence, region boundary agreement, and agreement of flux metadata using the approximately 140 regions in the May 2010-October 2010 time period. We envision several uses for these data

  12. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures

    SciTech Connect

    Endoh, H.; Okada, N.

    1986-01-01

    Total DNAs from various animals were transcribed in vitro in a HeLa cell extract, and it was found that one to several discrete RNAs were transcribed by RNA polymerase III. With tortoise (Geoclemys reevessi) and newt (Cynops pyrrhogaster), distinct 6.5S and 8S RNAs were transcribed from these respective DNAs. Representative phage clones carrying the 6.5S and 8S RNA genes were isolated from genomic libraries of these animals, and the sequences of these genes were determined. The 5' parts of highly repetitive and transcribable sequences of tortoise and newt were found to have close resemblance to tRNA/sub 1//sup Lys/ (rabbit) gene (78% homology) and a tRNA/sup Glu/ (Drosophila) gene (74% homology, not counting the aminoacyl stem region), respectively. The homologies extended to secondary structures, homologous nucleotides being located on similar secondary structures. It is proposed that many, if not all, highly repetitive and transcribable sequences detected by total DNA transcription have specific tRNA genes as their progenitors.

  13. Comparison of laboratory colonies and field populations of Tamarixia radiata, an ecto-parasitoid of the Asian Citrus Psyllid, using internal transcribed spacer and cytochrome oxidase subunit l DNA sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of Tamarixia radiata laboratory colonies derived from collections in China, northern Vietnam, Pakistan, and a mixed colony from Taiwan and southern Vietnam was evaluated using the internal transcribed spacer region 1 (ITS-1), internal transcribed spacer region 2 (ITS-2) and the...

  14. A Fractal Dimension Survey of Active Region Complexity

    NASA Technical Reports Server (NTRS)

    McAteer, R. T. James; Gallagher, Peter; Ireland, Jack

    2005-01-01

    A new approach to quantifying the magnetic complexity of active regions using a fractal dimension measure is presented. This fully-automated approach uses full disc MDI magnetograms of active regions from a large data set (2742 days of the SoHO mission; 9342 active regions) to compare the calculated fractal dimension to both Mount Wilson classification and flare rate. The main Mount Wilson classes exhibit no distinct fractal dimension distribution, suggesting a self-similar nature of all active regions. Solar flare productivity exhibits an increase in both the frequency and GOES X-ray magnitude of flares from regions with higher fractal dimensions. Specifically a lower threshold fractal dimension of 1.2 and 1.25 exists as a necessary, but not sufficient, requirement for an active region to produce M- and X-class flares respectively .

  15. GLOBAL DYNAMICS OF SUBSURFACE SOLAR ACTIVE REGIONS

    SciTech Connect

    Jouve, L.; Brun, A. S.

    2013-01-01

    We present three-dimensional numerical simulations of a magnetic loop evolving in either a convectively stable or unstable rotating shell. The magnetic loop is introduced into the shell in such a way that it is buoyant only in a certain portion in longitude, thus creating an {Omega}-loop. Due to the action of magnetic buoyancy, the loop rises and develops asymmetries between its leading and following legs, creating emerging bipolar regions whose characteristics are similar to those of observed spots at the solar surface. In particular, we self-consistently reproduce the creation of tongues around the spot polarities, which can be strongly affected by convection. We further emphasize the presence of ring-shaped magnetic structures around our simulated emerging regions, which we call 'magnetic necklace' and which were seen in a number of observations without being reported as of today. We show that those necklaces are markers of vorticity generation at the periphery and below the rising magnetic loop. We also find that the asymmetry between the two legs of the loop is crucially dependent on the initial magnetic field strength. The tilt angle of the emerging regions is also studied in the stable and unstable cases and seems to be affected both by the convective motions and the presence of a differential rotation in the convective cases.

  16. OBSERVING CORONAL NANOFLARES IN ACTIVE REGION MOSS

    SciTech Connect

    Testa, Paola; DeLuca, Ed; Golub, Leon; Korreck, Kelly; Weber, Mark; De Pontieu, Bart; Martinez-Sykora, Juan; Title, Alan; Hansteen, Viggo; Cirtain, Jonathan; Winebarger, Amy; Kobayashi, Ken; Kuzin, Sergey; Walsh, Robert; DeForest, Craig

    2013-06-10

    The High-resolution Coronal Imager (Hi-C) has provided Fe XII 193A images of the upper transition region moss at an unprecedented spatial ({approx}0.''3-0.''4) and temporal (5.5 s) resolution. The Hi-C observations show in some moss regions variability on timescales down to {approx}15 s, significantly shorter than the minute-scale variability typically found in previous observations of moss, therefore challenging the conclusion of moss being heated in a mostly steady manner. These rapid variability moss regions are located at the footpoints of bright hot coronal loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly in the 94 A channel, and by the Hinode/X-Ray Telescope. The configuration of these loops is highly dynamic, and suggestive of slipping reconnection. We interpret these events as signatures of heating events associated with reconnection occurring in the overlying hot coronal loops, i.e., coronal nanoflares. We estimate the order of magnitude of the energy in these events to be of at least a few 10{sup 23} erg, also supporting the nanoflare scenario. These Hi-C observations suggest that future observations at comparable high spatial and temporal resolution, with more extensive temperature coverage, are required to determine the exact characteristics of the heating mechanism(s).

  17. Software Displays Data on Active Regions of the Sun

    NASA Technical Reports Server (NTRS)

    Golightly, Mike; Weyland, Mark; Raben, Vern

    2011-01-01

    The Solar Active Region Display System is a computer program that generates, in near real time, a graphical display of parameters indicative of the spatial and temporal variations of activity on the Sun. These parameters include histories and distributions of solar flares, active region growth, coronal mass ejections, size, and magnetic configuration. By presenting solar-activity data in graphical form, this program accelerates, facilitates, and partly automates what had previously been a time-consuming mental process of interpretation of solar-activity data presented in tabular and textual formats. Intended for original use in predicting space weather in order to minimize the exposure of astronauts to ionizing radiation, the program might also be useful on Earth for predicting solar-wind-induced ionospheric effects, electric currents, and potentials that could affect radio-communication systems, navigation systems, pipelines, and long electric-power lines. Raw data for the display are obtained automatically from the Space Environment Center (SEC) of the National Oceanic and Atmospheric Administration (NOAA). Other data must be obtained from the NOAA SEC by verbal communication and entered manually. The Solar Active Region Display System automatically accounts for the latitude dependence of the rate of rotation of the Sun, by use of a mathematical model that is corrected with NOAA SEC active-region position data once every 24 hours. The display includes the date, time, and an image of the Sun in H light overlaid with latitude and longitude coordinate lines, dots that mark locations of active regions identified by NOAA, identifying numbers assigned by NOAA to such regions, and solar-region visual summary (SRVS) indicators associated with some of the active regions. Each SRVS indicator is a small pie chart containing five equal sectors, each of which is color-coded to provide a semiquantitative indication of the degree of hazard posed by one aspect of the activity at

  18. Reading cinnamon activates olfactory brain regions.

    PubMed

    González, Julio; Barros-Loscertales, Alfonso; Pulvermüller, Friedemann; Meseguer, Vanessa; Sanjuán, Ana; Belloch, Vicente; Avila, César

    2006-08-15

    Some words immediately and automatically remind us of odours, smells and scents, whereas other language items do not evoke such associations. This study investigated, for the first time, the abstract linking of linguistic and odour information using modern neuroimaging techniques (functional MRI). Subjects passively read odour-related words ('garlic', 'cinnamon', 'jasmine') and neutral language items. The odour-related terms elicited activation in the primary olfactory cortex, which include the piriform cortex and the amygdala. Our results suggest the activation of widely distributed cortical cell assemblies in the processing of olfactory words. These distributed neuron populations extend into language areas but also reach some parts of the olfactory system. These distributed neural systems may be the basis of the processing of language elements, their related conceptual and semantic information and the associated sensory information.

  19. Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast

    PubMed Central

    Conconi, Antonio; Bespalov, Vyacheslav A.; Smerdon, Michael J.

    2002-01-01

    Nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers (CPDs) was measured in the individual strands of transcriptionally active and inactive ribosomal genes of yeast. Ribosomal genes (rDNA) are present in multiple copies, but only a fraction of them is actively transcribed. Restriction enzyme digestion was used to specifically release the transcriptionally active fraction from yeast nuclei, and selective psoralen crosslinking was used to distinguish between active and inactive rDNA chromatin. Removal of CPDs was followed in both rDNA populations, and the data clearly show that strand-specific repair occurs in transcriptionally active rDNA while being absent in the inactive rDNA fraction. Thus, transcription-coupled repair occurs in RNA polymerase I-transcribed genes in yeast. Moreover, the nontranscribed strand of active rDNA is repaired faster than either strand of inactive rDNA, implying that NER has preferred access to the active, non-nucleosomal rDNA chromatin. Finally, restriction enzyme accessibility to active rDNA varies during NER, suggesting that there is a change in ribosomal gene chromatin structure during or soon after CPD removal. PMID:11782531

  20. 3D MHD Models of Active Region Loops

    NASA Technical Reports Server (NTRS)

    Ofman, Leon

    2004-01-01

    Present imaging and spectroscopic observations of active region loops allow to determine many physical parameters of the coronal loops, such as the density, temperature, velocity of flows in loops, and the magnetic field. However, due to projection effects many of these parameters remain ambiguous. Three dimensional imaging in EUV by the STEREO spacecraft will help to resolve the projection ambiguities, and the observations could be used to setup 3D MHD models of active region loops to study the dynamics and stability of active regions. Here the results of 3D MHD models of active region loops are presented, and the progress towards more realistic 3D MHD models of active regions. In particular the effects of impulsive events on the excitation of active region loop oscillations, and the generation, propagations and reflection of EIT waves are shown. It is shown how 3D MHD models together with 3D EUV observations can be used as a diagnostic tool for active region loop physical parameters, and to advance the science of the sources of solar coronal activity.

  1. Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription

    PubMed Central

    Li, Bing; Gogol, Madelaine; Carey, Mike; Pattenden, Samantha G.; Seidel, Chris; Workman, Jerry L.

    2007-01-01

    The presence of Set2-mediated methylation of H3K36 (K36me) correlates with transcription frequency throughout the yeast genome. K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Here, using a genome-wide approach, we report that the Set2–Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional readout for this pathway, we discovered that longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high-resolution tiling microarrays allowed us to identify a group of genes that rely on Set2–Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend on the same pathway to maintain a hypoacetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways. PMID:17545470

  2. ACTIVE REGION MORPHOLOGIES SELECTED FROM NEAR-SIDE HELIOSEISMIC DATA

    SciTech Connect

    MacDonald, G. A.; McAteer, R. T. J.; Henney, C. J.; Arge, C. N.; Díaz Alfaro, M.; González Hernández, I.; Lindsey, C.

    2015-07-01

    We estimate the morphology of near-side active regions using near-side helioseismology. Active regions from two data sets, Air Force Data Assimilative Photospheric flux Transport synchronic maps and Global Oscillation Network Group near-side helioseismic maps, were matched and their morphologies compared. Our algorithm recognizes 382 helioseismic active regions between 2002 April 25 and 2005 December 31 and matches them to their corresponding magnetic active regions with 100% success. A magnetic active region occupies 30% of the area of its helioseismic signature. Recovered helioseismic tilt angles are in good agreement with magnetic tilt angles. Approximately 20% of helioseismic active regions can be decomposed into leading and trailing polarity. Leading polarity components show no discernible scaling relationship, but trailing magnetic polarity components occupy approximately 25% of the area of the trailing helioseismic component. A nearside phase-magnetic calibration is in close agreement with a previous far-side helioseismic calibration and provides confidence that these morphological relationships can be used with far-side helioseismic data. Including far-side active region morphology in synchronic maps will have implications for coronal magnetic topology predictions and solar wind forecasts.

  3. Active Region Morphologies Selected From Near-side Helioseismic Data

    NASA Astrophysics Data System (ADS)

    MacDonald, Gordon Andrew; Henney, Carl; Diaz Alfaro, Manuel; Gonzalez Hernandez, Irene; Arge, Nick; Lindsey, Charles; McAteer, James

    2015-04-01

    We estimate the morphology of near-side active regions using near-side helioseismology. Active regions from two data sets, ADAPT synchronic maps and GONG near-side helioseismic maps, were matched and their morphologies compared. Our algorithm recognizes 382 helioseismic active regions between 2002 April 25 and 2005 December 31 and matches them to their corresponding magnetic active regions with 100% success. A magnetic active region occupies 30% of the area of its helioseismic signature. Recovered helioseismic tilt angles are in good agreement with magnetic tilt angles. Approximately 20% of helioseismic active regions can be decomposed into leading and trailing polarity. Leading polarity components show no discernible scaling relationship, but trailing magnetic polarity components occupy approximately 25% of the area of the trailing helioseismic component. A nearside phase-magnetic calibration is in close agreement with a previous far-side helioseismic calibration and provides confidence that these morphological relationships can be used with far-side helioseismic data. Including far-side active region morphology in synchronic maps will have implications for coronal magnetic topology predictions and solar wind forecasts.

  4. Active Region Morphologies Selected from Near-side Helioseismic Data

    NASA Astrophysics Data System (ADS)

    MacDonald, G. A.; Henney, C. J.; Díaz Alfaro, M.; González Hernández, I.; Arge, C. N.; Lindsey, C.; McAteer, R. T. J.

    2015-07-01

    We estimate the morphology of near-side active regions using near-side helioseismology. Active regions from two data sets, Air Force Data Assimilative Photospheric flux Transport synchronic maps and Global Oscillation Network Group near-side helioseismic maps, were matched and their morphologies compared. Our algorithm recognizes 382 helioseismic active regions between 2002 April 25 and 2005 December 31 and matches them to their corresponding magnetic active regions with 100% success. A magnetic active region occupies 30% of the area of its helioseismic signature. Recovered helioseismic tilt angles are in good agreement with magnetic tilt angles. Approximately 20% of helioseismic active regions can be decomposed into leading and trailing polarity. Leading polarity components show no discernible scaling relationship, but trailing magnetic polarity components occupy approximately 25% of the area of the trailing helioseismic component. A nearside phase-magnetic calibration is in close agreement with a previous far-side helioseismic calibration and provides confidence that these morphological relationships can be used with far-side helioseismic data. Including far-side active region morphology in synchronic maps will have implications for coronal magnetic topology predictions and solar wind forecasts.

  5. A Multi Wavelength Study of Active Region Development

    NASA Astrophysics Data System (ADS)

    Lara, A.; Gopalswamy, N.; Kundu, M. R.; Perez-Enriquez, R.; Koshiishi, H.; Enome, S.

    1996-05-01

    We report on a study of the evolution of several active regions during 1993 April 17-28 using data obtained at multiple wavelengths that probe various heights of the active region corona. We use simultaneous microwave (1.5 and 17 GHz) and Soft X-ray images obtained by the Very Large Array (VLA), the Nobeyama Radio Heliograph (NRH) and the Soft X-ray Telescope (SXT) on board the Yohkoh spacecraft. We also use photospheric magnetograms from Kitt Peak National Observatory to study the development of Solar Active Regions. We have followed the development of various observed parameters such as brightness temperature and polarization using radio images. The X-ray data were used to track the development of density and temperature of active regions. Using the fact that the quiet active region radiation is thermal and adopting proper emission mechanism at each frequency domain, we construct a consistent picture for the three dimensional structure of the active regions. Particular attention has been paid to the mode coupling observed at 17 GHz while the active regions crossed the solar disk.

  6. Regional Observation of Seismic Activity in Baekdu Mountain

    NASA Astrophysics Data System (ADS)

    Kim, Geunyoung; Che, Il-Young; Shin, Jin-Soo; Chi, Heon-Cheol

    2015-04-01

    Seismic unrest in Baekdu Mountain area between North Korea and Northeast China region has called attention to geological research community in Northeast Asia due to her historical and cultural importance. Seismic bulletin shows level of seismic activity in the area is higher than that of Jilin Province of Northeast China. Local volcanic observation shows a symptom of magmatic unrest in period between 2002 and 2006. Regional seismic data have been used to analyze seismic activity of the area. The seismic activity could be differentiated from other seismic phenomena in the region by the analysis.

  7. The Smad3 linker region contains a transcriptional activation domain.

    PubMed

    Wang, Guannan; Long, Jianyin; Matsuura, Isao; He, Dongming; Liu, Fang

    2005-02-15

    Transforming growth factor-beta (TGF-beta)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-beta/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-beta transcriptional activation responses, although it can be phosphorylated by the TGF-beta receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-beta. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control.

  8. Project to transcribe old ship logs provides important weather data

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-11-01

    Kathy Wendolkowski is a citizen scientist. It's a term that Wendolkowski considers far too lofty for what she claims is simply a happy addiction that she and others have for transcribing old logs from naval ship and other vessels. They perform this task to glean the regularly recorded weather data from those logs for the benefit of science. For Wendolkowski, though, greater satisfaction comes from reading what the logs also reveal about the daily lives of the sailors as well as any accompanying historical drama.

  9. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure.

    PubMed

    Coleman, Annette W

    2015-03-01

    rRNA is one of the few universal features of life, making it uniquely suited to assess phylogenetic relationships. The processing of the initial polycistronic rRNA transcript is also a conserved process, involving numerous cleavage events and the generation of secondary structures. The secondary structure of the internal transcribed spacer (ITS) regions of nuclear rRNA transcripts are well known for a wide variety of eukaryotes and have been used to aid in the alignment of these sequences for phylogenetic comparisons. By contrast, study of the processing of the initial rRNA transcripts has been largely limited to yeast, mice, rats, and humans. Here I examine the known cleavage sites in the two ITS regions and their positions relative to the secondary structure. A better understanding of the conservation of secondary structures and cleavage sites within the ITS regions will improve evolutionary inferences based on these sequences.

  10. Prediction of Active-Region CME Productivity from Magnetograms

    NASA Technical Reports Server (NTRS)

    Falconer, D. A.; Moore, R. L.; Gary, G. A.

    2004-01-01

    We report results of an expanded evaluation of whole-active-region magnetic measures as predictors of active-region coronal mass ejection (CME) productivity. Previously, in a sample of 17 vector magnetograms of 12 bipolar active regions observed by the Marshall Space Flight Center (MSFC) vector magnetograph, from each magnetogram we extracted a measure of the size of the active region (the active region s total magnetic flux a) and four measures of the nonpotentiality of the active region: the strong-shear length L(sub SS), the strong-gradient length L(sub SG), the net vertical electric current I(sub N), and the net-current magnetic twist parameter alpha (sub IN). This sample size allowed us to show that each of the four nonpotentiality measures was statistically significantly correlated with active-region CME productivity in time windows of a few days centered on the day of the magnetogram. We have now added a fifth measure of active-region nonpotentiality (the best-constant-alpha magnetic twist parameter (alpha sub BC)), and have expanded the sample to 36 MSFC vector magnetograms of 31 bipolar active regions. This larger sample allows us to demonstrate statistically significant correlations of each of the five nonpotentiality measures with future CME productivity, in time windows of a few days starting from the day of the magnetogram. The two magnetic twist parameters (alpha (sub 1N) and alpha (sub BC)) are normalized measures of an active region s nonpotentially in that they do not depend directly on the size of the active region, while the other three nonpotentiality measures (L(sub SS), L(sub SG), and I(sub N)) are non-normalized measures in that they do depend directly on active-region size. We find (1) Each of the five nonpotentiality measures is statistically significantly correlated (correlation confidence level greater than 95%) with future CME productivity and has a CME prediction success rate of approximately 80%. (2) None of the nonpotentiality

  11. Observed Helicity of Active Regions in Solar Cycle 21

    NASA Technical Reports Server (NTRS)

    Hagyard, M. J.; Pevtsov, A. A.; Blehm, Z.; Smith, J. E.; Six, Frank (Technical Monitor)

    2003-01-01

    We report the results of a study of helicity in solar active regions during the peak of activity in solar cycle 21 from observations with the Marshall Space Flight Center's solar vector magnetograph. Using the force-free parameter alpha as the proxy for helicity, we calculated an average value of alpha for each of 60 active regions from a total of 449 vector magnetograms that were obtained during the period 1980 March to November. The signs of these average values of alpha were correlated with the latitude of the active regions to test the hemispheric rule of helicity that has been proposed for solar magnetic fields: negative helicity predominant in northern latitudes, positive in the southern ones. We have found that of the 60 regions that were observed, 30 obey the hemispheric rule and 30 do not.

  12. Photospheric Magnetic Free Energy Density of Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Zhang, Hongqi

    2016-12-01

    We present the photospheric energy density of magnetic fields in two solar active regions (one of them recurrent) inferred from observational vector magnetograms, and compare it with other available differently defined energy parameters of magnetic fields in the photosphere. We analyze the magnetic fields in Active Regions NOAA 6580-6619-6659 and 11158. The quantity 1/4π{B}n\\cdot{B}p is an important energy parameter that reflects the contribution of magnetic shear to the difference between the potential (Bp) and the non-potential magnetic field (Bn), and also the contribution to the free magnetic energy near the magnetic neutral lines in the active regions. It is found that the photospheric mean magnetic energy density shows clear changes before the powerful solar flares in Active Region NOAA 11158, which is consistent with the change in magnetic fields in the flaring lower atmosphere.

  13. AFS dynamics in a short-lived active region

    NASA Astrophysics Data System (ADS)

    Zuccarello, F.; Battiato, V.; Contarino, L.; Romano, P.; Spadaro, D.; Vlahos, L.

    2005-11-01

    In the framework of the study on active region emergence, we report the results obtained from the analysis of the short-lived (7 days) active region NOAA 10407. The data used were acquired during an observational campaign carried out with the THEMIS telescope in IPM mode in July 2003, coordinated with other ground- and space-based instruments (INAF-OACT, DOT, BBSO, MDI/SOHO, EIT/SOHO, TRACE). We determined the morphological and magnetic evolution of NOAA 10407, as well as the velocity fields associated with its magnetic structures. Within the limits imposed by the spatial and temporal resolution of the images analyzed, the first evidence of the active region formation is initially observed in the transition region and lower corona, and later on (i.e. after about 7 h) in the inner layers, as found in a previous analysis concerning a long-lived, recurrent active region. The results also indicate that the AFS formed in the active region shows typical upward motion at the AFS's tops and downward motion at the footpoints. The velocity values relevant to the upward motions decrease over the evolution of the region, similarly to the case of the recurrent active region, while we notice an increasing trend in the downflow velocity during the early phases of the time interval analyzed by THEMIS. On the other hand, the AFS preceding legs show a higher downflow than the following ones, a result in contrast with that found in the long-lived active region. The chromospheric area overhanging the sunspot umbra shows an upward motion of ˜ 2 km s-1, while that above the pores shows a downward motion of ~4 km s-1.

  14. THE COLD SHOULDER: EMISSION MEASURE DISTRIBUTIONS OF ACTIVE REGION CORES

    SciTech Connect

    Schmelz, J. T.; Pathak, S.

    2012-09-10

    The coronal heating mechanism for active region core loops is difficult to determine because these loops are often not resolved and cannot be studied individually. Rather, we concentrate on the 'inter-moss' areas between loop footpoints. We use observations from the Hinode EUV Imaging Spectrometer and the X-Ray Telescope to calculate the emission measure distributions of eight inter-moss areas in five different active regions. The combined data sets provide both high- and low-temperature constraints and ensure complete coverage in the temperature range appropriate for active regions. For AR 11113, the emission can be modeled with heating events that occur on timescales less than the cooling time. The loops in the core regions appear to be close to equilibrium and are consistent with steady heating. The other regions studied, however, appear to be dominated by nanoflare heating. Our results are consistent with the idea that active region age is an important parameter in determining whether steady or nanoflare heating is primarily responsible for the core emission, that is, older regions are more likely to be dominated by steady heating, while younger regions show more evidence of nanoflares.

  15. Active Ageing Level of Older Persons: Regional Comparison in Thailand

    PubMed Central

    Haque, Md. Nuruzzaman

    2016-01-01

    Active ageing level and its discrepancy in different regions (Bangkok, Central, North, Northeast, and South) of Thailand have been examined for prioritizing the policy agenda to be implemented. Attempt has been made to test preliminary active ageing models for Thai older persons and hence active ageing index (AAI, ranges from 0 to 1) has been estimated. Using nationally representative data and confirmatory factor analysis approach, this study justified active ageing models for female and male older persons in Thailand. Results revealed that active ageing level of Thai older persons is not high (mean AAIs for female and male older persons are 0.64 and 0.61, resp., and those are significantly different (p < 0.001)). Mean AAI in Central region is lower than North, Northeast, and South regions but there is no significant difference in the latter three regions of Thailand. Special emphasis should be given to Central region and policy should be undertaken for increasing active ageing level. Implementation of an Integrated Active Ageing Package (IAAP), containing policies for older persons to improve their health and economic security, to promote participation in social groups and longer working lives, and to arrange learning programs, would be helpful for increasing older persons' active ageing level in Thailand. PMID:27375903

  16. DISTRIBUTION OF ELECTRIC CURRENTS IN SOLAR ACTIVE REGIONS

    SciTech Connect

    Török, T.; Titov, V. S.; Mikić, Z.; Leake, J. E.; Archontis, V.; Linton, M. G.; Dalmasse, K.; Aulanier, G.; Kliem, B.

    2014-02-10

    There has been a long-standing debate on the question of whether or not electric currents in solar active regions are neutralized. That is, whether or not the main (or direct) coronal currents connecting the active region polarities are surrounded by shielding (or return) currents of equal total value and opposite direction. Both theory and observations are not yet fully conclusive regarding this question, and numerical simulations have, surprisingly, barely been used to address it. Here we quantify the evolution of electric currents during the formation of a bipolar active region by considering a three-dimensional magnetohydrodynamic simulation of the emergence of a sub-photospheric, current-neutralized magnetic flux rope into the solar atmosphere. We find that a strong deviation from current neutralization develops simultaneously with the onset of significant flux emergence into the corona, accompanied by the development of substantial magnetic shear along the active region's polarity inversion line. After the region has formed and flux emergence has ceased, the strong magnetic fields in the region's center are connected solely by direct currents, and the total direct current is several times larger than the total return current. These results suggest that active regions, the main sources of coronal mass ejections and flares, are born with substantial net currents, in agreement with recent observations. Furthermore, they support eruption models that employ pre-eruption magnetic fields containing such currents.

  17. Photospheric Magnetic Diffusion by Measuring Moments of Active Regions

    NASA Astrophysics Data System (ADS)

    Engell, Alexander; Longcope, D.

    2013-07-01

    Photospheric magnetic surface diffusion is an important constraint for the solar dynamo. The HMI Active Region Patches (HARPs) program automatically identify all magnetic regions above a certain flux. In our study we measure the moments of ARs that are no longer actively emerging and can thereby give us good statistical constraints on photospheric diffusion. We also present the diffusion properties as a function of latitude, flux density, and single polarity (leading or following) within each HARP.

  18. Solar Irradiance Variations on Active Region Time Scales

    NASA Technical Reports Server (NTRS)

    Labonte, B. J. (Editor); Chapman, G. A. (Editor); Hudson, H. S. (Editor); Willson, R. C. (Editor)

    1984-01-01

    The variations of the total solar irradiance is an important tool for studying the Sun, thanks to the development of very precise sensors such as the ACRIM instrument on board the Solar Maximum Mission. The largest variations of the total irradiance occur on time scales of a few days are caused by solar active regions, especially sunspots. Efforts were made to describe the active region effects on total and spectral irradiance.

  19. 11p15-subband specific search for transcribed sequences using exon trapping

    SciTech Connect

    Loebbert, R.; Prawitt, D.; Monroe, D.

    1994-09-01

    Evidence from cytogenetic and molecular data suggest that the region 11p15 contains genes involved in different disorders, like Beckwith-Wiedemann syndrome (BWS), long QT syndrome (LQT), Usher syndrome type I and tumor development. Focusing on the subregion 11p15.1, we are isolating and characterizing new transcribed sequences. The applied strategy includes exon amplification and subsequent PCR screening of cDNA libraries. So far 100 YACs and 38 cosmid clones from 11p15.1-15.3 have been collected and are currently arrayed. 16 cosmids have been analyzed for transcribed sequences using the exon amplification scheme developed by Buckler et al. (1991). We were able to identify 18 exons that contain correct open reading frames and map back to the cosmid clones. A data base search revealed that two exons represent parts of known genes from this region (ST5 and AMPD3). Moreover, we identified one exon that represents an EGF-like repeat with homologies to various proteins. Using PCR and primers from the exon sequences, a fetal brain library, which has been arranged in the form of hierarchic arrayed phage pools, was screened. Up to now, two cDNA clones corresponding to different exons were isolated and are currently sequenced.

  20. The nature of chromospheric active regions on V410 Tauri

    NASA Astrophysics Data System (ADS)

    Mekkaden, M. V.; Pukalenthi, S.; Muneer, S.; Bastian, Anju Barbara

    2005-12-01

    We present spectroscopic observations in the region of H alpha and Li I lines of the weak emission T Tauri star V410 Tau obtained over 1999/2000, 2002/2003 and 2003/2004 seasons. The emission strength showed rotational modulation during the 1999/2000 season in such a way that the emis- sion strength is maximum at light minimum and vice versa. This indicates that the photospheric and chromospheric active regions overlap over shorter dura- tions of time and the lifetimes of chromospheric active regions are far shorter than the photospheric active regions. But the observations obtained during the 2003/2004 season do not follow the trend observed at earlier seasons. This can be due to the change in the location of chromospheric active regions. Another possibility is the occurrence of a major change in the photospheric active re- gions that have caused a redistribution of photospheric as well as chromospheric active regions. The Li I EW does not show any appreciable change over the four-year period.

  1. Twist of Magnetic Fields in Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Zhang, Hongqi; Bao, Shudong; Kuzanyan, Kirill M.

    2002-05-01

    We study the twist properties of photospheric magnetic fields in solar active regions using magnetographic data on 422 active regions obtained at the Huairou Solar Observing Station in 1988 1997. We calculate the mean twist (force-free field αf) of the active regions and compare it with the mean current-helicity density of these same active regions, h c =B ∥·(∇×B)∥. The latitude and longitude distributions and time dependence of these quantities is analyzed. These parameters represent two different tracers of the α effect in dynamo theory, so we might expect them to possess similar properties. However, apart from differences in their definitions, they also display differences associated with the technique used to recalculate the magnetographic data and with their different physical meanings. The distributions of the mean αf and h c both show hemispherical asymmetry—negative (positive) values in the northern (southern) hemisphere—although this tendency is stronger for h c. One reason for these differences may be the averaging procedure, when twists of opposite sign in regions with weak fields make a small contribution to the mean current-helicity density. Such transequatorial regularity is in agreement with the expectations of dynamo theory. In some active regions, the average αf and h c do not obey this transequatorial rule. As a whole, the mean twist of the magnetic fields αf of active regions does not vary significantly with the solar cycle. Active regions that do not follow the general behavior for αf do not show any appreciable tendency to cluster at certain longitudes, in contrast to results for h c noted in previous studies. We analyze similarities and differences in the distributions of these two quantities. We conclude that using only one of these tracers, such as αf, to search for signatures of the α effect can have disadvantages, which should be taken into account in future studies.

  2. SDO/HMI survey of emerging active regions for helioseismology

    NASA Astrophysics Data System (ADS)

    Schunker, H.; Braun, D. C.; Birch, A. C.; Burston, R. B.; Gizon, L.

    2016-11-01

    Context. Observations from the Solar Dynamics Observatory (SDO) have the potential for allowing the helioseismic study of the formation of hundreds of active regions, which would enable us to perform statistical analyses. Aims: Our goal is to collate a uniform data set of emerging active regions observed by the SDO/HMI instrument suitable for helioseismic analysis, where each active region is centred on a 60° × 60° area and can be observed up to seven days before emergence. Methods: We restricted the sample to active regions that were visible in the continuum and emerged into quiet Sun largely avoiding pre-existing magnetic regions. As a reference data set we paired a control region (CR), with the same latitude and distance from central meridian, with each emerging active region (EAR). The control regions do not have any strong emerging flux within 10° of the centre of the map. Each region was tracked at the Carrington rotation rate as it crossed the solar disk, within approximately 65° from the central meridian and up to seven days before, and seven days after, emergence. The mapped and tracked data, consisting of line-of-sight velocity, line-of-sight magnetic field, and intensity as observed by SDO/HMI, are stored in datacubes that are 410 min in duration and spaced 320 min apart. We call this data set, which is currently comprised of 105 emerging active regions observed between May 2010 and November 2012, the SDO Helioseismic Emerging Active Region (SDO/HEAR) survey. Results: To demonstrate the utility of a data set of a large number of emerging active regions, we measure the relative east-west velocity of the leading and trailing polarities from the line-of-sight magnetogram maps during the first day after emergence. The latitudinally averaged line-of-sight magnetic field of all the EARs shows that, on average, the leading (trailing) polarity moves in a prograde (retrograde) direction with a speed of 121 ± 22 m s-1 (-70 ± 13 m s-1) relative to the

  3. Earth resources-regional transfer activity contracts review

    NASA Technical Reports Server (NTRS)

    Bensko, J., Jr.; Daniels, J. L.; Downs, S. W., Jr.; Jones, N. L.; Morton, R. R.; Paludan, C. T.

    1977-01-01

    A regional transfer activity contracts review held by the Earth Resources Office was summarized. Contracts in the earth resources field primarily directed toward applications of satellite data and technology in solution of state and regional problems were reviewed. A summary of the progress of each contract was given in order to share experiences of researchers across a seven state region. The region included Missouri, Kentucky, Tennessee, Mississippi, Alabama, Georgia, and North Carolina. Research in several earth science disciplines included forestry, limnology, water resources, land use, geology, and mathematical modeling. The use of computers for establishment of information retrieval systems was also emphasized.

  4. Predictions of active region flaring probability using subsurface helicity measurements

    NASA Astrophysics Data System (ADS)

    Reinard, A. A.; Komm, R.; Hill, F.

    2010-12-01

    Solar flares are responsible for a number of hazardous effects on the earth such as disabling high-frequency radio communications, interfering with GPS measurements, and disrupting satellites. However, forecasting flare occurrence is currently very difficult. One possible means for predicting flare occurrence lies in helioseismology, i.e. analysis of the region below the active region for signs of an impending flare. Time series helioseismic data collected by the Global Oscillation Network Group (GONG) has been analyzed for a subset of active regions that produce large flares and a subset with very high magnetic field strength that produce no flares. A predictive parameter has been developed and analyzed using discriminant analysis as well as traditional forecasting tools such as the Heidke skill score. Preliminary results show that this parameter predicts the flaring probability of an active region 2-3 days in advance with a relatively high degree of success.

  5. Helium Line Formation and Abundance in a Solar Active Region

    NASA Astrophysics Data System (ADS)

    Mauas, P. J. D.; Andretta, V.; Falchi, A.; Falciani, R.; Teriaca, L.; Cauzzi, G.

    2005-01-01

    An observing campaign (SOHO JOP 139), coordinated between ground-based and Solar and Heliospheric Observatory (SOHO) instruments, has been planned to obtain simultaneous spectroheliograms of the same active region in several spectral lines. The chromospheric lines Ca II K, Hα, and Na I D, as well as He I 10830, 5876, 584, and He II 304 Å lines have been observed. The EUV radiation in the range λ<500 Å and in the range 260<λ<340 Å has also been measured at the same time. These simultaneous observations allow us to build semiempirical models of the chromosphere and low transition region of an active region, taking into account the estimated total number of photoionizing photons impinging on the target active region and their spectral distribution. We obtained a model that matches very well all the observed line profiles, using a standard value for the He abundance ([He]=0.1) and a modified distribution of microturbulence. For this model we study the influence of the coronal radiation on the computed helium lines. We find that, even in an active region, the incident coronal radiation has a limited effect on the UV He lines, while it is of fundamental importance for the D3 and 10830 Å lines. Finally, we build two more models, assuming values of He abundance [He]=0.07 and 1.5, only in the region where temperatures are >1×104 K. This region, between the chromosphere and transition region, has been indicated as a good candidate for processes that might be responsible for strong variations of [He]. The set of our observables can still be well reproduced in both cases, changing the atmospheric structure mainly in the low transition region. This implies that, to choose between different values of [He], it is necessary to constrain the transition region with different observables, independent of the He lines.

  6. Universities and Economic Development Activities: A UK Regional Comparison

    ERIC Educational Resources Information Center

    Decter, Moira; Cave, Frank; Rose, Mary; Peers, Gill; Fogg, Helen; Smith, Susan M.

    2011-01-01

    A number of UK universities prioritize economic development or regeneration activities and for some of these universities such activities are the main focus of their knowledge transfer work. This study compares two regions of the UK--the North West and the South East of England--which have very different levels of economic performance.…

  7. IFLA General Conference, 1985. Division on Regional Activities. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on regional library activities which were presented at the 1985 International Federation of Library Associations (IFLA) conference include: (1) "Importance of Information Resources in National Development with Particular Reference to the Asian Scene" (Yogendra P. Dubey, India); (2) "Report of the Activities of the Regional…

  8. Activated region fitting: a robust high-power method for fMRI analysis using parameterized regions of activation.

    PubMed

    Weeda, Wouter D; Waldorp, Lourens J; Christoffels, Ingrid; Huizenga, Hilde M

    2009-08-01

    An important issue in the analysis of fMRI is how to account for the spatial smoothness of activated regions. In this article a method is proposed to accomplish this by modeling activated regions with Gaussian shapes. Hypothesis tests on the location, spatial extent, and amplitude of these regions are performed instead of hypothesis tests of individual voxels. This increases power and eases interpretation. Simulation studies show robust hypothesis tests under misspecification of the shape model, and increased power over standard techniques especially at low signal-to-noise ratios. An application to real single-subject data also indicates that the method has increased power over standard methods.

  9. Dynamics of active regions observed with Hinode XRT

    NASA Astrophysics Data System (ADS)

    Sakao, Taro

    We present dynamics of active regions observed with the X-Ray Telescope (XRT) aboard Hinode. XRT is a grazing-incidence imager with a Walter Type-I-like mirror of 34 cm diameter with a back-illuminated CCD device. The XRT can image the X-ray corona of the Sun with angular resolution consistent with 1 arcsec CCD pixel size. In addition to this unprecedentedly-high angular resolution ever achieved as a solar X-ray telescope, enhanced sensitivity of the CCD towards longer X-ray wavelengths (particularly beyond 50 Angstroms) enables XRT to image, and perform temperature diagnostics on, a wide range of coronal plasmas from those as low as 1 MK to high-temperature plasmas even exceeding 10 MK. This adds a notable advantage to the XRT such that it can observe most, if not all, active phenomena taking place in and around active regions. Since the beginning of observations with XRT on 23 October 2006, the XRT has so far made various interesting observations regarding active regions. These include (1) continuous outflow of plasmas from the edge of a solar active region that is likely to be a source of (slow) solar wind, (2) clear signature of eruptions for activities even down to GOES B-level, (3) detailed structure and evolution of flaring loops, (4) formation of large-scale hot loops around active regions, and so on. Dynamic phenomena in and around active regions observed with Hinode XRT will be presented and their possible implications to the Sun-Earth connection investigation will be discussed.

  10. EVIDENCE OF IMPULSIVE HEATING IN ACTIVE REGION CORE LOOPS

    SciTech Connect

    Tripathi, Durgesh; Mason, Helen E.; Klimchuk, James A.

    2010-11-01

    Using a full spectral scan of an active region from the Extreme-Ultraviolet Imaging Spectrometer (EIS) we have obtained emission measure EM(T) distributions in two different moss regions within the same active region. We have compared these with theoretical transition region EMs derived for three limiting cases, namely, static equilibrium, strong condensation, and strong evaporation from Klimchuk et al. The EM distributions in both the moss regions are strikingly similar and show a monotonically increasing trend from log T[K] = 5.15-6.3. Using photospheric abundances, we obtain a consistent EM distribution for all ions. Comparing the observed and theoretical EM distributions, we find that the observed EM distribution is best explained by the strong condensation case (EM{sub con}), suggesting that a downward enthalpy flux plays an important and possibly dominant role in powering the transition region moss emission. The downflows could be due to unresolved coronal plasma that is cooling and draining after having been impulsively heated. This supports the idea that the hot loops (with temperatures of 3-5 MK) seen in the core of active regions are heated by nanoflares.

  11. Technical note: use of internal transcribed spacer for ruminal yeast identification in dairy cows.

    PubMed

    Vargas-Bello-Pérez, E; Cancino-Padilla, N; Romero, J

    2016-12-01

    Molecular techniques are important tools for microbiological studies in different habitats, and the internal transcribed spacer (ITS) has been proved to be useful for analyzing fungal diversity. The aim of this study was to use the ITS region to generate ruminal yeast profile and to identify ruminal yeast. DNA from ruminal digesta was extracted to amplify the ribosomal ITS region. The profile from the PCR products was visualized and the excised bands from the profile were identified as the genera Millerozyma, Pichia, Rhizomucor and Hyphopichia. Overall, the ITS resulted to be a simple, fast and sensitive approach that allowed profiling and identification of ruminal yeast that have not been previously described (Millerozyma and Hyphopichia) in the rumen microbial community.

  12. Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

    SciTech Connect

    Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; Hechmer, Aaron; Simirenko, Lisa; Stapleton, Mark; Luengo Hendriks, Cris L.; Chu, Hou Cheng; Ogawa, Nobuo; Inwood, William; Sementchenko, Victor; Beaton, Amy; Weiszmann, Richard; Celniker, Susan E.; Knowles, David W.; Gingeras, Tom; Speed, Terence P.; Eisen, Michael B.; Biggin, Mark D.

    2008-01-10

    Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early

  13. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

    PubMed Central

    Arner, Erik; Daub, Carsten O.; Vitting-Seerup, Kristoffer; Andersson, Robin; Lilje, Berit; Drabløs, Finn; Lennartsson, Andreas; Rönnerblad, Michelle; Hrydziuszko, Olga; Vitezic, Morana; Freeman, Tom C.; Alhendi, Ahmad M. N.; Arner, Peter; Axton, Richard; Baillie, J. Kenneth; Beckhouse, Anthony; Bodega, Beatrice; Briggs, James; Brombacher, Frank; Davis, Margaret; Detmar, Michael; Ehrlund, Anna; Endoh, Mitsuhiro; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Faulkner, Geoffrey J.; Ferrai, Carmelo; Fisher, Malcolm E.; Forrester, Lesley; Goldowitz, Daniel; Guler, Reto; Ha, Thomas; Hara, Mitsuko; Herlyn, Meenhard; Ikawa, Tomokatsu; Kai, Chieko; Kawamoto, Hiroshi; Khachigian, Levon M.; Klinken, S. Peter; Kojima, Soichi; Koseki, Haruhiko; Klein, Sarah; Mejhert, Niklas; Miyaguchi, Ken; Mizuno, Yosuke; Morimoto, Mitsuru; Morris, Kelly J.; Mummery, Christine; Nakachi, Yutaka; Ogishima, Soichi; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Qin, Xian-Yang; Roy, Sugata; Sato, Hiroki; Savvi, Suzana; Saxena, Alka; Schwegmann, Anita; Sugiyama, Daisuke; Swoboda, Rolf; Tanaka, Hiroshi; Tomoiu, Andru; Winteringham, Louise N.; Wolvetang, Ernst; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Zabierowski, Susan; Zhang, Peter; Abugessaisa, Imad; Bertin, Nicolas; Diehl, Alexander D.; Fukuda, Shiro; Furuno, Masaaki; Harshbarger, Jayson; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Ishizu, Yuri; Itoh, Masayoshi; Kawashima, Tsugumi; Kojima, Miki; Kondo, Naoto; Lizio, Marina; Meehan, Terrence F.; Mungall, Christopher J.; Murata, Mitsuyoshi; Nishiyori-Sueki, Hiromi; Sahin, Serkan; Nagao-Sato, Sayaka; Severin, Jessica; de Hoon, Michiel J. L.; Kawai, Jun; Kasukawa, Takeya; Lassmann, Timo; Suzuki, Harukazu; Kawaji, Hideya; Summers, Kim M.; Wells, Christine; Hume, David A.; Forrest, Alistair R. R.; Sandelin, Albin; Carninci, Piero; Hayashizaki, Yoshihide

    2015-01-01

    Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation. PMID:25678556

  14. Eruptions that Drive Coronal Jets in a Solar Active Region

    NASA Technical Reports Server (NTRS)

    Sterling, Alphonse C.; Moore, Ronald L.; Falconer, David A.; Panesar, Navdeep K.; Akiyama, Sachiko; Yashiro, Seiji; Gopalswamy, Nat

    2016-01-01

    Solar coronal jets are common in both coronal holes and in active regions (e.g., Shibata et al. 1992, Shimojo et al. 1996, Cirtain et al. 2007. Savcheva et al. 2007). Recently, Sterling et al. (2015), using data from Hinode/XRT and SDO/AIA, found that coronal jets originating in polar coronal holes result from the eruption of small-scale filaments (minifilaments). The jet bright point (JBP) seen in X-rays and hotter EUV channels off to one side of the base of the jet's spire develops at the location where the minifilament erupts, consistent with the JBPs being miniature versions of typical solar flares that occur in the wake of large-scale filament eruptions. Here we consider whether active region coronal jets also result from the same minifilament-eruption mechanism, or whether they instead result from a different mechanism (e.g. Yokoyama & Shibata 1995). We present observations of an on-disk active region (NOAA AR 11513) that produced numerous jets on 2012 June 30, using data from SDO/AIA and HMI, and from GOES/SXI. We find that several of these active region jets also originate with eruptions of miniature filaments (size scale 20'') emanating from small-scale magnetic neutral lines of the region. This demonstrates that active region coronal jets are indeed frequently driven by minifilament eruptions. Other jets from the active region were also consistent with their drivers being minifilament eruptions, but we could not confirm this because the onsets of those jets were hidden from our view. This work was supported by funding from NASA/LWS, NASA/HGI, and Hinode. A full report of this study appears in Sterling et al. (2016).

  15. Interplanetary planar magnetic structures associated with expanding active regions

    NASA Technical Reports Server (NTRS)

    Nakagawa, Tomoko; Uchida, Yutaka

    1995-01-01

    Planar magnetic structures are interplanetary objects whose magnetic field cannot be explained by Parker's solar wind model. They are characterized by two-dimensional structure of magnetic field that are highly variable and parallel to a plane which is inclined to the ecliptic plane. They appeared independently of interplanetary compression, solar flares, active prominences nor filament disappearances, but the sources often coincided with active regions. On the other hand, it has been discovered by the Yohkoh Soft X-ray telescope that active-region corona expand outwards at speeds of a few to a few tens of km/s near the Sun. The expansions occurred repeatedly, almost continually, even in the absence of any sizable flares. In the Yohkoh Soft X-ray images, the active-region corona seems to expand out into interplanetary space. Solar sources of interplanetary planar magnetic structures observed by Sakigake were examined by Yohkoh soft X-ray telescope. During a quiet period of the Sun from January 6 to November 11, 1993, there found 5 planar magnetic structures according to the criteria (absolute value of Bn)/(absolute value of B) less than 0.1 for planarity and (dB)/(absolute value of B) greater than 0.7 for variability of magnetic field, where Bn, dB, and the absolute value of B are field component normal to a plane, standard deviation, and average of the magnitude of the magnetic field, respectively. Sources of 4 events were on low-latitude (less than 5 degrees) active regions from which loop-like structures were expanding. The coincidence, 80%, is extremely high with respect to accidental coincidence, 7%, of Sakigake windows of solar wind observation with active regions. The last source was on loop-like features which seemed to be related with a mid-latitude (20 degrees) active region.

  16. Bimanual passive movement: functional activation and inter-regional coupling.

    PubMed

    Macaluso, Emiliano; Cherubini, Andrea; Sabatini, Umberto

    2007-01-01

    The aim of this study was to investigate intra-regional activation and inter-regional connectivity during passive movement. During fMRI, a mechanic device was used to move the subject's index and middle fingers. We assessed four movement conditions (unimanual left/right, bimanual symmetric/asymmetric), plus Rest. A conventional intra-regional analysis identified the passive stimulation network, including motor cortex, primary and secondary somatosensory cortex, plus the cerebellum. The posterior (sensory) part of the sensory-motor activation around the central sulcus showed a significant modulation according to the symmetry of the bimanual movement, with greater activation for asymmetric compared to symmetric movements. A second set of fMRI analyses assessed condition-dependent changes of coupling between sensory-motor regions around the superior central sulcus and the rest of the brain. These analyses showed a high inter-regional covariation within the entire network activated by passive movement. However, the specific experimental conditions modulated these patterns of connectivity. Highest coupling was observed during the Rest condition, and the coupling between homologous sensory-motor regions around the left and right central sulcus was higher in bimanual than unimanual conditions. These findings demonstrate that passive movement can affect the connectivity within the sensory-motor network. We conclude that implicit detection of asymmetry during bimanual movement relies on associative somatosensory region in post-central areas, and that passive stimulation reduces the functional connectivity within the passive movement network. Our findings open the possibility to combine passive movement and inter-regional connectivity as a tool to investigate the functionality of the sensory-motor system in patients with very poor mobility.

  17. TARPs: Tracked Active Region Patches from SoHO/MDI

    NASA Astrophysics Data System (ADS)

    Turmon, M.; Hoeksema, J. T.; Bobra, M.

    2013-12-01

    We describe progress toward creating a retrospective MDI data product consisting of tracked magnetic features on the scale of solar active regions, abbreviated TARPs (Tracked Active Region Patches). The TARPs are being developed as a backward-looking extension (covering approximately 3500 regions spanning 1996-2010) to the HARP (HMI Active Region Patch) data product that has already been released for HMI (2010-present). Like the HARPs, the MDI TARP data set is designed to be a catalog of active regions (ARs), indexed by a region ID number, analogous to a NOAA AR number, and time. TARPs from MDI are computed based on the 96-minute synoptic magnetograms and pseudo-continuum intensitygrams. As with the related HARP data product, the approximate threshold for significance is 100G. Use of both image types together allows faculae and sunspots to be separated out as sub-classes of activity, in addition to identifying the overall active region that the faculae/sunspots are part of. After being identified in single images, the magnetically-active patches are grouped and tracked from image to image. Merges among growing active regions, as well as faint active regions hovering at the threshold of detection, are handled automatically. Regions are tracked from their inception until they decay within view, or transit off the visible disk. The final data product is indexed by a nominal AR number and time. For each active region and for each time, a bitmap image is stored containing the precise outline of the active region. Additionaly, metadata such as areas and integrated fluxes are stored for each AR and for each time. Because there is a calibration between the HMI and MDI magnetograms (Liu, Hoeksema et al. 2012), it is straightforward to use the same classification and tracking rules for the HARPs (from HMI) and the MDI TARPs. We anticipate that this will allow a consistent catalog spanning both instruments. We envision several uses for the TARP data product, which will be

  18. Active Region Moss: Doppler Shifts from Hinode/EIS Observations

    NASA Technical Reports Server (NTRS)

    Tripathi, Durgesh; Mason, Helen E.; Klimchuk, James A.

    2012-01-01

    Studying the Doppler shifts and the temperature dependence of Doppler shifts in moss regions can help us understand the heating processes in the core of the active regions. In this paper we have used an active region observation recorded by the Extreme-ultraviolet Imaging Spectrometer (EIS) onboard Hinode on 12-Dec- 2007 to measure the Doppler shifts in the moss regions. We have distinguished the moss regions from the rest of the active region by defining a low density cut-off as derived by Tripathi et al. (2010). We have carried out a very careful analysis of the EIS wavelength calibration based on the method described in Young, O Dwyer and Mason (2012). For spectral lines having maximum sensitivity between log T = 5.85 and log T = 6.25 K, we find that the velocity distribution peaks at around 0 km/s with an estimated error of 4 km/s. The width of the distribution decreases with temperature. The mean of the distribution shows a blue shift which increases with increasing temperature and the distribution also shows asymmetries towards blue-shift. Comparing these results with observables predicted from different coronal heating models, we find that these results are consistent with both steady and impulsive heating scenarios. Further observational constraints are needed to distinguish between these two heating scenarios.

  19. Active region moss. Basic physical parameters and their temporal variation

    NASA Astrophysics Data System (ADS)

    Tripathi, D.; Mason, H. E.; Del Zanna, G.; Young, P. R.

    2010-07-01

    Context. Active region moss are transition region phenomena, first noted in the images recorded by the Transition Region and Coronal Explorer (TRACE) in λ171. Moss regions are thought to be the footpoints of hot loops (3-5 MK) seen in the core of active regions. These hot loops appear “fuzzy” (unresolved). Therefore, it is difficult to study the physical plasma parameters in individual hot core loops and hence their heating mechanisms. Moss regions provide an excellent opportunity to study the physics of hot loops. In addition, they allow us to study the transition region dynamics in the footpoint regions. Aims: To derive the physical plasma parameters such as temperature, electron density, and filling factors in moss regions and to study their variation over a short (an hour) and a long time period (5 consecutive days). Methods: Primarily, we have analyzed spectroscopic observations recorded by the Extreme-ultraviolet Imaging Spectrometer (EIS) aboard Hinode. In addition we have used supplementary observations taken from TRACE and the X-Ray Telescope (XRT) aboard Hinode. Results: The moss emission is strongest in the Fe XII and Fe XIII lines. Based on analyses using line ratios and emission measure we found that moss regions have a characteristic temperature of log T[K] = 6.2. The temperature structure in moss region remains almost identical from one region to another and it does not change with time. The electron densities measured at different locations in the moss regions using Fe XII ratios are about 1-3 × 1010 cm-3 and about 2-4 × 109 cm-3 using Fe XIII and Fe XIV. The densities in the moss regions are similar in different places and show very little variation over short and long time scales. The derived electron density substantially increased (by a factor of about 3-4 or even more in some cases) when a background subtraction was performed. The filling factor of the moss plasma can vary between 0.1-1 and the path length along which the emission

  20. On the Active Region Bright Grains Observed in the Transition Region Imaging Channels of IRIS

    NASA Astrophysics Data System (ADS)

    Skogsrud, H.; Rouppe van der Voort, L.; De Pontieu, B.

    2016-02-01

    The Interface Region Imaging Spectrograph (IRIS) provides spectroscopy and narrow band slit-jaw (SJI) imaging of the solar chromosphere and transition region at unprecedented spatial and temporal resolutions. Combined with high-resolution context spectral imaging of the photosphere and chromosphere as provided by the Swedish 1 m Solar Telescope (SST), we can now effectively trace dynamic phenomena through large parts of the solar atmosphere in both space and time. IRIS SJI 1400 images from active regions, which primarily sample the transition region with the Si iv 1394 and 1403 Å lines, reveal ubiquitous bright “grains” which are short-lived (two to five minute) bright roundish small patches of sizes 0.″5-1.″7 that generally move limbward with velocities up to about 30 km s-1. In this paper, we show that many bright grains are the result of chromospheric shocks impacting the transition region. These shocks are associated with dynamic fibrils (DFs), most commonly observed in Hα. We find that the grains show the strongest emission in the ascending phase of the DF, that the emission is strongest toward the top of the DF, and that the grains correspond to a blueshift and broadening of the Si iv lines. We note that the SJI 1400 grains can also be observed in the SJI 1330 channel which is dominated by C ii lines. Our observations show that a significant part of the active region transition region dynamics is driven from the chromosphere below rather than from coronal activity above. We conclude that the shocks that drive DFs also play an important role in the heating of the upper chromosphere and lower transition region.

  1. ON THE ACTIVE REGION BRIGHT GRAINS OBSERVED IN THE TRANSITION REGION IMAGING CHANNELS OF IRIS

    SciTech Connect

    Skogsrud, H.; Voort, L. Rouppe van der; Pontieu, B. De

    2016-02-01

    The Interface Region Imaging Spectrograph (IRIS) provides spectroscopy and narrow band slit-jaw (SJI) imaging of the solar chromosphere and transition region at unprecedented spatial and temporal resolutions. Combined with high-resolution context spectral imaging of the photosphere and chromosphere as provided by the Swedish 1 m Solar Telescope (SST), we can now effectively trace dynamic phenomena through large parts of the solar atmosphere in both space and time. IRIS SJI 1400 images from active regions, which primarily sample the transition region with the Si iv 1394 and 1403 Å lines, reveal ubiquitous bright “grains” which are short-lived (two to five minute) bright roundish small patches of sizes 0.″5–1.″7 that generally move limbward with velocities up to about 30 km s{sup −1}. In this paper, we show that many bright grains are the result of chromospheric shocks impacting the transition region. These shocks are associated with dynamic fibrils (DFs), most commonly observed in Hα. We find that the grains show the strongest emission in the ascending phase of the DF, that the emission is strongest toward the top of the DF, and that the grains correspond to a blueshift and broadening of the Si iv lines. We note that the SJI 1400 grains can also be observed in the SJI 1330 channel which is dominated by C ii lines. Our observations show that a significant part of the active region transition region dynamics is driven from the chromosphere below rather than from coronal activity above. We conclude that the shocks that drive DFs also play an important role in the heating of the upper chromosphere and lower transition region.

  2. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.

    PubMed

    Conti, Anastasia; Carnevali, Davide; Bollati, Valentina; Fustinoni, Silvia; Pellegrini, Matteo; Dieci, Giorgio

    2015-01-01

    Of the ∼ 1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼ 1300 Alu loci corresponding to detectable transcripts, with ∼ 120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.

  3. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data

    PubMed Central

    Conti, Anastasia; Carnevali, Davide; Bollati, Valentina; Fustinoni, Silvia; Pellegrini, Matteo; Dieci, Giorgio

    2015-01-01

    Of the ∼1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼1300 Alu loci corresponding to detectable transcripts, with ∼120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5′-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions. PMID:25550429

  4. Socioeconomic and regional differences in active transportation in Brazil

    PubMed Central

    de Sá, Thiago Hérick; Pereira, Rafael Henrique Moraes; Duran, Ana Clara; Monteiro, Carlos Augusto

    2016-01-01

    ABSTRACT OBJECTIVE To present national estimates regarding walking or cycling for commuting in Brazil and in 10 metropolitan regions. METHODS By using data from the Health section of 2008’s Pesquisa Nacional por Amostra de Domicílio (Brazil’s National Household Sample Survey), we estimated how often employed people walk or cycle to work, disaggregating our results by sex, age range, education level, household monthly income per capita, urban or rural address, metropolitan regions, and macro-regions in Brazil. Furthermore, we estimated the distribution of this same frequency according to quintiles of household monthly income per capita in each metropolitan region of the country. RESULTS A third of the employed men and women walk or cycle from home to work in Brazil. For both sexes, this share decreases as income and education levels rise, and it is higher among younger individuals, especially among those living in rural areas and in the Northeast region of the country. Depending on the metropolitan region, the practice of active transportation is two to five times more frequent among low-income individuals than among high-income individuals. CONCLUSIONS Walking or cycling to work in Brazil is most frequent among low-income individuals and the ones living in less economically developed areas. Active transportation evaluation in Brazil provides important information for public health and urban mobility policy-making PMID:27355465

  5. Urban, Rural, and Regional Variations in Physical Activity

    ERIC Educational Resources Information Center

    Martin, Sarah Levin; Kirkner, Gregory J.; Mayo, Kelly; Matthews, Charles E.; Durstine, Larry; Hebert, James R.

    2005-01-01

    Purpose: There is some speculation about geographic differences in physical activity (PA) levels. We examined the prevalence of physical inactivity (PIA) and whether US citizens met the recommended levels of PA across the United States. In addition, the association between PIA/PA and degree of urbanization in the 4 main US regions (Northeast,…

  6. Inferred flows of electric currents in solar active regions

    NASA Technical Reports Server (NTRS)

    Ding, Y. J.; Hong, Q. F.; Hagyard, M. J.; Deloach, A. C.

    1985-01-01

    Techniques to identify sources of major current systems in active regions and their channels of flow are explored. Measured photospheric vector magnetic fields together with high resolution white light and H-alpha photographs provide the data base to derive the current systems in the photosphere and chromosphere of a solar active region. Simple mathematical constructions of active region fields and currents are used to interpret these data under the assumptions that the fields in the lower atmosphere (below 200 km) may not be force free but those in the chromosphere and higher are. The results obtained for the complex active region AR 2372 are: (1) Spots exhibiting significant spiral structure in the penumbral filaments were the source of vertical currents at the photospheric surface; (2) Magnetic neutral lines where the transverse magnetic field was strongly sheared were channels along which a strong current system flowed; (3) The inferred current systems produced a neutral sheet and oppositely-flowing currents in the area of the magnetic delta configuration that was the site of flaring.

  7. IFLA General Conference, 1987. Division of Regional Activities. Papers.

    ERIC Educational Resources Information Center

    International Federation of Library Associations, The Hague (Netherlands).

    Six of the seven papers in this collection focus on regional library activities in Africa, Asia and Oceania, and Latin America and the Caribbean: (1) "Libraries and Information Services in a Changing World: The Challenges African Information Services Face at the End of the 1980s" (Dejen Abate, Ethiopia); (2) "The Computer and…

  8. Early life stress affects limited regional brain activity in depression.

    PubMed

    Du, Lian; Wang, Jingjie; Meng, Ben; Yong, Na; Yang, Xiangying; Huang, Qingling; Zhang, Yan; Yang, Lingling; Qu, Yuan; Chen, Zhu; Li, Yongmei; Lv, Fajin; Hu, Hua

    2016-05-03

    Early life stress (ELS) can alter brain function and increases the risk of major depressive disorder (MDD) in later life. This study investigated whether ELS contributes to differences in regional brain activity between MDD patients and healthy controls (HC), as measured by amplitude of low-frequency fluctuation (ALFF)/fractional (f)ALFF. Eighteen first-episode, treatment-naïve MDD patients and HC were assessed with the Childhood Trauma Questionnaire and resting-state functional magnetic resonance imaging. We compared ALFF/fALFF between MDD patients and HC, with or without controlling for ELS, and determined whether ELS level was correlated with regional brain activity in each group. After regressing out ELS, we found that ALFF increased in bilateral amygdala and left orbital/cerebellum, while fALFF decreased in left inferior temporal and right middle frontal gyri in MDD patients relative to controls. ELS positively correlated with regional activity in the left cerebellum in MDD and in the right post-central/inferior temporal/superior frontal cingulate, inferior frontal gyrus and bilateral cerebellum in HC. Our findings indicate that there is only very limited region showing correlation between ELS and brain activity in MDD, while diverse areas in HC, suggesting ELS has few impacts on MDD patients.

  9. A solar cycle timing predictor - The latitude of active regions

    NASA Technical Reports Server (NTRS)

    Schatten, Kenneth H.

    1990-01-01

    A 'Spoerer butterfly' method is used to examine solar cycle 22. It is shown from the latitude of active regions that the cycle can now be expected to peak near November 1989 + or - 8 months, basically near the latter half of 1989.

  10. Unwinding motion of a twisted active region filament

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Kong, D. F.; Liu, J. H.; Xu, C. L.

    2014-12-10

    To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament, we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.

  11. Early life stress affects limited regional brain activity in depression

    PubMed Central

    Du, Lian; Wang, Jingjie; Meng, Ben; Yong, Na; Yang, Xiangying; Huang, Qingling; Zhang, Yan; Yang, Lingling; Qu, Yuan; Chen, Zhu; Li, Yongmei; Lv, Fajin; Hu, Hua

    2016-01-01

    Early life stress (ELS) can alter brain function and increases the risk of major depressive disorder (MDD) in later life. This study investigated whether ELS contributes to differences in regional brain activity between MDD patients and healthy controls (HC), as measured by amplitude of low-frequency fluctuation (ALFF)/fractional (f)ALFF. Eighteen first-episode, treatment-naïve MDD patients and HC were assessed with the Childhood Trauma Questionnaire and resting-state functional magnetic resonance imaging. We compared ALFF/fALFF between MDD patients and HC, with or without controlling for ELS, and determined whether ELS level was correlated with regional brain activity in each group. After regressing out ELS, we found that ALFF increased in bilateral amygdala and left orbital/cerebellum, while fALFF decreased in left inferior temporal and right middle frontal gyri in MDD patients relative to controls. ELS positively correlated with regional activity in the left cerebellum in MDD and in the right post-central/inferior temporal/superior frontal cingulate, inferior frontal gyrus and bilateral cerebellum in HC. Our findings indicate that there is only very limited region showing correlation between ELS and brain activity in MDD, while diverse areas in HC, suggesting ELS has few impacts on MDD patients. PMID:27138376

  12. Doppler Shifts in Active Region Moss Using SOHO/SUMER

    NASA Astrophysics Data System (ADS)

    Winebarger, Amy; Tripathi, Durgesh; Mason, Helen E.; Del Zanna, Giulio

    2013-04-01

    The velocity of the plasma at the footpoint of hot loops in active region cores can be used to discriminate between different heating frequencies. Velocities on the order of a few kilometers per second would indicate low-frequency heating on sub-resolution strands, while velocities close to zero would indicate high-frequency (steady) heating. To discriminate between these two values requires accurate velocity measurements; previous velocity measurements suffer from large uncertainties, mainly due to the lack of an absolute wavelength reference scale. In this paper, we determine the velocity in the loop footpoints using observations from Solar Ultraviolet Measurements of Emitted Radiation (SUMER) on Solar and Heliospheric Observatory. We use neutral spectral lines to determine the wavelength scale of the observations with an uncertainty in the absolute velocity of <3.5 km s-1 and co-aligned Transition Region and Coronal Explorer (TRACE) images to identify footpoint regions. We studied three different active regions and found average redshifts in the Ne VIII 770 Å emission line (formed at 6 × 105 K) of 5.17 ± 5.37 km s-1 and average redshifts in the C IV 1548 and 1550 Å emission lines (formed at 1 × 105 K) of 13.94 ± 4.93 km s-1 and 14.91 ± 6.09 km s-1, respectively. We find no correlation between the brightness in the spectral line and the measured velocity, nor do we find correlation between the Ne VIII and C IV velocities measured co-spatially and co-temporally. SUMER scanned two of the active regions twice; in those active regions we find positive correlation between the co-spatial velocities measured during the first and second scans. These results provide definitive and quantitative measurements for comparisons with simulations of different coronal heating mechanisms.

  13. RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae.

    PubMed

    Volokhov, Dmitriy V; Simonyan, Vahan; Davidson, Maureen K; Chizhikov, Vladimir E

    2012-01-01

    Conventional classification of the species in the family Mycoplasmataceae is mainly based on phenotypic criteria, which are complicated, can be difficult to measure, and have the potential to be hampered by phenotypic deviations among the isolates. The number of biochemical reactions suitable for phenotypic characterization of the Mycoplasmataceae is also very limited and therefore the strategy for the final identification of the Mycoplasmataceae species is based on comparative serological results. However, serological testing of the Mycoplasmataceae species requires a performance panel of hyperimmune sera which contains anti-serum to each known species of the family, a high level of technical expertise, and can only be properly performed by mycoplasma-reference laboratories. In addition, the existence of uncultivated and fastidious Mycoplasmataceae species/isolates in clinical materials significantly complicates, or even makes impossible, the application of conventional bacteriological tests. The analysis of available genetic markers is an additional approach for the primary identification and phylogenetic classification of cultivable species and uncultivable or fastidious organisms in standard microbiological laboratories. The partial nucleotide sequences of the RNA polymerase β-subunit gene (rpoB) and the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known type strains and the available non-type strains of the Mycoplasmataceae species. In addition to the available 16S rRNA gene data, the ITS and rpoB sequences were used to infer phylogenetic relationships among these species and to enable identification of the Mycoplasmataceae isolates to the species level. The comparison of the ITS and rpoB phylogenetic trees with the 16S rRNA reference phylogenetic tree revealed a similar clustering patterns for the Mycoplasmataceae species, with minor discrepancies for a few species that demonstrated higher divergence of their ITS and rpoB in

  14. Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA.

    PubMed

    Varela, Eduardo S; Lima, João P M S; Galdino, Alexsandro S; Pinto, Luciano da S; Bezerra, Walderly M; Nunes, Edson P; Alves, Maria A O; Grangeiro, Thalles B

    2004-01-01

    The complete sequences of nuclear ribosomal DNA (nrDNA) internal transcribed spacer regions (ITS/5.8S) were determined for species belonging to six genera from the subtribe Diocleinae as well as for the anomalous genera Calopogonium and Pachyrhizus. Phylogenetic trees constructed by distance matrix, maximum parsimony and maximum likelihood methods showed that Calopogonium and Pachyrhizus were outside the clade Diocleinae (Canavalia, Camptosema, Cratylia, Dioclea, Cymbosema, and Galactia). This finding supports previous morphological, phytochemical, and molecular evidence that Calopogonium and Pachyrhizus do not belong to the subtribe Diocleinae. Within the true Diocleinae clade, the clustering of genera and species were congruent with morphology-based classifications, suggesting that ITS/5.8S sequences can provide enough informative sites to allow resolution below the genus level. This is the first evidence of the phylogeny of subtribe Diocleinae based on nuclear DNA sequences.

  15. Regional differences in rat conjunctival ion transport activities.

    PubMed

    Yu, Dongfang; Thelin, William R; Rogers, Troy D; Stutts, M Jackson; Randell, Scott H; Grubb, Barbara R; Boucher, Richard C

    2012-10-01

    Active ion transport and coupled osmotic water flow are essential to maintain ocular surface health. We investigated regional differences in the ion transport activities of the rat conjunctivas and compared these activities with those of cornea and lacrimal gland. The epithelial sodium channel (ENaC), sodium/glucose cotransporter 1 (Slc5a1), transmembrane protein 16 (Tmem16a, b, f, and g), cystic fibrosis transmembrane conductance regulator (Cftr), and mucin (Muc4, 5ac, and 5b) mRNA expression was characterized by RT-PCR. ENaC proteins were measured by Western blot. Prespecified regions (palpebral, fornical, and bulbar) of freshly isolated conjunctival tissues and cell cultures were studied electrophysiologically with Ussing chambers. The transepithelial electrical potential difference (PD) of the ocular surface was also measured in vivo. The effect of amiloride and UTP on the tear volume was evaluated in lacrimal gland excised rats. All selected genes were detected but with different expression patterns. We detected αENaC protein in all tissues, βENaC in palpebral and fornical conjunctiva, and γENaC in all tissues except lacrimal glands. Electrophysiological studies of conjunctival tissues and cell cultures identified functional ENaC, SLC5A1, CFTR, and TMEM16. Fornical conjunctiva exhibited the most active ion transport under basal conditions amongst conjunctival regions. PD measurements confirmed functional ENaC-mediated Na(+) transport on the ocular surface. Amiloride and UTP increased tear volume in lacrimal gland excised rats. This study demonstrated that the different regions of the conjunctiva exhibited a spectrum of ion transport activities. Understanding the specific functions of distinct regions of the conjunctiva may foster a better understanding of the physiology maintaining hydration of the ocular surface.

  16. Regional differences in rat conjunctival ion transport activities

    PubMed Central

    Yu, Dongfang; Thelin, William R.; Rogers, Troy D.; Stutts, M. Jackson; Randell, Scott H.; Grubb, Barbara R.

    2012-01-01

    Active ion transport and coupled osmotic water flow are essential to maintain ocular surface health. We investigated regional differences in the ion transport activities of the rat conjunctivas and compared these activities with those of cornea and lacrimal gland. The epithelial sodium channel (ENaC), sodium/glucose cotransporter 1 (Slc5a1), transmembrane protein 16 (Tmem16a, b, f, and g), cystic fibrosis transmembrane conductance regulator (Cftr), and mucin (Muc4, 5ac, and 5b) mRNA expression was characterized by RT-PCR. ENaC proteins were measured by Western blot. Prespecified regions (palpebral, fornical, and bulbar) of freshly isolated conjunctival tissues and cell cultures were studied electrophysiologically with Ussing chambers. The transepithelial electrical potential difference (PD) of the ocular surface was also measured in vivo. The effect of amiloride and UTP on the tear volume was evaluated in lacrimal gland excised rats. All selected genes were detected but with different expression patterns. We detected αENaC protein in all tissues, βENaC in palpebral and fornical conjunctiva, and γENaC in all tissues except lacrimal glands. Electrophysiological studies of conjunctival tissues and cell cultures identified functional ENaC, SLC5A1, CFTR, and TMEM16. Fornical conjunctiva exhibited the most active ion transport under basal conditions amongst conjunctival regions. PD measurements confirmed functional ENaC-mediated Na+ transport on the ocular surface. Amiloride and UTP increased tear volume in lacrimal gland excised rats. This study demonstrated that the different regions of the conjunctiva exhibited a spectrum of ion transport activities. Understanding the specific functions of distinct regions of the conjunctiva may foster a better understanding of the physiology maintaining hydration of the ocular surface. PMID:22814399

  17. The non-coding B2 RNA binds to the DNA cleft and active site region of RNA polymerase II

    PubMed Central

    Ponicsan, Steven L.; Houel, Stephane; Old, William M.; Ahn, Natalie G.; Goodrich, James A.; Kugel, Jennifer F.

    2013-01-01

    The B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III. The ~180 nt B2 RNA has been shown to potently repress mRNA transcription by binding tightly to RNA polymerase II (Pol II) and assembling with it into complexes on promoter DNA, where it keeps the polymerase from properly engaging the promoter DNA. Mammalian Pol II is a ~500 kD complex that contains 12 different protein subunits, providing many possible surfaces for interaction with B2 RNA. We found that the carboxy-terminal domain of the largest Pol II subunit was not required for B2 RNA to bind Pol II and repress transcription in vitro. To identify the surface on Pol II to which the minimal functional region of B2 RNA binds, we coupled multi-step affinity purification, reversible formaldehyde crosslinking, peptide sequencing by mass spectrometry, and analysis of peptide enrichment. The Pol II peptides most highly recovered after crosslinking to B2 RNA mapped to the DNA binding cleft and active site region of Pol II. These studies determine the location of a defined nucleic acid binding site on a large, native, multi-subunit complex and provide insight into the mechanism of transcriptional repression by B2 RNA. PMID:23416138

  18. Active sonar, beaked whales and European regional policy.

    PubMed

    Dolman, Sarah J; Evans, Peter G H; Notarbartolo-di-Sciara, Giuseppe; Frisch, Heidrun

    2011-01-01

    Various reviews, resolutions and guidance from international and regional fora have been produced in recent years that acknowledge the significance of marine noise and its potential impacts on cetaceans. Within Europe, ACCOBAMS and ASCOBANS have shown increasing attention to the issue. The literature highlights concerns surrounding the negative impacts of active sonar on beaked whales in particular, where concerns primarily relate to the use of mid-frequency active sonar (1-10kHz), as used particularly in military exercises. The authors review the efforts that European regional policies have undertaken to acknowledge and manage possible negative impacts of active sonar and how these might assist the transition from scientific research to policy implementation, including effective management and mitigation measures at a national level.

  19. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

    PubMed

    Harrison, Paul M; Zheng, Deyou; Zhang, Zhaolei; Carriero, Nicholas; Gerstein, Mark

    2005-01-01

    Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete protein-coding sequences. Processed pseudogenes (PPsigs) are made through mRNA retrotransposition. There is overwhelming genomic evidence for thousands of human PPsigs and also dozens of human processed genes that comprise complete retrotransposed copies of other genes. Here, we survey for an intermediate entity, the transcribed processed pseudogene (TPPsig), which is disabled but nonetheless transcribed. TPPsigs may affect expression of paralogous genes, as observed in the case of the mouse makorin1-p1 TPPsig. To elucidate their role, we identified human TPPsigs by mapping expressed sequences onto PPsigs and, reciprocally, extracting TPPsigs from known mRNAs. We consider only those PPsigs that are homologous to either non-mammalian eukaryotic proteins or protein domains of known structure, and require detection of identical coding-sequence disablements in both the expressed and genomic sequences. Oligonucleotide microarray data provide further expression verification. Overall, we find 166-233 TPPsigs ( approximately 4-6% of PPsigs). Proteins/transcripts with the highest numbers of homologous TPPsigs generally have many homologous PPsigs and are abundantly expressed. TPPsigs are significantly over-represented near both the 5' and 3' ends of genes; this suggests that TPPsigs can be formed through gene-promoter co-option, or intrusion into untranslated regions. However, roughly half of the TPPsigs are located away from genes in the intergenic DNA and thus may be co-opting cryptic promoters of undesignated origin. Furthermore, TPPsigs are unlike other PPsigs and processed genes in the following ways: (i) they do not show a significant tendency to either deposit on or originate from the X chromosome; (ii) only 5% of human TPPsigs have potential orthologs in mouse. This

  20. Static and Dynamic Modeling of a Solar Active Region

    NASA Astrophysics Data System (ADS)

    Warren, Harry P.; Winebarger, Amy R.

    2007-09-01

    Recent hydrostatic simulations of solar active regions have shown that it is possible to reproduce both the total intensity and the general morphology of the high-temperature emission observed at soft X-ray wavelengths using static heating models. These static models, however, cannot account for the lower temperature emission. In addition, there is ample observational evidence that the solar corona is highly variable, indicating a significant role for dynamical processes in coronal heating. Because they are computationally demanding, full hydrodynamic simulations of solar active regions have not been considered previously. In this paper we make first application of an impulsive heating model to the simulation of an entire active region, AR 8156 observed on 1998 February 16. We model this region by coupling potential field extrapolations to full solutions of the time-dependent hydrodynamic loop equations. To make the problem more tractable we begin with a static heating model that reproduces the emission observed in four different Yohkoh Soft X-Ray Telescope (SXT) filters and consider impulsive heating scenarios that yield time-averaged SXT intensities that are consistent with the static case. We find that it is possible to reproduce the total observed soft X-ray emission in all of the SXT filters with a dynamical heating model, indicating that nanoflare heating is consistent with the observational properties of the high-temperature solar corona. At EUV wavelengths the simulated emission shows more coronal loops, but the agreement between the simulation and the observation is still not acceptable.

  1. THE EVOLUTION OF DARK CANOPIES AROUND ACTIVE REGIONS

    SciTech Connect

    Wang, Y.-M.; Robbrecht, E.; Muglach, K. E-mail: eva.robbrecht@oma.be

    2011-05-20

    As observed in spectral lines originating from the chromosphere, transition region, and low corona, active regions are surrounded by an extensive 'circumfacular' area which is darker than the quiet Sun. We examine the properties of these dark moat- or canopy-like areas using Fe IX 17.1 nm images and line-of-sight magnetograms from the Solar Dynamics Observatory. The 17.1 nm canopies consist of fibrils (horizontal fields containing extreme-ultraviolet-absorbing chromospheric material) clumped into featherlike structures. The dark fibrils initially form a quasiradial or vortical pattern as the low-lying field lines fanning out from the emerging active region connect to surrounding network and intranetwork elements of opposite polarity. The area occupied by the 17.1 nm fibrils expands as supergranular convection causes the active-region flux to spread into the background medium; the outer boundary of the dark canopy stabilizes where the diffusing flux encounters a unipolar region of opposite sign. The dark fibrils tend to accumulate in regions of weak longitudinal field and to become rooted in mixed-polarity flux. To explain the latter observation, we note that the low-lying fibrils are more likely to interact with small loops associated with weak, opposite-polarity flux elements in close proximity, than with high loops anchored inside strong unipolar network flux. As a result, the 17.1 nm fibrils gradually become concentrated around the large-scale polarity inversion lines (PILs), where most of the mixed-polarity flux is located. Systematic flux cancellation, assisted by rotational shearing, removes the field component transverse to the PIL and causes the fibrils to coalesce into long PIL-aligned filaments.

  2. DIVERGENT HORIZONTAL SUB-SURFACE FLOWS WITHIN ACTIVE REGION 11158

    SciTech Connect

    Jain, Kiran; Tripathy, S. C.; Hill, F. E-mail: stripathy@nso.edu

    2015-07-20

    We measure the horizontal subsurface flow in a fast emerging active region (AR; NOAA 11158) using the ring-diagram technique and the Helioseismic and Magnetic Imager high spatial resolution Dopplergrams. This AR had a complex magnetic structure and displayed significant changes in morphology during its disk passage. Over a period of six days from 2011 February 11 to 16, the temporal variation in the magnitude of the total velocity is found to follow the trend of magnetic field strength. We further analyze regions of individual magnetic polarity within AR 11158 and find that the horizontal velocity components in these sub-regions have significant variation with time and depth. The leading and trailing polarity regions move faster than the mixed-polarity region. Furthermore, both zonal and meridional components have opposite signs for trailing and leading polarity regions at all depths showing divergent flows within the AR. We also find a sharp decrease in the magnitude of total horizontal velocity in deeper layers around major flares. It is suggested that the re-organization of magnetic fields during flares, combined with the sunspot rotation, decreases the magnitude of horizontal flows or that the flow kinetic energy has been converted into the energy released by flares. After the decline in flare activity and sunspot rotation, the flows tend to follow the pattern of magnetic activity. We also observe less variation in the velocity components near the surface but these tend to increase with depth, further demonstrating that the deeper layers are more affected by the topology of ARs.

  3. EUV analysis of an active region. [of solar corona in limb region

    NASA Technical Reports Server (NTRS)

    Raghavan, N.; Withbroe, G. L.

    1975-01-01

    A sequence of extreme-ultraviolet (EUV) spectroheliograms of McMath region No. 10283 were obtained by OSO-6. The lines O VI (1032 A) Mg X (625 A), Si XII (499 A), and Fe XVI (335 A) were used to determine coronal temperatures and densities above the active region. A comparison of theoretical and observed line ratios yielded coronal temperatures of 2.2 to 2.3 million K above the active region and 2.0 to 2.1 million K in the surrounding area. The temperatures derived from ratios involving the O VI intensities are systematically higher than the others. This is attributed to an error in the theoretical O VI intensities. The intensities observed above the limb are compared with intensities predicted by a simple model based on cylindrical geometry. The overall agreement shows that the assumption of an isothermal corona in hydrostatic equilibrium above the active region is a resonable working hypothesis and that the adopted geometrical model for the electron density distribution is adequate.

  4. The evolution and orientation of early cycle 22 active regions

    NASA Technical Reports Server (NTRS)

    Cannon, Anne T.; Marquette, William H.

    1991-01-01

    The evolution of six major active regions which appeared during the first phase of the present solar cycle (cycle 22) has been studied. It was found that the northern hemisphere regions exhibited a broad range of evolutionary behavior in which the commonly accepted 'normal pattern' (whereby the follower flux moves preferentially polewards ahead of the leader flux) is represented at one end of the range. At the other end of the range, the leader flux is displaced polewards of the follower flux. In the latter cases equatorward extensions of the polar coronal hole are noted.

  5. Extreme storm activity in North Atlantic and European region

    NASA Astrophysics Data System (ADS)

    Vyazilova, N.

    2010-09-01

    The extreme storm activity study over North Atlantic and Europe includes the analyses of extreme cyclone (track number, integral cyclonic intensity) and extreme storm (track number) during winter and summer seasons in the regions: 1) 55°N-80N, 50°W-70°E; 2) 30°N-55°N, 50°W-70°E. Extreme cyclones were selected based on cyclone centre pressure (P<=970 mbar). Extreme storms were selected from extreme cyclones based on wind velocity on 925 mbar. The Bofort scala was used for this goal. Integral cyclonic intensity (for region) includes the calculation cyclone centers number and sum of MSLP anomalies in cyclone centers. The analyses based on automated cyclone tracking algorithm, 6-hourly MSLP and wind data (u and v on 925 gPa) from the NCEP/NCAR reanalyses from January 1948 to March 2010. The comparision of mean, calculated for every ten years, had shown, that in polar region extreme cyclone and storm track number, and integral cyclonic intensity gradually increases and have maximum during last years (as for summer, as for winter season). Every ten years means for summer season are more then for winter season, as for polar, as for tropical region. Means (ten years) for tropical region are significance less then for polar region.

  6. PATTERNS OF ACTIVITY IN A GLOBAL MODEL OF A SOLAR ACTIVE REGION

    SciTech Connect

    Bradshaw, S. J.; Viall, N. M. E-mail: Nicholeen.M.Viall@nasa.gov

    2016-04-10

    In this work we investigate the global activity patterns predicted from a model active region heated by distributions of nanoflares that have a range of frequencies. What differs is the average frequency of the distributions. The activity patterns are manifested in time lag maps of narrow-band instrument channel pairs. We combine hydrodynamic and forward modeling codes with a magnetic field extrapolation to create a model active region and apply the time lag method to synthetic observations. Our aim is not to reproduce a particular set of observations in detail, but to recover some typical properties and patterns observed in active regions. Our key findings are the following. (1) Cooling dominates the time lag signature and the time lags between the channel pairs are generally consistent with observed values. (2) Shorter coronal loops in the core cool more quickly than longer loops at the periphery. (3) All channel pairs show zero time lag when the line of sight passes through coronal loop footpoints. (4) There is strong evidence that plasma must be re-energized on a timescale comparable to the cooling timescale to reproduce the observed coronal activity, but it is likely that a relatively broad spectrum of heating frequencies are operating across active regions. (5) Due to their highly dynamic nature, we find nanoflare trains produce zero time lags along entire flux tubes in our model active region that are seen between the same channel pairs in observed active regions.

  7. Armenia as a Regional Centre for Astronomy for Development activities

    NASA Astrophysics Data System (ADS)

    Mickaelian, A.

    2015-03-01

    The Byurakan Astrophysical Observatory (BAO, Armenia, http://www.bao.am) are among the candidate IAU Regional Nodes for Astronomy for Development activities. It is one of the main astronomical centers of the former Soviet Union and the Middle East region. At present there are 48 qualified researchers at BAO, including six Doctors of Science and 30 PhDs. Five important observational instruments are installed at BAO, the larger ones being 2.6m Cassegrain (ZTA-2.6) and 1m Schmidt (the one that provided the famous Markarian survey). BAO is regarded as a national scientific-educational center, where a number of activities are being organized, such as: international conferences (4 IAU symposia and 1 IAU colloquium, JENAM-2007, etc.), small workshops and discussions, international summer schools (1987, 2006, 2008 and 2010), and Olympiads. BAO collaborates with scientists from many countries. The Armenian Astronomical Society (ArAS, http://www.aras.am/) is an NGO founded in 2001; it has 93 members and it is rather active in the organization of educational, amateur, popular, promotional and other matters. The Armenian Virtual Observatory (ArVO, http://www.aras.am/Arvo/arvo.htm) is one of the 17 national VO projects forming the International Virtual Observatories Alliance (IVOA) and is the only VO project in the region serving also for educational purposes. A number of activities are planned, such as management, coordination and evaluation of the IAU programs in the area of development and education, establishment of the new IAU endowed lectureship program and organization of seminars and public lectures, coordination and initiation of fundraising activities for astronomy development, organization of regional scientific symposia, conferences and workshops, support to Galileo Teacher Training Program (GTTP), production/publication of educational and promotional materials, etc.

  8. Active region upflows. I. Multi-instrument observations

    NASA Astrophysics Data System (ADS)

    Vanninathan, K.; Madjarska, M. S.; Galsgaard, K.; Huang, Z.; Doyle, J. G.

    2015-12-01

    Context. We study upflows at the edges of active regions, called AR outflows, using multi-instrument observations. Aims: This study intends to provide the first direct observational evidence of whether chromospheric jets play an important role in furnishing mass that could sustain coronal upflows. The evolution of the photospheric magnetic field, associated with the footpoints of the upflow region and the plasma properties of active region upflows is investigated with the aim of providing information for benchmarking data-driven modelling of this solar feature. Methods: We spatially and temporally combine multi-instrument observations obtained with the Extreme-ultraviolet Imaging Spectrometer on board the Hinode, the Atmospheric Imaging Assembly and the Helioseismic Magnetic Imager instruments on board the Solar Dynamics Observatory and the Interferometric BI-dimensional Spectro-polarimeter installed at the National Solar Observatory, Sac Peak, to study the plasma parameters of the upflows and the impact of the chromosphere on active region upflows. Results: Our analysis shows that the studied active region upflow presents similarly to those studied previously, i.e. it displays blueshifted emission of 5-20 kms-1 in Fe xii and Fe xiii and its average electron density is 1.8 × 109 cm-3 at 1 MK. The time variation of the density is obtained showing no significant change (in a 3σ error). The plasma density along a single loop is calculated revealing a drop of 50% over a distance of ~20 000 km along the loop. We find a second velocity component in the blue wing of the Fe xii and Fe xiii lines at 105 kms-1 reported only once before. For the first time we study the time evolution of this component at high cadence and find that it is persistent during the whole observing period of 3.5 h with variations of only ±15 kms-1. We also, for the first time, study the evolution of the photospheric magnetic field at high cadence and find that magnetic flux diffusion is

  9. Coronal Jets from Minifilament Eruptions in Active Regions

    NASA Technical Reports Server (NTRS)

    Martinez, Francisco; Sterling, Alphonse C.; Falconer, David A.; Moore, Ronald L.

    2016-01-01

    Solar coronal jets are transient (frequently of lifetime approx.10 min) features that shoot out from near the solar surface, become much longer than their width, and occur in all solar regions, including coronal holes, quiet Sun, and active regions (e.g., Shimojo et al. 1996, Cirtain et al. 2007). Sterling et al. (2015) and other studies found that in coronal holes and in quiet Sun the jets result when small-scale filaments, called "minifilaments" erupt onto nearby open or high-reaching field lines. Additional studies found that coronal-jet-onset locations (and hence presumably the minifilament-eruption-onset locations) coincided with locations of magnetic-flux cancelation. For active region (AR) jets however the situation is less clear. Sterling et al. (2016) studied jets in one active region over a 24-hour period; they found that some AR jets indeed resulted from minifilament eruptions, usually originating from locations of episodes of magnetic-flux cancelation. In some cases however they could not determine whether flux was emerging or canceling at the polarity inversion line from which the minifilament erupted, and for other jets of that region minifilaments were not conclusively apparent prior to jet occurrence. Here we further study AR jets, by observing them in a single AR over a one-week period, using X-ray images from Hinode/XRT and EUV/UV images from SDO/AIA, and line-of-sight magnetograms and white-light intensity-grams from SDO/HMI. We initially identified 13 prominent jets in the XRT data, and examined corresponding AIA and HMI data. For at least several of the jets, our findings are consistent with the jets resulting from minifilament eruptions, and originating from sites of magnetic-field cancelation.

  10. Physical Properties of Cooling Plasma in Quiescent Active Region Loops

    NASA Astrophysics Data System (ADS)

    Landi, E.; Miralles, M. P.; Curdt, W.; Hara, H.

    2009-04-01

    In the present work, we use SOHO/SUMER, SOHO/UVCS, SOHO/EIT, SOHO/LASCO, STEREO/EUVI, and Hinode/EIS coordinated observations of an active region (AR 10989) at the west limb taken on 2008 April 8 to study the cooling of coronal loops. The cooling plasma is identified using the intensities of SUMER spectral lines emitted at temperatures in the 4.15 <= log T <= 5.45 range. EIS and SUMER spectral observations are used to measure the physical properties of the loops. We found that before cooling took place these loops were filled with coronal hole-like plasma, with temperatures in the 5.6 <= log T <= 5.9 range. SUMER spectra also allowed us to determine the plasma temperature, density, emission measure, element abundances, and dynamic status during the cooling process. The ability of EUVI to observe the emitting region from a different direction allowed us to measure the volume of the emitting region and estimate its emission measure. Comparison with values measured from line intensities provided us with an estimate of the filling factor. UVCS observations of the coronal emission above the active region showed no streamer structure associated with AR 10989 at position angles between 242°and 253fdg EIT, LASCO, and EUVI-A narrowband images and UVCS spectral observations were used to discriminate between different scenarios and monitor the behavior of the active region in time. The present study provides the first detailed measurements of the physical properties of cooling loops, a very important benchmark for theoretical models of loop cooling and condensation.

  11. Electric currents and coronal heating in NOAA active region 6952

    NASA Technical Reports Server (NTRS)

    Metcalf, T. R.; Canfield, R. C.; Hudson, H. S.; Mickey, D. L.; Wulser, J. -P.; Martens, P. C. H.; Tsuneta, S.

    1994-01-01

    We examine the spatial and temporal relationship between coronal structures observed with the soft X-ray telescope (SXT) on board the Yohkoh spacecraft and the vertical electric current density derived from photospheric vector magnetograms obtained using the Stokes Polarimeter at the Mees Solar Observatory. We focus on a single active region: AR 6952 which we observed on 7 days during 1991 December. For 11 independent maps of the vertical electric current density co-aligned with non-flaring X-ray images, we search for a morphological relationship between sites of high vertical current density in the photosphere and enhanced X-ray emission in the overlying corona. We find no compelling spatial or temporal correlation between the sites of vertical current and the bright X-ray structures in this active region.

  12. Evidence of active region imprints on the solar wind structure

    NASA Technical Reports Server (NTRS)

    Hick, P.; Jackson, B. V.

    1995-01-01

    A common descriptive framework for discussing the solar wind structure in the inner heliosphere uses the global magnetic field as a reference: low density, high velocity solar wind emanates from open magnetic fields, with high density, low speed solar wind flowing outward near the current sheet. In this picture, active regions, underlying closed magnetic field structures in the streamer belt, leave little or no imprint on the solar wind. We present evidence from interplanetary scintillation measurements of the 'disturbance factor' g that active regions play a role in modulating the solar wind and possibly contribute to the solar wind mass output. Hence we find that the traditional view of the solar wind, though useful in understanding many features of solar wind structure, is oversimplified and possibly neglects important aspects of solar wind dynamics

  13. Modeling the Subsurface Evolution of Active-Region Flux Tubes

    NASA Astrophysics Data System (ADS)

    Fan, Y.

    2009-12-01

    I present results from a set of 3-D spherical-shell MHD simulations of the buoyant rise of active region flux tubes in the solar interior that put new constraints on the initial twist of the subsurface tubes in order for them to emerge with tilt angles consistent with the observed Joy's law for the mean tilt of solar active regions. Due to asymmetric stretching of the Ω-shaped tube by the Coriolis force, a field strength asymmetry develops with the leading side having a greater field strength and thus being more cohesive compared to the following side. Furthermore, the magnetic flux in the leading leg shows more coherent values of local twist α ≡ JB / B2, whereas the values in the following leg show large fluctuations and are of mixed signs.

  14. Regional Blood-Brain Barrier Responses to Central Cholinergic Activity

    DTIC Science & Technology

    1989-07-30

    regions were of particular interest because they show the largest decreases in glucose metabolism following limbic seizures ( Ben - Ari et al., 1981). It is...following seizures ( Ben - Ari et. al., 1981). The piriform cortex-amygdala also appears to be a generator of epileptiform activity in a variety of seizure...produced by PTZ. Such studies are ongoing and the results will be given in subsequent reports. 11 REFERENCES Ben - Ari , Y., D. Richie, E. Tremblay and G

  15. Multi-wavelength Observations of Microflares Near an Active Region

    NASA Astrophysics Data System (ADS)

    Bein, B.; Veronig, A.; Rybak, J.; Gömöry, P.; Berkebile-Stoiser, S.; Sütterlin, P.

    We study the multi-wavelength characteristics of a microflaring active region (AR 10898) near disc centre. The analysed data were from the 4^{th} of July 2006, and were recorded by DOT (Hα, Ca II H), RHESSI (X-rays), TRACE (EUV) and SOHO/MDI (magnetograms). The identified microflare events were studied with respect to their magnetic field configuration and their multi-wavelength time evolution.

  16. A Survey of Nanoflare Properties in Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Viall, N. M.; Klimchuk, J. A.

    2013-12-01

    We investigate coronal heating using a systematic technique to analyze the properties of nanoflares in active regions (AR). Our technique computes cooling times, or time-lags, on a pixel-by-pixel basis using data taken with the Atmospheric Imaging Assembly onboard the Solar Dynamics Observatory. Our technique has the advantage that it allows us to analyze all of the coronal AR emission, including the so-called diffuse emission. We recently presented results using this time-lag analysis on NOAA AR 11082 (Viall & Klimchuk 2012) and found that the majority of the pixels contained cooling plasma along their line of sight, consistent with impulsive coronal nanoflare heating. Additionally, our results showed that the nanoflare energy is stronger in the AR core and weaker in the active region periphery. Are these results representative of the nanoflare properties exhibited in the majority of ARs, or is AR 11082 unique? Here we present the time-lag results for a survey of ARs and show that these nanoflare patterns are born out in other active regions, for a range of ages, magnetic complexity, and total unsigned magnetic flux. Other aspects of the nanoflare properties, however, turn out to be dependent on certain AR characteristics.

  17. The Intermediate-line Region in Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Adhikari, T. P.; Różańska, A.; Czerny, B.; Hryniewicz, K.; Ferland, G. J.

    2016-11-01

    We show that the recently observed suppression of the gap between the broad-line region (BLR) and the narrow-line region (NLR) in some active galactic nuclei (AGNs) can be fully explained by an increase of the gas density in the emitting region. Our model predicts the formation of the intermediate-line region (ILR) that is observed in some Seyfert galaxies by the detection of emission lines with intermediate-velocity FWHM ˜ 700-1200 km s-1. These lines are believed to be originating from an ILR located somewhere between the BLR and NLR. As was previously proved, the apparent gap is assumed to be caused by the presence of dust beyond the sublimation radius. Our computations with the use of the cloudy photoionization code show that the differences in the shape of the spectral energy distribution from the central region of AGNs do not diminish the apparent gap in the line emission in those objects. A strong discontinuity in the line emission versus radius exists for all lines at the dust sublimation radius. However, increasing the gas density to ˜{10}11.5 cm-3 at the sublimation radius provides the continuous line emission versus radius and fully explains the recently observed lack of apparent gap in some AGNs. We show that such a high density is consistent with the density of upper layers of an accretion disk atmosphere. Therefore, the upper layers of the disk atmosphere can give rise to the formation of observed emission-line clouds.

  18. Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

    PubMed Central

    Chakraborty, Anirban; Tapryal, Nisha; Venkova, Tatiana; Horikoshi, Nobuo; Pandita, Raj K.; Sarker, Altaf H.; Sarkar, Partha S.; Pandita, Tej K.; Hazra, Tapas K.

    2016-01-01

    DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ-expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome. PMID:27703167

  19. Medical Terminology of the Musculoskeletal System. Medical Records. Instructional Unit for the Medical Transcriber.

    ERIC Educational Resources Information Center

    Gosman, Minna L.

    Following an analysis of the task of transcribing as practiced in a health facility, this study guide was developed to teach the knowledge and skills required of a medical transcriber. The medical record department was identified as a major occupational area, and a task inventory for medical records was developed and used as a basis for a…

  20. Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens.

    PubMed

    Brännström, S; Morrison, D A; Mattsson, J G; Chirico, J

    2008-06-01

    We investigated the presence of the poultry red mite or the chicken mite, Dermanyssus gallinae De Geer, Acari: Dermanyssidae, in wild bird populations in four different geographical regions of Sweden. The mites identified as D. gallinae were compared genetically with D. gallinae from egg-producing poultry farms in the same regions. The small subunit (SSU) gene, the 5.8S ribosomal RNA (rRNA) gene and the two internal transcribed spacers (ITS) of the rRNA genes were used in the genetic analysis. All D. gallinae mites had identical SSU rRNA, 5.8S rRNA and ITS2 sequences independent of their origin. By contrast, we identified significant differences in the ITS1 sequences. Based on the differences in the ITS1 sequences, the mites could be divided into two genotypes, of wild and domesticated origin, with no variation within the groups. These results imply that wild bird populations are of low importance, if any, as natural reservoirs of D. gallinae in these four geographical regions of Sweden.

  1. Holocene fire activity in the Carpathian region: regional climate vs. local controls

    NASA Astrophysics Data System (ADS)

    Florescu, Gabriela; Feurdean, Angelica

    2015-04-01

    Introduction. Fire drives significant changes in ecosystem structure and function, diversity, species evolution, biomass dynamics and atmospheric composition. Palaeodata and model-based studies have pointed towards a strong connection between fire activity, climate, vegetation and people. Nevertheless, the relative importance of these factors appears to be strongly variable and a better understanding of these factors and their interaction needs a thorough investigation over multiple spatial (local to global) and temporal (years to millennia) scales. In this respect, sedimentary charcoal, associated with other proxies of climate, vegetation and human impact, represents a powerful tool of investigating changes in past fire activity, especially in regions with scarce fire dataset such as the CE Europe. Aim. To increase the spatial and temporal coverage of charcoal records and facilitate a more critical examination of the patterns, drivers and consequences of biomass burning over multiple spatial and temporal scales in CE Europe, we have investigated 6 fossil sequences in the Carpathian region (northern Romania). These are located in different geographical settings, in terms of elevation, vegetation composition, topography and land-use. Specific questions are: i) determine trends in timing and magnitude of fire activity, as well as similarities and differences between elevations; ii) disentangle the importance of regional from local controls in fire activity; iii) evaluate ecological consequences of fire on landscape composition, structure and diversity. Methods. We first determine the recent trends in fire activity (the last 150 years) from charcoal data and compare them with instrumental records of temperature, precipitation, site history and topography for a better understanding of the relationship between sedimentary charcoal and historical fire activity. We then statistically quantify centennial to millennial trends in fire activity (frequency, magnitude) based on

  2. Monitoring rice farming activities in the Mekong Delta region

    NASA Astrophysics Data System (ADS)

    Nguyen, S. T.; Chen, C. F.; Chen, C. R.; Chiang, S. H.; Chang, L. Y.; Khin, L. V.

    2015-12-01

    Half of the world's population depends on rice for survival. Rice agriculture thus plays an important role in the developing world's economy. Vietnam is one of the largest rice producers and suppliers on earth and more than 80% of the exported rice was produced from the Mekong Delta region, which is situated in the southwestern Vietnam and encompasses approximately 40,000 km2. Changes in climate conditions could likely trigger the increase of insect populations and rice diseases, causing the potential loss of rice yields. Monitoring rice-farming activities through crop phenology detection can provide policymakers with timely strategies to mitigate possible impacts on the potential yield as well as rice grain exports to ensure food security for the region. The main objective of this study is to develop a logistic-based algorithm to investigate rice sowing and harvesting activities from the multi-temporal Moderate Resolution Imaging Spectroradiometer (MODIS)-Landsat fusion data. We processed the data for two main cropping seasons (i.e., winter-spring and summer-autumn seasons) through a three-step procedure: (1) MODIS-Landsat data fusion, (2) construction of the time-series enhanced vegetation index 2 (EVI2) data, (3) rice crop phenology detection. The EVI2 data derived from the fusion results between MODIS and Landsat data were compared with that of Landsat data indicated close correlation between the two datasets (R2 = 0.93). The time-series EVI2 data were processed using the double logistic method to detect the progress of sowing and harvesting activities in the region. The comparisons between the estimated sowing and harvesting dates and the field survey data revealed the root mean squared error (RMSE) values of 8.4 and 5.5 days for the winter-spring crop and 9.4 and 12.8 days for the summer-autumn crop, respectively. This study demonstrates the effectiveness of the double logistic-based algorithm for rice crop monitoring from temporal MODIS-Landsat fusion data

  3. Density and Temperature Measurements in a Solar Active Region

    NASA Astrophysics Data System (ADS)

    Warren, Harry P.; Winebarger, Amy R.

    2003-10-01

    We present electron density and temperature measurements from an active region observed above the limb with the Solar Ultraviolet Measurements of Emitted Radiation spectrometer on the Solar and Heliospheric Observatory. Density-sensitive line ratios from Si VIII and S X indicate densities greater than 108 cm-3 as high as 200" (or 145 Mm) above the limb. At these heights, static, uniformly heated loop models predict densities close to 107 cm-3. Differential emission measure analysis shows that the observed plasma is nearly isothermal with a mean temperature of about 1.5 MK and a dispersion of about 0.2 MK. Both the differential emission measure and the Si XI/Si VIII line ratios indicate only small variations in the temperature at the heights observed. These measurements confirm recent observations from the Transition Region and Coronal Explorer of ``overdense'' plasma at temperatures near 1 MK in solar active regions. Time-dependent hydrodynamic simulations suggest that impulsive heating models can account for the large densities, but they have a difficult time reproducing the narrow range of observed temperatures. The observations of overdense, nearly isothermal plasma in the solar corona provide a significant challenge to theories of coronal heating.

  4. FORMATION OF CORONAL HOLES ON THE ASHES OF ACTIVE REGIONS

    SciTech Connect

    Karachik, Nina V.; Pevtsov, Alexei A.; Abramenko, Valentyna I. E-mail: apevtsov@nso.ed

    2010-05-10

    We investigate the formation of isolated non-polar coronal holes (CHs) on the remnants of decaying active regions (ARs) at the minimum/early ascending phase of sunspot activity. We follow the evolution of four bipolar ARs and measure several parameters of their magnetic fields including total flux, imbalance, and compactness. As regions decay, their leading and following polarities exhibit different dissipation rates: loose polarity tends to dissipate faster than compact polarity. As a consequence, we see a gradual increase in flux imbalance inside a dissipating bipolar region, and later a formation of a CH in place of more compact magnetic flux. Out of four cases studied in detail, two CHs had formed at the following polarity of the decaying bipolar AR, and two CHs had developed in place of the leading polarity field. All four CHs contain a significant fraction of magnetic field of their corresponding AR. Using potential field extrapolation, we show that the magnetic field lines of these CHs were closed on the polar CH at the North, which at the time of the events was in imbalance with the polar CH at the South. This topology suggests that the observed phenomenon may play an important role in transformation of toroidal magnetic field to poloidal field, which is a key step in transitioning from an old solar cycle to a new one. The timing of this observed transition may indicate the end of solar cycle 23 and the beginning of cycle 24.

  5. Active Region Oscillations: Results from SOHO JOP 097

    NASA Astrophysics Data System (ADS)

    O'Shea, E.; Fleck, B.; Muglach, K.; Sütterlin, P.

    2001-05-01

    We present here an analysis of data obtained in a sunspot region, using the Coronal Diagnostic Spectrometer (CDS) on SOHO. These data were obtained in the context of the Joint Observing Program (JOP) 97 which, together with CDS, included the Michelson Doppler Imaging (MDI) instrument on SOHO, the TRACE satellite and various ground based observatories, e.g. the DOT on La Palma. Using the lines of Fe XVI 335, Mg IX 368, He I 584, O III 599, Mg X 624 and O V 624 of CDS time series data were obtained in the pore and plage regions of sunspots associated with active regions AR 9166, 9166 and 9169 between September 19-29 2000. In addition to the time series datasets we also obtained 240 arcsec x 240 arcsec raster images of the sunspot regions examined. Using different time series analysis techniques we analyse the different periods of oscillation found in time series datasets and present the results here. This research is part of the European Solar Magnetometry Network supported by the EC through the TMR programme.

  6. Helioseismology of pre-emerging active regions. III. Statistical analysis

    SciTech Connect

    Barnes, G.; Leka, K. D.; Braun, D. C.; Birch, A. C.

    2014-05-01

    The subsurface properties of active regions (ARs) prior to their appearance at the solar surface may shed light on the process of AR formation. Helioseismic holography has been applied to samples taken from two populations of regions on the Sun (pre-emergence and without emergence), each sample having over 100 members, that were selected to minimize systematic bias, as described in Paper I. Paper II showed that there are statistically significant signatures in the average helioseismic properties that precede the formation of an AR. This paper describes a more detailed analysis of the samples of pre-emergence regions and regions without emergence based on discriminant analysis. The property that is best able to distinguish the populations is found to be the surface magnetic field, even a day before the emergence time. However, after accounting for the correlations between the surface field and the quantities derived from helioseismology, there is still evidence of a helioseismic precursor to AR emergence that is present for at least a day prior to emergence, although the analysis presented cannot definitively determine the subsurface properties prior to emergence due to the small sample sizes.

  7. Photometric observations of the energetics of small solar active regions

    SciTech Connect

    Lawrence, J.K.; Chapman, G.A. )

    1990-10-01

    The energetics of small solar active regions was investigated using for the analysis the photometric solar images taken from July 29 to September 6, 1984 with the San Fernando Observatory's 28-cm vacuum telescope, vacuum spectroheliograph, and dual 512 element Reticon linear diode arrays. Ten small newly formed regions were observed, whose entire sunspot evolution apparently occurred within the observed disk crossing. Seven of these showed a net energy excess of a few times 10 to the 33th ergs during this time. These results are discussed in connection with the 0.1 percent decline in solar irradiance observed by the SMM/ACRIM and Nimbus 7/ERB radiometers between 1980 and 1986. 35 refs.

  8. Multi-wavelength Observations of Solar Active Region NOAA 7154

    NASA Technical Reports Server (NTRS)

    Bruner, M. E.; Nitta, N. V.; Frank. Z. A.; Dame, L.; Suematsu, Y.

    2000-01-01

    We report on observations of a solar active region in May 1992 by the Solar Plasma Diagnostic Experiment (SPDE) in coordination with the Yohkoh satellite (producing soft X-ray images) and ground-based observatories (producing photospheric magnetograms and various filtergrams including those at the CN 3883 A line). The main focus is a study of the physical conditions of hot (T is approximately greater than 3 MK) coronal loops at their foot-points. The coronal part of the loops is fuzzy but what appear to be their footpoints in the transition region down to the photosphere are compact. Despite the morphological similarities, the footpoint emission at 10(exp 5) K is not quantitatively correlated with that at approximately 300 km above the tau (sub 5000) = 1 level, suggesting that the heat transport and therefore magnetic field topology in the intermediate layer is complicated. High resolution imaging observations with continuous temperature coverage are crucially needed.

  9. Influence of the Cardiac Myosin Hinge Region on Contractile Activity

    NASA Astrophysics Data System (ADS)

    Margossian, Sarkis S.; Krueger, John W.; Sellers, James R.; Cuda, Giovanni; Caulfield, James B.; Norton, Paul; Slayter, Henry S.

    1991-06-01

    The participation of cardiac myosin hinge in contractility was investigated by in vitro motility and ATPase assays and by measurements of sarcomere shortening. The effect on contractile activity was analyzed using an antibody directed against a 20-amino acid peptide within the hinge region of myosin. This antibody bound specifically at the hinge at a distance of 55 nm from the S1/S2 junction, was specific to human, dog, and rat cardiac myosins, did not crossreact with gizzard or skeletal myosin, and had no effect on ATPase activity of purified S1 and myofibrils. However, it completely suppressed the movement of actin filaments in in vitro motility assays and reduced active shortening of sarcomeres of skinned cardiac myocytes by half. Suppression of motion by the antihinge antibody may reflect a mechanical constraint imposed by the antibody upon the mobility of the S2 region of myosin. The results suggest that the steps in the mechanochemical energy transduction can be separately influenced through S2.

  10. High Spatial Resolution Fe XII Observations of Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Testa, Paola; De Pontieu, Bart; Hansteen, Viggo

    2016-08-01

    We use UV spectral observations of active regions with the Interface Region Imaging Spectrograph (IRIS) to investigate the properties of the coronal Fe xii 1349.4 Å emission at unprecedented high spatial resolution (˜0.33″). We find that by using appropriate observational strategies (i.e., long exposures, lossless compression), Fe xii emission can be studied with IRIS at high spatial and spectral resolution, at least for high-density plasma (e.g., post-flare loops and active region moss). We find that upper transition region (TR; moss) Fe xii emission shows very small average Doppler redshifts ({v}{{D}} ˜ 3 km s-1) as well as modest non-thermal velocities (with an average of ˜24 km s-1 and the peak of the distribution at ˜15 km s-1). The observed distribution of Doppler shifts appears to be compatible with advanced three-dimensional radiative MHD simulations in which impulsive heating is concentrated at the TR footpoints of a hot corona. While the non-thermal broadening of Fe xii 1349.4 Å peaks at similar values as lower resolution simultaneous Hinode Extreme Ultraviolet Imaging Spectrometer (EIS) measurements of Fe xii 195 Å, IRIS observations show a previously undetected tail of increased non-thermal broadening that might be suggestive of the presence of subarcsecond heating events. We find that IRIS and EIS non-thermal line broadening measurements are affected by instrumental effects that can only be removed through careful analysis. Our results also reveal an unexplained discrepancy between observed 195.1/1349.4 Å Fe xii intensity ratios and those predicted by the CHIANTI atomic database.

  11. THE EXPANSION OF ACTIVE REGIONS INTO THE EXTENDED SOLAR CORONA

    SciTech Connect

    Morgan, Huw; Jeska, Lauren; Leonard, Drew

    2013-06-01

    Advanced image processing of Large Angle and Spectrometric Coronagraph Experiment (LASCO) C2 observations reveals the expansion of the active region closed field into the extended corona. The nested closed-loop systems are large, with an apparent latitudinal extent of 50 Degree-Sign , and expanding to heights of at least 12 R{sub Sun }. The expansion speeds are {approx}10 km s{sup -1} in the AIA/SDO field of view, below {approx}20 km s{sup -1} at 2.3 R{sub Sun }, and accelerate linearly to {approx}60 km s{sup -1} at 5 R{sub Sun }. They appear with a frequency of one every {approx}3 hr over a time period of around three days. They are not coronal mass ejections (CMEs) since their gradual expansion is continuous and steady. They are also faint, with an upper limit of 3% of the brightness of background streamers. Extreme ultraviolet images reveal continuous birth and expansion of hot, bright loops from a new active region at the base of the system. The LASCO images show that the loops span a radial fan-like system of streamers, suggesting that they are not propagating within the main coronal streamer structure. The expanding loops brighten at low heights a few hours prior to a CME eruption, and the expansion process is temporarily halted as the closed field system is swept away. Closed magnetic structures from some active regions are not isolated from the extended corona and solar wind, but can expand to large heights in the form of quiescent expanding loops.

  12. Implications of Special Regions to Conducting Human Activities on Mars

    NASA Astrophysics Data System (ADS)

    Rummel, J. D.; Barlow, N. G.; Beaty, D. W.; Jones, M. A.; Hipkin, V.

    2014-12-01

    A MEPAG Science Analysis Group (SAG) has undertaken an analysis of Special Regions (SR) on Mars—regions where indigenous martian life could exist or where Earth microbes, if introduced, could survive and reproduce. The SR-SAG has considered the impact of SR on future human activities on the martian surface. Human exploration requires access to in-situ resources, some of which may be found in SR. Water and oxygen for ISRU are found in the atmosphere, surface/near-surface ice, hydrated minerals, and perchlorates. Water ice is most abundant at latitudes poleward of ~60 degrees, but polar darkness, cold temperatures, and CO2 degassing present hazards to human operations in these regions. Accessible water is more limited toward the equator, though temperature and solar energy conditions become more favorable. The possible presence of liquid water in Recurring Slope Lineae and active gullies leads to their treatment as SR. Fuel for surface operations and propellants for crew ascent could be manufactured from the martian atmosphere and surface materials, but dust in the atmosphere may clog ISRU equipment and perchlorate is toxic to humans. Power may be produced from solar or nuclear energy. Reliance on solar energy limits operations to the equatorial zone where easily accessible ice resources are limited. Nuclear power allows surface operations at a range of latitudes, but waste heat could convert some non-SR into SR. Radiation shielding is necessary for long-term human operations on Mars and could be obtained by deposition of regolith or by water storage in tanks or as ice around habitats, or the use of underground habitats. SR-SAG recognizes that it will be impossible for all human-associated processes and operations to be conducted within entirely closed systems. Protocols need to be established so (1) human missions to Mars will not contaminate SR nor be contaminated by materials from them, and (2) human activities on Mars will avoid converting areas into SR.

  13. Temporal evolution of continental lithospheric strength in actively deforming regions

    USGS Publications Warehouse

    Thatcher, W.; Pollitz, F.F.

    2008-01-01

    It has been agreed for nearly a century that a strong, load-bearing outer layer of earth is required to support mountain ranges, transmit stresses to deform active regions and store elastic strain to generate earthquakes. However the dept and extent of this strong layer remain controversial. Here we use a variety of observations to infer the distribution of lithospheric strength in the active western United States from seismic to steady-state time scales. We use evidence from post-seismic transient and earthquake cycle deformation reservoir loading glacio-isostatic adjustment, and lithosphere isostatic adjustment to large surface and subsurface loads. The nearly perfectly elastic behavior of Earth's crust and mantle at the time scale of seismic wave propagation evolves to that of a strong, elastic crust and weak, ductile upper mantle lithosphere at both earthquake cycle (EC, ???10?? to 103 yr) and glacio-isostatic adjustment (GIA, ???103 to 104 yr) time scales. Topography and gravity field correlations indicate that lithosphere isostatic adjustment (LIA) on ???106-107 yr time scales occurs with most lithospheric stress supported by an upper crust overlying a much weaker ductile subtrate. These comparisons suggest that the upper mantle lithosphere is weaker than the crust at all time scales longer than seismic. In contrast, the lower crust has a chameleon-like behavior, strong at EC and GIA time scales and weak for LIA and steady-state deformation processes. The lower crust might even take on a third identity in regions of rapid crustal extension or continental collision, where anomalously high temperatures may lead to large-scale ductile flow in a lower crustal layer that is locally weaker than the upper mantle. Modeling of lithospheric processes in active regions thus cannot use a one-size-fits-all prescription of rheological layering (relation between applied stress and deformation as a function of depth) but must be tailored to the time scale and tectonic

  14. Emission Measure Distribution and Heating of Two Active Region Cores

    NASA Technical Reports Server (NTRS)

    Tripathi, Durgesh; Klimchuk, James A.; Mason, Helen E.

    2011-01-01

    Using data from the Extreme-ultraviolet Imaging Spectrometer aboard Hinode, we have studied the coronal plasma in the core of two active regions. Concentrating on the area between opposite polarity moss, we found emission measure distributions having an approximate power-law form EM/T(exp 2.4) from log T = 5.55 up to a peak at log T = 6.57. The observations are explained extremely well by a simple nanoflare model. However, in the absence of additional constraints, the observations could possibly also be explained by steady heating.

  15. Hinode Observations of an Eruption from a Sigmoidal Active Region

    NASA Astrophysics Data System (ADS)

    Green, L. M.; Wallace, A. J.; Kliem, B.

    2012-08-01

    We analyse the evolution of a bipolar active region which produces an eruption during its decay phase. The soft X-ray arcade develops high shear over a time span of two days and transitions to sigmoidal shortly before the eruption. We propose that the continuous sigmoidal soft X-ray threads indicate that a flux rope has formed which is lying low in the solar atmosphere with a bald patch separatrix surface topology. The formation of the flux rope is driven by the photospheric evolution which is dominated by fragmentation of the main polarities, motion due to supergranular flows and cancellation at the polarity inversion line.

  16. SOI/MDI studies of active region seismology and evolution

    NASA Technical Reports Server (NTRS)

    Tarbell, Ted D.; Title, Alan; Hoeksema, J. Todd; Scherrer, Phil; Zweibel, Ellen

    1995-01-01

    The solar oscillations investigation (SOI) will study solar active regions using both helioseismic and conventional observation techniques. The Michelson Doppler imager (MDI) can perform Doppler continuum and line depth imagery and can produce longitudinal magnetograms, showing either the full disk or a high resolution field of view. A dynamics program of continuous full disk Doppler observations for two months per year, campaign programs of eight hours of continuous observation per day, and a synoptic magnetic program of about 15 full disk magnetograms per day, are planned. The scientific plans, measurements and observation programs, are described.

  17. Substrate-emitting semiconductor laser with a trapezoidal active region

    SciTech Connect

    Dikareva, N V; Nekorkin, S M; Karzanova, M V; Zvonkov, B N; Aleshkin, V Ya; Dubinov, A A; Afonenko, A A

    2014-04-28

    Semiconductor lasers with a narrow (∼2°) directional pattern in the planes both parallel and perpendicular to the p–n junction are fabricated. To achieve a low radiation divergence in the p–n junction plane, the active region in this plane was designed in the form of a trapezium. The narrow directional pattern in the plane perpendicular to the p–n junction was ensured by the use of a leaky mode, through which more than 90% of laser power was coupled out. (lasers)

  18. C IV Doppler shifts observed in active region filaments

    NASA Technical Reports Server (NTRS)

    Klimchuk, J. A.

    1986-01-01

    The Doppler shift properties of 21 active region filaments were studied using C IV Dopplergram data. Most are associated with corridors of weak magnetic field that separate opposite polarity strong fields seen in photospheric magnetograms. A majority of the filaments are relatively blue shifted, although several lie very close to the dividing lines between blue and red shift. Only one filament in the samples is clearly red shifted. A new calibration procedure for Dopplergrams indicates that sizable zero point offsets are often required. The center-to-limb behavior of the resulting absolute Doppler shifts suggests that filament flows are usually quite small. It is possible that they vanish.

  19. Chromospheric Evolution and the Flare Activity of Super-Active Region NOAA 6555

    NASA Technical Reports Server (NTRS)

    PrasadC, Debi; Ambastha, Ashok; Srivastava, Nandita; Tripathy, Sushanta C.; Hagyard, Mona J.

    1997-01-01

    Super-active region NOAA 6555 was highly flare productive during the period March 21st - 27th, 1991 of its disk passage. We have studied its chromospheric activity using high spatial resolution H alpha filtergrams taken at Udaipur along with MSFC vector magnetograms. A possible relationship of flare productivity and the variation in shear has been explored. Flares were generally seen in those subareas of the active region which possessed closed magnetic field configuration, whereas only minor flares and/or surges occurred in subareas showing open magnetic field configuration. Physical mechanisms responsible for the observed surges are also discussed.

  20. Sequence analysis of the ribosomal internal transcribed spacer DNA of the crayfish parasite Psorospermium haeckeli.

    PubMed

    Bangyeekhun, E; Ryynänen, H J; Henttonen, P; Huner, J V; Cerenius, L; Söderhäll, K

    2001-10-08

    Two morphotypes of the crayfish parasite Psorospermium haeckeli were isolated from 2 crayfish species of different geographical origin. The oval-shaped sporocysts were obtained from the epidermal and connective tissue beneath the carapace of the noble crayfish Astacus astacus from Sweden and Finland. Elongated spores were isolated from the abdominal muscle tissue of the red swamp crayfish Procambarus clarkii from USA. To compare genetic divergence of 2 morphotypes of the parasite, the ribosomal internal transcribed spacer (ITS) DNA (ITS 1 and ITS 2) and the 5.8S rRNA gene were cloned and sequenced. The analysed region is variable in length, with the ribosomal ITS sequence of the European morphotype longer than the North American one. Sequence diversity is found mainly in ITS 1 and ITS 2 regions, and there is 66% and 58% similarity between the 2 morphotypes, respectively. Thus, analysis of the ribosomal ITS DNA suggests that P. haeckeli forms obtained from Europe and North America are genetically diverse, which supports the previously reported morphological characteristics.

  1. CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella.

    PubMed

    Věchtová, Pavlína; Dalíková, Martina; Sýkorová, Miroslava; Žurovcová, Martina; Füssy, Zoltán; Zrzavá, Magda

    2016-08-01

    Satellite DNA (satDNA) is a non-coding component of eukaryotic genomes, located mainly in heterochromatic regions. Relevance of satDNA began to emerge with accumulating evidence of its potential yet hardly comprehensible role that it can play in the genome of many organisms. We isolated the first satDNA of the codling moth (Cydia pomonella, Tortricidae, Lepidoptera), a species with holokinetic chromosomes and a single large heterochromatic element, the W chromosome in females. The satDNA, called CpSAT-1, is located on all chromosomes of the complement, although in different amounts. Surprisingly, the satellite is almost missing in the heterochromatic W chromosome. Additionally, we isolated mRNA from all developmental stages (1st-5th instar larva, pupa, adult), both sexes (adult male and female) and several tissues (Malpighian tubules, gut, heart, testes, and ovaries) of the codling moth and showed the CpSAT-1 sequence was transcribed in all tested samples. Using CpSAT-1 specific primers we amplified, cloned and sequenced 40 monomers from cDNA and gDNA, respectively. The sequence analysis revealed a high mutation rate and the presence of potentially functional motifs, mainly in non-conserved regions of the monomers. Both the chromosomal distribution and the sequence analysis suggest that CPSAT-1 has no function in the C. pomonella genome.

  2. Sequence polymorphism in the ribosomal DNA internal transcribed spacers differs among Theileria species.

    PubMed

    Aktas, Münir; Bendele, Kylie G; Altay, Kürsat; Dumanli, Nazir; Tsuji, Masayoshi; Holman, Patricia J

    2007-07-20

    The genomic region spanning the two ribosomal RNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was cloned and sequenced from sixteen Theileria isolates. Each Theileria species possessed ITS1 and ITS2 of unique size(s) and species specific nucleotide sequences. Varying degrees of ITS1 and ITS2 intra- and inter-species sequence polymorphism were found among ruminant Theileria species. The spacers were most polymorphic in the agent of tropical theileriosis, Theileria annulata, and were more conserved in two benign species, Theileria buffeli and Theileria sergenti Chitose. Phylogenetic analysis of the rDNA ITS1-5.8S rRNA gene-ITS2 region clearly separated each taxon, placing them in three clusters. One held T. annulata, Theileria parva, and Theileria mutans, with the latter two most closely related. The second held T. sergenti Ikeda, T. sergenti Chitose, and T. buffeli, with the latter two most closely related. The third cluster held the Theileria ovis isolates.

  3. Internal transcribed spacer guided multiplex PCR for species identification of Convolvulus prostratus and Evolvulus alsinoides

    PubMed Central

    Sharma, Sonal; Shrivastava, Neeta

    2016-01-01

    Shankhpushpi is a reputed drug from an Indian system of medicine for treating mental disorders and enhancing memory. Two herbs, namely Convolvulus prostratus Forssk. and Evolvulus alsinoides (L.) L., are commonly known as Shankhpushpi. Ambiguous vernacular identity can affect the scientific validity of the Shankpushpi-based herbal drug therapy. In the present investigation, a novel and sensitive multiplex PCR method based on polymorphism in the internal transcribed spacer (ITS) region was developed to establish the molecular identity of C. prostratus and E. alsinoides. DNA was isolated and the ITS region was amplified, sequenced and assembled. Sequences were aligned to identify variable nucleotides in order to develop plant-specific primers. Primers were validated in singleplex reactions and eventually a multiplex assay was developed. This assay was tested for sensitivity and validated by amplifying DNA isolated from the simulated blended powdered plant material. Primers developed for C. prostratus resulted into a 200 bp amplicon and 596 bp for E. alsinoides. The assay was found to be sensitive enough for amplification of low quantities of DNA. The method can detect 10% of the mixing of plants with each other in blended material. This PCR assay can be used for rapid botanical identification of Shankhpushpi plant materials and will improve evidence-based herbal drug therapy. PMID:27175337

  4. The morphology of flare phenomena, magnetic fields, and electric currents in active regions. II - NOAA active region 5747 (1989 October)

    NASA Technical Reports Server (NTRS)

    Leka, K. D.; Canfield, Richard C.; Mcclymont, A. N.; De La Beaujardiere, J.-F.; Fan, Yuhong; Tang, F.

    1993-01-01

    The paper describes October 1989 observations in NOAA Active Region 5747 of the morphology of energetic electron precipitation and high-pressure coronal flare plasmas of three flares and their relation to the vector magnetic field and vertical electric currents. The H-alpha spectroheliograms were coaligned with the vector magnetograms using continuum images of sunspots, enabling positional accuracy of a few arcsec. It was found that, during the gradual phase, the regions of the H-alpha flare that show the effects of enhanced pressure in the overlying corona often encompass extrema of the vertical current density, consistent with earlier work showing a close relationship between H-alpha emission and line-of-sight currents. The data are also consistent with the overall morphology and evolution described by erupting-filament models such as those of Kopp and Pneuman (1976) and Sturrock (1989).

  5. Behaviour of oscillations in loop structures above active regions

    NASA Astrophysics Data System (ADS)

    Kolobov, D. Y.; Kobanov, N. I.; Chelpanov, A. A.; Kochanov, A. A.; Anfinogentov, S. A.; Chupin, S. A.; Myshyakov, I. I.; Tomin, V. E.

    2015-12-01

    In this study we combine the multiwavelength ultraviolet-optical (Solar Dynamics Observatory, SDO) and radio (Nobeyama Radioheliograph, NoRH) observations to get further insight into space-frequency distribution of oscillations at different atmospheric levels of the Sun. We processed the observational data on NOAA 11711 active region and found oscillations propagating from the photospheric level through the transition region upward into the corona. The power maps of low-frequency (1-2 mHz) oscillations reproduce well the fan-like coronal structures visible in the Fe IX 171 Å line. High frequency oscillations (5-7 mHz) propagate along the vertical magnetic field lines and concentrate inside small-scale elements in the umbra and at the umbra-penumbra boundary. We investigated the dependence of the dominant oscillation frequency upon the distance from the sunspot barycentre to estimate inclination of magnetic tubes in higher levels of sunspots where it cannot be measured directly, and found that this angle is close to 40° above the umbra boundaries in the transition region.

  6. Active Region Magnetic Structure Observed in the Photosphere and Chromosphere

    NASA Technical Reports Server (NTRS)

    Leka, K. D.; Metcalf, Thomas R.

    2001-01-01

    The magnetic flux above sunspots and plage in NOAA (National Oceanic and Atmospheric Administration) Active Region 8299 has been measured in the photosphere and the chromosphere. We investigate the vertical magnetic structure above the umbrae, penumbrae and plage regions using quantitative statistical comparisons of the photospheric and chromospheric vector magnetic flux data. The results include: (1) a decrease in flux with height, (2) the direct detection of the superpenumbral canopy in the chromosphere, (3) values for dB/dz which are consistent with earlier investigations when derived from a straight difference between the two datasets but quite low when derived from the delta x B = 0 condition, (4) a monolithic structure in the umbra which extends well into the upper chromosphere with a very complex and varied structure in the penumbra and plage, as evidenced by (5) a uniform magnetic scale height in the umbrae with an abrupt jump to widely varying scale heights in the penumbral and plage regions. Further, we find (6) evidence for a very large (delta z approximately equals 3Mm) height difference between the atmospheric layers sampled in the two magnetograms, almost a factor of three larger than that implied by atmospheric models. We additionally test the apropriateness of using photospheric magnetic flux as a boundary for field-line extrapolations, and find a better agreement with observed coronal structure when the chromospheric flux is used as a boundary.

  7. Photospheric electric current and transition region brightness within an active region

    NASA Technical Reports Server (NTRS)

    Deloach, A. C.; Hagyard, M. J.; Rabin, D.; Moore, R. L.; Smith, B. J., Jr.; West, E. A.; Tandberg-Hanssen, E.

    1984-01-01

    Distributions of vertical electrical current density J(z) calculated from vector measurements of the photospheric magnetic field are compared with ultraviolet spectroheliograms to investigate whether resistive heating is an important source of enhanced emission in the transition region. The photospheric magnetic fields in Active Region 2372 were measured on April 6 and 7, 1980 with the Marshall Space Flight Center vector magnetograph; ultraviolet wavelength spectroheliograms (L-alpha and N V 1239 A) were obtained with the UV Spectrometer and Polarimeter experiment aboard the Solar Maximum Mission satellite. Spatial registration of the J(z) (5 arcsec resolution) and UV (3 arcsec resolution) maps indicates that the maximum current density is cospatial with a minor but persistent UV enhancement, but there is little detected current associated with other nearby bright areas. It is concluded that, although resistive heating may be important in the transition region, the currents responsible for the heating are largely unresolved in the present measurements and have no simple correlation with the residual current measured on 5-arcsec scales.

  8. THE MAGNETIC CLASSIFICATION OF SOLAR ACTIVE REGIONS 1992–2015

    SciTech Connect

    Jaeggli, S. A.; Norton, A. A.

    2016-03-20

    The purpose of this Letter is to address a blindspot in our knowledge of solar active region (AR) statistics. To the best of our knowledge, there are no published results showing the variation of the Mount Wilson magnetic classifications as a function of solar cycle based on modern observations. We show statistics for all ARs reported in the daily Solar Region Summary from 1992 January 1 to 2015 December 31. We find that the α and β class ARs (including all sub-groups, e.g., βγ, βδ) make up fractions of approximately 20% and 80% of the sample, respectively. This fraction is relatively constant during high levels of activity; however, an increase in the α fraction to about 35% and and a decrease in the β fraction to about 65% can be seen near each solar minimum and are statistically significant at the 2σ level. Over 30% of all ARs observed during the years of solar maxima were appended with the classifications γ and/or δ, while these classifications account for only a fraction of a percent during the years near the solar minima. This variation in the AR types indicates that the formation of complex ARs may be due to the pileup of frequent emergence of magnetic flux during solar maximum, rather than the emergence of complex, monolithic flux structures.

  9. Multi-Wavelength Study of Active Region Loop Dynamics

    NASA Astrophysics Data System (ADS)

    Banerjee, D.

    2006-11-01

    Observations have revealed the existence of weak transient disturbances in extended coronal loop systems. These propagating disturbances (PDs) originate from small scale brightenings at the footpoints of the loops and propagate upward along the loops. In all cases observed, the projected propagation speed is close to, but below the expected sound speed in the loops. This suggests that the PDs could be interpreted as slow mode MHD waves. Interpreting the oscillation in terms of different wave modes and/or plasma motions always depend on the line of sight as we observe in the limb or on the center of the disk. The JOP 165 campaign will address some of these questions. MDI and TRACE photospheric and UV imaging of TRACE and SPIRIT have been acquired simultaneously with high temporal and spatial coverage along with the spectroscopic data from CDS. EIT was operated in the shutter-less mode to achieve high Cadence. Some of the off- limb active region dynamics and oscillations observed during this JOP campaign will be focused in this presentation. Plasma condensations and temporal variations in active region loops will be also addressed.

  10. Magnetic field measurements in and above a limb active region

    NASA Astrophysics Data System (ADS)

    Philip, Judge

    2013-07-01

    We analyze spectropolarimetric data of a limb active region (NOAA 11302) obtained on September 22nd 2011 using the Facility Infrared Spectrometer (FIRS) at the Dunn Solar Telescope (DST). Stokes profiles including lines of Si I 1028.7 nm and He I 1083 nm were obtained in three scans over a 45"x75" area. Simultaneous narrow band Ca II K and G-band intensity data were acquired with a cadence of 5s at the DST. The He I data show not only typical active region polarization signatures, but also signatures in plumes -- cool post flare loops -- which extend many Mm into the corona across the visible limb. The plumes have remarkably uniform brightness, and the plume plasma is significantly Doppler shifted as it drains from the corona. Using carefully constructed observing and calibration sequences and applying Principal Component Analysis to remove instrumental artifacts, we achieved a polarization sensitivity approaching 0.02%. With this sensitivity we attempt to diagnose the vector magnetic fields and plasma properties of chromospheric and cool coronal material in and above NOAA 11302. Inversions using various radiative transfer models in the HAZEL code are remarkably consistent with the idea that plume spectra are formed in a simple, slab-like geometry, but that the ``disk'' spectra are formed under more traditional models (Milne-Eddington). The inverted magnetic data of He I lines are compared with photospheric inversions of DST Si I and Fe I data from the Solar Dynamics Observatory.

  11. Material Supply and Magnetic Configuration of an Active Region Filament

    NASA Astrophysics Data System (ADS)

    Zou, P.; Fang, C.; Chen, P. F.; Yang, K.; Hao, Q.; Cao, Wenda

    2016-11-01

    It is important to study the fine structures of solar filaments with high-resolution observations, since it can help us understand the magnetic and thermal structures of the filaments and their dynamics. In this paper, we study a newly formed filament located inside the active region NOAA 11762, which was observed by the 1.6 m New Solar Telescope at Big Bear Solar Observatory from 16:40:19 UT to 17:07:58 UT on 2013 June 5. As revealed by the Hα filtergrams, cool material is seen to be injected into the filament spine with a speed of 5-10 km s-1. At the source of the injection, brightenings are identified in the chromosphere, which are accompanied by magnetic cancellation in the photosphere, implying the importance of magnetic reconnection in replenishing the filament with plasmas from the lower atmosphere. Counter-streamings are detected near one endpoint of the filament, with the plane-of-the-sky speed being 7-9 km s-1 in the Hα red-wing filtergrams and 9-25 km s-1 in the blue-wing filtergrams. The observations are indicative that this active region filament is supported by a sheared arcade without magnetic dips, and the counter-streamings are due to unidirectional flows with alternative directions, rather than due to the longitudinal oscillations of filament threads as in many other filaments.

  12. Photonic crystal lasers using wavelength-scale embedded active region

    NASA Astrophysics Data System (ADS)

    Matsuo, Shinji; Sato, Tomonari; Takeda, Koji; Shinya, Akihiko; Nozaki, Kengo; Kuramochi, Eiichi; Taniyama, Hideaki; Notomi, Masaya; Fujii, Takuro; Hasebe, Koichi; Kakitsuka, Takaaki

    2014-01-01

    Lasers with ultra-low operating energy are desired for use in chip-to-chip and on-chip optical interconnects. If we are to reduce the operating energy, we must reduce the active volume. Therefore, a photonic crystal (PhC) laser with a wavelength-scale cavity has attracted a lot of attention because a PhC provides a large Q-factor with a small volume. To improve this device's performance, we employ an embedded active region structure in which the wavelength-scale active region is buried with an InP PhC slab. This structure enables us to achieve effective confinement of both carriers and photons, and to improve the thermal resistance of the device. Thus, we have obtained a large external differential quantum efficiency of 55% and an output power of -10 dBm by optical pumping. For electrical pumping, we use a lateral p-i-n structure that employs Zn diffusion and Si ion implantation for p-type and n-type doping, respectively. We have achieved room-temperature continuous-wave operation with a threshold current of 7.8 µA and a maximum 3 dB bandwidth of 16.2 GHz. The results of an experimental bit error rate measurement with a 10 Gbit s-1 NRZ signal reveal the minimum operating energy for transferring a single bit of 5.5 fJ. These results show the potential of this laser to be used for very short reach interconnects. We also describe the optimal design of cavity quality (Q) factor in terms of achieving a large output power with a low operating energy using a calculation based on rate equations. When we assume an internal absorption loss of 20 cm-1, the optimized coupling Q-factor is 2000.

  13. Regional variation in myofilament length-dependent activation.

    PubMed

    Cazorla, Olivier; Lacampagne, Alain

    2011-07-01

    The Frank-Starling law is an important regulatory mechanism of the heart that links the end-diastolic volume with the systolic ejection fraction. This beat-to-beat regulation of the heart, underlined at the cellular level by higher myofilament calcium sensitivity at longer sarcomere length, is known as length-dependent activation or stretch sensitization of activation. However, the heart is structurally and functionally heterogeneous and asymmetrical. Specifically, contractile properties are not uniform within the left ventricle partly due to transmural differences in action potential waveforms and calcium homeostasis. The present review will focus on the role of the contractile machinery in the transmural contractile heterogeneity and its adaptation to changes in muscle strain. The expression of different myosin isoforms, the level of titin-based passive tension, and thin and thick sarcomeric regulatory proteins are considered to explain the regional cellular contractile properties. Finally, the importance of transmural heterogeneity of length-dependent activation and the consequences of its modification on the heart mechanics are discussed. Despite extensive research since the characterization of the Frank-Starling law, the molecular mechanisms by which strain information is transduced to the contractile machinery have not been fully determined yet.

  14. Repetitive Transcranial Magnetic Stimulation Activates Specific Regions in Rat Brain

    NASA Astrophysics Data System (ADS)

    Ji, Ru-Rong; Schlaepfer, Thomas E.; Aizenman, Carlos D.; Epstein, Charles M.; Qiu, Dike; Huang, Justin C.; Rupp, Fabio

    1998-12-01

    Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive technique to induce electric currents in the brain. Although rTMS is being evaluated as a possible alternative to electroconvulsive therapy for the treatment of refractory depression, little is known about the pattern of activation induced in the brain by rTMS. We have compared immediate early gene expression in rat brain after rTMS and electroconvulsive stimulation, a well-established animal model for electroconvulsive therapy. Our result shows that rTMS applied in conditions effective in animal models of depression induces different patterns of immediate-early gene expression than does electroconvulsive stimulation. In particular, rTMS evokes strong neural responses in the paraventricular nucleus of the thalamus (PVT) and in other regions involved in the regulation of circadian rhythms. The response in PVT is independent of the orientation of the stimulation probe relative to the head. Part of this response is likely because of direct activation, as repetitive magnetic stimulation also activates PVT neurons in brain slices.

  15. In-depth survey of sunspot and active region catalogs

    NASA Astrophysics Data System (ADS)

    Lefèvre, Laure; Clette, Frédéric; Baranyi, Tunde

    2011-08-01

    When consulting detailed photospheric catalogs for solar activity studies spanning long time intervals, solar physicists face multiple limitations in the existing catalogs: finite or fragmented time coverage, limited time overlap between catalogs and even more importantly, a mismatch in contents and conventions. In view of a study of new sunspot-based activity indices, we have conducted a comprehensive survey of existing catalogs. In a first approach, we illustrate how the information from parallel catalogs can be merged to form a much more comprehensive record of sunspot groups. For this, we use the unique Debrecen Photoheliographic Data (DPD), which is already a composite of several ground observatories and SOHO data, and the USAF/Mount Wilson catalog from the Solar Optical Observing Network (SOON). We also describe our semi-interactive cross-identification method, which was needed to match the non-overlapping solar active region nomenclature, the most critical and subtle step when working with multiple catalogs. This effort, focused here first on the last two solar cycles, should lead to a better central database collecting all available sunspot group parameters to address future solar cycle studies beyond the traditional sunspot index time series Ri.

  16. On the modified active region design of interband cascade lasers

    SciTech Connect

    Motyka, M.; Ryczko, K.; Dyksik, M.; Sęk, G.; Misiewicz, J.; Weih, R.; Dallner, M.; Kamp, M.; Höfling, S.

    2015-02-28

    Type II InAs/GaInSb quantum wells (QWs) grown on GaSb or InAs substrates and designed to be integrated in the active region of interband cascade lasers (ICLs) emitting in the mid infrared have been investigated. Optical spectroscopy, combined with band structure calculations, has been used to probe their electronic properties. A design with multiple InAs QWs has been compared with the more common double W-shaped QW and it has been demonstrated that it allows red shifting the emission wavelength and enhancing the transition oscillator strength. This can be beneficial for the improvements of the ICLs performances, especially when considering their long-wavelength operation.

  17. Chromospheric magnetic fields of an active region filament

    NASA Astrophysics Data System (ADS)

    Xu, Z.; Solanki, S.; Lagg, A.

    2012-06-01

    Vector magnetic fields of an active region filament are co-spatially and co-temporally mapped in photosphere and upper chromosphere, by using spectro-polarimetric observations made by Tenerife Infrared Polarimeter (TIP II) at the German Vacuum Tower Telescope (VTT). A Zeeman-based ME inversion is performed on the full Stokes vectors of both the photospheric Si I 1082.7 nm and the chromospheric He I 1083.0 nm lines. We found that the strong magnetic fields, with the field strength of 600 - 800 G in the He I line formation height, are not uncommon among AR filaments. But such strong magnetic field is not always found in AR filaments.

  18. SIGN SINGULARITY AND FLARES IN SOLAR ACTIVE REGION NOAA 11158

    SciTech Connect

    Sorriso-Valvo, L.; De Vita, G.; Kazachenko, M. D.; Krucker, S.; Welsch, B. T.; Fisher, G. H.; Primavera, L.; Servidio, S.; Lepreti, F.; Carbone, V.; Vecchio, A.

    2015-03-01

    Solar Active Region NOAA 11158 has hosted a number of strong flares, including one X2.2 event. The complexity of current density and current helicity are studied through cancellation analysis of their sign-singular measure, which features power-law scaling. Spectral analysis is also performed, revealing the presence of two separate scaling ranges with different spectral index. The time evolution of parameters is discussed. Sudden changes of the cancellation exponents at the time of large flares and the presence of correlation with Extreme-Ultra-Violet and X-ray flux suggest that eruption of large flares can be linked to the small-scale properties of the current structures.

  19. Focused ultrasound modulates region-specific brain activity

    PubMed Central

    Yoo, Seung-Schik; Bystritsky, Alexander; Lee, Jong-Hwan; Zhang, Yongzhi; Fischer, Krisztina; Min, Byoung-Kyong; McDannold, Nathan J.; Pascual-Leone, Alvaro; Jolesz, Ferenc A.

    2012-01-01

    We demonstrated the in vivo feasibility of using focused ultrasound (FUS) to transiently modulate (through either stimulation or suppression) the function of regional brain tissue in rabbits. FUS was delivered in a train of pulses at low acoustic energy, far below the cavitation threshold, to the animal's somatomotor and visual areas, as guided by anatomical and functional information from magnetic resonance imaging (MRI). The temporary alterations in the brain function affected by the sonication were characterized by both electrophysiological recordings and functional brain mapping achieved through the use of functional MRI (fMRI). The modulatory effects were bimodal, whereby the brain activity could either be stimulated or selectively suppressed. Histological analysis of the excised brain tissue after the sonication demonstrated that the FUS did not elicit any tissue damages. Unlike transcranial magnetic stimulation, FUS can be applied to deep structures in the brain with greater spatial precision. Transient modulation of brain function using image-guided and anatomically-targeted FUS would enable the investigation of functional connectivity between brain regions and will eventually lead to a better understanding of localized brain functions. It is anticipated that the use of this technology will have an impact on brain research and may offer novel therapeutic interventions in various neurological conditions and psychiatric disorders. PMID:21354315

  20. Slow Magnetosonic Waves and Fast Flows in Active Region Loops

    NASA Technical Reports Server (NTRS)

    Ofman, L.; Wang, T. J.; Davila, J. M.

    2012-01-01

    Recent extreme ultraviolet spectroscopic observations indicate that slow magnetosonic waves are present in active region (AR) loops. Some of the spectral data were also interpreted as evidence of fast (approx 100-300 km/s) quasiperiodic flows. We have performed three-dimensional magnetohydrodynamic (3D MHD) modeling of a bipolar AR that contains impulsively generated waves and flows in coronal loops. The model AR is initiated with a dipole magnetic field and gravitationally stratified density, with an upflow-driven steadily or periodically in localized regions at the footpoints of magnetic loops. The resulting flows along the magnetic field lines of the AR produce higher density loops compared to the surrounding plasma by injection of material into the flux tubes and the establishment of siphon flow.We find that the impulsive onset of flows with subsonic speeds result in the excitation of damped slow magnetosonic waves that propagate along the loops and coupled nonlinearly driven fast-mode waves. The phase speed of the slow magnetosonic waves is close to the coronal sound speed. When the amplitude of the driving pulses is increased we find that slow shock-like wave trains are produced. When the upflows are driven periodically, undamped oscillations are produced with periods determined by the periodicity of the upflows. Based on the results of the 3D MHD model we suggest that the observed slow magnetosonic waves and persistent upflows may be produced by the same impulsive events at the bases of ARs.

  1. The transcriptionally active regions in the genome of Bacillus subtilis

    PubMed Central

    Rasmussen, Simon; Nielsen, Henrik Bjørn; Jarmer, Hanne

    2009-01-01

    The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non-coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22, is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA. Through this work we have discovered a long conserved 3′ untranslated region (UTR) in a group of membrane-associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system. PMID:19682248

  2. Comparison of Solar Active Region Complexity Andgeomagnetic Activity from 1996 TO 2014

    NASA Astrophysics Data System (ADS)

    Tanskanen, E. I.; Nikbakhsh, S.; Perez-Suarez, D.; Hackman, T.

    2015-12-01

    We have studied the influence of magnetic complexity of solar Active Regions (ARs)on geomagnetic activity from 1996 to 2014. Sunspots are visual indicators of ARswhere the solar magnetic field is disturbed. We have used International, American,Space Environment Service Center (SESC) and Space Weather Prediction Center(SWPC) sunspot numbers to examine ARs. Major manifestations of solar magneticactivity, such as flares and Coronal Mass Ejections (CMEs), are associated withARs. For this study we chose the Mount Wilson scheme. It classifies ARs in terms oftheir magnetic topology from the least complex (?) to the most complex one ( ?).Several cases have been found where the more complex structures produce strongerflares and CMEs than the less complex ones. We have a list of identified substormsavailable with different phases and their durations. This will be compared to ourmagnetic complexity data to analyse the effects of active region magnetic complexityto the magnetic activity on the vicinity of the Earth.

  3. Molecular Systematics of Genus Atractylodes (Compositae, Cardueae): Evidence from Internal Transcribed Spacer (ITS) and trnL-F Sequences

    PubMed Central

    Peng, Hua-Sheng; Yuan, Qing-Jun; Li, Qian-Quan; Huang, Lu-Qi

    2012-01-01

    To determine the evolutionary relationships among all members of the genus Atractylodes (Compositae, Cardueae), we conducted molecular phylogenetic analyses of one nuclear DNA (nrDNA) region (internal transcribed spacer, ITS) and one chloroplast DNA (cpDNA) region (intergenic spacer region of trnL-F). In ITS and ITS + trnL-F trees, all members of Atractylodes form a monophyletic clade. Atractylodes is a sister group of the Carlina and Atractylis branch. Atractylodes species were distributed among three clades: (1) A. carlinoides (located in the lowest base of the Atractylodes phylogenetic tree), (2) A. macrocephala, and (3) the A. lancea complex, including A. japonica, A. coreana, A. lancea, A. lancea subsp. luotianensis, and A. chinensis. The taxonomic controversy over the classification of species of Atractylodes is mainly concentrated in the A. lancea complex. In base on molecular results, the intraspecific division of Atractylodes lancea is not supported, and A. coreana should be treated as a synonym A. chinensis. PMID:23203084

  4. Molecular systematics of Genus Atractylodes (Compositae, Cardueae): evidence from Internal Transcribed Spacer (ITS) and trnL-F sequences.

    PubMed

    Peng, Hua-Sheng; Yuan, Qing-Jun; Li, Qian-Quan; Huang, Lu-Qi

    2012-11-09

    To determine the evolutionary relationships among all members of the genus Atractylodes (Compositae, Cardueae), we conducted molecular phylogenetic analyses of one nuclear DNA (nrDNA) region (internal transcribed spacer, ITS) and one chloroplast DNA (cpDNA) region (intergenic spacer region of trnL-F). In ITS and ITS + trnL-F trees, all members of Atractylodes form a monophyletic clade. Atractylodes is a sister group of the Carlina and Atractylis branch. Atractylodes species were distributed among three clades: (1) A. carlinoides (located in the lowest base of the Atractylodes phylogenetic tree), (2) A. macrocephala, and (3) the A. lancea complex, including A. japonica, A. coreana, A. lancea, A. lancea subsp. luotianensis, and A. chinensis. The taxonomic controversy over the classification of species of Atractylodes is mainly concentrated in the A. lancea complex. In base on molecular results, the intraspecific division of Atractylodes lancea is not supported, and A. coreana should be treated as a synonym A. chinensis.

  5. Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin.

    PubMed Central

    Bazett-Jones, D P; Mendez, E; Czarnota, G J; Ottensmeyer, F P; Allfrey, V G

    1996-01-01

    We have characterized the structure of transcriptionally active nucleosome subunits using electron spectroscopic imaging. Individual nucleosomes were analyzed in terms of total mass, DNA and protein content, while the ensemble of images of active nucleosomes was used to calculate a three-dimensional reconstruction. Transcriptionally active nucleosomes were separated from inactive nucleosomes by mercury-affinity chromatography thus making it possible to compare their structures. The chromatographic results combined with electron spectroscopic imaging confirm that active nucleosomes unfold to form extended U-shaped particles. Phosphorus mapping indicated that the nucleosomal DNA also underwent a conformational change consistent with particle unfolding. The three-dimensional structure of the Hg-affinity purified nucleosomes determined using quaternion-assisted angular reconstitution methods unites and resolves the different electron microscopic views of the particle and is concordant with a sulphydryl-exposing disruption of the H3-H4 tetramer. PMID:8628657

  6. Cloud condensation nuclei activity and droplet activation kinetics of wet processed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2011-08-01

    This study reports laboratory measurements of particle size distributions, cloud condensation nuclei (CCN) activity, and droplet activation kinetics of wet generated aerosols from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. The dependence of critical supersaturation, sc, on particle dry diameter, Ddry, is used to characterize particle-water interactions and assess the ability of Frenkel-Halsey-Hill adsorption activation theory (FHH-AT) and Köhler theory (KT) to describe the CCN activity of the considered samples. Wet generated regional dust samples produce unimodal size distributions with particle sizes as small as 40 nm, CCN activation consistent with KT, and exhibit hygroscopicity similar to inorganic salts. Wet generated clays and minerals produce a bimodal size distribution; the CCN activity of the smaller mode is consistent with KT, while the larger mode is less hydrophilic, follows activation by FHH-AT, and displays almost identical CCN activity to dry generated dust. Ion Chromatography (IC) analysis performed on regional dust samples indicates a soluble fraction that cannot explain the CCN activity of dry or wet generated dust. A mass balance and hygroscopicity closure suggests that the small amount of ions (from low solubility compounds like calcite) present in the dry dust dissolve in the aqueous suspension during the wet generation process and give rise to the observed small hygroscopic mode. Overall these results identify an artifact that may question the atmospheric relevance of dust CCN activity studies using the wet generation method. Based on the method of threshold droplet growth analysis, wet generated mineral aerosols display similar activation kinetics compared to ammonium sulfate calibration aerosol. Finally, a unified CCN activity framework that accounts for concurrent effects of solute and adsorption is developed to describe the CCN activity of aged or hygroscopic dusts.

  7. Transcribing and digitizing eighteenth- and nineteenth-century letters for a historical digital repository.

    PubMed

    Dunster, Emily S; Kipnis, Daniel G; Angelo, F Michael

    2014-01-01

    In fall 2011, the Scott Memorial Library purchased 53 letters belonging to an 1841 graduate of Jefferson Medical College, John Plimpton Green. The library staff transcribed and digitized the letters, creating an online collection in the university's institutional repository, Jefferson Digital Commons. This article will detail the process of transcribing and digitizing the collection along with sharing statistics and the benefits of this project to global researchers.

  8. A Phylogenetic Analysis of Heterorhabditis (Nemata: Rhabditidae) Based on Internal Transcribed Spacer 1 DNA Sequence Data

    PubMed Central

    Adams, B. J.; Burnell, A. M.; Powers, T. O.

    1998-01-01

    Internal transcribed spacer 1 sequences were used to infer phylogenetic relationships among 8 of the 9 described species and one putative species of the entomopathogenic nematode genus Heterorhabditis. Sequences were aligned and optimized based on pairwise genetic distance and parsimony criteria and subjected to a variety of sequence alignment parameters. Phylogenetic trees were constructed with maximum parsimony, cladistic, distance, and maximum likelihood algorithms. Our results gave strong support for four pairs of sister species, while relationships between these pairs also were resolved but less well supported. The ITS1 region of the nuclear ribosomal repeat was a reliable source of homologous characters for resolving relationships between closely related taxa but provided more tenuous resolution among more divergent lineages. A high degree of sequence identity and lack of autapomorphic characters suggest that sister species pairs within three distinct lineages may be mutually conspecific. Application of these molecular data and current morphological knowledge to the delimitation of species is hindered by an incomplete understanding of their variability in natural populations. PMID:19274196

  9. Identification of dendrobium species used for herbal medicines based on ribosomal DNA internal transcribed spacer sequence.

    PubMed

    Takamiya, Tomoko; Wongsawad, Pheravut; Tajima, Natsuko; Shioda, Nao; Lu, Jun Feng; Wen, Chi Luan; Wu, Jin Bin; Handa, Takashi; Iijima, Hiroshi; Kitanaka, Susumu; Yukawa, Tomohisa

    2011-01-01

    Stems of genus Dendrobium (Orchidaceae) have been traditionally used as an herbal medicine (Dendrobii Herba) in Eastern Asia. Although demand for Dendrobium is increasing rapidly, wild resources are decreasing due to over-collection. This study aimed to identify plant sources of Dendrobii Herba on the market based on sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. We constructed an ITS1-5.8S-ITS2 sequence database of 196 Dendrobium species, and the database was employed to identify 21 herbal samples. We found that 13 Dendrobium species (D. catenatum, D. cucullatum, D. denudans, D. devonianum, D. eriiflorum, D. hancockii, D. linawianum, D. lituiflorum, D. loddigesii, D. polyanthum, D. primulinum, D. regium, and D. transparens) were possibly used as plant sources of Dendrobii Herba, and unidentified species allied to D. denudans, D. eriiflorum, D. gregulus, or D. hemimelanoglossum were also used as sources. Furthermore, it is clear that D. catenatum is one of the most important sources of Dendrobii Herba (5 out of 21 samples).

  10. Internal Transcribed Spacer Sequencing versus Biochemical Profiling for Identification of Medically Important Yeasts

    PubMed Central

    Ciardo, D. E.; Schär, G.; Böttger, E. C.; Altwegg, M.; Bosshard, P. P.

    2006-01-01

    In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region. PMID:16390952

  11. Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers.

    PubMed

    Peleg, Zvi; Fahima, Tzion; Abbo, Shahal; Krugman, Tamar; Saranga, Yehoshua

    2008-03-01

    Simple sequence repeat (SSR) markers have become a major tool in population genetic analyses. The anonymous genomic SSRs (gSSRs) have been recently supplemented with expressed sequence tag (EST) derived SSRs (eSSRs), which represent the transcribed regions of the genome. In the present study, we used 8 populations of wild emmer wheat (Triticum turgidum subsp. dicoccoides) to compare the usefulness of the two types of SSR markers in assessing allelic diversity and population structure. gSSRs revealed significantly higher diversity than eSSRs in terms of average number of alleles (14.92 vs. 7.4, respectively), polymorphic information content (0.87 vs. 0.68, respectively), and gene diversity (He; 0.55 vs. 0.38, respectively). Despite the overall differences in the level of diversity, Mantel tests for correlations between eSSR and gSSR pairwise genetic distances were found to be significant for each population as well as for all accessions jointly (RM=0.54, p=0.01). Various genetic structure analyses (AMOVA, PCoA, STRUCTURE, unrooted UPGMA tree) revealed a better capacity of eSSRs to distinguish between populations, while gSSRs showed a higher proportion of intrapopulation (among accessions) diversity. We conclude that eSSR and gSSR markers should be employed in conjunction to obtain a high inter- and intra-specific (or inter- and intra-varietal) distinctness.

  12. Long-Period ULF Wave Activity in the Cusp Region

    NASA Astrophysics Data System (ADS)

    Pilipenko, V.; Belakhovsky, V.; Engebretson, M. J.; Kozlovsky, A.

    2013-12-01

    We compare simultaneous observations of long-period ULF wave activity from the Svalbard/IMAGE and Greenland fluxgate magnetometer profiles covering the expected cusp geomagnetic latitudes. Irregular Pulsations at Cusp Latitudes (IPCL) and narrow-band Pc5 waves are found to be a ubiquitous element of ULF activity in the dayside high-latitude region. To identify the ionospheric projections of the cusp, we use the width of the return signal of the SuperDARN radar covering the Svalbard archipelago, predictions of empirical cusp models, and augmented whenever possible by DMSP identification of magnetospheric boundary domains. The meridional spatial structure of IPCL/Pc5 pulsation spectral power has been found to have a localized latitudinal peak, but not under the cusp proper as was previously thought, but several degrees southward from the equatorward cusp boundary. Possible mechanisms and their relevance to observational data are discussed. The occurrence of IPCL and Pc5 waves in the dayside boundary layers is a challenge to modelers, because so far their mechanism has not been firmly identified.

  13. E region electric field dependence of the solar activity

    NASA Astrophysics Data System (ADS)

    Denardini, C. M.; Moro, J.; Resende, L. C. A.; Chen, S. S.; Schuch, N. J.; Costa, J. E. R.

    2015-10-01

    We have being studying the zonal and vertical E region electric field components inferred from the Doppler shifts of type 2 echoes (gradient drift irregularities) detected with the 50 MHz backscatter coherent radar set at São Luis, Brazil (SLZ, 2.3°S, 44.2°W) during the solar cycle 24. In this report we present the dependence of the vertical and zonal components of this electric field with the solar activity, based on the solar flux F10.7. For this study we consider the geomagnetically quiet days only (Kp ≤ 3+). A magnetic field-aligned-integrated conductivity model was developed for proving the conductivities, using the IRI-2007, the MISIS-2000, and the IGRF-11 models as input parameters for ionosphere, neutral atmosphere, and Earth magnetic field, respectively. The ion-neutron collision frequencies of all the species are combined through the momentum transfer collision frequency equation. The mean zonal component of the electric field, which normally ranged from 0.19 to 0.35 mV/m between the 8 and 18 h (LT) in the Brazilian sector, show a small dependency with the solar activity. Whereas the mean vertical component of the electric field, which normally ranges from 4.65 to 10.12 mV/m, highlights the more pronounced dependency of the solar flux.

  14. The Voice Transcription Technique: Use of Voice Recognition Software to Transcribe Digital Interview Data in Qualitative Research

    ERIC Educational Resources Information Center

    Matheson, Jennifer L.

    2007-01-01

    Transcribing interview data is a time-consuming task that most qualitative researchers dislike. Transcribing is even more difficult for people with physical limitations because traditional transcribing requires manual dexterity and the ability to sit at a computer for long stretches of time. Researchers have begun to explore using an automated…

  15. The morphology of flare phenomena, magnetic fields, and electric currents in active regions. III - NOAA active region 6233 (1990 August)

    NASA Technical Reports Server (NTRS)

    De La Beaujardiere, J.-F.; Canfield, Richard C.; Leka, K. D.

    1993-01-01

    We investigate the spatial relationship between vertical electric currents and flare phenomena in NOAA Active Region 6233, which was observed 1990, August 28-31 at Mees Solar Observatory. The two flares studied are the 1N/M1.8 flare on August 28, 22:30 UT and the 1N/M1.6 flare on August 29, 20:35 UT. Using Stokes polarimetry we make magnetograms of the region and compute the vertical current density. Using H-alpha imaging spectroscopy we identify sites of intense nonthermal electron precipitation or of high coronal pressure. The precipitation in these flares is barely strong enough to be detectable. We find that both precipitation and high pressure tend to occur near vertical currents, but that neither phenomenon is cospatial with current maxima. In contrast with the conclusion of other authors, we argue that these observations do not support a current-interruption model for flares, unless the relevant currents are primarily horizontal. The magnetic morphology and temporal evolution of these flares suggest that an erupting filament model may be relevant, but this model does not explicitly predict the relationship between precipitation, high pressure, and vertical currents.

  16. ON MAGNETIC ACTIVITY BAND OVERLAP, INTERACTION, AND THE FORMATION OF COMPLEX SOLAR ACTIVE REGIONS

    SciTech Connect

    McIntosh, Scott W.; Leamon, Robert J.

    2014-11-20

    Recent work has revealed a phenomenological picture of the how the ∼11 yr sunspot cycle of the Sun arises. The production and destruction of sunspots is a consequence of the latitudinal-temporal overlap and interaction of the toroidal magnetic flux systems that belong to the 22 yr magnetic activity cycle and are rooted deep in the Sun's convective interior. We present a conceptually simple extension of this work, presenting a hypothesis on how complex active regions can form as a direct consequence of the intra- and extra-hemispheric interaction taking place in the solar interior. Furthermore, during specific portions of the sunspot cycle, we anticipate that those complex active regions may be particularly susceptible to profoundly catastrophic breakdown, producing flares and coronal mass ejections of the most severe magnitude.

  17. Contribution of regional brain melanocortin receptor subtypes to elevated activity energy expenditure in lean, active rats

    PubMed Central

    Shukla, Charu; Koch, Lauren G.; Britton, Steven L.; Cai, Minying; Hruby, Victor J.; Bednarek, Maria; Novak, Colleen M.

    2015-01-01

    Physical activity and non-exercise activity thermogenesis (NEAT) are crucial factors accounting for individual differences in body weight, interacting with genetic predisposition. In the brain, a number of neuroendocrine intermediates regulate food intake and energy expenditure (EE); this includes the brain melanocortin (MC) system, consisting of melanocortin peptides as well as their receptors (MCR). MC3R and MC4R have emerged as critical modulators of EE and food intake. To determine how variance in MC signaling may underlie individual differences in physical activity levels, we examined behavioral response to MC receptor agonists and antagonists in rats that show high and low levels of physical activity and NEAT, that is, high- and low-capacity runners (HCR, LCR), developed by artificial selection for differential intrinsic aerobic running capacity. Focusing on the hypothalamus, we identified brain region-specific elevations in expression of MCR 3, 4, and also MC5R, in the highly active, lean HCR relative to the less active and obesity-prone LCR. Further, the differences in activity and associated EE as a result of MCR activation or suppression using specific agonists and antagonists were similarly region-specific and directly corresponded to the differential MCR expression patterns. The agonists and antagonists investigated here did not significantly impact food intake at the doses used, suggesting that the differential pattern of receptor expression may by more meaningful to physical activity than to other aspects of energy balance regulation. Thus, MCR-mediated physical activity may be a key neural mechanism in distinguishing the lean phenotype and a target for enhancing physical activity and NEAT. PMID:26404873

  18. High resolution studies of complex solar active regions

    NASA Astrophysics Data System (ADS)

    Deng, Na

    Flares and Coronal Mass Ejections (CMEs) are energetic events, which can even impact the near-Earth environment and are the principal source of space weather. Most of them originate in solar active regions. The most violent events are produced in sunspots with a complex magnetic field topology. Studying their morphology and dynamics is helpful in understanding the energy accumulation and release mechanisms for flares and CMEs, which are intriguing problems in solar physics. The study of complex active regions is based on high-resolution observations from space missions and new instruments at the Big Bear Solar Observatory (BBSO). Adaptive optics (AO) in combination with image restoration techniques (speckle masking imaging) can achieve improved image quality and a spatial resolution (about 100 km on the solar surface) close to the diffraction limit of BBSO's 65 cm vacuum telescope. Dopplergrams obtained with a two-dimensional imaging spectrometer combined with horizontal flow maps derived with Local Correlation Tracking (LCT) provide precise measurements of the three-dimensional velocity field in sunspots. Magnetic field measurements from ground- and space-based instruments complement these data. At the outset of this study, the evolution and morphology of a typical round sunspot are described in some detail. The sunspot was followed from disk center to the limb, thus providing some insight into the geometry of the magnetic flux system. Having established a benchmark for a stable sunspot, the attention is turned to changes of the sunspot structure associated with flares and CMEs. Rapid penumbral decay and the strengthening of sunspot umbrae are manifestations of photospheric magnetic field changes after a flare. These sudden intensity changes are interpreted as a result of magnetic reconnection during the flare, which causes the magnetic field lines to be turned from more inclined to more vertical. Strong photospheric shear flows along the flaring magnetic

  19. Structural Determination of a Transcribing RNA Polymerase II Complex

    DTIC Science & Technology

    2000-05-01

    eukaryote- TFIIH, whose helicase activities melt DNA transcription initiation factor TFIIE, as re- specific subunits Rpbl0 and Rpbl2. Contact of...from a DNA template. Despite challenges involved in this project, a major achievement is at hand. Firstly, a mainchain model of RNA Polymerase II with...conducting research utilizing recombinant DNA technology, the investigator(s) adhered to current guidelines promulgated by the National Institutes of

  20. Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region.

    PubMed

    GokulRaj, Kathamuthu; Sundaresan, Natesan; Ganeshan, Enthai Jagan; Rajapriya, Pandi; Muthumary, Johnpaul; Sridhar, Jayavel; Pandi, Mohan

    2014-01-01

    Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal plants and characterized based on ITS2 sequence - secondary structure analysis. ITS2 secondary structures were elucidated with minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic relationships at different taxonomic levels due to their lesser length.

  1. Apparent and Intrinsic Evolution of Active Region Upflows

    NASA Astrophysics Data System (ADS)

    Baker, Deborah; Janvier, Miho; Démoulin, Pascal; Mandrini, Cristina H.

    2017-04-01

    We analyze the evolution of Fe xii coronal plasma upflows from the edges of ten active regions (ARs) as they cross the solar disk using the Hinode Extreme Ultraviolet Imaging Spectrometer (EIS) to do this. Confirming the results of Démoulin et al. ( Sol. Phys. 283, 341, 2013), we find that for each AR there is an observed long-term evolution of the upflows. This evolution is largely due to the solar rotation that progressively changes the viewpoint of dominantly stationary upflows. From this projection effect, we estimate the unprojected upflow velocity and its inclination to the local vertical. AR upflows typically fan away from the AR core by 40° to nearly vertical for the following polarity. The span of inclination angles is more spread out for the leading polarity, with flows angled from -29° (inclined toward the AR center) to 28° (directed away from the AR). In addition to the limb-to-limb apparent evolution, we identify an intrinsic evolution of the upflows that is due to coronal activity, which is AR dependent. Furthermore, line widths are correlated with Doppler velocities only for the few ARs with the highest velocities. We conclude that for the line widths to be affected by the solar rotation, the spatial gradient of the upflow velocities must be large enough such that the line broadening exceeds the thermal line width of Fe xii. Finally, we find that upflows occurring in pairs or multiple pairs are a common feature of ARs observed by Hinode/EIS, with up to four pairs present in AR 11575. This is important for constraining the upflow-driving mechanism as it implies that the mechanism is not local and does not occur over a single polarity. AR upflows originating from reconnection along quasi-separatrix layers between overpressure AR loops and neighboring underpressure loops is consistent with upflows occurring in pairs, unlike other proposed mechanisms that act locally in one polarity.

  2. Seismic activity of the San Francisco Bay region

    USGS Publications Warehouse

    Bakun, W.H.

    1999-01-01

    Moment magnitude M with objective confidence-level uncertainties are estimated for felt San Francisco Bay region earthquakes using Bakun and Wentworth's (1997) analysis strategy for seismic intensity observations. The frequency-magnitude distribution is well described for M ???5.5 events since 1850 by a Gutenberg-Richter relation with a b-value of 0.90. The seismic moment rate ??M0/yr since 1836 is 2.68 X 1018 N-m/yr (95% confidence range = 1.29 X 1018 N-m/yr to 4.07 X 1018 N-m/yr); the seismic moment rate since 1850 is nearly the same. ??M0/yr in the 56 years before 1906 is about 10 times that in the 70 years after 1906. In contrast, ??M0/yr since 1977 is about equal that in the 56 years before 1906. 80% (1?? = 14%) of the plate-motion moment accumulation rate is available for release in earthquakes. The historical ??M0/yr and the portion of the plate-motion moment accumulation rate available for release in earthquakes are used in a seismic cycle model to estimate the rate of seismic activity in the twenty-first century. High and low rates of future seismic activity are both permissible given the range of possible seismic-cycle recurrence times T and the uncertainties in the historical ??M0 and in the percentage of plate motion available for release in earthquakes. If the historical seismic moment rate is not greater than the estimated 2.68 X 1018 N-m/yr and the percentage of the plate-motion moment accumulation available for release in earthquakes is not less than the estimated 80%, then for all T, the rate of seismic moment release from now until the next 1906-sized shock will be comparable to the rate from 1836 to 1905 when M 6 1/2 shocks occurred every 15 to 20 years.

  3. FIP BIAS EVOLUTION IN A DECAYING ACTIVE REGION

    SciTech Connect

    Baker, D.; Yardley, S. L.; Driel-Gesztelyi, L. van; Long, D. M.; Green, L. M.; Brooks, D. H.; Démoulin, P.

    2015-04-01

    Solar coronal plasma composition is typically characterized by first ionization potential (FIP) bias. Using spectra obtained by Hinode’s EUV Imaging Spectrometer instrument, we present a series of large-scale, spatially resolved composition maps of active region (AR)11389. The composition maps show how FIP bias evolves within the decaying AR during the period 2012 January 4–6. Globally, FIP bias decreases throughout the AR. We analyzed areas of significant plasma composition changes within the decaying AR and found that small-scale evolution in the photospheric magnetic field is closely linked to the FIP bias evolution observed in the corona. During the AR’s decay phase, small bipoles emerging within supergranular cells reconnect with the pre-existing AR field, creating a pathway along which photospheric and coronal plasmas can mix. The mixing timescales are shorter than those of plasma enrichment processes. Eruptive activity also results in shifting the FIP bias closer to photospheric in the affected areas. Finally, the FIP bias still remains dominantly coronal only in a part of the AR’s high-flux density core. We conclude that in the decay phase of an AR’s lifetime, the FIP bias is becoming increasingly modulated by episodes of small-scale flux emergence, i.e., decreasing the AR’s overall FIP bias. Our results show that magnetic field evolution plays an important role in compositional changes during AR development, revealing a more complex relationship than expected from previous well-known Skylab results showing that FIP bias increases almost linearly with age in young ARs.

  4. Reverse transcription-polymerase chain reaction detection of transcribed sequences on human chromosome 21

    SciTech Connect

    Cheng, J.F.; Zhu, Y. )

    1994-03-15

    Seventy-four pairs of oligonucleotides derived from sequence-tagged sites (STSs) on the long arm of human chromosome 21, specifically from bands 21q22.1 to 21q22.3, were used in reverse transcription-polymerase chain reactions (RT-PCR) to detect the presence of expressed sequences in a fetal brain. These STSs included 69 that had not been related to transcribed sequences and 5 that had detected two known genes and three previously isolated cDNA clones. Of the 69 STSs analyzed in RT-PCR, 25 allowed amplification of specific cDNA fragments. The sizes of amplified cDNA fragments match those amplified from either human genomic DNA or somatic hybrid cells containing human chromosome 21. Of the 11 cDNA analyzed in Northern blot hybridizations, 6 hybridized to specific RNA species. The rapid screening for cDNA using previously mapped STSs has provided insight into the distribution of expressed sequences in this region of chromosome 21. Northern blot analysis of the amplified cDNA fragments has revealed interesting candidate genes in two disease loci. The marker D21S267 was previously mapped in the Down syndrome region of chromosome 21, and the marker D21S113 is closely linked to progressive myoclonus epilepsy. The cDNA fragments amplified using the primer sequences derived from D21S267 and D21S113 hybridized to 7- and 6.5-kb transcripts, respectively, which seems to express predominantly in brain. 37 refs., 3 figs., 1 tab.

  5. Structural and Functional Characterization of Noncoding Repetitive RNAs Transcribed in Stressed Human CellsD⃞

    PubMed Central

    Valgardsdottir, Rut; Chiodi, Ilaria; Giordano, Manuela; Cobianchi, Fabio; Riva, Silvano; Biamonti, Giuseppe

    2005-01-01

    Thermal and chemical stresses induce the formation in human cells of novel and transient nuclear structures called nuclear stress bodies (nSBs). These contain heat shock factor 1 (HSF-1) and a specific subset of pre-mRNA processing factors. Nuclear stress bodies are assembled on specific pericentromeric heterochromatic domains containing satellite III (SatIII) DNA. In response to stress, these domains change their epigenetic status from heterochromatin to euchromatin and are transcribed in poly-adenylated RNAs that remain associated with nSBs. In this article, we describe the cloning, sequencing, and functional characterization of these transcripts. They are composed of SatIII repeats and originate from the transcription of multiple sites within the SatIII arrays. Interestingly, the level of SatIII RNAs can be down-regulated both by antisense oligonucleotides and small interfering RNAs (siRNA). Knockdown of SatIII RNA by siRNAs requires the activity of Argonaute 2, a component of the RNA-induced silencing complex. Down-regulation of satellite III RNAs significantly affects the recruitment of RNA processing factors to nSBs without altering the association of HSF-1 with these structures nor the presence of acetylated histones within nSBs. Thus, satellite III RNAs have a major role in the formation of nSBs. PMID:15788562

  6. SIMULATION OF THE FORMATION OF A SOLAR ACTIVE REGION

    SciTech Connect

    Cheung, M. C. M.; Title, A. M.; Rempel, M.; Schuessler, M.

    2010-09-01

    We present a radiative magnetohydrodynamics simulation of the formation of an active region (AR) on the solar surface. The simulation models the rise of a buoyant magnetic flux bundle from a depth of 7.5 Mm in the convection zone up into the solar photosphere. The rise of the magnetic plasma in the convection zone is accompanied by predominantly horizontal expansion. Such an expansion leads to a scaling relation between the plasma density and the magnetic field strength such that B {proportional_to} rhov{sup 1/2}. The emergence of magnetic flux into the photosphere appears as a complex magnetic pattern, which results from the interaction of the rising magnetic field with the turbulent convective flows. Small-scale magnetic elements at the surface first appear, followed by their gradual coalescence into larger magnetic concentrations, which eventually results in the formation of a pair of opposite polarity spots. Although the mean flow pattern in the vicinity of the developing spots is directed radially outward, correlations between the magnetic field and velocity field fluctuations allow the spots to accumulate flux. Such correlations result from the Lorentz-force-driven, counterstreaming motion of opposite polarity fragments. The formation of the simulated AR is accompanied by transient light bridges between umbrae and umbral dots. Together with recent sunspot modeling, this work highlights the common magnetoconvective origin of umbral dots, light bridges, and penumbral filaments.

  7. Plasma Composition in a Sigmoidal Anemone Active Region

    NASA Astrophysics Data System (ADS)

    Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, L.; Green, L. M.; Steed, K.; Carlyle, J.

    2013-11-01

    Using spectra obtained by the EUV Imaging Spectrometer (EIS) instrument onboard Hinode, we present a detailed spatially resolved abundance map of an active region (AR)-coronal hole (CH) complex that covers an area of 359'' × 485''. The abundance map provides first ionization potential (FIP) bias levels in various coronal structures within the large EIS field of view. Overall, FIP bias in the small, relatively young AR is 2-3. This modest FIP bias is a consequence of the age of the AR, its weak heating, and its partial reconnection with the surrounding CH. Plasma with a coronal composition is concentrated at AR loop footpoints, close to where fractionation is believed to take place in the chromosphere. In the AR, we found a moderate positive correlation of FIP bias with nonthermal velocity and magnetic flux density, both of which are also strongest at the AR loop footpoints. Pathways of slightly enhanced FIP bias are traced along some of the loops connecting opposite polarities within the AR. We interpret the traces of enhanced FIP bias along these loops to be the beginning of fractionated plasma mixing in the loops. Low FIP bias in a sigmoidal channel above the AR's main polarity inversion line, where ongoing flux cancellation is taking place, provides new evidence of a bald patch magnetic topology of a sigmoid/flux rope configuration.

  8. Static and Impulsive Models of Solar Active Regions

    NASA Technical Reports Server (NTRS)

    Patsourakos, S.; Klimchuk, James A.

    2008-01-01

    The physical modeling of active regions (ARs) and of the global coronal is receiving increasing interest lately. Recent attempts to model ARs using static equilibrium models were quite successful in reproducing AR images of hot soft X-ray (SXR) loops. They however failed to predict the bright EUV warm loops permeating ARs: the synthetic images were dominated by intense footpoint emission. We demonstrate that this failure is due to the very weak dependence of loop temperature on loop length which cannot simultaneously account for both hot and warm loops in the same AR. We then consider time-dependent AR models based on nanoflare heating. We demonstrate that such models can simultaneously reproduce EUV and SXR loops in ARs. Moreover, they predict radial intensity variations consistent with the localized core and extended emissions in SXR and EUV AR observations respectively. We finally show how the AR morphology can be used as a gauge of the properties (duration, energy, spatial dependence, repetition time) of the impulsive heating.

  9. Active region emission measure distributions and implications for nanoflare heating

    SciTech Connect

    Cargill, P. J.

    2014-03-20

    The temperature dependence of the emission measure (EM) in the core of active regions coronal loops is an important diagnostic of heating processes. Observations indicate that EM(T) ∼ T{sup a} below approximately 4 MK, with 2 < a < 5. Zero-dimensional hydrodynamic simulations of nanoflare trains are used to demonstrate the dependence of a on the time between individual nanoflares (T{sub N} ) and the distribution of nanoflare energies. If T{sub N} is greater than a few thousand seconds, a < 3. For smaller values, trains of equally spaced nanoflares cannot account for the observed range of a if the distribution of nanoflare energies is either constant, randomly distributed, or a power law. Power law distributions where there is a delay between consecutive nanoflares proportional to the energy of the second nanoflare do lead to the observed range of a. However, T{sub N} must then be of the order of hundreds to no more than a few thousand seconds. If a nanoflare leads to the relaxation of a stressed coronal field to a near-potential state, the time taken to build up the required magnetic energy is thus too long to account for the EM measurements. Instead, it is suggested that a nanoflare involves the relaxation from one stressed coronal state to another, dissipating only a small fraction of the available magnetic energy. A consequence is that nanoflare energies may be smaller than previously envisioned.

  10. Active Region Emission Measure Distributions and Implications for Nanoflare Heating

    NASA Astrophysics Data System (ADS)

    Cargill, P. J.

    2014-03-01

    The temperature dependence of the emission measure (EM) in the core of active regions coronal loops is an important diagnostic of heating processes. Observations indicate that EM(T) ~ Ta below approximately 4 MK, with 2 < a < 5. Zero-dimensional hydrodynamic simulations of nanoflare trains are used to demonstrate the dependence of a on the time between individual nanoflares (TN ) and the distribution of nanoflare energies. If TN is greater than a few thousand seconds, a < 3. For smaller values, trains of equally spaced nanoflares cannot account for the observed range of a if the distribution of nanoflare energies is either constant, randomly distributed, or a power law. Power law distributions where there is a delay between consecutive nanoflares proportional to the energy of the second nanoflare do lead to the observed range of a. However, TN must then be of the order of hundreds to no more than a few thousand seconds. If a nanoflare leads to the relaxation of a stressed coronal field to a near-potential state, the time taken to build up the required magnetic energy is thus too long to account for the EM measurements. Instead, it is suggested that a nanoflare involves the relaxation from one stressed coronal state to another, dissipating only a small fraction of the available magnetic energy. A consequence is that nanoflare energies may be smaller than previously envisioned.

  11. Optical Properties of Active Regions in Terahertz Quantum Cascade Lasers

    NASA Astrophysics Data System (ADS)

    Dyksik, M.; Motyka, M.; Rudno-Rudziński, W.; Sęk, G.; Misiewicz, J.; Pucicki, D.; Kosiel, K.; Sankowska, I.; Kubacka-Traczyk, J.; Bugajski, M.

    2016-07-01

    In this work, AlGaAs/GaAs superlattice, with layers' sequence and compositions imitating the active and injector regions of a quantum cascade laser designed for emission in the terahertz spectral range, was investigated. Three independent absorption-like optical spectroscopy techniques were employed in order to study the band structure of the minibands formed within the conduction band. Photoreflectance measurements provided information about interband transitions in the investigated system. Common transmission spectra revealed, in the target range of intraband transitions, mainly a number of lines associated with the phonon-related processes, including two-phonon absorption. In contrast, differential transmittance realized by means of Fourier-transform spectroscopy was utilized to probe the confined states of the conduction band. The obtained energy separation between the second and third confined electron levels, expected to be predominantly contributing to the lasing, was found to be ~9 meV. The optical spectroscopy measurements were supported by numerical calculations performed in the effective mass approximation and XRD measurements for layers' width verification. The calculated energy spacings are in a good agreement with the experimental values.

  12. Plasma composition in a sigmoidal anemone active region

    SciTech Connect

    Baker, D.; Van Driel-Gesztelyi, L.; Green, L. M.; Carlyle, J.; Brooks, D. H.; Démoulin, P.; Steed, K.

    2013-11-20

    Using spectra obtained by the EUV Imaging Spectrometer (EIS) instrument onboard Hinode, we present a detailed spatially resolved abundance map of an active region (AR)-coronal hole (CH) complex that covers an area of 359'' × 485''. The abundance map provides first ionization potential (FIP) bias levels in various coronal structures within the large EIS field of view. Overall, FIP bias in the small, relatively young AR is 2-3. This modest FIP bias is a consequence of the age of the AR, its weak heating, and its partial reconnection with the surrounding CH. Plasma with a coronal composition is concentrated at AR loop footpoints, close to where fractionation is believed to take place in the chromosphere. In the AR, we found a moderate positive correlation of FIP bias with nonthermal velocity and magnetic flux density, both of which are also strongest at the AR loop footpoints. Pathways of slightly enhanced FIP bias are traced along some of the loops connecting opposite polarities within the AR. We interpret the traces of enhanced FIP bias along these loops to be the beginning of fractionated plasma mixing in the loops. Low FIP bias in a sigmoidal channel above the AR's main polarity inversion line, where ongoing flux cancellation is taking place, provides new evidence of a bald patch magnetic topology of a sigmoid/flux rope configuration.

  13. Oscillations in the Flaring Active Region NOAA 11272

    NASA Astrophysics Data System (ADS)

    Conde Cuellar, S. M.; Costa, J. E. R.; Cedeño Montaña, C. E.

    2016-11-01

    We studied waves seen during the class C1.9 flare that occurred in Active Region NOAA 11272 on SOL2011-08-17. We found standing waves with periods in the 9- and 19-minute band in six extreme ultraviolet (EUV) wavelengths of the SDO/AIA instrument. We succeeded in identifying the magnetic arc where the flare started and two neighbour loops that were disturbed in sequence. The analysed standing waves spatially coincide with these observed EUV loops. To study the wave characteristics along the loops, we extrapolated field lines from the line-of-sight magnetograms using the force-free approximation in the linear regime. We used atmosphere models to determine the mass density and temperature at each height of the loop. Then, we calculated the sound and Alfvén speeds using densities 108 ≲ ni ≲ 10^{17} cm^{-3} and temperatures 103 ≲ T ≲ 107 K. The brightness asymmetry in the observed standing waves resembles the Alfvén speed distribution along the loops, but the atmospheric model we used needs higher densities to explain the observed periods.

  14. THE ORIGIN OF NET ELECTRIC CURRENTS IN SOLAR ACTIVE REGIONS

    SciTech Connect

    Dalmasse, K.; Kliem, B.; Török, T.

    2015-09-01

    There is a recurring question in solar physics regarding whether or not electric currents are neutralized in active regions (ARs). This question was recently revisited using three-dimensional (3D) magnetohydrodynamic (MHD) numerical simulations of magnetic flux emergence into the solar atmosphere. Such simulations showed that flux emergence can generate a substantial net current in ARs. Other sources of AR currents are photospheric horizontal flows. Our aim is to determine the conditions for the occurrence of net versus neutralized currents with this second mechanism. Using 3D MHD simulations, we systematically impose line-tied, quasi-static, photospheric twisting and shearing motions to a bipolar potential magnetic field. We find that such flows: (1) produce both direct and return currents, (2) induce very weak compression currents—not observed in 2.5D—in the ambient field present in the close vicinity of the current-carrying field, and (3) can generate force-free magnetic fields with a net current. We demonstrate that neutralized currents are in general produced only in the absence of magnetic shear at the photospheric polarity inversion line—a special condition that is rarely observed. We conclude that  photospheric flows, as magnetic flux emergence, can build up net currents in the solar atmosphere, in agreement with recent observations. These results thus provide support for eruption models based on pre-eruption magnetic fields that possess a net coronal current.

  15. Magnetic Separatrix as the Source Region of the Plasma Supply for an Active-region Filament

    NASA Astrophysics Data System (ADS)

    Zou, P.; Fang, C.; Chen, P. F.; Yang, K.; Cao, Wenda

    2017-02-01

    Solar filaments can be formed via chromospheric evaporation followed by condensation in the corona or by the direct injection of cool plasma from the chromosphere to the corona. We here confirm with high-resolution Hα data observed by the 1.6 m New Solar Telescope of the Big Bear Solar Observatory on 2015 August 21 that an active-region filament is maintained by the continuous injection of cold chromospheric plasma. We find that the filament is rooted along a bright ridge in Hα, which corresponds to the intersection of a magnetic quasi-separatrix layer with the solar surface. This bright ridge consists of many small patches whose sizes are comparable to the width of the filament threads. It is found that upflows originate from the brighter patches of the ridge, whereas the downflows move toward the weaker patches of the ridge. The whole filament is composed of two opposite-direction streams, implying that longitudinal oscillations are not the only cause of the counterstreamings, and unidirectional siphon flows with alternative directions are another possibility.

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

    PubMed

    González, Angel; Mas, Albert

    2011-06-30

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

  17. Detection of multiple infections by Monocystis strains in a single earthworm host using ribosomal internal transcribed spacer sequence variation.

    PubMed

    Velavan, T P; Schulenburg, H; Michiels, N K

    2010-01-01

    Monocystis sp. are sporocyst-forming apicomplexan parasites common in seminal vesicles of the earthworm Lumbricus terrestris where they may account for temporary castration. This study describes the internal transcribed spacer (ITS) region of the ribosomal cistron of Monocystis sp. This region, including ITS-1, the 5.8S ribosomal RNA gene, and ITS-2, was PCR amplified, cloned, and sequenced for Monocystis sp. isolated from the seminal vesicles of several wild-caught L. terrestris. Our analysis revealed substantial polymorphisms, also within single host organisms, indicating intra-host diversity of parasites. These genetic markers are the first that allow distinction of Monocystis sp. genotypes, opening new avenues for the study of parasite diversity within and between hosts.

  18. Dynamics of radon activity due to earthquakes (by the example of Altai seismically active region)

    NASA Astrophysics Data System (ADS)

    Aptikaeva, O. I.; Shitov, A. V.

    2016-12-01

    The results of monitoring radon emanations in the territory of Gorno-Altaisk due to seismic activity and their influence on human health are considered. It is shown that the level of activity of subsoil radon in the vicinity of the fault zone in the territory of Gorno-Altaisk exceeds such a level recorded in Moscow by 3-4 times. There is ambiguity in the behavior of radon as a precursor of a seismic event. Some radon anomalies are synchronous with moments of earthquakes and others correspond to quiet periods. The radon activity is more closely associated with the earthquakes localized in the aftershock zone of the Chuya earthquake. This is assumed to be caused by the network of fluid-conducting channels within the active fault between this region and the observation station.

  19. A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.

    PubMed

    Svensson, J Peter; Shukla, Manu; Menendez-Benito, Victoria; Norman-Axelsson, Ulrika; Audergon, Pauline; Sinha, Indranil; Tanny, Jason C; Allshire, Robin C; Ekwall, Karl

    2015-06-01

    Nucleosome composition actively contributes to chromatin structure and accessibility. Cells have developed mechanisms to remove or recycle histones, generating a landscape of differentially aged nucleosomes. This study aimed to create a high-resolution, genome-wide map of nucleosome turnover in Schizosaccharomyces pombe. The recombination-induced tag exchange (RITE) method was used to study replication-independent nucleosome turnover through the appearance of new histone H3 and the disappearance or preservation of old histone H3. The genome-wide location of histones was determined by chromatin immunoprecipitation-exonuclease methodology (ChIP-exo). The findings were compared with diverse chromatin marks, including histone variant H2A.Z, post-translational histone modifications, and Pol II binding. Finally, genome-wide mapping of the methylation states of H4K20 was performed to determine the relationship between methylation (mono, di, and tri) of this residue and nucleosome turnover. Our analysis showed that histone recycling resulted in low nucleosome turnover in the coding regions of active genes, stably expressed at intermediate levels. High levels of transcription resulted in the incorporation of new histones primarily at the end of transcribed units. H4K20 was methylated in low-turnover nucleosomes in euchromatic regions, notably in the coding regions of long genes that were expressed at low levels. This transcription-dependent accumulation of histone methylation was dependent on the histone chaperone complex FACT. Our data showed that nucleosome turnover is highly dynamic in the genome and that several mechanisms are at play to either maintain or suppress stability. In particular, we found that FACT-associated transcription conserves histones by recycling them and is required for progressive H4K20 methylation.

  20. CONTRACTING AND ERUPTING COMPONENTS OF SIGMOIDAL ACTIVE REGIONS

    SciTech Connect

    Liu Rui; Wang Yuming; Liu Chang; Wang Haimin; Toeroek, Tibor

    2012-10-01

    It has recently been noted that solar eruptions can be associated with the contraction of coronal loops that are not involved in magnetic reconnection processes. In this paper, we investigate five coronal eruptions originating from four sigmoidal active regions, using high-cadence, high-resolution narrowband EUV images obtained by the Solar Dynamic Observatory (SDO). The magnitudes of the flares associated with the eruptions range from GOES class B to class X. Owing to the high-sensitivity and broad temperature coverage of the Atmospheric Imaging Assembly (AIA) on board SDO, we are able to identify both the contracting and erupting components of the eruptions: the former is observed in cold AIA channels as the contracting coronal loops overlying the elbows of the sigmoid, and the latter is preferentially observed in warm/hot AIA channels as an expanding bubble originating from the center of the sigmoid. The initiation of eruption always precedes the contraction, and in the energetically mild events (B- and C-flares), it also precedes the increase in GOES soft X-ray fluxes. In the more energetic events, the eruption is simultaneous with the impulsive phase of the nonthermal hard X-ray emission. These observations confirm that loop contraction is an integrated process in eruptions with partially opened arcades. The consequence of contraction is a new equilibrium with reduced magnetic energy, as the contracting loops never regain their original positions. The contracting process is a direct consequence of flare energy release, as evidenced by the strong correlation of the maximal contracting speed, and strong anti-correlation of the time delay of contraction relative to expansion, with the peak soft X-ray flux. This is also implied by the relationship between contraction and expansion, i.e., their timing and speed.

  1. Recurrent Jets Occurred Nearby Active Region NOAA 11931

    NASA Astrophysics Data System (ADS)

    Yu-kun, Hu; Zhi, Xu; Zhi-ke, Xue; Xiao-li, Yan; Yuan-deng, Shen; Ning, Wu; Jun, Lin

    2016-10-01

    According to the 171 Å observation of Solar Dynamics Observatory/Atmospheric Imaging Assembly (SDO/AIA) in 2013 December 25∼26, a series of homologous jets were continuously found in the southwestern area of the active region NOAA 11931, from which 12 typical jets were selected and studied in this paper. The magnetic field structures in most jets had an obviously untwisting motion in the ejection process, though a few of them didn't have. The process of some jets was divided into two phases: the slow ejection without untwisting, and the rapid untwisting ejection. Before some jets started, a bright point grew along the bottom of magnetic arcade, and extended from the end remote from the jet to the end proximate to the jet, and there were two parts of magnetic structures near the bottom of magnetic arcade untwisted simultaneously in the ejection process. During the final one jet, two magnetic arcades appeared successively in the southeastern end of the magnetic structure on the jet bottom, while a small magnetic loop emerged in the northwestern end. Compared with the line-of-sight magnetogram of SDO/Helioseismic and Magnetic Imager (SDO/HMI), in about 4 h before the first jet appeared, a pair of magnetic dipoles emerged from the bottom of magnetic structure, and continuously lifted during the whole jet event. Although overall the bottom magnetic field emerged before and after the 12 jets, but for each individual jet, the variation of the bottom magnetic field was different from one another: in some jets, the magnetic field near the magnetic arcade on the jet bottom exhibited both magnetic emergence and cancellation; but in other jets, the magnetic field near the jet bottom exhibited only an obvious emergence or cancellation.

  2. Diagnostics of Coronal Heating in Active-region Loops

    NASA Astrophysics Data System (ADS)

    Fludra, A.; Hornsey, C.; Nakariakov, V. M.

    2017-01-01

    Understanding coronal heating remains a central problem in solar physics. Many mechanisms have been proposed to explain how energy is transferred to and deposited in the corona. We summarize past observational studies that attempted to identify the heating mechanism and point out the difficulties in reproducing the observations of the solar corona from the heating models. The aim of this paper is to study whether the observed extreme ultraviolet (EUV) emission in individual coronal loops in solar active regions can provide constraints on the volumetric heating function, and to develop a diagnostic for the heating function for a subset of loops that are found close to static thermal equilibrium. We reconstruct the coronal magnetic field from Solar Dynamics Observatory/HMI data using a nonlinear force-free magnetic field model. We model selected loops using a one-dimensional stationary model, with a heating rate dependent locally on the magnetic field strength along the loop, and we calculate the emission from these loops in various EUV wavelengths for different heating rates. We present a method to measure a power index β defining the dependence of the volumetric heating rate EH on the magnetic field, {E}H\\propto {B}β , and controlling also the shape of the heating function: concentrated near the loop top, uniform and concentrated near the footpoints. The diagnostic is based on the dependence of the electron density on the index β. This method is free from the assumptions of the loop filling factor but requires spectroscopic measurements of the density-sensitive lines. The range of applicability for loops of different length and heating distributions is discussed, and the steps to solving the coronal heating problem are outlined.

  3. The SMM UV observations of Active Region 5395

    NASA Technical Reports Server (NTRS)

    Drake, Stephen A.; Gurman, Joseph B.

    1989-01-01

    The Ultraviolet Spectrometer and Polarimeter (UVSP) on the Solar Maximum Mission (SMM) spacecraft was used extensively to study the spatial morphology and time variability of solar active regions in the far UV (at approx. wavelength of 1370 A) since July 1985. The normal spatial resolution of UVSP observations in this 2nd-order mode is 10 sec., and the highest temporal resolution is 64 milliseconds. To make a full-field, 4 min. by 4 min. image this wavelength using 5 sec. raster steps takes about 3 minutes. UVSP can also make observations of the Sun at approx. wavelength of 2790 with 3 sec. spatial resolution when operated in its 1st-order mode; a full-field image at this wavelength (a so-called SNEW image) takes about 8 minutes. UVSP made thousands of observations (mostly in 2nd-order) of AR 5395 during its transit across the visible solar hemisphere (from 7 to 19 March, inclusive). During this period, UVSP's duty cycle for observing AR 5395 was roughly 40 percent, with the remaining 60 percent of the time being fairly evenly divided between aeronomy studies of the Earth's atmosphere and dead time due to Earth occultation of the Sun. UVSP observed many of the flares tagged to AR 5395, including 26 GOES M-level flares and 3 X-level flares, one of which produced so much UV emission that the safety software of UVSP turned off the detector to avoid damage due to saturation. Images and light curves of some of the more spectacular of the AR 5395 events are presented.

  4. Evidence of Twisted Flux-Tube Emergence in Active Regions

    NASA Astrophysics Data System (ADS)

    Poisson, M.; Mandrini, C. H.; Démoulin, P.; López Fuentes, M.

    2015-03-01

    Elongated magnetic polarities are observed during the emergence phase of bipolar active regions (ARs). These extended features, called magnetic tongues, are interpreted as a consequence of the azimuthal component of the magnetic flux in the toroidal flux-tubes that form ARs. We develop a new systematic and user-independent method to identify AR tongues. Our method is based on determining and analyzing the evolution of the AR main polarity inversion line (PIL). The effect of the tongues is quantified by measuring the acute angle [ τ] between the orientation of the PIL and the direction orthogonal to the AR main bipolar axis. We apply a simple model to simulate the emergence of a bipolar AR. This model lets us interpret the effect of magnetic tongues on parameters that characterize ARs ( e.g. the PIL inclination and the tilt angles, and their evolution). In this idealized kinematic emergence model, τ is a monotonically increasing function of the twist and has the same sign as the magnetic helicity. We systematically apply our procedure to a set of bipolar ARs (41 ARs) that were observed emerging in line-of-sight magnetograms over eight years. For most of the cases studied, the tongues only have a small influence on the AR tilt angle since tongues have a much lower magnetic flux than the more concentrated main polarities. From the observed evolution of τ, corrected for the temporal evolution of the tilt angle and its final value when the AR is fully emerged, we estimate the average number of turns in the subphotospherically emerging flux-rope. These values for the 41 observed ARs are below unity, except for one. This indicates that subphotospheric flux-ropes typically have a low amount of twist, i.e. highly twisted flux-tubes are rare. Our results demonstrate that the evolution of the PIL is a robust indicator of the presence of tongues and constrains the amount of twist in emerging flux-tubes.

  5. [Integration of activities of regional hospitals and territorial medical institutions].

    PubMed

    Murtazin, Z Ia; Blokhin, A B

    2000-01-01

    Medical and economic efficiency of regional therapeutic and prophylactic institutions is to develop in integration with therapeutic and prophylactic institutions of administrative territories of a subject of the federation, which necessitates modifications in the functions and organizational structure of organization and methodology departments of regional, central, and municipal hospitals.

  6. The Maximum Free Magnetic Energy Allowed in a Solar Active Region

    NASA Technical Reports Server (NTRS)

    Moore, Ronald L.; Falconer, David A.

    2009-01-01

    Two whole-active-region magnetic quantities that can be measured from a line-of-sight magnetogram are (sup L) WL(sub SG), a gauge of the total free energy in an active region's magnetic field, and sup L(sub theta), a measure of the active region's total magnetic flux. From these two quantities measured from 1865 SOHO/MDI magnetograms that tracked 44 sunspot active regions across the 0.5 R(sub Sun) central disk, together with each active region's observed production of CMEs, X flares, and M flares, Falconer et al (2009, ApJ, submitted) found that (1) active regions have a maximum attainable free magnetic energy that increases with the magnetic size (sup L) (sub theta) of the active region, (2) in (Log (sup L)WL(sub SG), Log(sup L) theta) space, CME/flare-productive active regions are concentrated in a straight-line main sequence along which the free magnetic energy is near its upper limit, and (3) X and M flares are restricted to large active regions. Here, from (a) these results, (b) the observation that even the greatest X flares produce at most only subtle changes in active region magnetograms, and (c) measurements from MSFC vector magnetograms and from MDI line-of-sight magnetograms showing that practically all sunspot active regions have nearly the same area-averaged magnetic field strength: =- theta/A approximately equal to 300 G, where theta is the active region's total photospheric flux of field stronger than 100 G and A is the area of that flux, we infer that (1) the maximum allowed ratio of an active region's free magnetic energy to its potential-field energy is 1, and (2) any one CME/flare eruption releases no more than a small fraction (less than 10%) of the active region's free magnetic energy. This work was funded by NASA's Heliophysics Division and NSF's Division of Atmospheric Sciences.

  7. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae

    PubMed Central

    Azvolinsky, Anna; Giresi, Paul G.; Lieb, Jason D.; Zakian, Virginia A.

    2009-01-01

    SUMMARY Replication forks face multiple obstacles that slow their progression. By two-dimensional gel analysis, yeast forks pause at stable DNA protein complexes, and this pausing is greatly increased in the absence of the Rrm3 helicase. We used a genome wide approach to identify 96 sites of very high DNA polymerase binding in wild type cells. Most of these binding sites were not previously identified pause sites. Rather, the most highly represented genomic category among high DNA polymerase binding sites was the open reading frames (ORFs) of highly transcribed RNA polymerase II genes. Twice as many pause sites were identified in rrm3 compared to wild type cells as pausing in this strain occurred at both highly transcribed RNA polymerase II genes and the previously identified protein DNA complexes. ORFs of highly transcribed RNA polymerase II genes are the first class of natural pause sites that are not exacerbated in rrm3 cells. PMID:19560424

  8. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer

    PubMed Central

    Ruegger, Paul M.; Clark, Robin T.; Weger, John R.; Braun, Jonathan; Borneman, James

    2014-01-01

    Current high throughput sequencing (HTS) methods are limited in their ability to resolve bacteria at or below the genus level. While the impact of this limitation may be relatively minor in whole-community analyses, it constrains the use of HTS as a tool for identifying and examining individual bacteria of interest. The limited resolution is a consequence of both short read lengths and insufficient sequence variation within the commonly targeted variable regions of the small-subunit rRNA (SSU) gene. The goal of this work was to improve the resolving power of bacterial HTS. We developed an assay targeting the hypervariable rRNA internal transcribed spacer (ITS) region residing between the SSU and large-subunit (LSU) rRNA genes. Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. This report presents a new HTS method for analyzing bacterial composition with improved capabilities. The greater resolving power enabled by the ITS region arises from its high sequence variation across a wide range of bacterial taxa and an associated decrease in taxonomic heterogeneity within its OTUs. Although the method should be adaptable to any HTS platform, this report presents PCR primers, amplification parameters, and protocols for Illumina-based analyses. PMID:25034229

  9. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer.

    PubMed

    Ruegger, Paul M; Clark, Robin T; Weger, John R; Braun, Jonathan; Borneman, James

    2014-10-01

    Current high throughput sequencing (HTS) methods are limited in their ability to resolve bacteria at or below the genus level. While the impact of this limitation may be relatively minor in whole-community analyses, it constrains the use of HTS as a tool for identifying and examining individual bacteria of interest. The limited resolution is a consequence of both short read lengths and insufficient sequence variation within the commonly targeted variable regions of the small-subunit rRNA (SSU) gene. The goal of this work was to improve the resolving power of bacterial HTS. We developed an assay targeting the hypervariable rRNA internal transcribed spacer (ITS) region residing between the SSU and large-subunit (LSU) rRNA genes. Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. This report presents a new HTS method for analyzing bacterial composition with improved capabilities. The greater resolving power enabled by the ITS region arises from its high sequence variation across a wide range of bacterial taxa and an associated decrease in taxonomic heterogeneity within its OTUs. Although the method should be adaptable to any HTS platform, this report presents PCR primers, amplification parameters, and protocols for Illumina-based analyses.

  10. The Limit of Magnetic-Shear Energy in Solar Active Regions

    NASA Technical Reports Server (NTRS)

    Moore, Ronald L.; Falconer, David A.; Sterling, Alphonse C.

    2013-01-01

    It has been found previously, by measuring from active ]region magnetograms a proxy of the free energy in the active region fs magnetic field, (1) that there is a sharp upper limit to the free energy the field can hold that increases with the amount of magnetic field in the active region, the active region fs magnetic flux content, and (2) that most active regions are near this limit when their field explodes in a CME/flare eruption. That is, explosive active regions are concentrated in a main ]sequence path bordering the free ]energy ]limit line in (flux content, free ]energy proxy) phase space. Here we present evidence that specifies the underlying magnetic condition that gives rise to the free ]energy limit and the accompanying main sequence of explosive active regions. Using a suitable free energy proxy measured from vector magnetograms of 44 active regions, we find evidence that (1) in active regions at and near their free ]energy limit, the ratio of magnetic ]shear free energy to the non ]free magnetic energy the potential field would have is of order 1 in the core field, the field rooted along the neutral line, and (2) this ratio is progressively less in active regions progressively farther below their free ]energy limit. Evidently, most active regions in which this core ]field energy ratio is much less than 1 cannot be triggered to explode; as this ratio approaches 1, most active regions become capable of exploding; and when this ratio is 1, most active regions are compelled to explode.

  11. The Limit of Magnetic-Shear Energy in Solar Active Regions

    NASA Technical Reports Server (NTRS)

    Moore, Ronald; Falconer, David; Sterling, Alphonse

    2012-01-01

    It has been found previously, by measuring from active-region magnetograms a proxy of the free energy in the active region's magnetic field, (1) that there is a sharp upper limit to the free energy the field can hold that increases with the amount of magnetic field in the active region, the active region's magnetic flux content, and (2) that most active regions are near this limit when their field explodes in a coronal mass ejection/flare eruption. That is, explosive active regions are concentrated in a main-sequence path bordering the free-energy-limit line in (flux content, free-energy proxy) phase space. Here, we present evidence that specifies the underlying magnetic condition that gives rise to the free-energy limit and the accompanying main sequence of explosive active regions. Using a suitable free-energy proxy measured from vector magnetograms of 44 active regions, we find evidence that (1) in active regions at and near their free-energy limit, the ratio of magnetic-shear free energy to the non-free magnetic energy the potential field would have is of the order of one in the core field, the field rooted along the neutral line, and (2) this ratio is progressively less in active regions progressively farther below their free-energy limit. Evidently, most active regions in which this core-field energy ratio is much less than one cannot be triggered to explode; as this ratio approaches one, most active regions become capable of exploding; and when this ratio is one, most active regions are compelled to explode.

  12. Transcribed sequences in the human genome to be held in San Francisco, November 7 and 8, 1992. Final report, September 1, 1992--August 31, 1993

    SciTech Connect

    Gardiner, K.

    1993-11-01

    The Second International Workshop on the Identification of Transcribed Sequences was held in San Francisco on November 7--8, 1992. The purpose of the workshop was to discuss and evaluate techniques for developing a complete transcriptional map of the human genome. Such a map requires the positions, sequences, and expression patterns of all genes. This goal is being approached from two different directions, each with strengths and weaknesses. One method is to identify the transcribed sequences from genomic DNA of a given region; the other is to systematically sequence and map cDNAs. The cDNA approach yields sequence information rapidly, but mapping each cDNA is a technical challenge. In the first approach, the map locations of genomic sequences are known at the outset, and the challenge is to identify exons. The efficient construction of a transcriptional map will require a diverse array of techniques.

  13. Analysis of body calcium (regional changes in body calcium by in vivo neutron activation analysis)

    NASA Technical Reports Server (NTRS)

    Suki, W.; Johnson, P. C.; Leblanc, A.; Evans, H. J.

    1981-01-01

    The effect of space flight on urine and fecal calcium loss was documented during the three long-term Skylab flights. Neutron activation analysis was used to determine regional calcium loss. Various designs for regional analysis were investigated.

  14. Demographic and Regional Determinants of Participation in Specific Exercise Activities

    DTIC Science & Technology

    1988-03-28

    Health and Physical Readiness Program. Questionnaires included self-report measures of the frequency and duration of 10 common exercise activities and... exercise behavior was assessed as the estimated frequency and duration of participation in each of ten types of physical activity . The recall method of...acceptable 6 method in the present study (3). The physical activities were aerobic dance/ exercise class, baseball, basketball, bicycling, calisthenics

  15. Changes in regional activity are accompanied with changes in inter-regional connectivity during 4 weeks motor learning.

    PubMed

    Ma, Liangsuo; Wang, Binquan; Narayana, Shalini; Hazeltine, Eliot; Chen, Xiying; Robin, Donald A; Fox, Peter T; Xiong, Jinhu

    2010-03-08

    Structural equation modeling (SEM) and fMRI were used to test whether changes in the regional activity are accompanied by changes in the inter-regional connectivity as motor practice progresses. Ten healthy subjects were trained to perform finger movement task daily for 4 weeks. Three sessions of fMRI images were acquired within 4 weeks. The changes in inter-regional connectivity were evaluated by measuring the effective connectivity between the primary motor area (M1), supplementary motor area (SMA), dorsal premotor cortex (PMd), basal ganglia (BG), cerebellum (CB), and posterior ventrolateral prefrontal cortex (pVLPFC). The regional activities in M1 and SMA increased from pre-training to week 2 and decreased from week 2 to week 4. The inter-regional connectivity generally increased in strength (with SEM path coefficients becoming more positive or negative) as practice progressed. The increases in the strength of the inter-regional connectivity may reflect long-term reorganization of the skilled motor network. We suggest that the performance gain was achieved by dynamically tuning the inter-regional connectivity in the motor network.

  16. LOW-LATITUDE CORONAL HOLES, DECAYING ACTIVE REGIONS, AND GLOBAL CORONAL MAGNETIC STRUCTURE

    SciTech Connect

    Petrie, G. J. D.; Haislmaier, K. J.

    2013-10-01

    We study the relationship between decaying active-region magnetic fields, coronal holes, and the global coronal magnetic structure using Global Oscillations Network Group synoptic magnetograms, Solar TErrestrial RElations Observatory extreme-ultraviolet synoptic maps, and coronal potential-field source-surface models. We analyze 14 decaying regions and associated coronal holes occurring between early 2007 and late 2010, 4 from cycle 23 and 10 from cycle 24. We investigate the relationship between asymmetries in active regions' positive and negative magnetic intensities, asymmetric magnetic decay rates, flux imbalances, global field structure, and coronal hole formation. Whereas new emerging active regions caused changes in the large-scale coronal field, the coronal fields of the 14 decaying active regions only opened under the condition that the global coronal structure remained almost unchanged. This was because the dominant slowly varying, low-order multipoles prevented opposing-polarity fields from opening and the remnant active-region flux preserved the regions' low-order multipole moments long after the regions had decayed. Thus, the polarity of each coronal hole necessarily matched the polar field on the side of the streamer belt where the corresponding active region decayed. For magnetically isolated active regions initially located within the streamer belt, the more intense polarity generally survived to form the hole. For non-isolated regions, flux imbalance and topological asymmetry prompted the opposite to occur in some cases.

  17. Lightning activity and aerosols in the Mediterranean region

    NASA Astrophysics Data System (ADS)

    Proestakis, E.; Kazadzis, S.; Lagouvardos, K.; Kotroni, V.; Kazantzidis, A.

    2016-03-01

    In the framework of this study, the effect of aerosols on lightning activity has been investigated for the first time over the broader Mediterranean Sea. Atmospheric optical depth data retrieved by MODIS on board Aqua satellite and cloud to ground lightning activity data provided by ZEUS network operated by the National Observatory of Athens were analyzed for a time period spanning from 01/01/2005 up to 31/12/2013. The results indicate the importance of aerosols in lightning modulation. The mean aerosol optical depth (AOD) values of the days with lightning activity were found to be higher than the mean seasonal AOD in 90% of the under study domain. Furthermore, the increasing rate of lightning activity with increasing aerosol loading was found to be more pronounced during summertime and for AOD values up to 0.4. Additionally, the spatial analysis showed that the percentage of days with lightning activity during summertime is increasing with increasing AOD. Finally, time series showed similar temporal behavior between AOD seasonal anomalies and days with lightning activity differences. Both the spatial and temporal analysis showed that lightning activity is correlated to AOD, a characteristic consistent for all seasons.

  18. Seismic activity monitoring in the Izvorul Muntelui dam region

    NASA Astrophysics Data System (ADS)

    Borleanu, Felix; Otilia Placinta, Anca; Popa, Mihaela; Adelin Moldovan, Iren; Popescu, Emilia

    2016-04-01

    Earthquakes occurrences near the artificial water reservoirs are caused by stress variation due to the weight of water, weakness of fractures or faults and increasing of pore pressure in crustal rocks. In the present study we aim to investigate how Izvorul Muntelui dam, located in the Eastern Carpathians influences local seismicity. For this purpose we selected from the seismic bulletins computed within National Data Center of National Institute for Earth Physics, Romania, crustal events occurred between 984 and 2015 in a range of 0.3 deg around the artificial lake. Subsequently to improve the seismic monitoring of the region we applied a cross-correlation detector on the continuous recordings of Bicaz (BIZ) seismic stations. Besides the tectonic events we detected sources within this region that periodically generate artificial evens. We couldn't emphasize the existence of a direct correlation between the water level variations and natural seismicity of the investigated area.

  19. 50 CFR 216.120 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... over the 5-year period of the regulations in this subpart, (3) Aircraft flight test operations, and (4... Flight Activities § 216.120 Specified activity and specified geographical region. (a) Regulations in...

  20. 50 CFR 216.120 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... in this subpart, (3) Aircraft flight test operations, and (4) Helicopter operations from Vandenberg... Flight Activities § 216.120 Specified activity and specified geographical region. (a) Regulations in...

  1. 50 CFR 216.120 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... in this subpart, (3) Aircraft flight test operations, and (4) Helicopter operations from Vandenberg... Flight Activities § 216.120 Specified activity and specified geographical region. (a) Regulations in...

  2. 50 CFR 216.120 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... over the 5-year period of the regulations in this subpart, (3) Aircraft flight test operations, and (4... Flight Activities § 216.120 Specified activity and specified geographical region. (a) Regulations in...

  3. Synthetic Physical Interactions Map Kinetochore-Checkpoint Activation Regions

    PubMed Central

    Ólafsson, Guðjón; Thorpe, Peter H.

    2016-01-01

    The spindle assembly checkpoint (SAC) is a key mechanism to regulate the timing of mitosis and ensure that chromosomes are correctly segregated to daughter cells. The recruitment of the Mad1 and Mad2 proteins to the kinetochore is normally necessary for SAC activation. This recruitment is coordinated by the SAC kinase Mps1, which phosphorylates residues at the kinetochore to facilitate binding of Bub1, Bub3, Mad1, and Mad2. There is evidence that the essential function of Mps1 is to direct recruitment of Mad1/2. To test this model, we have systematically recruited Mad1, Mad2, and Mps1 to most proteins in the yeast kinetochore, and find that, while Mps1 is sufficient for checkpoint activation, recruitment of either Mad1 or Mad2 is not. These data indicate an important role for Mps1 phosphorylation in SAC activation, beyond the direct recruitment of Mad1 and Mad2. PMID:27280788

  4. Solar irradiance modulation by active regions from 1969 through 1980

    SciTech Connect

    Schatten, K.H.; Miller, N.; Sofia, S.; Oster, L.

    1982-01-01

    The solar irradiance variations resulting from sunspot deficits and facular excesses in emission have been calculated from 1969 through 1980. Agreement appears to exist between our calculations and the major features seen with the Nimbus 7 cavity pyrheliometer and with both the major and minor features detected by The Solar Maximum Mission ACRIM experiment. The 12-year irradiance variations we calculate suggest a larger variance with increased solar activity, and little change in the average irradiance with solar activity. The largest excursions over these 12 years show a 0.4% variation. Removal of the activity influences upon solar irradiance during the numerous rocket experiments observing the solar ''constant'' may allow a better value for this quantity to be determined.

  5. Coronal Hole-Active Region-Current Sheet (CHARCS) Association with Intense Interplanetary and Geomagnetic Activity

    NASA Technical Reports Server (NTRS)

    Gonzalez, W. D.; Tsurutani, B. T.; McIntosh, P. S.; Gonzalez, A. L.

    1996-01-01

    Intense geomagnetic storms (Dstactive regions(flares and/or filament eruptions) ocurring close to the streamer belt and to growing low altitude coronal holes. It is also shown that such type of coronal holes had a dual-peak solar cycle distribution during solar cycle 21, similar to that previously reported for the above mentioned interplanetary and geomagnetic phenomena.

  6. Reliable differentiation of Meyerozyma guilliermondii from Meyerozyma caribbica by internal transcribed spacer restriction fingerprinting

    PubMed Central

    2014-01-01

    Background Meyerozyma guilliermondii (anamorph Candida guilliermondii) and Meyerozyma caribbica (anamorph Candida fermentati) are closely related species of the genetically heterogenous M. guilliermondii complex. Conventional phenotypic methods frequently misidentify the species within this complex and also with other species of the Saccharomycotina CTG clade. Even the long-established sequencing of large subunit (LSU) rRNA gene remains ambiguous. We also faced similar problem during identification of yeast isolates of M. guilliermondii complex from indigenous bamboo shoot fermentation in North East India. There is a need for development of reliable and accurate identification methods for these closely related species because of their increasing importance as emerging infectious yeasts and associated biotechnological attributes. Results We targeted the highly variable internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and identified seven restriction enzymes through in silico analysis for differentiating M. guilliermondii from M. caribbica. Fifty five isolates of M. guilliermondii complex which could not be delineated into species-specific taxonomic ranks by API 20 C AUX and LSU rRNA gene D1/D2 sequencing were subjected to ITS-restriction fragment length polymorphism (ITS-RFLP) analysis. TaqI ITS-RFLP distinctly differentiated the isolates into M. guilliermondii (47 isolates) and M. caribbica (08 isolates) with reproducible species-specific patterns similar to the in silico prediction. The reliability of this method was validated by ITS1-5.8S-ITS2 sequencing, mitochondrial DNA RFLP and electrophoretic karyotyping. Conclusions We herein described a reliable ITS-RFLP method for distinct differentiation of frequently misidentified M. guilliermondii from M. caribbica. Even though in silico analysis differentiated other closely related species of M. guilliermondii complex from the above two species, it is yet to be confirmed by in vitro analysis using reference

  7. Magnetic field configuration in a flaring active region

    NASA Astrophysics Data System (ADS)

    Palacios, J.; Balmaceda, L. A.; Vieira, L. E.

    2015-10-01

    The Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) provides continuous monitoring of the Sun's vector magnetic field through full-disk photospheric data with both high cadence and high spatial resolution. Here we investigate the evolution of AR 11249 from March 6 to March 7, 2012. We make use of HMI Stokes imaging, SDO/SHARPs, the HMI magnetic field line-of-sight (LOS) maps and the transverse components of the magnetic field as well as LOS velocity maps in order to detect regions with significant flux emergence and/or cancellation. In addition, we apply the Local Correlation Tracking (LCT) technique to the total and signed magnetic flux data and derive maps of horizontal velocity. From this analysis, we were able to pinpoint localized shear regions (and a shear channel) where penumbrae and pore formation areas, with strong linear polarization signals, are stretched and squeezed, showing also important downflows and upflows. We have also utilized Hinode/SP data and compared them to the HMI-SHARPs and the HMI-Stokes spectrograms. The aforementioned shear channel seems to correspond well with the X-class flare main channel of March 7 2012, as observed in AIA/SDO 171, 304 and 1600 Å.

  8. 78 FR 23951 - Powder River Regional Coal Team Activities: Notice of Public Meeting in Casper, Wyoming

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-23

    ... management activities in the Powder River Coal Production Region. DATES: The RCT meeting will begin at 9 a.m... Bureau of Land Management Powder River Regional Coal Team Activities: Notice of Public Meeting in Casper, Wyoming AGENCY: Bureau of Land Management, Interior. ACTION: Notice of public meeting. SUMMARY: The...

  9. Development of MHD Wave Diagnostic and Models of Coronal Active Regions

    NASA Astrophysics Data System (ADS)

    Ofman, L.; Thompson, B. J.; Davila, J. M.

    2004-05-01

    We investigate the generation, propagation, and damping of MHD waves in active regions, with the goal to develop a diagnostic tool of active region structure, dynamics, and stability. We used 3D MHD model to study the generation and the propagation of EIT waves in a simple model of an active regions, and the interaction of EIT waves with the active region magnetic field. We model the oscillation of active region loops numerically using the 3D MHD model active regions. Such oscillations have been recently observed by TRACE. We use photospheric magnetograms as the boundary conditions for the magnetic field model, and construct an initial field using force-free extrapolation. Finite plasma temperature, density, and gravity are included in the model. We construct loop density structures in the model, guided by TRACE and EIT observations in the EUV. We demonstrate that by comparing the results of the MHD models of waves in an active region to observations we will be able to construct a diagnostic tool for the physical properties of the active regions, such as magnetic field and density structure.

  10. The Atlantic Canada-New England Region and Environment. A Learning Activity Packet.

    ERIC Educational Resources Information Center

    Maine Univ., Orono. New England - Atlantic Provinces - Quebec Center.

    In this Learning Activity Packet (LAP) students examine the geographic and ecological bases of the Eastern international region. The overall objective of activities is to help students comprehend the man-earth relationship concept. By studying this familiar relevant region students gain geographic knowledge and skills applicable to other areas.…

  11. 50 CFR 216.240 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Active Sonar Training (AFAST) § 216.240 Specified activity and specified geographical region. (a... Navy is only authorized if it occurs incidental to the use of the following mid-frequency active sonar (MFAS) sources, high frequency active sonar (HFAS) sources, explosive sonobuoys, or similar sources,...

  12. 50 CFR 216.240 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Active Sonar Training (AFAST) § 216.240 Specified activity and specified geographical region. (a... Navy is only authorized if it occurs incidental to the use of the following mid-frequency active sonar (MFAS) sources, high frequency active sonar (HFAS) sources, explosive sonobuoys, or similar sources,...

  13. Active-region plages and the Hyades anomaly?

    NASA Technical Reports Server (NTRS)

    Labonte, B. J.; Rose, J. A.

    1985-01-01

    The Hyades are known to differ in their photometric properties (Crawford 1969; Campbell 1984) and spectral properties (Rose 1984) from field stars of similar metal abundance. Using spectra of solar plages, it is demonstrated that the Hyades spectral anomalies are caused by excess emission from magnetic regions (plages) on the surfaces of these cluster stars. It is further speculated that the Hyades photometric anomalies arise from the same cause, but photometric data on solar plages necessary to resolve this issue are not available. The Pleiades stars and a few extreme emission stars show similar spectral anomalies, but of such magnitude to indicate that plages on Pleiades stars have higher surface brightnesses than on the sun and do not merely cover a larger fraction of the stars.

  14. Temperature and density structure of a recurring active region jet

    NASA Astrophysics Data System (ADS)

    Mulay, Sargam M.; Zanna, Giulio Del; Mason, Helen

    2017-01-01

    Aims: We present a study of a recurring jet observed on October 31, 2011 by the Atmosphereic Imaging Assembly (AIA) on board the Solar Dynamic Observatory, the X-ray Telescope (XRT) and EUV Imaging Spectrometer (EIS) on board Hinode. We discuss the physical parameters of the jet that are obtained using imaging and spectroscopic observations, such as density, differential emission measure, peak temperature, velocity, and filling factor. Methods: A differential emission measure (DEM) analysis was performed at the region of the jet spire and the footpoint using EIS observations and also by combining AIA and XRT observations. The resulting EIS DEM curves were compared to those obtained with AIA-XRT. The DEM curves were used to create synthetic spectra with the CHIANTI atomic database. The predicted total count rates for each AIA channel were compared with the observed count rates. The effects of varying elemental abundances and the temperature range for the DEM inversion were investigated. Spectroscopic diagnostics were used to obtain an electron number density distribution for the jet spire and the jet footpoint. Results: The plasma along the line of sight in the jet spire and jet footpoint was found to be peak at 2.0 MK (log T [K] = 6.3). We calculated electron densities using the Fe XII (λ186/λ195) line ratio in the region of the spire (Ne = 7.6 × 1010 cm-3) and the footpoint (1.1 × 1011 cm-3). The plane-of-sky velocity of the jet is found to be 524 km s-1. The resulting EIS DEM values are in good agreement with those obtained from AIA-XRT. The synthetic spectra contributing to each AIA channel confirms the multi-thermal nature of the AIA channels in both regions. There is no indication of high temperatures, such as emission from Fe XVII (λ254.87) (log T [K] = 6.75) seen in the jet spire. In the case of the jet footpoint, synthetic spectra predict weak contributions from Ca XVII (λ192.85) and Fe XVII (λ254.87). With further investigation, we confirmed

  15. Variation of the internal transcribed spacer 1 sequence within individual strains and among different strains of Neospora caninum.

    PubMed

    Gondim, Luis F P; Laski, Paul; Gao, Liying; McAllister, Milton M

    2004-02-01

    Small differences have been reported in the internal transcribed spacer 1 (ITS1) region among strains of Neospora caninum. We compared ITS1 sequences among 6 N. caninum strains analyzed in our laboratory, including 2 strains that have not been examined previously (NC-Illinois and NC-Bahia). Five sequences showed 100% similarity and also were identical to 7 of 11 sequences that were previously reported by others. In contrast, initial attempts to sequence the ITS1 of NC-Bahia generated 12 nucleotide differences compared with the other 5 strains, and several ambiguous bases. However, the single band containing the ITS1 region, as observed after electrophoresis on a 2% agarose gel, became divided into 2 distinct bands when reanalyzed using 5 or 10% polyacrylamide gel electrophoresis (PAGE), and the ITS1 within these separate bands were sequenced without ambiguity. The other 5 N. caninum strains were also reexamined using PAGE, and in each strain 2 distinct bands were discovered. In comparison, 2 strains of Toxoplasma gondii continued to show only 1 band when examined using PAGE. The ITS1 sequence of NC-Bahia, from Brazil, differs in several base pairs from those of North American and European strains of N. caninum. Intrastrain variation of the ITS1 region appears to be common in N. caninum, in contrast to T. gondii.

  16. MAG4 Versus Alternative Techniques for Forecasting Active-Region Flare Productivity

    NASA Technical Reports Server (NTRS)

    Falconer, David A.; Moore, Ronald L.; Barghouty, Abdulnasser F.; Khazanov, Igor

    2014-01-01

    MAG4 is a technique of forecasting an active region's rate of production of major flares in the coming few days from a free-magnetic-energy proxy. We present a statistical method of measuring the difference in performance between MAG4 and comparable alternative techniques that forecast an active region's major-flare productivity from alternative observed aspects of the active region. We demonstrate the method by measuring the difference in performance between the "Present MAG4" technique and each of three alternative techniques, called "McIntosh Active-Region Class," "Total Magnetic Flux," and "Next MAG4." We do this by using (1) the MAG4 database of magnetograms and major-flare histories of sunspot active regions, (2) the NOAA table of the major-flare productivity of each of 60 McIntosh active-region classes of sunspot active regions, and (3) five technique-performance metrics (Heidke Skill Score, True Skill Score, Percent Correct, Probability of Detection, and False Alarm Rate) evaluated from 2000 random two-by-two contingency tables obtained from the databases. We find that (1) Present MAG4 far outperforms both McIntosh Active-Region Class and Total Magnetic Flux, (2) Next MAG4 significantly outperforms Present MAG4, (3) the performance of Next MAG4 is insensitive to the forward and backward temporal windows used, in the range of one to a few days, and (4) forecasting from the free-energy proxy in combination with either any broad category of McIntosh active-region classes or any Mount Wilson active-region class gives no significant performance improvement over forecasting from the free-energy proxy alone (Present MAG4).

  17. The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

    PubMed Central

    Bintu, Lacramioara; Kopaczynska, Marta; Hodges, Courtney; Lubkowska, Lucyna; Kashlev, Mikhail; Bustamante, Carlos

    2011-01-01

    Upon transcription, histones can either detach from DNA or transfer behind the polymerase through a process believed to involve template looping. The details governing nucleosomal fate during transcription are not well understood. Our atomic force microscopy images of RNA polymerase II-nucleosome complexes confirm the presence of looped transcriptional intermediates and provide mechanistic insight into the histone-transfer process via the distribution of transcribed nucleosome positions. Significantly, we find that a fraction of the transcribed nucleosomes are remodeled to hexasomes, and that this fraction depends on the transcription elongation rate. A simple model involving the kinetic competition between transcription elongation, histone transfer, and histone-histone dissociation quantitatively rationalizes our observations and unifies results obtained with other polymerases. Factors affecting the relative magnitude of these processes provide the physical basis for nucleosomal fate during transcription and, therefore, for the regulation of gene expression. PMID:22081017

  18. On the Non-Kolmogorov Nature of Flare-productive Solar Active Regions

    NASA Astrophysics Data System (ADS)

    Mandage, Revati S.; McAteer, R. T. James

    2016-12-01

    A magnetic power spectral analysis is performed on 53 solar active regions, observed from 2011 August to 2012 July. Magnetic field data obtained from the Helioseismic and Magnetic Imager, inverted as Active Region Patches, are used to study the evolution of the magnetic power index as each region rotates across the solar disk. Active regions are classified based on the numbers and sizes of solar flares they produce in order to study the relationship between flare productivity and the magnetic power index. The choice of window size and inertial range plays a key role in determining the correct magnetic power index. The overall distribution of magnetic power indices has a range of 1.0-2.5. Flare-quiet regions peak at a value of 1.6. However, flare-productive regions peak at a value of 2.2. Overall, the histogram of the distribution of power indices of flare-productive active regions is well separated from flare-quiet active regions. Only 12% of flare-quiet regions exhibit an index greater than 2, whereas 90% of flare-productive regions exhibit an index greater than 2. Flare-quiet regions exhibit a high temporal variance (i.e., the index fluctuates between high and low values), whereas flare-productive regions maintain an index greater than 2 for several days. This shows the importance of including the temporal evolution of active regions in flare prediction studies, and highlights the potential of a 2-3 day prediction window for space weather applications.

  19. Atmospheric energetics in regions of intense convective activity

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.

    1977-01-01

    Synoptic-scale budgets of kinetic and total potential energy are computed using 3- and 6-h data at nine times from NASA's fourth Atmospheric Variability Experiment (AVE IV). Two intense squall lines occurred during the period. Energy budgets for areas that enclose regions of intense convection are shown to have systematic changes that relate to the life cycles of the convection. Some of the synoptic-scale energy processes associated with the convection are found to be larger than those observed in the vicinity of mature cyclones. Volumes enclosing intense convection are found to have large values of cross-contour conversion of potential to kinetic energy and large horizontal export of kinetic energy. Although small net vertical transport of kinetic energy is observed, values at individual layers indicate large upward transport. Transfer of kinetic energy from grid to subgrid scales of motion occurs in the volumes. Latent heat release is large in the middle and upper troposphere and is thought to be the cause of the observed cyclic changes in the budget terms. Total potential energy is found to be imported horizontally in the lower half of the atmosphere, transported aloft, and then exported horizontally. Although local changes of kinetic energy and total potential energy are small, interaction between volumes enclosing convection with surrounding larger volumes is quite large.

  20. Image patch analysis of sunspots and active regions. I. Intrinsic dimension and correlation analysis

    NASA Astrophysics Data System (ADS)

    Moon, Kevin R.; Li, Jimmy J.; Delouille, Véronique; De Visscher, Ruben; Watson, Fraser; Hero, Alfred O.

    2016-01-01

    Context. The flare productivity of an active region is observed to be related to its spatial complexity. Mount Wilson or McIntosh sunspot classifications measure such complexity but in a categorical way, and may therefore not use all the information present in the observations. Moreover, such categorical schemes hinder a systematic study of an active region's evolution for example. Aims: We propose fine-scale quantitative descriptors for an active region's complexity and relate them to the Mount Wilson classification. We analyze the local correlation structure within continuum and magnetogram data, as well as the cross-correlation between continuum and magnetogram data. Methods: We compute the intrinsic dimension, partial correlation, and canonical correlation analysis (CCA) of image patches of continuum and magnetogram active region images taken from the SOHO-MDI instrument. We use masks of sunspots derived from continuum as well as larger masks of magnetic active regions derived from magnetogram to analyze separately the core part of an active region from its surrounding part. Results: We find relationships between the complexity of an active region as measured by its Mount Wilson classification and the intrinsic dimension of its image patches. Partial correlation patterns exhibit approximately a third-order Markov structure. CCA reveals different patterns of correlation between continuum and magnetogram within the sunspots and in the region surrounding the sunspots. Conclusions: Intrinsic dimension has the potential to distinguish simple from complex active regions. These results also pave the way for patch-based dictionary learning with a view toward automatic clustering of active regions.

  1. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

    PubMed Central

    Chan, Wen-Ling; Yuo, Chung-Yee; Yang, Wen-Kuang; Hung, Shih-Ya; Chang, Ya-Sian; Chiu, Chien-Chih; Yeh, Kun-Tu; Huang, Hsien-Da; Chang, Jan-Gowth

    2013-01-01

    Pseudogenes, especially those that are transcribed, may not be mere genomic fossils, but their biological significance remains unclear. Postulating that in the human genome, as in animal models, pseudogenes may function as gene regulators through generation of endo-siRNAs (esiRNAs), antisense RNAs or RNA decoys, we performed bioinformatic and subsequent experimental tests to explore esiRNA-mediated mechanisms of pseudogene involvement in oncogenesis. A genome-wide survey revealed a partial retrotranscript pseudogene ψPPM1K containing inverted repeats capable of folding into hairpin structures that can be processed into two esiRNAs; these esiRNAs potentially target many cellular genes, including NEK8. In 41 paired surgical specimens, we found significantly reduced expression of two predicted ψPPM1K-specific esiRNAs, and the cognate gene PPM1K, in hepatocellular carcinoma compared with matched non-tumour tissues, whereas the expression of target gene NEK8 was increased in tumours. Additionally, NEK8 and PPM1K were downregulated in stably transfected ψPPM1K-overexpressing cells, but not in cells transfected with an esiRNA1-deletion mutant of ψPPM1K. Furthermore, expression of NEK8 in ψPPM1K-transfected cells demonstrated that NEK8 can counteract the growth inhibitory effects of ψPPM1K. These findings indicate that a transcribed pseudogene can exert tumour-suppressor activity independent of its parental gene by generation of esiRNAs that regulate human cell growth. PMID:23376929

  2. Characterization of local self-similarity and criticality in the solar active regions

    NASA Astrophysics Data System (ADS)

    Rosa, R. R.; Vats, H. O.; Ramos, F. M.; Zanandrea, A.; Rodrigues Neto, C.; Fernandes, F. C. R.; Bolzan, M. J. A.; Rempel, E. L.; Brito, R. C.; Vijaykumar, N. L.; Sawant, H. S.

    From solar radio burst data we computed wavelet transforms and frequency distribution for investigation of self-similar temporal variability and power-laws, as the fundamental conditions for characterization of dynamical criticality (self or forced) in the solar active regions. The main result indicates that, as for the global activity, the local coronal magnetic field, in millisecond time scales, can be in a critical state where the dynamics of solar active regions works as avalanches of many small intermittent particle acceleration events.

  3. An Active Region Model for Capturing Fractal Flow Patterns inUnsaturated Soils: Model Development

    SciTech Connect

    Liu, Hui-Hai; Zhang, R.; Bodvarsson, Gudmundur S.

    2005-06-11

    Preferential flow commonly observed in unsaturated soils allows rapid movement of solute from the soil surface or vadose zone to the groundwater, bypassing a significant volume of unsaturated soil and increasing the risk of groundwater contamination. A variety of evidence indicates that complex preferential patterns observed from fields are fractals. In this study, we developed a relatively simple active region model to incorporate the fractal flow pattern into the continuum approach. In the model, the flow domain is divided into active and inactive regions. Flow occurs preferentially in the active region (characterized by fractals), and inactive region is simply bypassed. A new constitutive relationship (the portion of the active region as a function of saturation) was derived. The validity of the proposed model is demonstrated by the consistency between field observations and the new constitutive relationship.

  4. On Heating the Sun's Corona by Magnetic Explosions: Feasibility in Active Regions and prospects for Quiet Regions and Coronal Holes

    NASA Technical Reports Server (NTRS)

    Moore, Ronald L.; Falconer, D. A.; Porter, Jason G.; Suess, Steven T.

    1999-01-01

    We build a case for the persistent strong coronal heating in active regions and the pervasive quasi-steady heating of the corona in quiet regions and coronal holes being driven in basically the same way as the intense transient heating in solar flares: by explosions of sheared magnetic fields in the cores of initially closed bipoles. We begin by summarizing the observational case for exploding sheared core fields being the drivers of a wide variety of flare events, with and without coronal mass ejections. We conclude that the arrangement of an event's flare heating, whether there is a coronal mass ejection, and the time and place of the ejection relative to the flare heating are all largely determined by four elements of the form and action of the magnetic field: (1) the arrangement of the impacted, interacting bipoles participating in the event, (2) which of these bipoles are active (have sheared core fields that explode) and which are passive (are heated by injection from impacted active bipoles), (3) which core field explodes first, and (4) which core-field explosions are confined within the closed field of their bipoles and which ejectively open their bipoles. We then apply this magnetic-configuration framework for flare heating to the strong coronal heating observed by the Yohkoh Soft X-ray Telescope in an active region with strongly sheared core fields observed by the MSFC vector magnetograph. All of the strong coronal heating is in continually microflaring sheared core fields or in extended loops rooted against the active core fields. Thus, the strong heating occurs in field configurations consistent with the heating being driven by frequent core-field explosions that are smaller but similar to those in confined flares and flaring arches. From analysis of the thermal and magnetic energetics of two selected core-field microflares and a bright extended loop, we find that (1) it is energetically feasible for the sheared core fields to drive all of the coronal

  5. THE FORMATION AND MAGNETIC STRUCTURES OF ACTIVE-REGION FILAMENTS OBSERVED BY NVST, SDO, AND HINODE

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Wang, J. C.; Xiang, Y. Y.; Kong, D. F.; Yang, L. H.; Pan, G. M.

    2015-08-15

    To better understand the properties of solar active-region filaments, we present a detailed study on the formation and magnetic structures of two active-region filaments in active region NOAA 11884 during a period of four days. It is found that the shearing motion of the opposite magnetic polarities and the rotation of the small sunspots with negative polarity play an important role in the formation of two active-region filaments. During the formation of these two active-region filaments, one foot of the filaments was rooted in a small sunspot with negative polarity. The small sunspot rotated not only around another small sunspot with negative polarity, but also around the center of its umbra. By analyzing the nonlinear force-free field extrapolation using the vector magnetic fields in the photosphere, twisted structures were found in the two active-region filaments prior to their eruptions. These results imply that the magnetic fields were dragged by the shearing motion between opposite magnetic polarities and became more horizontal. The sunspot rotation twisted the horizontal magnetic fields and finally formed the twisted active-region filaments.

  6. Triggering an Eruptive Flare by Emerging Flux in a Solar Active-Region Complex

    NASA Astrophysics Data System (ADS)

    Louis, Rohan E.; Kliem, Bernhard; Ravindra, B.; Chintzoglou, Georgios

    2015-12-01

    A flare and fast coronal mass ejection originated between solar active regions NOAA 11514 and 11515 on 2012 July 1 (SOL2012-07-01) in response to flux emergence in front of the leading sunspot of the trailing region 11515. Analyzing the evolution of the photospheric magnetic flux and the coronal structure, we find that the flux emergence triggered the eruption by interaction with overlying flux in a non-standard way. The new flux neither had the opposite orientation nor a location near the polarity inversion line, which are favorable for strong reconnection with the arcade flux under which it emerged. Moreover, its flux content remained significantly smaller than that of the arcade ({≈} 40 %). However, a loop system rooted in the trailing active region ran in part under the arcade between the active regions, passing over the site of flux emergence. The reconnection with the emerging flux, leading to a series of jet emissions into the loop system, caused a strong but confined rise of the loop system. This lifted the arcade between the two active regions, weakening its downward tension force and thus destabilizing the considerably sheared flux under the arcade. The complex event was also associated with supporting precursor activity in an enhanced network near the active regions, acting on the large-scale overlying flux, and with two simultaneous confined flares within the active regions.

  7. Regional vulnerability of the hippocampus to repeated motor activity deprivation.

    PubMed

    Faraji, Jamshid; Soltanpour, Nabiollah; Moeeini, Reza; Hosseini, Seyed Abedin; Pakdel, Shiva; Moharrerie, Alireza; Arjang, Kaveh; Soltanpour, Nasrin; Metz, Gerlinde A S

    2016-03-15

    Spontaneous vertical and horizontal exploratory movements are integral components of rodent behavior. Little is known, however, about the structural and functional consequences of restricted spontaneous exploration. Here, we report two experiments to probe whether restriction in vertical activity (rearing) in rats could induce neuro-hormonal and behavioral disturbances. Rearing movements in rats were deprived for 3h/day for 30 consecutive days by placing the animal into a circular tunnel task. Rats temporarily deprived of rearing behavior showed elevated plasma corticosterone levels but no detectable psychological distress and/or anxiety-related behavior within an elevated plus maze. However, rats emitted a greater number of 22-kHz ultrasonic vocalizations and spent significantly more time vocalizing than controls when deprived of their rearing behavior. Despite intact spatial performance within wet- and dry-land spatial tasks, rearing-deprived rats also exhibited a significant alteration in search strategies within both spatial tasks along with reduced volume and neuron number in the hippocampal subregion CA2. These data suggest a new approach to test the importance of free exploratory behavior in endocrine and structural manifestations. The results support a central role of the CA2 in spontaneous exploratory behavior and vulnerability to psychological stress.

  8. A note on chromospheric fine structure at active region polarity boundaries.

    NASA Technical Reports Server (NTRS)

    Prata, S. W.

    1971-01-01

    High resolution H-alpha filtergrams from Big Bear Solar Observatory reveal that some filamentary features in active regions have fine structure and hence magnetic field transverse to the gross structure and the zero longitudinal field line. These features are distinct from the usual active region filament, in which fine structure, magnetic field, and filament are all parallel to the zero longitudinal field line. The latter occur on boundaries between regions of weaker fields, while the former occur at boundaries between regions of stronger field.

  9. Short-term disruption in regional left ventricular electrical conduction patterns increases interstitial matrix metalloproteinase activity

    PubMed Central

    Zavadzkas, Juozas A.; Rivers, William T.; McLean, Julie E.; Chang, Eileen I.; Bouges, Shenikqua; Matthews, Robert G.; Koval, Christine N.; Stroud, Robert E.; Spinale, Francis G.

    2010-01-01

    Increased matrix metalloproteinase (MMP) abundance occurs with adverse left ventricular (LV) remodeling in a number of cardiac disease states, including those induced by long-standing arrhythmias. However, whether regionally contained aberrant electrical activation of the LV, with consequent dyskinesia, alters interstitial MMP activation remained unknown. Electrical activation of the LV of pigs (n = 10, 30–35 kg) was achieved by pacing (150 beats/min) at left atrial and LV sites such that normal atrioventricular activation (60 min) was followed by regional early LV activation for 60 min within 1.5 cm of the paced site and restoration of normal atrioventricular pacing for 120 min. Regional shortening (piezoelectric crystals) and interstitial MMP activity (microdialysis with MMP fluorogenic substrate) at the LV pacing site and a remote LV site were monitored at 30-min intervals. During aberrant electrical stimulation, interstitial MMP activity at the paced site was increased (122 ± 4%) compared with the remote region (100%, P < 0.05). Restoration of atrioventricular pacing after the 60-min period of aberrant electrical activation normalized segmental shortening (8.5 ± 0.4%), but MMP activity remained elevated (121 ± 6%, P < 0.05). This study demonstrates that despite the restoration of mechanical function, disturbances in electrical conduction, in and of itself, can cause acute increases in regional in vivo MMP activation and, therefore, contribute to myocardial remodeling. PMID:20472759

  10. Short-term disruption in regional left ventricular electrical conduction patterns increases interstitial matrix metalloproteinase activity.

    PubMed

    Mukherjee, Rupak; Zavadzkas, Juozas A; Rivers, William T; McLean, Julie E; Chang, Eileen I; Bouges, Shenikqua; Matthews, Robert G; Koval, Christine N; Stroud, Robert E; Spinale, Francis G

    2010-07-01

    Increased matrix metalloproteinase (MMP) abundance occurs with adverse left ventricular (LV) remodeling in a number of cardiac disease states, including those induced by long-standing arrhythmias. However, whether regionally contained aberrant electrical activation of the LV, with consequent dyskinesia, alters interstitial MMP activation remained unknown. Electrical activation of the LV of pigs (n = 10, 30-35 kg) was achieved by pacing (150 beats/min) at left atrial and LV sites such that normal atrioventricular activation (60 min) was followed by regional early LV activation for 60 min within 1.5 cm of the paced site and restoration of normal atrioventricular pacing for 120 min. Regional shortening (piezoelectric crystals) and interstitial MMP activity (microdialysis with MMP fluorogenic substrate) at the LV pacing site and a remote LV site were monitored at 30-min intervals. During aberrant electrical stimulation, interstitial MMP activity at the paced site was increased (122 +/- 4%) compared with the remote region (100%, P < 0.05). Restoration of atrioventricular pacing after the 60-min period of aberrant electrical activation normalized segmental shortening (8.5 +/- 0.4%), but MMP activity remained elevated (121 +/- 6%, P < 0.05). This study demonstrates that despite the restoration of mechanical function, disturbances in electrical conduction, in and of itself, can cause acute increases in regional in vivo MMP activation and, therefore, contribute to myocardial remodeling.

  11. Novel mid-infrared lasers with compressively strained InAsSb active regions

    SciTech Connect

    Kurtz, S.R.; Biefeld, R.M.; Allerman, A.A.

    1997-02-01

    Mid-infrared lasers grown by MOCVD with AlAsSb claddings and strained InAsSb active regions are reported. A 3.8--3.9 {micro}m injection laser with a pseudomorphic InAsSb multiple quantum well active region lased at 210 K under pulsed operation. A semi-metal layer acts as an internal electron source for the injection laser. An optically pumped laser with an InAsSb/InAsP strained-layer superlattice active region was demonstrated at 3.7 {micro}m, 240 K.

  12. Development of a PCR assay based on the 16S-23S rDNA internal transcribed spacer for identification of strictly anaerobic bacterium Zymophilus.

    PubMed

    Felsberg, Jurgen; Jelínková, Markéta; Kubizniaková, Petra; Matoulková, Dagmar

    2015-06-01

    PCR-primers were designed for identification of strictly anaerobic bacteria of the genus Zymophilus based on genus-specific sequences of the 16S-23S rDNA internal transcribed spacer region. The specificity of the primers was tested against 37 brewery-related non-target microorganisms that could potentially occur in the same brewery specimens. None DNA was amplified from any of the non-Zymophilus strains tested including genera from the same family (Pectinatus, Megasphaera, Selenomonas), showing thus 100% specificity. PCR assay developed in this study allows an extension of the spectra of detected beer spoilage microorganisms in brewery laboratories.

  13. Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

    PubMed

    Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

    2016-02-01

    Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili.

  14. Leishmania major: genetic heterogeneity of Iranian isolates by single-strand conformation polymorphism and sequence analysis of ribosomal DNA internal transcribed spacer.

    PubMed

    Tashakori, Mahnaz; Mahnaz, Tashakori; Kuhls, Katrin; Katrin, Kuhls; Al-Jawabreh, Amer; Amer, Al-Jawabreh; Mauricio, Isabel L; Isabel, Mauricio; Schönian, Gabriele; Gabriele, Schönian; Farajnia, Safar; Safar, Farajnia; Alimohammadian, Mohammad Hossein; Hossein, Alimohammadian Mohammad

    2006-04-01

    Protozoan parasites of Leishmania major are the causative agents of cutaneous leishmaniasis in different parts of Iran. We applied PCR-based methods to analyze L. major parasites isolated from patients with active lesions from different geographic areas in Iran in order to understand DNA polymorphisms within L. major species. Twenty-four isolates were identified as L. major by RFLP analysis of the ribosomal internal transcribed spacer 1 (ITS1) amplicons. These isolates were further studied by single-strand conformation polymorphism (SSCP) analysis and sequencing of ITS1 and ITS2. Data obtained from SSCP analysis of the ITS1 and ITS2 loci revealed three and four different patterns among all studied samples, respectively. Sequencing of ITS1 and ITS2 confirmed the results of SSCP analysis and showed the potential of the PCR-SSCP method for assessing genetic heterogeneity within L. major. Different patterns in ITS1 were due to substitution of one nucleotide, whereas in ITS2 the changes were defined by variation in the number of repeats in two polymorphic microsatellites. In total five genotypic groups LmA, LmB, LmC, LmD and LmE were identified among L. major isolates. The most frequent genotype, LmA, was detected in isolates collected from different endemic areas of cutaneous leishmaniasis in Iran. Genotypes LmC, LmD and LmE were found only in the new focus of CL in Damghan (Semnan province) and LmB was identified exclusively among isolates of Kashan focus (Isfahan province). The distribution of genetic polymorphisms suggests the existence of distinct endemic regions of L. major in Iran.

  15. Mapping brain region activity during chewing: a functional magnetic resonance imaging study.

    PubMed

    Onozuka, M; Fujita, M; Watanabe, K; Hirano, Y; Niwa, M; Nishiyama, K; Saito, S

    2002-11-01

    Mastication has been suggested to increase neuronal activities in various regions of the human brain. However, because of technical difficulties, the fine anatomical and physiological regions linked to mastication have not been fully elucidated. Using functional magnetic resonance imaging during cycles of rhythmic gum-chewing and no chewing, we therefore examined the interaction between chewing and brain regional activity in 17 subjects (aged 20-31 years). In all subjects, chewing resulted in a bilateral increase in blood oxygenation level-dependent (BOLD) signals in the sensorimotor cortex, supplementary motor area, insula, thalamus, and cerebellum. In addition, in the first three regions, chewing of moderately hard gum produced stronger BOLD signals than the chewing of hard gum. However, the signal was higher in the cerebellum and not significant in the thalamus, respectively. These results suggest that chewing causes regional increases in brain neuronal activities which are related to biting force.

  16. Active region 11748: Recurring X-class flares, large scale dimmings and waves.

    NASA Astrophysics Data System (ADS)

    Davey, Alisdair R.; Malanushenko, Anna; McIntosh, Scott W.

    2014-06-01

    AR 11748 was a relatively compact active region that crossed the solar disk between 05/14/2013 and 05/26/2013. Despite its size it produced a number X-class flares, and global scale eruptive events that were captured by the SDO Feature Finding Team's (FFT) Dimming Region Detector. Using the results of this module and other FFT modules, we present an analysis of the this AR region and investigate why it was so globally impactful.

  17. HELIOSEISMOLOGY OF PRE-EMERGING ACTIVE REGIONS. II. AVERAGE EMERGENCE PROPERTIES

    SciTech Connect

    Birch, A. C.; Braun, D. C.; Leka, K. D.; Barnes, G.; Javornik, B.

    2013-01-10

    We report on average subsurface properties of pre-emerging active regions as compared to areas where no active region emergence was detected. Helioseismic holography is applied to samples of the two populations (pre-emergence and without emergence), each sample having over 100 members, which were selected to minimize systematic bias, as described in Leka et al. We find that there are statistically significant signatures (i.e., difference in the means of more than a few standard errors) in the average subsurface flows and the apparent wave speed that precede the formation of an active region. The measurements here rule out spatially extended flows of more than about 15 m s{sup -1} in the top 20 Mm below the photosphere over the course of the day preceding the start of visible emergence. These measurements place strong constraints on models of active region formation.

  18. Waste production and regional growth of marine activities an econometric model.

    PubMed

    Bramati, Maria Caterina

    2016-11-15

    Coastal regions are characterized by intense human activity and climatic pressures, often intensified by competing interests in the use of marine waters. To assess the effect of public spending on the regional economy, an econometric model is here proposed. Not only are the regional investment and the climatic risks included in the model, but also variables related to the anthropogenic pressure, such as population, economic activities and waste production. Feedback effects of economic and demographic expansion on the pollution of coastal areas are also considered. It is found that dangerous waste increases with growing shipping and transportation activities and with growing population density in non-touristic coastal areas. On the other hand, the amount of non-dangerous wastes increases with marine mining, defense and offshore energy production activities. However, lower waste production occurs in areas where aquaculture and touristic industry are more exploited, and accompanied by increasing regional investment in waste disposal.

  19. Lymphocyte Activation Dynamics Is Shaped by Hereditary Components at Chromosome Region 17q12-q21

    PubMed Central

    Carreras-Sureda, Amado; Rubio-Moscardo, Fanny; Olvera, Alex; Argilaguet, Jordi; Kiefer, Kerstin; Mothe, Beatriz; Meyerhans, Andreas; Brander, Christian

    2016-01-01

    Single nucleotide polymorphisms (SNPs) located in the chromosome region 17q12-q21 are risk factors for asthma. Particularly, there are cis-regulatory haplotypes within this region that regulate differentially the expression levels of ORMDL3, GSDMB and ZPBP2 genes. Remarkably, ORMDL3 has been shown to modulate lymphocyte activation parameters in a heterologous expression system. In this context, it has been shown that Th2 and Th17 cytokine production is affected by SNPs in this region. Therefore, we aim to assess the impact of hereditary components within region 17q12-q21 on the activation profile of human T lymphocytes, focusing on the haplotype formed by allelic variants of SNPs rs7216389 and rs12936231. We measured calcium influx and activation markers, as well as the proliferation rate upon T cell activation. Haplotype-dependent differences in mRNA expression levels of IL-2 and INF-γ were observed at early times after activation. In addition, the allelic variants of these SNPs impacted on the extent of calcium influx in resting lymphocytes and altered proliferation rates in a dose dependent manner. As a result, the asthma risk haplotype carriers showed a lower threshold of saturation during activation. Finally, we confirmed differences in activation marker expression by flow cytometry using phytohemagglutinin, a strong polyclonal stimulus. Altogether, our data suggest that the genetic component of pro-inflammatory pathologies present in this chromosome region could be explained by different T lymphocyte activation dynamics depending on individual allelic heredity. PMID:27835674

  20. Active region coronal loops observed at the total solar eclipse of February 16, 1980

    NASA Astrophysics Data System (ADS)

    Hanaoka, Yoishiro; Kurokawa, Hiroki; Saito, Sumisaburo

    Coronal loop structures above an active region observed at the total eclipse of February 16, 1980 in Kenya are analyzed. Temperatures and densities of the loops are derived from three monochromatic images of Fe X λ6374 (1×106K or cool corona), Fe XIV λ5303 (2×106K or hot corona), and continuum. These monochromatic images are processed for the analyses, and pure images of the active region corona are obtained. Results from a morphological diagnostics are presented.

  1. Dynamic activation of frontal, parietal, and sensory regions underlying anticipatory visual spatial attention.

    PubMed

    Simpson, Gregory V; Weber, Darren L; Dale, Corby L; Pantazis, Dimitrios; Bressler, Steven L; Leahy, Richard M; Luks, Tracy L

    2011-09-28

    Although it is well established that multiple frontal, parietal, and occipital regions in humans are involved in anticipatory deployment of visual spatial attention, less is known about the electrophysiological signals in each region across multiple subsecond periods of attentional deployment. We used MEG measures of cortical stimulus-locked, signal-averaged (event-related field) activity during a task in which a symbolic cue directed covert attention to the relevant location on each trial. Direction-specific attention effects occurred in different cortical regions for each of multiple time periods during the delay between the cue and imperative stimulus. A sequence of activation from V1/V2 to extrastriate, parietal, and frontal regions occurred within 110 ms after cue, possibly related to extraction of cue meaning. Direction-specific activations ∼300 ms after cue in frontal eye field (FEF), lateral intraparietal area (LIP), and cuneus support early covert targeting of the cued location. This was followed by coactivation of a frontal-parietal system [superior frontal gyrus (SFG), middle frontal gyrus (MFG), LIP, anterior intraparietal sulcus (IPSa)] that may coordinate the transition from targeting the cued location to sustained deployment of attention to both space and feature in the last period. The last period involved direction-specific activity in parietal regions and both dorsal and ventral sensory regions [LIP, IPSa, ventral IPS, lateral occipital region, and fusiform gyrus], which was accompanied by activation that was not direction specific in right hemisphere frontal regions (FEF, SFG, MFG). Behavioral performance corresponded with the magnitude of attention-related activity in different brain regions at each time period during deployment. The results add to the emerging electrophysiological characterization of different cortical networks that operate during anticipatory deployment of visual spatial attention.

  2. HARPs: Tracked Active Region Patch Data Product from SDO/HMI

    NASA Astrophysics Data System (ADS)

    Turmon, M.; Hoeksema, J. T.; Sun, X.; Bobra, M.

    2012-12-01

    We describe an HMI data product consisting of tracked magnetic features on the scale of solar active regions, abbreviated HARPs (HMI Active Region Patches). The HARP data series has been helpful for subsetting individual active regions, for development of near-real-time (NRT) space weather indices for individual active regions, and for defining closed magnetic structures for computationally-intensive algorithms like vector field disambiguation. The data series builds upon the 720s cadence activity masks, which identify large-scale instantaneously-observed magnetic features. Using these masks as a starting point, large spatially-coherent structures are identified using convolution with a longitudinally-extended kernel on a spherical domain. The resulting set of identified regions is then tracked from image to image. The metric for inter-image association is area of overlap between the best current estimate of AR location, as predicted by temporally extrapolating each currently tracked object, and the set of instantaneously-observed magnetic structures. Once completed tracks have been extracted, they are made into a standardized HARP data series by finding the smallest constant-angular-velocity box, of constant width in latitude and longitude, that encompasses all appearances of the active region. This data product is currently available, in definitive and near-real-time forms, with accompanying region-strength, location, and NOAA-AR metadata, on HMI's Joint Science Operations Center (JSOC) data portal.; HARP outlines for three days (2001 February 14, 15, and 16, 00:00 TAI, flipped N-S, selected from the 12-minute cadence original data product). HARPs are shown in the same color (some colors repeated) with a thin white box surrounding each HARP. HARPs are tracked and associated from image to image. HARPs, such as the yellow one in the images above, need not be connected regions. Merges and splits, such as the light blue region, are accounted for automatically.

  3. Compact sources of suprathermal microwave emission detected in quiescent active regions during lunar occultations

    NASA Astrophysics Data System (ADS)

    Correia, E.; Kaufmann, P.; Strauss, F. M.

    1992-04-01

    Solar quiescent active regions are known to exhibit radio emission from discrete structures. The knowledge of their dimensions and brightness temperatures is essential for understanding the physics of quiescent, confined plasma regions. Solar eclipses of 10 August, 1980 and 26 January, 1990, observed with high sensitivity and high time resolution at 22 GHz, allowed an unprecedented opportunity to identify Fresnel diffraction effects during lunar occultations of active regions. The results indicate the presence of quiescent discrete sources smaller than one arcsec in one dimension. Assuming symmetrical sources, their brightness temperatures were larger than 2 x 10 exp 7 K and 8 x 10 exp 7 K, for the 1980 and 1990 observations, respectively.

  4. MAG4 versus alternative techniques for forecasting active region flare productivity

    PubMed Central

    Falconer, David A; Moore, Ronald L; Barghouty, Abdulnasser F; Khazanov, Igor

    2014-01-01

    MAG4 is a technique of forecasting an active region's rate of production of major flares in the coming few days from a free magnetic energy proxy. We present a statistical method of measuring the difference in performance between MAG4 and comparable alternative techniques that forecast an active region's major-flare productivity from alternative observed aspects of the active region. We demonstrate the method by measuring the difference in performance between the “Present MAG4” technique and each of three alternative techniques, called “McIntosh Active-Region Class,” “Total Magnetic Flux,” and “Next MAG4.” We do this by using (1) the MAG4 database of magnetograms and major flare histories of sunspot active regions, (2) the NOAA table of the major-flare productivity of each of 60 McIntosh active-region classes of sunspot active regions, and (3) five technique performance metrics (Heidke Skill Score, True Skill Score, Percent Correct, Probability of Detection, and False Alarm Rate) evaluated from 2000 random two-by-two contingency tables obtained from the databases. We find that (1) Present MAG4 far outperforms both McIntosh Active-Region Class and Total Magnetic Flux, (2) Next MAG4 significantly outperforms Present MAG4, (3) the performance of Next MAG4 is insensitive to the forward and backward temporal windows used, in the range of one to a few days, and (4) forecasting from the free-energy proxy in combination with either any broad category of McIntosh active-region classes or any Mount Wilson active-region class gives no significant performance improvement over forecasting from the free-energy proxy alone (Present MAG4). Key Points Quantitative comparison of performance of pairs of forecasting techniques Next MAG4 forecasts major flares more accurately than Present MAG4 Present MAG4 forecast outperforms McIntosh AR Class and total magnetic flux PMID:26213517

  5. EVIDENCE THAT TEMPORAL CHANGES IN SOLAR SUBSURFACE HELICITY PRECEDE ACTIVE REGION FLARING

    SciTech Connect

    Reinard, A. A.; Komm, R.; Hill, F.

    2010-02-20

    We report on the analysis of subsurface vorticity/helicity measurements for flare producing and quiet active regions. We have developed a parameter to investigate whether large, decreasing kinetic helicity density commonly occurs prior to active region flaring. This new parameter is effective at separating flaring and non-flaring active regions and even separates among C-, M-, and X-class flare producing regions. In addition, this parameter provides advance notice of flare occurrence, as it increases 2-3 days before the flare occurs. These results are striking on an average basis, though on an individual basis there is still considerable overlap between flare associated and non-flare associated values. We propose the following qualitative scenario for flare production: subsurface rotational kinetic energy twists the magnetic field lines into an unstable configuration, resulting in explosive reconnection and a flare.

  6. MAGNETIC FIELD TOPOLOGY AND THE THERMAL STRUCTURE OF THE CORONA OVER SOLAR ACTIVE REGIONS

    SciTech Connect

    Schrijver, Carolus J.; DeRosa, Marc L.; Title, Alan M.

    2010-08-20

    Solar extreme ultraviolet (EUV) images of quiescent active-region coronae are characterized by ensembles of bright 1-2 MK loops that fan out from select locations. We investigate the conditions associated with the formation of these persistent, relatively cool, loop fans within and surrounding the otherwise 3-5 MK coronal environment by combining EUV observations of active regions made with TRACE with global source-surface potential-field models based on the full-sphere photospheric field from the assimilation of magnetograms that are obtained by the Michelson Doppler Imager (MDI) on SOHO. We find that in the selected active regions with largely potential-field configurations these fans are associated with (quasi-)separatrix layers (QSLs) within the strong-field regions of magnetic plage. Based on the empirical evidence, we argue that persistent active-region cool-loop fans are primarily related to the pronounced change in connectivity across a QSL to widely separated clusters of magnetic flux, and confirm earlier work that suggested that neither a change in loop length nor in base field strengths across such topological features are of prime importance to the formation of the cool-loop fans. We discuss the hypothesis that a change in the distribution of coronal heating with height may be involved in the phenomenon of relatively cool coronal loop fans in quiescent active regions.

  7. Satellite-tagged transcribing sequences in Bubalus bubalis genome undergo programmed modulation in meiocytes: possible implications for transcriptional inactivation.

    PubMed

    Chattopadhyay, M; Gangadharan, S; Kapur, V; Azfer, M A; Prakash, B; Ali, S

    2001-09-01

    We cloned and sequenced a 1378 bp BamHI satellite DNA fraction from the water buffalo Bubalus bubalis and have studied its expression in different tissues. The GC-rich sequences of the resultant contig pDS5 crosshybridize only with bovid DNA and are not conserved evolutionarily. Typing of buffalo genomic DNA using pDS5 with several restriction enzymes revealed multilocus monomorphic bands. Similar typing of cattle, buffalo, goat, sheep, and gaur genomic DNA revealed variations in copy number and allele length giving rise to species-specific band patterns. Expression study of pDS5 in bubaline samples by RNA slot-blot, Northern blot, and RT-PCR showed various levels of signal in all the somatic tissues and germline cells except heart. A GenBank database search revealed homology of pDS5 sequences in the 5' region from nt 1-1261 with collagen gene. An AluI typing analysis of DNA from bubaline semen samples showed consistent loss of two bands. The presence of corresponding bands in somatic tissues suggests a sequence modulation within the pDS5 array in meiocytes during spermatogenesis, which is restored in the somatic cells after fertilization. Modulation of the satellite-tagged transcribing sequence in the meiocytes may be a mechanism of its inactivation.

  8. Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals.

    PubMed

    Chow, S; Ueno, Y; Toyokawa, M; Oohara, I; Takeyama, H

    2009-01-01

    Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 sequences (118 to 422 bp) with lower GC content (35.8% to 61.7%) than the other animal taxa. Mollusca and Crustacea were diverse groups with respect to ITS1 length, ranging from 108 to 1,118 and 182 to 1,613 bp, respectively. No universal relationship between length and GC content was observed. Our data indicated that ITS1 has a limited utility for phylogenetic analysis as obtaining confident sequence alignment was often impossible between different genera of the same family and even between congeneric species.

  9. Genetic variability in Melipona quinquefasciata (Hymenoptera, Apidae, Meliponini) from northeastern Brazil determined using the first internal transcribed spacer (ITS1).

    PubMed

    Pereira, J O P; Freitas, B M; Jorge, D M M; Torres, D C; Soares, C E A; Grangeiro, T B

    2009-01-01

    Melipona quinquefasciata is a ground-nesting South American stingless bee whose geographic distribution was believed to comprise only the central and southern states of Brazil. We obtained partial sequences (about 500-570 bp) of first internal transcribed spacer (ITS1) nuclear ribosomal DNA from Melipona specimens putatively identified as M. quinquefasciata collected from different localities in northeastern Brazil. To confirm the taxonomic identity of the northeastern samples, specimens from the state of Goiás (Central region of Brazil) were included for comparison. All sequences were deposited in GenBank (accession numbers EU073751-EU073759). The mean nucleotide divergence (excluding sites with insertions/deletions) in the ITS1 sequences was only 1.4%, ranging from 0 to 4.1%. When the sites with insertions/deletions were also taken into account, sequence divergences varied from 0 to 5.3%. In all pairwise comparisons, the ITS1 sequence from the specimens collected in Goiás was most divergent compared to the ITS1 sequences of the bees from the other locations. However, neighbor-joining phylogenetic analysis showed that all ITS1 sequences from northeastern specimens along with the sample of Goiás were resolved in a single clade with a bootstrap support of 100%. The ITS1 sequencing data thus support the occurrence of M. quinquefasciata in northeast Brazil.

  10. Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Coutinho, João Paulo; Carvalho, Ana; Lima-Brito, José

    2014-11-26

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. In this study, co-dominant ITS PCR-RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR-RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR-RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area.

  11. Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction–restriction fragment length polymorphism

    PubMed Central

    Coutinho, João Paulo; Carvalho, Ana; Lima-Brito, José

    2015-01-01

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) techniques. In this study, co-dominant ITS PCR–RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR–RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR–RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area. PMID:25429047

  12. 50 CFR 217.151 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... activity and specified geographical region. (a) Regulations in this subpart apply only to Port Dolphin Energy LLC (Port Dolphin) and those persons it authorizes to conduct activities on its behalf for the... incidental to construction and operation of the Port Dolphin Deepwater Port (Port). (b) The taking of...

  13. 50 CFR 217.151 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... activity and specified geographical region. (a) Regulations in this subpart apply only to Port Dolphin Energy LLC (Port Dolphin) and those persons it authorizes to conduct activities on its behalf for the... incidental to construction and operation of the Port Dolphin Deepwater Port (Port). (b) The taking of...

  14. Problems and Perspectives on the Evaluation of Regional and National Computer-Related Educational Activity.

    ERIC Educational Resources Information Center

    Collis, Betty

    Although the importance of systematic evaluation of educational policy and practice is well established, various problems confound the intention of evaluating regional or national activity with regard to computer-related activities in education. At least two of these problems relate to a general conception of the appropriate entry points for…

  15. 50 CFR 217.170 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Operation and Maintenance of the Neptune Liquefied Natural Gas Facility Off Massachusetts § 217.170 Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune LNG LLC (Neptune) and those persons it authorizes to conduct activities on its behalf for the...

  16. 50 CFR 217.170 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Operation and Maintenance of the Neptune Liquefied Natural Gas Facility Off Massachusetts § 217.170 Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune LNG LLC (Neptune) and those persons it authorizes to conduct activities on its behalf for the...

  17. 50 CFR 217.170 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Operation and Maintenance of the Neptune Liquefied Natural Gas Facility Off Massachusetts § 217.170 Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune LNG LLC (Neptune) and those persons it authorizes to conduct activities on its behalf for the...

  18. 50 CFR 217.170 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Operation and Maintenance of the Neptune Liquefied Natural Gas Facility Off Massachusetts § 217.170 Specified activity and specified geographical region. (a) Regulations in this subpart apply only to Neptune LNG LLC (Neptune) and those persons it authorizes to conduct activities on its behalf for the...

  19. Regional Quality Assurance Activity in Higher Education in Southeast Asia: Its Characteristics and Driving Forces

    ERIC Educational Resources Information Center

    Umemiya, Naoki

    2008-01-01

    This article analyses the characteristics and driving forces of regional quality assurance activity in Southeast Asia, which has been actively promoted in recent years by the ASEAN University Network, an organisation for higher education under the auspices of the Association of Southeast Asian Nations (ASEAN). There are now more collaborative…

  20. Study of the magnetospheres of active regions on the sun by radio astronomy techniques

    NASA Astrophysics Data System (ADS)

    Bogod, V. M.; Kal'tman, T. I.; Peterova, N. G.; Yasnov, L. V.

    2017-01-01

    In the 1990s, based on detailed studies of the structure of active regions (AR), the concept of the magnetosphere of the active region was proposed. This includes almost all known structures presented in the active region, ranging from the radio granulation up to noise storms, the radiation of which manifests on the radio waves. The magnetosphere concept, which, from a common point of view, considers the manifestations of the radio emission of the active region as a single active complex, allows one to shed light on the relation between stable and active processes and their interrelations. It is especially important to identify the basic ways of transforming nonthermal energy into thermal energy. A dominant role in all processes is attributed to the magnetic field, the measurement of which on the coronal levels can be performed by radio-astronomical techniques. The extension of the wavelength range and the introduction of new tools and advanced modeling capabilities makes it possible to analyze the physical properties of plasma structures in the AR magnetosphere and to evaluate the coronal magnetic fields at the levels of the chromosphere-corona transition zone and the lower corona. The features and characteristics of the transition region from the S component to the B component have been estimated.

  1. Venezuelan equine encephalitis virus activity in the Gulf Coast region of Mexico, 2003-2010.

    PubMed

    Adams, A Paige; Navarro-Lopez, Roberto; Ramirez-Aguilar, Francisco J; Lopez-Gonzalez, Irene; Leal, Grace; Flores-Mayorga, Jose M; Travassos da Rosa, Amelia P A; Saxton-Shaw, Kali D; Singh, Amber J; Borland, Erin M; Powers, Ann M; Tesh, Robert B; Weaver, Scott C; Estrada-Franco, Jose G

    2012-01-01

    Venezuelan equine encephalitis virus (VEEV) has been the causative agent for sporadic epidemics and equine epizootics throughout the Americas since the 1930s. In 1969, an outbreak of Venezuelan equine encephalitis (VEE) spread rapidly from Guatemala and through the Gulf Coast region of Mexico, reaching Texas in 1971. Since this outbreak, there have been very few studies to determine the northward extent of endemic VEEV in this region. This study reports the findings of serologic surveillance in the Gulf Coast region of Mexico from 2003-2010. Phylogenetic analysis was also performed on viral isolates from this region to determine whether there have been substantial genetic changes in VEEV since the 1960s. Based on the findings of this study, the Gulf Coast lineage of subtype IE VEEV continues to actively circulate in this region of Mexico and appears to be responsible for infection of humans and animals throughout this region, including the northern State of Tamaulipas, which borders Texas.

  2. Venezuelan Equine Encephalitis Virus Activity in the Gulf Coast Region of Mexico, 2003–2010

    PubMed Central

    Adams, A. Paige; Navarro-Lopez, Roberto; Ramirez-Aguilar, Francisco J.; Lopez-Gonzalez, Irene; Leal, Grace; Flores-Mayorga, Jose M.; Travassos da Rosa, Amelia P. A.; Saxton-Shaw, Kali D.; Singh, Amber J.; Borland, Erin M.; Powers, Ann M.; Tesh, Robert B.; Weaver, Scott C.; Estrada-Franco, Jose G.

    2012-01-01

    Venezuelan equine encephalitis virus (VEEV) has been the causative agent for sporadic epidemics and equine epizootics throughout the Americas since the 1930s. In 1969, an outbreak of Venezuelan equine encephalitis (VEE) spread rapidly from Guatemala and through the Gulf Coast region of Mexico, reaching Texas in 1971. Since this outbreak, there have been very few studies to determine the northward extent of endemic VEEV in this region. This study reports the findings of serologic surveillance in the Gulf Coast region of Mexico from 2003–2010. Phylogenetic analysis was also performed on viral isolates from this region to determine whether there have been substantial genetic changes in VEEV since the 1960s. Based on the findings of this study, the Gulf Coast lineage of subtype IE VEEV continues to actively circulate in this region of Mexico and appears to be responsible for infection of humans and animals throughout this region, including the northern State of Tamaulipas, which borders Texas. PMID:23133685

  3. Effect of acute and chronic administration of methamphetamine on activator protein-1 binding activities in the rat brain regions.

    PubMed

    Akiyama, K; Ishihara, T; Kashihara, K

    1996-10-31

    The activator protein-1 (AP-1) binding activities in the three brain regions (striatum, nucleus accumbens, cingulate cortex) increased after a single methamphetamine (METH, 4 mg/kg) injection and reached maximum levels after 180 min. Pretreatment with SCH 23390 (0.5 mg/kg), a selective dopamine D1 receptor antagonist, significantly inhibited the enhanced AP-1 binding activities induced by acute METH (4 mg/kg) administration. In chronic experiments, rats were pretreated with METH (4 mg/kg) or saline for 14 days. The AP-1 binding activities after a 1-week abstinence from chronic administration of MAP increased significantly in all the brain regions compared with those of the saline-treated controls, whereas after a 4-week abstinence, the AP-1 binding activity decreased significantly in the cingulate cortex, but not striatum or nucleus accumbens, compared with the saline-treated control group. A METH challenge after a 4-week abstinence period induced significantly more intense stereotypy, but lower AP-1 binding activities in all the brain regions of rats treated with repeated METH than repeated saline injections. The super-shift assay revealed that after a 1- or 4-week abstinence, there was no significant difference between the Fos-related antigens (Fras) contents of the saline- and METH-treated groups in any brain region examined, and that the Jun family protein levels of the METH-treated group increased significantly in the striatum and nucleus accumbens after a 1-, but not 4-, week abstinence. These results suggest that chronic METH administration leads to delayed decay of the induced AP-1 binding activities and Jun component levels after abstinence for up to 1 week, but results in no change in or decreases these activities and attenuates METH challenge-induced AP-1 binding activities after abstinence for 4 weeks.

  4. The Main Sequence of Explosive Solar Active Regions: Discovery and Interpretation

    DTIC Science & Technology

    2009-01-01

    from equilibrium between input of free energy to an explosive active region’s magnetic field in the chromosphere and corona by contortion of the field...coronal mass ejections (CMEs) – Sun: flares 1. INTRODUCTION For an active region’s chromospheric and coronal magnetic field to be able to...reason for this trend is that in the smaller active regions near the front the maximum rate of buildup of free energy in the field in the chromosphere

  5. Regional distribution pattern of groundwater heavy metals resulting from agricultural activities

    NASA Astrophysics Data System (ADS)

    Nouri, J.; Mahvi, A. H.; Jahed, G. R.; Babaei, A. A.

    2008-09-01

    Contaminations of groundwater by heavy metals due to agricultural activities are growing recently. The objective of this study was to evaluate and map regional patterns of heavy metals (Cd, Zn and Cu) in groundwater on a plain with high agricultural activities. The study was conducted to investigate the concentration of heavy metals and distribution in groundwater in regions of Shush Danial and Andimeshk aquifers in the southern part of Iran. Presently, groundwater is the only appropriate and widely used source of drinking water for rural and urban communities in this region. The region covers an area of 1,100 km2 between the Dez and Karkhe rivers, which lead to the Persian Gulf. For this study, the region was divided into four sub-regions A, B, C and D. Additionally, 168 groundwater samples were collected from 42 water wells during the earlier months of 2004. The flame atomic absorption spectrometry (AAS-Flame) was used to measure the concentration of heavy metals in water samples and the Surfer software was used for determination of the contour map of metal distribution. The results demonstrated that in all of the samples, Cd and Zn concentrations were below the EPA MCLG and EPA secondary standard, respectively. However, the Cu contents of 4.8 % of all samples were higher than EPA MCL. It is also indicated that the concentrations of metals were more pronounced at the southern part of the studied region than at the others. The analysis of fertilizers applied for agricultural activities at this region also indicated that a great majority of the above-mentioned heavy metals were discharged into the environment. Absence of confining layers, proximity to land surface, excess agricultural activities in the southern part and groundwater flow direction that is generally from the north to the southern parts in this area make the southern region of the Shush plain especially vulnerable to pollution by heavy metals than by other contaminants.

  6. High endocytotic activity occurs periodically in the endplate region of denervated mouse striated muscle fibers.

    PubMed

    Lawoko, G; Tågerud, S

    1995-08-01

    High endocytotic activity after denervation of skeletal muscle occurs in a proportion of muscle fibers (both slow and fast fiber types) in the endplate region. The present study was performed in order to examine if a periodicity in the endocytotic activity could explain why the process is not observed in all fibers at a given time. Three markers, horseradish peroxidase (HRP), rhodamine B isothiocyanate-labeled dextran, and fluorescein isothiocyanate-labeled dextran were used to demonstrate endocytotic activity of muscle fibers of the denervated mouse hemidiaphragm in vivo. Acetylcholine esterase staining was used in conjunction with HRP uptake to determine the proportion of denervated muscle fibers with endocytotic activity in the endplate region at any one time. The results show that 25-50% of the muscle fibers display high endocytotic activity in the endplate region at a given time 10 days after denervation. The existence of a periodicity in this endocytotic activity is suggested by results obtained using two different endocytotic markers administered at time intervals of 0-7 days. We conclude that loss of contact with the innervating motorneuron induces a high endocytotic activity which occurs periodically in the perisynaptic region of skeletal muscle fibers.

  7. Optimization of object region and boundary extraction by energy minimization for activity recognition

    NASA Astrophysics Data System (ADS)

    Albalooshi, Fatema A.; Asari, Vijayan K.

    2013-05-01

    Automatic video segmentation for human activity recognition has played an important role in several computer vision applications. Active contour model (ACM) has been used extensively for unsupervised adaptive segmentation and automatic object region and boundary extraction in video sequences. This paper presents optimizing Active Contour Model using recurrent architecture for automatic object region and boundary extraction in human activity video sequences. Taking advantage of the collective computational ability and energy convergence capability of the recurrent architecture, energy function of Active Contour Model is optimized with lower computational time. The system starts with initializing recurrent architecture state based on the initial boundary points and ends up with final contour which represent actual boundary points of human body region. The initial contour of the Active Contour Model is computed using background subtraction based on Gaussian Mixture Model (GMM) such that background model is built dynamically and regularly updated to overcome different challenges including illumination changes, camera oscillations, and changes in background geometry. The recurrent nature is useful for dealing with optimization problems due to its dynamic nature, thus, ensuring convergence of the system. The proposed boundary detection and region extraction can be used for real time processing. This method results in an effective segmentation that is less sensitive to noise and complex environments. Experiments on different databases of human activity show that our method is effective and can be used for real-time video segmentation.

  8. Tectonic and Hydrological Activities on Xanadu, Hotei and Tui Regions on Titan

    NASA Astrophysics Data System (ADS)

    Mitri, G.; Di Marco, C.; Di Achille, G.; Lunine, J. I.; Flamini, E.; Meriggiola, R.; Poggiali, V.

    2012-12-01

    Xanadu (~10°S, 120°W), Tui (~24°S, 125°W) and Hotei (~26°S, 78°W) regions are three adjacent geomorphic provinces located on Titan's leading hemisphere. The interpretation of the geological activities of these regions is not unique. Radebaugh et al. (2010) proposed that complex geological activity occurred to form the highlands regions of Xanadu where first compression occurred, and subsequently extensional tectonism and erosion by methane precipitation. However, Brown et al. (2011) proposed that Xanadu is a wide and ancient impact crater basin. Nelson et al. (2009) observed surface reflectance variability at the Hotei region suggesting that such surface variability might be due to surface activity potentially related to cryovolcanic activity. Wide lobate features in the Tui and Hotei regions were identified using Cassini VIMS (Barnes et al. 2009) and RADAR observations (Walls et al. 2009) and were interpreted as cryovolcanic flows. However, Moore and Howard (2010) suggested that the observed lobate features in both regions might be paleolakes. We produced a geomorphological map encompassing the Xanadu, Tui and Hotei regions. Our geomorphological analysis is based on the Synthetic Aperture Radar images from the Cassini RADAR. We also used topographic data from radar altimeter and SAR-Topography technique datasets. We show that Xanadu is a dissected plateau whose formation most likely involved crustal uplift produced by compressional tectonic activity. We also show that both the Tui and Hotei regions present characteristics of closed drainage basins with an inflow of liquids from the highlands of Xanadu and a lack of outflow, suggesting that Hotei and Tui are endorheic basins that might contain ephemeral lakes currently appearing as dry lakebeds. Such lakebeds are likely filled with liquid hydrocarbons only during rare periods of significant rainfall and dry out due to evaporation.

  9. Analysis of Seismic Activity of the last 15 Years Nearby Puerto Rico and Caribbean Region.

    NASA Astrophysics Data System (ADS)

    Huerta-Lopez, C. I.; Torres-Ortíz, D. M.; Fernández-Heredia, A. I.; Martínez-Cruzado, J. A.

    2015-12-01

    An earthquake catalog of the seismicity occurred during the last 15 years in the Caribbean region, nearby the vicinity of Puerto Rico Island (PRI) was compiled in order to capture the big picture of the regional seismic activity ratio and in particular at the epicentral regions of several historical and instrumentally recorded (during 2008-20015) large to moderate magnitude earthquakes occurred nearby PRI in onshore and offshore, which include the M6.4 earthquake of 01/13/2014, the largest earthquake recorded instrumentally nearby PRI. From the point of view of joint temporal-spatial distribution of epicenters, episodic temporal-spatial seismic activity is clearly seen as temporal-spatial concentrations during certain time intervals in different regions. These localized concentrations of epicenters that occur during certain time intervals in well localized/concentrated regions may suggest "seismic gaps" that shows no regular time interval, neither spatial pattern. In the epicentral region of the M6.4 01/13/2014 earthquake and the historical Mona Passage M7.5 earthquake of 10/11/1918, episodic concentrations in time and space of small magnitude earthquakes epicenters is evident, however do not show temporal pattern. Preliminary results of statistical analysis of an ongoing research in terms of the parameter b (Gutenberg-Richter relationship), and the Omori's law with the aim to relate the tectonic framework of the region (or sub-regions) such as structural heterogeneity stress are here presented/discussed.

  10. Minifilament Eruptions that Drive Coronal Jets in a Solar Active Region

    NASA Astrophysics Data System (ADS)

    Sterling, Alphonse C.; Moore, Ronald L.; Falconer, David; Panesar, Navdeep; Akiyama, Sachiko; Yashiro, Seiji; Gopalswamy, Nat

    2016-05-01

    Solar coronal jets are common in both coronal holes and in active regions. Recently, Sterling et al. (2015), using data from Hinode/XRT and SDO/AIA, found that coronal jets originating in polar coronal holes result from the eruption of small-scale filaments (minifilaments). The jet bright point (JBP) seen in X-rays and hotter EUV channels off to one side of the base of the jet's spire develops at the location where the minifilament erupts, consistent with the JBPs being miniature versions of typical solar flares that occur in the wake of large-scale filament eruptions. Here we consider whether active region coronal jets also result from the same minifilament-eruption mechanism, or whether they instead result from a different mechanism, such as the hitherto popular ``emerging flux'' model for jets. We present observations of an on-disk active region that produced numerous jets on 2012 June 30, using data from SDO/AIA and HMI, and from GOES/SXI. We find that several of these active region jets also originate with eruptions of miniature filaments (size scale ~20'') emanating from small-scale magnetic neutral lines of the region. This demonstrates that active region coronal jets are indeed frequently driven by minifilament eruptions. Other jets from the active region were also consistent with their drivers being minifilament eruptions, but we could not confirm this because the onsets of those jets were hidden from our view. This work was supported by funding from NASA/LWS, NASA/HGI, and Hinode.

  11. Variegation of comet 67P/Churyumov-Gerasimenko in regions showing activity

    NASA Astrophysics Data System (ADS)

    Oklay, N.; Vincent, J.-B.; Fornasier, S.; Pajola, M.; Besse, S.; Davidsson, B. J. R.; Lara, L. M.; Mottola, S.; Naletto, G.; Sierks, H.; Barucci, A. M.; Scholten, F.; Preusker, F.; Pommerol, A.; Masoumzadeh, N.; Lazzarin, M.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; A'Hearn, M. F.; Bertaux, J.-L.; Bertini, I.; Bodewits, D.; Cremonese, G.; Da Deppo, V.; Debei, S.; De Cecco, M.; Fulle, M.; Groussin, O.; Gutiérrez, P. J.; Güttler, C.; Hall, I.; Hofmann, M.; Hviid, S. F.; Ip, W.-H.; Jorda, L.; Keller, H. U.; Knollenberg, J.; Kovacs, G.; Kramm, J.-R.; Kührt, E.; Küppers, M.; Lin, Z.-Y.; Lopez Moreno, J. J.; Marzari, F.; Moreno, F.; Shi, X.; Thomas, N.; Toth, I.; Tubiana, C.

    2016-02-01

    Aims.We carried out an investigation of the surface variegation of comet 67P/Churyumov-Gerasimenko, the detection of regions showing activity, the determination of active and inactive surface regions of the comet with spectral methods, and the detection of fallback material. Methods: We analyzed multispectral data generated with Optical, Spectroscopic, and Infrared Remote Imaging System (OSIRIS) narrow angle camera (NAC) observations via spectral techniques, reflectance ratios, and spectral slopes in order to study active regions. We applied clustering analysis to the results of the reflectance ratios, and introduced the new technique of activity thresholds to detect areas potentially enriched in volatiles. Results: Local color inhomogeneities are detected over the investigated surface regions. Active regions, such as Hapi, the active pits of Seth and Ma'at, the clustered and isolated bright features in Imhotep, the alcoves in Seth and Ma'at, and the large alcove in Anuket, have bluer spectra than the overall surface. The spectra generated with OSIRIS NAC observations are dominated by cometary emissions of around 700 nm to 750 nm as a result of the coma between the comet's surface and the camera. One of the two isolated bright features in the Imhotep region displays an absorption band of around 700 nm, which probably indicates the existence of hydrated silicates. An absorption band with a center between 800-900 nm is tentatively observed in some regions of the nucleus surface. This absorption band can be explained by the crystal field absorption of Fe2+, which is a common spectral feature seen in silicates.

  12. Evidence for Widespread Cooling in an Active Region Observed with the SDO Atmospheric Imaging Assembly

    NASA Technical Reports Server (NTRS)

    Viall, Nicholeen M.; Klimchuk, James A.

    2012-01-01

    A well known behavior of EUV light curves of discrete coronal loops is that the peak intensities of cooler channels or spectral lines are reached at progressively later times. This time lag is understood to be the result of hot coronal loop plasma cooling through these lower respective temperatures. However, loops typically comprise only a minority of the total emission in active regions. Is this cooling pattern a common property of active region coronal plasma, or does it only occur in unique circumstances, locations, and times? The new SDO/AIA data provide a wonderful opportunity to answer this question systematically for an entire active region. We measure the time lag between pairs of SDO/AIA EUV channels using 24 hours of images of AR 11082 observed on 19 June 2010. We find that there is a time-lag signal consistent with cooling plasma, just as is usually found for loops, throughout the active region including the diffuse emission between loops for the entire 24 hour duration. The pattern persists consistently for all channel pairs and choice of window length within the 24 hour time period, giving us confidence that the plasma is cooling from temperatures of greater than 3 MK, and sometimes exceeding 7 MK, down to temperatures lower than approx. 0.8 MK. This suggests that the bulk of the emitting coronal plasma in this active region is not steady; rather, it is dynamic and constantly evolving. These measurements provide crucial constraints on any model which seeks to describe coronal heating.

  13. Different Modes of Turbulence in the Active Regions of the Solar Photosphere

    NASA Astrophysics Data System (ADS)

    Kozak, L. V.; Kostik, R. I.; Cheremnykh, O. K.

    In work the range of different methods for the analysis of characteristics of turbulent processes in the active regions of the solar photosphere has been used. The changes of fluctuations distribution function and its moments were analyzed, spectral analysis was carried out.It was found out from the observations of active region carried out with the 70-cm vacuum tower telescope VTT in Isanie (Tenerife Island, Spain) that the turbulent processes in the sun photosphere are characterized by two different spectra of turbulence. The first one of them is well known Kolmohorov spectrum, which describes the plasma with zero mean magnetic field. The second one is the Kraichnan spectrum with a different from zero mean magnetic field. Transition from one spectrum type to another one occurs at scale of 3 Mm.We have to note that the scale 3 Mm corresponds to one of mesogranulation and testifies about non-zero mean magnetic fields for the consideration of regions exceeding the granulation in active regions of the photosphere. Besides, this clears the possibility of appearance of selforganizing magnetic plasma structures such as spots, active regions and complexes of activity.

  14. Measurements of cloud condensation nuclei activity and droplet activation kinetics of wet processed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2011-04-01

    This study reports laboratory measurements of particle size distributions, cloud condensation nuclei (CCN) activity, and droplet activation kinetics of wet generated aerosols from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. The dependence of critical supersaturation, sc, on particle dry diameter, Ddry, is used to characterize particle-water interactions and assess the ability of Frenkel-Halsey-Hill adsorption activation theory (FHH-AT) and Köhler theory (KT) to describe the CCN activity of the considered samples. Regional dust samples produce unimodal size distributions with particle sizes as small as 40 nm, CCN activation consistent with KT, and exhibit hygroscopicity similar to inorganic salts. Clays and minerals produce a bimodal size distribution; the CCN activity of the smaller mode is consistent with KT, while the larger mode is less hydrophilic, follows activation by FHH-AT, and displays almost identical CCN activity to dry generated dust. Ion Chromatography (IC) analysis performed on regional dust samples indicates a soluble fraction that cannot explain the CCN activity of dry or wet generated dust. A mass balance and hygroscopicity closure suggests that the small amount of ions (of low solubility compounds like calcite) present in the dry dust dissolve in the aqueous suspension during the wet generation process and give rise to the observed small hygroscopic mode. Overall these results identify an artifact that may question the atmospheric relevance of dust CCN activity studies using the wet generation method. Based on a threshold droplet growth analysis, wet generated mineral aerosols display similar activation kinetics compared to ammonium sulfate calibration aerosol. Finally, a unified CCN activity framework that accounts for concurrent effects of solute and adsorption is developed to describe the CCN activity of aged or hygroscopic dusts.

  15. Genetic Analysis of a Temporally Transcribed Chemotaxis Gene Cluster Caulobacter Crescentus

    PubMed Central

    Alley, MRK.; Gomes, S. L.; Alexander, W.; Shapiro, L.

    1991-01-01

    Caulobacter crescentus performs chemotaxis by short intermittent reversals of rotation of its single polar flagellum. Tn5 insertions causing a general chemotaxis phenotype, an inability to reverse swimming direction and to form large swarm colonies, have been mapped to an 8-kb region of the C. crescentus genome. These Tn5 mutations had different effects on the methyl-accepting chemotaxis proteins (MCP), and the activities of methyltransferase and methylesterase. The Tn5 insertion mutant SC1130 had no cross-reacting MCP and had reduced levels of activity of the methyltransferase and methylesterase. Other mutants bearing Tn5 insertions retained cross-reacting MCP activity and were altered only in their methyltransferase and methylesterase activities. Using a cosmid library we isolated a clone that complemented SC1130. Complementation studies of the Tn5 mutants using derivatives of the cosmid clone showed that all the Tn5 insertions lie within a single operon that appears to encode many chemotaxis genes. The first gene in this operon was shown to encode an MCP by immuno-blot analysis of strains carrying β-galactosidase protein fusions to portions of the operon. The promoter of this operon was located by chromosomal integration of subclones of this region and by identifying DNA fragments that were capable of expressing lacZ transcriptional fusions. The transcription of the che operon occurred at a defined time in the cell cycle, prior to cell division. PMID:1660425

  16. Temperature structure of active regions deduced from helium-like sulphur lines

    NASA Technical Reports Server (NTRS)

    Watanabe, Tetsuya; Hara, Hirohisa; Shimizu, Toshifumi; Hiei, Eijiro; Bentley, Robert D.; Lang, James; Phillips, Kenneth J. H.; Pike, C. David; Fludra, Andrzej; Bromage, Barbara J. I.

    1995-01-01

    Solar active-region temperatures have been determined from the full-Sun spectra of helium-like sulfur (S XV) observed by the Bragg Crystal Spectrometer on Board the Yohkoh satellite. The average temperature deduced from S XV is demonstrated to vary with the solar activity level: A temperature of 2.5 x 10(exp 6) K is derived from the spectra taken during low solar activity, similar to the general corona, while 4 x 10(exp 6) K is obtained during a higher activity phase. For the latter, the high- temperature tail of the differential emission measure of active regions is found most likely due to the superposition of numerous flare-like events (micro/nano-flares).

  17. Antioxidant activities of Sarcodon imbricatum wildly grown in the Black Sea Region of Turkey

    PubMed Central

    Özen, Tevfik; Türkekul, İbrahim

    2010-01-01

    The antioxidant activities of the methanol extract of Sarcodon imbricatum wildly grown in the Black Sea Region of Turkey were investigated in this study. Antioxidant activities were evaluated in terms of total antioxidant activity, reducing power, metal chelating ability, inhibition of linoleic acid peroxidation, superoxide, peroxide and hydrogen peroxide scavenging effects. Various antioxidant activities were compared to references antioxidants such as α-tocopherol, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), and trolox. In total antioxidant (12674.45 μmol α-tocopherol/g of extract), superoxide scavenging (53.74%) and peroxide scavenging activity (45.73%), the methanol extract of Sarcodon imbricatum showed stronger activity patterns than that of references antioxidants. Reducing power, metal chelating activity and free radical (DPPH•) scavenging activity was increased with the increasing concentration. The contents of total phenolic, flavonoid, anthocyanin, ascorbic acid, β-carotene and lycopene of Sarcodon imbricatum were determined and found to be noteworthy. PMID:20668572

  18. An EEG Finger-Print of fMRI deep regional activation.

    PubMed

    Meir-Hasson, Yehudit; Kinreich, Sivan; Podlipsky, Ilana; Hendler, Talma; Intrator, Nathan

    2014-11-15

    This work introduces a general framework for producing an EEG Finger-Print (EFP) which can be used to predict specific brain activity as measured by fMRI at a given deep region. This new approach allows for improved EEG spatial resolution based on simultaneous fMRI activity measurements. Advanced signal processing and machine learning methods were applied on EEG data acquired simultaneously with fMRI during relaxation training guided by on-line continuous feedback on changing alpha/theta EEG measure. We focused on demonstrating improved EEG prediction of activation in sub-cortical regions such as the amygdala. Our analysis shows that a ridge regression model that is based on time/frequency representation of EEG data from a single electrode, can predict the amygdala related activity significantly better than a traditional theta/alpha activity sampled from the best electrode and about 1/3 of the times, significantly better than a linear combination of frequencies with a pre-defined delay. The far-reaching goal of our approach is to be able to reduce the need for fMRI scanning for probing specific sub-cortical regions such as the amygdala as the basis for brain-training procedures. On the other hand, activity in those regions can be characterized with higher temporal resolution than is obtained by fMRI alone thus revealing additional information about their processing mode.

  19. Seasonal forecasting of lightning and thunderstorm activity in tropical and temperate regions of the world.

    PubMed

    Dowdy, Andrew J

    2016-02-11

    Thunderstorms are convective systems characterised by the occurrence of lightning. Lightning and thunderstorm activity has been increasingly studied in recent years in relation to the El Niño/Southern Oscillation (ENSO) and various other large-scale modes of atmospheric and oceanic variability. Large-scale modes of variability can sometimes be predictable several months in advance, suggesting potential for seasonal forecasting of lightning and thunderstorm activity in various regions throughout the world. To investigate this possibility, seasonal lightning activity in the world's tropical and temperate regions is examined here in relation to numerous different large-scale modes of variability. Of the seven modes of variability examined, ENSO has the strongest relationship with lightning activity during each individual season, with relatively little relationship for the other modes of variability. A measure of ENSO variability (the NINO3.4 index) is significantly correlated to local lightning activity at 53% of locations for one or more seasons throughout the year. Variations in atmospheric parameters commonly associated with thunderstorm activity are found to provide a plausible physical explanation for the variations in lightning activity associated with ENSO. It is demonstrated that there is potential for accurately predicting lightning and thunderstorm activity several months in advance in various regions throughout the world.

  20. Seasonal forecasting of lightning and thunderstorm activity in tropical and temperate regions of the world

    PubMed Central

    Dowdy, Andrew J.

    2016-01-01

    Thunderstorms are convective systems characterised by the occurrence of lightning. Lightning and thunderstorm activity has been increasingly studied in recent years in relation to the El Niño/Southern Oscillation (ENSO) and various other large-scale modes of atmospheric and oceanic variability. Large-scale modes of variability can sometimes be predictable several months in advance, suggesting potential for seasonal forecasting of lightning and thunderstorm activity in various regions throughout the world. To investigate this possibility, seasonal lightning activity in the world’s tropical and temperate regions is examined here in relation to numerous different large-scale modes of variability. Of the seven modes of variability examined, ENSO has the strongest relationship with lightning activity during each individual season, with relatively little relationship for the other modes of variability. A measure of ENSO variability (the NINO3.4 index) is significantly correlated to local lightning activity at 53% of locations for one or more seasons throughout the year. Variations in atmospheric parameters commonly associated with thunderstorm activity are found to provide a plausible physical explanation for the variations in lightning activity associated with ENSO. It is demonstrated that there is potential for accurately predicting lightning and thunderstorm activity several months in advance in various regions throughout the world. PMID:26865431

  1. Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio.

    PubMed

    Minamoto, Toshifumi; Uchii, Kimiko; Takahara, Teruhiko; Kitayoshi, Takumi; Tsuji, Satsuki; Yamanaka, Hiroki; Doi, Hideyuki

    2017-03-01

    The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.

  2. Genetic diversity of Ephedra plants in mongolia inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

    PubMed

    Kitani, Yuki; Zhu, Shu; Batkhuu, Javzan; Sanchir, Chinbat; Komatsu, Katsuko

    2011-01-01

    Ephedrae herba has been used for treating colds, relieving coughs and asthma from ancient times. We previously reported the distribution of Ephedra sinica, E. equisetina, E. przewalskii, E. regeliana, E. monosperma and Ephedra sp. in Mongolia, and among them E. sinica and E. equisetina were potential new resources of Ephedrae herba of Japanese pharmacopoeia grade, based on our field survey and subsequent molecular and chemical assessments. However, the Ephedra population in southwestern areas showed a high possibility of having hybrid origins. Further field surveys in southwestern areas, and sequence analysis of the partial nuclear internal transcribed spacer 1 (ITS1) region, besides trnK and 18S ribosomal RNA (rRNA) gene regions, were conducted in order to obtain detailed evidence of hybridization status. As a result, the distribution of E. glauca in western area and E. lomatolepis in western-most area was confirmed. The ITS sequences from all 8 Ephedra species collected in Mongolia were roughly divided into 5 types (types I-V). Type II sequence, having several additive nucleotides, was found in Ephedra sp., E. glauca, E. regeliana and E. sinica, which provided useful information for tracing hybrid origins. Morphological, genetic and distribution evidence suggested that the hybridization of Ephedra species occurred widely in southwestern Mongolia, and several Ephedra species including E. przewalkskii and E. intermedia were involved in these events. Integrated with our previous report, trnK-, 18S- and ITS-types from pure lines of each species are proposed. In addition, we propose a practicable method for detecting additive peaks on a direct sequencing electropherogram.

  3. RAPD and internal transcribed spacer sequence analyses reveal Zea nicaraguensis as a section Luxuriantes species close to Zea luxurians.

    PubMed

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-04-15

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species.

  4. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens.

    PubMed

    Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D; Callac, Philippe

    2016-01-01

    The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.

  5. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

    PubMed Central

    Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D.; Callac, Philippe

    2016-01-01

    The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

  6. X-ray structures associated with disappearing H-alpha filaments in active regions

    NASA Technical Reports Server (NTRS)

    Kahler, S. W.

    1980-01-01

    The paper examines the relationship between active region disappearing H-alpha filaments and the associated coronal X-ray structures observed both before the disappearance event and afterwards. The events chosen for the study were selected from a list of active region X-ray transients observed in the images from the X-ray telescope on Skylab and from a list compiled by Webb (1976) of sudden disappearances of filaments during the Skylab period. Results indicate no distinction between the disappearing and the remaining active region filaments in terms of their pre-event associated X-ray emission features. However, X-ray brightenings were associated in a nearly one-to-one correspondence with disappearing portions of the filaments.

  7. The Central California Regional Obesity Prevention Program: Changing Nutrition and Physical Activity Environments in California's Heartland

    PubMed Central

    Samuels, Sarah E.; Capitman, John; Ruwe, Mathilda; Boyle, Maria; Flores, George

    2010-01-01

    The goals of the Central California Regional Obesity Prevention Program (CCROPP) are to promote safe places for physical activity, increase access to fresh fruits and vegetables, and support community and youth engagement in local and regional efforts to change nutrition and physical activity environments for obesity prevention. CCROPP has created a community-driven policy and environmental change model for obesity prevention with local and regional elements in low-income, disadvantaged ethnic and rural communities in a climate of poor resources and inadequate infrastructure. Evaluation data collected from 2005–2009 demonstrate that CCROPP has made progress in changing nutrition and physical activity environments by mobilizing community members, engaging and influencing policymakers, and forming organizational partnerships. PMID:20864732

  8. UVCS Observations of Slow Plasma Flow in the Corona Above Active Regions

    NASA Astrophysics Data System (ADS)

    Woo, R.; Habbal, S. R.

    2005-05-01

    The elusive source of slow solar wind has been the subject of ongoing discussion and debate. Observations of solar wind speed near the Earth orbit, first with IPS (interplanetary scintillation) and later with Ulysses in situ measurements, have suggested that some slow solar wind may be associated with active regions (Kojima & Kakinuma 1987; Woo, Habbal & Feldman 2004). The ability of SOHO UVCS Doppler dimming measurements to provide estimates of solar wind speed in the corona (Kohl et al. 1995) has made it possible to investigate the distribution of flow near the Sun. In this paper, we will present results confirming that active regions are one of the sources of slow wind. Insight into the relationship between coronal streamers, active regions and plasma flow will also be discussed.

  9. Yeast tRNA3Leu gene transcribed and spliced in a HeLa cell extract.

    PubMed Central

    Standring, D N; Venegas, A; Rutter, W J

    1981-01-01

    A cloned yeast tRNA3Leu gene containing a 33-base intervening sequence (IVS) is selectively transcribed by a soluble extract from HeLa cells. The 130-nucleotide tRNA3Leu precursor RNA formed is colinear with the gene and contains approximately 4 leader nucleotides and up to 9 trailer nucleotides. The IVS is accurately and efficiently removed by an endogenous HeLa excision-ligase activity to yield the spliced tRNA, the free IVS, and the half-tRNA intermediates. The splicing reaction occurs without prior 5' and 3' maturation of the precursor but, with this exception, this pattern of synthesis and subsequent maturation of the tRNA3Leu precursor conforms to the scheme for tRNA biosynthesis deduced for the xenopus system. Indeed, the two systems utilize similar or identical tRNA3Leu precursors. Our results stress the extraordinary conservation of tRNA biosynthesis in eukaryotes and demonstrate that a HeLa extract provides a useful system for investigating this process. Images PMID:6796956

  10. Active Region Moss: Doppler Shifts from Hinode/Extreme-ultraviolet Imaging Spectrometer Observations

    NASA Astrophysics Data System (ADS)

    Tripathi, Durgesh; Mason, Helen E.; Klimchuk, James A.

    2012-07-01

    Studying the Doppler shifts and the temperature dependence of Doppler shifts in moss regions can help us understand the heating processes in the core of the active regions. In this paper, we have used an active region observation recorded by the Extreme-ultraviolet Imaging Spectrometer (EIS) on board Hinode on 2007 December 12 to measure the Doppler shifts in the moss regions. We have distinguished the moss regions from the rest of the active region by defining a low-density cutoff as derived by Tripathi et al. in 2010. We have carried out a very careful analysis of the EIS wavelength calibration based on the method described by Young et al. in 2012. For spectral lines having maximum sensitivity between log T = 5.85 and log T = 6.25 K, we find that the velocity distribution peaks at around 0 km s-1 with an estimated error of 4-5 km s-1. The width of the distribution decreases with temperature. The mean of the distribution shows a blueshift which increases with increasing temperature and the distribution also shows asymmetries toward blueshift. Comparing these results with observables predicted from different coronal heating models, we find that these results are consistent with both steady and impulsive heating scenarios. However, the fact that there are a significant number of pixels showing velocity amplitudes that exceed the uncertainty of 5 km s-1 is suggestive of impulsive heating. Clearly, further observational constraints are needed to distinguish between these two heating scenarios.

  11. Associations of season and region on objectively assessed physical activity and sedentary behaviour.

    PubMed

    Hagströmer, Maria; Rizzo, Nico S; Sjöström, Michael

    2014-01-01

    Seasonal and regional variation may influence physical activity (PA) patterns. These associations are in need of further investigation. The objective of the current study was to examine the association of season and region on objectively measured PA. The study was designed as a cross-sectional study with 1172 participants living in Sweden. Data on PA were collected throughout a calendar year using accelerometry. Regions were categorised as south (Götaland), central (Svealand) and north (Norrland). Outcome variables included accelerometer-measured mean counts per minute, sedentary time and time in low intensity and moderate-intensity physical activity (MVPA) or greater. ANCOVA was used to determine the associations of season and region with PA, adjusting for sex, age, body mass index (BMI) and education. The results showed that during the Spring season more time was spent in MVPA than during the Autumn. For participants living in the south of Sweden, a significant trend for season was found for MVPA, with Spring having the highest MVPA (P = 0.025). Season had a borderline significant association with MVPA or higher intensity activities (P = 0.051). No significant effects of region or season on total PA, low-intensity PA and sedentary periods of time were observed. The results indicate that studies conducted in a population living in high latitudes, may not be significantly affected by seasonality or region when assessing PA.

  12. Hot Plasma from Solar Active Region Cores: a Test of AC and DC Coronal Heating Models?

    NASA Astrophysics Data System (ADS)

    Schmelz, J. T.; Asgari-Targhi, M.; Christian, G. M.; Dhaliwal, R. S.; Pathak, S.

    2015-06-01

    Direct current (DC) models of solar coronal heating invoke magnetic reconnection to convert magnetic free energy into heat, whereas alternating current (AC) models invoke wave dissipation. In both cases the energy is supplied by photospheric footpoint motions. For a given footpoint velocity amplitude, DC models predict lower average heating rates but greater temperature variability when compared to AC models. Therefore, evidence of hot plasma (T > 5 MK) in the cores of active regions could be one of the ways for current observations to distinguish between AC and DC models. We have analyzed data from the X-Ray Telescope (XRT) and the Atmospheric Imaging Assembly for 12 quiescent active region cores, all of which were observed in the XRT Be_thick channel. We did Differential Emission Measure (DEM) analysis and achieved good fits for each data set. We then artificially truncated the hot plasma of the DEM model at 5 MK and examined the resulting fits to the data. For some regions in our sample, the XRT intensities continued to be well-matched by the DEM predictions, even without the hot plasma. This truncation, however, resulted in unacceptable fits for the other regions. This result indicates that the hot plasma is present in these regions, even if the precise DEM distribution cannot be determined with the data available. We conclude that reconnection may be heating the hot plasma component of these active regions.

  13. Signatures of Slow Solar Wind Streams from Active Regions in the Inner Corona

    NASA Astrophysics Data System (ADS)

    Slemzin, V.; Harra, L.; Urnov, A.; Kuzin, S.; Goryaev, F.; Berghmans, D.

    2013-08-01

    The identification of solar-wind sources is an important question in solar physics. The existing solar-wind models ( e.g., the Wang-Sheeley-Arge model) provide the approximate locations of the solar wind sources based on magnetic field extrapolations. It has been suggested recently that plasma outflows observed at the edges of active regions may be a source of the slow solar wind. To explore this we analyze an isolated active region (AR) adjacent to small coronal hole (CH) in July/August 2009. On 1 August, Hinode/EUV Imaging Spectrometer observations showed two compact outflow regions in the corona. Coronal rays were observed above the active-region coronal hole (ARCH) region on the eastern limb on 31 July by STEREO-A/EUVI and at the western limb on 7 August by CORONAS- Photon/TESIS telescopes. In both cases the coronal rays were co-aligned with open magnetic-field lines given by the potential field source surface model, which expanded into the streamer. The solar-wind parameters measured by STEREO-B, ACE, Wind, and STEREO-A confirmed the identification of the ARCH as a source region of the slow solar wind. The results of the study support the suggestion that coronal rays can represent signatures of outflows from ARs propagating in the inner corona along open field lines into the heliosphere.

  14. HOT PLASMA FROM SOLAR ACTIVE REGION CORES: A TEST OF AC AND DC CORONAL HEATING MODELS?

    SciTech Connect

    Schmelz, J. T.; Christian, G. M.; Dhaliwal, R. S.; Pathak, S.; Asgari-Targhi, M.

    2015-06-20

    Direct current (DC) models of solar coronal heating invoke magnetic reconnection to convert magnetic free energy into heat, whereas alternating current (AC) models invoke wave dissipation. In both cases the energy is supplied by photospheric footpoint motions. For a given footpoint velocity amplitude, DC models predict lower average heating rates but greater temperature variability when compared to AC models. Therefore, evidence of hot plasma (T > 5 MK) in the cores of active regions could be one of the ways for current observations to distinguish between AC and DC models. We have analyzed data from the X-Ray Telescope (XRT) and the Atmospheric Imaging Assembly for 12 quiescent active region cores, all of which were observed in the XRT Be-thick channel. We did Differential Emission Measure (DEM) analysis and achieved good fits for each data set. We then artificially truncated the hot plasma of the DEM model at 5 MK and examined the resulting fits to the data. For some regions in our sample, the XRT intensities continued to be well-matched by the DEM predictions, even without the hot plasma. This truncation, however, resulted in unacceptable fits for the other regions. This result indicates that the hot plasma is present in these regions, even if the precise DEM distribution cannot be determined with the data available. We conclude that reconnection may be heating the hot plasma component of these active regions.

  15. Determining the solar wind speed above active regions using remote radio-wave observations.

    PubMed

    Bougeret, J L; Fainberg, J; Stone, R G

    1983-11-04

    A new technique has made it possible to measure the velocity of portions of the solar wind during its flow outward from the sun. This analysis utilizes spacecraft (ISEE-3) observations of radio emission generated in regions of the solar wind associated with solar active regions. By tracking the source of these radio waves over periods of days, it is possible to measure the motion of the emission regions. Evidence of solar wind acceleration during this outward flow, consistent with theoretical models, has also been obtained.

  16. Determining the solar wind speed above active regions using remote radio-wave observations

    NASA Technical Reports Server (NTRS)

    Fainberg, J.; Stone, R. G.; Bougeret, J.-L.

    1983-01-01

    A new technique has made it possible to measure the velocity of portions of the solar wind during its flow outward from the sun. This analysis utilizes spacecraft (ISEE-3) observations of radio emission generated in regions of the solar wind associated with solar active regions. By tracking the source of these radio waves over periods of days, it is possible to measure the motion of the emission regions. Evidence of solar wind acceleration during this outward flow, consistent with theoretical models, has also been obtained.

  17. Relationship between the photospheric Poynting flux and the active region luminosity

    NASA Astrophysics Data System (ADS)

    Kazachenko, Maria D.; Canfield, Richard C.; Fisher, George H.; Hudson, Hugh S.; Welsch, Brian

    2014-06-01

    How does energy radiated by active regions compare with magnetic energy that propagates lower across the photosphere? This is a fundamental question for energy storage and release in active regions, yet it is presently poorly understood. In this work we quantify and compare both energy terms using SDO observations of the active region (AR) 11520. To quantify the magnetic energy crossing the photosphere, or the Poynting flux, we need to know both the magnetic field vector B and electric field vector E as well. Our current electric field inversion technique, PDFI, combines the Poloidal-Toroidal-Decomposition method with information from Doppler measurements, Fourier local correlation tracking (FLCT) results, and the ideal MHD constraint, to determine the electric field from vector magnetic field and Doppler data. We apply the PDFI method to a sequence of Helioseismic and Magnetic Imager (HMI/SDO) vector magnetogram data, to find the electric-field and hence the Poynting-flux evolution in AR 11520. We find that most of the magnetic energy in this AR is injected in the range of $10^7$ to $10^8$ $ergs/{cm^2 s}$, with the largest fluxes reaching $10^{10}$ $ergs/{cm^2 s}$. Integrating over the active region this yields a total energy of order $10^{28}$ ergs/s. To quantify the active region luminosity, we use EUV Variability Experiment (EVE) and Atmospheric Imaging Assembly (AIA) spectrally resolved observations. We find the active region luminosity of order $10^{28}$ ergs/s. We compare derived magnetic and radiated energy fluxes on different temporal and spatial scales and estimate their uncertainties. We also discuss the roles that potential/non-potential and emerging/shearing terms play in the total magnetic energy budget.

  18. Explosive events in active region observed by IRIS and SST/CRISP

    NASA Astrophysics Data System (ADS)

    Huang, Z.; Madjarska, M. S.; Scullion, E. M.; Xia, L.-D.; Doyle, J. G.; Ray, T.

    2017-01-01

    Transition-region explosive events (EEs) are characterized by non-Gaussian line profiles with enhanced wings at Doppler velocities of 50-150 km s-1. They are believed to be the signature of solar phenomena that are one of the main contributors to coronal heating. The aim of this study is to investigate the link of EEs to dynamic phenomena in the transition region and chromosphere in an active region. We analyse observations simultaneously taken by the Interface Region Imaging Spectrograph (IRIS) in the Si IV 1394 Å line and the slit-jaw (SJ) 1400 Å images, and the Swedish 1-m Solar Telescope in the Hα line. In total 24 events were found. They are associated with small-scale loop brightenings in SJ 1400 Å images. Only four events show a counterpart in the Hα-35 km s-1 and Hα+35 km s-1 images. Two of them represent brightenings in the conjunction region of several loops that are also related to a bright region (granular lane) in the Hα-35 km s-1 and Hα+35 km s-1 images. 16 are general loop brightenings that do not show any discernible response in the Hα images. Six EEs appear as propagating loop brightenings, from which two are associated with dark jet-like features clearly seen in the Hα-35 km s-1 images. We found that chromospheric events with jet-like appearance seen in the wings of the Hα line can trigger EEs in the transition region and in this case the IRIS Si IV 1394 Å line profiles are seeded with absorption components resulting from Fe II and Ni II. Our study indicates that EEs occurring in active regions have mostly upper-chromosphere/transition-region origin. We suggest that magnetic reconnection resulting from the braidings of small-scale transition region loops is one of the possible mechanisms of energy release that are responsible for the EEs reported in this paper.

  19. Detailed correlation of type III radio bursts with H alpha activity. I - Active region of 22 May 1970.

    NASA Technical Reports Server (NTRS)

    Kuiper, T. B. H.; Pasachoff, J. M.

    1973-01-01

    Comparison of observations of type III impulsive radio bursts made at the Clark Lake Radio Observatory with high-spatial-resolution cinematographic observations taken at the Big Bear Solar Observatory. Use of the log-periodic radio interferometer makes it possible to localize the radio emission uniquely. This study concentrates on the particularly active region close to the limb on May 22, 1970. Sixteen of the 17 groups were associated with some H alpha activity, 11 of them with the start of such activity.

  20. A regional reconstruction of debris-flow activity in the Northern Calcareous Alps, Austria

    NASA Astrophysics Data System (ADS)

    Procter, Emily; Bollschweiler, Michelle; Stoffel, Markus; Neumann, Mathias

    2011-09-01

    Dendrogeomorphic dating of historical debris-flow events is a highly valuable tool for improving historical records in the field of natural hazard management. Previous dendrogeomorphic investigations generally have focused on case studies of single torrents; however, regional investigations may offer a more accurate reconstruction of regional patterns of activity and therefore may have an advantage over individual cases. The aim of the study is to provide a regional reconstruction of debris-flow events for a site in the Northern Calcareous Alps of western Austria (Gamperdonatal, Vorarlberg) and to document spatial and temporal morphological changes in individual and neighboring torrents. Analysis of 442 trees (268 Pinus mugo ssp. uncinata, 164 Picea abies, and 10 Abies alba) allowed identification of 579 growth disturbances corresponding to 63 debris-flow events since A.D. 1839. The majority of growth disturbances were in the form of growth suppression or release (76%) owing to the nature of both the deposited material and the process characteristics. Regional patterns of event frequency indicated a paucity of activity in the early to mid-twentieth century and increased activity since A.D. 1948, whereby large events were followed by subsequent years of continued activity of smaller magnitude. Patterns of frequency could be attributed primarily to spatiotemporal changes in channel morphology, but may also be reflective of changes in transport conditions within the valley. This study provides the first regional investigation in the Austrian Alps and contributes to the documentation of tree responses to geomorphic disturbances in calcareous material.

  1. Light Bridge in a Developing Active Region. I. Observation of Light Bridge and its Dynamic Activity Phenomena

    NASA Astrophysics Data System (ADS)

    Toriumi, Shin; Katsukawa, Yukio; Cheung, Mark C. M.

    2015-10-01

    Light bridges, the bright structures that divide the umbra of sunspots and pores into smaller pieces, are known to produce a wide variety of activity events in solar active regions (ARs). It is also known that the light bridges appear in the assembling process of nascent sunspots. The ultimate goal of this series of papers is to reveal the nature of light bridges in developing ARs and the occurrence of activity events associated with the light bridge structures from both observational and numerical approaches. In this first paper, exploiting the observational data obtained by Hinode, the Interface Region Imaging Spectrograph, and the Solar Dynamics Observatory, we investigate the detailed structure of the light bridge in NOAA AR 11974 and its dynamic activity phenomena. As a result, we find that the light bridge has a weak, horizontal magnetic field, which is transported from the interior by a large-scale convective upflow and is surrounded by strong, vertical fields of adjacent pores. In the chromosphere above the bridge, a transient brightening occurs repeatedly and intermittently, followed by a recurrent dark surge ejection into higher altitudes. Our analysis indicates that the brightening is the plasma heating due to magnetic reconnection at lower altitudes, while the dark surge is the cool, dense plasma ejected from the reconnection region. From the observational results, we conclude that the dynamic activity observed in a light bridge structure such as chromospheric brightenings and dark surge ejections are driven by magnetoconvective evolution within the light bridge and its interaction with the surrounding magnetic fields.

  2. A viable non-axisymmetric non-force-free field to represent solar active regions

    NASA Astrophysics Data System (ADS)

    Prasad, A.; Bhattacharyya, R.

    2016-11-01

    A combination of analytical calculations and vectormagnetogram data is utilized to develop a non-axisymmetric non-force-free magnetic field and assess its viability in describing solar active regions. For that purpose, we construct a local spherical shell where a planar surface, tangential to the inner sphere, represents a Cartesian cutout of an active region. The magnetic field defined on the surface is then correlated with magnetograms. The analysis finds that the non-axisymmetric non-force-free magnetic field, obtained by a superposition of two linear-force-free fields, correlates reasonably well with magnetograms.

  3. Comparison of the activity measurements in nuclear medicine services in the Brazilian northeast region.

    PubMed

    de Farias Fragoso, Maria da Conceição; de Albuquerque, Antônio Morais; de Oliveira, Mércia L; de Lima, Fabiana Farias; Barreto, Flávio Chiappetta Paes; de Andrade Lima, Ricardo

    2013-12-01

    The Northeastern Regional Centre for Nuclear Sciences (CRCN-NE), National Nuclear Energy Commission, has organized for the first time in nuclear medicine services (NMSs) in the Brazilian northeast region a comparison of activity measurements for (99m)Tc, (131)I, (67)Ga, (201)Tl and (57)Co. This tool is widely utilized to evaluate not only the accuracy of radionuclide calibrators, but also the competence of NMSs to measure the activity of the radiopharmaceuticals and the performance of the personnel involved in these measurements. The comparison results showed that 90% of the results received from participants are within the ±10% limit established by the Brazilian Norm.

  4. RESEARCH PAPER: A logistic model for magnetic energy storage in solar active regions

    NASA Astrophysics Data System (ADS)

    Wang, Hua-Ning; Cui, Yan-Mei; He, Han

    2009-06-01

    Previous statistical analyses of a large number of SOHO/MDI full disk longitudinal magnetograms provided a result that demonstrated how responses of solar flares to photospheric magnetic properties can be fitted with sigmoid functions. A logistic model reveals that these fitted sigmoid functions might be related to the free energy storage process in solar active regions. Although this suggested model is rather simple, the free energy level of active regions can be estimated and the probability of a solar flare with importance over a threshold can be forecast within a given time window.

  5. The birthplaces of active regions and X-ray bright points. [on sun

    NASA Technical Reports Server (NTRS)

    Howard, R.; Fritzova-Svestkova, L.; Svestka, Z.

    1979-01-01

    A comparison of soft X-ray pictures of the Sun (S-054 experiment of Skylab) with K-line spectroheliograms (Mount Wilson) shows that the X-ray bright points tend to emerge randomly throughout the Ca network pattern. However, all those bright points that developed into active regions emerged at the boundaries of network cells. This suggests that the magnetic flux of active regions comes from greater depths in the convection zone that the shallow flux that gives rise to the random emergence of bright points.

  6. Space-weather Parameters for 1,000 Active Regions Observed by SDO/HMI

    NASA Astrophysics Data System (ADS)

    Bobra, M.; Liu, Y.; Hoeksema, J. T.; Sun, X.

    2013-12-01

    We present statistical studies of several space-weather parameters, derived from observations of the photospheric vector magnetic field by the Helioseismic and Magnetic Imager (HMI) aboard the Solar Dynamics Observatory, for a thousand active regions. Each active region has been observed every twelve minutes during the entirety of its disk passage. Some of these parameters, such as energy density and shear angle, indicate the deviation of the photospheric magnetic field from that of a potential field. Other parameters include flux, helicity, field gradients, polarity inversion line properties, and measures of complexity. We show that some of these parameters are useful for event prediction.

  7. Karyotypes, C-banding, and chromosomal location of active nucleolar organizing regions in Tapinoma (Hymenoptera, Formicidae).

    PubMed

    Palomeque, T; Chica, E; Cano, M A; Díaz de la Guardia, R

    1988-04-01

    The haploid and diploid karyotypes of Tapinoma erraticum (n = 8) and Tapinoma nigerrimum (n = 9) were analyzed using C-banding and observation of NOR sites. C-banding showed the existence of heterochromatin in the paracentromeric regions of all chromosomes. The analysis of NOR sites in these species proved the existence of primary activity NOR in one or two chromosomes, respectively, whereas the other chromosomes showed secondary activity NOR, expressed only in a minority of cells. In both species the NOR were located in paracentromeric regions. These results are discussed in relation to a hypothesis of chromosome differentiation of these species.

  8. Real-Time CME Forecasting Using HMI Active-Region Magnetograms and Flare History

    NASA Technical Reports Server (NTRS)

    Falconer, David; Moore, Ron; Barghouty, Abdulnasser F.; Khazanov, Igor

    2011-01-01

    We have recently developed a method of predicting an active region s probability of producing a CME, an X-class Flare, an M-class Flare, or a Solar Energetic Particle Event from a free-energy proxy measured from SOHO/MDI line-of-sight magnetograms. This year we have added three major improvements to our forecast tool: 1) Transition from MDI magnetogram to SDO/HMI magnetogram allowing us near-real-time forecasts, 2) Automation of acquisition and measurement of HMI magnetograms giving us near-real-time forecasts (no older than 2 hours), and 3) Determination of how to improve forecast by using the active region s previous flare history in combination with its free-energy proxy. HMI was turned on in May 2010 and MDI was turned off in April 2011. Using the overlap period, we have calibrated HMI to yield what MDI would measure. This is important since the value of the free-energy proxy used for our forecast is resolution dependent, and the forecasts are made from results of a 1996-2004 database of MDI observations. With near-real-time magnetograms from HMI, near-real-time forecasts are now possible. We have augmented the code so that it continually acquires and measures new magnetograms as they become available online, and updates the whole-sun forecast from the coming day. The next planned improvement is to use an active region s previous flare history, in conjunction with its free-energy proxy, to forecast the active region s event rate. It has long been known that active regions that have produced flares in the past are likely to produce flares in the future, and that active regions that are nonpotential (have large free-energy) are more likely to produce flares in the future. This year we have determined that persistence of flaring is not just a reflection of an active region s free energy. In other words, after controlling for free energy, we have found that active regions that have flared recently are more likely to flare in the future.

  9. RPMA (Real Property Maintenance Activities) Consolidation Activities in the National Capital Region. Volume 1. Main Report.

    DTIC Science & Technology

    1984-05-01

    planning the activities of future IPCs. Pre-IPC Activities Participating installations should have been directed through command channels to take the...the task with minimal impact on the existing A workload, and (2) ensure that the request for inforniation is formal and sent through channels . Planners...34... . .•.....¢,.. -...... ,- % * .*. ...... ....... .°. •.-.-.-. •..... 39. The District init inttei the cofl ract Ior <I’MA t i i on;, e i, ( I i HQDA through command channels . 40

  10. T7 RNA polymerase cannot transcribe through a highly knotted DNA template.

    PubMed Central

    Portugal, J; Rodríguez-Campos, A

    1996-01-01

    The ability of T7 RNA polymerase to transcribe a plasmid DNA in vitro in its linear, supercoiled, relaxed and knotted forms was analysed. Similar levels of transcription were found on each template with the exception of plasmids showing varying degrees of knotting (obtained using stoichiometric amounts of yeast topoisomerase II). A purified fraction of knotted DNA with a high number of nodes (crosses) was found to be refractory to transcription. The unknotting of the knotted plasmids, using catalytic amounts of topoisomerase II, restored their capacity as templates for transcription to levels similar to those obtained for the other topological forms. These results demonstrate that highly knotted DNA is the only topological form of DNA that is not a template for transcription. We suggest that the regulation of transcription, which depends on the topological state of the template, might be related to the presence of knotted DNA with different number of nodes. PMID:9016657

  11. Photobleaching reveals complex effects of inhibitors on transcribing RNA polymerase II in living cells

    SciTech Connect

    Fromaget, Maud; Cook, Peter R. . E-mail: peter.cook@path.ox.ac.uk

    2007-08-15

    RNA polymerase II transcribes most eukaryotic genes. Photobleaching studies have revealed that living Chinese hamster ovary cells expressing the catalytic subunit of the polymerase tagged with the green fluorescent protein contain a large rapidly exchanging pool of enzyme, plus a smaller engaged fraction; genetic complementation shows this tagged polymerase to be fully functional. We investigated how transcriptional inhibitors - some of which are used therapeutically - affect the engaged fraction in living cells using fluorescence loss in photobleaching; all were used at concentrations that have reversible effects. Various kinase inhibitors (roscovitine, DRB, KM05283, alsterpaullone, isoquinolinesulfonamide derivatives H-7, H-8, H-89, H-9), proteasomal inhibitors (lactacystin, MG132), and an anti-tumour agent (cisplatin) all reduced the engaged fraction; an intercalator (actinomycin D), two histone deacetylase inhibitors (trichostatin A, sodium butyrate), and irradiation with ultra-violet light all increased it. The polymerase proves to be both a sensitive sensor and effector of the response to these inhibitors.

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

    PubMed

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

    2012-05-01

    The present article deals with the polymerase chain reaction (PCR)-based genotoxicity evaluation of neonicotinoid pesticides, imidacloprid and thiamethoxam, by using the genome of a mosquito Anopheles stephensi taken as an experimental model. After treatment of the second instar larvae with LC(20) of the pesticides for 24 h, the induced nucleotide sequence variations in the internal transcribed spacer 2 (ITS2) of freshly hatched unfed control and treated individuals was studied from the sequence alignment data and the mutations in the form of insertion, deletion and substitution of bases were recorded. Measurable differences, indicative of the genetic damage due to imidacloprid and thiamethoxam were observed when ITS2 sequences of control and treated individuals were compared. It was found that imidacloprid-treated individual had 8 deletions, 29 insertions, 18 transitions and 33 transversions, whereas thiamethoxam-treated individual had 10 deletions, 8 insertions, 47 transitions and 68 transversions.

  13. Forward modeling transient brightenings and microflares around an active region observed with Hi-C

    SciTech Connect

    Kobelski, Adam R.; McKenzie, David E.

    2014-10-20

    Small-scale flare-like brightenings around active regions are among the smallest and most fundamental of energetic transient events in the corona, providing a testbed for models of heating and active region dynamics. In a previous study, we modeled a large collection of these microflares observed with Hinode/X-Ray Telescope (XRT) using EBTEL and found that they required multiple heating events, but could not distinguish between multiple heating events on a single strand, or multiple strands each experiencing a single heating event. We present here a similar study, but with extreme-ultraviolet data of Active Region 11520 from the High Resolution Coronal Imager (Hi-C) sounding rocket. Hi-C provides an order of magnitude improvement to the spatial resolution of XRT, and a cooler temperature sensitivity, which combine to provide significant improvements to our ability to detect and model microflare activity around active regions. We have found that at the spatial resolution of Hi-C (≈0.''3), the events occur much more frequently than expected (57 events detected, only 1 or 2 expected), and are most likely made from strands of the order of 100 km wide, each of which is impulsively heated with multiple heating events. These findings tend to support bursty reconnection as the cause of the energy release responsible for the brightenings.

  14. Regional NAD(P)H:quinone oxidoreductase activity in Alzheimer's disease.

    PubMed

    SantaCruz, Karen S; Yazlovitskaya, Eugenia; Collins, Julie; Johnson, Jeff; DeCarli, Charles

    2004-01-01

    Converging evidence supports the role of oxidative stress in the pathology of Alzheimer's disease (AD). This notion is further supported by recent findings of increased NAD(P)H:quinone oxidodreductase (NQO1) activity, a potent antioxidant system, in association with hippocampal AD pathology. If increased NQO1 activity is truly related to the AD process, however, we would expect to see regional co-localization of NQO1 activity with AD pathology throughout affected brain regions and the absence of NQO1 activity in regions unaffected by AD. We examined this hypothesis by measuring NQO1 enzymatic activity and NQO1 immunohistochemical staining in regions commonly affected by the AD process such as frontal cortex and compared this to regions generally unaffected by the AD process such as occipital cortex, cerebellum, and substantia nigra for a group of AD patients and controls. The ratio of frontal to cerebellar NQO1 enzymatic activity was significantly increased in patients with AD (2.07 +/- 1.90) versus controls (0.60 +/- 0.31; P < 0.03). Moreover, regional immunohistochemical staining revealed specific localization of NQO1 staining to astrocytes and neurites surrounding senile plaques. The extent of immunohistochemical staining also closely correlated with the extent of local AD pathology across the various brain regions examined. Neuronal NQO1 staining seen in frontal cortex of AD patients was absent in frontal cortex of controls, but was found to the same extent in neurons of the substantia nigra of both AD patients and controls. We conclude that NQO1 activity co-localizes closely with AD pathology supporting a presumed role as an antioxidant system upregulated in response to the oxidative stress of the AD process. The antioxidant role for NQO1 is further supported by finding increased neuronal NQO1 activity in substantia nigra neurons of both AD patients and controls as this neuronal population is known to be under constant oxidative stress. While requiring further

  15. Efficient regeneration by activation of neurogenesis in homeostatically quiescent regions of the adult vertebrate brain.

    PubMed

    Berg, Daniel A; Kirkham, Matthew; Beljajeva, Anna; Knapp, Dunja; Habermann, Bianca; Ryge, Jesper; Tanaka, Elly M; Simon, András

    2010-12-01

    In contrast to mammals, salamanders and teleost fishes can efficiently repair the adult brain. It has been hypothesised that constitutively active neurogenic niches are a prerequisite for extensive neuronal regeneration capacity. Here, we show that the highly regenerative salamander, the red spotted newt, displays an unexpectedly similar distribution of active germinal niches with mammals under normal physiological conditions. Proliferation zones in the adult newt brain are restricted to the forebrain, whereas all other regions are essentially quiescent. However, ablation of midbrain dopamine neurons in newts induced ependymoglia cells in the normally quiescent midbrain to proliferate and to undertake full dopamine neuron regeneration. Using oligonucleotide microarrays, we have catalogued a set of differentially expressed genes in these activated ependymoglia cells. This strategy identified hedgehog signalling as a key component of adult dopamine neuron regeneration. These data show that brain regeneration can occur by activation of neurogenesis in quiescent brain regions.

  16. Brain regional development of the activity of alpha-ketoglutarate dehydrogenase complex in the rat.

    PubMed

    Buerstatte, C R; Behar, K L; Novotny, E J; Lai, J C

    2000-12-29

    This study was initiated to test the hypothesis that the development of alpha-ketoglutarate dehydrogenase complex (KGDHC) activity, like that of pyruvate dehydrogenase complex, is one of the late developers of tricarboxylic acid (TCA) cycle enzymes. The postnatal development of KGDHC in rat brain exhibits four distinct region-specific patterns. The age-dependent increases in olfactory bulb (OB) and hypothalamus (HYP) form one pattern: low in postnatal days (P) 2 and 4, KGDHC activity rose linearly to attain adult level at P30. The increases in mid-brain (MB) and striatum (ST) constitute a second pattern: being <40% of adult level at P2 and P4, KGDHC activity rose steeply between P10 and P17 and attained adult level by P30. The increases in cerebellum (CB), cerebral cortex (CC), and hippocampus (HIP) form a third pattern: being 25-30% of adult level at P2 and P4, KGDHC activity doubled between P10 and P17 and rose to adult level by P30. KGDHC activity development is unique in pons and medulla (PM): being >60% of the adult level at P2, it rose rapidly to adult level by P10. Thus, KGDHC activity develops earlier in phylogenetically older regions (PM) than in phylogenetically younger regions (CB, CC, HIP). Being lowest in activity among all TCA cycle enzymes, KGDHC activity in any region at any age will exert a limit on the maximum TCA cycle flux therein. The results may have functional and pathophysiological implications in control of brain glucose oxidative metabolism, energy metabolism, and neurotransmitter syntheses.

  17. Cyclone activity in the Arctic from an ensemble of regional climate models (Arctic CORDEX)

    NASA Astrophysics Data System (ADS)

    Akperov, Mirseid; Mokhov, Igor; Rinke, Annette; Handorf, Doerthe; Dethloff, Klaus

    2016-04-01

    The ability of the regional climate models (Arctic CORDEX) to simulate cyclone activity for the Arctic region is investigated. 10 regional climate models (RCMs), including models with and w/o "nudging" are considered. Comparing the characteristics of cyclone activity with the use of an ensemble of RCM's hindcast simulations and ERA-Interim reanalysis for four seasons (winter, spring, summer, autumn) and for last decades, biases in cyclone frequency, intensity and size over the Arctic (region ca. north of 60°N) are quantified. In spite of these biases RCM's are able to represent the characteristics of cyclone activity in the Arctic region, in particular RCM's with "nudging". The spread across the models are estimated. Additionally, the characteristics of extreme mesocyclones (polar lows) are investigated. The ability of RCM's and reanalyses (ERA-Interim, Arctic system reanalysis - ASR) to represent polar lows over the Barents and Kara Seas in comparison with satellite observations is assessed. Reanalyses and RCM's with high spatial resolution are able to represent ca. 50% of the observed polar lows.

  18. Flow and magnetic field properties in the trailing sunspots of active region NOAA 12396

    NASA Astrophysics Data System (ADS)

    Verma, M.; Denker, C.; Böhm, F.; Balthasar, H.; Fischer, C. E.; Kuckein, C.; Bello González, N.; Berkefeld, T.; Collados, M.; Diercke, A.; Feller, A.; González Manrique, S. J.; Hofmann, A.; Lagg, A.; Nicklas, H.; Orozco Suárez, D.; Pator Yabar, A.; Rezaei, R.; Schlichenmaier, R.; Schmidt, D.; Schmidt, W.; Sigwarth, M.; Sobotka, M.; Solanki, S. K.; Soltau, D.; Staude, J.; Strassmeier, K. G.; Volkmer, R.; von der Lühe, O.; Waldmann, T.

    2016-11-01

    Improved measurements of the photospheric and chromospheric three-dimensional magnetic and flow fields are crucial for a precise determination of the origin and evolution of active regions. We present an illustrative sample of multi-instrument data acquired during a two-week coordinated observing campaign in August 2015 involving, among others, the GREGOR solar telescope (imaging and near-infrared spectroscopy) and the space missions Solar Dynamics Observatory (SDO) and Interface Region Imaging Spectrograph (IRIS). The observations focused on the trailing part of active region NOAA 12396 with complex polarity inversion lines and strong intrusions of opposite polarity flux. The GREGOR Infrared Spectrograph (GRIS) provided Stokes IQUV spectral profiles in the photospheric Si I λ1082.7 nm line, the chromospheric He I λ1083.0 nm triplet, and the photospheric Ca I λ1083.9 nm line. Carefully calibrated GRIS scans of the active region provided maps of Doppler velocity and magnetic field at different atmospheric heights. We compare quick-look maps with those obtained with the ``Stokes Inversions based on Response functions'' (SIR) code, which furnishes deeper insight into the magnetic properties of the region. We find supporting evidence that newly emerging flux and intruding opposite polarity flux are hampering the formation of penumbrae, i.e., a penumbra fully surrounding a sunspot is only expected after cessation of flux emergence in proximity to the sunspots.

  19. Differential Activation Patterns in the Same Brain Region Led to Opposite Emotional States

    PubMed Central

    Shibata, Kazuhisa; Watanabe, Takeo; Kawato, Mitsuo; Sasaki, Yuka

    2016-01-01

    In human studies, how averaged activation in a brain region relates to human behavior has been extensively investigated. This approach has led to the finding that positive and negative facial preferences are represented by different brain regions. However, using a functional magnetic resonance imaging (fMRI) decoded neurofeedback (DecNef) method, we found that different patterns of neural activations within the cingulate cortex (CC) play roles in representing opposite directions of facial preference. In the present study, while neutrally preferred faces were presented, multi-voxel activation patterns in the CC that corresponded to higher (or lower) preference were repeatedly induced by fMRI DecNef. As a result, previously neutrally preferred faces became more (or less) preferred. We conclude that a different activation pattern in the CC, rather than averaged activation in a different area, represents and suffices to determine positive or negative facial preference. This new approach may reveal the importance of an activation pattern within a brain region in many cognitive functions. PMID:27608359

  20. Seasonal distribution of microbial activity in bioaerosols in the outdoor environment of the Qingdao coastal region

    NASA Astrophysics Data System (ADS)

    Zhong, Xi; Qi, Jianhua; Li, Hongtao; Dong, Lijie; Gao, Dongmei

    2016-09-01

    Microbial activities in the atmosphere can indicate the physiological processes of microorganisms and can indirectly affect cloud formation and environmental health. In this study, the microbial activity in bioaerosols collected in the Qingdao coastal region was investigated using the fluorescein diacetate (FDA) hydrolysis method to detect the enzyme activity of microorganisms. The results showed that the microbial activity ranged from 5.49 to 102 ng/m3 sodium fluorescein from March 2013 to February 2014; the average value was 34.4 ng/m3. Microbial activity has no statistical correlation with total microbial quantity. Multiple linear regression analysis showed that meteorological factors such as atmospheric temperature, relative humidity and wind speed accounted for approximately 35.7% of the variation of the microbial activity, although their individual impacts on microbial activity varied. According to the correlation analysis, atmospheric temperature and wind speed had a significant positive and negative influence on microbial activity, respectively, whereas relative humidity and wind direction had no significant influence. The seasonal distribution of microbial activity in bioaerosols was in the order of summer > autumn > winter > spring, with high fluctuations in the summer and autumn. Microbial activity in bioaerosols differed in different weather conditions such as the sunny, foggy, and hazy days of different seasons. Further in situ observations in different weather conditions at different times and places are needed to understand the seasonal distribution characteristics of microbial activity in bioaerosols and the influence factors of microbial activity.

  1. Identifying induced seismicity in active tectonic regions: A case study of the San Joaquin Basin, California

    NASA Astrophysics Data System (ADS)

    Aminzadeh, F.; Göbel, T.

    2013-12-01

    Understanding the connection between petroleum-industry activities, and seismic event occurrences is essential to monitor, quantify, and mitigate seismic risk. While many studies identified anthropogenically-induced seismicity in intraplate regions where background seismicity rates are generally low, little is known about how to distinguish naturally occurring from induced seismicity in active tectonic regions. Further, it is not clear how different oil and gas operational parameters impact the frequency and magnitude of the induced seismic events. Here, we examine variations in frequency-size and spatial distributions of seismicity within the Southern Joaquin basin, an area of both active petroleum production and active fault systems. We analyze a newly available, high-quality, relocated earthquake catalog (Hauksson et al. 2012). This catalog includes many seismic events with magnitudes up to M = 4.5 within the study area. We start by analyzing the overall quality and consistence of the seismic catalog, focusing on temporal variations in seismicity rates and catalog completeness which could indicate variations in network sensitivity. This catalog provides relatively homogeneous earthquake recordings after 1981, enabling us to compare seismicity rates before and after the beginning of more pervasive petroleum-industry activities, for example, hydraulic-fracturing and waste-water disposals. We conduct a limited study of waste-water disposal wells to establish a correlation between seismicity statistics (i.e. rate changes, fractal dimension, b-value) within specific regions and anthropogenic influences. We then perform a regional study, to investigate spatial variations in seismicity statistics which are then correlated to oil field locations and well densities. In order to distinguish, predominantly natural seismicity from induced seismicity, we perform a spatial mapping of b-values and fractal dimensions of earthquake hypocenters. Seismic events in the proximity to

  2. Cross-modal activation of auditory regions during visuo-spatial working memory in early deafness.

    PubMed

    Ding, Hao; Qin, Wen; Liang, Meng; Ming, Dong; Wan, Baikun; Li, Qiang; Yu, Chunshui

    2015-09-01

    Early deafness can reshape deprived auditory regions to enable the processing of signals from the remaining intact sensory modalities. Cross-modal activation has been observed in auditory regions during non-auditory tasks in early deaf subjects. In hearing subjects, visual working memory can evoke activation of the visual cortex, which further contributes to behavioural performance. In early deaf subjects, however, whether and how auditory regions participate in visual working memory remains unclear. We hypothesized that auditory regions may be involved in visual working memory processing and activation of auditory regions may contribute to the superior behavioural performance of early deaf subjects. In this study, 41 early deaf subjects (22 females and 19 males, age range: 20-26 years, age of onset of deafness < 2 years) and 40 age- and gender-matched hearing controls underwent functional magnetic resonance imaging during a visuo-spatial delayed recognition task that consisted of encoding, maintenance and recognition stages. The early deaf subjects exhibited faster reaction times on the spatial working memory task than did the hearing controls. Compared with hearing controls, deaf subjects exhibited increased activation in the superior temporal gyrus bilaterally during the recognition stage. This increased activation amplitude predicted faster and more accurate working memory performance in deaf subjects. Deaf subjects also had increased activation in the superior temporal gyrus bilaterally during the maintenance stage and in the right superior temporal gyrus during the encoding stage. These increased activation amplitude also predicted faster reaction times on the spatial working memory task in deaf subjects. These findings suggest that cross-modal plasticity occurs in auditory association areas in early deaf subjects. These areas are involved in visuo-spatial working memory. Furthermore, amplitudes of cross-modal activation during the maintenance stage were

  3. Inventory of non-federally funded marine pollution research, development, and monitoring activities: West Coast region

    SciTech Connect

    Canton, G.M.; Opresko, D.M.; Weaver, R.S.

    1987-12-01

    Knowledge of current marine pollution research and monitoring programs is an important factor in planning and guiding future national efforts to control such pollution. To supplement these reports on Federal activities, NMPPO published a series of reports in 1980 on non-federally funded marine pollution research and monitoring activities in various regions. The following document presents an update of one of these reports. It presents an inventory of the non-federally funded research and monitoring projects for the West Coast region of the United States. It is one in a series of four updates that will collectively provide an updated inventory of non-federally funded projects for all the coastal regions of the United States.

  4. Temperature and Abundance Variations of an Active Region in Three Solar Rotations

    NASA Astrophysics Data System (ADS)

    Ko, Y.; Fludra, A.; Raymond, J. C.

    2002-12-01

    Active region 9718 (AR 9718) appeared at the east limb on November 26, 2001 which was newly formed when it was at the backside of the Sun. It survives through three solar rotations -- AR 9755 and AR 9798 for subsequent rotations. AR 9798 decayed to no visible sunspot before it reached the west limb. SOHO/UVCS observed this region four times, as part of SOHO JOP 151, when it was at the limbs (AR 9718 at the west limb, AR 9755 at both the east and west limbs, and AR 9798 at the west limb). SOHO/CDS made observations when AR 9718 and AR 9755 were at the west limb. We investigate the temperature and abundance variations of this active region during its lifetime, and look for possible correlations between these physical parameters and its magnetic characteristics.

  5. Dynamics in Restructuring Active Regions Observed During Soho/Yohkoh/Gbo Campaigns

    NASA Astrophysics Data System (ADS)

    Schmieder, B.; Deng, Y.; Mandrini, C. H.; Rudawy, P.; Nitta, N.; Mason, H.; Fletcher, L.; Martens, P.; Brynildsen, N.

    JOP17 and JOP 33 are SOHO Joint Observing Programs in collaboration with Yohkoh/SXT and ground based observatories (GBO's), dedicated to observe dynamical events through the atmosphere. During runs of these programs we observed in restructuring active regions (ARs), surges, subflares, bright knots, but not large flares and jets. From these observations we have been able to derive some of the responses of the coronal and chromospheric plasma to the evolution of the photospheric magnetic field. Emerging flux in an AR led to the formation of Arch Filament Systems in the chromosphere, hot loops and knots in the transition region, and X-ray loops. Frequent surges have been observed in relation to parasitic or mixed polarities, but coronal jets have not yet been found. We discuss the possible mechanisms acting during the restructuring of the active regions (reconnection or ``sea-serpent'' geometries)

  6. "Power, Regulation and Physically Active Identities": The Experiences of Rural and Regional Living Adolescent Girls

    ERIC Educational Resources Information Center

    Casey, M.; Mooney, A.; Smyth, J.; Payne, W.

    2016-01-01

    Drawing on interpretations of Foucault's techniques of power, we explored the discourses and power relations operative between groups of girls that appeared to influence their participation in Physical Education (PE) and outside of school in sport and physical activity (PA) in rural and regional communities. Interviews and focus groups were…

  7. CURRENT HELICITY OF ACTIVE REGIONS AS A TRACER OF LARGE-SCALE SOLAR MAGNETIC HELICITY

    SciTech Connect

    Zhang, H.; Gao, Y.; Xu, H.; Moss, D.; Kleeorin, N.; Rogachevskii, I.; Kuzanyan, K.; Sokoloff, D.

    2012-05-20

    We demonstrate that the current helicity observed in solar active regions traces the magnetic helicity of the large-scale dynamo generated field. We use an advanced two-dimensional mean-field dynamo model with dynamo saturation based on the evolution of the magnetic helicity and algebraic quenching. For comparison, we also studied a more basic two-dimensional mean-field dynamo model with simple algebraic alpha-quenching only. Using these numerical models we obtained butterfly diagrams both for the small-scale current helicity and also for the large-scale magnetic helicity, and compared them with the butterfly diagram for the current helicity in active regions obtained from observations. This comparison shows that the current helicity of active regions, as estimated by -A {center_dot} B evaluated at the depth from which the active region arises, resembles the observational data much better than the small-scale current helicity calculated directly from the helicity evolution equation. Here B and A are, respectively, the dynamo generated mean magnetic field and its vector potential. A theoretical interpretation of these results is given.

  8. "Not Greenies" at School: Investigating the Discourses of Environmental Activism in Regional Australia

    ERIC Educational Resources Information Center

    Whitehouse, Hilary

    2014-01-01

    Implementing environmental activism at school can be socially risky business. This paper explores the narratives of three women who undertook award winning environmental projects in two regional Australian schools. Tara (student, age 15) and Andrea (principal, age 42) document the complex and courageous social negotiations they were forced to…

  9. Impact-related Events on Active Tectonic Regions Defined by Its Age, Shocked Minerals and Compositions

    NASA Astrophysics Data System (ADS)

    Miura, Y.; Hirota, A.; Gorton, M.; Kedves, M.

    2002-03-01

    New type of impact-related event is defined at active tectonic region by using semi-circular structure, bulk XRF compositions with mixed data, shocked quartz grains with the PDFs texture, and Fe-Ni content. Example is discussed in Takamatsu MKT crater in Japan.

  10. Directory of Facilities. Development Activities in the Marine Environment of the Coastal Plains Region.

    ERIC Educational Resources Information Center

    Hill, Philip G.

    Described in this directory are marine activities on the coasts of North Carolina, South Carolina, and Georgia, and the adjacent offshore area, known administratively as the Coastal Plains Region. The facilities for each state are described within these categories: educational institutions, state agencies, federal agencies, and industrial…

  11. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

    PubMed Central

    Ernst, Jason; Melnikov, Alexandre; Zhang, Xiaolan; Wang, Li; Rogov, Peter; Mikkelsen, Tarjei S.; Kellis, Manolis

    2016-01-01

    Massively parallel reporter assays (MPRA) enable nucleotide-resolution dissection of transcriptional regulatory regions, such as enhancers, but only few regions at a time. Here, we present a combined experimental and computational approach, Sharpr-MPRA, that allows high-resolution analysis of thousands of regions simultaneously. Sharpr-MPRA combines dense tiling of overlapping MPRA constructs with a probabilistic graphical model to recognize functional regulatory nucleotides, and to distinguish activating and repressive nucleotides, using their inferred contribution to reporter gene expression. We use Sharpr-MPRA to test 4.6 million nucleotides spanning 15,000 putative regulatory regions tiled at 5-nucleotide resolution in two human cell types. Our results recover known cell type-specific regulatory motifs and evolutionarily-conserved nucleotides, and distinguish known activating and repressive motifs. Our results also show that endogenous chromatin state and DNA accessibility are both predictive of regulatory function in reporter assays, identify retroviral elements with activating roles, and uncover ‘attenuator’ motifs with repressive roles in active chromatin. PMID:27701403

  12. 50 CFR 217.140 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... specified geographical region. (a) Regulations in this subpart apply only to BP Exploration (Alaska) Inc. (BP) and those persons it authorizes to conduct activities on its behalf for the taking of marine... Area. (b) The taking of marine mammals by BP may be authorized in a Letter of Authorization only if...

  13. Magnetoseismology of Active Regions using Multi-wavelength Observations from GONG and SDO

    NASA Astrophysics Data System (ADS)

    Tripathy, Sushanta; Jain, Kiran; Kholikov, Shukur; Hill, Frank; Cally, Paul

    2016-05-01

    The structure and dynamics of active regions beneath the surface show significant uncertainties due to our limited understanding of the wave interaction with magnetic field. Recent numerical simulations further demonstrate that the atmosphere above the photospheric levels also modifies the seismic observables at the surface. Thus the key to improve helioseismic interpretation beneath the active regions requires a synergy between models and helioseismic inferences from observations. In this context, using data from Global Oscillation Network Group and from Helioseismic Magnetic Imager and Atmospheric Imaging Assembly onboard Solar Dynamics Observatory, we characterize the spatio-temporal power distribution in and around active regions. Specifically, we focus on the power enhancements seen around active regions as a function of wave frequencies, strength, inclination of magnetic field and observation height as well as the relative phases of the observables and their cross-coherence functions. It is expected that these effects will help us to comprehend the interaction of acoustic waves with magnetic field in the solar photosphere.

  14. Regional cholinesterase activity in white-throated sparrow brain is differentially affected by acephate (Orthene?)

    USGS Publications Warehouse

    Vyas, N.B.; Kuenzel, W.J.; Hill, E.F.; Romo, G.A.; Komaragiri, M.V.S.

    1996-01-01

    Effects of a 14-day dietary exposure to an organophosphorus pesticide, acephate (acetylphosphoramidothioic acid O,S-dimethyl ester), were determined on cholinesterase activity in three regions (basal ganglia, hippocampus, and hypothalamus) of the white-throated sparrow, Zonotrichia albicollis, brain. All three regions experienced depressed cholinesterase activity between 0.5-2 ppm acephate. The regions exhibited cholinesterase recovery at 2-16 ppm acephate; however, cholinesterase activity dropped and showed no recovery at higher dietary levels (>16 ppm acephate). Evidence indicates that the recovery is initiated by the magnitude of depression, not the duration. In general, as acephate concentration increased, differences in ChE activity among brain regions decreased. Three terms are introduced to describe ChE response to acephate exposure: (1) ChE resistance threshold, (2) ChE compensation threshold, and (3) ChE depression threshold. It is hypothesized that adverse effects to birds in the field may occur at pesticide exposure levels customarily considered negligible.

  15. Coupled-resonator vertical-cavity lasers with two active gain regions

    DOEpatents

    Fischer, Arthur J.; Choquette, Kent D.; Chow, Weng W.

    2003-05-20

    A new class of coupled-resonator vertical-cavity semiconductor lasers has been developed. These lasers have multiple resonant cavities containing regions of active laser media, resulting in a multi-terminal laser component with a wide range of novel properties.

  16. THE LIFETIME OF H ALPHA-STRUCTURES IN ACTIVE REGIONS ON THE SUN,

    DTIC Science & Technology

    During the last two quarters of 1966 time series of exposures of active regions on the sun were obtained at the Solar Observatory at Harestua using the Zeiss Coude refractor and a Lyot monochromator. By a graphic method the mean lifetime of 574 fibrills taken from 81 selected areas is found to be 4 hours. (Author)

  17. 50 CFR 217.60 - Specified activity and specified geographical region.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... geographical region. (a) Regulations in this subpart apply only to the 30th Space Wing, United States Air Force... OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE MARINE MAMMALS REGULATIONS GOVERNING THE.... Air Force Launches, Aircraft and Helicopter Operations, and Harbor Activities Related to...

  18. Magnetic Characteristics of Active Region Heating Observed with TRACE, SOHO/EIT, and Yohkoh/SXT

    NASA Technical Reports Server (NTRS)

    Porter, J. G.; Falconer, D. A.; Moore, R. L.; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Over the past several years, we have reported results from studies that have compared the magnetic structure and heating of the transition region and corona (both in active regions and in the quiet Sun) by combining X-ray and EUV images from Yohkoh and Solar and Heliospheric Observatory (SOHO) with photospheric magnetograms from ground-based observatories. Our findings have led us to the hypothesis that most heating throughout the corona is driven from near and below the base of the corona by eruptive microflares occurring in compact low-lying "core magnetic fields (i.e., fields rooted along and closely enveloping polarity inversion lines in the photospheric magnetic flux). We now extend these studies, comparing sequences of UV images from Transition Region and Coronal Explorer (TRACE) with longitudinal magnetograms from Kitt Peak and vector magnetograms from MUSIC. These comparisons confirm the previous results regarding the importance of core-field activity to active region heating. Activity in fields associated with satellite polarity inclusions and/or magnetically sheared configurations is especially prominent. This work is funded by NASA's Office of Space Science through the Sun-Earth Connection Guest Investigator Program and the Solar Physics Supporting Research and Technology Program.

  19. FLOWS AT THE EDGE OF AN ACTIVE REGION: OBSERVATION AND INTERPRETATION

    SciTech Connect

    Boutry, C.; Buchlin, E.; Vial, J.-C.; Regnier, S.

    2012-06-10

    Upflows observed at the edges of active regions have been proposed as the source of the slow solar wind. In the particular case of Active Region (AR) 10942, where such an upflow has been already observed, we want to evaluate the part of this upflow that actually remains confined in the magnetic loops that connect AR 10942 to AR 10943. Both active regions were visible simultaneously on the solar disk and were observed by STEREO/SECCHI EUVI. Using Hinode/EIS spectra, we determine the Doppler shifts and densities in AR 10943 and AR 10942 in order to evaluate the mass flows. We also perform magnetic field extrapolations to assess the connectivity between AR 10942 and AR 10943. AR 10943 displays a persistent downflow in Fe XII. Magnetic extrapolations including both ARs show that this downflow can be connected to the upflow in AR 10942. We estimate that the mass flow received by AR 10943 areas connected to AR 10942 represents about 18% of the mass flow from AR 10942. We conclude that the upflows observed on the edge of active regions represent either large-scale loops with mass flowing along them (accounting for about one-fifth of the total mass flow in this example) or open magnetic field structures where the slow solar wind originates.

  20. How Much Energy Can Be Stored in Solar Active Region Magnetic Fields?

    NASA Astrophysics Data System (ADS)

    Linker, J.; Downs, C.; Torok, T.; Titov, V. S.; Lionello, R.; Mikic, Z.; Riley, P.

    2015-12-01

    Major solar eruptions such as X-class flares and very fast coronal mass ejections usually originate in active regions on the Sun. The energy that powers these events is believed to be stored as free magnetic energy (energy above the potential field state) prior to eruption. While coronal magnetic fields are not in general force-free, active regions have very strong magnetic fields and at low coronal heights the plasma beta is therefore very small, making the field (in equilibrium) essentially force-free. The Aly-Sturrock theorem shows that the energy of a fully force-free field cannot exceed the energy of the so-called open field. If the theorem holds, this places an upper limit on the amount of free energy that can be stored: the maximum free energy (MFE) is the difference between the open field energy and the potential field energy of the active region. In thermodynamic MHD simulations of a major eruption (the July 14, 2000 'Bastille' day event) and a modest event (February 13, 2009, we have found that the MFE indeed bounds the energy stored prior to eruption. We compute the MFE for major eruptive events in cycles 23 and 24 to investigate the maximum amount of energy that can be stored in solar active regions.Research supported by AFOSR, NASA, and NSF.

  1. Active region plasma outflows as sources of slow/intermediate solar wind

    NASA Astrophysics Data System (ADS)

    van Driel-Gesztelyi, Lidia M.

    2015-08-01

    L. van Driel-Gesztelyi (1,2,3), D. Baker (1), P. Démoulin (2), Culhane, J.L. (1), M.L. DeRosa (4) C.H. Mandrini (5,6), D.H. Brooks (7), A.N. Fazakerley (1), L.K. Harra (1), L. Zhao (7), T.H. Zurbuchen (7), F.A. Nuevo (5,6), A.M. Vásquez (5,6), G.D. Cristiani (5,6) M. Pick (2)1) UCL/MSSL, UK, (2) Paris Observatory, LESIA, CNRS, France, (3) Konkoly Observatory, Hungary, (4) Lockheed Martin Solar and Astrophysics Laboratory, USA, (5) IAFE, CONICET-UBA, Argentina (6) FCEN, UBA, Argentina (7) Dept. of Atmospheric, Oceanic and Earth Sciences, Univ. of Michigan, USAWe analyse plasma upflows of tens of km/s from the edges of solar active regions discovered by Hinode/EIS and investigate whether or not they become outflows, i.e. find their way into the solar wind. We analyse two magnetic configurations: bipolar and quadrupolar and find that the active region plasma may be directly channeled into the solar wind via interchange reconnection at a high-altitude null point above the active region especially when active regions are located besides coronal holes or in a more complex way via multiple reconnections even fro