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Sample records for neuraminidase na sequences

  1. Cloning of neuraminidase (NA) gene and identification of its antiviral ...

    African Journals Online (AJOL)

    ... the sialic acid receptor required by virus infection of the host cell surface which protects the host from virus damage. In order to explore a new idea to use neuraminidase (NA) gene and produce disease-resistant transgenic poultry, prokaryotic expression vector pGEX-NA was constructed to make NA polyclone antibody.

  2. Cloning of neuraminidase (NA) gene and identification of its antiviral ...

    African Journals Online (AJOL)

    user

    2012-06-12

    Jun 12, 2012 ... neuraminidase (NA) gene and produce disease-resistant transgenic poultry, prokaryotic expression ... transfected cells were challenged by Newcastle disease virus (NDV), the morphology of CEF cells were observed to detect the .... eukaryotic expression vector pcDNA3.0-NA and pcDNA3.0/EGFP-. NA.

  3. Baculovirus Surface Display Using Infuenza Neuraminidase (NA Transmembrane Anchor

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    Irisa Trianti

    2016-11-01

    Full Text Available Baculovirus surface display has been employed as an excellent tools for presentation of foreign peptides and proteins on virus surface with native conformation, functions and immunogenicity. A baculovirus major envelope protein, gp64, or a capsid protein, vp39 are generally used as fusion partners for displaying of polypeptides on the surface of virions. Alternatively, a membrane anchoring domain of vesicular stomatitis virus G protein (VSV-G can also be used. In this study, an influenza neuraminidase (NA was proposed as a new membrane anchor for the display of Angiotensin II (AngII, DRVYIHPFHL, peptides. The AngII peptides were inserted into NA by replacing NA amino acid number 60-67 with AngII, and then integrated into a baculovirus genome. A recombinant baculovirus expressing the NA fusion-AngII peptides was generated from infected insect cells. Those peptides were found to express and translocated on the membrane of the baculovirus infected insect cell (Sf9 cell as detected by immunocytochemistry using anti-AngII monoclonal antibody. Upon budding of the recombinant baculovirus progenies through the insect cells membrane, the recombinant NA-AngII peptides was acquired to envelopes of the new baculovirus progenies. The conformation of NA on baculovirus surface was not affected by the deletion, as the 55 kDa band of NA can be detected from Western Blotting analysis by specific anti-NA monoclonal antibody. In addition, the same protein was also found by anti-AngII antibody indicating that the AngII peptides had been successfully fused with the recombinant NA. Interestingly, electron microscopy analysis demonstrated that not only the recombinant baculovirus displaying AngII peptides were generated by infected insect cells, but also the NA virus-like-particle displaying AngII peptides.

  4. Partial antiviral activities detection of chicken Mx jointing with neuraminidase gene (NA against Newcastle disease virus.

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    Yani Zhang

    Full Text Available As an attempt to increase the resistance to Newcastle Disease Virus (NDV and so further reduction of its risk on the poultry industry. This work aimed to build the eukaryotic gene co-expression plasmid of neuraminidase (NA gene and myxo-virus resistance (Mx and detect the gene expression in transfected mouse fibroblasts (NIH-3T3 cells, it is most important to investigate the influence of the recombinant plasmid on the chicken embryonic fibroblasts (CEF cells. cDNA fragment of NA and mutant Mx gene were derived from pcDNA3.0-NA and pcDNA3.0-Mx plasmid via PCR, respectively, then NA and Mx cDNA fragment were inserted into the multiple cloning sites of pVITRO2 to generate the eukaryotic co-expression plasmid pVITRO2-Mx-NA. The recombinant plasmid was confirmed by restriction endonuclease treatment and sequencing, and it was transfected into the mouse fibroblasts (NIH-3T3 cells. The expression of genes in pVITRO2-Mx-NA were measured by RT-PCR and indirect immunofluorescence assay (IFA. The recombinant plasmid was transfected into CEF cells then RT-PCR and the micro-cell inhibition tests were used to test the antiviral activity for NDV. Our results showed that co-expression vector pVITRO2-Mx-NA was constructed successfully; the expression of Mx and NA could be detected in both NIH-3T3 and CEF cells. The recombinant proteins of Mx and NA protect CEF cells from NDV infection until after 72 h of incubation but the individually mutagenic Mx protein or NA protein protects CEF cells from NDV infection till 48 h post-infection, and co-transfection group decreased significantly NDV infection compared with single-gene transfection group (P<0. 05, indicating that Mx-NA jointing contributed to delaying the infection of NDV in single-cell level and the co-transfection of the jointed genes was more powerful than single one due to their synergistic effects.

  5. Sequence analysis of haemagglutinin and neuraminidase of H1N1 strain from a patient coinfected with Mycobacterium tuberculosis.

    Science.gov (United States)

    Alghamdi, Ahmed N; Mahfouz, Mohammad E; Hamdi, Fahd A; Al Aboud, Daifullah; Al-Laylah, Tawfiq Z; Alotaibi, Mohammed I; Al-Thomali, Khalid W A; Abdel-Moneim, Ahmed S

    2017-08-01

    The 2009 H1N1 pandemic (H1N1pdm09) was associated with a considerable influenza-related morbidity and mortality. Among the complications, Mycobacterial tuberculosis was recorded as a coinfection with influenza in rare cases. The full-length sequences of the viral haemagglutinin and neuraminidase of H1N1pdm09 influenza A virus were analyzed from a recently infected patient. The patient was chronically infected with Mycobacterium tuberculosis. Molecular modelling and in-silico docking of the virus, and other selected strains with the drug oseltamivir were conducted and compared. Sequence analysis of the viral haemagglutinin revealed it to be closely related to the 6B.1 clade, with high identity to the circulating H1N1pdm09 strains, and confirmed that the virus still harbouring high affinity to the α-2,6-sialic acid human receptor. The viral neuraminidase showed high identity to the neuraminidase of the recently circulating strains of the virus with no evidence of the development of oseltamivir-resistant mutants. Regular monitoring of the circulating strains is recommended to screen for a possible emergence of drug-resistant strains. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

    Science.gov (United States)

    Mochizuki, Yuji; Yamashita, Katsumi; Fukuzawa, Kaori; Takematsu, Kazutomo; Watanabe, Hirofumi; Taguchi, Naoki; Okiyama, Yoshio; Tsuboi, Misako; Nakano, Tatsuya; Tanaka, Shigenori

    2010-06-01

    Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.

  7. The I427T neuraminidase (NA) substitution, located outside the NA active site of an influenza A(H1N1)pdm09 variant with reduced susceptibility to NA inhibitors, alters NA properties and impairs viral fitness.

    Science.gov (United States)

    Tu, Véronique; Abed, Yacine; Barbeau, Xavier; Carbonneau, Julie; Fage, Clément; Lagüe, Patrick; Boivin, Guy

    2017-01-01

    Emergence of pan neuraminidase inhibitor (NAI)-resistant variants constitutes a serious clinical concern. An influenza A(H1N1)pdm09 variant containing the I427T/Q313R neuraminidase (NA) substitutions was previously identified in a surveillance study. Although these changes are not part of the NA active site, the variant showed reduced susceptibility to many NAIs. In this study, we investigated the mechanism of resistance for the I427T/Q313R substitution and its impact on the NA enzyme and viral fitness. Recombinant wild-type (WT), I427T/Q313R and I427T A(H1N1)pdm09 viruses were generated by reverse genetics and tested for their drug susceptibilities, enzymatic properties and replication kinetics in vitro as well as their virulence in mice. Molecular dynamics (MD) simulations were performed for NA structural analysis. The I427T substitution, which was responsible for the resistance phenotype observed in the double (I427T/Q313R) mutant, induced 17-, 56-, 7-, and 14-fold increases in IC50 values against oseltamivir, zanamivir, peramivir and laninamivir, respectively. The I427T substitution alone or combined to Q313R significantly reduced NA affinity. The I427T/Q313R and to a lesser extent I427T recombinant viruses displayed reduced viral titers vs WT in vitro. In experimentally-infected mice, the mortality rates were 62.5%, 0% and 14.3% for the WT, I417T/Q313R and I427T viruses, respectively. There were about 2.5- and 2-Log reductions in mean lung viral titers on day 5 post-infection for the I427T/Q313R and I427T mutants, respectively, compared to WT. Results from simulations revealed that the I427T change indirectly altered the stability of the catalytic R368 residue of the NA enzyme causing its reduced binding to the substrate/inhibitor. This study demonstrates that the I427T/Q313R mutant, not only alters NAI susceptibility but also compromises NA properties and viral fitness, which could explain its infrequent detection in clinic. Copyright © 2016 Elsevier B

  8. Improvement of influenza vaccine strain A/Vietnam/1194/2004 (H5N1) growth with the neuraminidase packaging sequence from A/Puerto Rico/8/34.

    Science.gov (United States)

    Pan, Weiqi; Dong, Zhenyuan; Meng, Weixu; Zhang, Wei; Li, Ting; Li, Chufang; Zhang, Beiwu; Chen, Ling

    2012-02-01

    H5N1 influenza candidate vaccine viruses were developed using the "6+2" approach. The hemagglutinin (HA) and neuraminidase (NA) genes were derived from the popular H5N1 virus and the remaining six internal segments were derived from the A/Puerto Rico/8/34 strain (H1N1, PR8). However, some of these candidate strains have been reported to produce relatively low yields in vaccine manufacture. In this study, we found that the NA vRNA of the A/Vietnam/1194/2004 strain (H5N1, VN1194) was poorly packaged into recombinant viruses with a backbone of PR8 genes, which resulted in the formation of defective virions that did not include the NA vRNA in the genome. Using recombinant DNA techniques, we constructed a chimeric NA gene with the coding region of VN1194 NA flanked by the packaging signal sequence of the PR8 NA gene (41 bp form the 3' end of the vRNA and 67 bp from the 5' end). The packaging of the NA vRNA was restored to normal levels in the recombinant viruses containing the chimeric NA gene. Recombinant viruses containing the chimeric NA replicated much better in chicken embryonated eggs than viruses with the wild-type NA from VN1194. These findings suggest a novel strategy to improve in ovo growth of vaccine strains and to increase the number of vaccine doses available to save people if a pandemic were to occur.

  9. [Accessing the features of surface neuraminidase (N1) of influenza A virus presenting on the platforms for anti-NA Abs screening].

    Science.gov (United States)

    Huang, Lan; Qin, Kun; Zhou, Jian-fang; Shu, Yue-long; Wei, Hong

    2013-02-01

    To understand if the Neuraminidase (N1) of Influenza A virus at the surface of yeast-displaying system, eukaryotic expression system and the infected cells could be used for anti-NA Abs screening, their activities and bindings to five candidate Abs were assayed. The surface NA expression was obtained by transfecting by recombinant NA constructors with specific tag-labels or live virus infection. The functional activity was measured by the fluorescent assay. Their bindings to the Abs were detected by flow cytometry. The surface NAs presenting on the yeast-displaying system and eukaryotic expression system exhibited functional NA activities as the NA at the surface of virus-infected cells which showed affinities to Ab1, 4, and 5. The same bindings to Abl and 5 were found in the surface NA expressed by eukaryotic expression system while minor binding was observed in the yeast displayed-NA. The epitopes of yeast-displayed NA may be different from the NAs present at eukaryotic expression system and the infected cells which more likely suitable for the screening of anti-NA Abs.

  10. Single electrode genosensor for simultaneous determination of sequences encoding hemagglutinin and neuraminidase of avian influenza virus type H5N1.

    Science.gov (United States)

    Grabowska, Iwona; Malecka, Kamila; Stachyra, Anna; Góra-Sochacka, Anna; Sirko, Agnieszka; Zagórski-Ostoja, Włodzimierz; Radecka, Hanna; Radecki, Jerzy

    2013-11-05

    The duo-genosensor consisting of two different oligonucleotide probes immobilized covalently on the surface of one gold electrode via Au-S bond formation was used for simultaneous determination of two different oligonucleotide targets. One of the probes, decorated on its 5'-end with ferrocene (SH-ssDNA-Fc), is complementary to the cDNA representing a sequence encoding part of H5 hemagglutinin from H5N1 virus. The second probe, decorated on its 5'-end with methylene blue (SH-ssDNA-MB), is complementary to cDNA representing the fragment of N1 neuraminidase from the same virus. The presence of both probes on the surface of gold electrodes was confirmed with Osteryoung square-wave voltammetry (OSWV). The changes in redox activity of both redox active complexes before and after the hybridization process were used as analytical signal. The peak at +400 ± 2 mV was observed in the presence of 40 nM ssDNA used as a target for SH-ssDNA-Fc probe. This peak increased with the increase of concentration of target ssDNA. It indicates the "signal on" mode of analytical signal generation. The peak at -250 ± 4 mV, characteristic for SH-ssDNA-MB probe, was decreasing with the increase of the concentration of the complementary ssDNA target starting from 8 to 100 nM. This indicates the generation of electrochemical signal according to the "signal off" mode. The proposed duo-genosensor is capable of simultaneous, specific, and good sensitivity probing for the sequences derived from genes encoding two main markers of the influenza virus, hemagglutinin and neuraminidase.

  11. A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus

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    Chen Wenbin

    2008-07-01

    Full Text Available Abstract Background The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes. Results Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97% cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. Conclusion Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.

  12. Inhibition of neuraminidase by Ganoderma triterpenoids and implications for neuraminidase inhibitor design

    Science.gov (United States)

    Zhu, Qinchang; Bang, Tran Hai; Ohnuki, Koichiro; Sawai, Takashi; Sawai, Ken; Shimizu, Kuniyoshi

    2015-01-01

    Neuraminidase (NA) inhibitors are the dominant antiviral drugs for treating influenza in the clinic. Increasing prevalence of drug resistance makes the discovery of new NA inhibitors a high priority. Thirty-one triterpenoids from the medicinal mushroom Ganoderma lingzhi were analyzed in an in vitro NA inhibition assay, leading to the discovery of ganoderic acid T-Q and TR as two inhibitors of H5N1 and H1N1 NAs. Structure-activity relationship studies revealed that the corresponding triterpenoid structure is a potential scaffold for the design of NA inhibitors. Using these triterpenoids as probes we found, through further in silico docking and interaction analysis, that interactions with the amino-acid residues Arg292 and/or Glu119 of NA are critical for the inhibition of H5N1 and H1N1. These findings should prove valuable for the design and development of NA inhibitors. PMID:26307417

  13. Homology modelling and insilico analysis of neuraminidase protein in H1N1 Influenza A virus

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    Abhilash Manohar

    2011-02-01

    Full Text Available In this work, modelling of Neuraminidase protein of Influenza A virus (A/Himeji/1/2009(H1N1 neuraminidase (NA protein was done using Modeller 9V2. Modelled structure was submitted to protein model database and could be downloaded using accession number PM0075830. The modelled protein structure was subjected to In silco analysis using various bioinformatics tools. Two anti-influenza drugs currently being used to treat infected patients are oseltamivir (Tamiflu and zanamivir (Relenza, both of which target the neuraminidase enzyme of the virus. Reports of the emergence of drug resistance make the development of new anti-influenza molecules a priority. Hence the modelled structure of H1NI Neuraminidase could be very useful for in silico analysis of potential neuraminidase inhibitors.

  14. Neuraminidase Inhibitory Activity and Constituent Characterization of Fagopyrum dibotrys

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    Xiang Zhang

    2017-11-01

    Full Text Available This study aimed to identify a new biological activity of the widely distributed species Fagopyrum dibotrys. Four F. dibotrys extracts (ethyl acetate (EA, petroleum ether (P, ethanol (E, and water (W were explored for their anti-neuraminidase (NA activity. A total of 32 compounds were identified using UHPLC-Q-Exactive Orbitrap HRMS in the EA extract, which had the best NA inhibitory effects. We used the docking data for supporting compounds’ anti-neuraminidase activity. Among them, five compounds including one flavonoid, three organic acids, and one glucoside were discovered for the first time in F. dibotrys. Docking studies and NA activity assay revealed the remarkable NA inhibitory activity of eight components in EA extract, especially rutin, hesperidin, procyanidin B2, and quercitrin. Therefore, F. dibotrys could be used to develop anti-influenza drugs.

  15. Neuraminidase-mediated haemagglutination of recent human influenza A(H3N2) viruses is determined by arginine 150 flanking the neuraminidase catalytic site.

    Science.gov (United States)

    Mögling, Ramona; Richard, Mathilde J; Vliet, Stefan van der; Beek, Ruud van; Schrauwen, Eefje J A; Spronken, Monique I; Rimmelzwaan, Guus F; Fouchier, Ron A M

    2017-06-01

    Over the last decade, an increasing proportion of circulating human influenza A(H3N2) viruses exhibited haemagglutination activity that was sensitive to neuraminidase inhibitors. This change in haemagglutination as compared to older circulating A(H3N2) viruses prompted an investigation of the underlying molecular basis. Recent human influenza A(H3N2) viruses were found to agglutinate turkey erythrocytes in a manner that could be blocked with either oseltamivir or neuraminidase-specific antisera, indicating that agglutination was driven by neuraminidase, with a low or negligible contribution of haemagglutinin. Using representative virus recombinants it was shown that the haemagglutinin of a recent A(H3N2) virus indeed had decreased activity to agglutinate turkey erythrocytes, while its neuraminidase displayed increased haemagglutinating activity. Viruses with chimeric and mutant neuraminidases were used to identify the amino acid substitution histidine to arginine at position 150 flanking the neuraminidase catalytic site as the determinant of this neuraminidase-mediated haemagglutination. An analysis of publicly available neuraminidase gene sequences showed that viruses with histidine at position 150 were rapidly replaced by viruses with arginine at this position between 2005 and 2008, in agreement with the phenotypic data. As a consequence of neuraminidase-mediated haemagglutination of recent A(H3N2) viruses and poor haemagglutination via haemagglutinin, haemagglutination inhibition assays with A(H3N2) antisera are no longer useful to characterize the antigenic properties of the haemagglutinin of these viruses for vaccine strain selection purposes. Continuous monitoring of the evolution of these viruses and potential consequences for vaccine strain selection remains important.

  16. Catalytically defective ganglioside neuraminidase in mucolipidosis IV

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Yoseph, Y.; Momoi, T.; Hahn, L.C.; Nadler, H.L. (Wayne State Univ., Detroit, MI (USA))

    1982-01-01

    Cultured skin fibroblasts from patients with mucolipidosis IV were found to be deficient in neuraminidase activity toward GDsub(la) and GDsub(lb) gangliosides radiolabelled in C/sub 3/ and C/sub 7/ analogs of their sialic acid residues. Neuraminidase activities toward 4-methylumbelliferyl-N-acetyl-neuraminic acid, neuraminlactose, and radiolabelled neuraminlactitol, fetuin and ..cap alpha../sub 1/-acid glycoprotein were within the range of normal controls. Fibroblasts from parents of patients with mucolipidosis IV demonstrated intermediate levels of ganglioside neuraminidase activity and normal levels of glycoprotein neuraminidase activity. The redidual acidic neuraminidase activity toward GDsub(1a) ganglioside in the patients' fibroblasts did not differ from that of controls in its pH optimum and thermostability, but had an abnormal apparent Ksub(m) which was about 18 times higher than that of the normal enzyme. These findings suggest that mucolipidosis IV is a ganglioside sialidosis due to a catalytically defective ganglioside neuraminidase.

  17. A complete analysis of HA and NA genes of influenza A viruses.

    LENUS (Irish Health Repository)

    Shi, Weifeng

    2010-12-01

    More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.

  18. Antibody against Microbial Neuraminidases Recognizes Human Sialidase 3 (NEU3: the Neuraminidase/Sialidase Superfamily Revisited

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    Chiguang Feng

    2017-06-01

    Full Text Available Neuraminidases (NAs are critical virulence factors for several microbial pathogens. With a highly conserved catalytic domain, a microbial NA “superfamily” has been proposed. We previously reported that murine polymorphonuclear leukocyte (PMN sialidase activity was important in leukocyte trafficking to inflamed sites and that antibodies to Clostridium perfringens NA recognized a cell surface molecule(s, presumed to be a sialidase of eukaryotic origin on interleukin-8-stimulated human and murine PMNs. These antibodies also inhibited cell sialidase activity both in vitro and, in the latter instance, in vivo. We therefore hypothesized that mammalian sialidases share structural homology and epitopes with microbial NAs. We now report that antibodies to one of the isoforms of C. perfringens NA, as well as anti-influenza virus NA serum, recognize human NEU3 but not NEU1 and that antibodies to C. perfringens NA inhibit NEU3 enzymatic activity. We conclude that the previously described microbial NA superfamily extends to human sialidases. Strategies designed to therapeutically inhibit microbial NA may need to consider potential compromising effects on human sialidases, particularly those expressed in cells of the immune system.

  19. Screening for Neuraminidase Inhibitory Activity in Traditional Chinese Medicines Used to Treat Influenza

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    Xian-Ying Yang

    2016-08-01

    Full Text Available Objective: To screen for influenza virus neuraminidase inhibition and to provide a reference for the clinical treatment of influenza using traditional Chinese medicines (TCM. In this study, 421 crude extracts (solubilized with petroleum ether, ethanol, ethyl acetate, and aqueous solvents were obtained from 113 TCM. The medicine extracts were then reacted with oseltamivir, using 2’-(4-methylumbelliferyl-α-D-N-acetylneuraminic acid (MUNANA as the substrate, to determine influenza virus neuraminidase activity using a standard fluorimetric assay. It was found that Chinese medicine extracts from Pyrola calliantha, Cynanchum wilfordii, Balanophora involucrata and Paeonia delavayi significantly inhibited neuraminidase activity at a concentration of 40 μg/mL. Dose-dependent inhibitory assays also revealed significant inhibition. The IC50 range of the TCM extracts for influenza virus neuraminidase was approximately 12.66–34.85 μg/mL, respectively. Some Chinese medicines have clear anti-influenza viral effects that may play an important role in the treatment of influenza through the inhibition of viral neuraminidase. The results of this study demonstrated that plant medicines can serve as a useful source of neuraminidase (NA inhibitors and further investigation into the pharmacologic activities of these extracts is warranted.

  20. Law of iterated logarithm for NA sequences with non-identical ...

    Indian Academy of Sciences (India)

    Based on a law of the iterated logarithm for independent random variables sequences, an iterated logarithm theorem for NA sequences with non-identical distributions is obtained. The proof is based on a Kolmogrov-type exponential inequality.

  1. Law of iterated logarithm for NA sequences with non-identical ...

    Indian Academy of Sciences (India)

    There are many results about law of iterated logarithm for independent random variables sequences. ... As for negatively associated (NA) random variables, Joag [2] gave the following defi- nition. DEFINITION [2] ... Recently, some authors focused on the problem of limiting behavior of partial sums of. NA sequences. Su et al ...

  2. Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016.

    Science.gov (United States)

    Gubareva, Larisa V; Besselaar, Terry G; Daniels, Rod S; Fry, Alicia; Gregory, Vicki; Huang, Weijuan; Hurt, Aeron C; Jorquera, Patricia A; Lackenby, Angie; Leang, Sook-Kwan; Lo, Janice; Pereyaslov, Dmitriy; Rebelo-de-Andrade, Helena; Siqueira, Marilda M; Takashita, Emi; Odagiri, Takato; Wang, Dayan; Zhang, Wenqing; Meijer, Adam

    2017-10-01

    Four World Health Organization (WHO) Collaborating Centres for Reference and Research on Influenza and one WHO Collaborating Centre for the Surveillance, Epidemiology and Control of Influenza (WHO CCs) assessed antiviral susceptibility of 14,330 influenza A and B viruses collected by WHO-recognized National Influenza Centres (NICs) between May 2015 and May 2016. Neuraminidase (NA) inhibition assay was used to determine 50% inhibitory concentration (IC50) data for NA inhibitors (NAIs) oseltamivir, zanamivir, peramivir and laninamivir. Furthermore, NA sequences from 13,484 influenza viruses were retrieved from public sequence databases and screened for amino acid substitutions (AAS) associated with reduced inhibition (RI) or highly reduced inhibition (HRI) by NAIs. Of the viruses tested by WHO CCs 93% were from three WHO regions: Western Pacific, the Americas and Europe. Approximately 0.8% (n = 113) exhibited either RI or HRI by at least one of four NAIs. As in previous seasons, the most common NA AAS was H275Y in A(H1N1)pdm09 viruses, which confers HRI by oseltamivir and peramivir. Two A(H1N1)pdm09 viruses carried a rare NA AAS, S247R, shown in this study to confer RI/HRI by the four NAIs. The overall frequency of A(H1N1)pdm09 viruses containing NA AAS associated with RI/HRI was approximately 1.8% (125/6915), which is slightly higher than in the previous 2014-15 season (0.5%). Three B/Victoria-lineage viruses contained a new AAS, NA H134N, which conferred HRI by zanamivir and laninamivir, and borderline HRI by peramivir. A single B/Victoria-lineage virus harboured NA G104E, which was associated with HRI by all four NAIs. The overall frequency of RI/HRI phenotype among type B viruses was approximately 0.6% (43/7677), which is lower than that in the previous season. Overall, the vast majority (>99%) of the viruses tested by WHO CCs were susceptible to all four NAIs, showing normal inhibition (NI). Hence, NAIs remain the recommended antivirals for treatment of

  3. Neuraminidase deficiency: case report and review of the phenotype.

    Science.gov (United States)

    Young, I D; Young, E P; Mossman, J; Fielder, A R; Moore, J R

    1987-01-01

    A 12 year old boy with neuraminidase deficiency (sialidosis, mucolipidosis I) is described. His clinical features included coarse facies, cherry red spot, ataxia, myoclonus, and dysotosis multiplex. The level of neuraminidase activity in cultured fibroblasts was very low and intermediate levels were observed in both parents. The clinical disorders associated with neuraminidase deficiency are reviewed. Images PMID:3585942

  4. Crystal Structures of Respiratory Pathogen Neuraminidases

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L

    2009-01-01

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.

  5. Regulation of neuraminidase expression in Streptococcus pneumoniae

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    Gualdi Luciana

    2012-09-01

    Full Text Available Abstract Background Sialic acid (N-acetylneuraminic acid; NeuNAc is one of the most important carbohydrates for Streptococcus pneumoniae due of its role as a carbon and energy source, receptor for adhesion and invasion and molecular signal for promotion of biofilm formation, nasopharyngeal carriage and invasion of the lung. Results In this work, NeuNAc and its metabolic derivative N-acetyl mannosamine (ManNAc were used to analyze regulatory mechanisms of the neuraminidase locus expression. Genomic and metabolic comparison to Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii and Streptococcus sanguinis elucidates the metabolic association of the two amino sugars to different parts of the locus coding for the two main pneumococcal neuraminidases and confirms the substrate specificity of the respective ABC transporters. Quantitative gene expression analysis shows repression of the locus by glucose and induction of all predicted transcriptional units by ManNAc and NeuNAc, each inducing with higher efficiency the operon encoding for the transporter with higher specificity for the respective amino sugar. Cytofluorimetric analysis demonstrated enhanced surface exposure of NanA on pneumococci grown in NeuNAc and ManNAc and an activity assay allowed to quantify approximately twelve times as much neuraminidase activity on induced cells as opposed to glucose grown cells. Conclusions The present data increase the understanding of metabolic regulation of the nanAB locus and indicate that experiments aimed at the elucidation of the relevance of neuraminidases in pneumococcal virulence should possibly not be carried out on bacteria grown in glucose containing media.

  6. Droplet digital PCR to investigate quasi-species at codons 119 and 275 of the A(H1N1)pdm09 neuraminidase during zanamivir and oseltamivir therapies.

    Science.gov (United States)

    Abed, Yacine; Carbonneau, Julie; L'Huillier, Arnaud G; Kaiser, Laurent; Boivin, Guy

    2017-04-01

    The H275Y and E119D neuraminidase (NA) mutations constitute important molecular markers of resistance to NA inhibitors in A(H1N1) pdm09 viruses. We used reverse transcriptase-droplet digital PCR amplification (RT-ddPCR) to analyze quasi-species at codons 275 and 119 of the NA in A(H1N1) pdm09 viruses recovered from an immuncompromised patient who received oseltamivir and zanamivir therapies. RT-ddPCR assays detected and quantified H275Y and E119D mutations with an efficiency that was comparable to that of high throughput sequencing (HiSeq 2500 Illumina, San Diego, CA) technology. With its sensitivity and reproducibility, RT-ddPCR could be a reliable method for accurate detection and quantification of major NAI-resistance mutations in clinical settings. J. Med. Virol. 89:737-741, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. In silico molecular modeling of neuraminidase enzyme H1N1 avian influenza virus and docking with zanamivir ligands

    Directory of Open Access Journals (Sweden)

    Muthiyan Ramachandran

    2012-12-01

    Full Text Available Objective: Neuraminidase is an enzyme aspartic protease that is essential for the life cycle of H1N1. Methods: Constructed a model of Neuraminidase enzyme the 3D structure as template using with Modeller software. The Neuraminidase enzyme model was predicted and validated by Procheck, What check, Errat, Verify-3D and AutoDock web server for reliability. Results: The Modeller homology-modeling algorithm was demonstrated excellent accuracy in blind predictions. The Neuraminidase enzyme model built with little, 35% identity could be accurate enough to be successfully used in receptor based rational drug design. The closest homologue with the highest sequence identity 100% was selected. Zanamivir drug and analogues were retrieved from PubChem database, as well as subjected to docking interaction with Neuraminidase enzyme used AutoDock programme. Based on the root mean square deviation and lowest binding energy values the best docking orientation was selected. The better lowest binding energy value -6.91 was selected of CID_25209232. Conclusions: This study will be used in broad screening of inhibitors of the protein. However, further implemented experimental and clinical verification is needed to establishment these analogues as drug.

  8. Purification and properties of rabbit spermatozoal acrosomal neuraminidase.

    Science.gov (United States)

    Srivastava, P N; Abou-Issa, H

    1977-01-01

    Treatment of rabbit spermatozoa with 50mM-MgCl2 removes the plasma and the outer acrosomal membranes. Subsequent treatment with the detergents Hyamine 2389 and Triton X-100 solubilizes spermatozoal neuraminidase bound to the inner acrosomal membrane. The enzyme was further purified by DEAE-cellulose, Sephadex G-150 and Bio-Gel P-300 column chromato. The enzyme showed a single major band, with the possibility of some minor contaminants, on disc-gel electrophoresis. It had a specific activity of 0.37 micronmal of sialic acid released/min per mg with purified boar Cowper's-gland mucin as the substrate. The enzyme had marked specificity for 2 leads to 6'-linked sialic acid in glycoproteins. The Km of spermatozoal neuraminidase was 1.72 X 10(-6)M with Cowper's-gland mucin, 1.17 X 10(-5)M with fetuin and 8.8 X 10(-4)M with sialyl-lactose as a substrates. The Vmax. was 0.112 micronmol/min per mg with the Cowper's-gland mucin, 0.071 micronmol/min per mg with fetuin and 0.033 micronmol/min per mg with sialyl-lactose as substrate. The enzyme hydrolysed sheep submaxillary-gland mucin as readily as the Cowper's-gland mucin. The optimum of enzyme activity was at pH 5.0 on the Cowper's-gland mucin and at pH4.3 on sialyl-lactose. The enzyme activity was unaffected by 20mM-Na+ and-K+, but was inhibited by 20mM-Ca2+,-Mn2+,-Co2+ and -Cu2+. The enzyme was unstable in dilute solutions, but could be stored indefinitely freeze-dried at --20 degrees C. Images PLATE 1 PMID:66917

  9. Lactococcus lactis displayed neuraminidase confers cross protective immunity against influenza A viruses in mice.

    Science.gov (United States)

    Lei, Han; Peng, Xiaojue; Zhao, Daxian; Ouyang, Jiexiu; Jiao, Huifeng; Shu, Handing; Ge, Xinqi

    2015-02-01

    Influenza A viruses pose a serious threat to public health. Current influenza A vaccines predominantly focus on hemagglutinin (HA) and show strain-specific protection. Neuraminidase (NA) is much less studied in the context of humoral immunity against influenza A viruses. The purpose of this study is to evaluate the cross protective immunity of NA presented on Lactococcus lactis (L.lactis) surface against homologous and heterologous influenza A viruses in the mouse model. L.lactis/pNZ8110-pgsA-NA was constructed in which pgsA was used as an anchor protein. Mice vaccinated orally with L.lactis/pNZ8110-pgsA-NA could elicit significant NA-specific serum IgG and mucosa IgA antibodies, as well as neuraminidase inhibition (NI) titers. Importantly, L.lactis/pNZ8110-pgsA-NA provided 80% protection against H5N1, 60% protection against H3N2 and H1N1, respectively. These findings suggest that recombinant L.lactis/pNZ110-pgsA-NA in the absence of adjuvant via oral administration can be served as an effective vaccine candidate against diverse strains of influenza A viruses. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. The low-pH stability discovered in neuraminidase of 1918 pandemic influenza A virus enhances virus replication.

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    Tadanobu Takahashi

    Full Text Available The "Spanish" pandemic influenza A virus, which killed more than 20 million worldwide in 1918-19, is one of the serious pathogens in recorded history. Characterization of the 1918 pandemic virus reconstructed by reverse genetics showed that PB1, hemagglutinin (HA, and neuraminidase (NA genes contributed to the viral replication and virulence of the 1918 pandemic influenza virus. However, the function of the NA gene has remained unknown. Here we show that the avian-like low-pH stability of sialidase activity discovered in the 1918 pandemic virus NA contributes to the viral replication efficiency. We found that deletion of Thr at position 435 or deletion of Gly at position 455 in the 1918 pandemic virus NA was related to the low-pH stability of the sialidase activity in the 1918 pandemic virus NA by comparison with the sequences of other human N1 NAs and sialidase activity of chimeric constructs. Both amino acids were located in or near the amino acid resides that were important for stabilization of the native tetramer structure in a low-pH condition like the N2 NAs of pandemic viruses that emerged in 1957 and 1968. Two reverse-genetic viruses were generated from a genetic background of A/WSN/33 (H1N1 that included low-pH-unstable N1 NA from A/USSR/92/77 (H1N1 and its counterpart N1 NA in which sialidase activity was converted to a low-pH-stable property by a deletion and substitutions of two amino acid residues at position 435 and 455 related to the low-pH stability of the sialidase activity in 1918 NA. The mutant virus that included "Spanish Flu"-like low-pH-stable NA showed remarkable replication in comparison with the mutant virus that included low-pH-unstable N1 NA. Our results suggest that the avian-like low-pH stability of sialidase activity in the 1918 pandemic virus NA contributes to the viral replication efficiency.

  11. Measurement of the time sequence of Na2 spectra by using a boxcar averager

    Science.gov (United States)

    Lu, Zhiwei; Wang, Qi L.; Ma, Zuguang

    1993-05-01

    A simple experimental method is proposed to measure the time sequence by using a Boxcar Averager, in which the time-resolved spectrum of every pulse is measured independently, and it is used on UV dye laser excited Na2 molecules.

  12. Neuraminidase-Mediated, NKp46-Dependent Immune-Evasion Mechanism of Influenza Viruses

    Directory of Open Access Journals (Sweden)

    Yotam Bar-On

    2013-04-01

    Full Text Available Natural killer (NK cells play an essential role in the defense against influenza virus, one of the deadliest respiratory viruses known today. The NKp46 receptor, expressed by NK cells, is critical for controlling influenza infections, as influenza-virus-infected cells are eliminated through the recognition of the viral hemagglutinin (HA protein by NKp46. Here, we describe an immune-evasion mechanism of influenza viruses that is mediated by the neuraminidase (NA protein. By using various NA blockers, we show that NA removes sialic acid residues from NKp46 and that this leads to reduced recognition of HA. Furthermore, we provide in vivo and in vitro evidence for the existence of this NA-mediated, NKp46-dependent immune-evasion mechanism and demonstrate that NA inhibitors, which are commonly used for the treatment of influenza infections, are useful not only as blockers of virus budding but also as boosters of NKp46 recognition.

  13. Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zhengliang L., E-mail: Leon.wu@bio-techne.com [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Zhou, Hui [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States); Ethen, Cheryl M. [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Reinhold, Vernon N., E-mail: Vernon.Reinhold@unh.edu [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States)

    2016-04-29

    The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and {sup 3}H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. - Graphical abstract: Proposed mechanism for how core-fucose prohibits the tetramerization of the 1918 pandemic viral neuraminidase. Only the cross section of the stalk region with two N-linked glycans are depicted for clarity. (A) Carbohydrate–carbohydrate interaction on non-fucosylated monomer allows tetramerization. (B) Core-fucosylation disrupts the interaction and prevents the tetramerization. - Highlights: • Expressed 1918 pandemic influenza viral neuraminidase has inactive and active forms. • The inactive form contains high level of core-6 fucose, while the active form lacks such modification. • Core fucose could interfere the oligomerization of the neuraminidase and thus its activation. • This discovery may explain

  14. Purification and renaturation of membrane neuraminidase from Haemophilus parasuis.

    Science.gov (United States)

    Lichtensteiger, Carol A; Vimr, Eric R

    2003-05-02

    Haemophilus parasuis, which causes polyserositis, polysynovitis, meningitis, septicemia, and pneumonia in pigs, has emerged as an increasing problem in modern swine production systems. Co-factors for and the pathogenesis of H. parasuis disease are not defined. One of the potential virulence factors of H. parasuis is its neuraminidase (sialidase). While purifying the H. parasuis neuraminidase from the membrane fraction, we developed a protocol to renature enzymatic activity after enzyme preparations were resolved electrophorectically in denaturing polyacrylamide gels. The H. parasuis neuraminidase co-resolved with recombinant neuraminidase of Vibrio cholera; thus its apparent molecular mass is 82 kilodalton (kDa). The H. parasuis neuraminidase was associated with the membrane fraction and the purification protocol removed over 99% of the H. parasuis cell protein while retaining over 90% of the neuraminidase activity. Purified protein will provide another avenue to clone the neuraminidase gene that has been refractory to cloning and the protocol will be a means to purify recombinant protein. Copyright 2003 Elsevier Science B.V.

  15. Positive Selection on Hemagglutinin and Neuraminidase Genes of H1N1 Influenza Viruses

    LENUS (Irish Health Repository)

    Li, Wenfu

    2011-04-21

    Abstract Background Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. Results Phylogenetic analysis revealed that both HA and NA genes have evolved into five distinct clusters, with further analyses indicating that the pandemic 2009 strains have experienced the strongest positive selection. We also found evidence of strong selection acting on the seasonal human H1N1 isolates. However, swine viruses from North America and Eurasia were under weak positive selection, while there was no significant evidence of positive selection acting on the avian isolates. A site-by-site analysis revealed that the positively selected sites were located in both of the cleaved products of HA (HA1 and HA2), as well as NA. In addition, the pandemic 2009 strains were subject to differential selection pressures compared to seasonal human, North American swine and Eurasian swine H1N1 viruses. Conclusions Most of these positively and\\/or differentially selected sites were situated in the B-cell and\\/or T-cell antigenic regions, suggesting that selection at these sites might be responsible for the antigenic variation of the viruses. Moreover, some sites were also associated with glycosylation and receptor-binding ability. Thus, selection at these positions might have helped the pandemic 2009 H1N1 viruses to adapt to the new hosts after they were introduced from pigs to humans. Positive selection on position 274 of NA protein, associated with drug resistance, might account for the prevalence of drug-resistant variants of seasonal human H1N1 influenza viruses, but there was no evidence that positive selection was responsible for the spread of the drug resistance of the pandemic H1N1 strains.

  16. Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase

    Directory of Open Access Journals (Sweden)

    Nandy Ashesh

    2010-02-01

    Full Text Available Abstract Background Catalytic activity of influenza neuraminidase (NA facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene. Results We extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514 and H1N1 swine flu sequences (425 accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure. Conclusion The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in

  17. Cloning of neuraminidase (NA) gene and identification of its antiviral ...

    African Journals Online (AJOL)

    user

    2012-06-12

    Jun 12, 2012 ... characters of isolates of Pasteurella multocida obtained from back‐yard poultry and from two outbreaks of avian cholera in avifauna in Denmark. Avian Pathol., 27(4): 373-381. Cong YL, Liu JH (2008). Molecular mechanism of the role of hemagglutinin of influenza virus in interspecies transmission. Chin. J.

  18. Structure Prediction and Analysis of Neuraminidase Sequence Variants

    Science.gov (United States)

    Thayer, Kelly M.

    2016-01-01

    Analyzing protein structure has become an integral aspect of understanding systems of biochemical import. The laboratory experiment endeavors to introduce protein folding to ascertain structures of proteins for which the structure is unavailable, as well as to critically evaluate the quality of the prediction obtained. The model system used is the…

  19. Radioassay method of neuraminidase towards N-acetylneuraminosyl hexasaccharides

    Energy Technology Data Exchange (ETDEWEB)

    Kuriyama, M.; Someya, F.; Yamada, T.; Miyatake, T. (Tokyo Metropolitan Research Lab. of Public Health (Japan))

    1982-02-26

    The authors have devised a sensitive method to assay for neuraminidase activities towards ..cap alpha..-(2..-->..3)-N-acetylneuraminosyl hexasaccharide and ..cap alpha..-(2..-->..6)-N-acetylneuraminosyl hexasaccharide, which were isolated from the urine of a patient with adult sialidosis with partial deficiency of ..beta..-galactosidase. Standard assay conditions for the determination of these neuraminidase activities were established and the radiolabeled reduced derivatives of these substrates were used. The fibroblast neuraminidase had its maximum activity at pH 4.0-4.2, with Ksub(m) values of 2.22 x 10/sup -3/ and 4.17 x 10/sup -3/ mol/l and Vsub(max) values of 76.9 and 28.6 nmol.mg/sup -1/ protein.h/sup -1/ towards the 2..-->..3 isomer and the 2..-->..6 isomer, respectively. Neuraminidase deficiencies were found in the fibroblasts of adult sialidosis, mucolipidosis II and III. These studies were compared with the neuraminidase activity towards ..cap alpha..-(2..-->..3)-N-acetylneuraminosyl lactose.

  20. EFFICIENCY AND SAFETY OF NEURAMINIDASE INHIBITOR OSELTAMIVIR FOR CHILDREN

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    A.S. Darmanyan

    2007-01-01

    Full Text Available Every year 3 to 5 million people suffer from flu. Children are most susceptible to flu. At the moment, the main methods of flu prophylaxis and treatment are flu vaccination and antivirus medications. Of the tested anti virus medications, 3 groups are most interesting and interferon inductors, м 2=channel blockers (derivative of adamantine and neuraminidase inhibitors. neuraminidase inhibitors are a brand new type of virus infection therapy — they selectively inhibit activity of flu virus neuraminidases, which restrains virus from getting into the cell, exit of virion from the cell before the reproduction cycle is over and new cells are affected. Oseltamivir — one of the new neuraminidase inhibitors — can be used for a safe and efficient flu treatment and prophylaxis among adults; yet recently this medication has been authorized for children over 1 year of age, basing upon the findings of randomized controlled surveys. Data shows that usage of oseltamivir reduces the period of diseases and severity of acute flu symptoms for children with no side diseases, as well as for children suffering from cardiovascular and bronchopulmonary system diseases; besides this medication reduces the risk of secondary flu complications.Key words: neuraminidase inhibitors, oseltamivir, flu, bird flu, antivirus medications.

  1. Estimation of the neuraminidase content of influenza viruses and split-product vaccines by immunochromatography.

    Science.gov (United States)

    Tanimoto, Takeshi; Nakatsu, Ritsuko; Fuke, Isao; Ishikawa, Toyokazu; Ishibashi, Masahide; Yamanishi, Kouichi; Takahashi, Michiaki; Tamura, Shin-ichi

    2005-08-31

    The neuraminidase (NA) of the influenza virus, as well as the hemagglutinin, is the most important protective components in the vaccine. However, the NA content of the vaccine remains to be standardized because of the labile nature of this glycoprotein during various chemical treatments and storage. In the present study, the NA content of the split-product (SP) vaccine (virus treated with ether then formalin) was estimated together with that of the virus by an immunochoromatography technique using monoclonal antibodies (mAbs) to viral NA for A/Panama/2007/99 (A/Pa) (H3N2), B/Shangdong/7/97 (B/S) or A/New Caledonia/20/99 (A/NC) (H1N1) viral strains. In the new method, the NA catalytic activity of each fraction from steps of NA purification was measured as an index of NA content. The NA level of A/Pa, B/S or A/NC viral particles was estimated at 6.9+/-0.9, 7.6+/-0.8 or 8.5+/-1.7% of total viral protein (not significant difference between viral strains). The NA level of the corresponding A/Pa, B/S or A/NC vaccines was estimated at 9.6+/-1.5, 12.7+/-0.4 or 12.2+/-1.2% of the total vaccine protein (a significant difference between each strain of virus and its vaccine). These results suggest that the NA content in the N1, N2 or B type NA virus ranges from 5 to 11% of the total viral protein, and that the NA level in each split-product vaccine is 1.4- to 1.6-fold higher than that in the corresponding viral particles. They also suggest that the NA content can be estimated by the immunochoromatography technique using anti-viral NA mAbs.

  2. Optimizing Viral Protein Yield of Influenza Virus Strain A/Vietnam/1203/2004 by Modification of the Neuraminidase Gene▿

    OpenAIRE

    Adamo, Joan E.; Liu, Teresa; Schmeisser, Falko; Ye, Zhiping

    2009-01-01

    The preparation of high-yield prepandemic influenza virus H5N1 strains has presented a challenge to both researchers and vaccine manufacturers. The reasons for the relatively low yield of the H5N1 strains are not fully understood, but it might be partially dependent on the interactions between the hemagglutinin (HA) or neuraminidase (NA) surface glycoprotein and other influenza virus proteins. In this study, we have constructed chimeras between the A/Puerto Rico/8/34 (PR8) NA gene and the A/V...

  3. Structural basis for a class of nanomolar influenza A neuraminidase inhibitors

    Science.gov (United States)

    Kerry, Philip S.; Mohan, Sankar; Russell, Rupert J. M.; Bance, Nicole; Niikura, Masahiro; Pinto, B. Mario

    2013-10-01

    The influenza virus neuraminidase (NA) is essential for the virus life cycle. The rise of resistance mutations against current antiviral therapies has increased the need for the development of novel inhibitors. Recent efforts have targeted a cavity adjacent to the catalytic site (the 150-cavity) in addition to the primary catalytic subsite in order to increase specificity and reduce the likelihood of resistance. This study details structural and in vitro analyses of a class of inhibitors that bind uniquely in both subsites. Crystal structures of three inhibitors show occupation of the 150-cavity in two distinct and novel binding modes. We believe these are the first nanomolar inhibitors of NA to be characterized in this way. Furthermore, we show that one inhibitor, binding within the catalytic site, offers reduced susceptibility to known resistance mutations via increased flexibility of a pendant pentyloxy group and the ability to pivot about a strong hydrogen-bonding network.

  4. Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja.

    Science.gov (United States)

    Ji, Wei; Li, Yong; Li, Jie; Dai, Cui-hong; Wang, Xi; Bai, Xi; Cai, Hua; Yang, Liang; Zhu, Yan-ming

    2006-02-22

    Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining. As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109) leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST) sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO) hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443-DT084445). The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants.

  5. Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja

    Directory of Open Access Journals (Sweden)

    Cai Hua

    2006-02-01

    Full Text Available Abstract Background Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining. Results As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109 leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443~DT084445. Conclusion The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants.

  6. Syntheses and neuraminidase inhibitory activity of multisubstituted cyclopentane amide derivatives.

    Science.gov (United States)

    Chand, Pooran; Babu, Y Sudhakar; Bantia, Shanta; Rowland, Scott; Dehghani, Ali; Kotian, Pravin L; Hutchison, Tracy L; Ali, Shoukath; Brouillette, Wayne; El-Kattan, Yahya; Lin, Tsu-Hsing

    2004-04-08

    In further studies aimed toward identifying effective and safe inhibitors of influenza neuraminidases, we synthesized a series of multisubstituted cyclopentane amide derivatives. Amides prepared were 14 examples of N-substituted alkyl or aralkyl types from primary amines, 13 examples of the N,N-disubstituted alkyl, aralkyl, or substituted-alkyl type from secondary amines, and 12 examples from cycloaliphatic or substituted cycloaliphatic secondary amines. These compounds bearing two chiral centers, at position-1 in the ring and position-1' in the side chain attached at position 3, were tested for their ability to inhibit A and B forms of influenza neuraminidase. The 1-ethylpropylamide, diethylamide, dipropylamide, and 4-morpholinylamide showed very good inhibitory activity (IC(50) = 0.015-0.080 microM) vs the neuraminidase A form, but modest activity (IC(50) = 3.0-9.2 microM) vs the neuraminidase B form. Since the parent amides bear two chiral centers (C-1 and C-1'), three of the better inhibitors were tested at higher levels of diastereomeric purity. The diastereomers corresponding to the active forms of the 1-(ethyl)propylamide, the diethylamide, and the dipropylamide (all of the same configuration at the C-1' chiral center), and the diastereomer of the diethylamide representing the active form at both C-1' and C-1 were isolated or synthesized from precursors that were isolated as diastereomers. These diastereomers showed some improvement in neuraminidase inhibition over the parent diastereomeric mixtures. 1-Carboxy-1-hydroxy derivatives of the best active compounds, the diethylamide and the dipropylamide, were also prepared. These compounds were not as active as the compounds without the 1-hydroxy group. In an in vivo study, the C-1' active isomer of the diethylamide from the 1-carboxy series was tested in influenza-infected mice by oral and intranasal administration and found to be very effective only intranasally in preventing weight loss at doses as low as 0

  7. A generic system for the expression and purification of soluble and stable influenza neuraminidase.

    Directory of Open Access Journals (Sweden)

    Peter M Schmidt

    Full Text Available The influenza surface glycoprotein neuraminidase (NA is essential for the efficient spread of the virus. Antiviral drugs such as Tamiflu (oseltamivir and Relenza (zanamivir that inhibit NA enzyme activity have been shown to be effective in the treatment of influenza infections. The recent 'swine flu' pandemic and world-wide emergence of Tamiflu-resistant seasonal human influenza A(H1N1 H(274Y have highlighted the need for the ongoing development of new anti-virals, efficient production of vaccine proteins and novel diagnostic tools. Each of these goals could benefit from the production of large quantities of highly pure and stable NA. This publication describes a generic expression system for NAs in a baculovirus Expression Vector System (BEVS that is capable of expressing milligram amounts of recombinant NA. To construct NAs with increased stability, the natural influenza NA stalk was replaced by two different artificial tetramerization domains that drive the formation of catalytically active NA homotetramers: GCN4-pLI from yeast or the Tetrabrachion tetramerization domain from Staphylothermus marinus. Both recombinant NAs are secreted as FLAG-tagged proteins to allow for rapid and simple purification. The Tetrabrachion-based NA showed good solubility, increased stability and biochemical properties closer to the original viral NA than the GCN4-pLI based construct. The expressed quantities and high quality of the purified recombinant NA suggest that this expression system is capable of producing recombinant NA for a broad range of applications including high-throughput drug screening, protein crystallisation, or vaccine development.

  8. Neuraminidase-mediated, NKp46-dependent immune-evasion mechanism of influenza viruses.

    Science.gov (United States)

    Bar-On, Yotam; Glasner, Ariella; Meningher, Tal; Achdout, Hagit; Gur, Chamutal; Lankry, Dikla; Vitenshtein, Alon; Meyers, Adrienne F A; Mandelboim, Michal; Mandelboim, Ofer

    2013-04-25

    Natural killer (NK) cells play an essential role in the defense against influenza virus, one of the deadliest respiratory viruses known today. The NKp46 receptor, expressed by NK cells, is critical for controlling influenza infections, as influenza-virus-infected cells are eliminated through the recognition of the viral hemagglutinin (HA) protein by NKp46. Here, we describe an immune-evasion mechanism of influenza viruses that is mediated by the neuraminidase (NA) protein. By using various NA blockers, we show that NA removes sialic acid residues from NKp46 and that this leads to reduced recognition of HA. Furthermore, we provide in vivo and in vitro evidence for the existence of this NA-mediated, NKp46-dependent immune-evasion mechanism and demonstrate that NA inhibitors, which are commonly used for the treatment of influenza infections, are useful not only as blockers of virus budding but also as boosters of NKp46 recognition. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Synthesis of Sulfo-Sialic Acid Analogues: Potent Neuraminidase Inhibitors in Regards to Anomeric Functionality.

    Science.gov (United States)

    Vavricka, Christopher J; Muto, Chiaki; Hasunuma, Tomohisa; Kimura, Yoshinobu; Araki, Michihiro; Wu, Yan; Gao, George F; Ohrui, Hiroshi; Izumi, Minoru; Kiyota, Hiromasa

    2017-08-15

    The design, synthesis and application of N-acetylneuraminic acid-derived compounds bearing anomeric sulfo functional groups are described. These novel compounds, which we refer to as sulfo-sialic acid analogues, include 2-decarboxy-2-deoxy-2-sulfo-N-acetylneuraminic acid and its 4-deoxy-3,4-dehydrogenated pseudoglycal. While 2-decarboxy-2-deoxy-2-sulfo-N-acetylneuraminic acid contains no further modifications of the 2-deoxy-pyranose ring, it is still a more potent inhibitor of avian-origin H5N1 neuraminidase (NA) and drug-resistant His275Tyr NA as compared to the oxocarbenium ion transition state analogue 2,3-dehydro-2-deoxy-N-acetylneuraminic acid. The sulfo-sialic acid analogues described in this report are also more potent inhibitors of influenza NA (up to 40-fold) and bacterial NA (up to 8.5-fold) relative to the corresponding anomeric phosphonic acids. These results confirm that this novel anomeric sulfo modification offers great potential to improve the potency of next-generation NA inhibitors including covalent inhibitors.

  10. Design, in silico studies, synthesis and in vitro evaluation of oseltamivir derivatives as inhibitors of neuraminidase from influenza A virus H1N1.

    Science.gov (United States)

    Neri-Bazán, Rocío M; García-Machorro, Jazmín; Méndez-Luna, David; Tolentino-López, Luis E; Martínez-Ramos, Federico; Padilla-Martínez, Itzia I; Aguilar-Faisal, Leopoldo; Soriano-Ursúa, Marvin A; Trujillo-Ferrara, José G; Fragoso-Vázquez, M Jonathan; Barrón, Blanca L; Correa-Basurto, José

    2017-03-10

    Since the neuraminidase (NA) enzyme of the influenza A virus plays a key role in the process of release of new viral particles from a host cell, it is often a target for new drug design. The emergence of NA mutations, such as H275Y, has led to great resistance against neuraminidase inhibitors, including oseltamivir and zanamivir. Hence, we herein designed a set of derivatives by modifying the amine and/or carboxylic groups of oseltamivir. After being screened for their physicochemical (Lipinski's rule) and toxicological properties, the remaining compounds were submitted to molecular and theoretical studies. The docking simulations provided insights into NA recognition patterns, demonstrating that oseltamivir modified at the carboxylic moiety and coupled with anilines had higher affinity and a better binding pose for NA than the derivatives modified at the amine group. Based on these theoretical studies, the new oseltamivir derivatives may have higher affinity to mutant variants and possibly to other viral subtypes. Accordingly, two compounds were selected for synthesis, which together with their respective intermediates were evaluated for their cytotoxicity and antiviral activities. Their biological activity was then tested in cells infected with the A/Puerto Rico/916/34 (H1N1) influenza virus, and virus yield reduction assays were performed. Additionally, by measuring neuraminidase activity with the neuraminidase assay kit it was found that the compounds produced inhibitory activity on this enzyme. Finally, the infected cells were analysed with atomic force microscopy (AFM), observing morphological changes strongly suggesting that these compounds interfered with cellular release of viral particles. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  11. Positive regulation of insulin signaling by neuraminidase 1.

    Science.gov (United States)

    Dridi, Larbi; Seyrantepe, Volkan; Fougerat, Anne; Pan, Xuefang; Bonneil, Eric; Thibault, Pierre; Moreau, Allain; Mitchell, Grant A; Heveker, Nikolaus; Cairo, Christopher W; Issad, Tarik; Hinek, Alexander; Pshezhetsky, Alexey V

    2013-07-01

    Neuraminidases (sialidases) catalyze the removal of sialic acid residues from sialylated glycoconjugates. We now report that mammalian neuraminidase 1 (Neu1), in addition to its catabolic function in lysosomes, is transported to the cell surface where it is involved in the regulation of insulin signaling. Insulin binding to its receptor rapidly induces interaction of the receptor with Neu1, which hydrolyzes sialic acid residues in the glycan chains of the receptor and, consequently, induces its activation. Cells from sialidosis patients with a genetic deficiency of Neu1 show impairment of insulin-induced phosphorylation of downstream protein kinase AKT, and treatment of these cells with purified Neu1 restores signaling. Genetically modified mice with ∼10% of the normal Neu1 activity exposed to a high-fat diet develop hyperglycemia and insulin resistance twice as fast as their wild-type counterparts. Together, these studies identify Neu1 as a novel component of the signaling pathways of energy metabolism and glucose uptake.

  12. Exploring the chemical space of influenza neuraminidase inhibitors

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    Nuttapat Anuwongcharoen

    2016-04-01

    Full Text Available The fight against the emergence of mutant influenza strains has led to the screening of an increasing number of compounds for inhibitory activity against influenza neuraminidase. This study explores the chemical space of neuraminidase inhibitors (NAIs, which provides an opportunity to obtain further molecular insights regarding the underlying basis of their bioactivity. In particular, a large set of 347 and 175 NAIs against influenza A and B, respectively, was compiled from the literature. Molecular and quantum chemical descriptors were obtained from low-energy conformational structures geometrically optimized at the PM6 level. The bioactivities of NAIs were classified as active or inactive according to their half maximum inhibitory concentration (IC50 value in which IC50 < 1µM and ≥ 10µM were defined as active and inactive compounds, respectively. Interpretable decision rules were derived from a quantitative structure–activity relationship (QSAR model established using a set of substructure descriptors via decision tree analysis. Univariate analysis, feature importance analysis from decision tree modeling and molecular scaffold analysis were performed on both data sets for discriminating important structural features amongst active and inactive NAIs. Good predictive performance was achieved as deduced from accuracy and Matthews correlation coefficient values in excess of 81% and 0.58, respectively, for both influenza A and B NAIs. Furthermore, molecular docking was employed to investigate the binding modes and their moiety preferences of active NAIs against both influenza A and B neuraminidases. Moreover, novel NAIs with robust binding fitness towards influenza A and B neuraminidase were generated via combinatorial library enumeration and their binding fitness was on par or better than FDA-approved drugs. The results from this study are anticipated to be beneficial for guiding the rational drug design of novel NAIs for treating influenza

  13. Neuraminidase as an enzymatic marker for detecting airborne Influenza virus and other viruses.

    Science.gov (United States)

    Turgeon, Nathalie; Toulouse, Marie-Josée; Ho, Jim; Li, Dongqing; Duchaine, Caroline

    2017-02-01

    Little information is available regarding the effectiveness of air samplers to collect viruses and regarding the effects of sampling processes on viral integrity. The neuraminidase enzyme is present on the surface of viruses that are of agricultural and medical importance. It has been demonstrated that viruses carrying this enzyme can be detected using commercial substrates without having to process the sample by methods such as RNA extraction. This project aims at evaluating the effects of 3 aerosol-sampling devices on the neuraminidase enzyme activity of airborne viruses. The purified neuraminidase enzymes from Clostridium perfringens, a strain of Influenza A (H1N1) virus, the FluMist influenza vaccine, and the Newcastle disease virus were used as models. The neuraminidase models were aerosolized in aerosol chambers and sampled with 3 different air samplers (SKC BioSampler, 3-piece cassettes with polycarbonate filters, and Coriolis μ) to assess the effect on neuraminidase enzyme activity. Our results demonstrated that Influenza virus and Newcastle disease virus neuraminidase enzymes are resistant to aerosolization and sampling with all air samplers tested. Moreover, we demonstrated that the enzymatic neuraminidase assay is as sensitive as RT-qPCR for detecting low concentrations of Influenza virus and Newcastle disease virus. Therefore, given the sensitivity of the assay and its compatibility with air sampling methods, viruses carrying the neuraminidase enzyme can be rapidly detected from air samples using neuraminidase activity assay without having to preprocess the samples.

  14. Using Common Spatial Distributions of Atoms to Relate Functionally Divergent Influenza Virus N10 and N11 Protein Structures to Functionally Characterized Neuraminidase Structures, Toxin Cell Entry Domains, and Non-Influenza Virus Cell Entry Domains

    Science.gov (United States)

    Weininger, Arthur; Weininger, Susan

    2015-01-01

    The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell

  15. Structural Characterization of the 1918 Influenza H1N1 Neuraminidase

    Energy Technology Data Exchange (ETDEWEB)

    Xu, X.; Zhu, X.; Dwek, R.A.; Stevens, J.; Wilson, I.A.

    2009-05-28

    Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 'Spanish flu' (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-{angstrom} and 1.45-{angstrom} resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.

  16. Peramivir susceptibilities of recombinant influenza A and B variants selected with various neuraminidase inhibitors.

    Science.gov (United States)

    Fage, Clément; Tu, Véronique; Carbonneau, Julie; Abed, Yacine; Boivin, Guy

    2017-03-22

    Peramivir is a parenteral neuraminidase inhibitor (NAI) approved for treating influenza infections in a few countries. We determined peramivir susceptibilities of several uncharacterized influenza A and B neuraminidase (NA) and haemagglutinin (HA) mutants selected with different NAIs. Recombinant wild-type (WT) and mutant NA proteins were expressed in 293T cells and susceptibility to peramivir, oseltamivir and zanamivir was determined by NA inhibition assay using the MUNANA substrate. Recombinant/reassortant influenza A(H1N1), A(H3N2) and B HA mutants were rescued by reverse genetics and assessed by plaque size or viral yield assays for drug susceptibility. Recombinant R152K, I222K/T, G248R+I266V, Q312R+I427T and R371K (A[H1N1]pdm09); E41G, 1222L/V, Q226H and S247P (A[H3N2]) and D198Y, A246D/S/T and G402S (B) mutant NA proteins (N2 numbering) were analysed. Peramivir exhibited the lowest IC50 values against both influenza A and B WT NAs. Peramivir and oseltamivir generally shared similar phenotypes. Of note, peramivir retained activity against I222K/T (A[H1N1]pdm09), I222L/V (A[H3N2]) and A246T (B) mutants, which had reduced inhibition (RI) or highly RI (HRI) against oseltamivir. Cross-RI/HRI against the three NAIs was observed for R152K, R371K and Q312R+I427T (A[H1N1]pdm09); S247P (A[H3N2]) and D198Y (B) mutants. All tested recombinant/reassortant R208K (A/Puerto Rico/8/34 [H1N1]); A28T, R124M and K189E (A/Victoria/3/75 [H3N2]) and T139N (B/Phuket/3073/13) HA mutants were susceptible to peramivir in cell culture experiments. Peramivir is highly active against seasonal influenza subtypes. Although peramivir and oseltamivir generally share similar phenotypes, peramivir still possesses activity against some variants with RI/HRI against oseltamivir. Finally, NAI-induced HA substitutions alone did not significantly impact NAI susceptibility.

  17. Neuraminidase stalk length and additional glycosylation of the hemagglutinin influence the virulence of influenza H5N1 viruses for mice.

    Science.gov (United States)

    Matsuoka, Yumiko; Swayne, David E; Thomas, Colleen; Rameix-Welti, Marie-Anne; Naffakh, Nadia; Warnes, Christine; Altholtz, Melanie; Donis, Ruben; Subbarao, Kanta

    2009-05-01

    Following circulation of avian influenza H5 and H7 viruses in poultry, the hemagglutinin (HA) can acquire additional glycosylation sites, and the neuraminidase (NA) stalk becomes shorter. We investigated whether these features play a role in the pathogenesis of infection in mammalian hosts. From 1996 to 2007, H5N1 viruses with a short NA stalk have become widespread in several avian species. Compared to viruses with a long-stalk NA, viruses with a short-stalk NA showed a decreased capacity to elute from red blood cells and an increased virulence in mice, but not in chickens. The presence of additional HA glycosylation sites had less of an effect on virulence than did NA stalk length. The short-stalk NA of H5N1 viruses circulating in Asia may contribute to virulence in humans.

  18. Sialidosis and galactosialidosis: chromosomal assignment of two genes associated with neuraminidase-deficiency disorders

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, O.T.; Henry, W.M.; Haley, L.L.; Byers, M.G.; Eddy, R.L.; Shows, T.B.

    1986-03-01

    The inherited human disorders sialidosis and galactosialidosis are the result of deficiencies of glycoprotein-specific ..cap alpha..-neuraminidase (acylneuraminyl hydrolase, EC 3.2.1.18; sialidase) activity. Two genes were determined to be necessary for expression of neuraminidase by using human-mouse somatic cell hybrids segregating human chromosomes. A panel of mouse RAG-human hybrid cells demonstrated a single-gene requirement for human neuraminidase and allowed assignment of this gene to the (pter ..-->.. q23) region of chromosome 10. A second panel of mouse thymidine kinase (TK)-deficient LM/TK/sup -/-human hybrid cells demonstrated that human neuraminidase activity required both chromosomes 10 and 20 to be present. Analysis of human neuraminidase expression in interspecific hybrid cells or polykaryocytes formed from fusion of mouse RAG or LM/TK/sup -/ cell lines with human sialidosis or galactosialidosis fibroblasts indicated that the RAG cell line complemented the galactosialidosis defect, but the LM/TK/sup -/ cell line did not. This eliminates the requirement for this gene in RAG-human hybrid cells and explains the different chromosome requirements of these two hybrid panels. Fusion of LM/TK/sup -/ cell hybrids lacking chromosome 10 or 20 and neuraminidase-deficient fibroblasts confirmed by complementation analysis that the sialidosis disorder results from a mutation on chromosome 10, presumably encoding the neuraminidase structural gene. Galactosialidosis is caused by a mutation in a second gene required for neuraminidase expression located on chromosome 20.

  19. Pitfalls in Diagnosing Neuraminidase Deficiency : Psychosomatics and Normal Sialic Acid Excretion

    NARCIS (Netherlands)

    Schene, Imre F; Ayuso, Viera Kalinina|info:eu-repo/dai/nl/33793259X; de Sain-van der Velden, Monique|info:eu-repo/dai/nl/304817910; van Gassen, Koen L I|info:eu-repo/dai/nl/304819417; Cuppen, Inge|info:eu-repo/dai/nl/314436529; van Hasselt, Peter M|info:eu-repo/dai/nl/304814423; Visser, Gepke|info:eu-repo/dai/nl/229317057

    2015-01-01

    Neuraminidase deficiency (mucolipidosis I, sialidosis types I and II, cherry-red spot myoclonus syndrome) is a lysosomal storage disorder with an expanding clinical phenotype. Here, we report the striking diagnostic history of late-onset neuraminidase deficiency in two sisters, currently aged 14

  20. Structural basis for substrate specificity of mammalian neuraminidases.

    Directory of Open Access Journals (Sweden)

    Victoria Smutova

    Full Text Available The removal of sialic acid (Sia residues from glycoconjugates in vertebrates is mediated by a family of neuraminidases (sialidases consisting of Neu1, Neu2, Neu3 and Neu4 enzymes. The enzymes play distinct physiological roles, but their ability to discriminate between the types of linkages connecting Sia and adjacent residues and between the identity and arrangement of the underlying sugars has never been systematically studied. Here we analyzed the specificity of neuraminidases by studying the kinetics of hydrolysis of BODIPY-labeled substrates containing common mammalian sialylated oligosaccharides: 3'Sia-LacNAc, 3'SiaLac, SiaLex, SiaLea, SiaLec, 6'SiaLac, and 6'SiaLacNAc. We found significant differences in substrate specificity of the enzymes towards the substrates containing α2,6-linked Sia, which were readily cleaved by Neu3 and Neu1 but not by Neu4 and Neu2. The presence of a branching 2-Fuc inhibited Neu2 and Neu4, but had almost no effect on Neu1 or Neu3. The nature of the sugar residue at the reducing end, either glucose (Glc or N-acetyl-D-glucosamine (GlcNAc had only a minor effect on all neuraminidases, whereas core structure (1,3 or 1,4 bond between D-galactose (Gal and GlcNAc was found to be important for Neu4 strongly preferring β3 (core 1 to β4 (core 2 isomer. Neu3 and Neu4 were in general more active than Neu1 and Neu2, likely due to their preference for hydrophobic substrates. Neu2 and Neu3 were examined by molecular dynamics to identify favorable substrate orientations in the binding sites and interpret the differences in their specificities. Finally, using knockout mouse models, we confirmed that the substrate specificities observed in vitro were recapitulated in enzymes found in mouse brain tissues. Our data for the first time provide evidence for the characteristic substrate preferences of neuraminidases and their ability to discriminate between distinct sialoside targets.

  1. Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function.

    Science.gov (United States)

    Zhang, Li; Ai, Hai-Xin; Li, Shi-Meng; Qi, Meng-Yuan; Zhao, Jian; Zhao, Qi; Liu, Hong-Sheng

    2017-10-10

    In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score, with a root-mean-square error of 1.46, Pearson's correlation coefficient of 0.707, and Spearman's rank correlation coefficient of 0.707 in a 5-fold cross-validation study. The performance of RF-NA-Score in a docking-based virtual screening of NA inhibitors was evaluated with a dataset containing 281 NA inhibitors and 322 noninhibitors. Compared with other docking-rescoring virtual screening strategies, rescoring with RF-NA-Score significantly improved the efficiency of virtual screening, and a strategy that averaged the scores given by RF-NA-Score, based on the binding conformations predicted with AutoDock, AutoDock Vina, and LeDock, was shown to be the best strategy. This strategy was then applied to the virtual screening of NA inhibitors in the SPECS database. The 100 selected compounds were tested in an in vitro H7N9 NA inhibition assay, and two compounds with novel scaffolds showed moderate inhibitory activities. These results indicate that RF-NA-Score improves the efficiency of virtual screening for NA inhibitors, and can be used successfully to identify new NA inhibitor scaffolds. Scoring functions specific for other drug targets could also be established with the same method.

  2. Isolation of Panels of Llama Single-Domain Antibody Fragments Binding All Nine Neuraminidase Subtypes of Influenza A Virus

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    Guus Koch

    2013-04-01

    Full Text Available Avian influenza A virus comprises sixteen hemagglutinin (HA and nine neuraminidase (NA subtypes (N1–N9. To isolate llama single-domain antibody fragments (VHHs against all N subtypes, four llamas were immunized with mixtures of influenza viruses. Selections using influenza virus yielded predominantly VHHs binding to the highly immunogenic HA and nucleoprotein. However, selection using enzymatically active recombinant NA (rNA protein enabled us to isolate NA binding VHHs. Some isolated VHHs cross-reacted to other N subtypes. These were subsequently used for the capture of N subtypes that could not be produced as recombinant protein (rN6 or were enzymatically inactive (rN1, rN5 in phage display selection, yielding novel VHHs. In total we isolated 188 NA binding VHHs, 64 of which were expressed in yeast. Most VHHs specifically recognize a single N subtype, but some VHHs cross-react with other N-subtypes. At least one VHH bound to all N subtypes, except N4, identifying a conserved antigenic site. Thus, this work (1 describes methods for isolating NA binding VHHs, (2 illustrates the suitability of llama immunization with multiple antigens for retrieving many binders against different antigens and (3 describes 64 novel NA binding VHHs, including a broadly reactive VHH, which can be used in various assays for influenza virus subtyping, detection or serology.

  3. Splice donor site mutation in the lysosomal neuraminidase gene causing exon skipping and complete loss of enzyme activity in a sialidosis patient.

    Science.gov (United States)

    Penzel, R; Uhl, J; Kopitz, J; Beck, M; Otto, H F; Cantz, M

    2001-07-20

    Sialidosis is a lysosomal storage disease caused by the deficiency of alpha-N-acetylneuraminidase (NEU1; sialidase), the key enzyme for the intralysosomal catabolism of sialylated glycoconjugates. We have identified a homozygous transversion in the last intron (IVSE +1 G>C) in neu1 of a sialidosis patient. Sequencing of the truncated cDNA revealed an alternatively spliced neu1 transcript which lacks the complete sequence of exon 5. Skipping of exon 5 leads to a frameshift and results in a premature termination codon. This is the first description of an intronic point mutation causing a complete deficiency of the lysosomal neuraminidase activity.

  4. Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naïve midgut.

    Science.gov (United States)

    Cramaro, Wibke J; Revets, Dominique; Hunewald, Oliver E; Sinner, Regina; Reye, Anna L; Muller, Claude P

    2015-10-28

    In Europe, Ixodes ricinus ticks are the most important vectors of diseases threatening humans, livestock, wildlife and companion animals. Nevertheless, genomic sequence information is missing and functional annotation of transcripts and proteins is limited. This lack of information is restricting studies of the vector and its interactions with pathogens and hosts. Here we present and integrate the first analysis of the I. ricinus genome with the transcriptome and proteome of the unfed I. ricinus midgut. Whole genome sequencing was performed on I. ricinus ticks and the sequences were de novo assembled. In parallel, I. ricinus ticks were dissected and the midgut transcriptome sequenced. Both datasets were integrated by transcript discovery analysis to identify putative genes and genome contigs were screened for homology. An alignment-based and a motif-search-based approach were combined for the annotation of the midgut transcriptome. Additionally, midgut proteins were identified and annotated by mass spectrometry with public databases and the in-house built transcriptome database as references and results were cross-validated. The de novo assembly of 1 billion DNA sequences to a reference genome of 393 Mb length provides an unprecedented insight into the I. ricinus genome. A homology search revealed sequences in the assembled genome contigs homologous to 89% of the I. scapularis genome scaffolds indicating coverage of most genome regions. We identified moreover 6,415 putative genes. More than 10,000 transcripts from naïve midgut were annotated with respect of predicted function and/or cellular localization. By combining an alignment-based with a motif-search-based annotation approach, we doubled the number of annotations throughout all functional categories. In addition, 574 gel spots were significantly identified by mass spectrometry (pricinus, paving the way for further in-depth analysis of the most important European disease vector and its interactions with

  5. Neuraminidase activity provides a practical read-out for a high throughput influenza antiviral screening assay

    Directory of Open Access Journals (Sweden)

    Wu Meng

    2008-09-01

    Full Text Available Abstract Background The emergence of influenza strains that are resistant to commonly used antivirals has highlighted the need to develop new compounds that target viral gene products or host mechanisms that are essential for effective virus replication. Existing assays to identify potential antiviral compounds often use high throughput screening assays that target specific viral replication steps. To broaden the search for antivirals, cell-based replication assays can be performed, but these are often labor intensive and have limited throughput. Results We have adapted a traditional virus neutralization assay to develop a practical, cell-based, high throughput screening assay. This assay uses viral neuraminidase (NA as a read-out to quantify influenza replication, thereby offering an assay that is both rapid and sensitive. In addition to identification of inhibitors that target either viral or host factors, the assay allows simultaneous evaluation of drug toxicity. Antiviral activity was demonstrated for a number of known influenza inhibitors including amantadine that targets the M2 ion channel, zanamivir that targets NA, ribavirin that targets IMP dehydrogenase, and bis-indolyl maleimide that targets protein kinase A/C. Amantadine-resistant strains were identified by comparing IC50 with that of the wild-type virus. Conclusion Antivirals with specificity for a broad range of targets are easily identified in an accelerated viral inhibition assay that uses NA as a read-out of replication. This assay is suitable for high throughput screening to identify potential antivirals or can be used to identify drug-resistant influenza strains.

  6. Neuraminidase 1 is a Negative Regulator of Lysosomal Exocytosis

    Science.gov (United States)

    Yogalingam, Gouri; Bonten, Erik J.; van de Vlekkert, Diantha; Hu, Huimin; Moshiach, Simon; Connell, Samuel A.; d’Azzo, Alessandra

    2009-01-01

    SUMMARY Lysosomal exocytosis is a Ca2+-regulated mechanism that involves proteins responsible for cytoskeletal attachment and fusion of lysosomes with the plasma membrane. However, whether luminal lysosomal enzymes contribute to this process remains unknown. Here we show that neuraminidase Neu1 negatively regulates lysosomal exocytosis in hematopoietic cells by processing the sialic acids on the lysosomal membrane protein Lamp-1. In macrophages from Neu1-deficient mice, a model of the disease sialidosis, and in patients’ fibroblasts, oversialylated Lamp-1 enhances lysosomal exocytosis. Silencing of Lamp-1 reverts this phenotype by interfering with the docking of lysosomes at the plasma membrane. In Neu1-/- mice the excessive exocytosis of serine proteases in the bone niche leads to inactivation of extracellular serpins, premature degradation of VCAM-1, and loss of bone marrow retention. Our findings uncover an unexpected mechanism influencing lysosomal exocytosis and argue that exacerbations of this process form the basis for certain genetic diseases. PMID:18606142

  7. Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase.

    Science.gov (United States)

    Wu, Zhengliang L; Zhou, Hui; Ethen, Cheryl M; N Reinhold, Vernon

    2016-04-29

    The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and (3)H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Influenza virus uses its neuraminidase protein to evade the recognition of two activating NK cell receptors.

    Science.gov (United States)

    Bar-On, Yotam; Seidel, Einat; Tsukerman, Pinchas; Mandelboim, Michal; Mandelboim, Ofer

    2014-08-01

    Natural Killer (NK) cells play a central role in the defense against viral infections and in the elimination of transformed cells. The recognition of pathogen-infected and tumor cells is controlled by inhibitory and activating receptors. We have previously shown that among the activating (killer) NK cell receptors the natural cytotoxicity receptors, NKp44 and NKp46, interact with the viral hemagglutinin (HA) protein expressed on the cell surface of influenza-virus-infected cells. We further showed that the interaction between NKp44/NKp46 and viral HA is sialic-acid dependent and that the recognition of HA by NKp44 and NKp46 leads to the elimination of the infected cells. Here we demonstrate that the influenza virus developed a counter-attack mechanism and that the virus uses its neuraminidase (NA) protein to prevent the recognition of HA by both the NKp44 and NKp46 receptors, resulting in reduced elimination of the infected cells by NK cells. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Synergistic Antiviral Activity of S-033188/S-033447, a Novel Inhibitor of Influenza Virus Cap-Dependent Endonuclease, in Combination with Neuraminidase Inhibitors In Vitro

    OpenAIRE

    Kitano, Mitsutaka; Yamamoto, Atsuko; Noshi, Takeshi; Kawai, Makoto; Yoshida, Ryu; Sato, Akihiko; Shishido, Takao; Naito, Akira

    2017-01-01

    Abstract Background S-033447, an active form of orally available prodrug S-033188, is a novel small molecule inhibitor of cap-dependent endonuclease that is essential for influenza virus transcription and replication. In this study, we evaluated the inhibitory effect of S-033188 in combination with neuraminidase inhibitors on the replication of influenza A/H1N1 virus in cultured cells. Methods The inhibitory effects of S-033447 in combination with NA inhibitors on the cytopathic effect of A/P...

  10. Sialidosis and galactosialidosis: chromosomal assignment of two genes associated with neuraminidase-deficiency disorders.

    Science.gov (United States)

    Mueller, O T; Henry, W M; Haley, L L; Byers, M G; Eddy, R L; Shows, T B

    1986-01-01

    The inherited human disorders sialidosis and galactosialidosis are the result of deficiencies of glycoprotein-specific alpha-neuraminidase (acylneuraminyl hydrolase, EC 3.2.1.18; sialidase) activity. Two genes were determined to be necessary for expression of neuraminidase by using human-mouse somatic cell hybrids segregating human chromosomes. A panel of mouse RAG-human hybrid cells demonstrated a single-gene requirement for human neuraminidase and allowed assignment of this gene to the (pter----q23) region of chromosome 10. A second panel of mouse thymidine kinase (TK)-deficient LM/TK- -human hybrid cells demonstrated that human neuraminidase activity required both chromosomes 10 and 20 to be present. Analysis of human neuraminidase expression in interspecific hybrid cells or polykaryocytes formed from fusion of mouse RAG (hypoxanthine/guanine phosphoribosyltransferase deficient) or LM/TK- cell lines with human sialidosis or galactosialidosis fibroblasts indicated that the RAG cell line complemented the galactosialidosis defect, but the LM/TK- cell line did not. This eliminates the requirement for this gene in RAG-human hybrid cells and explains the different chromosome requirements of these two hybrid panels. Fusion of LM/TK- cell hybrids lacking chromosome 10 or 20 (phenotype 10+,20- and 10-,20+) and neuraminidase-deficient fibroblasts confirmed by complementation analysis that the sialidosis disorder results from a mutation on chromosome 10, presumably encoding the neuraminidase structural gene. Galactosialidosis is caused by a mutation in a second gene required for neuraminidase expression located on chromosome 20. PMID:3081902

  11. Neuraminidase production by a Streptococcus sanguis strain associated with subacute bacterial endocarditis.

    OpenAIRE

    Straus, D. C.; Portnoy-Duran, C

    1983-01-01

    The properties of an extracellular neuraminidase produced by a Streptococcus sanguis strain (isolated from a confirmed case of subacute bacterial endocarditis) during growth in a defined medium was examined in this investigation. This enzyme, isolated from concentrated culture supernatants of S. sanguis biotype II, was active against human alpha-1 acid glycoprotein, N-acetylneuramin lactose, bovine submaxillary mucin, and fetuin. Neuraminidase production paralleled bacterial growth in defined...

  12. Electron-ion collisional ionization cross sections and rates for the Na isoelectronic sequence

    CERN Document Server

    Chen, C Y; Wang, Y S; Yang, F J; Xu, X J; Sun, Y S

    2001-01-01

    In this paper, we present the electron-impact ionization cross sections for eight highly charged Na-like ions in the range 18<=Z<=39 calculated by means of a distorted-wave Born exchange approximation method including relativistic corrections. Direct ionization from the ground and excited states (n=3-5) is calculated. For the ground state, contributions due to excitation-autoionization are also calculated, taking account of branching ratios and configuration interaction. A systematic study of the dependence of the cross sections on impact energy and nuclear charge is carried out for the direct ionization of all states and for excitation-autoionization. The results of the calculations are fitted by empirical formulas to facilitate use in practical applications; the fitted values are found to be in good agreement with the calculated results. An accurate empirical formula for calculating ionization rates is also given.

  13. Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors.

    Directory of Open Access Journals (Sweden)

    Kai-Cheng Hsu

    Full Text Available Infection with influenza virus is a major public health problem, causing serious illness and death each year. Emergence of drug-resistant influenza virus strains limits the effectiveness of drug treatment. Importantly, a dual H275Y/I223R mutation detected in the pandemic influenza A 2009 virus strain results in multidrug resistance to current neuraminidase (NA drugs. Therefore, discovery of new agents for treating multiple drug-resistant (MDR influenza virus infections is important. Here, we propose a parallel screening strategy that simultaneously screens wild-type (WT and MDR NAs, and identifies inhibitors matching the subsite characteristics of both NA-binding sites. These may maintain their potency when drug-resistant mutations arise. Initially, we analyzed the subsite of the dual H275Y/I223R NA mutant. Analysis of the site-moiety maps of NA protein structures show that the mutant subsite has a relatively small volume and is highly polar compared with the WT subsite. Moreover, the mutant subsite has a high preference for forming hydrogen-bonding interactions with polar moieties. These changes may drive multidrug resistance. Using this strategy, we identified a new inhibitor, Remazol Brilliant Blue R (RB19, an anthraquinone dye, which inhibited WT NA and MDR NA with IC(50 values of 3.4 and 4.5 µM, respectively. RB19 comprises a rigid core scaffold and a flexible chain with a large polar moiety. The former interacts with highly conserved residues, decreasing the probability of resistance. The latter forms van der Waals contacts with the WT subsite and yields hydrogen bonds with the mutant subsite by switching the orientation of its flexible side chain. Both scaffolds of RB19 are good starting points for lead optimization. The results reveal a parallel screening strategy for identifying resistance mechanisms and discovering anti-resistance neuraminidase inhibitors. We believe that this strategy may be applied to other diseases with high

  14. Neuraminidase activity of blue eye disease porcine rubulavirus: Specificity, affinity and inhibition studies.

    Science.gov (United States)

    Santos-López, Gerardo; Borraz-Argüello, María T; Márquez-Domínguez, Luis; Flores-Alonso, Juan Carlos; Ramírez-Mendoza, Humberto; Priem, Bernard; Fort, Sébastien; Vallejo-Ruiz, Verónica; Reyes-Leyva, Julio; Herrera-Camacho, Irma

    2017-10-01

    Porcine rubulavirus (PorPV), also known as La Piedad Michoacan Virus (LPMV) causes encephalitis and reproductive failure in newborn and adult pigs, respectively. The hemagglutinin-neuraminidase (HN) glycoprotein is the most exposed and antigenic of the virus proteins. HN plays central roles in PorPV infection; i.e., it recognizes sialic acid-containing cell receptors that mediate virus attachment and penetration; in addition, its neuraminidase (sialic acid releasing) activity has been proposed as a virulence factor. This work describes the purification and characterization of PorPV HN protein (isolate PAC1). The specificity of neuraminidase is restricted to sialyl(α2,3)lactose (3SL). HN showed typical Michaelis-Menten kinetics with fetuin as substrate (km=0.029μM, Vmax=522.8nmolmin-1mg-1). When 3SL was used as substrate, typical cooperative kinetics were found (S50=0.15μM, Vmax=154.3nmolmin-1mg-1). The influenza inhibitor zanamivir inhibited the PorPV neuraminidase with IC50 of 0.24μM. PorPV neuraminidase was activated by Ca2+ and inhibited by nucleoside triphosphates with the level of inhibition depending on phosphorylation level. The present results open possibilities to study the role of neuraminidase in the pathogenicity of PorPV infection and its potential inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Vaccine-associated enhanced respiratory disease is influenced by haemagglutinin and neuraminidase in whole inactivated influenza virus vaccines.

    Science.gov (United States)

    Rajão, Daniela S; Chen, Hongjun; Perez, Daniel R; Sandbulte, Matthew R; Gauger, Phillip C; Loving, Crystal L; Shanks, G Dennis; Vincent, Amy

    2016-07-01

    Multiple subtypes and many antigenic variants of influenza A virus (IAV) co-circulate in swine in the USA, complicating effective use of commercial vaccines to control disease and transmission. Whole inactivated virus (WIV) vaccines may provide partial protection against IAV with substantial antigenic drift, but have been shown to induce vaccine-associated enhanced respiratory disease (VAERD) when challenged with an antigenic variant of the same haemagglutinin (HA) subtype. This study investigated the role the immune response against HA, neuraminidase (NA) and nucleoprotein (NP) may play in VAERD by reverse engineering vaccine and challenge viruses on a common backbone and using them in a series of vaccination/challenge trials. Mismatched HA between vaccine and challenge virus was necessary to induce VAERD. However, vaccines containing a matched NA abrogated the VAERD phenomenon induced by the HA mismatch and this was correlated with NA-inhibiting (NI) antibodies. Divergence between the two circulating swine N2 lineages (92 % identity) resulted in a loss of NI cross-reactivity and also resulted in VAERD with the mismatched HA. The NP lineage selected for use in the WIV vaccine strains did not affect protection or pathology. Thus the combination of HA and NA in the vaccine virus strains played a substantial role in vaccine protection versus immunopathology, suggesting that vaccines that target the HA protein alone could be more prone to VAERD due to the absence of cross-protective NI antibodies.

  16. The M segment of the 2009 pandemic influenza virus confers increased neuraminidase activity, filamentous morphology, and efficient contact transmissibility to A/Puerto Rico/8/1934-based reassortant viruses.

    Science.gov (United States)

    Campbell, Patricia J; Danzy, Shamika; Kyriakis, Constantinos S; Deymier, Martin J; Lowen, Anice C; Steel, John

    2014-04-01

    The 2009 H1N1 lineage represented the first detection of a novel, highly transmissible influenza A virus genotype: six gene segments originated from the North American triple-reassortant swine lineage, and two segments, NA and M, derived from the Eurasian avian-like swine lineage. As neither parental lineage transmits efficiently between humans, the adaptations and mechanisms underlying the pandemic spread of the swine-origin 2009 strain are not clear. To help identify determinants of transmission, we used reverse genetics to introduce gene segments of an early pandemic isolate, A/Netherlands/602/2009 [H1N1] (NL602), into the background of A/Puerto Rico/8/1934 [H1N1] (PR8) and evaluated the resultant viruses in a guinea pig transmission model. Whereas the NL602 virus spread efficiently, the PR8 virus did not transmit. Swapping of the HA, NA, and M segments of NL602 into the PR8 background yielded a virus with indistinguishable contact transmissibility to the wild-type pandemic strain. Consistent with earlier reports, the pandemic M segment alone accounted for much of the improvement in transmission. To aid in understanding how the M segment might affect transmission, we evaluated neuraminidase activity and virion morphology of reassortant viruses. Transmission was found to correlate with higher neuraminidase activity and a more filamentous morphology. Importantly, we found that introduction of the pandemic M segment alone resulted in an increase in the neuraminidase activity of two pairs of otherwise isogenic PR8-based viruses. Thus, our data demonstrate the surprising result that functions encoded by the influenza A virus M segment impact neuraminidase activity and, perhaps through this mechanism, have a potent effect on transmissibility. Our work uncovers a previously unappreciated mechanism through which the influenza A virus M segment can alter the receptor-destroying activity of an influenza virus. Concomitant with changes to neuraminidase activity, the M

  17. The special neuraminidase stalk-motif responsible for increased virulence and pathogenesis of H5N1 influenza A virus.

    Directory of Open Access Journals (Sweden)

    Hongbo Zhou

    Full Text Available The variation of highly pathogenic avian influenza H5N1 virus results in gradually increased virulence in poultry, and human cases continue to accumulate. The neuraminidase (NA stalk region of influenza virus varies considerably and may associate with its virulence. The NA stalk region of all N1 subtype influenza A viruses can be divided into six different stalk-motifs, H5N1/2004-like (NA-wt, WSN-like, H5N1/97-like, PR/8-like, H7N1/99-like and H5N1/96-like. The NA-wt is a special NA stalk-motif which was first observed in H5N1 influenza virus in 2000, with a 20-amino acid deletion in the 49(th to 68(th positions of the stalk region. Here we show that there is a gradual increase of the special NA stalk-motif in H5N1 isolates from 2000 to 2007, and notably, the special stalk-motif is observed in all 173 H5N1 human isolates from 2004 to 2007. The recombinant H5N1 virus with the special stalk-motif possesses the highest virulence and pathogenicity in chicken and mice, while the recombinant viruses with the other stalk-motifs display attenuated phenotype. This indicates that the special stalk-motif has contributed to the high virulence and pathogenicity of H5N1 isolates since 2000. The gradually increasing emergence of the special NA stalk-motif in H5N1 isolates, especially in human isolates, deserves attention by all.

  18. Encoding and recall of finger sequences in experienced pianists compared with musically naïve controls: a combined behavioral and functional imaging study.

    Science.gov (United States)

    Pau, S; Jahn, G; Sakreida, K; Domin, M; Lotze, M

    2013-01-01

    Long-term intensive sensorimotor training alters functional representation of the motor and sensory system and might even result in structural changes. However, there is not much knowledge about how previous training impacts learning transfer and functional representation. We tested 14 amateur pianists and 15 musically naïve participants in a short-term finger sequence training procedure, differing considerably from piano playing and measured associated functional representation with functional magnetic resonance imaging. The conditions consisted of encoding a finger sequence indicated by hand symbols ("sequence encoding") and subsequently replaying the sequence from memory, both with and without auditory feedback ("sequence retrieval"). Piano players activated motor areas and the mirror neuron system more strongly than musically naïve participants during encoding. When retrieving the sequence, musically naïve participants showed higher activation in similar brain areas. Thus, retrieval activations of naïve participants were comparable to encoding activations of piano players, who during retrieval performed the sequences more accurately despite lower motor activations. Interestingly, both groups showed primary auditory activation even during sequence retrieval without auditory feedback, supporting previous reports about coactivation of the auditory cortex after learned association with motor performance. When playing with auditory feedback, only pianists lateralized to the left auditory cortex. During encoding activation in left primary somatosensory cortex in the height of the finger representations had a predictive value for increased motor performance later on (error rates). Contrarily, decreased performance was associated with increased visual cortex activation during encoding. Our study extends previous reports about training transfer of motor knowledge resulting in superior training effects in musicians. Performance increase went along with activity in

  19. Dual Acting Neuraminidase Inhibitors Open New Opportunities to Disrupt the Lethal Synergism between Streptococcus pneumoniae and Influenza Virus

    Directory of Open Access Journals (Sweden)

    Elisabeth eWalther

    2016-03-01

    Full Text Available Secondary infections with Streptococcus pneumoniae cause severe pneumonia and enhance lethality during influenza epidemics and pandemics. Structural and functional similarities with viral neuraminidase (NA suggest that the highly prevalent pneumococcal NAs, NanA and NanB, might contribute to this lethal synergism by supporting viral replication and that dual acting NA inhibitors (NAIs will disrupt it. To verify this hypothesis, NanA and NanB were expressed in E. coli. After confirming their activity in enzyme assays, in vitro models with influenza virus A/Jena/8178/09 (Jena/8178 and the recombinant NanA or NanB (rNanA and rNanB were established in A549 and MDCK cells to mimic the role of these pneumococcal NAs during co-infection. Studies on the influence of both NAs on viral receptor expression, spread, and yield revealed a distinct effect of NanA and NanB on viral replication in these in vitro models. Both enzymes were able to support Jena/8178 replication at certain concentrations. This synergism was disrupted by the NAIs oseltamivir, DANA, katsumadain A, and artocarpin exerting an inhibitory effect on viral NA and NanA. Interestingly, katsumadain A and artocarpin inhibited rNanA and rNanB similarly. Zanamivir did not show activity. These results demonstrate a key role of pneumococcal NAs in the lethal synergism with influenza viruses and reveal opportunities for its effective disruption.

  20. QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR

    Science.gov (United States)

    Zheng, Mingyue; Yu, Kunqian; Liu, Hong; Luo, Xiaomin; Chen, Kaixian; Zhu, Weiliang; Jiang, Hualiang

    2006-09-01

    The recent wide spreading of the H5N1 avian influenza virus (AIV) in Asia, Europe and Africa and its ability to cause fatal infections in human has raised serious concerns about a pending global flu pandemic. Neuraminidase (NA) inhibitors are currently the only option for treatment or prophylaxis in humans infected with this strain. However, drugs currently on the market often meet with rapidly emerging resistant mutants and only have limited application as inadequate supply of synthetic material. To dig out helpful information for designing potent inhibitors with novel structures against the NA, we used automated docking, CoMFA, CoMSIA, and HQSAR methods to investigate the quantitative structure-activity relationship for 126 NA inhibitors (NIs) with great structural diversities and wide range of bioactivities against influenza A virus. Based on the binding conformations discovered via molecular docking into the crystal structure of NA, CoMFA and CoMSIA models were successfully built with the cross-validated q 2 of 0.813 and 0.771, respectively. HQSAR was also carried out as a complementary study in that HQSAR technique does not require 3D information of these compounds and could provide a detailed molecular fragment contribution to the inhibitory activity. These models also show clearly how steric, electrostatic, hydrophobicity, and individual fragments affect the potency of NA inhibitors. In addition, CoMFA and CoMSIA field distributions are found to be in well agreement with the structural characteristics of the corresponding binding sites. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction should be useful in developing novel potent NA inhibitors.

  1. Unprecedented phase transition sequence in the perovskite Li0.2Na0.8NbO3

    Directory of Open Access Journals (Sweden)

    Charlotte A. L. Dixon

    2017-05-01

    Full Text Available The perovskite Li0.2Na0.8NbO3 is shown, by powder neutron diffraction, to display a unique sequence of phase transitions at elevated temperature. The ambient temperature polar phase (rhombohedral, space group R3c transforms via a first-order transition to a polar tetragonal phase (space group P42mc in the region 150–300°C; these two phases correspond to Glazer tilt systems a−a−a− and a+a+c−, respectively. At 500°C a ferroelectric–paraelectric transition takes place from P42mc to P42/nmc, retaining the a+a+c− tilt. Transformation to a single-tilt system, a0a0c+ (space group P4/mbm, occurs at 750°C, with the final transition to the aristotype cubic phase at 850°C. The P42mc and P42/nmc phases have each been seen only once and twice each, respectively, in perovskite crystallography, in each case in compositions prepared at high pressure.

  2. Regeneration of membrane sialic acid after neuraminidase treatment of leukemic granulocytes.

    Science.gov (United States)

    Taub, R N; Hindenburg, A A; Baker, M A

    1985-01-01

    Granulocytes from patients with chronic myelogenous leukemia (CML) were studied for their ability to regenerate surface sialic acid following treatment with Vibrio cholera neuraminidase (VCN) in vitro. Immediately after neuraminidase treatment, CML and normal granulocytes showed similar incorporation of radioactivity after surface labelling with sodium periodate/potassium-H3-borohydride (PI/BH3(4)). CML granulocytes treated with neuraminidase then incubated for 18 h in nutrient medium showed strikingly increased PI/BH3(4) labelling, usually greater than initial pretreatment values, consistent with a rapid reappearance of sialic acid in the cell membrane. This pattern was not seen in normal granulocytes. The aberrant regeneration of sialic acid in CML granulocytes in vitro could be inhibited by addition of 3 X 10(-6) M retinoic acid, suggesting either a direct effect on membrane glycoconjugate synthesis or an association with granulocyte differentiation.

  3. Transforming growth factor-β: activation by neuraminidase and role in highly pathogenic H5N1 influenza pathogenesis.

    Directory of Open Access Journals (Sweden)

    Christina M Carlson

    2010-10-01

    Full Text Available Transforming growth factor-beta (TGF-β, a multifunctional cytokine regulating several immunologic processes, is expressed by virtually all cells as a biologically inactive molecule termed latent TGF-β (LTGF-β. We have previously shown that TGF-β activity increases during influenza virus infection in mice and suggested that the neuraminidase (NA protein mediates this activation. In the current study, we determined the mechanism of activation of LTGF-β by NA from the influenza virus A/Gray Teal/Australia/2/1979 by mobility shift and enzyme inhibition assays. We also investigated whether exogenous TGF-β administered via a replication-deficient adenovirus vector provides protection from H5N1 influenza pathogenesis and whether depletion of TGF-β during virus infection increases morbidity in mice. We found that both the influenza and bacterial NA activate LTGF-β by removing sialic acid motifs from LTGF-β, each NA being specific for the sialic acid linkages cleaved. Further, NA likely activates LTGF-β primarily via its enzymatic activity, but proteases might also play a role in this process. Several influenza A virus subtypes (H1N1, H1N2, H3N2, H5N9, H6N1, and H7N3 except the highly pathogenic H5N1 strains activated LTGF-β in vitro and in vivo. Addition of exogenous TGF-β to H5N1 influenza virus-infected mice delayed mortality and reduced viral titers whereas neutralization of TGF-β during H5N1 and pandemic 2009 H1N1 infection increased morbidity. Together, these data show that microbe-associated NAs can directly activate LTGF-β and that TGF-β plays a pivotal role protecting the host from influenza pathogenesis.

  4. Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction.

    Science.gov (United States)

    Li, Yan; Wu, Tao; Qi, Xian; Ge, Yiyue; Guo, Xiling; Wu, Bin; Yu, Huiyan; Zhu, Yefei; Shi, Zhiyang; Wang, Hua; Cui, Lunbiao; Zhou, Minghao

    2013-12-01

    A novel reassortant influenza A (H7N9) virus emerged recently in China. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The sensitivity of the assay was determined to be 10 RNA copies per reaction for both HA and NA genes. No cross-reactivity was observed with other influenza virus subtypes or respiratory tract viruses. One hundred and forty-six clinical and environmental specimens were tested and compared with reference methods and were found to be consistent. The assay is suitable for large-scale screening due to short turnaround times and high specificity, sensitivity, and reproducibility. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Sialidosis Type 1 with a Novel Mutation in the Neuraminidase-1 (NEU1) Gene.

    Science.gov (United States)

    Gowda, Vykuntaraju K; Srinivasan, Varun M; Benakappa, Naveen; Benakappa, Asha

    2017-05-01

    A patient with Sialidosis type 1 with a novel variation in neuraminidase-1 (NEU1) is described. The patient developed ataxia and myoclonus at 9 y of age. He was born to a second degree consanguineous marriage couple. On examination child had cerebellar signs and bilateral macular cherry-red spots. MRI of the brain and electroencephalogram were normal. The enzyme analysis revealed deficiency of neuraminidase. Genetic analysis identified novel homozygous missense mutation c.742G > T (p.G248C) in exon 4 of NEU1 gene. At 13 y of age, the ataxia and had myoclonus progressed.

  6. A contributing role for anti-neuraminidase antibodies on immunity to pandemic H1N1 2009 influenza A virus.

    Directory of Open Access Journals (Sweden)

    Glendie Marcelin

    Full Text Available Exposure to contemporary seasonal influenza A viruses affords partial immunity to pandemic H1N1 2009 influenza A virus (pH1N1 infection. The impact of antibodies to the neuraminidase (NA of seasonal influenza A viruses to cross-immunity against pH1N1 infection is unknown.Antibodies to the NA of different seasonal H1N1 influenza strains were tested for cross-reactivity against A/California/04/09 (pH1N1. A panel of reverse genetic (rg recombinant viruses was generated containing 7 genes of the H1N1 influenza strain A/Puerto Rico/08/34 (PR8 and the NA gene of either the pandemic H1N1 2009 strain (pH1N1 or one of the following contemporary seasonal H1N1 strains: A/Solomon/03/06 (rg Solomon or A/Brisbane/59/07 (rg Brisbane. Convalescent sera collected from mice infected with recombinant viruses were measured for cross-reactive antibodies to pH1N1 via Hemagglutinin Inhibition (HI or Enzyme-Linked Immunosorbent Assay (ELISA. The ectodomain of a recombinant NA protein from the pH1N1 strain (pNA-ecto was expressed, purified and used in ELISA to measure cross-reactive antibodies. Analysis of sera from elderly humans immunized with trivalent split-inactivated influenza (TIV seasonal vaccines prior to 2009 revealed considerable cross-reactivity to pNA-ecto. High titers of cross-reactive antibodies were detected in mice inoculated with either rg Solomon or rg Brisbane. Convalescent sera from mice inoculated with recombinant viruses were used to immunize naïve recipient Balb/c mice by passive transfer prior to challenge with pH1N1. Mice receiving rg California sera were better protected than animals receiving rg Solomon or rg Brisbane sera.The NA of contemporary seasonal H1N1 influenza strains induces a cross-reactive antibody response to pH1N1 that correlates with reduced lethality from pH1N1 challenge, albeit less efficiently than anti-pH1N1 NA antibodies. These findings demonstrate that seasonal NA antibodies contribute to but are not sufficient for cross

  7. Proteome Response of Chicken Embryo Fibroblast Cells to Recombinant H5N1 Avian Influenza Viruses with Different Neuraminidase Stalk Lengths.

    Science.gov (United States)

    Li, Yongtao; Ming, Fan; Huang, Huimin; Guo, Kelei; Chen, Huanchun; Jin, Meilin; Zhou, Hongbo

    2017-01-12

    The variation on neuraminidase (NA) stalk region of highly pathogenic avian influenza H5N1 virus results in virulence change in animals. In our previous studies, the special NA stalk-motif of H5N1 viruses has been demonstrated to play a significant role in the high virulence and pathogenicity in chickens. However, the molecular mechanisms underlying the pathogenicity of viruses with different NA stalk remain poorly understood. This study presents a comprehensive characterization of the proteome response of chicken cells to recombinant H5N1 virus with stalk-short NA (rNA-wt) and the stalkless NA mutant virus (rSD20). 208 proteins with differential abundance profiles were identified differentially expressed (DE), and these proteins were mainly related to stress response, transcription regulation, transport, metabolic process, cellular component and cytoskeleton. Through Ingenuity Pathways Analysis (IPA), the significant biological functions of DE proteins represented included Post-Translational Modification, Protein Folding, DNA Replication, Recombination and Repair. It was interesting to find that most DE proteins were involved in the TGF-β mediated functional network. Moreover, the specific DE proteins may play important roles in the innate immune responses and H5N1 virus replication. Our data provide important information regarding the comparable host response to H5N1 influenza virus infection with different NA stalk lengths.

  8. Systematic review of influenza resistance to the neuraminidase inhibitors

    Directory of Open Access Journals (Sweden)

    Boivin Guy

    2011-05-01

    Full Text Available Abstract Background Antivirals play a critical role in the prevention and the management of influenza. One class of antivirals, neuraminidase inhibitors (NAIs, is effective against all human influenza viruses. Currently there are two NAI drugs which are licensed worldwide: oseltamivir (Tamiflu® and zanamivir (Relenza®; and two drugs which have received recent approval in Japan: peramivir and laninamivir. Until recently, the prevalence of antiviral resistance has been relatively low. However, almost all seasonal H1N1 strains that circulated in 2008-09 were resistant to oseltamivir whereas about 1% of tested 2009 pandemic H1N1 viruses were found to be resistant to oseltamivir. To date, no studies have demonstrated widespread resistance to zanamivir. It seems likely that the literature on antiviral resistance associated with oseltamivir as well as zanamivir is now sufficiently comprehensive to warrant a systematic review. The primary objectives were to systematically review the literature to determine the incidence of resistance to oseltamivir, zanamivir, and peramivir in different population groups as well as assess the clinical consequences of antiviral resistance. Methods We searched MEDLINE and EMBASE without language restrictions in September 2010 to identify studies reporting incidence of resistance to oseltamivir, zanamivir, and peramivir. We used forest plots and meta-analysis of incidence of antiviral resistance associated with the three NAIs. Subgroup analyses were done across a number of population groups. Meta-analysis was also performed to evaluate associations between antiviral resistance and clinical complications and symptoms. Results We identified 19 studies reporting incidence of antiviral resistance. Meta-analysis of 15 studies yielded a pooled incidence rate for oseltamivir resistance of 2.6% (95%CI 0.7% to 5.5%. The incidence rate for all zanamivir resistance studies was 0%. Only one study measured incidence of antiviral

  9. A Viable Recombinant Rhabdovirus Lacking Its Glycoprotein Gene and Expressing Influenza Virus Hemagglutinin and Neuraminidase Is a Potent Influenza Vaccine

    Science.gov (United States)

    Ryder, Alex B.; Buonocore, Linda; Vogel, Leatrice; Nachbagauer, Raffael; Krammer, Florian

    2014-01-01

    ABSTRACT The emergence of novel influenza viruses that cause devastating human disease is an ongoing threat and serves as an impetus for the continued development of novel approaches to influenza vaccines. Influenza vaccine development has traditionally focused on producing humoral and/or cell-mediated immunity, often against the viral surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Here, we describe a new vaccine candidate that utilizes a replication-defective vesicular stomatitis virus (VSV) vector backbone that lacks the native G surface glycoprotein gene (VSVΔG). The expression of the H5 HA of an H5N1 highly pathogenic avian influenza virus (HPAIV), A/Vietnam/1203/04 (VN1203), and the NA of the mouse-adapted H1N1 influenza virus A/Puerto Rico/8/34 (PR8) in the VSVΔG vector restored the ability of the recombinant virus to replicate in cell culture, without the requirement for the addition of trypsin. We show here that this recombinant virus vaccine candidate was nonpathogenic in mice when given by either the intramuscular or intranasal route of immunization and that the in vivo replication of VSVΔG-H5N1 is profoundly attenuated. This recombinant virus also provided protection against lethal H5N1 infection after a single dose. This novel approach to vaccination against HPAIVs may be widely applicable to other emerging strains of influenza virus. IMPORTANCE Preparation for a potentially catastrophic influenza pandemic requires novel influenza vaccines that are safe, can be produced and administered quickly, and are effective, both soon after administration and for a long duration. We have created a new influenza vaccine that utilizes an attenuated vesicular stomatitis virus (VSV) vector, to deliver and express influenza virus proteins against which vaccinated animals develop potent antibody responses. The influenza virus hemagglutinin and neuraminidase proteins, expressed on the surface of VSV particles, allowed this vaccine to grow in cell

  10. A viable recombinant rhabdovirus lacking its glycoprotein gene and expressing influenza virus hemagglutinin and neuraminidase is a potent influenza vaccine.

    Science.gov (United States)

    Ryder, Alex B; Buonocore, Linda; Vogel, Leatrice; Nachbagauer, Raffael; Krammer, Florian; Rose, John K

    2015-03-01

    The emergence of novel influenza viruses that cause devastating human disease is an ongoing threat and serves as an impetus for the continued development of novel approaches to influenza vaccines. Influenza vaccine development has traditionally focused on producing humoral and/or cell-mediated immunity, often against the viral surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). Here, we describe a new vaccine candidate that utilizes a replication-defective vesicular stomatitis virus (VSV) vector backbone that lacks the native G surface glycoprotein gene (VSVΔG). The expression of the H5 HA of an H5N1 highly pathogenic avian influenza virus (HPAIV), A/Vietnam/1203/04 (VN1203), and the NA of the mouse-adapted H1N1 influenza virus A/Puerto Rico/8/34 (PR8) in the VSVΔG vector restored the ability of the recombinant virus to replicate in cell culture, without the requirement for the addition of trypsin. We show here that this recombinant virus vaccine candidate was nonpathogenic in mice when given by either the intramuscular or intranasal route of immunization and that the in vivo replication of VSVΔG-H5N1 is profoundly attenuated. This recombinant virus also provided protection against lethal H5N1 infection after a single dose. This novel approach to vaccination against HPAIVs may be widely applicable to other emerging strains of influenza virus. Preparation for a potentially catastrophic influenza pandemic requires novel influenza vaccines that are safe, can be produced and administered quickly, and are effective, both soon after administration and for a long duration. We have created a new influenza vaccine that utilizes an attenuated vesicular stomatitis virus (VSV) vector, to deliver and express influenza virus proteins against which vaccinated animals develop potent antibody responses. The influenza virus hemagglutinin and neuraminidase proteins, expressed on the surface of VSV particles, allowed this vaccine to grow in cell culture and induced a

  11. Chalcones as novel influenza A (H1N1) neuraminidase inhibitors from Glycyrrhiza inflata

    DEFF Research Database (Denmark)

    Dao, Trong Tuan; Nguyen, Phi Hung; Lee, Hong Sik

    2011-01-01

    -8) chalcones were isolated as active principles from the acetone extract of Glycyrrhiza inflata. Compounds 3 and 6 without prenyl group showed strong inhibitory effects on various neuraminidases from influenza viral strains, H1N1, H9N2, novel H1N1 (WT), and oseltamivir-resistant novel H1N1 (H274Y) expressed...

  12. Clinical presentation of congenital sialidosis in a patient with a neuraminidase gene frameshift mutation.

    Science.gov (United States)

    Buchholz, T; Molitor, G; Lukong, K E; Praun, M; Genzel-Boroviczény, O; Freund, M; Pshezhetsky, A V; Schulze, A

    2001-01-01

    Congenital sialidosis is a rare lysosomal storage disease caused by a primary neuraminidase deficiency which results from defects in the neuraminidase gene on chromosome 6p. The inheritance is autosomal recessive. Patients exhibit excessive urinary excretion of bound sialic acid and decreased or undetectable amounts of neuraminidase activity in various tissues. The clinical expression is variable, but ascites and hepatosplenomegaly are hallmarks of the disease. Skeletal abnormalities, facial dysmorphism and inguinal herniae have been described in most of the few reported cases. We describe a baby girl with biochemically proven sialidosis, who in addition to the above clinical features, had severely dilated coronary arteries, excessive retinal vascular tortuosity and an erythematous, macular rash. Homozygosity for a frameshift mutation at residue 623 of the neuraminidase cDNA was found. We speculate that the additional features found in our patient might be associated with the here described genotype of congenital sialidosis. Severely dilated coronary arteries, excessive retinal vascular tortuosity and an erythematous macular rash might be associated features of congenital sialidosis.

  13. Novel mutations in lysosomal neuraminidase identify functional domains and determine clinical severity in sialidosis.

    Science.gov (United States)

    Bonten, E J; Arts, W F; Beck, M; Covanis, A; Donati, M A; Parini, R; Zammarchi, E; d'Azzo, A

    2000-11-01

    Lysosomal neuraminidase is the key enzyme for the intralysosomal catabolism of sialylated glycoconjugates and is deficient in two neurodegenerative lysosomal disorders, sialidosis and galactosialidosis. Here we report the identification of eight novel mutations in the neuraminidase gene of 11 sialidosis patients with various degrees of disease penetrance. Comparison of the primary structure of human neuraminidase with the primary and tertiary structures of bacterial sialidases indicated that most of the single amino acid substitutions occurred in functional motifs or conserved residues. On the basis of the subcellular distribution and residual catalytic activity of the mutant neuraminidases we assigned the mutant proteins to three groups: (i) catalytically inactive and not lysosomal; (ii) catalytically inactive, but localized in lysosome; and (iii) catalytically active and lysosomal. In general, there was a close correlation between the residual activity of the mutant enzymes and the clinical severity of disease. Patients with the severe infantile type II disease had mutations from group I, whereas patients with a mild form of type I disease had at least one mutation from group III. Mutations from the second group were mainly found in juvenile type II patients with intermediate clinical severity. Overall, our findings explain the clinical heterogeneity observed in sialidosis and may help in the assignment of existing or new allelic combinations to specific phenotypes.

  14. Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y.

    Science.gov (United States)

    Burnham, Andrew J; Baranovich, Tatiana; Marathe, Bindumadhav M; Armstrong, Jianling; Webster, Robert G; Govorkova, Elena A

    2014-05-01

    Influenza B viruses cause annual outbreaks of respiratory illness in humans and are increasingly recognized as a major cause of influenza-associated pediatric mortality. Neuraminidase (NA) inhibitors (NAIs) are the only available therapy for patients infected with influenza B viruses, and the potential emergence of NAI-resistant viruses is a public health concern. The NA substitutions located within the enzyme active site could not only reduce NAI susceptibility of influenza B virus but also affect virus fitness. In this study, we investigated the effect of single NA substitutions on the fitness of influenza B/Yamanashi/166/1998 viruses (Yamagata lineage). We generated recombinant viruses containing either wild-type (WT) NA or NA with a substitution in the catalytic (R371K) or framework (E119A, D198E, D198Y, I222T, H274Y, and N294S) residues. We assessed NAI susceptibility, NA biochemical properties, NA protein expression, and virus replication in vitro and in differentiated normal human bronchial epithelial (NHBE) cells. Our results showed that four NA substitutions (D198E, I222T, H274Y, and N294S) conferred reduced inhibition by oseltamivir and three (E119A, D198Y, and R371K) conferred highly reduced inhibition by oseltamivir, zanamivir, and peramivir. All NA substitutions, except for D198Y and R371K, were genetically stable after seven passages in MDCK cells. Cell surface NA protein expression was significantly increased by H274Y and N294S substitutions. Viruses with the E119A, I222T, H274Y, or N294S substitution were not attenuated in replication efficiency in vitro or in NHBE cells. Overall, viruses with the E119A or H274Y NA substitution possess fitness comparable to NAI-susceptible virus, and the acquisition of these substitutions by influenza B viruses should be closely monitored.

  15. [The use of ultra deep sequencing technique in the screening program on HIV-1 drug resistance mutation among ART-naїve patients in Hunan province].

    Science.gov (United States)

    He, Jianmei; Zou, Xiaobai; Chen, Xi; Zheng, Jun

    2014-10-01

    To determine the prevalence rates of nucleotide reverse-transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI)TDRs among HIV-1 ART-naїve patients in Hunan province using the ultra deep sequencing (UDS) technique. ART-naїve subjects diagnosed in Hunan between 2010 and 2011 were evaluated by both UDS technique and Sanger sequencing techniques, to the 1% variant level. Mutations were scored using the Stanford HIVdb algorithm to infer the status on drug resistance. UDS method was performed on 90 ART-naїve subjects that seeking service of care, in Hunan. In total, 42.2% (38/90) of the subjects showed major NRTI or nonnucleoside reverse transcriptase inhibitor NNRTI TDRs by UDS technique, at a HIV variant frequency level of ≥1%, 15.6% (14/90) showed NRTI TDR, 16.7% (15/90) showed a major NNRTI TDR and 10% (9/90) were both resistant to NRTI and NNRTI when variants were analyzed by Stanford HIVdb. ART-naїve subjects from Hunan province, which had been predominately infected by subtype AE, would frequently possess HIV variants with NRTI/NNRTI TDRs that would affect the use of first line ART in the region, identified by the UDS technique. Further studies were needed to describe the prevalence of TDRs and to gather related information.

  16. Characterization of the neuraminidase genes from human influenza A viruses circulating in Iran from 2010 to 2015.

    Science.gov (United States)

    Moasser, Elham; Behzadian, Farida; Moattari, Afagh; Fotouhi, Fatemeh; Zaraket, Hassan

    2017-10-31

    Characterization of influenza viruses is critical for detection of new emerging variants. Herein, we analyzed the genetic diversity and drug susceptibility of the neuraminidase gene (NAs) expressed by influenza A/H1N1pdm09 and A/H3N2 viruses circulating in Iran from 2010 to 2015. We genetically analyzed the NAs of 38 influenza A/H1N1pdm09 and 35 A/H3N2 isolates. The Iranian A/H1N1pdm09 viruses belonged to seven genogroups/subgenogroups, with the dominant groups being genogroups 6B and 6C. The A/H3N2 isolates fell into six gneogroups/subgenogroups, with the dominant genogroups being 3C and 3C.2a. The most common mutations detected among the A/H1N1pdm09 viruses included N44S, V106I, N200S, and N248D. All H1N1pdm09 viruses were genetically susceptible to the NAIs. However, one A/H1N1pdm09 virus from the 2013-2014 season possessed an NA-S247N mutation, which reduces the susceptibility to oseltamivir. In case of H3N2, none of the analyzed Iranian strains carried a substitution that might affect its susceptibility to NAIs. The ongoing evolution of influenza viruses and the detect of influenza viruses with reduced susceptibility to NAIs warrants continuous monitoring of the circulating strains.

  17. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

    Science.gov (United States)

    Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

    2014-01-01

    Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

  18. Second Sialic Acid Binding Site in Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications for Fusion

    OpenAIRE

    Zaitsev, Viatcheslav; von Itzstein, Mark; Groves, Darrin; Kiefel, Milton; Takimoto, Toru; Portner, Allen; Taylor, Garry

    2004-01-01

    Paramyxoviruses are the leading cause of respiratory disease in children. Several paramyxoviruses possess a surface glycoprotein, the hemagglutinin-neuraminidase (HN), that is involved in attachment to sialic acid receptors, promotion of fusion, and removal of sialic acid from infected cells and progeny virions. Previously we showed that Newcastle disease virus (NDV) HN contained a pliable sialic acid recognition site that could take two states, a binding state and a catalytic state. Here we ...

  19. Microcapsules functionalized with neuraminidase can enter vascular endothelial cells in vitro.

    Science.gov (United States)

    Liu, Weizhi; Wang, Xiaocong; Bai, Ke; Lin, Miao; Sukhorukov, Gleb; Wang, Wen

    2014-12-06

    Microcapsules made of polyelectrolyte multilayers exhibit no or low toxicity, appropriate mechanical stability, variable controllable degradation and can incorporate remote release mechanisms triggered by various stimuli, making them well suited for targeted drug delivery to live cells. This study investigates interactions between microcapsules made of synthetic (i.e. polystyrenesulfonate sodium salt/polyallylamine hydrochloride) or natural (i.e. dextran sulfate/poly-L-arginine) polyelectrolyte and human umbilical vein endothelial cells with particular focus on the effect of the glycocalyx layer on the intake of microcapsules by endothelial cells. Neuraminidase cleaves N-acetyl neuraminic acid residues of glycoproteins and targets the sialic acid component of the glycocalyx on the cell membrane. Three-dimensional confocal images reveal that microcapsules, functionalized with neuraminidase, can be internalized by endothelial cells. Capsules without neuraminidase are blocked by the glycocalyx layer. Uptake of the microcapsules is most significant in the first 2 h. Following their internalization by endothelial cells, biodegradable DS/PArg capsules rupture by day 5; however, there is no obvious change in the shape and integrity of PSS/PAH capsules within the period of observation. Results from the study support our hypothesis that the glycocalyx functions as an endothelial barrier to cross-membrane movement of microcapsules. Neuraminidase-loaded microcapsules can enter endothelial cells by localized cleavage of glycocalyx components with minimum disruption of the glycocalyx layer and therefore have high potential to act as drug delivery vehicles to reach tissues beyond the endothelial barrier of blood vessels. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  20. Financial conflicts of interest and conclusions about neuraminidase inhibitors for influenza: an analysis of systematic reviews.

    Science.gov (United States)

    Dunn, Adam G; Arachi, Diana; Hudgins, Joel; Tsafnat, Guy; Coiera, Enrico; Bourgeois, Florence T

    2014-10-07

    Industry funding and financial conflicts of interest may contribute to bias in the synthesis and interpretation of scientific evidence. To examine the association between financial conflicts of interest and characteristics of systematic reviews of neuraminidase inhibitors. Retrospective analysis. Reviews that examined the use of neuraminidase inhibitors in the prophylaxis or treatment of influenza, were published between January 2005 and May 2014, and used a systematic search protocol. Two investigators blinded to all information regarding the review authors independently assessed the presentation of evidence on the use of neuraminidase inhibitors as favorable or not favorable. Financial conflicts of interest were identified using the index reviews, other publications, and Web-based searches. Associations between financial conflicts of interest, favorability assessments, and presence of critical appraisals of evidence quality were analyzed. Twenty-six systematic reviews were identified, of which 13 examined prophylaxis and 24 examined treatment, accounting for 37 distinct assessments. Among assessments associated with a financial conflict of interest, 7 of 8 (88%) were classified as favorable, compared with 5 of 29 (17%) among those without a financial conflict of interest. Reviewers without financial conflicts of interest were more likely to include statements about the quality of the primary studies than those with financial conflicts of interest. The heterogeneity in populations and outcomes examined in the reviews precluded analysis of the contribution of selective inclusion of evidence on the discordance of the assessments made in the reviews. Many of the systematic reviews had overlapping authorship. Reviewers with financial conflicts of interest may be more likely to present evidence about neuraminidase inhibitors in a favorable manner and recommend the use of these drugs than reviewers without financial conflicts of interest. Australian National Health and

  1. Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Nanyu Han

    Full Text Available It is critical to understand the molecular basis of the drug resistance of influenza viruses to efficiently treat this infectious disease. Recently, H1N1 strains of influenza A carrying a mutation of Q136K in neuraminidase were found. The new strain showed a strong Zanamivir neutralization effect. In this study, normal molecular dynamics simulations and metadynamics simulations were employed to explore the mechanism of Zanamivir resistance. The wild-type neuraminidase contained a 3(10 helix before the 150 loop, and there was interaction between the 150 and 430 loops. However, the helix and the interaction between the two loops were disturbed in the mutant protein due to interaction between K136 and nearby residues. Hydrogen-bond network analysis showed weakened interaction between the Zanamivir drug and E276/D151 on account of the electrostatic interaction between K136 and D151. Metadynamics simulations showed that the free energy landscape was different in the mutant than in the wild-type neuraminidase. Conformation with the global minimum of free energy for the mutant protein was different from the wild-type conformation. While the drug fit completely into the active site of the wild-type neuraminidase, it did not match the active site of the mutant variant. This study indicates that the altered hydrogen-bond network and the deformation of the 150 loop are the key factors in development of Zanamivir resistance. Furthermore, the Q136K mutation has a variable effect on conformation of different N1 variants, with conformation of the 1918 N1 variant being more profoundly affected than that of the other N1 variants studied in this paper. This observation warrants further experimental investigation.

  2. Aggregation of Streptococcus sanguis by a neuraminidase-sensitive component of serum and crevicular fluid.

    OpenAIRE

    Morris, E. J.; McBride, B. C.

    1983-01-01

    A number of strains of Streptococcus sanguis were found to aggregate in nonimmune serum and in crevicular fluid. All strains which aggregated in serum also aggregated in saliva, but some strains which aggregated in saliva did not aggregate in serum. Aggregation was destroyed by treatment of serum or crevicular fluid with neuraminidase and was inhibited by gangliosides. Treatment of serum with proteases reduced aggregating activity. Adsorption of serum to hydroxyapatite did not reduce the aggr...

  3. OPPORTUNITIES FOR APPLICATION OF THE NEURAMINIDASE INHIBITORS IN TREATMENT AND PREVENTION OF THE FLU

    Directory of Open Access Journals (Sweden)

    Yu.B. Belan

    2007-01-01

    Full Text Available Flu viruses cause yearly epidemics with the lesion of approximately 20% of population. during the increase of the flu sickness rate, it is necessary to take urgent anti epidemic and treatment steps aimed to reduce the spread of an infection as soon as possible and incorporating the application of the specific antiviral medications. The major aims for prescription of the specific antiviral medications in flu treatment are to reduce the duration and severity of the leading disease symptoms, risks of complications, as well as to prevent the lethal out comes. There were developed medications, effectively inhibiting the replication of B flu virus. At present, there are the 1st generation medications available — adamantane derivatives (amantadine and rimantadine and the 2nd generation medications — neuraminidase inhibitors (oseltamivir and zanamivir. The fast increase of the flu virus resistance towards adamantanes determine the necessity of a wider application of neuraminidase inhibitors, which are highly effective in respect flu viruses of A and B, as well as avian flu virus (h5n1.Key words: neuraminidase inhibitors, adamantanes, oseltamivir, zanamivir, h3n2, h5n1.

  4. 'a'-Position-mutated and G4-mutated hemagglutinin-neuraminidase proteins of Newcastle disease virus impair fusion and hemagglutinin-neuraminidase-fusion interaction by different mechanisms.

    Science.gov (United States)

    Chu, Fu-lu; Wen, Hong-ling; Zhang, Wen-qiang; Lin, Bin; Zhang, Yan; Sun, Cheng-xi; Ren, Gui-jie; Song, Yan-yan; Wang, Zhiyu

    2013-01-01

    To determine the effects of heptad repeat regions (HRs) and N-linked carbohydrate sites of the Newcastle disease virus hemagglutinin-neuraminidase (HN) protein on fusion of HN and fusion (F) proteins and HN-F interaction. We mutated six 'a' residues in the HRs and four asparagines in N-linked carbohydrate sites to alanine in the HN protein. A vaccinia-T7 RNA polymerase expression system was used to express HN cDNAs in BHK-21 cells to determine the HN functions. Deglycosylation was treated with PGNase F digestion. The formation of HN-F protein complexes was determined by the coimmunoprecipitation assay. Each HR-mutated protein interfered with fusion and the HN-F interaction. The G4-mutated protein not only impaired fusion and HN-F interaction but also decreased activities in cell fusion promotion, hemadsorption and neuraminidase. It is assumed that two different mechanisms for mutations in these two regions are responsible for the decreased fusion promotion activity and the reduced ability of interaction with F protein. Mutations in the HRs impair fusion and HN-F interaction by altering the transmission of a signal from the globular domain to the F-specific region in the stalk, but the G4 mutation modulates fusion and HN-F interaction by the misfolding of some important structures. Copyright © 2012 S. Karger AG, Basel.

  5. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  6. Replication of H9 influenza viruses in the human ex vivo respiratory tract, and the influence of neuraminidase on virus release.

    Science.gov (United States)

    Chan, Renee W Y; Chan, Louisa L Y; Mok, Chris K P; Lai, Jimmy; Tao, Kin P; Obadan, Adebimpe; Chan, Michael C W; Perez, Daniel R; Peiris, J S Malik; Nicholls, John M

    2017-07-24

    H9N2 viruses are the most widespread influenza viruses in poultry in Asia. We evaluated the infection and tropism of human and avian H9 influenza virus in the human respiratory tract using ex vivo respiratory organ culture. H9 viruses infected the upper and lower respiratory tract and the majority of H9 viruses had a decreased ability to release virus from the bronchus rather than the lung. This may be attributed to a weak neuraminidase (NA) cleavage of carbon-6-linked sialic acid (Sia) rather than carbon-3-linked Sia. The modified cleavage of N-acetlylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) by NA in H9 virus replication was observed by reverse genetics, and recombinant H9N2 viruses with amino acids (38KQ) deleted in the NA stalk, and changing the amino acid at position 431 from Proline-to-Lysine. Using recombinant H9 viruses previously evaluated in the ferret, we found that viruses which replicated well in the ferret did not replicate to the same extent in the human ex vivo cultures. The existing risk assessment models for H9N2 viruses in ferrets may not always have a strong correlation with the replication in the human upper respiratory tract. The inclusion of the human ex vivo cultures would further strengthen the future risk-assessment strategies.

  7. High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors.

    Directory of Open Access Journals (Sweden)

    Rodrigo Pessôa

    Full Text Available An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs.The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2 and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses.No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR and reverse transcriptase (RT regions of the HIV-1 pol gene was 44.5% (57/128, including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI. Of the 57 subjects, 43 (75.4% harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7% had detectable minority resistant variants to NRTIs, 6 (13.9% to NNRTIs, and 16 (37.2% to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis.Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these

  8. Zanamivir immobilized magnetic beads for voltammetric measurement of neuraminidase at gold-modified boron doped diamond electrode

    Energy Technology Data Exchange (ETDEWEB)

    Wahyuni, Wulan Tri, E-mail: wulantriws@gmail.com [Department of Chemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Kampus IPB Darmaga, Bogor 16680 (Indonesia); Department of Chemistry, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); Ivandini, Tribidasari A.; Saepudin, Endang [Department of Chemistry, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); Einaga, Yasuaki [Department of Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama 223-8522 (Japan); CREST, JST, 3-14-1 Hiyoshi, Yokohama 223-8522 (Japan)

    2016-04-19

    Biomolecule modified magnetic beads has been widely used in separation and sensing process. This study used streptavidin modified magnetic beads to immobilize biotin modified zanamivir. Biotin-streptavidin affinity facilitates immobilization of zanamivir on magnetic beads. Then interaction of zanamivir and neuraminidase was adopted as basic for enzyme detection. Detection of neuraminidase was performed at gold modified BDD using cyclic voltammetry technique. The measurement was carried out based on alteration of electrochemical signals of working electrode as neuraminidase response. The result showed that zanamivir was successfully immobilized on magnetic beads. The optimum amount of magnetic beads for zanamivir immobilization was 120 ug. Linear responses of neuraminidase were detected in concentration range of 0-15 mU. Detection limit (LOD) of measurement was 2.32 mU (R2 = 0.959) with precision as % RSD of 1.41%. Measurement of neuraminidase on magnetic beads could be also performed in the presence of mucin matrix. The linearity range was 0-8 mU with LOD of 0.64 mU (R2 = 0.950) and % RSD of 7.25%.

  9. Intestinal neuraminidase activity of suckling rats and other mammals. Relationship to the sialic acid content of milk.

    Science.gov (United States)

    Dickson, J J; Messer, M

    1978-02-15

    1. The neuraminidase activity of homogenates of the mucosa of the middle and distal thirds of the small intestine of rats increased about 5-fold between birth and 4 to 8 days of age, and then gradually declined to the much lower adult activity by 24 days. No comparable changes occurred in the proximal third. 2. In 8-day-old rats, the neuraminidase activity of the middle and distal thirds of the small intestine was about 10 times greater than that of the proximal third, 20 times greater than that of the colon and at least 100 times greater than that of the liver, brain, gastric mucosa or pancreas. 3. In all other species investigated (mice, rabbits, cats and guinea pigs), the neuraminidase activity of the middle and distal thirds of the small intestine was greater in suckling animals than in adults. 4. The sialic acid content of rat milk increased about 2-fold between birth and 8 days post partum and then declined. 5. There was a highly significant positive correlation between the intestinal neuraminidase activity of suckling animals of various species and ages and the sialic acid content of milk obtained from the corresponding species and stage of lactation. 6. It is suggested that the intestinal neuraminidase of suckling mammals functions primarily to remove sialic acid from various components of milk, thus providing sialic acid for the synthesis of sialoglycoproteins and gangliosides by the young.

  10. Neuraminidase production by a Streptococcus sanguis strain associated with subacute bacterial endocarditis.

    Science.gov (United States)

    Straus, D C; Portnoy-Duran, C

    1983-01-01

    The properties of an extracellular neuraminidase produced by a Streptococcus sanguis strain (isolated from a confirmed case of subacute bacterial endocarditis) during growth in a defined medium was examined in this investigation. This enzyme, isolated from concentrated culture supernatants of S. sanguis biotype II, was active against human alpha-1 acid glycoprotein, N-acetylneuramin lactose, bovine submaxillary mucin, and fetuin. Neuraminidase production paralleled bacterial growth in defined medium and was maximal in the early stationary phase of growth but decreased dramatically, probably owing to protease production, during the late stationary phase. The enzyme was purified to near homogeneity by a combination of salt fractionation, ion-exchanged chromatography on DEAE-Sephacel, and gel filtration on Sephadex G-200. These procedures yielded an enzyme preparation that possessed a specific activity of 174.4 mumol of sialic acid released per min per mg of protein against human alpha-1 acid glycoprotein. The Km value for this enzyme with human alpha-1 acid glycoprotein as substrate was 2.5 X 10(-3) M, and the enzyme possessed a pH optimum of 6.5. The S. sanguis neuraminidase had a molecular weight of approximately 85,000 as estimated by gel filtration and approximately 90,000 when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme was stable at temperatures of 4 and 37 degrees C for 3 h, but approximately 50% of the enzymatic activity was lost within 30 min at 50 degrees C, with 100% of the enzymatic activity being destroyed within 10 min at temperatures of greater than or equal to 65 degrees C. Images PMID:6874067

  11. Neuraminidase inhibitory polyketides from the marine-derived fungus Phoma herbarum.

    Science.gov (United States)

    Zhang, Gao Fei; Han, Wen Bo; Cui, Jiang Tao; Ng, Seik Weng; Guo, Zhi Kai; Tan, Ren Xiang; Ge, Hui Ming

    2012-01-01

    Two new polyketides, arthropsadiol C (1) and massarilactone H (2), together with six known derivatives (3-8) were isolated from the culture broth of the marine-derived fungus Phoma herbarum. Their structures were elucidated on the basis of spectroscopic methods, including 2D NMR techniques. Compounds 2, 4, 5, and 8 showed moderate neuraminidase inhibitory activity with IC(50) values ranging from 4.15 to 9.16 µM. © Georg Thieme Verlag KG Stuttgart · New York.

  12. The equilibrium constant for the interaction between a monoclonal Fab fragment and an influenza virus neuraminidase.

    Science.gov (United States)

    Jackson, D C; Howlett, G J; Nestorowicz, A; Webster, R G

    1983-03-01

    The affinity or equilibrium constant between an Fab fragment derived from monoclonal IgG directed against influenza virus neuraminidase was measured as 4.1 X 10(7) M-1. The method, which makes use of an air-driven ultracentrifuge, is simple and uses extremely small amounts (10(-11) mol) of material. Furthermore, interpretation of the data is based on sound theoretical considerations. The technique also allows m.w. of the interacting species to be measured and the stoichiometry of the reaction to be determined.

  13. Structure-function analysis of two variants of mumps virus hemagglutinin-neuraminidase protein

    Directory of Open Access Journals (Sweden)

    Gerardo Santos-López

    Full Text Available A point mutation from guanine (G to adenine (A at nucleotide position 1081 in the hemagglutinin-neuraminidase (HN gene has been associated with neurovirulence of Urabe AM9 mumps virus vaccine. This mutation corresponds to a glutamic acid (E to lysine (K change at position 335 in the HN glycoprotein. We have experimentally demonstrated that two variants of Urabe AM9 strain (HN-A1081 and HN-G1081 differ in neurotropism, sialic acidbinding affinity and neuraminidase activity. In the present study, we performed a structure-function analysis of that amino acid substitution; the structures of HN protein of both Urabe AM9 strain variants were predicted. Based on our analysis, the E/K mutation changes the protein surface properties and to a lesser extent their conformations, which in turn reflects in activity changes. Our modeling results suggest that this E/K interchange does not affect the structure of the sialic acid binding motif; however, the electrostatic surface differs drastically due to an exposed short alpha helix. Consequently, this mutation may affect the accessibility of HN to substrates and membrane receptors of the host cells. Our findings appear to explain the observed differences in neurotropism of these vaccine strains.

  14. Susceptibility of influenza viruses circulating in Western Saudi Arabia to neuraminidase inhibitors

    Directory of Open Access Journals (Sweden)

    Ahmed M. Tolah

    2016-04-01

    Full Text Available Objectives: To investigate the sensitivity of circulating influenza viruses in Western Saudi Arabia to neuraminidase inhibitors (NAIs; mainly, zanamivir and oseltamivir. Methods: Respiratory samples were collected from patients presenting with respiratory symptoms to King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia (KSA between September 2013 and October 2014. All samples were tested prospectively by real-time reverse-transcription polymerase chain reaction for influenza A and B viruses. Positive samples were then inoculated on Madin-Darby Canine Kidney (MDCK cells and isolated viruses were examined for their sensitivity to NAIs using fluorescent neuraminidase inhibition assay. Results: Out of 406 tested samples, 25 samples (6.2% were positive for influenza A/pdmH1N1 virus, one sample (0.25% was positive for influenza A/H3N2 virus, and 7 samples (1.7% were positive for influenza B Yamagata-like virus. Screening of isolated influenza A and B viruses (9 out of 33 for their sensitivity to NAIs showed no significant resistance to available NAIs. Conclusion: Our results show that circulating influenza viruses in Jeddah are still sensitive to NAIs.

  15. Analysis of Anti-Influenza Virus Neuraminidase Antibodies in Children, Adults, and the Elderly by ELISA and Enzyme Inhibition: Evidence for Original Antigenic Sin.

    Science.gov (United States)

    Rajendran, Madhusudan; Nachbagauer, Raffael; Ermler, Megan E; Bunduc, Paul; Amanat, Fatima; Izikson, Ruvim; Cox, Manon; Palese, Peter; Eichelberger, Maryna; Krammer, Florian

    2017-03-21

    Antibody responses to influenza virus hemagglutinin provide protection against infection and are well studied. Less is known about the human antibody responses to the second surface glycoprotein, neuraminidase. Here, we assessed human antibody reactivity to a panel of N1, N2, and influenza B virus neuraminidases in different age groups, including children, adults, and the elderly. Using enzyme-linked immunosorbent assays (ELISA), we determined the breadth, magnitude, and isotype distribution of neuraminidase antibody responses to historic, current, and avian strains, as well as to recent isolates to which these individuals have not been exposed. It appears that antibody levels against N1 neuraminidases were lower than those against N2 or B neuraminidases. The anti-neuraminidase antibody levels increased with age and were, in general, highest against strains that circulated during the childhood of the tested individuals, providing evidence for "original antigenic sin." Titers measured by ELISA correlated well with titers measured by the neuraminidase inhibition assays. However, in the case of the 2009 pandemic H1N1 virus, we found evidence of interference from antibodies binding to the conserved stalk domain of the hemagglutinin. In conclusion, we found that antibodies against the neuraminidase differ in magnitude and breadth between subtypes and age groups in the human population. (This study has been registered at ClinicalTrials.gov under registration no. NCT00336453, NCT00539981, and NCT00395174.)IMPORTANCE Anti-neuraminidase antibodies can afford broad protection from influenza virus infection in animal models and humans. However, little is known about the breadth and magnitude of the anti-neuraminidase response in the human population. Here we assessed antibody levels of children, adults, and the elderly against a panel of N1, N2, and type B influenza virus neuraminidases. We demonstrated that antibody levels measured by ELISA correlate well with functional

  16. Baicalein, Ethyl Acetate, and Chloroform Extracts of Scutellaria baicalensis Inhibit the Neuraminidase Activity of Pandemic 2009 H1N1 and Seasonal Influenza A Viruses

    Directory of Open Access Journals (Sweden)

    Mann-Jen Hour

    2013-01-01

    Full Text Available This study rated antiviral activity of Scutellaria baicalensis Georgi (S. baicalensis extracts against influenza A virus subtypes, for example, pandemic 2009 H1N1, seasonal H1N1 and H3N2. Ethyl acetate (EtOAc and chloroform extracts inhibited in vitro neuraminidase (NA enzymatic activity and viral replication more than methanol (MeOH extract. EtOAc extract demonstrated NA inhibition IC50 values ranging from 73.16 to 487.40 μg/mL and plaque reduction IC50 values ranging from 23.7 to 27.4 μg/mL. Chloroform extract showed antiviral activities with plaque reduction IC50 values ranging from 14.16 to 41.49 μg/mL Time-of-addition assay indicated that EtOAc and chloroform extracts also significantly inhibited virus yields after infection. HPLC analysis demonstrated that baicalin was dominant in the MeOH extract; baicalein and chrysin were rich in the EtOAc and chloroform extracts. Molecular simulation revealed baicalein hydrogen bonding with Glu277 as well as hydrophobic and Van der Waals interactions with Ile222, Arg224, Ser246, and Tyr347 in NA1 active sites of NA1. Baicalein inhibited in vitro replication of influenza A viruses pandemic 2009 H1N1 (IC50 = 0.018 μM and seasonal 2007 H1N1 using plaque reduction assays. A combination of low-dose baicalein with other anti-influenza agents could be applicable for development of alternative remedies treating influenza A virus infection.

  17. Molecular basis for broad neuraminidase immunity: conserved epitopes in seasonal and pandemic H1N1 as well as H5N1 influenza viruses.

    Science.gov (United States)

    Wan, Hongquan; Gao, Jin; Xu, Kemin; Chen, Hongjun; Couzens, Laura K; Rivers, Katie H; Easterbrook, Judy D; Yang, Kevin; Zhong, Lei; Rajabi, Mohsen; Ye, Jianqiang; Sultana, Ishrat; Wan, Xiu-Feng; Liu, Xiufan; Perez, Daniel R; Taubenberger, Jeffery K; Eichelberger, Maryna C

    2013-08-01

    Influenza A viruses, including H1N1 and H5N1 subtypes, pose a serious threat to public health. Neuraminidase (NA)-related immunity contributes to protection against influenza virus infection. Antibodies to the N1 subtype provide protection against homologous and heterologous H1N1 as well as H5N1 virus challenge. Since neither the strain-specific nor conserved epitopes of N1 have been identified, we generated a panel of mouse monoclonal antibodies (MAbs) that exhibit different reactivity spectra with H1N1 and H5N1 viruses and used these MAbs to map N1 antigenic domains. We identified 12 amino acids essential for MAb binding to the NA of a recent seasonal H1N1 virus, A/Brisbane/59/2007. Of these, residues 248, 249, 250, 341, and 343 are recognized by strain-specific group A MAbs, while residues 273, 338, and 339 are within conserved epitope(s), which allows cross-reactive group B MAbs to bind the NAs of seasonal H1N1 and the 1918 and 2009 pandemic (09pdm) H1N1 as well as H5N1 viruses. A single dose of group B MAbs administered prophylactically fully protected mice against lethal challenge with seasonal and 09pdm H1N1 viruses and resulted in significant protection against the highly pathogenic wild-type H5N1 virus. Another three N1 residues (at positions 396, 397, and 456) are essential for binding of cross-reactive group E MAbs, which differ from group B MAbs in that they do not bind 09pdm H1N1 viruses. The identification of conserved N1 epitopes reveals the molecular basis for NA-mediated immunity between H1N1 and H5N1 viruses and demonstrates the potential for developing broadly protective NA-specific antibody treatments for influenza.

  18. Composition of hemagglutinin and neuraminidase affects the antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses.

    Science.gov (United States)

    Shirakura, Masayuki; Kawaguchi, Akira; Tashiro, Masato; Nobusawa, Eri

    2013-01-01

    To improve the hemagglutinin (HA) antigen yield of influenza A(H1N1)pdm09 candidate vaccine viruses, we generated 7:1, 6:2, and 5:3 genetic reassortant viruses between wild-type (H1N1)pdm09 (A/California/7/2009) (Cal7) and a high-yielding master virus, A/Puerto Rico/8/34 (PR8). These viruses contained the HA; HA and neuraminidase (NA); and HA, NA, and M genes, respectively, derived from Cal7, on a PR8 backbone. The influence of the amino acid residue at position 223 in Cal7 HA on virus growth and HA antigen yield differed between these reassortant viruses. NIIDRG-7, a 7:1 virus possessing arginine at position 223, exhibited a 10-fold higher 50% egg infectious dose (EID(50)) (10.0 log(10)EID(50)/ml) than the 5:3 and 6:2 viruses. It also had 1.5- to 3-fold higher protein (13.8 μg/ml of allantoic fluids) and HA antigen (4.1 μg/ml of allantoic fluids) yields than the 5:3 and 6:2 viruses, which possessed identical Cal7 HA proteins. However, the HA antigen yield of the other 7:1 virus, which possessed glutamine at position 223 was 60% of that of NIIDRG-7. In addition, a novel 6:2 virus possessing Cal7 HA and the NA of A/Wisconsin/10/98 (a triple reassortant swine-like H1N1 virus), produced 107% of the HA yield of NIIDRG-7. In this study, we showed that the balance between HA and NA in the influenza A(H1N1)pdm09 virus affects its protein and antigen yield.

  19. C-Methylated Flavonoids from Cleistocalyx operculatus and Their Inhibitory Effects on Novel Influenza A (H1N1) Neuraminidase

    DEFF Research Database (Denmark)

    Dao, Trong-Tuan; Tung, Bui-Thanh; Nguyen, Phi-Hung

    2010-01-01

    As part of an ongoing study focused on the discovery of anti-influenza agents from plants, four new (1-4) and 10 known (5-14) C-methylated flavonoids were isolated from a methanol extract of Cleistocalyx operculatus buds using an influenza H1N1 neuraminidase inhibition assay. Compounds 4, 7, 8...

  20. Correlation of haemagglutinin-neuraminidase and fusion protein content with protective antibody response after immunisation with inactivated Newcastle disease vaccines.

    NARCIS (Netherlands)

    Maas, R.A.; Komen, M.; Diepen, van M.; Oei, H.L.; Claassen, I.J.T.M.

    2003-01-01

    The correlation between the antigen content of inactivated Newcastle disease (ND) oil emulsion-vaccines and the serological response after immunisation was studied. The haemagglutinin-neuraminidase (HN) and fusion (F) proteins of Newcastle disease virus (NDV) were quantified in 33 inactivated

  1. Financial competing interests were associated with favorable conclusions and greater author productivity in nonsystematic reviews of neuraminidase inhibitors.

    Science.gov (United States)

    Dunn, Adam G; Zhou, Xujuan; Hudgins, Joel; Arachi, Diana; Mandl, Kenneth D; Coiera, Enrico; Bourgeois, Florence T

    2016-12-01

    To characterize the conclusions and production of nonsystematic reviews about neuraminidase inhibitors relative to financial competing interests held by the authors. We searched for articles about neuraminidase inhibitors and influenza (January 2005 to April 2015), identifying nonsystematic reviews and grading them according to the favorable/nonfavorable presentation of evidence on safety and efficacy. We recorded financial competing interests disclosed in the reviews and from other articles written by their authors. We measured associations between competing interests, author productivity, and conclusions. Among 213 nonsystematic reviews, 138 (65%) presented favorable conclusions. Financial competing interests were identified for 26% (137/532) of authors; 51% (108/213) of reviews were associated with a financial competing interest. Reviews produced exclusively by authors with financial competing interests (33%; 71/213) were more likely to present favorable conclusions than reviews with no competing interests (risk ratio 1.27; 95% confidence interval 1.03-1.55). Authors with financial competing interests published more articles about neuraminidase inhibitors than their counterparts. Half of nonsystematic reviews about neuraminidase inhibitors included an author with a financial competing interest. Reviews produced exclusively by these authors were more likely to present favorable conclusions, and authors with financial competing interests published a greater number of reviews. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations.

    Science.gov (United States)

    Tam, Nguyen Minh; Nguyen, Minh Tho; Ngo, Son Tung

    2017-08-24

    The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0.82 and error of σΔGexp=2.2kcal/mol. The results were observed using Amber99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Virtual screening of Indonesian flavonoid as neuraminidase inhibitor of influenza a subtype H5N1

    Science.gov (United States)

    Parikesit, A. A.; Ardiansah, B.; Handayani, D. M.; Tambunan, U. S. F.; Kerami, D.

    2016-02-01

    Highly Pathogenic Avian Influenza (HPAI) H5N1 poses a significant threat to animal and human health worldwide. The number of H5N1 infection in Indonesia is the highest during 2005-2013, with a mortality rate up to 83%. A mutation that occurred in H5N1 strain made it resistant to commercial antiviral agents such as oseltamivir and zanamivir, so the more potent antiviral agent is needed. In this study, virtual screening of Indonesian flavonoid as neuraminidase inhibitor of H5N1 was conducted. Total 491 flavonoid compound obtained from HerbalDB were screened. Molecular docking was performed using MOE 2008.10. This research resulted in Guajavin B as the best ligand.

  4. Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hua; Carney, Paul J.; Mishin, Vasiliy P.; Guo, Zhu; Chang, Jessie C.; Wentworth, David E.; Gubareva, Larisa V.; Stevens, James; Schultz-Cherry, S.

    2016-04-06

    ABSTRACT

    During 2014, a subclade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus caused poultry outbreaks around the world. In late 2014/early 2015, the virus was detected in wild birds in Canada and the United States, and these viruses also gave rise to reassortant progeny, composed of viral RNA segments (vRNAs) from both Eurasian and North American lineages. In particular, viruses were found with N1, N2, and N8 neuraminidase vRNAs, and these are collectively referred to as H5Nx viruses. In the United States, more than 48 million domestic birds have been affected. Here we present a detailed structural and biochemical analysis of the surface antigens of H5N1, H5N2, and H5N8 viruses in addition to those of a recent human H5N6 virus. Our results with recombinant hemagglutinin reveal that these viruses have a strict avian receptor binding preference, while recombinantly expressed neuraminidases are sensitive to FDA-approved and investigational antivirals. Although H5Nx viruses currently pose a low risk to humans, it is important to maintain surveillance of these circulating viruses and to continually assess future changes that may increase their pandemic potential.

    IMPORTANCEThe H5Nx viruses emerging in North America, Europe, and Asia pose a great public health concern. Here we report a molecular and structural study of the major surface proteins of several H5Nx influenza viruses. Our results improve the understanding of these new viruses and provide important information on their receptor preferences and susceptibilities to antivirals, which are central to pandemic risk assessment.

  5. Integrin-mediated cell migration is blocked by inhibitors of human neuraminidase.

    Science.gov (United States)

    Jia, Feng; Howlader, Md Amran; Cairo, Christopher W

    2016-09-01

    Integrins are critical receptors in cell migration and adhesion. A number of mechanisms are known to regulate the function of integrins, including phosphorylation, conformational change, and cytoskeletal anchoring. We investigated whether native neuraminidase (Neu, or sialidase) enzymes which modify glycolipids could play a role in regulating integrin-mediated cell migration. Using a scratch assay, we found that exogenously added Neu3 and Neu4 activity altered rates of cell migration. We observed that Neu4 increased the rate of migration in two cell lines (HeLa, A549); while Neu3 only increased migration in HeLa cells. A bacterial neuraminidase was able to increase the rate of migration in HeLa, but not in A549 cells. Treatment of cells with complex gangliosides (GM1, GD1a, GD1b, and GT1b) resulted in decreased cell migration rates, while LacCer was able to increase rates of migration in both lines. Importantly, our results show that treatment of cells with inhibitors of native Neu enzymes had a dramatic effect on the rates of cell migration. The most potent compound tested targeted the human Neu4 isoenzyme, and was able to substantially reduce the rate of cell migration. We found that the lateral mobility of integrins was reduced by treatment of cells with Neu3, suggesting that Neu3 enzyme activity resulted in changes to integrin-co-receptor or integrin-cytoskeleton interactions. Finally, our results support the hypothesis that inhibitors of human Neu can be used to investigate mechanisms of cell migration and for the development of anti-adhesive therapies. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. [High-yield reassortant virus containing hemagglutinin and neuraminidase genes of pandemic influenza A/Moscowl/01/2009 (H1N1) virus].

    Science.gov (United States)

    Ignat'eva, A V; Rudneva, I A; Timofeeva, T A; Shilov, A A; Zaberezhnyĭ, A D; Aliper, T I; Kaverin, N V; L'vov, D K

    2011-01-01

    The crossing of influenza A/Moscow/01/2009 (H1N1) virus and reassortant strain X31 (H3N2) containing the genes of internal and non-structural proteins of A/Puerto Rico/8/34 (H1N1) strain gave rise to reassortant virus ReM8. The reassortant contained hemagglutinin (HA) and neuraminidase (NA) genes of pandemic 2009 influenza virus and 6 genes of high-yield A/Puerto Rico/8/34 (H1N1) strain. The reassortant ReM8 produced higher yields in the embryonated chicken eggs than the parent pandemic virus, as suggested by infectivity and HA activity titration as well as by ELISA and the measurement of HA protein content by scanning electrophoresis in polyacrylamide gel slabs. High immunogenicity of ReM8 reassortant was demonstrated by immune protection studies in mice. The reassortant virus ReM8 is suitable as a candidate strain for the production of inactivated and subunit influenza vaccines.

  7. Neuraminidase Activity in Streptococcus sanguis and in the Viridans Group, and Occurrence of Acylneuraminate Lyase in Viridans Organisms Isolated from Patients with Septicemia

    Science.gov (United States)

    Müller, H. E.

    1974-01-01

    The enzyme neuraminidase (EC 3.2.1.18) was found to be strongly active in different types of Streptococcus sanguis and S. viridans, and, in addition, the occurrence of the enzyme acylneuraminate pyruvate lyase (EC 4.1.3.3) was described in S. viridans. The enzyme-active bacteria strains were isolated from blood cultures of patients with septicemia. Whereas S. sanguis lost its strong neuraminidase activity after some weeks, S. viridans retained its enzyme activity for a long time in culture. Immunoelectrophoretic studies of the blood cultures of patients with streptococcal infections showed the loss of neuraminic acid in most glycoproteins of the serum, proving the in vivo action of neuraminidase. The pathogenic role of neuraminidase is discussed in streptococcal septicemia from the viewpoint of present knowledge. Images PMID:4816461

  8. Sequenciamento de DNA de nova geração e suas aplicações na genômica de plantas Next generation DNA sequencing and its applications in plant genomics

    Directory of Open Access Journals (Sweden)

    Mayra Costa da Cruz Gallo de Carvalho

    2010-03-01

    Full Text Available As plataformas de sequenciamento de nova geração são uma alternativa poderosa para estudos de genômica estrutural e funcional. Na genômica de plantas, os trabalhos com as novas plataformas têm sido destinados ao sequenciamento de transcritos, ressequenciamento ou sequenciamento de novo de genomas plastidiais. Neste trabalho, são detalhadas as tecnologias das plataformas mais utilizadas atualmente, bem como é revisada a aplicação dessas tecnologias na genômica estrutural e funcional de plantas.The next-generation DNA sequencing technologies are a powerful alternative to studies in structural and functional genomics. In plant genomics studies, the work with these new platforms has been used for the sequencing of transcripts, re-sequencing, and the de novo sequencing of plastid genomes. This research details the technological principles of the next-generation DNA sequencing platforms most used and reviews its application in structural and functional plant genomics.

  9. Adamantane and Neuraminidase resistant influenza A/H3N2 isolated in Iran from 2005 to 2013

    Directory of Open Access Journals (Sweden)

    Jila Yavarian

    2014-04-01

    Conclusion: This study showed circulating A/H3N2 viruses was resistant to adaman-tanes but susceptible to neuraminidase inhibitors. The national data analyzed in this re-search may help increase knowledge about influenza virus antiviral drug resistance, which is a global public health concern. The authors suggested continuing this study and also the investigation of antiviral drug resistance of influenza A/H1N1 and B viruses.

  10. Prognosis of hospitalized patients with 2009 H1N1 influenza in Spain: influence of neuraminidase inhibitors

    Science.gov (United States)

    Delgado-Rodríguez, Miguel; Castilla, Jesús; Godoy, Pere; Martín, Vicente; Soldevila, Nuria; Alonso, Jordi; Astray, Jenaro; Baricot, Maretva; Cantón, Rafael; Castro, Ady; Gónzález-Candelas, Fernando; Mayoral, José María; Quintana, José María; Pumarola, Tomás; Tamames, Sonia; Sáez, Marc; Domínguez, Angela

    2012-01-01

    Background The H1N1 influenza pandemic strain has been associated with a poor prognosis in hospitalized patients. The present report evaluates the factors influencing prognosis. Methods A total of 813 patients hospitalized with H1N1 influenza in 36 hospitals (nationwide) in Spain were analysed. Detailed histories of variables preceding hospital admission were obtained by interview, validating data on medications and vaccine with their attending physicians. Data on treatment and complications during hospital stay were recorded. As definition of poor outcome, the endpoints of death and admission to intensive care were combined; and as a further outcome, length of stay was used. Results The mean age was 38.5 years (SD 22.8 years). There were 10 deaths and 79 admissions to intensive care (combined, 88). The use of neuraminidase inhibitors was reported by 495 patients (60.9%). The variables significantly associated with a poor outcome were diabetes (OR = 2.21, 95% CI = 1.21–4.02), corticosteroid therapy (OR = 3.37, 95% CI = 1.39–8.20) and use of histamine-2 receptor antagonists (OR = 2.68, 95% CI = 1.14–6.36), while the use of neuraminidase inhibitors (OR = 0.57, 95% CI = 0.34–0.94) was protective. Neuraminidase inhibitors within the first 2 days after the influenza onset reduced hospital stay by a mean of 1.9 days (95% CI = 4.7–6.6). Conclusions The use of neuraminidase inhibitors decreases the length of hospital stay and admission to intensive care and/or death. PMID:22467633

  11. Assessment of Streptococcus pneumoniae Capsule in Conjunctivitis and Keratitis in vivo Neuraminidase Activity Increases in Nonencapsulated Pneumococci following Conjunctival Infection

    Science.gov (United States)

    Norcross, Erin W.; Tullos, Nathan A.; Taylor, Sidney D.; Sanders, Melissa E.; Marquart, Mary E.

    2010-01-01

    Purpose The pneumococcal capsule is required for pathogenesis in systemic infections, yet reports show most conjunctivitis outbreaks are caused by nonencapsulated pneumococci, while keratitis infections are caused by encapsulated strains. This study aims to determine the effect of capsule in pneumococcal keratitis and conjunctivitis in rabbit models of infection. Methods A capsule-deficient isogenic mutant was created using homologous transformation. Parent and mutant strains were injected within the upper bulbar conjunctiva (conjunctivitis) or into the corneal stroma (keratitis) of New Zealand white rabbits. Clinical examinations were performed 24 and 48 hr post-infection at which time corneas or conjunctivae were removed, homogenized, and plated to determine the recovered bacterial load. Whole eyes were removed for histological examination. The neuraminidase activity was determined following in vitro and in vivo growth. Results There were no significant differences in clinical scores between the eyes infected with the parent or mutant for either infection, nor was there a difference in the amount of bacteria recovered from the cornea. In the conjunctivae, however, the mutant strain was cleared by the host faster than the parent strain. Histological examination showed slightly more infiltrating polymorphonuclear leukocytes (PMN) and macrophages in the conjunctivae infected with the parent strain. The neuraminidase activity of both strains was not significantly different when the strains were grown in vitro. However, the neuraminidase activity of the parent was significantly less than that of the mutant at 3 and 12 hr post conjunctival infection. Conclusions Although more outbreaks of pneumococcal conjunctivitis are tied to nonencapsulated S. pneumoniae strains, this study showed that an encapsulated strain was capable of establishing conjunctivitis in a rabbit injection model and survive attack by the host immune system longer than its nonencapsulated isogenic

  12. Kinetic, thermodynamic and structural analysis of tamiphosphor binding to neuraminidase of H1N1 (2009) pandemic influenza

    Czech Academy of Sciences Publication Activity Database

    Albinana, C. B.; Machara, A.; Řezáčová, Pavlína; Pachl, Petr; Konvalinka, Jan; Kožíšek, Milan

    2016-01-01

    Roč. 121, Oct 4 (2016), s. 100-109 ISSN 0223-5234 R&D Projects: GA ČR GA13-19561S; GA MŠk LO1302; GA MŠk(CZ) LO1304 Institutional support: RVO:61388963 Keywords : influenza neuraminidase * oseltamivir * tamiphosphor * isothermal titration calorimetry * crystal structure * lattice-translocation defect Subject RIV: CE - Biochemistry Impact factor: 4.519, year: 2016

  13. Ependymal denudation, aqueductal obliteration and hydrocephalus after a single injection of neuraminidase into the lateral ventricle of adult rats.

    Science.gov (United States)

    Grondona, J M; Pérez-Martín, M; Cifuentes, M; Pérez, J; Jiménez, A J; Pérez-Fígares, J M; Fernández-Llebrez, P

    1996-09-01

    To investigate the role of sialic acid in the ependyma of the rat brain, we injected neuraminidase from Clostridium perfingens into the lateral ventricle of 86 adult rats that were sacrificed at various time intervals. After administration of 10 micrograms neuraminidase, ciliated cuboidal ependymal cells of the lateral ventricles, third ventricle, cerebral aqueduct, and the rostral half of the fourth ventricle died and detached. The ependymal regions sealed by tight junctions such as the choroid plexus and the subcommissural organ were not affected. Debris was removed by infiltrating neutrophils and macrophagic cells. At the same time, after ependymal disappearance, the aqueduct was obliterated. In this region, mitoses were evident and cystic ependymal cells were frequent. Hydrocephalus of the lateral and third ventricles was evident 4 days after neuraminidase injection. Gliosis was restricted to the dorsal telencephalic wall of the injected lateral ventricle. It is thought that cleavage of sialic acid from ependymal surface glycoproteins or glycolipids, likely involved in cell adhesion, led to the detaching and death of the ependymal cells. Thereafter, ependymal loss, together with edema, led to fusion of the lateral walls of the cerebral aqueduct and this in turn provoked hydrocephalus of the third and lateral ventricles. This model of experimental hydrocephalus is compared with other models, in particular those of hydrocephalus after viral invasion of the cerebral ventricles.

  14. Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases:a homology modeling and flexible docking study

    Directory of Open Access Journals (Sweden)

    MARIJA L. MIHAJLOVIC

    2009-01-01

    Full Text Available In the context of the recent pandemic threat by the worldwide spread of H5N1 avian influenza, novel insights into the mechanism of ligand binding and interaction between various inhibitors (zanamivir – ZMV, oseltamivir – OTV, 2,3-didehydro-2-deoxy-N-acetylneuraminic acid – DANA, peramivir – PMV and neuraminidases (NA are of vital importance for the structure-based design of new anti-viral drugs. To address this issue, three-dimensional models of H5N1-NA and N9-NA were generated by homology modeling. Traditional residues within the active site throughout the family of NA protein structures were found to be highly conserved in H5N1-NA. A subtle variation between lipophilic and hydrophilic environments in H5N1-NA with respect to N9-NA was observed, thus shedding more light on the high resistance of some H5N1 strains to various NA inhibitors. Based on these models, an ArgusLab4/AScore flexible docking study was performed. The conformational differences between OTV bound to H5N1-NA and OTV bound to N9-NA were structurally identified and quantified. A slight difference of less than 1 kcal mol-1 between the OTV-N9 and OTV-N1 binding free energies is in agreement with the experimentally predicted free energy difference. The conformational differences between ZMV and OTV bound to either H5N1-NA or N9-NA were structurally identified. The binding free energies of the ZMV complexes, being slightly higher than those of OTV, are not in agreement with what was previously proposed using homology modeling. The differences between ZMV and OTV are suggested to be ascribed to the presence/absence of Asn166 in the active cavity of ZMV/OTV in H5N1-NA, and to the presence/absence of Ser165 in the binding site of ZMV/OTV in N9-NA. The charge distribution was evaluated using the semi-empirical AM1 method. The trends of the AM1 charges of the ZMV and OTV side chains in the complexes deviate from those previously reported.

  15. Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.

    Directory of Open Access Journals (Sweden)

    Wangchao Lou

    Full Text Available Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that

  16. Clinical Effectiveness of Peramivir in Comparison with Other Neuraminidase Inhibitors in Pediatric Influenza Patients

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    Toshiyuki Hikita

    2012-01-01

    Full Text Available The currently used antivirals in the treatment of influenza in Japan include amantadine, oseltamivir, zanamivir, laninamivir, and peramivir. We compared the efficacy of intravenous peramivir with that of other neuraminidase inhibitors for treating pediatric influenza. The present study included 223 influenza patients (≤18 years who presented at the Hikita Pediatric Clinic between February and April 2011. We compared fever duration after starting treatment with antiviral drugs. Because inhalation drugs are difficult to use in <5-year-old patients and because of the potential adverse effects of oseltamivir in teenagers, we created two different age groups (<10-year-old group and 5–18-year-old group to evaluate treatment results. In influenza A patients between 5 and 18 years old, the median fever duration after treatment with zanamivir was 2 days, compared with 1 day for peramivir (=0.0242. In influenza B patients between 5 and 18 years old, the median fever duration after treatment with laninamivir was 3 days, compared with 1 day for peramivir (=0.0097. We found no significant difference for any of the other combinations of drug/disease type/age groups. No adverse effects were observed with the antiviral drugs used. The results suggest that peramivir is very useful in pediatric influenza patients.

  17. The accuracy and timeliness of neuraminidase inhibitor dispensing data for predicting laboratory-confirmed influenza.

    Science.gov (United States)

    Papenburg, J; Charland, K M; DE Serres, G; Buckeridge, D L

    2016-06-01

    Neuraminidase inhibitor (NI) dispensing has emerged as a possible automated data source for influenza surveillance. We aimed to evaluate its timeliness, correlation, and predictive accuracy in relation to influenza activity in Quebec, Canada, 2010-2013. Our secondary objective was to use the same metrics to compare NI dispensing to visits for influenza-like illness (ILI) in emergency departments (EDs). Provincial weekly counts of positive influenza laboratory tests were used as a reference measure for the level of influenza circulation. We applied ARIMA models to account for serial correlation. We computed cross-correlations to measure the strengths of association and lead-lag relationships between NI dispensing, ILI ED visits, and our reference indicator. Finally, using an ARIMA model, we evaluated the ability of NI dispensing and ILI ED visits to predict laboratory-confirmed influenza. NI dispensing was significantly correlated (R = 0·68) with influenza activity with no lag. The maximal correlation of ILI ED visits was not as strong (R = 0·50). Both NI dispensing and ILI ED visits were significant predictors of laboratory-confirmed influenza in a multivariable model; predictive potential was greatest when NI counts were lagged to precede laboratory surveillance by 2 weeks. We conclude that NI dispensing data provides timely and valuable information for influenza surveillance.

  18. Protective Protein/Cathepsin A Rescues N-glycosylation defects in Neuraminidase-1

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    Wang, Dongning; Zaitsev, Slava; Taylor, Garry; d’Azzo, Alessandra; Bonten, Erik

    2009-01-01

    Background Neuraminidase-1 (NEU1) catabolizes the hydrolysis of sialic acids from sialo-glycoconjugates. NEU1 depends on its interaction with the protective protein/cathepsin A (PPCA) for lysosomal compartmentalization and catalytic activation. Murine NEU1 contains 4 N-glycosylation sites, 3 of which are conserved in the human enzyme. The expression of NEU1 gives rise to differentially glycosylated proteins. Methods We generated single-point mutations in mouse NEU1 at each of the 4 N-glycosylation sites. Mutant enzymes were expressed in NEU1-deficient cells in the presence and absence of PPCA. Results All 4 N-glycosylation variants were targeted to the lysosomal/endosomal compartment. All N-glycans, with the exception of the most C-terminal glycan, were important for maintaining stability or catalytic activity. The loss of catalytic activity caused by the deletion of the second N-glycan was rescued by increasing PPCA expression. Similar results were obtained with a human NEU1 N-glycosylation mutant identified in a sialidosis patient. Conclusions The N-terminal N-glycan of NEU1 is indispensable for its function, whereas the C-terminal N-glycan appears to be non-essential. The omission of the second N-glycan can be compensated for by upregulating the expression of PPCA. General Significance These findings could be relevant for the design of target therapies for patients carrying specific NEU1 mutations. PMID:19714866

  19. Aggregation of Streptococcus sanguis by a neuraminidase-sensitive component of serum and crevicular fluid.

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    Morris, E J; McBride, B C

    1983-01-01

    A number of strains of Streptococcus sanguis were found to aggregate in nonimmune serum and in crevicular fluid. All strains which aggregated in serum also aggregated in saliva, but some strains which aggregated in saliva did not aggregate in serum. Aggregation was destroyed by treatment of serum or crevicular fluid with neuraminidase and was inhibited by gangliosides. Treatment of serum with proteases reduced aggregating activity. Adsorption of serum to hydroxyapatite did not reduce the aggregating activity. The aggregating factor was partially purified by gel filtration and polyacrylamide gel electrophoresis and was found to be an acidic glycoprotein with a molecular weight of greater than 200,000, comprised of subunits with molecular weights of approximately 100,000. It did not appear to be an immunoglobulin and could not be identified with any other serum component tested. The possible role of the aggregating factor in providing nonimmune protection against colonization of S. sanguis in the gingival crevice and blood is discussed. Images PMID:6358038

  20. New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability

    Science.gov (United States)

    Maurice, Pascal; Baud, Stéphanie; Bocharova, Olga V.; Bocharov, Eduard V.; Kuznetsov, Andrey S.; Kawecki, Charlotte; Bocquet, Olivier; Romier, Beatrice; Gorisse, Laetitia; Ghirardi, Maxime; Duca, Laurent; Blaise, Sébastien; Martiny, Laurent; Dauchez, Manuel; Efremov, Roman G.; Debelle, Laurent

    2016-12-01

    Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139-159 (TM1) and 316-333 (TM2) - as potential transmembrane (TM) domains. In membrane mimicking environments, the corresponding peptides form stable α-helices and TM2 is suited for self-association. This was confirmed with full-size NEU1 by co-immunoprecipitations from membrane preparations and split-ubiquitin yeast two hybrids. The TM2 region was shown to be critical for dimerization since introduction of point mutations within TM2 leads to disruption of NEU1 dimerization and decrease of sialidase activity in membrane. In conclusion, these results bring new insights in the molecular organization of membrane-bound NEU1 and demonstrate, for the first time, the presence of two potential TM domains that may anchor NEU1 in the membrane, control its dimerization and sialidase activity.

  1. Estimating the Fitness Advantage Conferred by Permissive Neuraminidase Mutations in Recent Oseltamivir-Resistant A(H1N1)pdm09 Influenza Viruses

    Science.gov (United States)

    Butler, Jeff; Hooper, Kathryn A.; Petrie, Stephen; Lee, Raphael; Maurer-Stroh, Sebastian; Reh, Lucia; Guarnaccia, Teagan; Baas, Chantal; Xue, Lumin; Vitesnik, Sophie; Leang, Sook-Kwan; McVernon, Jodie; Kelso, Anne; Barr, Ian G.; McCaw, James M.; Bloom, Jesse D.; Hurt, Aeron C.

    2014-01-01

    Oseltamivir is relied upon worldwide as the drug of choice for the treatment of human influenza infection. Surveillance for oseltamivir resistance is routinely performed to ensure the ongoing efficacy of oseltamivir against circulating viruses. Since the emergence of the pandemic 2009 A(H1N1) influenza virus (A(H1N1)pdm09), the proportion of A(H1N1)pdm09 viruses that are oseltamivir resistant (OR) has generally been low. However, a cluster of OR A(H1N1)pdm09 viruses, encoding the neuraminidase (NA) H275Y oseltamivir resistance mutation, was detected in Australia in 2011 amongst community patients that had not been treated with oseltamivir. Here we combine a competitive mixtures ferret model of influenza infection with a mathematical model to assess the fitness, both within and between hosts, of recent OR A(H1N1)pdm09 viruses. In conjunction with data from in vitro analyses of NA expression and activity we demonstrate that contemporary A(H1N1)pdm09 viruses are now more capable of acquiring H275Y without compromising their fitness, than earlier A(H1N1)pdm09 viruses circulating in 2009. Furthermore, using reverse engineered viruses we demonstrate that a pair of permissive secondary NA mutations, V241I and N369K, confers robust fitness on recent H275Y A(H1N1)pdm09 viruses, which correlated with enhanced surface expression and enzymatic activity of the A(H1N1)pdm09 NA protein. These permissive mutations first emerged in 2010 and are now present in almost all circulating A(H1N1)pdm09 viruses. Our findings suggest that recent A(H1N1)pdm09 viruses are now more permissive to the acquisition of H275Y than earlier A(H1N1)pdm09 viruses, increasing the risk that OR A(H1N1)pdm09 will emerge and spread worldwide. PMID:24699865

  2. Cross-reactive neuraminidase antibodies afford partial protection against H5N1 in mice and are present in unexposed humans.

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    Matthew R Sandbulte

    2007-02-01

    Full Text Available BACKGROUND: A pandemic H5N1 influenza outbreak would be facilitated by an absence of immunity to the avian-derived virus in the human population. Although this condition is likely in regard to hemagglutinin-mediated immunity, the neuraminidase (NA of H5N1 viruses (avN1 and of endemic human H1N1 viruses (huN1 are classified in the same serotype. We hypothesized that an immune response to huN1 could mediate cross-protection against H5N1 influenza virus infection. METHODS AND FINDINGS: Mice were immunized against the NA of a contemporary human H1N1 strain by DNA vaccination. They were challenged with recombinant A/Puerto Rico/8/34 (PR8 viruses bearing huN1 (PR8-huN1 or avN1 (PR8-avN1 or with H5N1 virus A/Vietnam/1203/04. Additional naïve mice were injected with sera from vaccinated mice prior to H5N1 challenge. Also, serum specimens from humans were analyzed for reactivity with avN1. Immunization elicited a serum IgG response to huN1 and robust protection against the homologous challenge virus. Immunized mice were partially protected from lethal challenge with H5N1 virus or recombinant PR8-avN1. Sera transferred from immunized mice to naïve animals conferred similar protection against H5N1 mortality. Analysis of human sera showed that antibodies able to inhibit the sialidase activity of avN1 exist in some individuals. CONCLUSIONS: These data reveal that humoral immunity elicited by huN1 can partially protect against H5N1 infection in a mammalian host. Our results suggest that a portion of the human population could have some degree of resistance to H5N1 influenza, with the possibility that this could be induced or enhanced through immunization with seasonal influenza vaccines.

  3. Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1pdm09 influenza viruses.

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    Jeff Butler

    2014-04-01

    Full Text Available Oseltamivir is relied upon worldwide as the drug of choice for the treatment of human influenza infection. Surveillance for oseltamivir resistance is routinely performed to ensure the ongoing efficacy of oseltamivir against circulating viruses. Since the emergence of the pandemic 2009 A(H1N1 influenza virus (A(H1N1pdm09, the proportion of A(H1N1pdm09 viruses that are oseltamivir resistant (OR has generally been low. However, a cluster of OR A(H1N1pdm09 viruses, encoding the neuraminidase (NA H275Y oseltamivir resistance mutation, was detected in Australia in 2011 amongst community patients that had not been treated with oseltamivir. Here we combine a competitive mixtures ferret model of influenza infection with a mathematical model to assess the fitness, both within and between hosts, of recent OR A(H1N1pdm09 viruses. In conjunction with data from in vitro analyses of NA expression and activity we demonstrate that contemporary A(H1N1pdm09 viruses are now more capable of acquiring H275Y without compromising their fitness, than earlier A(H1N1pdm09 viruses circulating in 2009. Furthermore, using reverse engineered viruses we demonstrate that a pair of permissive secondary NA mutations, V241I and N369K, confers robust fitness on recent H275Y A(H1N1pdm09 viruses, which correlated with enhanced surface expression and enzymatic activity of the A(H1N1pdm09 NA protein. These permissive mutations first emerged in 2010 and are now present in almost all circulating A(H1N1pdm09 viruses. Our findings suggest that recent A(H1N1pdm09 viruses are now more permissive to the acquisition of H275Y than earlier A(H1N1pdm09 viruses, increasing the risk that OR A(H1N1pdm09 will emerge and spread worldwide.

  4. SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests

    Science.gov (United States)

    Tsukamoto, K.; Javier, P.C.; Shishido, M.; Noguchi, D.; Pearce, J.; Kang, H.-M.; Jeong, O.M.; Lee, Y.-J.; Nakanishi, K.; Ashizawa, T.

    2012-01-01

    Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10 1.5, 10 2.3, and 10 3.1 50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples. Copyright ?? 2012, American Society for Microbiology. All Rights Reserved.

  5. Computational design of drug candidates for influenza A virus subtype H1N1 by inhibiting the viral neuraminidase-1 enzyme

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    Tambunan Usman Sumo Friend

    2014-06-01

    Full Text Available It is critical to seek potential alternative treatments for H1N1 infections by inhibiting neuraminidase-1 enzyme. One of the viable options for inhibiting the activity of neuraminidase- 1 is peptide drug design. In order to increase peptide stability, cyclization is necessary to prevent its digestion by protease enzyme. Cyclization of peptide ligands by formation of disulfide bridges is preferable for designing inhibitors of neuraminidase-1 because of their high activity and specificity. Here we designed ligands by using molecular docking, drug scan and dynamics computational methods. Based on our docking results, short polypeptides of cystein-arginine-methionine-tyrosine- -proline-cysteine (CRMYPC and cysteine-arginine-aspargine- phenylalanine-proline-cysteine (CRNFPC have good residual interactions with the target and the binding energy ΔGbinding of -31.7402 and -31.0144 kcal mol-1, respectively. These values are much lower than those of the standards, and it means that both ligands are more accessible to ligand-receptor binding. Based on drug scan results, both of these ligands are neither mutagenic nor carcinogenic. They also show good oral bioavailability. Moreover, both ligands show relatively stable molecular dynamics progression of RMSD vs. time plot. However, based on our metods, the CRMYPC ligand has sufficient hydrogen bonding interactions with residues of the active side of neuraminidase-1 and can be therefore proposed as a potential inhibitor of neuraminidase-1

  6. Neuraminidase inhibitor resistance in influenza: assessing the danger of its generation and spread.

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    Andreas Handel

    2007-12-01

    Full Text Available Neuraminidase Inhibitors (NI are currently the most effective drugs against influenza. Recent cases of NI resistance are a cause for concern. To assess the danger of NI resistance, a number of studies have reported the fraction of treated patients from which resistant strains could be isolated. Unfortunately, those results strongly depend on the details of the experimental protocol. Additionally, knowing the fraction of patients harboring resistance is not too useful by itself. Instead, we want to know how likely it is that an infected patient can generate a resistant infection in a secondary host, and how likely it is that the resistant strain subsequently spreads. While estimates for these parameters can often be obtained from epidemiological data, such data is lacking for NI resistance in influenza. Here, we use an approach that does not rely on epidemiological data. Instead, we combine data from influenza infections of human volunteers with a mathematical framework that allows estimation of the parameters that govern the initial generation and subsequent spread of resistance. We show how these parameters are influenced by changes in drug efficacy, timing of treatment, fitness of the resistant strain, and details of virus and immune system dynamics. Our study provides estimates for parameters that can be directly used in mathematical and computational models to study how NI usage might lead to the emergence and spread of resistance in the population. We find that the initial generation of resistant cases is most likely lower than the fraction of resistant cases reported. However, we also show that the results depend strongly on the details of the within-host dynamics of influenza infections, and most importantly, the role the immune system plays. Better knowledge of the quantitative dynamics of the immune response during influenza infections will be crucial to further improve the results.

  7. Effects of vaccination and the new neuraminidase inhibitor, laninamivir, on influenza infection.

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    Takuro Mizuno

    Full Text Available BACKGROUND: Evidence of the effectiveness of influenza vaccination in children and elderly adults is limited, although this population has the highest risk for influenza infection. MATERIALS AND METHODS: We enrolled 4443 participants, aged 3-97 years, who had influenza-kit-positive results during seasons 2007-12, including 2135 with influenza A, 534 with A/H1N1, and 1643 with influenza B. Eligible subjects completed a questionnaire to identify past influenza infection and vaccination history. For the diagnosis of current influenza infection, subjects were examined, and pharyngeal swabs were collected and tested using the Capilia flu rapid diagnosis kit to confirm influenza infection. An interim analysis was performed using clinician-based surveillance data for the entire four seasons of influenza infection in Japan. RESULTS: In 3035 adults aged 14-64 years, administration of the influenza vaccine significantly reduced the frequency of infection (P65 years significantly. Laninamivir, oseltamivir phosphate, zanamivir hydrate, and amantadine hydrochloride were administered to 1381, 2432, 1044, and 100 patients, respectively. They were effective in >97% of patients, with no significant differences being found. Adverse effects were few. However, the recurrence rate of influenza infection after treatment was significantly reduced in patients who received laninamivir compared with that in those who received oseltamivir and zanamivir (P<0.01. The effectiveness of laninamivirdid not decrease. CONCLUSIONS: The vaccines administered had limited efficacy in reducing the frequency of influenza infection in young adults. Laninamivir significantly reduced the recurrence of influenza infection when compared with other neuraminidase inhibitors.

  8. Preterm human milk contains a large pool of latent TGF-β, which can be activated by exogenous neuraminidase

    Science.gov (United States)

    Namachivayam, Kopperuncholan; Blanco, Cynthia L.; Frost, Brandy L.; Reeves, Aaron A.; Jagadeeswaran, Ramasamy; MohanKumar, Krishnan; Safarulla, Azif; Mandal, Partha; Garzon, Steven A.; Raj, J. Usha

    2013-01-01

    Human milk contains substantial amounts of transforming growth factor (TGF)-β, particularly the isoform TGF-β2. We previously showed in preclinical models that enterally administered TGF-β2 can protect against necrotizing enterocolitis (NEC), an inflammatory bowel necrosis of premature infants. In this study we hypothesized that premature infants remain at higher risk of NEC than full-term infants, even when they receive their own mother's milk, because preterm human milk contains less bioactive TGF-β than full-term milk. Our objective was to compare TGF-β bioactivity in preterm vs. full-term milk and identify factors that activate milk-borne TGF-β. Mothers who delivered between 23 0/7 and 31 6/7 wk or at ≥37 wk of gestation provided milk samples at serial time points. TGF-β bioactivity and NF-κB signaling were measured using specific reporter cells and in murine intestinal tissue explants. TGF-β1, TGF-β2, TGF-β3, and various TGF-β activators were measured by real-time PCR, enzyme immunoassays, or established enzymatic activity assays. Preterm human milk showed minimal TGF-β bioactivity in the native state but contained a large pool of latent TGF-β. TGF-β2 was the predominant isoform of TGF-β in preterm milk. Using a combination of several in vitro and ex vivo models, we show that neuraminidase is a key regulator of TGF-β bioactivity in human milk. Finally, we show that addition of bacterial neuraminidase to preterm human milk increased TGF-β bioactivity. Preterm milk contains large quantities of TGF-β, but most of it is in an inactive state. Addition of neuraminidase can increase TGF-β bioactivity in preterm milk and enhance its anti-inflammatory effects. PMID:23558011

  9. Methanolic soluble fractions of lingzhi or reishi medicinal mushroom, Ganoderma lucidum (higher Basidiomycetes) extract inhibit neuraminidase activity in Newcastle disease virus (LaSota).

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    Shamaki, Bala U; Sandabe, Umar K; Ogbe, Adamu O; Abdulrahman, Fanna I; El-Yuguda, Abdul-Dahiru

    2014-01-01

    The antineuraminidase activity of different organic soluble fractions of Ganoderma lucidum extract was investigated using inhibition of hemagglutination and elution of chicken erythrocytes by Newcastle disease virus (NDV). Fractions of methanol, ethylacetate, and normal butanol (n-butanol) of the G. lucidum were tested against neuraminidase producing NDV as antigen. Different dilutions of the organic soluble fractions inhibited elution of 1% red blood cells by neuraminidase of NDV While the methanolic and n-butanol extracts inhibited neuraminidase activity even at a dilution of 1:16 and that of ethylacetate fraction inhibited even at 1:32 respectively. This finding indicates that G. lucidum has some antineuraminidase activity against NDV and may be exploited in the management of NDV infection.

  10. Controlled clinical trial of adjuvant immunotherapy with BCG and neuraminidase-treated autologous tumour cells in large bowel cancer.

    Science.gov (United States)

    Gray, B N; Walker, C; Andrewartha, L; Freeman, S; Bennett, R C

    1989-01-01

    A controlled, randomised clinical trial of immunotherapy was performed in 301 patients with stage B or C colorectal cancer. The immunotherapy treatment consisted of 18 vaccinations over a 2 year period following surgery with a combination of BCG given by scarification plus subcutaneous injection of Vibrio cholera neuraminidase (VCN)-modified autologous tumour cells. Five year follow-up has now been completed in all patients. The immunotherapy did not alter either the disease-free interval or the overall survival of patients in comparison with a control group of patients not receiving immunotherapy.

  11. Identification of potential B cell epitope determinants by computer techniques, in hemagglutinin-neuraminidase from the porcine rubulavirus La Piedad Michoacan.

    Science.gov (United States)

    Zenteno-Cuevas, Roberto; Huerta-Yepez, Sara; Reyes-Leyva, Julio; Hernández-Jáuregui, Pablo; González-Bonilla, Cesar; Ramírez-Mendoza, Humberto; Agundis, Concepción; Zenteno, Edgar

    2007-01-01

    Hemagglutinin-neuraminidase (HN) from porcine rubulavirus La Piedad Michoacan (RvpLPM) is one of the most antigenic proteins known, and is responsible for virus-host cell interaction. We analyzed the amino acid sequence of HN, using computer-assisted techniques to identify B cell epitopes. From a pool of 18 possible antigenic peptides, we evaluated the antigenicity of the 2 peptides with the highest scores and the 1 with lowest score. Antibodies from RvpLPM-infected pigs recognized the synthesized HN-A, HN-B, and HN-R peptides (optical density [OD]: 0.33 +/- 0.02 for HN-A, 0.20 +/- 0.02 for HN-B, and 0.07 +/- 0.01 for HN-R); bovine serum albumin-coupled HN-A and HN-B induced rabbit anti-RvpLPM antibodies (OD: 0.39 +/- 0.01 for HN-A and 0.35 +/- 0.02 for HN-B). Loop 5 from the outer membrane protein, OmpC, from Salmonella typhi was replaced with HN-B; this protein was then expressed in Escherichia coli UH302. BALB/c mice were challenged intraperitoneally or orogastrically with the fusion protein expressed in E. coli and murine antibodies obtained from both types of administration inhibited virus-hemagglutinating activity, as did the antibodies from RvpLPM-infected swine. These results suggest that HN-A and HN-B are peptides involved in RvpLPM cell carbohydrate recognition, and could therefore be considered potential targets for vaccine and diagnostic procedures development.

  12. Synergistic Antiviral Activity of S-033188/S-033447, a Novel Inhibitor of Influenza Virus Cap-Dependent Endonuclease, in Combination with Neuraminidase Inhibitors In Vitro

    Science.gov (United States)

    Kitano, Mitsutaka; Yamamoto, Atsuko; Noshi, Takeshi; Kawai, Makoto; Yoshida, Ryu; Sato, Akihiko; Shishido, Takao; Naito, Akira

    2017-01-01

    Abstract Background S-033447, an active form of orally available prodrug S-033188, is a novel small molecule inhibitor of cap-dependent endonuclease that is essential for influenza virus transcription and replication. In this study, we evaluated the inhibitory effect of S-033188 in combination with neuraminidase inhibitors on the replication of influenza A/H1N1 virus in cultured cells. Methods The inhibitory effects of S-033447 in combination with NA inhibitors on the cytopathic effect of A/PR/8/34 strain in Madin–Darby canine kidney cells cultured for 2 days were tested and EC50 were determined. The combination index (CI), which were obtained when S-033188 and NA inhibitor were added at the closest ratio of each EC50 value, were used for the evaluation of these combinational effects (Table 1). CI values were calculated by the Chou and Talalay method, in which combinational effect were determined according to the criteria as follows: synergistic if CI ≤ 0.8, additive if 0.8 < CI < 1.2, and antagonistic if CI ≥ 1.2. CI = (DA/A + B)/DA + (DB/A + B)/DB + (DA/A + B × DB/A + B)/(DA × DB) DA: the EC50 of S-033447 DB: the EC50 of NA inhibitor DA/A + B: the concentration of S-033447 giving 50% inhibition in combination with NA inhibitor at the closest ratio of each EC50 value DB/A + B: the concentration of NA inhibitor giving 50% inhibition in combination with S-033447 at the closest ratio of each EC50 value Results All CI values were lower than 0.8, under the condition that both S-033447 and NA inhibitor (oseltamivir acid, zanamivir hydrate, laninamivir, or peramivir trihydrate) were added at the closest ratio of each EC50 value (Table 1). Conclusion S-033447 in combination with oseltamivir acid, zanamivir hydrate, laninamivir, or peramivir trihydrate synergistically inhibited the replication of influenza A/H1N1 virus in MDCK cells. Table 1. Combination effect of S-033447 and NA inhibitor in MDCK cells infected with A/PR/8/34 strain Substance A

  13. Genome Sequence of a Reassortant H5N1 Avian Influenza Virus Isolated from Domestic Green-Winged Teal.

    Science.gov (United States)

    Xiong, Chaochao; Liu, Qian; Chen, Quanjiao; Chen, Jianjun

    2013-08-15

    An avian influenza virus strain, A/domestic green-winged teal/Hunan/3450/2006(H5N1) (DGW-T3450), was isolated from domestic green-winged teals. Genome analysis demonstrated that DGW-T3450 is a novel reassortant strain. The hemagglutinin (HA) and neuraminidase (NA) genes of this strain originated from H5N1 viruses circulating in poultry, while its remaining genes are derived from multiple ancestors, including viruses like those that infect wild birds.

  14. Charged amino acid variability related to N-glyco -sylation and epitopes in A/H3N2 influenza: Hem -agglutinin and neuraminidase.

    Science.gov (United States)

    Huang, Zhong-Zhou; Yu, Liang; Huang, Ping; Liang, Li-Jun; Guo, Qing

    2017-01-01

    The A/H3N2 influenza viruses circulated in humans have been shown to undergo antigenic drift, a process in which amino acid mutations result from nucleotide substitutions. There are few reports regarding the charged amino acid mutations. The purpose of this paper is to explore the relations between charged amino acids, N-glycosylation and epitopes in hemagglutinin (HA) and neuraminidase (NA). A total of 700 HA genes (691 NA genes) of A/H3N2 viruses were chronologically analyzed for the mutational variants in amino acid features, N-glycosylation sites and epitopes since its emergence in 1968. It was found that both the number of HA N-glycosylation sites and the electric charge of HA increased gradually up to 2016. The charges of HA and HA1 increased respectively 1.54-fold (+7.0 /+17.8) and 1.08-fold (+8.0/+16.6) and the number of NGS in nearly doubled (7/12). As great diversities occurred in 1990s, involving Epitope A, B and D mutations, the charged amino acids in Epitopes A, B, C and D in HA1 mutated at a high frequency in global circulating strains last decade. The charged amino acid mutations in Epitopes A (T135K) has shown high mutability in strains near years, resulting in a decrease of NGT135-135. Both K158N and K160T not only involved mutations charged in epitope B, but also caused a gain of NYT158-160. Epitope B and its adjacent N-glycosylation site NYT158-160 mutated more frequently, which might be under greater immune pressure than the rest. The charged amino acid mutations in A/H3N2 Influenza play a significant role in virus evolution, which might cause an important public health issue. Variability related to both the epitopes (A and B) and N-glycosylation is beneficial for understanding the evolutionary mechanisms, disease pathogenesis and vaccine research.

  15. Differential actions of proteinases and neuraminidase on mammalian erythrocyte surface and its impact on erythrocyte agglutination by concanavalin A.

    Science.gov (United States)

    Sharma, Savita; Gokhale, Sadashiv M

    2012-12-01

    Action of proteinases viz. trypsin and chymotrypsin, and neuraminidase on intact erythrocyte membrane proteins and glycophorins (sialoglycoproteins) exposed to cell surface and its impact on lectin (concanavalin A)-mediated agglutination were studied in Homo sapiens (human), Capra aegagrus hircus (goat) and Bubalus bubalis (buffalo). Membrane proteins and glycophorins analysis by SDS-PAGE as visualized by coomassie brilliant blue and periodic acid-schiff stains, respectively, and agglutination behaviour revealed marked differences: 1) there were prominent dissimilarities in the number and molecular weights of glycophorins in human, goat and buffalo erythrocyte membranes; 2) proteinase action(s) on human and buffalo erythrocyte surface membrane proteins and glycophorins showed similarity but was found different in goat; 3) significant differences in erythrocyte agglutinability with concanavalin A can be attributed to differences in membrane composition and alterations in the surface proteins after enzyme treatment; 4) a direct correlation was found between degradation of glycophorins and concanavalin A agglutinability; 5) action of neuraminidase specifically indicated the negative role of cell surface sialic acids in determining concanavalin A agglutinability of goat and buffalo erythrocytes, similar to human. Present studies clearly indicate that there are some basic differences in human, goat and buffalo erythrocyte membrane proteins, especially with respect to glycophorins, which determine the concanavalin A-mediated agglutination in enzyme treated erythrocytes.

  16. Different Origins of Newcastle Disease Virus Hemagglutinin-Neuraminidase Protein Modulate the Replication Efficiency and Pathogenicity of the Virus

    Directory of Open Access Journals (Sweden)

    Ji-hui Jin

    2017-08-01

    Full Text Available To investigate the exact effects of different origins of Newcastle disease virus (NDV hemagglutinin-neuraminidase (HN protein to the biological characteristics of the virus, we systematically studied the correlation between the HN protein and NDV virulence by exchanging the HN of velogenic or lentogenic NDV strains with the HN from other strains of different virulence. The results revealed that the rSG10 or rLaSota derivatives bearing the HN gene of other viruses exhibited decreased or increased hemadsorption (HAd, neuraminidase and fusion promotion activities. In vitro and in vivo tests further showed that changes in replication level, tissue tropism and virulence of the chimeric viruses were also consistent with these biological activities. These findings demonstrated that the balance among three biological activities caused variation in replication and pathogenicity of the virus, which was closely related to the origin of the HN protein. Our study highlights the importance of the HN glycoprotein in modulating the virulence of NDV and contributes to a more complete understanding of the virulence of NDV.

  17. Potent bacterial neuraminidase inhibitors, anthraquinone glucosides from Polygonum cuspidatum and their inhibitory mechanism.

    Science.gov (United States)

    Uddin, Zia; Song, Yeong Hun; Curtis-Long, Marcus J; Kim, Jeong Yoon; Yuk, Heung Joo; Park, Ki Hun

    2016-12-04

    P. cuspidatum is a popular Chinese medicinal herb, having a long history of usage in traditional Chinese medicine for the treatment of several inflammatory diseases in the form of powders and decoctions. Similarly there are many reports that P. cuspidatum has antibacterial and anti-inflammatory effects, both of which are properties associated with compounds having activity against bacterial neuraminidase (BNA). We investigated whether P. cuspidatum's metabolites exhibited BNA inhibition. Consistent with our hypothesis, we found several inhibitors from the methanol extract of this plant, and then fully characterized their inhibitory mechanisms. Activity guided separation of methanol extract led to isolation of individual constituents, and subsequently their structures were elucidated by spectroscopic analysis. Detailed kinetic behaviors of BNA inhibitors were explored by showing the changes of Km and Vmax, the ratios of KI/KIS and Kik/Kiv, and fluorescence quenching effect. This study attempted to isolate the responsible metabolites and elucidate the BNA inhibitory mechanism. The principal BNA inhibitory compounds (2-6) were identified as emodin (2), physcion-8-O-β-D-glucopyranoside (3), emodin-8-O-β-D-glucopyranoside (4), emodin-1-O-β-D-glucopyranoside (5), and 2-methoxy-6-acetyl-7-methyljuglone (6). Unexpectedly, anthraquinone glucosides (3-5) were much more potent than their corresponding aglycones (1 and 2). For example, emodin (2) had an IC50=5.4μM, whereas its glucosides (4 and 5) had IC50=0.85μM and 0.43μM respectively. A similar trend was observed with physcion (1, IC50>200μM) and its glucoside (3, IC50=6.2μM). The anthraquinone (2) was mixed type I inhibitor, whereas its glucosides (4 and 5) were noncompetitive. In addition, the fluorescence quenching study showed that the affinity constants (KSV) of inhibitors increased in proportion to their inhibitory potencies. Furthermore, we quantified the major and minor metabolites through UPLC

  18. H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

    NARCIS (Netherlands)

    E. van der Vries (Erhard); P.J. Collins (Patrick ); S.G. Vachieri (Sebastien); X. Xiong (Xiaoli); J. Liu (Jinhua); P.A. Walker (Philip); L.F. Haire (Lesley ); A.J. Hay (Alan); M. Schutten (Martin); A.D.M.E. Osterhaus (Albert); S.R. Martin (Steve ); C.A. Boucher (Charles); J.J. Skehel (John ); S.J. Gamblin (Steve )

    2012-01-01

    textabstractTwo classes of antiviral drugs, neuraminidase inhibitors and adamantanes, are approved for prophylaxis and therapy against influenza virus infections. A major concern is that antiviral resistant viruses emerge and spread in the human population. The 2009 pandemic H1N1 virus is already

  19. Two single mutations in the fusion protein of Newcastle disease virus confer hemagglutinin-neuraminidase independent fusion promotion and attenuate the pathogenicity in chickens

    Science.gov (United States)

    The fusion (F) protein of Newcastle disease virus (NDV) plays an important role in viral infection and pathogenicity through mediating membrane fusion between the virion and host cells in the presence of the hemagglutinin-neuraminidase (HN). Previously, we obtained a velogenic NDV genotype VII muta...

  20. Sequence diversity in the coat protein gene of Lettuce big-vein associated virus and Mirafiori lettuce big-vein virus infecting lettuce in Brazil Variabilidade genética na porção codificadora para a proteína capsidial do Lettuce big-vein associated virus e Mirafiori lettuce big-vein virus provenientes de alface no Brasil

    Directory of Open Access Journals (Sweden)

    Márcio Martinello Sanches

    2008-06-01

    Full Text Available Lettuce big vein associated virus (LBVaV and Mirafiori lettuce big vein virus (MLBVV have been found in mixed infection in Brazil causing the lettuce big vein disease. Analysis of part of the coat protein (CP gene of Brazilian isolates of LBVaV collected from lettuce, showed at least 93% amino acid sequence identity with other LBVaV isolates. Genetic diversity among MLBVV CP sequences was higher when compared to LBVaV CP sequences, with amino acid sequence identity ranging between 91% to 100%. Brazilian isolates of MLBVV belong to subgroup A, with one RsaI restriction site on the coat protein gene. There is no indication for a possible geografical origin for the Brazilian isolates of LBVaV and MLBVV.Lettuce big vein associated virus (LBVaV e Mirafiori lettuce big vein virus (MLBVV têm sido encontrados em infecções mistas no Brasil, causando a doença conhecida como engrossamento das nervuras da alface. Análise de parte do gene da proteína capsidial (CP de isolados brasileiros de LBVaV coletados em alface, indicou que estes possuem identidade superior a 93% com isolados coletados em diferentes regiões geográficas. A diversidade genética entre a CP de isolados de MLBVV de alface foi maior comparada às sequências da CP de LBVaV, com a identidade de aminoácidos variando entre 91 a 100%. Os isolados brasileiros de MLBVV pertencem ao subgrupo A, com um único sítio de restrição RsaI no gene da proteína capsidial. Não há indicação para uma provável origem geográfica dos isolados brasileiros de MLBVV e LBVaV.

  1. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1 pandemic.

    Directory of Open Access Journals (Sweden)

    Juan Téllez-Sosa

    Full Text Available BACKGROUND: Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The "deep sequencing" approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. METHODOLOGY AND PRINCIPAL FINDINGS: We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1 pandemic (A(H1N1pdm virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n  =  299 taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July to second wave (September-November of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. CONCLUSIONS: NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that

  2. Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children

    Directory of Open Access Journals (Sweden)

    Tom Jefferson

    Full Text Available BACKGROUND:Neuraminidase inhibitors (NIs are stockpiled and recommended by public health agencies for treating and preventing seasonal and pandemic influenza. They are used clinically worldwide.OBJECTIVE:To describe the potential benefits and harms of NIs for influenza in all age groups by reviewing all clinical study reports of published and unpublished randomised, placebo-controlled trials and regulatory comments.METHODSSearch methods: We searched trial registries, electronic databases (to 22 July 2013 and regulatory archives, and corresponded with manufacturers to identify all trials. We also requested clinical study reports. We focused on the primary data sources of manufacturers but we checked that there were no published randomised controlled trials (RCTs from non-manufacturer sources by running electronic searches in the following databases: the Cochrane Central Register of Controlled Trials (CENTRAL, MEDLINE, MEDLINE (Ovid, EMBASE, Embase.com, PubMed (not MEDLINE, the Database of Reviews of Effects, the NHS Economic Evaluation Database and the Health Economic Evaluations Database.Selection criteria: Randomised, placebo-controlled trials on adults and children with confirmed or suspected exposure to naturally occurring influenza.Data collection and analysis: We extracted clinical study reports and assessed risk of bias using purpose-built instruments. We analysed the effects of zanamivir and oseltamivir on time to first alleviation of symptoms, influenza outcomes, complications, hospitalisations and adverse events in the intention-to-treat (ITT population. All trials were sponsored by the manufacturers.MAIN RESULTS: We obtained 107 clinical study reports from the European Medicines Agency (EMA, GlaxoSmithKline and Roche. We accessed comments by the US Food and Drug Administration (FDA, EMA and Japanese regulator. We included 53 trials in Stage 1 (a judgement of appropriate study design and 46 in Stage 2 (formal analysis, including 20

  3. Neuraminidase inhibitors for influenza: a systematic review and meta-analysis of regulatory and mortality data.

    Science.gov (United States)

    Heneghan, Carl J; Onakpoya, Igho; Jones, Mark A; Doshi, Peter; Del Mar, Chris B; Hama, Rokuro; Thompson, Matthew J; Spencer, Elizabeth A; Mahtani, Kamal R; Nunan, David; Howick, Jeremy; Jefferson, Tom

    2016-01-01

    BACKGROUND Neuraminidase inhibitors (NIs) are stockpiled and recommended by public health agencies for treating and preventing seasonal and pandemic influenza. They are used clinically worldwide. OBJECTIVES To (1) describe the potential benefits and harms of NIs for influenza in all age groups by reviewing all clinical study reports (CSRs) of published and unpublished randomised, placebo-controlled trials and regulatory comments; and (2) determine the effect of oseltamivir (Tamiflu(®), Roche) treatment on mortality in patients with 2009A/H1N1 influenza. METHODS We searched trial registries, electronic databases and corresponded with regulators and sponsors to identify randomised trials of NIs. We requested full CSRs and accessed regulators' comments. We included only those trials for which we had CSRs. To examine the effects of oseltamivir on 2009A/H1N1 influenza mortality, we requested individual patient data (IPD) from corresponding authors of all included observational studies. RESULTS Effect of oseltamivir and zanamivir (Relenza®, GlaxoSmithKline) in the prevention and treatment of influenza: Oseltamivir reduced the time to first alleviation of symptoms in adults by 16.8 hours [95% confidence interval (CI) 8.4 to 25.1 hours]. Zanamivir reduced the time to first alleviation of symptoms in adults by 0.60 days (95% CI 0.39 to 0.81 days). Oseltamivir reduced unverified pneumonia in adult treatment [risk difference (RD) 1.00%, 95% CI 0.22% to 1.49%]; similar findings were observed with zanamivir prophylaxis in adults (RD 0.32%, 95% CI 0.09% to 0.41%). Oseltamivir treatment of adults increased the risk of nausea (RD 3.66%, 95% CI 0.90% to 7.39%) and vomiting (RD 4.56%, 95% CI 2.39% to 7.58%). In the treatment of children, oseltamivir induced vomiting (RD 5.34%, 95% CI 1.75% to 10.29%). Both oseltamivir and zanamivir prophylaxis reduced the risk of symptomatic influenza in individuals (oseltamivir RD 3.05%, 95% CI 1.83% to 3.88%; zanamivir RD 1.98%, 95% CI 0.98% to

  4. Toxin a from Clostridium difficile binds to rabbit erythrocyte glycolipids with therminal Gal. cap alpha. 1-3Gal. beta. 1-4GlcNaC sequences

    Energy Technology Data Exchange (ETDEWEB)

    Clark, G.F.; Krivan, H.; Wilkins, T.; Smith, D.F.

    1987-05-01

    Toxin A is one of two clostridial toxins implicated as the causative agent of pseudomembranous colitis in patients undergoing postoperative antibiotic therapy. Evidence that the carbohydrate binding determinant for this toxin is a glycoconjugate(s) with non-reducing Gal..cap alpha..1-3Gal..beta..1-4GlcNAc has recently been reported. Specific agglutination of rabbit erythrocytes by Toxin A is inhibited by bovine thyroglobulin and prevented by pretreatment of cells with ..cap alpha..-galactosidase. Total lipid extracts from rabbit erythrocytes were subjected to thin layer chromatography and the chromatogram overlaid with purified /sup 125/I-labeled Toxin A. Two major and several minor toxin-binding glycolipids were detected following autoradiography. The major toxin-binding glycolipids were identified as pentasaccharide- and decasaccharide-ceramides expressing terminal Gal..cap alpha..1-3Gal..beta..1-4GlcNAc sequences. Treatment of the toxin-binding glycolipids with ..cap alpha..-galactosidase abolished binding. Forsmann glycolipid, globoside, Gal..cap alpha..1-4 Gal..beta..1-4Glc-cer, and Gal..cap alpha..1-3Gal..beta..1-4Glc-cer did not bind the toxin. These observations are consistent with the proposed carbohydrate specificity of the toxin for the non-reducing terminal sequence, Gal..cap alpha..1-3Gal..beta..1-4GlcNAc.

  5. Active 1918 pandemic flu viral neuraminidase has distinct N-glycan profile and is resistant to trypsin digestion.

    Science.gov (United States)

    Wu, Zhengliang L; Ethen, Cheryl; Hickey, Gregg E; Jiang, Weiping

    2009-02-13

    The 1918 pandemic flu virus caused one of the most deadly pandemics in human history. To search for unique structural features of the neuraminidase from this virus that might have contributed to its unusual virulence, we expressed this enzyme. The purified enzyme appeared as a monomer, a dimer and a tetramer, with only the tetramer being active and therefore biologically relevant. The monomer and the dimer could not be oligomerized into the tetramer in solution, suggesting that some unique structural features were required for oligomerization and activation. These features could be related to N-glycosylation, because the tetramer displayed different N-glycans than the monomer and the dimer. Furthermore, the tetramer was found to be resistant to trypsin digestion, which may give the virus the capability to invade tissues that are normally not infected by influenza viruses and make the virus more robust for infection.

  6. Using High-Throughput Sequencing to Leverage Surveillance of Genetic Diversity and Oseltamivir Resistance: A Pilot Study during the 2009 Influenza A(H1N1) Pandemic

    Science.gov (United States)

    Téllez-Sosa, Juan; Rodríguez, Mario Henry; Gómez-Barreto, Rosa E.; Valdovinos-Torres, Humberto; Hidalgo, Ana Cecilia; Cruz-Hervert, Pablo; Luna, René Santos; Carrillo-Valenzo, Erik; Ramos, Celso; García-García, Lourdes; Martínez-Barnetche, Jesús

    2013-01-01

    Background Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS) has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The “deep sequencing” approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. Methodology and Principal Findings We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1) pandemic (A(H1N1)pdm) virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n  =  299) taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July) to second wave (September-November) of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. Conclusions NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that the approach

  7. (H5N1) strain neuraminidase expressed in yeast Pichia pastoris

    Indian Academy of Sciences (India)

    2014-03-20

    Mar 20, 2014 ... The colonies were subcultured on YPD broth and gene integration was confirmed as described at ww.invitrogen.com/content/sfs/manuals/pich_man.pdf. 2.4 Expression of rNA in Pichia pastoris. The positive transformants were inoculated into 2 mL of. Buffered Glycerol-complex Medium (BMGY) media and.

  8. Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins.

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    Amelia M Clark

    Full Text Available Antigenic drift of the hemagglutinin (HA and neuraminidase (NA influenza virus proteins contributes to reduced vaccine efficacy. To analyze antigenic drift in human seasonal H1N1 viruses derived from the 2009 pandemic H1N1 virus (pH1N1-like viruses accounts for the limited effectiveness (around 40% of vaccination against pH1N1-like viruses during the 2015-2016 season, nasal washes/swabs collected from adult subjects in the Rochester, NY area, were used to sequence and isolate the circulating viruses. The HA and NA proteins from viruses circulating during the 2015-2016 season encoded eighteen and fourteen amino acid differences, respectively, when compared to A/California/04/2009, a strain circulating at the origin of the 2009 pandemic. The circulating strains belonged to subclade 6B.1, defined by HA amino acid substitutions S101N, S179N, and I233T. Hemagglutination-inhibiting (HAI and HA-specific neutralizing serum antibody (Ab titers from around 50% of pH1N1-like virus-infected subjects and immune ferrets were 2-4 fold lower for the 2015-2016 circulating strains compared to the vaccine strain. In addition, using a luminex-based mPlex HA assay, the binding of human sera from subjects infected with pH1N1-like viruses to the HA proteins from circulating and vaccine strains was not identical, strongly suggesting antigenic differences in the HA protein. Additionally, NA inhibition (NAI Ab titers in human sera from pH1N1-like virus-infected subjects increased after the infection and there were measurable antigenic differences between the NA protein of circulating strains and the vaccine strain using both ferret and human antisera. Despite having been vaccinated, infected subjects exhibited low HAI Ab titers against the vaccine and circulating strains. This suggests that poor responses to the H1N1 component of the vaccine as well as antigenic differences in the HA and NA proteins of currently circulating pH1N1-like viruses could be contributing to

  9. In vitro neuraminidase inhibitory concentration (IC50) of four neuraminidase inhibitors against clinical isolates of the influenza viruses circulating in the 2010-2011 to 2014-2015 Japanese influenza seasons.

    Science.gov (United States)

    Ikematsu, Hideyuki; Kawai, Naoki; Iwaki, Norio; Kashiwagi, Seizaburo

    2016-09-01

    To assess the extent of viral resistance to the four neuraminidase inhibitors (NAIs), we measured their 50% inhibitory concentration (IC50) for influenza virus isolates from the 2014-2015 influenza season for comparison with those circulating in the 2010-2011 to 2013-2014 influenza seasons. Viral isolation was done with specimens obtained prior to treatment, and the type and subtype of influenza was determined by RT-PCR using type- and subtype-specific primers. The IC50 was determined by a neuraminidase inhibition assay using a fluorescent substrate. IC50 was measured for 200 influenza A(H3N2) and 19 influenza B in the 2014-2015 season, and no virus with highly reduced sensitivity to the four NAIs was detected. The ratios of the geometric means of the A(H3N2) IC50s of 2014-2015 to those of the 2010-2011, 2011-2012, 2012-2013, and 2013-2014 seasons ranged from 0.72 to 1.05, 0.82 to 1.22, 0.69 to 1.00, and 0.70 to 1.03, respectively. The ratios of the geometric mean of the B IC50s to the previous four seasons ranged from 0.59 to 1.28, 0.66 to 1.34, 0.84 to 1.21, and 1.06 to 1.47, respectively. There was no trend in the change of the IC50s for A(H3N2) or B. Significant differences were found in some seasons, but the differences in the IC50s were all less than two fold. These results show change in the geometric mean IC50 by season but with no trend, which indicates that the influence of viral mutation on the effectiveness of these NAIs was minute for A(H3N2) and B over the past five seasons. Copyright © 2016 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  10. H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis.

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    Erhard van der Vries

    2012-09-01

    Full Text Available Two classes of antiviral drugs, neuraminidase inhibitors and adamantanes, are approved for prophylaxis and therapy against influenza virus infections. A major concern is that antiviral resistant viruses emerge and spread in the human population. The 2009 pandemic H1N1 virus is already resistant to adamantanes. Recently, a novel neuraminidase inhibitor resistance mutation I223R was identified in the neuraminidase of this subtype. To understand the resistance mechanism of this mutation, the enzymatic properties of the I223R mutant, together with the most frequently observed resistance mutation, H275Y, and the double mutant I223R/H275Y were compared. Relative to wild type, K(M values for MUNANA increased only 2-fold for the single I223R mutant and up to 8-fold for the double mutant. Oseltamivir inhibition constants (K(I increased 48-fold in the single I223R mutant and 7500-fold in the double mutant. In both cases the change was largely accounted for by an increased dissociation rate constant for oseltamivir, but the inhibition constants for zanamivir were less increased. We have used X-ray crystallography to better understand the effect of mutation I223R on drug binding. We find that there is shrinkage of a hydrophobic pocket in the active site as a result of the I223R change. Furthermore, R223 interacts with S247 which changes the rotamer it adopts and, consequently, binding of the pentoxyl substituent of oseltamivir is not as favorable as in the wild type. However, the polar glycerol substituent present in zanamivir, which mimics the natural substrate, is accommodated in the I223R mutant structure in a similar way to wild type, thus explaining the kinetic data. Our structural data also show that, in contrast to a recently reported structure, the active site of 2009 pandemic neuraminidase can adopt an open conformation.

  11. Neuraminidase-1, a Subunit of the Cell Surface Elastin Receptor, Desialylates and Functionally Inactivates Adjacent Receptors Interacting with the Mitogenic Growth Factors PDGF-BB and IGF-2

    Science.gov (United States)

    Hinek, Aleksander; Bodnaruk, Tetyana D.; Bunda, Severa; Wang, Yanting; Liu, Kela

    2008-01-01

    We recently established that the elastin-binding protein, which is identical to the spliced variant of β-galactosidase, forms a cell surface-targeted complex with two proteins considered “classic lysosomal enzymes”: protective protein/cathepsin A and neuraminidase-1 (Neu1). We also found that cell surface-residing Neu1 can desialylate neighboring microfibrillar glycoproteins and facilitate the deposition of insoluble elastin, which contributes to the maintenance of cellular quiescence. Here we provide evidence that cell surface-residing Neu1 contributes to a novel mechanism that limits cellular proliferation by desialylating cell membrane-residing sialoglycoproteins that directly propagate mitogenic signals. We demonstrated that treatment of cultured human aortic smooth muscle cells (SMCs) with either a sialidase inhibitor or an antibody that blocks Neu1 activity induced significant up-regulation in SMC proliferation in response to fetal bovine serum. Conversely, treatment with Clostridium perfringens neuraminidase (which is highly homologous to Neu1) decreased SMC proliferation, even in cultures that did not deposit elastin. Further, we found that pretreatment of aortic SMCs with exogenous neuraminidase abolished their mitogenic responses to recombinant platelet-derived growth factor (PDGF)-BB and insulin-like growth factor (IGF)-2 and that sialidosis fibroblasts (which are exclusively deficient in Neu1) were more responsive to PDGF-BB and IGF-2 compared with normal fibroblasts. Furthermore, we provide direct evidence that neuraminidase caused the desialylation of both PDGF and IGF-1 receptors and diminished the intracellular signals induced by the mitogenic ligands PDGF-BB and IGF-2. PMID:18772331

  12. Synthesis of a cluster-forming sialylthio-D-galactose fullerene conjugate and evaluation of its interaction with influenza virus hemagglutinin and neuraminidase.

    Science.gov (United States)

    Tollas, Szilvia; Bereczki, Ilona; Borbás, Anikó; Batta, Gyula; Vanderlinden, Evelien; Naesens, Lieve; Herczegh, Pál

    2014-06-01

    In order to obtain self assembling, multivalent ligand for influenza virus hemagglutinin α-N-acetylneuraminyl-(2-6)-D-galactopyranose has been synthesized and bonded to a water soluble fullerene derivative using 1,3-dipolar cycloaddition click reaction. The aggregating amphiphilic compound did not inhibit the influenza virus hemagglutinin, but it proved to be an inhibitor of its neuraminidase with a 50% inhibitory concentration of 81 μM. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Neuraminidase inhibitors in the treatment and post exposure prevention of influenza

    Directory of Open Access Journals (Sweden)

    von der Schulenburg, Johann-Matthias

    2006-01-01

    Full Text Available Introduction: Influenza is a viral respiratory infection which presents itself as an acute febrile disease. It is contracted by virus-laden respiratory secretions from infected individuals. Symptoms usually last three to seven days and are accompanied by severely limited activities during this time. A definite diagnosis, however, can only be made by laboratory analysis. Every year, about 20% of children and 5% of adults develop symptomatic influenza of the serotypes A or B worldwide. Typical complications of influenza include viral or bacterial infections, as well as deterioration of an existing cardio-vascular or respiratory disease which may lead to hospitalization and death. Current policy recommends that individuals, who are at-risk of developing serious complications (patients over sixty years of age or patients with concomitant chronic diseases, as well as people in direct contact with high risk patients (i.e. nursing staff in living and care facilities, should be annually vaccinated with inactivated influenza strains. Various pharmaceutical agents for the treatment and prophylaxis of influenza have been approved. Amantadine, which inhibits the viral M2-ion channel, is only effective in influenza-serotype A. Neuraminidase inhibitors (NI represent a new class of antivirals for prophylaxis and treatment of influenza A and B. NI interrupt various central functions that are vital for the life cycle and spreading of the virus. Two drugs of this substance class, Zanamivir (RelenzaTM and Oseltamivir (Tamiflu®, are licensed for the treatment of influenza. For adults and teenagers over thirteen years of age Oseltamivir is also approved for the prophylaxis of influenza. Zanamivir is a powder which needs to be inhaled, whereas Oseltamivir is licensed as a capsule for oral administration. M2-inhibitors and NI are only effective at an early stage of the influenza infection, i.e. during the first 36 to 48 hours after symptom onset, before replication

  14. Biological Characterizations of H5Nx Avian Influenza Viruses Embodying Different Neuraminidases

    Directory of Open Access Journals (Sweden)

    Yuandi Yu

    2017-06-01

    Full Text Available The H5 subtype virus of Highly Pathogenic Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. Until 2010, H5N1 subtype virus was the major genotype in China. Since 2011, reassortant H5N2, H5N6, and H5N8 viruses were identified in domestic poultry in China. The clade 2.3.4.4 H5N6 and H5N8 AIV has now spread to most of China. Clade 2.3.4.4 H5N6 virus has caused 17 human deaths. However, the prevalence, pathogenicity, and transmissibility of the distinct NA reassortment with H5 subtypes viruses (H5Nx is unknown. We constructed five clade 2.3.4.4 reassortant H5Nx viruses that shared the same HA and six internal gene segments. The NA gene segment was replaced with N1, N2, N6, ΔN6 (with an 11 amino acid deletion at the 58th to 68th of NA stalk region, and N8 strains, respectively. The reassortant viruses with distinct NAs of clade 2.3.4.4 H5 subtype had different degrees of fitness. All reassortant H5Nx viruses formed plaques on MDCK cell monolayers, but the ΔH5N6 grew more efficiently in mammalian and avian cells. The reassortant H5Nx viruses were more virulent in mice as compared to the H5N2 virus. The H5N6 and H5N8 reassortant viruses exhibited enhanced pathogenicity and transmissibility in chickens as compared to the H5N1 reassortant virus. We suggest that comprehensive surveillance work should be undertaken to monitor the H5Nx viruses.

  15. Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children.

    Science.gov (United States)

    Jefferson, Tom; Jones, Mark A; Doshi, Peter; Del Mar, Chris B; Hama, Rokuro; Thompson, Matthew J; Spencer, Elizabeth A; Onakpoya, Igho; Mahtani, Kamal R; Nunan, David; Howick, Jeremy; Heneghan, Carl J

    2014-04-10

    Neuraminidase inhibitors (NIs) are stockpiled and recommended by public health agencies for treating and preventing seasonal and pandemic influenza. They are used clinically worldwide. To describe the potential benefits and harms of NIs for influenza in all age groups by reviewing all clinical study reports of published and unpublished randomised, placebo-controlled trials and regulatory comments. We searched trial registries, electronic databases (to 22 July 2013) and regulatory archives, and corresponded with manufacturers to identify all trials. We also requested clinical study reports. We focused on the primary data sources of manufacturers but we checked that there were no published randomised controlled trials (RCTs) from non-manufacturer sources by running electronic searches in the following databases: the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, MEDLINE (Ovid), EMBASE, Embase.com, PubMed (not MEDLINE), the Database of Reviews of Effects, the NHS Economic Evaluation Database and the Health Economic Evaluations Database. Randomised, placebo-controlled trials on adults and children with confirmed or suspected exposure to naturally occurring influenza. We extracted clinical study reports and assessed risk of bias using purpose-built instruments. We analysed the effects of zanamivir and oseltamivir on time to first alleviation of symptoms, influenza outcomes, complications, hospitalisations and adverse events in the intention-to-treat (ITT) population. All trials were sponsored by the manufacturers. We obtained 107 clinical study reports from the European Medicines Agency (EMA), GlaxoSmithKline and Roche. We accessed comments by the US Food and Drug Administration (FDA), EMA and Japanese regulator. We included 53 trials in Stage 1 (a judgement of appropriate study design) and 46 in Stage 2 (formal analysis), including 20 oseltamivir (9623 participants) and 26 zanamivir trials (14,628 participants). Inadequate reporting put most of the

  16. Neuraminidase Inhibition Primes Short-Term Depression and Suppresses Long-Term Potentiation of Synaptic Transmission in the Rat Hippocampus

    Directory of Open Access Journals (Sweden)

    Alina Savotchenko

    2015-01-01

    Full Text Available Neuraminidase (NEU is a key enzyme that cleaves negatively charged sialic acid residues from membrane proteins and lipids. Clinical and basic science studies have shown that an imbalance in NEU metabolism or changes in NEU activity due to various pathological conditions parallel with behavior and cognitive impairment. It has been suggested that the decreases of NEU activity could cause serious neurological consequences. However, there is a lack of direct evidences that modulation of endogenous NEU activity can impair neuronal function. Using combined rat entorhinal cortex/hippocampal slices and a specific inhibitor of NEU, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (NADNA, we examined the effect of downregulation of NEU activity on different forms of synaptic plasticity in the hippocampal CA3-to-CA1 network. We show that NEU inhibition results in a significant decrease in long-term potentiation (LTP and an increase in short-term depression. Synaptic depotentiation restores LTP in NADNA-pretreated slices to the control level. These data suggest that short-term NEU inhibition produces the LTP-like effect on neuronal network, which results in damping of further LTP induction. Our findings demonstrate that downregulation of NEU activity could have a major impact on synaptic plasticity and provide a new insight into the cellular mechanism underlying behavioral and cognitive impairment associated with abnormal metabolism of NEU.

  17. Analisando a implementação de uma abordagem CTS na sala de aula de química Analysing a teaching sequence with STS approach applied in the chemistry classroom

    Directory of Open Access Journals (Sweden)

    Ruth do Nascimento Firme

    2011-01-01

    Full Text Available Neste artigo, analisamos como dois professores de química desenvolveram, em sala de aula, uma intervenção didática previamente planejada com enfoque CTS, buscando identificar obstáculos e dificuldades para o estabelecimento de uma prática docente pautada nessa perspectiva de ensino. As aulas foram filmadas, transcritas e os dados analisados a partir da dinâmica discursiva estabelecida entre professores e alunos. A análise apontou que dificuldades no desenvolvimento das atividades podem estar associadas não somente à prática docente, mas também a fatores tais como: ausência de informações técnicas e científicas sobre o tema; velocidade da inovação tecnológica; complexidade cientifica na abordagem de alguns temas; dificuldade em articular adequadamente conceitos científicos com questões tecnológicas, associadas a um tema social relevante; e dificuldade de material didático que suporte as discussões de temas específicos na sala de aula.In this work, we have analyzed how two Chemistry's teachers developed a planned teaching sequence starting from a STS perspective in their classrooms, trying to identify obstacles and difficulties in engaging this pedagogical practice and taking into account this perspective for science teaching. Lessons were video recorded, transcribed and data were analyzed considering the discursive dynamic established between the teacher and the students. Data analysis showed that possible obstacles to developing didactic activities cannot be associated only with the teacher's practice and experience, but also can be related to aspects, such as: the lack of technical information about the theme studied; continuous improvement related to the technological artifacts; themes requiring a more complex scientific understanding; difficulties in properly putting together scientific concepts and technology implicated with relevant social problems; and difficulty with appropriate didactical sources to approach

  18. Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein.

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    Gallen B Triana-Baltzer

    2009-11-01

    Full Text Available Antiviral drug resistance for influenza therapies remains a concern due to the high prevalence of H1N1 2009 seasonal influenza isolates which display H274Y associated oseltamivir-resistance. Furthermore, the emergence of novel H1N1 raises the potential that additional reassortments can occur, resulting in drug resistant virus. Thus, additional antiviral approaches are urgently needed. DAS181 (Fludase, a sialidase fusion protein, has been shown to have inhibitory activity against a large number of seasonal influenza strains and a highly pathogenic avian influenza (HPAI strain (H5N1. Here, we examine the in vitro activity of DAS181 against a panel of 2009 oseltamivir-resistant seasonal H1N1 clinical isolates. The activity of DAS181 against nine 2009, two 2007, and two 2004 clinical isolates of seasonal IFV H1N1 was examined using plaque number reduction assay on MDCK cells. DAS181 strongly inhibited all tested isolates. EC50 values remained constant against isolates from 2004, 2007, and 2009, suggesting that there was no change in DAS181 sensitivity over time. As expected, all 2007 and 2009 isolates were resistant to oseltamivir, consistent with the identification of the H274Y mutation in the NA gene of all these isolates. Interestingly, several of the 2007 and 2009 isolates also exhibited reduced sensitivity to zanamivir, and accompanying HA mutations near the sialic acid binding site were observed. DAS181 inhibits IFV that is resistant to NAIs. Thus, DAS181 may offer an alternative therapeutic option for seasonal or pandemic IFVs that become resistant to currently available antiviral drugs.

  19. Avian adeno-associated virus-based expression of Newcastle disease virus hemagglutinin-neuraminidase protein for poultry vaccination.

    Science.gov (United States)

    Perozo, F; Villegas, P; Estevez, C; Alvarado, I R; Purvis, L B; Saume, E

    2008-06-01

    The avian adeno-associated virus (AAAV) is a replication-defective nonpathogenic virus member of the family Parvoviridae that has been proved to be useful as a viral vector for gene delivery. The use of AAAV for transgenic expression of Newcastle disease virus (NDV) hemagglutinin-neuraminidase (HN) protein and its ability to induce immunity in chickens were assessed. Proposed advantages of this system include no interference with maternal antibodies, diminished immune response against the vector, and the ability to accommodate large fragments of genetic information. In this work the generation of recombinant AAAV virions expressing the HN protein (rAAAV-HN) was demonstrated by electron microscopy, immunocytochemistry, and western blot analysis. Serological evidence of HN protein expression after in ovo or intramuscular inoculation of the recombinant virus in specific-pathogen-free chickens was obtained. Serum from rAAAV-HN-vaccinated birds showed a systemic immune response evidenced by NDV-specific enzyme-linked immunosorbent assay and hemagglutination inhibition testing. Positive virus neutralization in embryonated chicken eggs and indirect immunofluorescence detection of NDV infected cells by serum from rAAAV-HN vaccinated birds is also reported. A vaccine-challenge experiment in commercial broiler chickens using a Venezuelan virulent viscerotropic strain of NDV was performed. All unvaccinated controls died within 5 days postchallenge. Protection up to 80% was observed in birds vaccinated in ovo and revaccinated at 7 days of age with the rAAAV-HN. The results demonstrate the feasibility of developing and using an AAAV-based gene delivery system for poultry vaccination.

  20. Cross-neutralization between three mumps viruses & mapping of haemagglutinin-neuraminidase (HN) epitopes.

    Science.gov (United States)

    Vaidya, Sunil R; Dvivedi, Garima M; Jadhav, Santoshkumar M

    2016-01-01

    The reports from the countries where mumps vaccine is given as routine immunization suggest differences in mumps virus neutralizing antibody titres when tested with vaccine and wild type viruses. Such reports are unavailable from countries like India where mumps vaccine is not included in routine immunization. We, therefore, undertook this study to understand the cross-neutralization activity of Indian mumps viruses. By using commercial mumps IgG enzyme immunoassay (EIA) and a rapid focus reduction neutralization test (FRNT), a panel of serum samples was tested. The panel consisted of 14 acute and 14 convalescent serum samples collected during a mumps outbreak and 18 archived serum samples. Two wild types (genotypes C and G) and Leningrad-Zagreb vaccine strain (genotype N) were used for the challenge experiments and FRNT titres were determined and further compared. The HN protein sequence of three mumps viruses was analyzed for the presence of key epitopes. All serum samples effectively neutralized mumps virus wild types and a vaccine strain. However, significantly lower FRNT titres were noted to wild types than to vaccine strain (Pmumps virus strains, however, higher level of FRNT titres was detected for mumps virus vaccine strain compared to Indian wild type isolates.

  1. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  2. Antiviral resistance due to deletion in the neuraminidase gene and defective interfering-like viral polymerase basic 2 RNA of influenza A virus subtype H3N2

    DEFF Research Database (Denmark)

    Trebbien, Ramona; Christiansen, Claus Bohn; Fischer, Thea Kølsen

    2018-01-01

    two major out-of-frame deletions in the polymerase basic 2 (PB2) gene, indicating defective interfering-like viral RNA. Conclusions: The viruses harboring the 245–248 deletion in the neuraminidase gene were still present after discontinuation of oseltamivir treatment and passages in cell cultures...... to zanamivir. Nine days after discontinuation of oseltamivir treatment the deleted H3N2 virus was still present in the patient. After three passages of the deleted virus in cell culture, the deletion was retained. Several variant mutations appeared in the other genes of the H3N2 virus, where most striking were...

  3. Cross-neutralization between three mumps viruses & mapping of haemagglutinin-neuraminidase (HN epitopes

    Directory of Open Access Journals (Sweden)

    Sunil R Vaidya

    2016-01-01

    Full Text Available Background & objectives: The reports from the countries where mumps vaccine is given as routine immunization suggest differences in mumps virus neutralizing antibody titres when tested with vaccine and wild type viruses. Such reports are unavailable from countries like India where mumps vaccine is not included in routine immunization. We, therefore, undertook this study to understand the cross-neutralization activity of Indian mumps viruses. Methods: By using commercial mumps IgG enzyme immunoassay (EIA and a rapid focus reduction neutralization test (FRNT, a panel of serum samples was tested. The panel consisted of 14 acute and 14 convalescent serum samples collected during a mumps outbreak and 18 archived serum samples. Two wild types (genotypes C and G and Leningrad-Zagreb vaccine strain (genotype N were used for the challenge experiments and FRNT titres were determined and further compared. The HN protein sequence of three mumps viruses was analyzed for the presence of key epitopes. Results: All serum samples effectively neutralized mumps virus wild types and a vaccine strain. However, significantly lower FRNT titres were noted to wild types than to vaccine strain (P<0.05. The comparison between EIA and FRNT results revealed 95.6 per cent agreement. No amino acid changes were seen in the epitopes in the Indian wild type strains. All potential N-linked glycosylation sites were observed in Indian strains. Interpretation & conclusions:Good cross-neutralization activity was observed for three mumps virus strains, however, higher level of FRNT titres was detected for mumps virus vaccine strain compared to Indian wild type isolates.

  4. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 2. Computational titration and pH effects in molecular models of neuraminidase-inhibitor complexes.

    Science.gov (United States)

    Fornabaio, Micaela; Cozzini, Pietro; Mozzarelli, Andrea; Abraham, Donald J; Kellogg, Glen E

    2003-10-09

    One factor that can strongly influence predicted free energy of binding is the ionization state of functional groups on the ligands and at the binding site at which calculations are performed. This analysis is seldom performed except in very detailed computational simulations. In this work, we address the issues of (i) modeling the complexity resulting from the different ionization states of ligand and protein residues involved in binding, (ii) if, and how, computational methods can evaluate the pH dependence of ligand inhibition constants, and (iii) how to score the protonation-dependent models. We developed a new and fairly rapid protocol called "computational titration" that enables parallel modeling of multiple ionization ensembles for each distinct protonation level. Models for possible protonation combinations for site/ligand ionizable groups are built, and the free energy of interaction for each of them is quantified by the HINT (Hydropathic INTeractions) software. We applied this procedure to the evaluation of the binding affinity of nine inhibitors (six derived from 2,3-didehydro-2-deoxy-N-acetylneuraminic acid, DANA) of influenza virus neuraminidase (NA), a surface glycoprotein essential for virus replication and thus a pharmaceutically relevant target for the design of anti-influenza drugs. The three-dimensional structures of the NA enzyme-inhibitor complexes indicate considerable complexity as the ligand-protein recognition site contains several ionizable moieties. Each computational titration experiment reveals a peak HINT score as a function of added protons. This maximum HINT score indicates the optimum pH (or the optimum protonation state of each inhibitor-protein binding site) for binding. The pH at which inhibition is measured and/or crystals were grown and analyzed can vary from this optimum. A protonation model is proposed for each ligand that reconciles the experimental complex structure with measured inhibition and the free energy of binding

  5. Virus-like particles displaying H5, H7, H9 hemagglutinins and N1 neuraminidase elicit protective immunity to heterologous avian influenza viruses in chickens.

    Science.gov (United States)

    Pushko, Peter; Tretyakova, Irina; Hidajat, Rachmat; Zsak, Aniko; Chrzastek, Klaudia; Tumpey, Terrence M; Kapczynski, Darrell R

    2017-01-15

    Avian influenza (AI) viruses circulating in wild birds pose a serious threat to public health. Human and veterinary vaccines against AI subtypes are needed. Here we prepared triple-subtype VLPs that co-localized H5, H7 and H9 antigens derived from H5N1, H7N3 and H9N2 viruses. VLPs also contained influenza N1 neuraminidase and retroviral gag protein. The H5/H7/H9/N1/gag VLPs were prepared using baculovirus expression. Biochemical, functional and antigenic characteristics were determined including hemagglutination and neuraminidase enzyme activities. VLPs were further evaluated in a chicken AI challenge model for safety, immunogenicity and protective efficacy against heterologous AI viruses including H5N2, H7N3 and H9N2 subtypes. All vaccinated birds survived challenges with H5N2 and H7N3 highly pathogenic AI (HPAI) viruses, while all controls died. Immune response was also detectable after challenge with low pathogenicity AI (LPAI) H9N2 virus suggesting that H5/H7/H9/N1/gag VLPs represent a promising approach for the development of broadly protective AI vaccine. Copyright © 2016. Published by Elsevier Inc.

  6. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...... and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  8. Genetic drift of HA and NA in Danish swine influenza virus from the period 2003-2012

    DEFF Research Database (Denmark)

    Fobian, Kristina; Breum, Solvej Østergaard; Hjulsager, Charlotte Kristiane

    2012-01-01

    The aim of this study is to analyze; the genetic drift in hemagglutinin (HA) and neuraminidase (NA) genes from influenza viruses isolated from Danish swine over the past decade; the antigenic evolution and relatedness between swine influenza virus strains of the H1 subtype by antigenic cartograph...... and along with the monitoring of antigenic changes in hemagglutinin subtypes it will be possible to ensure a continuous efficacy of influenza virus vaccines.......The aim of this study is to analyze; the genetic drift in hemagglutinin (HA) and neuraminidase (NA) genes from influenza viruses isolated from Danish swine over the past decade; the antigenic evolution and relatedness between swine influenza virus strains of the H1 subtype by antigenic cartography....... Currently at least three influenza A subtypes (H1N1, H1N2 and H3N2) are endemic in the Danish swine population, and since 2010 the pandemic virus (H1N1pdm09) have also frequently been detected. The focus in this study will be on H1N1 and H1N2, since the prevalence of H3N2 have declined over the past years...

  9. Improved immunogenicity of Newcastle disease virus inactivated vaccine following DNA vaccination using Newcastle disease virus hemagglutinin-neuraminidase and fusion protein genes.

    Science.gov (United States)

    Firouzamandi, Masoumeh; Moeini, Hassan; Hosseini, Davood; Bejo, Mohd Hair; Omar, Abdul Rahman; Mehrbod, Parvaneh; Ideris, Aini

    2016-03-01

    The present study describes the development of DNA vaccines using the hemagglutinin-neuraminidase (HN) and fusion (F) genes from AF2240 Newcastle disease virus strain, namely pIRES/HN, pIRES/F and pIRES-F/HN. Transient expression analysis of the constructs in Vero cells revealed the successful expression of gene inserts in vitro. Moreover, in vivo experiments showed that single vaccination with the constructed plasmid DNA (pDNA) followed by a boost with inactivated vaccine induced a significant difference in enzyme-linked immunosorbent assay antibody levels (p inactivated vaccine alone. Taken together, these results indicated that recombinant pDNA could be used to increase the efficacy of the inactivated vaccine immunization procedure.

  10. Filament-producing mutants of influenza A/Puerto Rico/8/1934 (H1N1 virus have higher neuraminidase activities than the spherical wild-type.

    Directory of Open Access Journals (Sweden)

    Jill Seladi-Schulman

    Full Text Available Influenza virus exhibits two morphologies - spherical and filamentous. Strains that have been grown extensively in laboratory substrates are comprised predominantly of spherical virions while clinical or low passage isolates produce a mixture of spheres and filamentous virions of varying lengths. The filamentous morphology can be lost upon continued passage in embryonated chicken eggs, a common laboratory substrate for influenza viruses. The fact that the filamentous morphology is maintained in nature but lost in favor of a spherical morphology in ovo suggests that filaments confer a selective advantage within the infected host that is not necessary for growth in laboratory substrates. Indeed, we have recently shown that filament-producing variant viruses are selected upon passage of the spherical laboratory strain A/Puerto Rico/8/1934 (H1N1 [PR8] in guinea pigs. Toward determining the nature of the selective advantage conferred by filaments, we sought to identify functional differences between spherical and filamentous particles. We compared the wild-type PR8 virus to two previously characterized recombinant PR8 viruses in which single point mutations within M1 confer a filamentous morphology. Our results indicate that these filamentous PR8 mutants have higher neuraminidase activities than the spherical PR8 virus. Conversely, no differences were observed in HAU:PFU or HAU:RNA ratios, binding avidity, sensitivity to immune serum in hemagglutination inhibition assays, or virion stability at elevated temperatures. Based on these results, we propose that the pleomorphic nature of influenza virus particles is important for the optimization of neuraminidase functions in vivo.

  11. COMPARATIVE MODELLING PROTEIN VAKSIN NA BTB H5N1 MENGGUNAKAN SWISS MODEL

    Directory of Open Access Journals (Sweden)

    Fitri Amelia

    2016-09-01

    Full Text Available Vaccine sequence of Neuraminidase BTB from previous research was studied by using swiss model server. Protein template was gotten from RSCB database by comparing the vaccine sequence with PDB database. HTY protein was used as a template for this vaccine. Template had 0.00e-1 E value, and 97% identity. The protein vaccine that has been modelled by swiss model had  good quality as immune inducer. Base on ramachandran plot analysis, protein model 1, 2, and 3 have amino acid residues in favoured region higher than 70%. They are 82,0% and 78,2%. Model 1 has the lowest non glysine amino acid residues in disallowed region area, that is 0%.   3D Structure of vaccine had 2086  hits of similarity with database on NCBI   Key words: comparing modelling, H5N1 vaccine, swiss model

  12. Impact of a large deletion in the neuraminidase protein identified in a laninamivir-selected influenza A/Brisbane/10/2007 (H3N2) variant on viral fitness in vitro and in ferrets.

    Science.gov (United States)

    Ann, Julie; Abed, Yacine; Beaulieu, Edith; Bouhy, Xavier; Joly, Marie-Hélène; Dubé, Karen; Carbonneau, Julie; Hamelin, Marie-Eve; Mallett, Corey; Boivin, Guy

    2016-03-01

    Viral fitness of a laninamivir-selected influenza A/Brisbane/10/2007-like (H3N2) isolate (LRVp9) containing a 237-amino acid neuraminidase deletion and a P194L hemagglutinin mutation was evaluated in vitro and in ferrets. LRVp9 and the wild-type (WT) virus showed comparable replication kinetics in MDCK-ST6GalI cells. Cultured virus was recovered between days 2 and 5 post-infection in nasal washes (NW) from the 4 WT-infected ferrets whereas no virus was recovered from the LRVp9-infected animals. There was a ≥1 log reduction in viral RNA copies/μl of NW for LRVp9 compared to WT at most time points. The large neuraminidase deletion compromises viral infectivity in vivo. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  13. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_se...quence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  14. Cloning, expression and sequence diversity of iss gene from avian pathogenic Escherichia coli (APEC isolated in Brazil / Clonagem, expressão e diversidade na seqüência do gene iss de Escherichia coli patogênica para aves (APEC, isolada no Brasil

    Directory of Open Access Journals (Sweden)

    Marilda Carlos Vidotto

    2010-09-01

    Full Text Available A proteína Iss (increased serum survival é uma importante característica de resistência ao sistema complemento da Escherichia coli patogênica para aves (APEC. Os objetivos deste trabalho foram clonar e verificar a diversidade da seqüência do gene iss de APEC e caracterizar a proteína Iss recombinante. O gene iss de 309 bp foi amplificado por PCR, clonado e expresso na E. coli BL21 (DE3 utilizando o vetor pET SUMO. O gene iss da APEC9 foi classificado como iss tipo 1 pela diferenciação entre 3 tipos de iss alelos. A proteína Iss foi expressa pela indução com IPTG, purificada em coluna com resina ligada ao íon níquel e utilizada na imunização de galinhas poedeiras. Anticorpos da classe IgY anti rIss reagiram com a proteina rIss, a qual apresentou massa molecular de 22 kDa, correspondendo 11kDa da Iss e 11 kDa da proteína SUMO. The Iss (Increased serum survival protein is an important characteristic of resistance to complement system of avian pathogenic Escherichia coli (APEC. The objectives of this work were to cloning and verify the sequence diversity of iss gene from APEC and characterize the recombinant Iss protein. The iss gene of 309 bp was amplified by PCR, cloned and expressed in E. coli BL21 (DE3 using the pET SUMO vector. The iss gene from APEC9 strain was classified as iss type 1 by differentiation of the three iss gene allele types. The protein was expressed by induction of IPTG and purified in resin charged with the nickel ion. Antibodies IgY anti rIss reacted with rIss showing a molecular mass of 22 kDa, corresponding 11KDa of Iss protein and 11 KDa SUMO protein.

  15. Seqüência Latossolo Amarelo - Podzólico Amarelo - Areias Quartzosas sob material da formação barreiras na região de Tucuruí, estado do Pará Oxisol-Ultisol-Entisol sequence developed from clayey material near Tucuruí region, Pará state, Brazil

    Directory of Open Access Journals (Sweden)

    J.A.M. Demattê

    1994-08-01

    Full Text Available Estudou-se uma seqüência de Latossolo Amarelo-Podzólico Amarelo-Areia Quartzosa desenvolvida em sedimentos da Formação Barreiras. A área se localiza no sul do Pará, nas proximidades entre Tucuruí e o Rio Moju, distando 65km da Usina Hidroelétrica de Tucuruí. Foi escolhida uma encosta de aproximadamente 1500 metros formada por Latossolo na parte alta e Podzólico Amarelo na encosta, ambos argilosos, terminando em amplo vale de fundo arenoso, com forte hidromorfísmo. Os regimes de temperatura são isohipertérmico e hipertérmico e os de umidade ústico e áquico, nas partes elevadas e fundo do vale, respectivamente. Foram abertas quatro trincheiras ao longo da encosta e feitas oito tradagens para apoio. O material de origem é representado pela caolinita. Verificou-se que a diferenciação lateral dos solos: Latossolo Amarelo na parte alta, Podzólico Latossólico na encosta e Areia Quartzosa no fundo do vale, pode ser devida principalmente a processos de remoção e/ou destruição de finos (argila silicatada + óxidos. O encharcamento temporário e a gleização acentuada, exerceram papel preponderante na diferenciação da seqüência estudada.The objective of this work was to study the genesis of an Oxisol-Ultisol-Entisol sequence, developed from sediments of the Barreiras Formation in the Tucurui region. The area is located about 65 km from Tucurui. In this area a soil topo sequence was selected, represented by a clayey oxisol in the higher parts, a clayey ultisol in the middle part, ending in an ample valley of sandy botton, with strong hidromorphism. The temperature regimes are isohyperthermic and hyperthermic and the moisture regimes are udic and aquic, in the higher parts and valley botton, respectively. Four profiles were examined and auger samples were taken in eight representative sites. The parent material is represented by clayey sediments from the Barreiras Formation. Chemically, the soils are leached with high aluminum

  16. Wheat germ cell-free system-based production of hemagglutinin-neuraminidase protein of human parainfluenza virus type 3: generation and characterization of monoclonal antibody

    Directory of Open Access Journals (Sweden)

    Satoko eMatsunaga

    2014-05-01

    Full Text Available Human parainfluenza virus 3 (HPIV3 commonly causes respiratory disorders in infants and young children. Monoclonal antibodies (MAbs have been produced to several components of HPIV3 and commercially available. However, the utility of these antibodies for several immunological and proteomic assays for understanding the nature of HPIV3 infection remain to be characterized. Herein, we report the development and characterization of monoclonal antibodies against hemagglutinin-neuraminidase (HN of HPIV3. A recombinant full-length HPIV3-HN was successfully synthesized using the wheat-germ cell-free protein production system. After immunization and cell fusion, 36 mouse hybridomas producing MAbs to HPIV3-HN were established. The MAbs obtained were fully characterized using ELISA, immunoblotting and immunofluorescent analyses. Of the MAbs tested, single clone was found to be applicable in both flow cytometry and immunoprecipitation procedures. By utilizing the antibody, we newly identified HPIV3-HN binding host proteins via immunoprecipitation-based mass spectrometry analysis. This study provides the availability of our newly-developed MAbs as a valuable tool for the study of HPIV3 infection as well as the several diagnostic tests of this virus.

  17. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  18. The in vivo efficacy of neuraminidase inhibitors cannot be determined from the decay rates of influenza viral titers observed in treated patients

    Science.gov (United States)

    Palmer, John; Dobrovolny, Hana M.; Beauchemin, Catherine A. A.

    2017-01-01

    Antiviral therapy is a first line of defence against new influenza strains. Current pandemic preparations involve stock- piling oseltamivir, an oral neuraminidase inhibitor (NAI), so rapidly determining the effectiveness of NAIs against new viral strains is vital for deciding how to use the stockpile. Previous studies have shown that it is possible to extract the drug efficacy of antivirals from the viral decay rate of chronic infections. In the present work, we use a nonlinear mathematical model representing the course of an influenza infection to explore the possibility of extracting NAI drug efficacy using only the observed viral titer decay rates seen in patients. We first show that the effect of a time-varying antiviral concentration can be accurately approximated by a constant efficacy. We derive a relationship relating the true treatment dose and time elapsed between doses to the constant drug dose required to approximate the time- varying dose. Unfortunately, even with the simplification of a constant drug efficacy, we show that the viral decay rate depends not just on drug efficacy, but also on several viral infection parameters, such as infection and production rate, so that it is not possible to extract drug efficacy from viral decay rate alone.

  19. Production of an enzymatically active and immunogenic form of ectodomain of Porcine rubulavirus hemagglutinin-neuraminidase in the yeast Pichia pastoris.

    Science.gov (United States)

    Cerriteño-Sánchez, José Luis; Santos-López, Gerardo; Rosas-Murrieta, Nora Hilda; Reyes-Leyva, Julio; Cuevas-Romero, Sandra; Herrera-Camacho, Irma

    2016-04-10

    Blue-eye disease (BED) of swine is a viral disease endemic in Mexico. The etiological agent is a paramyxovirus classified as Porcine rubulavirus (PoRV-LPMV), which exhibits in its envelope the hemagglutinin-neuraminidase (HN) glycoprotein, the most immunogenic and a major target for vaccine development. We report in this study the obtaining of ectodomain of PoRV HN (eHN) through the Pichia pastoris expression system. The expression vector (pPICZαB-HN) was integrated by displacement into the yeast chromosome and resulted in a Mut(+) phenotype. Expressed eHN in the P. pastoris X33 strain was recovered from cell-free medium, featuring up to 67 nmol/min/mg after 6 days of expression. eHN was recognized by the serum of infected pigs with strains currently circulating in the Mexican Bajio region. eHN induces antibodies in mice after 28 days of immunization with specific recognition in ELISA test. These antibodies were able to inhibit >80% replication by viral neutralization assays in cell culture. These studies show the obtaining of a protein with similar characteristics to the native HN and which may be a candidate to propose a vaccine or to use the antigen in a serologic diagnostic test. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. 6SLN-lipo PGA specifically catches (coats) human influenza virus and synergizes neuraminidase-targeting drugs for human influenza therapeutic potential.

    Science.gov (United States)

    Sriwilaijaroen, Nongluk; Suzuki, Katsuhiko; Takashita, Emi; Hiramatsu, Hiroaki; Kanie, Osamu; Suzuki, Yasuo

    2015-10-01

    The purpose of this study was to develop a new compound to overcome influenza epidemics and pandemics as well as drug resistance. We synthesized a new compound carrying: (i) Neu5Acα2-6Galβ1-4GlcNAc (6SLN) for targeting immutable haemagglutinins (HAs) unless switched from human-type receptor preference; (ii) an acyl chain (lipo) for locking the compound with the viral HA via hydrophobic interactions; and (iii) a flexible poly-α-L-glutamic acid (PGA) for enhancing the compound solubility and for coating the viral surface, precluding accessibility of the PGA-coated virus to the negatively charged sialic acid on the host cell surface. 6SLN-lipo PGA appears to subvert binding of pandemic H1 and seasonal H3 HAs to receptors, as assessed by using guinea pig erythrocytes, which is critical for virus entry into host cells for multiplication. It shows high potency with IC50 values in the range of 300-500 nM against multiplication of both influenza pandemic H1N1/2009 and seasonal H3N2/2004 viruses in cell culture. It acts in synergism with either of the two FDA-approved neuraminidase inhibitor (NAI) clinical drugs, zanamivir (Relenza(®)) and oseltamivir carboxylate (active form of Tamiflu(®)), and it has the potential to aid NAI drugs to achieve complete clearance of the virus from the culture. 6SLN-lipo PGA is a new potential candidate drug for influenza control and is an attractive candidate for use in combination with an NAI drug for minimized toxicity, delayed development of resistance, prevention and treatment with the potential for eradication of human influenza. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Evidence synthesis and decision modelling to support complex decisions: stockpiling neuraminidase inhibitors for pandemic influenza usage [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Samuel I. Watson

    2017-03-01

    Full Text Available Objectives: The stockpiling of neuraminidase inhibitor (NAI antivirals as a defence against pandemic influenza is a significant public health policy decision that must be made despite a lack of conclusive evidence from randomised controlled trials regarding the effectiveness of NAIs on important clinical end points such as mortality. The objective of this study was to determine whether NAIs should be stockpiled for treatment of pandemic influenza on the basis of current evidence. Methods: A decision model for stockpiling was designed. Data on previous pandemic influenza epidemiology was combined with data on the effectiveness of NAIs in reducing mortality obtained from a recent individual participant meta-analysis using observational data. Evidence synthesis techniques and a bias modelling method for observational data were used to incorporate the evidence into the model. The stockpiling decision was modelled for adults (≥16 years old and the United Kingdom was used as an example. The main outcome was the expected net benefits of stockpiling in monetary terms. Health benefits were estimated from deaths averted through stockpiling. Results: After adjusting for biases in the estimated effectiveness of NAIs, the expected net benefit of stockpiling in the baseline analysis was £444 million, assuming a willingness to pay of £20,000/QALY ($31,000/QALY. The decision would therefore be to stockpile NAIs. There was a greater probability that the stockpile would not be utilised than utilised. However, the rare but catastrophic losses from a severe pandemic justified the decision to stockpile. Conclusions: Taking into account the available epidemiological data and evidence of effectiveness of NAIs in reducing mortality, including potential biases, a decision maker should stockpile anti-influenza medication in keeping with the postulated decision rule.

  2. Chimeric Bovine Respiratory Syncytial Virus with Attachment and Fusion Glycoproteins Replaced by Bovine Parainfluenza Virus Type 3 Hemagglutinin-Neuraminidase and Fusion Proteins

    Science.gov (United States)

    Stope, Matthias B.; Karger, Axel; Schmidt, Ulrike; Buchholz, Ursula J.

    2001-01-01

    Chimeric bovine respiratory syncytial viruses (BRSV) expressing glycoproteins of bovine parainfluenza virus type 3 (BPIV-3) instead of BRSV glycoproteins were generated from cDNA. In the BRSV antigenome cDNA, the open reading frames of the major BRSV glycoproteins, attachment protein G and fusion protein F, were replaced individually or together by those of the BPIV-3 hemagglutinin-neuraminidase (HN) and/or fusion (F) glycoproteins. Recombinant virus could not be recovered from cDNA when the BRSV F open reading frame was replaced by the BPIV-3 F open reading frame. However, cDNA recovery of the chimeric virus rBRSV-HNF, with both glycoproteins replaced simultaneously, and of the chimeric virus rBRSV-HN, with the BRSV G protein replaced by BPIV-3 HN, was successful. The replication rates of both chimeras were similar to that of standard rBRSV. Moreover, rBRSV-HNF was neutralized by antibodies specific for BPIV-3, but not by antibodies specific to BRSV, demonstrating that the BRSV glycoproteins can be functionally replaced by BPIV-3 glycoproteins. In contrast, rBRSV-HN was neutralized by BRSV-specific antisera, but not by BPIV-3 specific sera, showing that infection of rBRSV-HN is mediated by BRSV F. Hemadsorption of cells infected with rBRSV-HNF and rBRSV-HN proved that BPIV-3 HN protein expressed by rBRSV is functional. Colocalization of the BPIV-3 glycoproteins with BRSV M protein was demonstrated by confocal laser scan microscopy. Moreover, protein analysis revealed that the BPIV-3 glycoproteins were present in chimeric virions. Taken together, these data indicate that the heterologous glycoproteins were not only expressed but were incorporated into the envelope of recombinant BRSV. Thus, the envelope glycoproteins derived from a member of the Respirovirus genus can together functionally replace their homologs in a Pneumovirus background. PMID:11533200

  3. Supply of neuraminidase inhibitors related to reduced influenza A (H1N1 mortality during the 2009-2010 H1N1 pandemic: an ecological study.

    Directory of Open Access Journals (Sweden)

    Paula E Miller

    Full Text Available BACKGROUND: The influenza A (H1N1 pandemic swept across the globe from April 2009 to August 2010 affecting millions. Many WHO Member States relied on antiviral drugs, specifically neuraminidase inhibitors (NAIs oseltamivir and zanamivir, to treat influenza patients in critical condition. Such drugs have been found to be effective in reducing severity and duration of influenza illness, and likely reduced morbidity during the pandemic. However, it is less clear whether NAIs used during the pandemic reduced H1N1 mortality. METHODS: Country-level data on supply of oseltamivir and zanamivir were used to predict H1N1 mortality (per 100,000 people from July 2009 to August 2010 in forty-two WHO Member States. Poisson regression was used to model the association between NAI supply and H1N1 mortality, with adjustment for economic, demographic, and health-related confounders. RESULTS: After adjustment for potential confounders, each 10% increase in kilograms of oseltamivir, per 100,000 people, was associated with a 1.6% reduction in H1N1 mortality over the pandemic period (relative rate (RR = 0.84 per log increase in oseltamivir supply. While the supply of zanamivir was considerably less than that of oseltamivir in each Member State, each 10% increase in kilogram of active zanamivir, per 100,000, was associated with a 0.3% reduction in H1N1 mortality (RR = 0.97 per log increase. CONCLUSION: While there are limitations to the ecologic nature of these data, this analysis offers evidence of a protective relationship between antiviral drug supply and influenza mortality and supports a role for influenza antiviral use in future pandemics.

  4. Anti-Tumor Effects of an Oncolytic Adenovirus Expressing Hemagglutinin-Neuraminidase of Newcastle Disease Virus in Vitro and in Vivo

    Directory of Open Access Journals (Sweden)

    Dongyun He

    2014-02-01

    Full Text Available Oncolytic virotherapy has been an attractive drug platform for targeted therapy of cancer over the past few years. Viral vectors can be used to target and lyse cancer cells, but achieving good efficacy and specificity with this treatment approach is a major challenge. Here, we assessed the ability of a novel dual-specific anti-tumor oncolytic adenovirus, expressing the hemagglutinin-neuraminidase (HN gene from the Newcastle disease virus under the human telomerase reverse transcriptase (hTERT promoter (Ad-hTERTp-E1a-HN, to inhibit esophageal cancer EC-109 cells in culture and to reduce tumor burden in xenografted BALB/c nude mice. In vitro, infection with Ad-hTERT-E1a-HN could inhibit the growth of EC-109 cells significantly and also protect normal human liver cell line L02 from growth suppression in 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT assays. Ad-hTERT-E1a-HN also effectively and selectively decreased the sialic acid level on EC-109 cells, but not on L02 cells. Furthermore, Ad-hTERT-E1a-HN was shown to induce the apoptosis pathway via acridine orange and ethidium bromide staining (AO/EB staining, increase reactive oxygen species (ROS, reduce mitochondrial membrane potential and release cytochrome c. In vivo, xenografted BALB/c nude mice were treated via intratumoral or intravenous injections of Ad-hTERT-E1a-HN. Although both treatments showed an obvious suppression in tumor volume, only Ad-hTERT-E1a-HN delivered via intratumoral injection elicited a complete response to treatment. These results reinforced previous findings and highlighted the potential therapeutic application of Ad-hTERT-E1a-HN for treatment of esophageal cancer in clinical trials.

  5. Supply of neuraminidase inhibitors related to reduced influenza A (H1N1) mortality during the 2009-2010 H1N1 pandemic: an ecological study.

    Science.gov (United States)

    Miller, Paula E; Rambachan, Aksharananda; Hubbard, Roderick J; Li, Jiabai; Meyer, Alison E; Stephens, Peter; Mounts, Anthony W; Rolfes, Melissa A; Penn, Charles R

    2012-01-01

    The influenza A (H1N1) pandemic swept across the globe from April 2009 to August 2010 affecting millions. Many WHO Member States relied on antiviral drugs, specifically neuraminidase inhibitors (NAIs) oseltamivir and zanamivir, to treat influenza patients in critical condition. Such drugs have been found to be effective in reducing severity and duration of influenza illness, and likely reduced morbidity during the pandemic. However, it is less clear whether NAIs used during the pandemic reduced H1N1 mortality. Country-level data on supply of oseltamivir and zanamivir were used to predict H1N1 mortality (per 100,000 people) from July 2009 to August 2010 in forty-two WHO Member States. Poisson regression was used to model the association between NAI supply and H1N1 mortality, with adjustment for economic, demographic, and health-related confounders. After adjustment for potential confounders, each 10% increase in kilograms of oseltamivir, per 100,000 people, was associated with a 1.6% reduction in H1N1 mortality over the pandemic period (relative rate (RR) = 0.84 per log increase in oseltamivir supply). While the supply of zanamivir was considerably less than that of oseltamivir in each Member State, each 10% increase in kilogram of active zanamivir, per 100,000, was associated with a 0.3% reduction in H1N1 mortality (RR = 0.97 per log increase). While there are limitations to the ecologic nature of these data, this analysis offers evidence of a protective relationship between antiviral drug supply and influenza mortality and supports a role for influenza antiviral use in future pandemics.

  6. Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.

    Science.gov (United States)

    Ahn, Insung; Son, Hyeon Seok

    2012-02-01

    In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series codon substitution patterns resulted dramatic changes of BLAST results in influenza A/H1N1, providing a possibility of developing a method for predicting the viral evolution in silico. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Thermodynamics of Ga ternary alloys with Na and In, Sn or Zn

    Energy Technology Data Exchange (ETDEWEB)

    Dergacheva, M.B. [Institute of Org. Catalysis and Electrochem. NAN RK, Almaty (Kazakhstan); Shatrova, E.G. [Institute of Org. Catalysis and Electrochem. NAN RK, Almaty (Kazakhstan); Harina, O.V. [Institute of Org. Catalysis and Electrochem. NAN RK, Almaty (Kazakhstan)

    1996-12-01

    Thermodynamic properties of ternary liquid Ga alloys, containing Na (X{sub Na} = 0.025 to 0.045) and In, Sn or Zn have been determined by e.m.f. measurements. The partial thermodynamic properties of Na ({alpha}{sub Na}, {gamma}{sub Na}, {Delta} anti G{sub Na}, {Delta} anti S{sub Na}) have been calculated. The interaction of Na with the other components decreases in the following sequence: In => Sn => Zn. The liquidus temperatures of the investigated ternary alloys have been also determined. (orig.)

  8. Newcastle Disease Virus Establishes Persistent Infection in Tumor Cells In Vitro: Contribution of the Cleavage Site of Fusion Protein and Second Sialic Acid Binding Site of Hemagglutinin-Neuraminidase.

    Science.gov (United States)

    Rangaswamy, Udaya S; Wang, Weijia; Cheng, Xing; McTamney, Patrick; Carroll, Danielle; Jin, Hong

    2017-08-15

    Newcastle disease virus (NDV) is an oncolytic virus being developed for the treatment of cancer. Following infection of a human ovarian cancer cell line (OVCAR3) with a recombinant low-pathogenic NDV, persistent infection was established in a subset of tumor cells. Persistently infected (PI) cells exhibited resistance to superinfection with NDV and established an antiviral state, as demonstrated by upregulation of interferon and interferon-induced genes such as myxoma resistance gene 1 (Mx1) and retinoic acid-inducing gene-I (RIG-I). Viruses released from PI cells induced higher cell-to-cell fusion than the parental virus following infection in two tumor cell lines tested, HT1080 and HeLa, and remained attenuated in chickens. Two mutations, one in the fusion (F) protein cleavage site, F117S (F117S), and another in hemagglutinin-neuraminidase (HN), G169R (HN169R), located in the second sialic acid binding region, were responsible for the hyperfusogenic phenotype. F117S improves F protein cleavage efficiency, facilitating cell-to-cell fusion, while HN169R possesses a multifaceted role in contributing to higher fusion, reduced receptor binding, and lower neuraminidase activity, which together result in increased fusion and reduced viral replication. Thus, establishment of persistent infection in vitro involves viral genetic changes that facilitate efficient viral spread from cell to cell as a potential mechanism to escape host antiviral responses. The results of our study also demonstrate a critical role in the viral life cycle for the second receptor binding region of the HN protein, which is conserved in several paramyxoviruses.IMPORTANCE Oncolytic Newcastle disease virus (NDV) could establish persistent infection in a tumor cell line, resulting in a steady antiviral state reflected by constitutively expressed interferon. Viruses isolated from persistently infected cells are highly fusogenic, and this phenotype has been mapped to two mutations, one each in the

  9. Comparison of mutation patterns in full-genome A/H3N2 influenza sequences obtained directly from clinical samples and the same samples after a single MDCK passage.

    Directory of Open Access Journals (Sweden)

    Hong Kai Lee

    Full Text Available Human influenza viruses can be isolated efficiently from clinical samples using Madin-Darby canine kidney (MDCK cells. However, this process is known to induce mutations in the virus as it adapts to this non-human cell-line. We performed a systematic study to record the pattern of MDCK-induced mutations observed across the whole influenza A/H3N2 genome. Seventy-seven clinical samples collected from 2009-2011 were included in the study. Two full influenza genomes were obtained for each sample: one from virus obtained directly from the clinical sample and one from the matching isolate cultured in MDCK cells. Comparison of the full-genome sequences obtained from each of these sources showed that 42% of the 77 isolates had acquired at least one MDCK-induced mutation. The presence or absence of these mutations was independent of viral load or sample origin (in-patients versus out-patients. Notably, all the five hemagglutinin missense mutations were observed at the hemaggutinin 1 domain only, particularly within or proximal to the receptor binding sites and antigenic site of the virus. Furthermore, 23% of the 77 isolates had undergone a MDCK-induced missense mutation, D151G/N, in the neuraminidase segment. This mutation has been found to be associated with reduced drug sensitivity towards the neuraminidase inhibitors and increased viral receptor binding efficiency to host cells. In contrast, none of the neuraminidase sequences obtained directly from the clinical samples contained the D151G/N mutation, suggesting that this mutation may be an indicator of MDCK culture-induced changes. These D151 mutations can confound the interpretation of the hemagglutination inhibition assay and neuraminidase inhibitor resistance results when these are based on MDCK isolates. Such isolates are currently in routine use in the WHO influenza vaccine and drug-resistance surveillance programs. Potential data interpretation miscalls can therefore be avoided by careful

  10. Glycosylation alters steady-state inactivation of sodium channel Nav1.9/NaN in dorsal root ganglion neurons and is developmentally regulated.

    Science.gov (United States)

    Tyrrell, L; Renganathan, M; Dib-Hajj, S D; Waxman, S G

    2001-12-15

    Na channel NaN (Na(v)1.9) produces a persistent TTX-resistant (TTX-R) current in small-diameter neurons of dorsal root ganglia (DRG) and trigeminal ganglia. Na(v)1.9-specific antibodies react in immunoblot assays with a 210 kDa protein from the membrane fractions of adult DRG and trigeminal ganglia. The size of the immunoreactive protein is in close agreement with the predicted Na(v)1.9 theoretical molecular weight of 201 kDa, suggesting limited glycosylation of this channel in adult tissues. Neonatal rat DRG membrane fractions, however, contain an additional higher molecular weight immunoreactive protein. Reverse transcription-PCR analysis did not show additional longer transcripts that could encode the larger protein. Enzymatic deglycosylation of the membrane preparations converted both immunoreactive proteins into a single faster migrating band, consistent with two states of glycosylation of Na(v)1.9. The developmental change in the glycosylation state of Na(v)1.9 is paralleled by a developmental change in the gating of the persistent TTX-R Na(+) current attributable to Na(v)1.9 in native DRG neurons. Whole-cell patch-clamp analysis demonstrates that the midpoint of steady-state inactivation is shifted 7 mV in a hyperpolarized direction in neonatal (postnatal days 0-3) compared with adult DRG neurons, although there is no significant difference in activation. Pretreatment of neonatal DRG neurons with neuraminidase causes an 8 mV depolarizing shift in the midpoint of steady-state inactivation of Na(v)1.9, making it indistinguishable from that of adult DRG neurons. Our data show that extensive glycosylation of rat Na(v)1.9 is developmentally regulated and changes a critical property of this channel in native neurons.

  11. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_se...quence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  12. The sequence of sequencers: The history of sequencing DNA

    Science.gov (United States)

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  13. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  14. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  15. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. Mumps virus F gene and HN gene sequencing as a molecular tool to study mumps virus transmission.

    Science.gov (United States)

    Gouma, Sigrid; Cremer, Jeroen; Parkkali, Saara; Veldhuijzen, Irene; van Binnendijk, Rob S; Koopmans, Marion P G

    2016-11-01

    Various mumps outbreaks have occurred in the Netherlands since 2004, particularly among persons who had received 2 doses of measles, mumps, and rubella (MMR) vaccination. Genomic typing of pathogens can be used to track outbreaks, but the established genotyping of mumps virus based on the small hydrophobic (SH) gene sequences did not provide sufficient resolution. Therefore, we expanded the sequencing to include fusion (F) gene and haemagglutinin-neuraminidase (HN) gene sequences in addition to the SH gene sequences from 109 mumps virus genotype G strains obtained between 2004 and mid 2015 in the Netherlands. When the molecular information from these 3 genes was combined, we were able to identify separate mumps virus clusters and track mumps virus transmission. The analyses suggested that multiple mumps virus introductions occurred in the Netherlands between 2004 and 2015 resulting in several mumps outbreaks throughout this period, whereas during some local outbreaks the molecular data pointed towards endemic circulation. Combined analysis of epidemiological data and sequence data collected in 2015 showed good support for the phylogenetic clustering. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Empirical insights into the stochasticity of small RNA sequencing

    OpenAIRE

    Qin, Li-Xuan; Tuschl, Thomas; Singer, Samuel

    2016-01-01

    The choice of stochasticity distribution for modeling the noise distribution is a fundamental assumption for the analysis of sequencing data and consequently is critical for the accurate assessment of biological heterogeneity and differential expression. The stochasticity of RNA sequencing has been assumed to follow Poisson distributions. We collected microRNA sequencing data and observed that its stochasticity is better approximated by gamma distributions, likely because of the stochastic na...

  18. Route, mechanism, and implications of proton import during Na+/K+ exchange by native Na+/K+-ATPase pumps

    Science.gov (United States)

    Vedovato, Natascia

    2014-01-01

    A single Na+/K+-ATPase pumps three Na+ outwards and two K+ inwards by alternately exposing ion-binding sites to opposite sides of the membrane in a conformational sequence coupled to pump autophosphorylation from ATP and auto-dephosphorylation. The larger flow of Na+ than K+ generates outward current across the cell membrane. Less well understood is the ability of Na+/K+ pumps to generate an inward current of protons. Originally noted in pumps deprived of external K+ and Na+ ions, as inward current at negative membrane potentials that becomes amplified when external pH is lowered, this proton current is generally viewed as an artifact of those unnatural conditions. We demonstrate here that this inward current also flows at physiological K+ and Na+ concentrations. We show that protons exploit ready reversibility of conformational changes associated with extracellular Na+ release from phosphorylated Na+/K+ pumps. Reversal of a subset of these transitions allows an extracellular proton to bind an acidic side chain and to be subsequently released to the cytoplasm. This back-step of phosphorylated Na+/K+ pumps that enables proton import is not required for completion of the 3 Na+/2 K+ transport cycle. However, the back-step occurs readily during Na+/K+ transport when external K+ ion binding and occlusion are delayed, and it occurs more frequently when lowered extracellular pH raises the probability of protonation of the externally accessible carboxylate side chain. The proton route passes through the Na+-selective binding site III and is distinct from the principal pathway traversed by the majority of transported Na+ and K+ ions that passes through binding site II. The inferred occurrence of Na+/K+ exchange and H+ import during the same conformational cycle of a single molecule identifies the Na+/K+ pump as a hybrid transporter. Whether Na+/K+ pump–mediated proton inflow may have any physiological or pathophysiological significance remains to be clarified. PMID

  19. Testing Na+ in blood

    OpenAIRE

    Lava, Sebastiano A.G.; Bianchetti, Mario G.; Milani, Gregorio P.

    2016-01-01

    Abstract Both direct potentiometry and indirect potentiometry are currently used for Na+ testing in blood. These measurement techniques show good agreement as long as protein and lipid concentrations in blood remain normal. In severely ill patients, indirect potentiometry commonly leads to relevant errors in Na+ estimation: 25% of specimens show a disagreement between direct and indirect potentiometry, which is ?4 mmol/L (mostly spuriously elevated Na+ level due to low circulating albumin con...

  20. Supply of neuraminidase inhibitors related to reduced influenza A (H1N1) mortality during the 2009-2010 H1N1 pandemic: summary of an ecological study.

    Science.gov (United States)

    Miller, Paula E; Rambachan, Aksharananda; Hubbard, Roderick J; Li, Jiabai; Meyer, Alison E; Stephens, Peter; Mounts, Anthony W; Rolfes, Melissa A; Penn, Charles R

    2013-09-01

    When the influenza A (H1N1) pandemic spread across the globe from April 2009 to August 2010, many WHO Member States used antiviral drugs, specifically neuraminidase inhibitors (NAIs) oseltamivir and zanamivir, to treat influenza patients in critical condition. Antivirals have been found to be effective in reducing severity and duration of influenza illness, and likely reduce morbidity; however, it is unclear whether NAIs used during the pandemic reduced H1N1 mortality. To assess the association between antivirals and influenza mortality, at an ecologic level, country-level data on supply of oseltamivir and zanamivir were compared to laboratory-confirmed H1N1 deaths (per 100 000 people) from July 2009 to August 2010 in 42 WHO Member States. From this analysis, it was found that each 10% increase in kilograms of oseltamivir, per 100 000 people, was associated with a 1·6% reduction in H1N1 mortality over the pandemic period [relative rate (RR) = 0·84 per log increase in oseltamivir supply]. Each 10% increase in kilogram of active zanamivir, per 100 000, was associated with a 0·3% reduction in H1N1 mortality (RR = 0·97 per log increase). While limitations exist in the inference that can be drawn from an ecologic evaluation, this analysis offers evidence of a protective relationship between antiviral drug supply and influenza mortality and supports a role for influenza antiviral use in future pandemics. This article summarises the original study described previously, which can be accessed through the following citation: Miller PE, Rambachan A, Hubbard RJ, Li J, Meyer AE, et al. (2012) Supply of Neuraminidase Inhibitors Related to Reduced Influenza A (H1N1) Mortality during the 2009-2010 H1N1 Pandemic: An Ecological Study. PLoS ONE 7(9): e43491. © 2013 Blackwell Publishing Ltd.

  1. VPLIV AMBROZIJE NA ZDRAVJE

    OpenAIRE

    Tramšek, Dejan

    2015-01-01

    Izhodišča: V raziskavi smo se osredotočili na opis različnih vrst ambrozije. Opisali smo tudi rastline, ki so v veliki meri podobne ambroziji. Ob vsem tem pa seveda vpliv ambrozije na zdravje ljudi, predvsem alergij. Predstavili smo posamezne alergije, opisali način preprečevanja in zdravljenja le-teh in simptome, ki alergije spremljajo. Za omejitev in zmanjšanje pojava alergij na ambrozijo pa je to rastlino potrebno odstraniti oz. zamejiti. Odločili smo se, da v diplomskem delu predstavimo ...

  2. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki

    2015-09-01

    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  3. A designated centre for people with disabilities operated by St Joseph's Foundation, Limerick

    LENUS (Irish Health Repository)

    Shi, Weifeng

    2010-12-01

    More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.

  4. A designated centre for people with disabilities operated by Ability West, Galway

    LENUS (Irish Health Repository)

    Shi, Weifeng

    2010-12-01

    More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.

  5. A designated centre for people with disabilities operated by St Christopher's Services Limited, Longford

    LENUS (Irish Health Repository)

    Shi, Weifeng

    2010-12-01

    More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.

  6. St Ita's Community Hospital, Newcastlewest, Limerick.

    LENUS (Irish Health Repository)

    Shi, Weifeng

    2010-12-01

    More and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.

  7. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  8. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  9. Complete genome sequence of Fer-de-Lance Virus reveals a novel gene in reptilian Paramyxoviruses

    Science.gov (United States)

    Kurath, G.; Batts, W.N.; Ahne, W.; Winton, J.R.

    2004-01-01

    The complete RNA genome sequence of the archetype reptilian paramyxovirus, Fer-de-Lance virus (FDLV), has been determined. The genome is 15,378 nucleotides in length and consists of seven nonoverlapping genes in the order 3??? N-U-P-M-F-HN-L 5???, coding for the nucleocapsid, unknown, phospho-, matrix, fusion, hemagglutinin-neuraminidase, and large polymerase proteins, respectively. The gene junctions contain highly conserved transcription start and stop signal sequences and tri-nucleotide intergenic regions similar to those of other Paramyxoviridae. The FDLV P gene expression strategy is like that of rubulaviruses, which express the accessory V protein from the primary transcript and edit a portion of the mRNA to encode P and I proteins. There is also an overlapping open reading frame potentially encoding a small basic protein in the P gene. The gene designated U (unknown), encodes a deduced protein of 19.4 kDa that has no counterpart in other paramyxoviruses and has no similarity with sequences in the National Center for Biotechnology Information database. Active transcription of the U gene in infected cells was demonstrated by Northern blot analysis, and bicistronic N-U mRNA was also evident. The genomes of two other snake paramyxovirus genotypes were also found to have U genes, with 11 to 16% nucleotide divergence from the FDLV U gene. Pairwise comparisons of amino acid identities and phylogenetic analyses of all deduced FDLV protein sequences with homologous sequences from other Paramyxoviridae indicate that FDLV represents a new genus within the subfamily Paramyxovirinae. We suggest the name Ferlavirus for the new genus, with FDLV as the type species.

  10. The LHC Sequencer

    CERN Document Server

    Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris

    2011-01-01

    The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.

  11. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  12. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  13. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  14. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  15. Tratamento de esgoto sanitário em reator híbrido em bateladas sequenciais: eficiência e estabilidade na remoção de matéria orgânica e nutrientes (N, P Sewage treatment in a sequencing batch hybrid reactor: efficiency and stability in organic matter and nutrient (N, P removal

    Directory of Open Access Journals (Sweden)

    Luiz Gonzaga Lamego Neto

    2011-12-01

    Full Text Available Este trabalho apresenta os resultados de estudo sobre o comportamento de um reator híbrido, operado em bateladas sequenciais, na remoção conjunta de matéria carbonácea, nitrogênio e fósforo de esgoto sanitário. Operado em ciclos de 8 horas de duração, o reator possuía em seu interior um suporte fixo com rede de nylon. Foram testadas cargas compreendidas entre 0,39 e 1,35 kgDQO.m-3.dia-1, 42 e 60 gN-NH4-.m-3.dia e 51 e 70 gP-PO4-.m-3.dia. O reator funcionou como um sistema estável e apresentou boas condições de depuração. A remoção da matéria carbonácea mostrou-se elevada, com eficiências médias de 92% de DBO5 e 80% de DQO. A remoção de nutrientes variou entre 59 e 71% para nitrogênio total e entre 45 e 67% para fósforo total. Tanto no lodo em suspensão, quanto no biofilme, foi observada a ocorrência de bactérias oxidadoras de amônio e micro-organismos responsáveis pela desnitrificação e remoção biológica de fósforo.This paper presents the results about the behavior of a sequencing batch hybrid reactor on combined removal of carbonaceous matter, nitrogen and phosphorus from sewage. Operated in 8-hour cycles, the reactor had a nylon net fixed inside. Loads between 0.39 and 1.35 kg COD.m-3.day-1, 42 and 60 gN-NH4-m-3.day-1 and 51 and 70 gP-PO4-m-3.day-1 were tested. The reactor operated as a stable system and showed good depuration conditions. The carbonaceous matter removal was high, with 92 and 80% efficiencies average to BOD5 and COD, respectively. The nutrients removal varied between 59 and 71% for total nitrogen and between 45 and 67% for total phosphorus. In both, sludge in suspension and the biofilm, occurrence of ammonium-oxidizing bacteria and microorganisms responsible for denitrification and biological phosphorus removal was observed.

  16. Whole-body magnetic resonance imaging for staging and follow-up of pediatric patients with Hodgkin's lymphoma: comparison of different sequences; Aplicacao da ressonancia magnetica de corpo inteiro para o estadiamento e acompanhamento de pacientes com linfoma de Hodgkin na faixa etaria infanto-juvenil: comparacao entre diferentes sequencias

    Energy Technology Data Exchange (ETDEWEB)

    Nava, Daniel; Oliveira, Heverton Cesar de, E-mail: daniel@centrus.com.b [Universidade Federal de Sao Paulo (UNIFESP/EPM), SP (Brazil). Dept. de Diagnostico por Imagem; Luisi, Flavio Augusto; Lederman, Henrique Manoel [Universidade Federal de Sao Paulo (UNIFESP/IOP/GRAACC), SP (Brazil). Inst. de Oncologia Pediatrica. Grupo de Apoio ao Adolescente e a Crianca com Cancer; Ximenes, Andrea Regina da Silveira [Clinica Centrus, Campinas, SP (Brazil)

    2011-07-01

    Objective: to compare the performance of the T1, T2, STIR and DWIBS (diffusion-weighted whole-body imaging with background body signal suppression) sequences in the staging and follow-up of pediatric patients with Hodgkin's lymphoma in lymph node chains, parenchymal organs and bone marrow, and to evaluate interobserver agreement. Materials and methods: the authors studied 12 patients with confirmed diagnosis of Hodgkin's lymphoma. The patients were referred for whole body magnetic resonance imaging with T1-weighted, T2-weighted, STIR and DWIBS sequences. Results: the number of lymph node sites characterized as affected by the disease on T1- and T2-weighted sequences showed similar results (8 sites for both sequences), but lower than DWIBS and STIR sequences (11 and 12 sites, respectively). The bone marrow involvement by lymphoma showed the same values for the T1-, T2-weighted and DWIBS sequences (17 lesions), higher than the value found on STIR (13 lesions). A high rate of interobserver agreement was observed as the four sequences were analyzed. Conclusion: STIR and DWIBS sequences detected the highest number of lymph node sites characterized as affected by the disease. Similar results were demonstrated by all the sequences in the evaluation of parenchymal organs and bone marrow. A high interobserver agreement was observed as the four sequences were analyzed. (author)

  17. At NA2

    CERN Multimedia

    1977-01-01

    One of the NA2 calorimeter sections is moved in. The NA2 calorimeter was divided in two halves, to the left and the right of the beam, each half consisting of sheets of passive high Z material interleaved with blades of plastic scintillators. The photo shows on the right, the upstream 'electron' module with eleven lead plates for a total radiation length of 20.

  18. Double sequence core theorems

    Directory of Open Access Journals (Sweden)

    Richard F. Patterson

    1999-01-01

    Full Text Available In 1900, Pringsheim gave a definition of the convergence of double sequences. In this paper, that notion is extended by presenting definitions for the limit inferior and limit superior of double sequences. Also the core of a double sequence is defined. By using these definitions and the notion of regularity for 4-dimensional matrices, extensions, and variations of the Knopp Core theorem are proved.

  19. Efficient probability sequence

    OpenAIRE

    Regnier, Eva

    2014-01-01

    A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficient forecasting systems, including memorylessness and increasing discrimination. These results suggest tests for efficiency and ...

  20. Efficient probability sequences

    OpenAIRE

    Regnier, Eva

    2014-01-01

    DRMI working paper A probability sequence is an ordered set of probability forecasts for the same event. Although single-period probabilistic forecasts and methods for evaluating them have been extensively analyzed, we are not aware of any prior work on evaluating probability sequences. This paper proposes an efficiency condition for probability sequences and shows properties of efficiency forecasting systems, including memorylessness and increasing discrimination. These res...

  1. [Study on factors influencing DNA sequencing by automatic genetic analyzer].

    Science.gov (United States)

    Yan, Shaofei; Wang, Wei; Xu, Jin; Bai, Li; Gan, Xin; Li, Fengqin

    2015-05-01

    To acquire accurate and successful DNA sequencing in a cost-effective way by ABI3500xl automatic genetic analyzer. BigDye was diluted to 8, 16 and 32 times in PCR product sequencing. Three different methods including CENTRI-SEP kit, BigDye cleaning beads and ethanol-NaAc-EDTA were used to purify the sequencing PCR products. The results of DNA sequencing were correct when BigDye was diluted up to 16 times. The misreading of nucleic acid bases was found as BigDye was diluted to 32 times. All three purification methods provided acceptable DNA sequencing results. In terms of method for purification of PCR products, the CENTRI-SEP Kit was the most expensive but time-saving (0.5 h), while ethanol-NaAc-EDTA method was the most economical but time-consuming (2 h). The BigDye cleaning beads method was of a suitable purification time (1 h) but not fit for high-throughput DNA sequencing. BigDye should be diluted up to 16 times in DNA sequencing by ABI3500xl DNA analyzer. Although all three purification methods may promise DNA sequencing results with good quality, it is necessary to choose an appropriate one to keep the balance between time and cost on the basis of the lab condition.

  2. Minimax-robust prediction problem for stochastic sequences with stationary increments and cointegrated sequences

    Directory of Open Access Journals (Sweden)

    Maksym Luz

    2015-05-01

    Full Text Available The problem of optimal estimation of the linear functionals $A {\\xi}=\\sum_{k=0}^{\\infty}a (k\\xi(k$ and $A_N{\\xi}=\\sum_{k=0}^{N}a (k\\xi(k$ which depend on the unknown values of a stochastic sequence $\\xi(m$ with stationary $n$th increments is considered. Estimates are obtained which are based on observations of the sequence $\\xi(m+\\eta(m$ at points of time $m=-1,-2,\\ldots$, where the sequence $\\eta(m$ is stationary and uncorrelated with the sequence $\\xi(m$. Formulas for calculating the mean-square errors and spectral characteristics of the optimal estimates of the functionals are derived in the case of spectral certainty, where spectral densities of the sequences $\\xi(m$ and $\\eta(m$ are exactly known. These results are applied for solving extrapolation problem for cointegrated sequences. In the case where spectral densities of the sequences are not known exactly, but sets of admissible spectral densities are given, the minimax-robust method of estimation is applied. Formulas that determine the least favorable spectral densities and minimax spectral characteristics are proposed for some special classes of admissible densities. 

  3. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin sequence (or syndrome) is a condition in which an infant has a smaller than normal lower jaw, a tongue ... The exact causes of Pierre Robin sequence are unknown. It may be ... jaw develops slowly before birth, but may grow faster during ...

  4. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  5. sequences in Chickpea

    African Journals Online (AJOL)

    Milena

    Author(s) retain the copyright of this article http://www.academicjournals.org/AJB. African Journal of Biotechnology. Full Length Research Paper. Evaluation of genetic divergence and phylogenetic relationship using sequence-tagged microsatellite. (STMS) sequences in Chickpea (Cicer arietinum L.) genotypes. Himanshu ...

  6. Sequences, Series, and Mathematica.

    Science.gov (United States)

    Mathews, John H.

    1992-01-01

    Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of sequences and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about sequences. (MDH)

  7. Gêneros orais na escola

    OpenAIRE

    Teixeira,Lucia

    2012-01-01

    O artigo analisa a utilização da noção de gênero na escola fundamental, detendo-se sobre o ensino dos gêneros orais. Apresenta postulados teóricos de Bakhtin e incorpora a contribuição da semiótica discursiva e as sugestões metodológicas da pedagogia de ensino de línguas desenvolvida na Universidade de Genebra. Em seguida, propõe exemplo prático de aplicação do conceito ao desenvolvimento da expressão oral em sala de aula.

  8. Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan

    Directory of Open Access Journals (Sweden)

    Mizuta Katsumi

    2011-12-01

    Full Text Available Abstract Background Human parainfluenza virus type 1 (HPIV1 causes various acute respiratory infections (ARI. Hemagglutinin-neuraminidase (HN glycoprotein of HPIV1 is a major antigen. However, the molecular epidemiology and genetic characteristics of such ARI are not exactly known. Recent studies suggested that a phylogenetic analysis tool, namely the maximum likelihood (ML method, may be applied to estimate the evolutionary time scale of various viruses. Thus, we conducted detailed genetic analyses including homology analysis, phylogenetic analysis (using both the neighbor joining (NJ and ML methods, and analysis of the pairwise distances of HN gene in HPIV1 isolated from patients with ARI in Yamagata prefecture, Japan. Results A few substitutions of nucleotides in the second binding site of HN gene were observed among the present isolates. The strains were classified into two major clusters in the phylogenetic tree by the NJ method. Another phylogenetic tree constructed by the ML method showed that the strains diversified in the late 1980s. No positively selected sites were found in the present strains. Moreover, the pairwise distance among the present isolates was relatively short. Conclusions The evolution of HN gene in the present HPIV1 isolates was relatively slow. The ML method may be a useful phylogenetic method to estimate the evolutionary time scale of HPIV and other viruses.

  9. Nanotechnology and Nanopore Sequencing.

    Science.gov (United States)

    Abedini-Nassab, Roozbeh

    2017-01-01

    DNA sequencing is one of the crucially important tasks in the fields of genetics and cellular biology, which is benefiting from nanotechnology. DNA carries genetic information and sequencing it in a quick way helps researchers in achieving essential goals, including personalized medicine. Solid state nanopores potentially can offer more durability, in sequencing biomolecules, over the proteinbased nanopores. In recent years, various ideas are introduced towards the goal of fast and low cost sequencing. In this review article recent advances presented in journal articles as well as patents in this field, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  10. Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin- and neuraminidase-specific tetra- and triplex real-time RT-PCRs

    DEFF Research Database (Denmark)

    Henritzi, Dinah; Zhao, Na; Starick, Elke

    2016-01-01

    Background A diversifying pool of mammalian-adapted influenza A viruses (IAV) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV isolated from swine....... Swine influenza viruses (SIV) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV in Europe is poorly understood. Objectives Efficient SIV surveillance programmes depend on sensitive and specific...... algorithm is proposed for the combined detection in clinical samples and subtyping of SIV strains currently circulating in Europe that is based on a generic, M-gene-specific influenza A virus RT-qPCR. In a second step, positive samples are examined by tetraplex HA- and triplex NA-specific RT...

  11. At NA5

    CERN Multimedia

    1978-01-01

    The NA5 experiment is shown at the start of the setting up in beam H2 of hall EHN1. It was designed by the Bari- Cracow-Liverpool-Munich (MPI) Collaboration to study hard hadron-hadron collisions with a streamer chamber vertex spectrometer and a calorimeter trigger. The beam from target T2 enters from the left. E

  12. Riso na epilepsia

    Directory of Open Access Journals (Sweden)

    Edymar Jardim

    1967-06-01

    Full Text Available São estudados três casos de síndrome convulsiva temporal, com manifestações concomitantes de riso na sua fase inicial. As características principais foram a imotivação e á incoercibilidade do riso. Esses sintomas desapareceram com o uso de anticonvulsivantes.

  13. Biotecnologia na agricultura

    Directory of Open Access Journals (Sweden)

    Helaine Carrer

    2010-01-01

    Full Text Available A expectativa de o crescimento populacional atingir 9 bilhões de habitantes em 2050 em adição às questões da sustentabilidade e do aquecimento global nos desafiam a aumentar a oferta de alimentos. Uma metodologia alternativa que contribua para a redução do impacto desse cenário envolve a biotecnologia, que, nas últimas décadas, trouxe marcantes oportunidades tecnológicas na agricultura, resultando em relevante desenvolvimento na obtenção de novas variedades de plantas, na melhoria da qualidade de diversos alimentos e atualmente também na bioenergia. As técnicas biotecnológicas envolvendo os marcadores moleculares, a genômica e a transformação genética estão transformando a agricultura e são discutidas neste artigo.The expected population growth to reach 9 billion by 2050 in addition to issues of sustainability and global warming challenges us to increase the supply of food. An alternative approach to help reducing the impact of this scenario involves biotechnology which in recent decades has brought remarkable technological opportunities in the agriculture that resulted in relevant development in obtaining new plant varieties, improved quality of different foods, and now also in bioenergy. The biotechnology techniques involving molecular markers, genomics and genetic transformation are transforming agriculture and will be discussed in this article.

  14. At NA3

    CERN Multimedia

    1977-01-01

    The NA3 experiment was setup in beam H8 in the Hall EHN1 by the CERN-College de France-Orsay-Palaiseau-Saclay Collaboration to study the hadronic production of high pT leptons and hadrons. The photo shows in the background (centre) the electromagnetic calorimeter.

  15. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  16. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  17. Evolution of DNA sequencing.

    Science.gov (United States)

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  18. How should we sequence and combine novel therapies in CLL?

    Science.gov (United States)

    Davids, Matthew S

    2017-12-08

    With the recent approval of several effective and well-tolerated novel agents (NAs), including ibrutinib, idelalisib, venetoclax, and obinutuzumab, patients with chronic lymphocytic leukemia (CLL) have more therapeutic options than ever before. The availability of these agents is both an important advance for patients but also a challenge for practicing hematologist/oncologists to learn how best to sequence NAs, both with respect to chemoimmunotherapy (CIT) and to other NAs. The sequencing of NAs in clinical practice should be guided both by an individual patient's prognostic markers, such as FISH and immunoglobulin heavy chain variable region (IGHV)-mutation status, as well as the patient's medical comorbidities and goals of care. For older, frailer patients with lower-risk CLL prognostic markers, NA monotherapy may remain a mainstay of CLL treatment for years to come. For younger, fitter patients and those with higher-risk CLL, such as del(17p) or unmutated IGHV, combination approaches may prove to be more valuable than NA monotherapy. Trials are currently evaluating the efficacy of several such combination approaches, including NA plus anti-CD20 monoclonal antibody, NA plus NA (with or without anti-CD20 monoclonal antibody), and NA plus CIT. Given the tremendous efficacy of the already approved NAs, as well as the promising data for next generation NAs, the development of well-tolerated, highly effective combination strategies with curative potential for patients with CLL has become a realistic goal. © 2016 by The American Society of Hematology. All rights reserved.

  19. Delayed Sequence Intubation

    DEFF Research Database (Denmark)

    Weingart, Scott D; Trueger, N Seth; Wong, Nelson

    2015-01-01

    , patients were paralyzed and intubated. The primary outcome of this study was the difference in oxygen saturations after maximal attempts at preoxygenation before delayed sequence intubation compared with saturations just before intubation. Predetermined secondary outcomes and complications were also...... assessed. RESULTS: A total of 62 patients were enrolled: 19 patients required delayed sequence intubation to allow nonrebreather mask, 39 patients required it to allow NIPPV, and 4 patients required it for nasogastric tube placement. Saturations increased from a mean of 89.9% before delayed sequence...... intubation to 98.8% afterward, with an increase of 8.9% (95% confidence interval 6.4% to 10.9%). Thirty-two patients were in a predetermined group with high potential for critical desaturation (pre-delayed sequence intubation saturations ≤93%). All of these patients increased their saturations post...

  20. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  1. Repeat Sequence Proteins as Matrices for Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

    2009-01-01

    Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

  2. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  3. What's Decidable About Sequences?

    OpenAIRE

    Furia, Carlo A.

    2010-01-01

    We present a first-order theory of sequences with integer elements, Presburger arithmetic, and regular constraints, which can model significant properties of data structures such as arrays and lists. We give a decision procedure for the quantifier-free fragment, based on an encoding into the first-order theory of concatenation; the procedure has PSPACE complexity. The quantifier-free fragment of the theory of sequences can express properties such as sortedness and injectivity, as well as Bool...

  4. O JORNALISTA NA PESQUISA E NA ARTE

    Directory of Open Access Journals (Sweden)

    Beatriz Marocco

    2013-06-01

    Full Text Available O jornalista tem sido objeto das artes e das ciências. Nesta incisão no tema do painel “Configurações e perspectivas da pesquisa em jornalismo no Brasil em diálogo com os estudos latinoamericanos em jornalismo”, realizado no Encontro Nacional da Sociedade Brasileira de Pesquisadores em Jornalismo/SBPJor (Curitiba, 10/11/2012, reconheci que o âmbito acadêmico projeta dois tipos de ação: em rede de pesquisadores de diferentes países e regiões do mundo, com participação de países da América Latina, na pesquisa colaborativa e em projetos de investigação com outras bases de colaboração. Ambas as modalidades dialogam com a produção do cinema e da literatura – que visibiliza a grande potência do profissional para tramas e tensões. 

  5. Sequence Classification: 894488 [

    Lifescience Database Archive (English)

    Full Text Available itions of high Na+, alkaline pH, and cell wall stress; Frt1p || http://www.ncbi.nlm.nih.gov/protein/6324901 ... ...culum membrane protein that is a substrate of the phosphatase calcineurin, interacts with homolog Frt2p, promotes cell growth in cond

  6. Romanskoe vlijanie na staroserbskij sintaksis

    OpenAIRE

    Pavlović Slobodan

    2010-01-01

    V nastojaščej rabote rassmatrivajutsja kontekstual'nye aspekty vlijanija romanskogo substrata i adstrata na staroserbskij sintaksis. Na sintaksis staroserbskogo razgovornogo jazyka mogli vlijat' vlašskie, dalmatinskie i ital'janskie dialekty. Na sintaksis staroserbskoj pis'mennosti (krome serbsko-slavjanskogo jazyka i romanskogo substrata) okazali vlijanie latinskij i ital'janskij jazyki, poskol'ku na territorii rasprostranenija serbskogo jazyka peresekalis' dve velikie kul'tury: Pax Sl...

  7. Preparing for NA4

    CERN Multimedia

    CERN PhotoLab

    1977-01-01

    Here, in one of the EF workshop, Albert Duchêne works on a pretty piece of mechanics. A few others await to be attended on the left. There are indications that the pipes were meant to house the carbon target (subdivided in eight sections) to be installed inside the toroid magnet of the NA4 experiment. The external strips were designed to possibly correct the magnetic field (???).

  8. Hidroma subdural na fossa posterior

    Directory of Open Access Journals (Sweden)

    José Carlos Vasques

    1970-03-01

    Full Text Available Os autores relatam um caso de hidroma subdural na fossa craniana posterior conseqüente a traumatismo na região occipital. O paciente foi operado com pleno sucesso. A raridade da localização de hidroma na fossa posterior é salientada, sendo discutidos os possíveis mecanismos etio-patogênicos.

  9. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  10. Sialyltransferase and Neuraminidase Levels/Ratios and Sialic Acid Levels in Peripheral Blood B Cells Correlate with Measures of Disease Activity in Patients with Systemic Lupus Erythematosus and Rheumatoid Arthritis: A Pilot Study.

    Directory of Open Access Journals (Sweden)

    Lieh-Bang Liou

    Full Text Available We attempted to determine whether the level of enzymes sialyltransferase (ST and neuraminidase (Neu and sialic acid (SIA in patients with systemic lupus erythematosus (SLE correlates with the SLE Disease Activity Index (SLEDAI and in patients with rheumatoid arthritis (RA correlates with the Disease Activity Score28 (DAS28.We examined cell-surface levels of ST6Gal-1, Neu1, ST3Gal-1, Neu3, α-2,6-SIA, and α-2,3-SIA by using fluorescent anti-enzyme antibodies, fluorescent-conjugated Sambucus nigra lectin, and fluorescent-conjugated Maackia amurensis lectin on blood cells in SLE and RA patients and assessed correlations of these levels with SLEDAI and with DAS28. Areas under the curve (AUC were calculated for different variables against SLEDAI.The B-cell ST3Gal-1/Neu3 ratio positively correlated with SLEDAI scores (ρ = 0.409 and P = 0.002, statistically significant after Bonferroni' correction for multiple analyses.. It was supported by the inverse correlation of B-cell Neu3 levels with SLEDAI scores (ρ = -0.264, P = 0.048. The B-cell ST3Gal-1/Neu3 ratio against SLEDAI yielded an AUC of 0.689, which was comparable to that of anti-dsDNA levels at 0.635. In contrast, both ST3Gal-1 and Neu3 levels of RA B cells (r = 0.376, P = 0.013; r = 0.425, P = 0.005, respectively correlated positively with high disease-activity DAS28 scores.B-cell ST3Gal-1/Neu3 ratios in SLE and B-cell ST3Gal-1 and Neu3 levels in RA with high disease-activity DAS28 scores correlated with disease activity measures and may be useful in monitoring disease activities.

  11. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  12. The CERES / NA45 experiment

    CERN Multimedia

    Laurent Guiraud

    2000-01-01

    Ceres is one of the second generation heavy ion experiments at CERN's SPS. It is dedicated to the study of electron-positron pairs in relativistic nuclear collisions. NA45 is one of the seven experiments (NA44, NA45, NA49, NA50, NA52, WA97/NA57 and WA98) involved in CERN's Heavy Ion programme which provided evidence for the existence of a new state of matter, the quark-gluon plasma. In this state, quarks, instead of being bound up into more complex particles such as protons and neutrons, are liberated and roam freely. Theory predicts that this state must have existed at about 10 microseconds after the Big Bang, before the formation of matter as we know it today.

  13. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  14. na Perua

    Directory of Open Access Journals (Sweden)

    Jorge Carvalho

    1989-01-01

    Full Text Available Antes de se caracterizar como tentativa de ensaio ou de análise a qualquer coisa, o presente artigo tem, antes de mais nada, a pretensão de se constituir uma provocação ao debate acerca da questão do esporte na escola. A provocação parte basicamente do relato da minha experiência pessoal como Secretário da Educação do Município de Aracaju, cargo que exerci no período de 1º de janeiro de 1986 a 27 de janeiro de 1987.

  15. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  16. Sequence Classification: 893720 [

    Lifescience Database Archive (English)

    Full Text Available ial ribosomal protein of the large subunit; MRP51 exhibits genetic interactions with mutations in the COX2 and COX3 mRNA 5'-untransla...ted leader sequences; Mrp51p || http://www.ncbi.nlm.nih.gov/protein/6325139 ...

  17. Goldbach Partitions and Sequences

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 11. Goldbach Partitions and Sequences. Subhash Kak. General Article Volume 19 Issue 11 November 2014 pp 1028-1037. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/019/11/1028-1037 ...

  18. The Compliment Sequence.

    Science.gov (United States)

    Sims, Anntarie L.

    1989-01-01

    Describes and examines 150 tape-recorded compliment sequences. Reports that the course and outcome of compliments and compliment responses are affected by: (1) the way a compliment is worded; (2) the type of statement that precedes or follows the compliment; and (3) the status and sex of the compliment participants. (RAE)

  19. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  20. absolutely regular random sequences

    Directory of Open Access Journals (Sweden)

    Michel Harel

    1996-01-01

    Full Text Available In this paper, the central limit theorems for the density estimator and for the integrated square error are proved for the case when the underlying sequence of random variables is nonstationary. Applications to Markov processes and ARMA processes are provided.

  1. Comprometimento pulmonar na leptospirose

    Directory of Open Access Journals (Sweden)

    Jorge Eduardo Manhães de Carvalho

    1992-03-01

    Full Text Available Em 23 pacientes com leptospirose apresentando comprometimento pulmonar, internados no Hospital Universitário Antônio Pedro da XJFF, Niterói, hemoptise e hemoptóicos foram observados em 21,7% e 30,4%, respectivajnente. Gasometria arterial revelou hipoxemia e hipocapnia na maioria dos casos. Radiografia de tórax em 15 pacientes mostrou comprometimento alveolar em 60%, comprometimento intersticial-reticular em 6%, padrão misto (alveolar e intersticial em20%e ausência de alterações radiológicas em 14%. A necrópsiade 13 pacientes mostrou edema, congestão e hemorragia nos pulmões em 100% dos casos. A hemorragia foi focal em 46% e difusa em 54% dos casos. Houve formação de membrana hialina em 30% e trombos de fibrina em 46% dos pulmões estudados, o que estabelece o diagnóstico da coagulação intravascular disseminada e a ocorrência da síndrome de angústia respiratória na leptospirose.

  2. Vrapci na tlu

    Directory of Open Access Journals (Sweden)

    Ana Ille Horvat

    2017-12-01

    Full Text Available Princeze nikada ne umiru. Udaju se i žive sretno do kraja života. "Ideja će mi sinuti kad se najmanje budem nadala", kaže Alice, "uvijek je tako. Neću očajavati." Upravo sjedi na kauču držeći bilježnicu u rukama u koju je trenutak prije, velikim štampanim slovima na vrhu lista, upisala "ideje za Afonsov rođendan". Pažljivo je povukla pet strelica i svaku označila brojem. Poslije toga nije napisala više ništa. Ovo je već sedmi popis koji radi otkako je sjela. Pogleda uprta prema dnevnom boravku, oko kažiprsta lijeve ruke mota plamen jarkoplave kose, kao u lutke."Kako se to smišlja neka ideja", upita se šapatom koji je uvježbala još u mladosti, "kako?"

  3. Rare kaon decays (NA48/2 and NA62)

    OpenAIRE

    Goudzovski, Evgueni

    2013-01-01

    The rare decay $K^\\pm\\to\\pi^\\pm\\gamma\\gamma$ has been recently measured from data samples collected by the NA48/2 and NA62 experiments at CERN. These measurements are presented, including model-independent spectrum measurements and fits to the Chiral Perturbation Theory description. The rare decay $K^\\pm\\to\\pi^\\pm\\gamma\\gamma$ has been recently measured from data samples collected by the NA48/2 and NA62 experiments at CERN. These measurements are presented, including model-independent spec...

  4. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  5. Role of divalent cations, pH, cytoskeleton componentes and surface charge on the adhesion of Trichomonas vaginalis to a polystyrene substrate Papel de cátions divalentes, pH, componentes de citoesqueleto e carga de superfície na adesão de Trichomonas vaginalis a um substrato de poliestireno

    Directory of Open Access Journals (Sweden)

    Fernando Costa e Silva Filho

    1987-09-01

    Full Text Available The process of adhesion of three different strains of Trichomonas vaginalis to a polystyrene substrate was analysed. The process of adhesion was dependent on the time of incubation and the pH of the phosphate-buffered solution (PBS in which the parasites were suspended. The highest indices of adhesion were observed after an incubation time of 60 min at pH 6.6. The adhesion index increased when the parasites were incubated in the presence of culture media or when Ca++ or Mg++ was added to the PBS solution, whereas cytochalasin B, trypsin or neuraminidase reduced adhesion. Incubation of the parasites in the presence of poly-L-lysine facilitated the process of adhesion. Incubation of the parasites or polystyrene beads in the presence of poly-L-lysine led to important changes in their surface charge.O processo de adesão de três cepas de Trichomonas vaginalis a um substrato de poliestireno foi estudado. Verificou-se que este processo depende do tempo de incubação e do pH da solução salina em que os parasitos se encontram. A maior taxa de adesão foi observada após 60 minutos de incubação a pH 6,6. A adesão é mior se Ca++ ou Mg++ for adicionado ao meio. Tratamento das células em citocalasina B, tripsina ou neuraminidase reduz a adesão enquanto tratamento com poli-L-lisina facilita esta adesão. Incubação dos parasitos ou esferas de poliestireno na presença de poli-L-lisina provoca alterações importantes na carga de superfície.

  6. Swaps in protein sequences.

    Science.gov (United States)

    Fliess, Amit; Motro, Benny; Unger, Ron

    2002-08-01

    An important question in protein evolution is to what extent proteins may have undergone swaps (switches of domain or fragment order) during evolution. Such events might have occurred in several forms: Swaps of short fragments, swaps of structural and functional motifs, or recombination of domains in multidomain proteins. This question is important for the theoretical understanding of the evolution of proteins, and has practical implications for using swaps as a design tool in protein engineering. In order to analyze the question systematically, we conducted a large scale survey of possible swaps and permutations among all pairs of protein from the Swissport database. A swap is defined as a specific kind of sequence mutation between two proteins in which two fragments that appear in both sequences have different relative order in the two sequences. For example, aXbYc and dYeXf are defined as a swap, where X and Y represent sequence fragments that switched their order. Identifying such swaps is difficult using standard sequence comparison packages. One of the main problems in the analysis stems from the fact that many sequences contain repeats, which may be identified as false-positive swaps. We have used two different approaches to detect pairs of proteins with swaps. The first approach is based on the predefined list of domains in Pfam. We identified all the proteins that share at least two domains and analyzed their relative order, looking for pairs in which the order of these domains was switched. We designed an algorithm to distinguish between real swaps and duplications. In the second approach, we used Blast to detect pairs of proteins that share several fragments. Then, we used an automatic procedure to select pairs that are likely to contain swaps. Those pairs were analyzed visually, using a graphical tool, to eliminate duplications. Combining these approaches, about 140 different cases of swaps in the Swissprot database were found (after eliminating

  7. Published sequences do not support transfer of oseltamivir resistance mutations from avian to human influenza A virus strains.

    Science.gov (United States)

    Norberg, Peter; Lindh, Magnus; Olofsson, Sigvard

    2015-03-28

    Tamiflu (oseltamivir phosphate ester, OE) is a widely used antiviral active against influenza A virus. Its active metabolite, oseltamivir carboxylate (OC), is chemically stable and secreted into wastewater treatment plants. OC contamination of natural habitats of waterfowl might induce OC resistance in influenza viruses persistently infecting waterfowl, and lead to transfer of OC-resistance from avian to human influenza. The aim of this study was to evaluate whether such has occurred. A genomics approach including phylogenetic analysis and probability calculations for homologous recombination was applied on altogether 19,755 neuraminidase (N1 and N2) genes from virus sampled in humans and birds, with and without resistance mutations. No evidence for transfer of OE resistance mutations from avian to human N genes was obtained, and events suggesting recombination between human and avian influenza virus variants could not be traced in the sequence material studied. The results indicate that resistance in influenza viruses infecting humans is due to the selection pressure posed by the global OE administration in humans rather than transfer from avian influenza A virus strains carrying mutations induced by environmental exposure to OC.

  8. Transposon facilitated DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  9. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...

  10. Moebius syndrome (moebius sequence)

    OpenAIRE

    A.A. Desai; Bansal, Sandeep

    1999-01-01

    Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.

  11. Moebius syndrome (moebius sequence).

    Science.gov (United States)

    Desai, A A; Bansal, S

    1999-10-01

    Moebius Syndrome is one of the rare disorder amongst the oromandibular limb hypogenesis. It is of a unknown atiology with sporadic occurrence in which there is congenital bilateral facial palsy,-bilateral involvement of abducent nerve along with other cranial nerves like III, V, IX, X, Xllth and the patient having masklike expressionless face. We are reporting a case of Moebius Sequence who presented to us in the department of ENT and Head and Neck Surgery, Baroda.

  12. NA48 prototype calorimeter

    CERN Multimedia

    1990-01-01

    This is a calorimeter, a detector which measures the energy of particles. When in use, it is filled with liquid krypton at -152°C. Electrons and photons passing through interact with the krypton, creating a shower of charged particles which are collected on the copper ribbons. The ribbons are aligned to an accuracy of a tenth of a millimetre. The folding at each end allows them to be kept absolutely flat. Each shower of particles also creates a signal in scintillating material embedded in the support disks. These flashes of light are transmitted to electronics by the optical fibres along the side of the detector. They give the time at which the interaction occurred. The photo shows the calorimeter at NA48, a CERN experiment which is trying to understand the lack of anti-matter in the Universe today.

  13. O real na psicose

    Directory of Open Access Journals (Sweden)

    Maurício Castejón Herrmann

    2004-06-01

    Full Text Available Este artigo discute a noção de real na psicose, a partir das formulações de Lacan sobre o tema, presentes no Seminário 3 - As Psicoses, no Seminário 20 - Mais, Ainda e no texto Televisão. Considerando-se que a concepção de real tem uma indicação clínica, a hipótese que se formula é a de que a noção de real trabalhada no Seminário 20, Mais, Ainda representa uma continuidade da concepção de real desenvolvida no Seminário 3, As Psicoses

  14. Na Cauda do Cometa

    Science.gov (United States)

    Voelzke, M. R.

    2009-01-01

    Quando viam um cometa, os antigos gregos imaginavam uma estrela com uma vasta cabeleira. Não à toa, a palavra deriva do termo koma, que significa cabelo. Constituídos por fragmentos de gelo e gases, os cometas possuem um núcleo sólido, que pode ter vários quilômetros de diâmetro, e uma cauda que sempre aponta na direção contrária ao Sol, devido aos ventos solares. Graças à aparência de pontos luminosos em movimento (ao contrário de outros astros, que parecem estáticos), esses corpos celestes foram interpretados por diferentes povos com muito misticismo, inspirando mitos tanto de boas-novas como de maus presságios. Conheça algumas dessas histórias:

  15. Athéna

    OpenAIRE

    Camps, G.

    2013-01-01

    Dès l’époque archaïque le culte d’Athéna fut important à Cyrène au point qu’on a pu se demander si cette importance ne s’expliquait pas par l’existence d’une divinité libyque qui aurait été identifiée à la déesse guerrière et industrieuse. A l’appui de cette opinion, on peut retenir plusieurs données de qualités diverses. Il faut citer en premier lieu la déesse égypto-libyque Nît, très ancienne mais particulièrement adorée durant l’époque saïte, au moment où la Basse-Egypte est soumise à une ...

  16. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  17. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  18. Comprometimento pulmonar na leptospirose

    Directory of Open Access Journals (Sweden)

    Jorge Eduardo Manhães de Carvalho

    1992-03-01

    Full Text Available Em 23 pacientes com leptospirose apresentando comprometimento pulmonar, internados no Hospital Universitário Antônio Pedro da XJFF, Niterói, hemoptise e hemoptóicos foram observados em 21,7% e 30,4%, respectivajnente. Gasometria arterial revelou hipoxemia e hipocapnia na maioria dos casos. Radiografia de tórax em 15 pacientes mostrou comprometimento alveolar em 60%, comprometimento intersticial-reticular em 6%, padrão misto (alveolar e intersticial em20%e ausência de alterações radiológicas em 14%. A necrópsiade 13 pacientes mostrou edema, congestão e hemorragia nos pulmões em 100% dos casos. A hemorragia foi focal em 46% e difusa em 54% dos casos. Houve formação de membrana hialina em 30% e trombos de fibrina em 46% dos pulmões estudados, o que estabelece o diagnóstico da coagulação intravascular disseminada e a ocorrência da síndrome de angústia respiratória na leptospirose.Tostudy thepulmonary complications in leptospirosis case records of 23 such patients admitted at the Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói, Brasil, were reviewed. Hemoptysis were seen in 21.7% and sputal blood in 30.4% of patients. Arterial gasometry detected hypoxemia and hypocapnia in most cases. Thoracic radiology showed an alveolar pattern in 60% of the patients, alveolo-interstitial in 20%, interstitial in 6%, and in 14% the lungs were considered to be normal Necropsy of 13 cases showed edema, congestion and hemorrhage in the lungs in all cases. Hyaline membrane was found in 30% and fibrin thrombi in 46% of these cases, resulting in a diagnosis of adult respiratory distress syndrome and acute disseminated intravascular coagulation (consumption coagulopathy in leptospirosis.

  19. A ENGENHARIA NA ESCOLA

    Directory of Open Access Journals (Sweden)

    Valéria Pelizzer Casara

    2015-04-01

    Full Text Available Este projeto teve por objetivo principal mostrar às jovens do ensino médio, como as áreas de exatas e de engenharia podem estar inseridas em situações rotineiras por elas vivenciadas e incentivá-las para ingressarem nessas áreas. O projeto foi executado na escola de ensino Médio Nelson Horostecki na cidade de Chapecó, Santa Catarina. Mostrou-se de forma simples que as áreas de exatas e de engenharia têm aplicações práticas nas nossas vidas. No desenvolvimento do projeto, realizaram-se oficinas na escola cujo tema principal abordado foi o processo de fabricação do chocolate, visto que o mesmo é um produto muito apreciado pelas adolescentes. Dentro dessa temática, foram trabalhadas as questões que envolvem conhecimentos das áreas de exatas e de engenharia, mais especificamente a Engenharia Ambiental. O projeto auxiliou na formação cidadã e também na escolha profissional das meninas. Muitas das alunas participantes nunca haviam tido contato direto com alunos graduandos de cursos na área das exatas. Mais ainda, este projeto oportunizou a aproximação da universidade com a comunidade externa. Palavras-chave: Extensão Universitária, Ciências Exatas e Engenharia, Chocolate, Oficinas.   Engineering in the school Abstract: The main objective of this project was to show high school female students how the exact sciences and engineering can be included in their routine situations encouraging them to entering in these areas. The project was carried out at the Nelson Horostecki High School in Chapecó, Santa Catarina State, Brazil. It was showed in a simple manner how exact sciences and engineering have practical applications in our lives. Workshops were conducted in the school during the execution of the project in which the main subject was the chocolate manufacturing process, since chocolate is a product greatly appreciated by the young female people. Within this matter, the activities were performed using the knowledge of

  20. Kaon experiments at CERN: NA48 and NA62

    CERN Document Server

    INSPIRE-00293758

    2012-01-01

    Searches for violation of lepton flavour universality and lepton number conservation in kaon decays by the NA62 and NA48/2 experiments at CERN, status and future plans of the CERN kaon programme are presented. A precision measurement of the helicity-suppressed ratio $R_K$ of the $K^\\pm\\to e^\\pm\

  1. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  2. Plant DNA sequencing for phylogenetic analyses: from plants to sequences.

    Science.gov (United States)

    Neves, Susana S; Forrest, Laura L

    2011-01-01

    DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.

  3. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  4. Gene silencing reveals multiple functions of Na+/K+-ATPase in the salmon louse (Lepeophtheirus salmonis).

    Science.gov (United States)

    Komisarczuk, Anna Z; Kongshaug, Heidi; Nilsen, Frank

    2018-01-12

    Na+/K+-ATPase has a key function in a variety of physiological processes including membrane excitability, osmoregulation, regulation of cell volume, and transport of nutrients. While knowledge about Na+/K+-ATPase function in osmoregulation in crustaceans is extensive, the role of this enzyme in other physiological and developmental processes is scarce. Here, we report characterization, transcriptional distribution and likely functions of the newly identified L. salmonis Na+/K+-ATPase (LsalNa+/K+-ATPase) α subunit in various developmental stages. The complete mRNA sequence was identified, with 3003 bp open reading frame encoding a putative protein of 1001 amino acids. Putative protein sequence of LsalNa+/K+-ATPase revealed all typical features of Na+/K+-ATPase and demonstrated high sequence identity to other invertebrate and vertebrate species. Quantitative RT-PCR analysis revealed higher LsalNa+/K+-ATPase transcript level in free-living stages in comparison to parasitic stages. In situ hybridization analysis of copepodids and adult lice revealed LsalNa+/K+-ATPase transcript localization in a wide variety of tissues such as nervous system, intestine, reproductive system, and subcuticular and glandular tissue. RNAi mediated knock-down of LsalNa+/K+-ATPase caused locomotion impairment, and affected reproduction and feeding. Morphological analysis of dsRNA treated animals revealed muscle degeneration in larval stages, severe changes in the oocyte formation and maturation in females and abnormalities in tegmental glands. Thus, the study represents an important foundation for further functional investigation and identification of physiological pathways in which Na+/K+-ATPase is directly or indirectly involved. Copyright © 2018. Published by Elsevier Inc.

  5. Novel expressed sequence tag- simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  6. Romanskoe vlijanie na staroserbskij sintaksis

    Directory of Open Access Journals (Sweden)

    Pavlović Slobodan

    2010-01-01

    Full Text Available V nastojaščej rabote rassmatrivajutsja kontekstual'nye aspekty vlijanija romanskogo substrata i adstrata na staroserbskij sintaksis. Na sintaksis staroserbskogo razgovornogo jazyka mogli vlijat' vlašskie, dalmatinskie i ital'janskie dialekty. Na sintaksis staroserbskoj pis'mennosti (krome serbsko-slavjanskogo jazyka i romanskogo substrata okazali vlijanie latinskij i ital'janskij jazyki, poskol'ku na territorii rasprostranenija serbskogo jazyka peresekalis' dve velikie kul'tury: Pax Slavia Orthodoxa i Pax Romana Catholica. Sintaksičeskoe vlijanie latinskogo i ital'janskogo jazykov na staro-serbskuju pis'mennost' osuščestvljalos' prežde vsego čerez zapadnye obrazcy delovoj perepiski. [Projekat Ministarstva nauke Republike Srbije: Istorija srpskog jezika

  7. Valores na escola

    Directory of Open Access Journals (Sweden)

    Menin Maria Suzana De Stefano

    2002-01-01

    Full Text Available Neste texto pretende-se discorrer sobre valores morais na escola e suas implicações para a formação de professores. Para tanto discutir-se-á, em primeiro lugar, e brevemente, o que são valores morais, ou éticos, e como a escola pode situar-se em relação a eles. Em seguida, serão relatadas algumas observações a respeito de valores de professores e práticas daí decorrentes. São comentados resultados de pesquisa que ilustram a transmissão de valores de forma doutrinal e a educação moral e cívica tal como realizada na ditadura militar, e, por outro lado, a posição relativista e/ou de laissez-faire que certas escolas podem adotar, metodologicamente, sobre a educação em valores. Finalmente, defender-se-á a idéia de que é necessária uma discussão sobre valores pelos diversos membros da escola e uma opção por uma metodologia para ensiná-los, seja os professores, em sua formação inicial e continuada, seja os alunos. A teoria de desenvolvimento moral de Jean Piaget será apresentada como uma referência possível para a educação em valores. Exemplos de situações escolares de conflito de valores entre direção, pais e alunos são discutidas para ilustrar como uma escola pode adotar um procedimento democrático de educação em valores, que se apresenta como um terceiro caminho possível de educação moral nas escolas, além das posições doutrinárias ou relativistas.

  8. Pathotypic and Sequence Characterization of Newcastle Disease Viruses from Vaccinated Chickens Reveals Circulation of Genotype II, IV and XIII and in India.

    Science.gov (United States)

    Jakhesara, S J; Prasad, V V S P; Pal, J K; Jhala, M K; Prajapati, K S; Joshi, C G

    2016-10-01

    Newcastle disease virus (NDV) causes a highly contagious disease which continuously haunts the global poultry industry. The nature and molecular epidemiology of NDVs prevalent in recent outbreaks in India is poorly understood. This study aimed to characterize NDVs prevalent in vaccinated flocks in India using whole-genome sequencing and biological pathotyping. Twelve field isolates were collected from outbreaks which occurred in different parts of India and characterized as velogenic based on their intracerebral pathogenicity index (ICPI) and amino acid sequence at the F protein cleavage site. All 12 of the field isolates and five commonly used vaccine strains were selected for whole-genome sequencing using Ion Torrent PGM technology, yielding complete genome sequences for ten field isolates and all vaccine strains. The genome of all isolates was found to be 15 192 nt long with a high level of conservation across multiple genomic features with APMV-I viruses. Phylogenetic analysis and evolutionary distance calculations placed the isolates in genotypes II, IV and XIII. Revisiting other recently reported strains provided preliminary evidence of genotypes VI, VII and XVIII circulating in India. Comparison between the field and vaccine virus sequences revealed unique genomic and amino acid differences in important antigenic regions of the F and hemagglutinin-neuraminidase (HN) genes which can be targeted for site directed mutagenesis to evaluate the impact of these substitutions on virus pathogenicity. This study highlights the requirement to evaluate current vaccines through systematic protection assays to determine protection efficacy against field isolates. © 2014 Blackwell Verlag GmbH.

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

    Science.gov (United States)

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

    2015-12-15

    CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Tuning of the sequence technique

    OpenAIRE

    Laude, Dominique; Baudrie, Véronique; Elghozi, Jean-Luc

    2009-01-01

    The sequence method was first described in cats, and applied in different species including humans. Up to now, there is no systematic study of the spontaneous baroreflex sensitivity (BRS) estimated by the sequence method to mice.

  11. O SUBLIME NA MODERNIDADE

    Directory of Open Access Journals (Sweden)

    Martha de Almeida

    2009-03-01

    Full Text Available A obra Uma investigação filosófica sobre a origem de nossas idéias do sublime e dobelo, do sensualista inglês Edmund Burke (1757, data as origens do sublime na Modernidade. Nosublime ocorre é um prazer ligado à dor, um "horror delicioso" que sentimos quando acreditamosque estamos em perigo sem que isso esteja ocorrendo realmente. Em O mundo como Vontade erepresentação Schopenhauer assume as influências que sofreu de Kant no que diz respeito à suainterpretação sobre o belo e o sublime, porém difere dele quanto à natureza dessa impressão. ParaSchopenhauer a experiência estética pressupõe a dissolução da subjetividade num movimento decontemplação das idéias livre do querer imposto pela vontade individual. As idéias deSchopenhauer influenciaram a estética do Nietzsche de O nascimento da tragédia.

  12. A aposta na filosofia

    Directory of Open Access Journals (Sweden)

    Márcio Suzuki

    2011-12-01

    Full Text Available Para Hume, filosofar é uma atividade semelhante às demais ocupações humanas. A decisão que leva à atividade filosófica é menos resultado de uma argumentação teórica do que fruto de um cálculo prático, que é entendido como uma caça ou um jogo. O objetivo deste trabalho será o de mostrar que no jogo filosófico perde quem joga sério demais. A aposta na filosofia tem que passar pelo bom humor e pela diversão: uma resposta a Pascal?For Hume, philosophy is in itself neither more nor less important than other human activities. On the contrary, it can be explained from its resemblance with game and hunting. If one chooses to dedicate himself to philosophy, his decision is not the consequence of logical reasoning, but depends on practical evaluation, which has something to do with gambling. The following text tries to show that in philosophy, like in other games, the loser will be the one who plays too earnestly. The philosophical game requires good humour and some relaxation: Is this a good answer to Pascal's pari?

  13. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  14. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  15. Eficiência do reator seqüencial em batelada (RSB na remoção de nitrogênio no tratamento de esgoto doméstico com DQO baixa The sequencing batch reactor (SBR efficiency in the removal of nitrogen on the treatment of domestic sewage with low COD

    Directory of Open Access Journals (Sweden)

    Luiz Fernando de Abreu Cybis

    2004-09-01

    Full Text Available Este trabalho tem como objetivo avaliar a eficiência e a estabilidade do RSB na remoção de nitrogênio no tratamento de esgoto doméstico com DQO baixa. O reator utilizado no experimento possui volume de trabalho de 600 L e trata 1200 L/d de esgoto bruto em três bateladas de oito horas. A partir dos dados obtidos na pesquisa, observou-se que o reator seqüencial em batelada possibilitou a remoção média de nitrogênio total igual a 88 % no tratamento de esgoto doméstico com DQO média de 257 mg/L. A remoção de DQO foi de 90 %, a média da alcalinidade total no efluente foi 72 mgCaCO3/L e o índice volumétrico de lodo médio ficou em 86 mL/g. Estes resultados indicam que é possível utilizar RSB para o tratamento de esgoto doméstico com matéria orgânica reduzida sem comprometer a qualidade do efluente, a remoção de nitrogênio e a estabilidade operacional do sistema.This work had the objective of evaluating the SBR efficiency and stability in the removal of nitrogen on the treatment of domestic sewage with low COD. The reactor used in the experiment has a working volume of 600 L, and treats 1200 L/d of raw sewage in three 8-hour cycles. From the data gathered during the research, it was realized that the SBR fostered an average removal of total nitrogen equal to 88% in the treatment of a domestic sewage with an average COD of 257 mg/L. The COD removal was 90%, the final effluent total alkalinity was 72 mgCaCO3/L, and the sludge volumetric index was 86 mL/g. The results indicate that is possible to use SBR for the treatment of domestic sewage with low organic matter without compromising the final effluent quality, the nitrogen removal ability, and the stability of the system.

  16. Multiple sequence alignments of partially coding nucleic acid sequences

    Directory of Open Access Journals (Sweden)

    Fried Claudia

    2005-06-01

    Full Text Available Abstract Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however, only a part of the sequence of interest is translated. On the other hand, overlapping reading frames may encode multiple alternative proteins, possibly with intermittent non-coding parts. Examples are, in particular, RNA virus genomes. Results The standard scoring scheme for nucleic acid alignments can be extended to incorporate simultaneously information on translation products in one or more reading frames. Here we present a multiple alignment tool, codaln, that implements a combined nucleic acid plus amino acid scoring model for pairwise and progressive multiple alignments that allows arbitrary weighting for almost all scoring parameters. Resource requirements of codaln are comparable with those of standard tools such as ClustalW. Conclusion We demonstrate the applicability of codaln to various biologically relevant types of sequences (bacteriophage Levivirus and Vertebrate Hox clusters and show that the combination of nucleic acid and amino acid sequence information leads to improved alignments. These, in turn, increase the performance of analysis tools that depend strictly on good input alignments such as methods for detecting conserved RNA secondary structure elements.

  17. Sequence Factorial and Its Applications

    Science.gov (United States)

    Asiru, Muniru A.

    2012-01-01

    In this note, we introduce sequence factorial and use this to study generalized M-bonomial coefficients. For the sequence of natural numbers, the twin concepts of sequence factorial and generalized M-bonomial coefficients, respectively, extend the corresponding concepts of factorial of an integer and binomial coefficients. Some latent properties…

  18. The advantages of SMRT sequencing.

    Science.gov (United States)

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-07-03

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  19. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked ...

  20. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large and com...

  1. Region segmentation along image sequence

    Energy Technology Data Exchange (ETDEWEB)

    Monchal, L.; Aubry, P.

    1995-12-31

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs.

  2. Children's discrimination of vowel sequences

    Science.gov (United States)

    Coady, Jeffry A.; Kluender, Keith R.; Evans, Julia

    2003-10-01

    Children's ability to discriminate sequences of steady-state vowels was investigated. Vowels (as in ``beet,'' ``bat,'' ``bought,'' and ``boot'') were synthesized at durations of 40, 80, 160, 320, 640, and 1280 ms. Four different vowel sequences were created by concatenating different orders of vowels for each duration, separated by 10-ms intervening silence. Thus, sequences differed in vowel order and duration (rate). Sequences were 12 s in duration, with amplitude ramped linearly over the first and last 2 s. Sequence pairs included both same (identical sequences) and different trials (sequences with vowels in different orders). Sequences with vowel of equal duration were presented on individual trials. Children aged 7;0 to 10;6 listened to pairs of sequences (with 100 ms between sequences) and responded whether sequences sounded the same or different. Results indicate that children are best able to discriminate sequences of intermediate-duration vowels, typical of conversational speaking rate. Children were less accurate with both shorter and longer vowels. Results are discussed in terms of auditory processing (shortest vowels) and memory (longest vowels). [Research supported by NIDCD DC-05263, DC-04072, and DC-005650.

  3. Relationship between intracellular Na+ concentration and reduced Na+ affinity in Na+,K+-ATPase mutants causing neurological disease

    DEFF Research Database (Denmark)

    Toustrup-Jensen, Mads Schak; Einholm, Anja P.; Schack, Vivien

    2014-01-01

    The neurological disorders familial hemiplegic migraine type 2 (FHM2), alternating hemiplegia of childhood (AHC), and rapid-onset dystonia parkinsonism (RDP) are caused by mutations of Na+,K+-ATPase α2- and α3-isoforms, expressed in glial and neuronal cells, respectively. Although these disorders...... mutations that increase Na+ affinity were found to reduce [Na+]i. It is concluded that the Na+ affinity of the Na+,K+-ATPase is an important determinant of [Na+]i....

  4. Hemisferectomia na hemiplegia infantil

    Directory of Open Access Journals (Sweden)

    Rolando A. Tenuto

    1956-03-01

    Full Text Available Os autores relatam o caso de um paciente com 18 anos de idade, portador de paralisia cerebral instalada aos 4 anos de idade após moléstia febril prolongada (hemiplegia esquerda, crises convulsivas generalizadas, freqüentes e rebeldes à medicação, deficiência mental e alterações de conduta. O eletrencefalograma e o pneumencefalograma revelaram alterações graves do hemisfério direito; tendo o primeiro destes exames demonstrado a existência de perturbações propagadas ao outro hemisfério. Foi praticada a hemisferectomia direita. Durante o ato cirúrgico, por exigência técnica foram extirpados, além do hemisfério cerebral, os dois terços rostrais do núcleo caudado e o núcleo amigdalóide. No pós-operatório foi intercorrência de osteomielite e meningite, medicadas com antibióticos e seqüestrectomia. Apesar da complicação pós-operatória, instalou-se progressiva melhora em relação à conduta social; diminuiu também a espasticidade no membro inferior esquerdo e não mais se repetiram as crises convulsivas. Não foram observadas modificações quanto ao rendimento intelectual e quanto aos distúrbios sensitivos que existiam antes da intervenção cirúrgica. O exame neurocular mostrou hemianopsia homônima esquerda. Êstes resultados são concordantes com os assinalados na literatura sobre o assunto.

  5. TRGOVANJE NA IZBRANEM TRGU - FOREX

    OpenAIRE

    Ambrož, Sabina

    2012-01-01

    V delu diplomskega seminarja je obravnavana tematika trgovanja na valutnem trgu. Trgovanje z valutami je v zadnjem desetletju doseglo velik razvoj, močno pa je narasla tudi priljubljenost valutnega trga Forex, saj se zaradi enostavnega pristopa in možnosti velikih zaslužkov zanj odloča vse več posameznikov. V teoretičnem delu povzamemo ključne elemente, ki jih mora poznati začetnik na tem trgu. V empiričnem delu pa poskušamo na praktičnem primeru pokazati primer trgovanja s trendom in vstopom...

  6. Integrated and Differentiated Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Murat Kirişci

    2015-01-01

    Full Text Available In this paper, we investigate integrated and differentiated sequence spaces which emerge from the concept of the sequence space $\\ell_{1}$. The integrated and differentiated sequence spaces were initiated by Goes and Goes [4]. The main propose of the present paper, we study matrix domains and some properties of the integrated and differentiated sequence spaces. In Section 3, we compute the alpha-, beta- and gamma duals of these spaces. Afterward, we characterize the matrix classes of these spaces with well-known sequence spaces.

  7. Asteroid Ida Rotation Sequence

    Science.gov (United States)

    1994-01-01

    This montage of 14 images (the time order is right to left, bottom to top) shows Ida as it appeared in the field of view of Galileo's camera on August 28, 1993. Asteroid Ida rotates once every 4 hours, 39 minutes and clockwise when viewed from above the north pole; these images cover about one Ida 'day.' This sequence has been used to create a 3-D model that shows Ida to be almost croissant shaped. The earliest view (lower right) was taken from a range of 240,000 kilometers (150,000 miles), 5.4 hours before closest approach. The asteroid Ida draws its name from mythology, in which the Greek god Zeus was raised by the nymph Ida.

  8. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  9. Tuning of influenza A virus neuraminidase activity

    NARCIS (Netherlands)

    Dai, Meiling

    2017-01-01

    Influenza A viruses (IAVs) are zoonotic pathogens that constantly circulate in a wide variety of species, including birds, pigs and humans. In humans, IAVs cause seasonal epidemics and occasional influenza pandemics. Annual epidemics caused by seasonal IAVs usually lead to millions of human

  10. Results from NA61/SHINE

    Directory of Open Access Journals (Sweden)

    Unger M.

    2013-06-01

    Full Text Available In this paper we summarize recent results from NA61/SHINE relevant for heavy ion physics, neutrino oscillations and the interpretation of air showers induced by ultra-high energy cosmic rays.

  11. ŠOLANJE NA DOMU

    OpenAIRE

    Horvat, Anja

    2016-01-01

    Pravica do izobraževanja in pridobivanja (ne)formalnih veščin in spretnosti je temeljna človekova pravica in svoboščina. Dobra izobrazba človeka duhovno bogati, plemeniti in širi njegova obzorja. Šolanje oz. izobraževanje na domu je ena od možnosti za izvajanje izobraževanja na osnovnošolski ravni, ki ga v Republiki Sloveniji ureja Zakon o osnovni šoli (1996, 5. in 88. člen). Ta predpisuje obvezne učne vsebine in načine preverjanja znanja, od izvajalcev poučevanja na domu pa ne zahteva do...

  12. Beam monitoring at NA2

    CERN Multimedia

    1978-01-01

    Claus Goessling working on the beam Cerenkov counter of NA2. The muon beam enters from left the hall EHN2 and the last element of the beam transport. On background is the access door on the Jura side.

  13. Na via do Behemoth

    Directory of Open Access Journals (Sweden)

    Gérard Rabinovitch

    2008-06-01

    Full Text Available O momento nazista permanece um enigma impensado de que a cultura contemporânea continua cativa. O autor levanta a hipótese de que a persistência desse enigma e seus estragos duráveis se devem à insistência dos pensamentos político, sociológico e filosófico em construírem o nazismo à luz da metáfora hobbesiana do Leviatã. Propõe retomar a questão do nazismo sob a perspectiva do Behemoth, antônimo do Leviatã. Para tanto, sugere a necessidade de retornar a Freud e à psicanálise, balizas de um possível novo pensamento do político que escrutine a destrutividade nazista. Propõe ainda sondar as homologias entre nazismo, corjas e máfias, com base na figura da " heroicização da violência" que lhes seria comum. E avança um modelo " econômico" : a quimera, suscetível de capturar o caráter heterotópico e heterocrônico de sua construção criminosa.The paths of Behemoth. The Nazi moment remains as the thoughtless enigma of which contemporary culture is still captive. The author raises the hypothesis where the persistency of this enigma and its durable damages are due to the insistence of the political, social and philosophical thoughts in building the Nazism at the view of the Hobbesian metaphor of Leviathan. It is here proposed to resume the Nazism matter under Behemoth's perspective, antonym to Leviathan. For such, it is suggested a necessity to look back at Freud and the psychoanalysis, structured by a possible new political thought which scrutinizes the destructivity of the Nazism. It is also here proposed to gaze at the homologies between Nazism, mafias and gangs, with a base in the figure of " violence as a heroically act" that are their common ground. The author also advances an economical model: the chimera susceptible to capture the heterotopic and heterochronic character of its criminal construction.

  14. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  15. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage........ In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  16. A possible mechanism for low affinity of silkworm Na+/K+-ATPase for K.

    Science.gov (United States)

    Homareda, Haruo; Otsu, Masahiro; Yamamoto, Sachiko; Ushimaru, Makoto; Ito, Sayaka; Fukutomi, Toshiyuki; Jo, Taeho; Eishi, Yoshinobu; Hara, Yukichi

    2017-12-01

    The affinity for K+ of silkworm nerve Na+/K+-ATPase is markedly lower than that of mammalian Na+/K+-ATPase (Homareda 2010). In order to obtain clues on the molecular basis of the difference in K+ affinities, we cloned cDNAs of silkworm (Bombyx mori) nerve Na+/K+-ATPase α and β subunits, and analyzed the deduced amino acid sequences. The molecular masses of the α and β subunits were presumed to be 111.5 kDa with ten transmembrane segments and 37.7 kDa with a single transmembrane segment, respectively. The α subunit showed 75% identity and 93% homology with the pig Na+/K+-ATPase α1 subunit. On the other hand, the amino acid identity of the β subunit with mammalian counterparts was as low as 30%. Cloned α and β cDNAs were co-expressed in cultured silkworm ovary-derived cells, BM-N cells, which lack endogenous Na+/K+-ATPase. Na+/K+-ATPase expressed in the cultured cells showed a low affinity for K+ and a high affinity for Na+, characteristic of the silkworm nerve Na+/K+-ATPase. These results suggest that the β subunit is responsible for the affinity for K+ of Na+/K+-ATPase.

  17. The EMBL Nucleotide Sequence Database.

    Science.gov (United States)

    Kanz, Carola; Aldebert, Philippe; Althorpe, Nicola; Baker, Wendy; Baldwin, Alastair; Bates, Kirsty; Browne, Paul; van den Broek, Alexandra; Castro, Matias; Cochrane, Guy; Duggan, Karyn; Eberhardt, Ruth; Faruque, Nadeem; Gamble, John; Diez, Federico Garcia; Harte, Nicola; Kulikova, Tamara; Lin, Quan; Lombard, Vincent; Lopez, Rodrigo; Mancuso, Renato; McHale, Michelle; Nardone, Francesco; Silventoinen, Ville; Sobhany, Siamak; Stoehr, Peter; Tuli, Mary Ann; Tzouvara, Katerina; Vaughan, Robert; Wu, Dan; Zhu, Weimin; Apweiler, Rolf

    2005-01-01

    The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.

  18. Large-Scale Sequence Comparison.

    Science.gov (United States)

    Lal, Devi; Verma, Mansi

    2017-01-01

    There are millions of sequences deposited in genomic databases, and it is an important task to categorize them according to their structural and functional roles. Sequence comparison is a prerequisite for proper categorization of both DNA and protein sequences, and helps in assigning a putative or hypothetical structure and function to a given sequence. There are various methods available for comparing sequences, alignment being first and foremost for sequences with a small number of base pairs as well as for large-scale genome comparison. Various tools are available for performing pairwise large sequence comparison. The best known tools either perform global alignment or generate local alignments between the two sequences. In this chapter we first provide basic information regarding sequence comparison. This is followed by the description of the PAM and BLOSUM matrices that form the basis of sequence comparison. We also give a practical overview of currently available methods such as BLAST and FASTA, followed by a description and overview of tools available for genome comparison including LAGAN, MumMER, BLASTZ, and AVID.

  19. Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant

    OpenAIRE

    Leipold, Enrico; Hanson-Kahn, Andrea; Frick, Miya; Gong, Ping; Bernstein, Jonathan A.; Voigt, Martin; Katona, Istvan; Oliver Goral, R.; Altm?ller, Janine; N?rnberg, Peter; Weis, Joachim; H?bner, Christian A.; Heinemann, Stefan H.; Kurth, Ingo

    2015-01-01

    Gain-of-function mutations in the human SCN11A-encoded voltage-gated Na+ channel NaV1.9 cause severe pain disorders ranging from neuropathic pain to congenital pain insensitivity. However, the entire spectrum of the NaV1.9 diseases has yet to be defined. Applying whole-exome sequencing we here identify a missense change (p.V1184A) in NaV1.9, which leads to cold-aggravated peripheral pain in humans. Electrophysiological analysis reveals that p.V1184A shifts the voltage dependence of channel op...

  20. Dependence of shake probability on nuclear charge in Li-, Na- and K-like ions

    Energy Technology Data Exchange (ETDEWEB)

    Kupliauskiene, A. [Vilnius University Institute of Theoretical Physics and Astronomy, A. Gostauto 12, LT-01108 Vilnius (Lithuania)]. E-mail: akupl@itpa.lt; Glemza, K. [Vilnius University, Saul e-dot tekio 9, LT-10222 Vilnius (Lithuania)

    2005-07-01

    In sudden perturbation approximation, the probability of the shake-up process accompanying inner-shell ionization is calculated for the isoelectronic sequences of Li-, Na- and K-like ions in the ground and excited np and nd states. Numerical solutions of Hartree-Fock equations and hydrogen-like radial orbitals are used. Very large differences between the results of both approximations for all ions and strong dependences on ion charge are obtained at the beginning of the isoelectronic sequences.

  1. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  2. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  3. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  4. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  5. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  6. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  7. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  8. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  9. Sanger dideoxy sequencing of DNA.

    Science.gov (United States)

    Walker, Sarah E; Lorsch, Jon

    2013-01-01

    While the ease and reduced cost of automated DNA sequencing has largely obviated the need for manual dideoxy sequencing for routine purposes, specific applications require manual DNA sequencing. For instance, in studies of enzymes or proteins that bind or modify DNA, a DNA ladder is often used to map the site at which an enzyme is bound or a modification occurs. In these cases, the Sanger method for dideoxy sequencing provides a rapid and facile method for producing a labeled DNA ladder. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  11. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  12. Eletrocauterio na cesarea : complicações na ferida cirurgica

    OpenAIRE

    Cristiane Menabo Moreira

    2010-01-01

    Resumo: Objetivo: Avaliar a efetividade e segurança do uso do eletrocautério para coagulação na da ferida operatória da cesárea. Métodos: Foi realizado um ensaio clínico piloto duplo cego controlado aleatorizado. Mulheres com indicação de cesárea, com até uma cesárea prévia, que fizeram pré-natal foram aleatorizadas na hora da cirurgia para uso ou não de eletrocautério para coagulação. As 224 voluntárias que participaram foram examinadas na alta hospitalar (3o dia) e pós-alta, no 7°.ao 10° di...

  13. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  14. Application of the Photomodeler software and Matlab environment for analysisof objects movement parameters based on image sequences. (Polish Title: Wykorzystanie pakietu Photomodeler oraz środowiska Matlab, do badania parametrów ruchu obiektów na podstawie obrazów sekwencyjnych)

    Science.gov (United States)

    Markowski, T.

    2013-12-01

    Analysis of objects movement parameters is the area of interest of scientists representing many disciplines. Technological progress provides improvement of research methods. One of them is photogrammetry, and more specifically, close-range image sequences processing. Much research on different approaches to this issue are conducted all over the world. Proposed solution is to carry out photogrammetric measurements using one of the standard programs for close-range objects 3D modeling - PhotoModeler software and their mathematical processing using popular computing environment - Matlab software. Application of existing software's functionality, in many cases seems to be less costly than development and then implementation of specialized measuring and computing applications, dedicated to analysis of movement parameters. Considered solution is based primarily on the appropriate transformations of the frame of reference with respect to which the movement takes place. Automatic coded targets measurements and bundle adjustment, carried out using PhotoModeler software, were used in the research. In order to calculate objects movements parameters, there were further repeated isometric coordinates transformations, numerical differentiation in method of difference quotient and orientation by iterative tabulation with intervals narrowing additionally applied by building own Matlab environment functions. A number of experiments were performed using registration in the form of films from JVC GZ-HD5 digital video camera and films and series of photographs from Nikon D5000 digital photographic camera. Accomplished experiments covered different objects of movement parameters analysis and also distinct movement types. There were also three different versions of established frame of reference -movement of the camera in relation to surroundings, movement of the object in relation to the camera and movement of the object in relation to surrounding. Carried out research revealed that

  15. ChPT tests at NA48 and NA62

    Directory of Open Access Journals (Sweden)

    Gonnella Francesco

    2014-01-01

    Full Text Available Final results from an analysis of about 400 K± → π±γγ rare decay candidates collected by the NA48/2 and NA62 experiments at CERN during low intensity runs with minimum bias trigger configurations are presented. The results include a model-independent decay rate measurement and fits to Chiral Perturbation Theory (ChPT description. The data support the ChPT prediction for a cusp in the di-photon invariant mass spectrum at the two pion threshold.

  16. Corpo e sexualidade na gravidez

    Directory of Open Access Journals (Sweden)

    Natalúcia Matos Araújo

    2012-06-01

    Full Text Available Estudo etnográfico que teve como objetivo compreender como as gestantes vivenciam os processos fisiológicos do seu corpo durante a gestação e a sua repercussão na sexualidade. A pesquisa envolveu sete mulheres residentes em bairro popular de São Paulo. Na coleta de dados, utilizou-se observação participante e entrevista com questões norteadoras. Os dados foram apresentados na forma de narrativa e posteriormente organizados nas categorias: Percebendo as transformações corporais; Convivendo com as mudanças no corpo; Sentimentos e sensações na vida sexual durante a gestação e imaginando o corpo e a sexualidade após a gestação. As mulheres referiram-se às transformações do corpo como desconfortos e expressaram a preocupação de que fossem definitivas. Expressaram o desejo de que, após o parto, o corpo volte a ser como era e que volte a sentir desejo sexual. O reconhecimento destes fatos constitui-se numa ferramenta primordial na adequação das práticas profissionais.

  17. All new for NA62

    CERN Multimedia

    Antonella Del Rosso

    2012-01-01

    This week sees the start of the first run of the new NA62 experiment. This will be a unique opportunity for the collaboration to test its new beam, new detectors and new data acquisition system before the physics run in 2014. Speaking to the Bulletin, the NA62 technical coordinator Ferdinand Hahn shares the many challenges that the various teams faced to be on time for beam. Ready, steady, start!   A Large Angle Veto detector (white) in place in the NA62 decay volume (blue). With components from almost all the detectors in place downstream of the decay point of the mother particles – the kaons – and of the KTAG detector that tags the kaons before they decay, NA62 is ready for its first technical run. This unique run will test all the equipment as well as the trigger and the data acquisition systems. “This year, we will have about five weeks of beam from the SPS before the long shutdown of all the CERN machines,” says Ferdinand Hahn, NA62 Technical Co-...

  18. A reference human genome dataset of the BGISEQ-500 sequencer.

    Science.gov (United States)

    Huang, Jie; Liang, Xinming; Xuan, Yuankai; Geng, Chunyu; Li, Yuxiang; Lu, Haorong; Qu, Shoufang; Mei, Xianglin; Chen, Hongbo; Yu, Ting; Sun, Nan; Rao, Junhua; Wang, Jiahao; Zhang, Wenwei; Chen, Ying; Liao, Sha; Jiang, Hui; Liu, Xin; Yang, Zhaopeng; Mu, Feng; Gao, Shangxian

    2017-05-01

    BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.

  19. gigapanorama of NA 62 cavern

    CERN Multimedia

    Brice, Maximilien

    2015-01-01

    The image shows the new rare Kaon decay experiment at CERN, called NA62. The NA62 experiment is 270 metres long and includes a 120-metre-long vacuum tank, shown here, housing several of the particle detectors. (Note: the experiment axis is a straight line, the curving of the tank is an optical effect of the photo.) Kaons are particles that decay into lighter elementary particles. The kaon decay processes are mostly well known, except for some very rare decay modes. For example, NA62 is investigating a rare decay predicted by the Standard Model in which a kaon decays into one pion and two neutrinos. This process occurs only once every 10 billion decays. The understanding of such ultra-rare decays are of great importance because they test the Standard Model in energy ranges not accessible by direct measurements. They are therefore complementary to the measurements at the LHC. ultra high definition on demand (photolab@cern.ch).

  20. Alcool e drogas na esquizofrenia

    OpenAIRE

    Marilia Montoya Boscolo

    2000-01-01

    Resumo: O objetivo deste trabalho é estudar o fenômeno do uso de álcool e drogas ilícitas (maconha e cocaína) na esquizoftenia. Trata-se de estudo comparativo, casocontrole, de dois grupos de esquizoftênicos pareados para sexo e idade, que preencheram os critérios diagnósticos do DSMIV para esquizoftenia. O grupo caso é definido por esquizofrênicos que têm história de ter feito uso de álcool, pelo menos no último mês e/ ou história de ter feito uso de drogas (maconha e cocaína), pelo menos al...

  1. OGLAŠEVANJE NA FACEBOOKU

    OpenAIRE

    Renko, Katica

    2013-01-01

    V magistrskem delu smo se seznanili z oglaševanjem na Facebooku. S pregledom gradiva, ki nam je ponujeno, smo preverili pogoje, načine, oblike … oglaševanja, ki pa smo jih s pregledom situacije v praksi preverili in dopolnili. Ob zaključku dela lahko rečemo, da je oglaševanje preko FB enostavnejše, cenejše, dostopnejše, omogoča nam ažurnost in samo komunikacijo z naslovniki, ki so potencialni kupci naših ponudb. Množični mediji nam omogočajo mnogotero obliko oglaševanja. Izbrana oblika ponuja...

  2. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. A criterion for regular sequences

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    D P PATIL1, U STORCH2 and J ST ¨UCKRAD3. 1Department of Mathematics, Indian Institute of Science, Bangalore 560 012, India ... For general notations in com- mutative algebra we also refer to [1]. ... Note that every sequence is a strongly regular as well as regular sequence on the zero module. Further, it is clear that a ...

  4. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  5. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  6. Diesel Mechanics: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a diesel mechanics vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  7. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  8. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

    Science.gov (United States)

    This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

  9. Combinatorial representations of token sequences

    NARCIS (Netherlands)

    Elzinga, C.H.

    2005-01-01

    This paper presents new representations of token sequences, with and without associated quantities, in Euclidean space. The representations are free of assumptions about the nature of the sequences or the processes that generate them. Algorithms and applications from the domains of structured

  10. Multiplex Evaluation of Influenza Neutralizing Antibodies with Potential Applicability to In-Field Serological Studies

    National Research Council Canada - National Science Library

    Molesti, Eleonora; Wright, Edward; Terregino, Calogero; Rahman, Rafat; Cattoli, Giovanni; Temperton, Nigel J

    2014-01-01

    .... Retroviral pseudotypes bearing influenza haemagglutinin (HA) and neuraminidase (NA) envelope glycoproteins represent a flexible platform for sensitive, readily standardized influenza serological assays...

  11. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S.K.

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  12. HERKUL NA BRAČU

    OpenAIRE

    Cambi, Nenad

    2013-01-01

    U radu se raspravlja o reljefu Herkula uklesanom u litici pred ulazom u kamenolomu Rasohe. Figure uklesane u stijeni su kultni reljefi božanstva koje se časti u prirodnom okruženju. Herkulov reljef je kultna slika na ulazu u kamenolom pred kojim su se prinosile žrtve na kamenom žrtveniku. Također se raspravlja o natpisu sa žrtvenika posvećenom Herkulu iz kamenoloma Stražišće i donosi ispravak pogrešnog čitanja natpisa. Donose se i drugi nalazi iz kamenoloma Dalmcije koji ...

  13. Control of polymorphism in NaNbO(3) by hydrothermal synthesis.

    Science.gov (United States)

    Modeshia, Deena R; Darton, Richard J; Ashbrook, Sharon E; Walton, Richard I

    2009-01-07

    The metastable ilmenite polymorph of NaNbO(3), instead of the expected perovskite polymorph, may be prepared directly in one step under mild hydrothermal conditions by lowering pH and using close to stoichiometric amounts of metal precursors; in situ energy-dispersive X-ray diffraction shows that crystallisation occurs rapidly via a sequence of intermediate crystalline phases.

  14. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from......Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS......) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time...

  15. NA60 frees the quarks

    CERN Multimedia

    2003-01-01

    Fitted with new state-of-the-art silicon detectors, NA60 is prepared to study the phase transition from confined hadronic matter to a deconfined (free) quark-gluon plasma, a state of matter which probably existed an instant after the Big Bang.

  16. NA62: Hidden Sector Physics

    CERN Document Server

    Cesarotti, Carissa Joyce

    2016-01-01

    Modern experimental physics is often probing for new physics by either finding deviations from predictions on extremely precise measurements, or by looking for a new signal that cannot be explained with existing models. The NA62 experiment at CERN does the former by measuring the ultra-rare decay $K^+ \\rightarrow \\pi^+ \

  17. EMC anténa

    OpenAIRE

    Tenora, Jan

    2016-01-01

    Cílem této diplomové práce bylo navrhnout anténu pracující ve frekvenčním pásmu 30 MHz až 1 GHz. Navržená bikónická anténa vyžaduje ke správné funkci symetrické napájení, proto bylo dále nutné navrhnout vhodný symetrizační člen sestavený z diskrétních součástek. Navržená anténa byla také zkonstruována a měřením byl ověřen její činitel odrazu na vstupu, zisk a směrové charakteristiky. Tato diplomová práce dále obsahuje seznámení čtenáře s principy měření úrovně rušivých signálů v oblasti EMC p...

  18. Optimal sequence for Parrondo games

    Science.gov (United States)

    Dinis, Luis

    2008-02-01

    An algorithm based on backward induction is devised in order to compute the optimal sequence of games to be played in Parrondo games. The algorithm can be used to find the optimal sequence for any finite number of turns or in the steady state, showing that ABABB… is the sequence with the highest steady state average gain. The algorithm can also be generalized to find the optimal adaptive strategy in a multiplayer version of the games, where a finite number of players may choose, at every turn, the game the whole ensemble should play.

  19. Phylogenetic analysis of influenza A viruses (H3N2 circulating in Zhytomyr region during 2013–2014 epidemic season

    Directory of Open Access Journals (Sweden)

    Boyalska O. G.

    2015-06-01

    Full Text Available Aim. To perform phylogenetic analysis of the hemagglutinin (HA and neuraminidase (NA genes of influenza A(H3N2 viruses circulating in the Zhytomyr region during 2013–2014 epidemic season. To make comparison of the HA and NA genes sequences of the Zhytomyr region isolates with the HA and NA genes sequences of influenza viruses circulating in the world. Methods. Laboratory diagnosis was conducted by real-time polymerase chain reaction (RT-PCR. In this study the sequencing and phylogenetic analysis were carried out. Results. For the first time the genes of influenza A(H3N2 viruses isolated in the Zhytomyr region during 2013–2014 epidemic season, coding hemagglutinin and neuraminidase were compared with their orthologs. According to the results of this comparison the phylogenetic tree was constructed. Additionally, the amino acid substitutions of the influenza viruses circulating in Ukraine and worldwide were analyzed. Conclusions. The nucleotide sequences of the influenza A(H3N2 viruses genes HA and NA isolated in the Zhytomyr region were identified. Based on the nucleotide sequences of HA and NA we constructed the influenza virus phylogenetic tree demonstrating that the virus isolated in the Zhytomyr region was closely related to the Ukrainian isolate from Kharkov and in the world to the isolates from Germany, Romania, Italy.

  20. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  1. The Dynamics of DNA Sequencing.

    Science.gov (United States)

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  2. Photodesorption of Na atoms from rough Na surfaces

    DEFF Research Database (Denmark)

    Balzer, Frank; Gerlach, R.; Manson, J.R.

    1997-01-01

    We investigate the desorption of Na atoms from large Na clusters deposited on dielectric surfaces. High-resolution translational energy distributions of the desorbing atoms are determined by three independent methods, two-photon laser-induced fluorescence, as well as single-photon and resonance......-enhanced two-photon ionization techniques. Upon variation of surface temperature and for different substrates (mica vs lithium fluoride) clear non-Maxwellian time-of-flight distributions are observed with a cos θ angular dependence and most probable kinetic energies below that expected of atoms desorbing from...... atoms are scattered by surface vibrations. Recent experiments providing time constants for the decay of the optical excitations in the clusters support this model. The excellent agreement between experiment and theory indicates the importance of both absorption of the laser photons via direct excitation...

  3. Sequencing Centers Panel at SFAF

    Energy Technology Data Exchange (ETDEWEB)

    Schilkey, Faye [NCGR; Ali, Johar [OICR; Grafham, Darren [Wellcome Trust Sanger Institute; Muzny, Donna [Baylor College of Medicine; Fulton, Bob [Washington University; Fitzgerald, Mike [Broad Institute; Hostetler, Jessica [J. Craig Venter Institute; Daum, Chris [DOE Joint Genome Institute

    2010-06-02

    From left to right: Faye Schilkey of NCGR, Johar Ali of OICR, Darren Grafham of Wellcome Trust Sanger Institute, Donna Muzny of the Baylor College of Medicine, Bob Fulton of Washington University, Mike Fitzgerald of the Broad Institute, Jessica Hostetler of the J. Craig Venter Institute and Chris Daum of the DOE Joint Genome Institute discuss sequencing technologies, applications and pipelines on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  4. DNA sequences at a glance.

    Directory of Open Access Journals (Sweden)

    Armando J Pinho

    Full Text Available Data summarization and triage is one of the current top challenges in visual analytics. The goal is to let users visually inspect large data sets and examine or request data with particular characteristics. The need for summarization and visual analytics is also felt when dealing with digital representations of DNA sequences. Genomic data sets are growing rapidly, making their analysis increasingly more difficult, and raising the need for new, scalable tools. For example, being able to look at very large DNA sequences while immediately identifying potentially interesting regions would provide the biologist with a flexible exploratory and analytical tool. In this paper we present a new concept, the "information profile", which provides a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The computation of the information profiles is computationally tractable: we show that it can be done in time proportional to the length of the sequence. We also describe a tool to compute the information profiles of a given DNA sequence, and use the genome of the fission yeast Schizosaccharomyces pombe strain 972 h(- and five human chromosomes 22 for illustration. We show that information profiles are useful for detecting large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms. The comparison scale can be varied, allowing the users to zoom-in on specific details, or obtain a broad overview of a long segment. Software applications have been made available for non-commercial use at http://bioinformatics.ua.pt/software/dna-at-glance.

  5. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  6. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  7. Direct Detection of Unnatural DNA Nucleotides dNaM and d5SICS using the MspA Nanopore.

    Directory of Open Access Journals (Sweden)

    Jonathan M Craig

    Full Text Available Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules.

  8. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the

  9. Tree morphisms, transducers, and integer sequences

    OpenAIRE

    Sunic, Zoran

    2006-01-01

    The notion of transducer integer sequences is considered through a series of examples. By definition, transducer integer sequences are integer sequences produced, under a suitable interpretation, by finite automata encoding tree morphisms (length and prefix preserving transformations of words). Transducer integer sequences are related to the notion of self-similar groups and semigroups, as well as to the notion of automatic sequences.

  10. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  11. Solid-phase sequencing on the gas-phase sequencer.

    Science.gov (United States)

    Sarin, V K; Kim, Y; Fox, J L

    1986-05-01

    Automated Edman degradation has been successfully used for determining the primary structure of numerous peptides and proteins. Quantitative solid-phase Edman degradation has great potential use for amino acid sequence analysis of synthetic peptides assembled on resin support by the Merrifield procedure. We report here the combined use of a modified gas-phase sequencer program and our improved reversed-phase HPLC analysis for PTH-amino acids to carry out the sequence analysis on synthesized peptide resins. This approach is far more sensitive than using glass beads on the conventional solid-phase sequencer. The peptide was assembled on copoly (styrene-1% divinylbenzene) resin beads at an initial substitution of 0.54 mmol/g. On a routine basis, 10-15 resin beads are used, and a repetitive yield of 94% is obtained: as few as 4 beads can be successfully sequenced. The HPLC PTH-amino acid analysis is sensitive down to subpicomole quantities. This procedure offers a sensitive and rapid analytical tool for checking the purity of peptides as they are being assembled on solid support.

  12. Sequencing and comparative analysis of the gorilla MHC genomic sequence

    Science.gov (United States)

    Wilming, Laurens G.; Hart, Elizabeth A.; Coggill, Penny C.; Horton, Roger; Gilbert, James G. R.; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L.

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  13. Nax loci affect SOS1-like Na+/H+ exchanger expression and activity in wheat.

    Science.gov (United States)

    Zhu, Min; Shabala, Lana; Cuin, Tracey A; Huang, Xin; Zhou, Meixue; Munns, Rana; Shabala, Sergey

    2016-02-01

    Salinity stress tolerance in durum wheat is strongly associated with a plant's ability to control Na(+) delivery to the shoot. Two loci, termed Nax1 and Nax2, were recently identified as being critical for this process and the sodium transporters HKT1;4 and HKT1;5 were identified as the respective candidate genes. These transporters retrieve Na(+) from the xylem, thus limiting the rates of Na(+) transport from the root to the shoot. In this work, we show that the Nax loci also affect activity and expression levels of the SOS1-like Na(+)/H(+) exchanger in both root cortical and stelar tissues. Net Na(+) efflux measured in isolated steles from salt-treated plants, using the non-invasive ion flux measuring MIFE technique, decreased in the sequence: Tamaroi (parental line)>Nax1=Nax2>Nax1:Nax2 lines. This efflux was sensitive to amiloride (a known inhibitor of the Na(+)/H(+) exchanger) and was mirrored by net H(+) flux changes. TdSOS1 relative transcript levels were 6-10-fold lower in Nax lines compared with Tamaroi. Thus, it appears that Nax loci confer two highly complementary mechanisms, both of which contribute towards reducing the xylem Na(+) content. One enhances the retrieval of Na(+) back into the root stele via HKT1;4 or HKT1;5, whilst the other reduces the rate of Na(+) loading into the xylem via SOS1. It is suggested that such duality plays an important adaptive role with greater versatility for responding to a changing environment and controlling Na(+) delivery to the shoot. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  14. Economia na consulta de Endodontia

    OpenAIRE

    Pinto, Diogo Filipe Cardoso

    2016-01-01

    Introdução: Em Portugal a realidade actual, clínica e financeira do exercício da Medicina Dentária é bem distinta da do final do séc. XX devido à pletora de Médicos Dentistas e à baixa de honorários por acto Médico registada nos últimos anos. Objectivos: Este trabalho teve como objectivo perceber um pouco sobre os detalhes a ter em consideração aquando da abertura de uma clínica centrada na realização de tratamentos na área da Endodontia, e como publicitá-la de forma legal e apelativa. Pre...

  15. ULIČNA LUTKOVNA PREDSTAVA

    OpenAIRE

    Novak, Natalija

    2016-01-01

    V diplomski nalogi z naslovom Ulična lutkovna predstava je predstavljena priprava in izvedba gledališko-lutkovne predstave, ki smo jo izvedli v okviru programa Šole uličnega gledališča, pod vodstvom gledališča Ane Monro. V teoretičnem delu smo na podlagi strokovne literature predstavili dejavnost uličnega gledališča, njegove zvrsti, vlogo prostora in publike v uličnem gledališču ter kratko zgodovino le-tega. Predstavili smo tudi gledališče Ane Monro, ki je glavni organizator Šole uličnega ...

  16. Carne suína

    OpenAIRE

    Ortigara, Claudino

    2000-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico. A carne suína é a fonte de proteína animal mais consumida no mundo. No entanto, em muitos países e em especial no Brasil o consumo per capita é muito baixo. Como conseqüência disso, limita-se o crescimento do segmento produtivo e uma série de benefícios socioeconômicos que são gerados pela atividade suinocultura.Com esse trabalho, buscamos uma explicação para entender a resistência da população ao consum...

  17. NA64 Status Report 2017

    CERN Document Server

    Gninenko, Sergei

    2017-01-01

    The experiment NA64 is aimed at a direct search for invisible decays of sub-GeV dark photons (A′). The main goal in 2016 was to probe a region of the A′ parameter space, particularly interesting for the explanation of the muon g − 2 anomaly. The status and results from two NA64 runs in July and October 2016, obtained, respectively, with 2.75×109 and 4×1010 accumulated electron on target are reported. A feasibility study of the search for the X → e+e− decay of a new light X boson, which could explain a recently observed excess of e+e− events from excited 8Be transitions is also presented.

  18. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  19. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans. © 2013 Wiley Periodicals, Inc.

  20. Influence of NaOH solution on the synthesis of fly ash geopolymer

    Energy Technology Data Exchange (ETDEWEB)

    Ubolluk Rattanasak; Prinya Chindaprasirt [Burapha University, Chonburi (Thailand). Department of Chemistry

    2009-10-15

    A study was conducted on leaching of fly ash mixed with NaOH solution and on mixing procedure for preparing geopolymer. Leaching of SiO{sub 2} and Al{sub 2}O{sub 3} was investigated by mixing fly ash with NaOH solution for different time intervals and leachates were analyzed in terms of silica and alumina contents. To make geopolymer paste, separate mixing and normal mixing were used. For separate mixing, NaOH solution was mixed with fly ash for the first 10 min; subsequently sodium silicate solution was added into the mixture. For normal mixing, fly ash, sodium hydroxide and sodium silicate solution were incorporated and mixed at the same time. Geopolymers were cured at 65{sup o}C for 48 h. Microstructure of paste and compressive strength of mortar were investigated. Results revealed that solubility of fly ash depended on concentration of NaOH and duration of mixing with NaOH. For mixing procedure, separate mixing gave slightly better strength mortar than normal mixing. High strength geopolymer mortar up to 70.0 MPa was obtained when the mixture was formulated with 10 M NaOH and sodium silicate to NaOH ratio of 1.0, and the separate mixing sequence was used.

  1. NA

    OpenAIRE

    Gleeson, David A.

    1998-01-01

    With advancements in the fields of propulsion, aerodynamics, structures, materials and controls, the routine exploration of hypersonic, atmospheric flight has become a more feasible concept. Thus, there is a need for efficient and effective hypersonic configurations. Current studies in configuration efficiency and effectiveness seem to be concentrated in aircraft subsystem design, especially propulsion systems, rather than at the conceptual aircraft system design level. This thesis attempts t...

  2. Emerged HA and NA mutants of the pandemic influenza H1N1 viruses with increasing epidemiological significance in Taipei and Kaohsiung, Taiwan, 2009-10.

    Directory of Open Access Journals (Sweden)

    Chuan-Liang Kao

    Full Text Available The 2009 influenza pandemic provided an opportunity to observe dynamic changes of the hemagglutinin (HA and neuraminidase (NA of pH1N1 strains that spread in two metropolitan areas--Taipei and Kaohsiung. We observed cumulative increases of amino acid substitutions of both HA and NA that were higher in the post-peak than in the pre-peak period of the epidemic. About 14.94% and 3.44% of 174 isolates had one and two amino acids changes, respective, in the four antigenic sites. One unique adaptive mutation of HA2 (E374K was first detected three weeks before the epidemic peak. This mutation evolved through the epidemic, and finally emerged as the major circulated strain, with significantly higher frequency in the post-peak period than in the pre-peak (64.65% vs 9.28%, p<0.0001. E374K persisted until ten months post-nationwide vaccination without further antigenic changes (e.g. prior to the highest selective pressure. In public health measures, the epidemic peaked at seven weeks after oseltamivir treatment was initiated. The emerging E374K mutants spread before the first peak of school class suspension, extended their survival in high-density population areas before vaccination, dominated in the second wave of class suspension, and were fixed as herd immunity developed. The tempo-spatial spreading of E374K mutants was more concentrated during the post-peak (p = 0.000004 in seven districts with higher spatial clusters (p<0.001. This is the first study examining viral changes during the naïve phase of a pandemic of influenza through integrated virological/serological/clinical surveillance, tempo-spatial analysis, and intervention policies. The vaccination increased the percentage of E374K mutants (22.86% vs 72.34%, p<0.001 and significantly elevated the frequency of mutations in Sa antigenic site (2.36% vs 23.40%, p<0.001. Future pre-vaccination public health efforts should monitor amino acids of HA and NA of pandemic influenza viruses isolated at

  3. Genetics Home Reference: isolated Pierre Robin sequence

    Science.gov (United States)

    ... Conditions Isolated Pierre Robin sequence Isolated Pierre Robin sequence Printable PDF Open All Close All Enable Javascript ... view the expand/collapse boxes. Description Pierre Robin sequence is a set of abnormalities affecting the head ...

  4. Genetics Home Reference: isolated lissencephaly sequence

    Science.gov (United States)

    ... Home Health Conditions Isolated lissencephaly sequence Isolated lissencephaly sequence Printable PDF Open All Close All Enable Javascript ... view the expand/collapse boxes. Description Isolated lissencephaly sequence (ILS) is a condition that affects brain development ...

  5. A Demonstration of Automated DNA Sequencing.

    Science.gov (United States)

    Latourelle, Sandra; Seidel-Rogol, Bonnie

    1998-01-01

    Details a simulation that employs a paper-and-pencil model to demonstrate the principles behind automated DNA sequencing. Discusses the advantages of automated sequencing as well as the chemistry of automated DNA sequencing. (DDR)

  6. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  7. 23Na Magnetic Resonance Imaging of the Lower Leg of Acute Heart Failure Patients during Diuretic Treatment.

    Directory of Open Access Journals (Sweden)

    Matthias Hammon

    Full Text Available Na+ can be stored in muscle and skin without commensurate water accumulation. The aim of this study was to assess Na+ and H2O in muscle and skin with MRI in acute heart failure patients before and after diuretic treatment and in a healthy cohort.Nine patients (mean age 78 years; range 58-87 and nine age and gender-matched controls were studied. They underwent 23Na/1H-MRI at the calf with a custom-made knee coil. Patients were studied before and after diuretic therapy. 23Na-MRI gray-scale measurements of Na+-phantoms served to quantify Na+-concentrations. A fat-suppressed inversion recovery sequence was used to quantify H2O content.Plasma Na+-levels did not change during therapy. Mean Na+-concentrations in muscle and skin decreased after furosemide therapy (before therapy: 30.7±6.4 and 43.5±14.5 mmol/L; after therapy: 24.2±6.1 and 32.2±12.0 mmol/L; p˂0.05 and p˂0.01. Water content measurements did not differ significantly before and after furosemide therapy in muscle (p = 0.17 and only tended to be reduced in skin (p = 0.06. Na+-concentrations in calf muscle and skin of patients before and after diuretic therapy were significantly higher than in healthy subjects (18.3±2.5 and 21.1±2.3 mmol/L.23Na-MRI shows accumulation of Na+ in muscle and skin in patients with acute heart failure. Diuretic treatment can mobilize this Na+-deposition; however, contrary to expectations, water and Na+-mobilization are poorly correlated.

  8. Statistical properties of DNA sequences

    Science.gov (United States)

    Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

    1995-01-01

    We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

  9. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  10. Diffusion of propylene adsorbed in Na-Y and Na-ZSM5 zeolites ...

    Indian Academy of Sciences (India)

    Here we report the quasielastic neutron scattering and FTIR studies on the dynamics of propylene adsorbed in Na-Y and Na-ZSM5 zeolites. QENS data show that although the mechanism of translational motion of propylene is jump diffusion in both the cases of Na-Y and Na-ZSM5 zeolites, the diffusivity is affected by the ...

  11. Diffusion of propylene adsorbed in Na-Y and Na-ZSM5 zeolites ...

    Indian Academy of Sciences (India)

    Abstract. Here we report the quasielastic neutron scattering and FTIR studies on the dynamics of propylene adsorbed in Na-Y and Na-ZSM5 zeolites. QENS data show that although the mechanism of translational motion of propylene is jump diffusion in both the cases of Na-Y and Na-ZSM5 zeolites, the diffusivity is affected ...

  12. Na+,K+-ATPase Na+ affinity in rat skeletal muscle fiber types

    DEFF Research Database (Denmark)

    Kristensen, Michael; Juel, Carsten

    2010-01-01

    Previous studies in expression systems have found different ion activation of the Na(+)/K(+)-ATPase isozymes, which suggest that different muscles have different ion affinities. The rate of ATP hydrolysis was used to quantify Na(+),K(+)-ATPase activity, and the Na(+) affinity of Na(+),K(+)-ATPase...

  13. Dijagnostičko-terapijski pristup pacijentu sa sumnjom na alergiju na penicilin

    OpenAIRE

    Stanić Benić, Mirjana; Vlahović-Palčvevski, Vera

    2016-01-01

    Iako se ne zna točna učestalost alergije na lijekove, pripisuje joj se oko 1/10 svih neželjenih reakcija na lijekove. Neželjene reakcije na penicilin javljaju se u 0,7 – 10 % ljudi koji primaju penicilin. Stvarna učestalost alergije na penicilin još je manja, budući da su se u prošlosti mnoge nealergijske nuspojave antibiotika pripisivale alergiji. U pacijenata kod kojih postoji sumnja na alergiju na penicilin važno je utvrditi alergološki status. Nepotrebno izbjegavanje upotrebe penicilina, ...

  14. New and advanced sequences for 23Na NMR imaging, implemented on a 7 T system

    DEFF Research Database (Denmark)

    Laustsen, Christoffer

    2009-01-01

    Introduction   Ischemia occurs when there is little or no blood flow to a given tissue. With the loss of essential oxygen and nutrients, essential function ceases and eventually the cells die. One of the initial functions that breaks down is the active transport of ions and water across the cell...... sodium is excited then it is possible to follow the sodium gradient over time and to determine the cell state earlier than today.   Methods   1. Implementation of multi quantum coherence techniques for sodium pool quantification   2. Development and implementation of the Non Negative Least Square (NNLS...

  15. Crowdsourcing: impactos na performance na venda de produtos

    OpenAIRE

    Alves, Milton Ruiz Rodrigues

    2015-01-01

    Vivemos num momento em que as expectativas de pensadores como Lévy (1998), se concretizaram. O consumidor mudou, passou a exigir um diálogo entre a empresa e a sociedade. Esse novo cenário cobrou da tecnologia formas de aperfeiçoar e agilizar este processo de comunicação, plataformas baseadas na internet que propiciem e incentivam a troca de informações. Nesta esfera surgiu o crowdsourcing, com a disponibilização do capital intelectual das massas, que acabou por mudar a form...

  16. As atitudes do terapeuta na teoria centrada na pessoa

    OpenAIRE

    Carreteiro, Tereza Cristina Othenio Cordeiro

    1981-01-01

    Este trabalho procede a um exame arqueológico das atitudes terapêuticas ao longo do desenvolvimento da teoria Rogeriana. Estuda-se o processo evolutivo que compõe o referido corpo teórico. Inicialmente, é feita uma breve apresentação de Carl Rogers, precursor da Abordagem Centrada na Pessoa. São discorridos aspectos pessoais e profissionais do autor assim como suas principais contribuições no campo da Psicologia clínica. A teoria é decomposta em três fases principais: pré história da empat...

  17. Priklop perifernih naprav na Raspberry Pi

    OpenAIRE

    Fabčič, Simon

    2015-01-01

    Moje diplomsko delo obravnava povezovanje perifernih naprav na Raspberry Pi. Najprej je predstavljena oprema, ki sem jo potreboval pri pisanju. Kot glavno strojno opremo sem uporabil enoploščni računalnik Raspberry Pi (model B) in nanj namestil operacijski sistem Raspbian. Na njem je bilo že pred naloženo razvojno okolje za programski jezik Python, ki sem ga tudi uporabljal. Nato sem prikazal, kako na Raspberry Pi na različne načine in prek raznih protokolov povežemo periferne naprave ter dig...

  18. Upravnopravna regulacija prava na pristup informacijama

    OpenAIRE

    Basta, Đurđica

    2016-01-01

    Pravo na pristup informacijama čini jedan od ključnih elemenata informacijskoga upravnog prava. U većini zemalja, uključujući Hrvatsku, pravo na pristup informacijama javnog sektora relativno je novo pravo. Uz Ustav RH kao temeljni dokument, od ožujka 2013. na snazi je novi, drugi hrvatski Zakon o pravu na pristup informacijama. Kritike na račun pravnog okvira kao i institucionalne podrške njegovoj provedbi doveli su do izmjena Zakona 2010. odnosno 2011., a 2013. i do donošenja...

  19. Sequence alignment with tandem duplication

    Energy Technology Data Exchange (ETDEWEB)

    Benson, G. [Mount Sinai School of Medicine, New York, NY (United States)

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  20. Twenty years of bacterial genome sequencing.

    Science.gov (United States)

    Loman, Nicholas J; Pallen, Mark J

    2015-12-01

    Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.

  1. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  2. Operator Ideal of Cesaro Type Sequence Spaces Involving Lacunary Sequence

    Directory of Open Access Journals (Sweden)

    Awad A. Bakery

    2014-01-01

    Full Text Available The aim of this paper is to give the sufficient conditions on the sequence space Cesθ,p defined in Lim (1977 such that the class of all bounded linear operators between any arbitrary Banach spaces with nth approximation numbers of the bounded linear operators in Cesθ,p form an operator ideal.

  3. Variability in Measures of Exhaled Breath Na, Influence of pulmonary Blood Flow and salivary Na

    Directory of Open Access Journals (Sweden)

    Courtney M. Wheatley

    2010-04-01

    Full Text Available The assessment of inflammatory markers and ions in exhaled breath condensate (EBC is being utilized more frequently in diseases such as asthma and cystic fibrosis with marked variability in EBC measures, including those of exhaled Na + . We sought to determine if variability in exhaled Na + was due to differences in pulmonary blood flow (PBF or Na + in the mouth (salivary Na + . We measured exhaled Na + three times with coinciding sampling of salivary Na + and assessment of PBF (using acetylene rebreathing in 13 healthy subjects (54% female, age = 27 ± 7 yrs., ht. = 172 ± 10 cm, wt. = 70 ± 21 kg, BMI = 22 ± 7 kg/m 2 mean ± SD. Exhaled Na + averaged 2.7 ± 1.2 mmol/l, and salivary Na + averaged 5.51 ± 4.58 mmol/l. The coefficients of variation across all three measures in all 13 subjects averaged 30% for exhaled Na + and 83% for salivary Na + , within subjects the variability across the three measures averaged 30% for exhaled Na + and 38% for salivary Na + . Across all three measures in all 13 subjects the relationship between PBF and exhaled Na + averaged 0.027 ( P = 0.87, and the relationship between salivary Na + and exhaled Na + concentrations averaged 0.59 ( P = 0.001. Also, we sought to determine the relationship between exhaled Na + and serum Na + in an addition 20 subjects. There was a moderate and significant relationship between serum Na + and exhaled Na + (r = 0.37, P = 0.04. These findings suggest there that the variability in exhaled Na + is caused, at least in part, by droplet formation from within the mouth as turbulent air passes through and that there is a flux of ions from the pulmonary blood into the airways.

  4. Istraživanje uticaja nekih parametara na osetljivost eksplozivnih materija na toplotni impuls

    OpenAIRE

    Jeremić Radun

    2002-01-01

    Ispitivana je osetljivost nekoliko vrsta eksplozivnih materija na toplotni impuls merenjem vremena zadrške u zavisnosti od temperature. Na osnovu eksperimentalnih rezultata određene su vrednosti energije aktivacije i predeksponencijalni faktori u jednačini Semjonova. Istraživan je i uticaj mase ispitivanog uzorka, granulacije i veličine kristala eksploziva na osetljivost na toplotni impuls. Pokazano je da ovi parametri imaju značajan uticaj na osetljivost eksplozivnih materija, pa je neophodn...

  5. Exome sequencing for syndrome diagnostics

    DEFF Research Database (Denmark)

    Østergaard, Elsebet; Risom, Lotte; Ek, Jakob

    2017-01-01

    The majority of rare congenital disorders and syndromes have a genetic cause, but the diagnostic rate using standard workup is only around 50%. Whole exome and whole genome sequencing methods have improved the genetic diagnosis of syndromes during the latest few years. This article is a presentat......The majority of rare congenital disorders and syndromes have a genetic cause, but the diagnostic rate using standard workup is only around 50%. Whole exome and whole genome sequencing methods have improved the genetic diagnosis of syndromes during the latest few years. This article...

  6. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  7. Comparison of two commercial broadrange PCR and sequencing assays for identification of bacteria in culture-negative clinical samples

    DEFF Research Database (Denmark)

    Stavnsbjerg, Camilla; Frimodt-Moller, Niels; Moser, Claus Ernst

    2017-01-01

    Background Culturing has long been the gold standard for detecting aetiologic agents in bacterial infections. In some cases, however, culturing fails to detect the infection. To further investigate culture-negative samples, amplification and subsequent sequencing of the 16S rRNA gene is often...... in a real-time PCR and sequenced. Results 22 of 76 samples (28.9%) were positive for bacteria with the UMD SelectNA, which was significantly more (p = 0.0055) than the MicroSeq ID where 11 of 76 samples (14.5%) were positive. The UMD SelectNA assay identified more relevant bacterial pathogens than the Micro...

  8. Silicene for Na-ion battery applications

    KAUST Repository

    Zhu, Jiajie

    2016-08-19

    Na-ion batteries are promising candidates to replace Li-ion batteries in large scale applications because of the advantages in natural abundance and cost of Na. Silicene has potential as the anode in Li-ion batteries but so far has not received attention with respect to Na-ion batteries. In this context, freestanding silicene, a graphene-silicene-graphene heterostructure, and a graphene-silicene superlattice are investigated for possible application in Na-ion batteries, using first-principles calculations. The calculated Na capacities of 954mAh/g for freestanding silicene and 730mAh/g for the graphenesilicene superlattice (10% biaxial tensile strain) are highly competitive and potentials of >0.3 V against the Na/Na potential exceed the corresponding value of graphite. In addition, the diffusion barriers are predicted to be <0.3 eV.

  9. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    Energy Technology Data Exchange (ETDEWEB)

    Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

    2009-05-20

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

    Full Text Available Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb and 7 (1.1 Mb from an individual from the International HapMap Project (NA12872. We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

  11. Sequences.

    Science.gov (United States)

    Cwirko-Godycki, Jerzy

    This collection of activities resulted from a visit by the Polish author to the Teachers' Center Project at Southern Illinois University at Edwardsville in 1980. The set of 30 activity sheets involve blocks with various types of patterns depicted. Directions for using each sheet and questions to be answered are then given. Elementary school…

  12. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates.

    Science.gov (United States)

    Thabet, Rahma; Rouault, J-D; Ayadi, Habib; Leignel, Vincent

    2016-01-01

    The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. VPLIV VODENJA NA RAZVOJ ORGANIZACIJE

    OpenAIRE

    Rauš, Ivo

    2010-01-01

    Ključno vlogo pri razvoju človeških potencialov in sproščanju posameznikovih notranjih zmožnosti imajo njihovi neposredni vodje. Le ti naj bi skrbeli za ustvarjanje takega delovnega okolja, ki bo spodbujalo ustvarjalne dosežke, inovativnost, izvirnost idej, pripadnost in timsko sodelovanje. Vodenje zavzema prvo mesto na lestvici ključnih managerskih izzivov sedanjosti in srednjeročne prihodnosti, o čemer govorijo tudi številne zadnje raziskave ameriških in evropskih strokovnjakov za razvoj...

  14. Chiaroscuro: a luz na sombra

    OpenAIRE

    Flamínio Jallageas de Lima Cardoso

    2015-01-01

    Este ensaio objetiva refletir sobre minha série fotográfica Chiaroscuro, na qual trabalho constrastes entre luz e sombra e as consequentes representações de vazio e memória. Para tanto, elejo os teóricos da antropologia da imagem Jacques Rancière, Georges Didi-Huberman, Victor Stoichita e Hans Belting como meus interlocutores. Uma vez que um dos propósitos deste trabalho abrange observar possíveis inter-relações entre a série e alguns artistas contemporâneos, estabeleço reflexões acerca da pr...

  15. Na alvorada de um sport

    OpenAIRE

    Sartori, Carina

    2013-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas, Programa de Pós-graduação em História, Florianópolis, 2013 Em Florianópolis, a primeira Sociedade de Regatas organizada, meados do século XIX, contaria com a participação dos Coronéis da Marinha e da Escola de Menores e Marinheiros da Canhoneira. Na virada do século, a fundação do Clube 29 de Abril permitiria que as atividades relacionadas ao Remo fossem oferecidas a todos que se associ...

  16. A virtude na psicologia positiva

    OpenAIRE

    Cardoso, José Augusto Rento

    2014-01-01

    O presente trabalho de psicologia teórica trata-se de um estudo crítico do conceito de virtude na Psicologia Positiva. Definida como movimento por alguns e como um novo campo por outros, a Psicologia Positiva reúne sob um mesmo “guarda-chuva” diversos estudos, passados e presentes, de várias áreas da Psicologia, como a Psicologia da Personalidade, a Psicologia Social, a Psicologia do Desenvolvimento e a Psicologia Moral. No presente trabalho, a mesma é compreendida como uma perspectiva e um m...

  17. Tortura : na atividade policial investigativa

    OpenAIRE

    Giudice de Argollo, Helvécio

    2003-01-01

    Este trabalho versa sobre o fenômeno social da tortura; do seu sentido polissêmico, do seu aspecto multifacetado e dos desafios que engendra, notadamente da sua perseverança nas sociedades, a despeito do banimento pelos textos legais, tanto no plano do direito transnacional quanto na maioria dos ordenamentos jurídicos do mundo ocidental. A tortura tem uma história que se confunde com a história da própria humanidade e, nesse sentido, o seu estudo desafia um périplo histórico...

  18. The NA62 RICH detector

    Energy Technology Data Exchange (ETDEWEB)

    Lenti, Massimo, E-mail: lenti@fi.infn.i [Sezione dell' INFN di Firenze, I-50019 Sesto Fiorentino (Italy)

    2011-05-21

    The NA62 RICH must separate charged pions from muons in a 15-35 GeV/c momentum range. The detector will have a 17 m long, 4 m wide cylindrical vessel, filled with neon at an atmospheric pressure. A mosaic of 20 mirrors, with 17 m focal length will be placed at the downstream end of the vessel while 2000 single anode photomultipliers will be placed at the upstream part. Two test beams were held at CERN in 2007 and 2009 with a RICH prototype. A muon suppression factor greater than 100 was validated.

  19. New results from NA49

    CERN Document Server

    Afanasiev, S V; Bächler, J; Barna, D; Barnby, L S; Bartke, Jerzy; Barton, R A; Behler, M; Betev, L; Bialkowska, H; Billmeier, A; Blume, C; Blyth, C O; Boimska, B; Botje, M; Bracinik, J; Brady, F P; Bramm, R; Brun, R; Buncic, P; Carr, L; Cebra, D; Cerny, V; Cooper, G E; Cramer, J G; Csató, P; Dinkelaker, P; Eckardt, V; Eckhardt, F; Ferenc, D; Filip, P; Fischer, H G; Foder, Z; Foka, P Y; Freund, P; Friese, V; Gál, J; Ganz, R E; Gazdzicki, M; Georgopoulos, G; Gladysz-Dziadus, E; Harris, J W; Hegyi, S; Höhne, C; Igo, G; Jacobs, P; Jones, P G; Kadija, K; Kolesnikov, V I; Kollegger, T; Kowalski, M; Kraus, I; Kreps, M; Lasiuk, B; Van Leeuwen, M; Lévai, Peter; Malakhov, A I; Margetis, S; Markert, C; Mayes, B W; Melkumov, G L; Mischke, A; Molnár, J; Nelson, J M; Odyniec, Grazyna Janina; Oldenburg, M; Pálla, G; Panagiotou, A D; Perl, K; Petridis, A; Pikna, M; Pinsky, L; Poskanzer, A M; Prindle, D J; Pühlhofer, F; Putschke, J; Reid, J G; Renfordt, A; Retyk, W; Ritter, H G; Röhrich, D; Roland, C; Roland, G; Rybicki, A; Sammer, T; Sann, H; Schäfer, E; Schmitz, N; Seyboth, P; Siklér, F; Sitár, B; Skrzypczak, E; Snellings, R; Squier, G T A; Stock, Reinhard; Ströbele, H; Susa, T; Szentpétery, I; Sziklai, J; Toy, M; Trainor, T A; Trentalange, S; Ullrich, T S; Varga, D; Vassiliou, Maria; Veres, G I; Vesztergombi, G; Voloshin, S A; Vranic, D; Wang, F; Weerasundara, D D; Wenig, S; Wetzler, A; Whitten, C; Xu, N; Yates, T A; Koo, I K; Zaranek, J; Zimányi, J

    2002-01-01

    Recent results of the NA49 experiment are presented. These cover first results on pion and kaon production, HBT, and charge fluctuations from Pb+Pb reactions at 40 AGeV and their comparison to 158 AGeV beam energy. Furthermore a study on baryon number transfer in p+p, centrality selected p+Pb and Pb+Pb collisions at 158 AGeV and new results on the system size dependence of kaon yields, including C+C and Si+Si data, are presented. Additionally, a first result on Lambda Lambda correlations is shown. (11 refs).

  20. Characteristics of NaNO3-Promoted CdO as a Midtemperature CO2 Absorbent.

    Science.gov (United States)

    Kim, Kang-Yeong; Kwak, Jin-Su; An, Young-In; Oh, Kyung-Ryul; Kwon, Young-Uk

    2017-06-28

    In this study, we explored the reaction system CdO(s) + CO2(g) ⇄ CdCO3(s) as a model system for CO2 capture agent in the intermediate temperature range of 300-400 °C. While pure CdO does not react with CO2 at all up to 500 °C, CdO mixed with an appropriate amount of NaNO3 (optimal molar ratio NaNO3/CdO = 0.14) greatly enhances the conversion of CdO into CdCO3 up to ∼80% (5.68 mmol/g). These NaNO3-promoted CdO absorbents can undergo many cycles of absorption and desorption by temperature swing between 300 and 370 °C under a 100% CO2 condition. Details of how NaNO3 promotes the CO2 absorption of CdO have been delineated through various techniques using thermogravimetry, coupled with X-ray diffraction and electron microscopy. On the basis of the observed data, we propose a mechanism of CO2 absorption and desorption of NaNO3-promoted CdO. The absorption proceeds through a sequence of events of CO2 adsorption on the CdO surface covered by NaNO3, dissolution of so-formed CdCO3, and precipitation of CdCO3 particles in the NaNO3 medium. The desorption occurs through the decomposition of CdCO3 in the dissolved state in the NaNO3 medium where CdO nanoparticles are formed dispersed in the NaNO3 medium. The CdO nanoparticles are aggregated into micrometer-large particles with smooth surfaces and regular shapes.

  1. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda.

    Directory of Open Access Journals (Sweden)

    Chao He

    Full Text Available Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX, Na+/Ca2+/K+ exchangers (NCKX, and Ca2+/Cation exchangers (CCX. In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics.

  2. Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda.

    Science.gov (United States)

    He, Chao; O'Halloran, Damien M

    2014-01-01

    Na+/Ca2+ exchangers are low affinity, high capacity transporters that rapidly transport calcium at the plasma membrane, mitochondrion, endoplasmic (and sarcoplasmic) reticulum, and the nucleus. Na+/Ca2+ exchangers are widely expressed in diverse cell types where they contribute homeostatic balance to calcium levels. In animals, Na+/Ca2+ exchangers are divided into three groups based upon stoichiometry: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers (NCKX), and Ca2+/Cation exchangers (CCX). In mammals there are three NCX genes, five NCKX genes and one CCX (NCLX) gene. The genome of the nematode Caenorhabditis elegans contains ten Na+/Ca2+ exchanger genes: three NCX; five CCX; and two NCKX genes. Here we set out to characterize structural and taxonomic specializations within the family of Na+/Ca2+ exchangers across the phylum Nematoda. In this analysis we identify Na+/Ca2+ exchanger genes from twelve species of nematodes and reconstruct their phylogenetic and evolutionary relationships. The most notable feature of the resulting phylogenies was the heterogeneous evolution observed within exchanger subtypes. Specifically, in the case of the CCX exchangers we did not detect members of this class in three Clade III nematodes. Within the Caenorhabditis and Pristionchus lineages we identify between three and five CCX representatives, whereas in other Clade V and also Clade IV nematode taxa we only observed a single CCX gene in each species, and in the Clade III nematode taxa that we sampled we identify NCX and NCKX encoding genes but no evidence of CCX representatives using our mining approach. We also provided re-annotation for predicted CCX gene structures from Heterorhabditis bacteriophora and Caenorhabditis japonica by RT-PCR and sequencing. Together, these findings reveal a complex picture of Na+/Ca2+ transporters in nematodes that suggest an incongruent evolutionary history of proteins that provide central control of calcium dynamics.

  3. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  4. 3 Tesla (23)Na magnetic resonance imaging during aerobic and anaerobic exercise.

    Science.gov (United States)

    Hammon, Matthias; Grossmann, Susan; Linz, Peter; Kopp, Christoph; Dahlmann, Anke; Janka, Rolf; Cavallaro, Alexander; Uder, Michael; Titze, Jens

    2015-09-01

    The aim of the work described here was to determine the feasibility of monitoring Na(+) concentration and distribution in muscle/skin during aerobic/anaerobic exercise with (23)Na magnetic resonance imaging (MRI). The Na(+) concentration and water content of muscle/skin of the left lower leg of six healthy subjects (mean age, 26 years; range, 22-30 years; three men and three women) were assessed before and after aerobic/anaerobic cycle ergometry and during recovery with 3-T (23)Na/(1)H MRI. (23)Na MRI was performed with a custom-made knee coil. A gradient echo sequence with an acquisition time of 3.25 minutes, echo time of 2.07 ms, repetition time of 100 ms, and spatial resolution of 3 × 3 × 30 mm(3) was applied. Phantoms with increasing sodium concentration served for quantification via linear extrapolation. Blood values were determined by blood gas analysis. The concentration of Na(+) significantly increased during anaerobic exercise in all muscle compartments except the medial gastrocnemius muscle, whereas no significant change was observed in most muscle compartments during aerobic exercise (only the soleus muscle exhibited a significant increase in Na(+) concentration during aerobic exercise: 1.6 ± 1.5 mmol/kg, 4.5%, P = .046). During anaerobic exercise, the mean Na(+) concentration of the triceps surae and the whole leg increased by 9.0% (3.1 ± 2.1 mmol/kg, P = .016) and 6.5% (2.2 ± 1.3 mmol/kg, P anaerobic exercise. Na(+) concentration significantly decreased during recovery after anaerobic and aerobic exercise in all muscle compartments except the soleus. The Na(+) concentration of the skin did not significantly change during anaerobic/aerobic exercise. Sodium(23) MRI allows reliable and noninvasive visualization and quantification of Na(+) concentration and distribution in muscle and skin during exercise. (23)Na MRI can be used to gain new insights into Na(+) homeostasis, presumably leading to better comprehension of pathophysiology. Copyright © 2015

  5. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Jonathan Z Li

    Full Text Available The impact of raltegravir-resistant HIV-1 minority variants (MVs on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs.A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser.Illumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001. Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454.In participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.

  6. O ATLETISMO NA PERSPECTIVA EDUCACIONAL

    Directory of Open Access Journals (Sweden)

    Leandro Araujo de Sousa

    2017-06-01

    Full Text Available A educação física escolar deve proporcionar experiências aos alunos para o seu desenvolvimento integral. As aulas muitas vezes são reduzidas ao ensino de esportes tradicionais, o que limita o repertório de movimentos dos alunos. Dessa forma o presente estudo de revisão objetiva problematizar o atletismo no ambiente escolar e propor possibilidades pedagógicas para seu ensino. Nesta pesquisa propomos tratar o ensino do atletismo na escola, caracterizando-o pelo seu repertório de movimentos que são naturais ao ser humano, como correr, saltar e lançar, o que possibilita maior praticidade em sua aplicação pedagógica, porém essas possibilidades não são consideradas no ambiente educacional. Diante dos dados encontrados, sugerimos que esse esporte seja abordado de forma multidimensional no ambiente escolar contextualizando-o à visão de algumas correntes teóricas. Nessa perspectiva do esporte educacional, o atletismo pode, assim como deve ser trabalhado nas aulas de educação física como instrumento pedagógico de ensino e auxiliar na formação do aluno de forma global.

  7. Identidades Homossexuais na Territorialidade Tradicionalista

    Directory of Open Access Journals (Sweden)

    Edipo Djavan dos Reis Göergen

    2015-12-01

    Full Text Available Este artigo apresenta o debate teórico que sustenta a pesquisa de mestrado desenvolvida pelo autor. Tendo por base suas vivências em contextos de tradicionalismo gaúcho, o autor deste trabalho tem percebido a grande quantidade de homossexuais, ou indivíduos que se auto-denominam não-heterossexuais, integrando as atividades artísticas do Movimento Tradicionalista Gaúcho, ou a territorialidade tradicionalista. Interessado em investigar tal fenômeno, o autor tem desenvolvido o projeto de pesquisa “Os Espaços Paradoxais de Relações Homoeróticas na Territorialidade Tradicionalista”, sob orientação do prof. Dr. Benhur Pinós da Costa, no Programa de Pós-Graduação em Geografia (UFSM. Para que essa pesquisa seja realizada, levam-se em conta as relações de gênero e de sexualidade que estão envolvidas no tema. Dessa forma, por ainda se tratarem de temáticas tidas como insignificantes na sociedade em geral e marginalizadas no campo científico, para que o presente trabalho fosse empreendido, buscou-se amparo teórico nas geografias feministas e queer, segmentos contemporâneos da ciência geográfica.

  8. Multiple Strand Sequencing Using the Elaboration Theory.

    Science.gov (United States)

    Beissner, Katherine; Reigeluth, Charles M.

    This study examined the sequencing of instruction in a course in physical therapy. In the first phase, a procedural elaboration sequence was designed using the Simplifying Assumptions Method. In the second phase, a prescriptive-theoretical elaboration sequence independent of the procedural sequence was designed. A descriptive-theoretical…

  9. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

  10. Micotoxinas e Micotoxicoses na Avicultura

    Directory of Open Access Journals (Sweden)

    Santurio JM

    2000-01-01

    Full Text Available Esta revisão tem como objetivo principal mostrar, baseado em dezenas de pesquisas realizadas, os efeitos tóxicos das micotoxinas aflatoxinas, tricotecenos, zealenona e fumonisinas sobre o desempenho das aves. O descobrimento das propriedades hepatotóxicas e hepatocarcinogênicas de algumas linhagens de Aspergillus flavus e A. parasiticus em perus, na Inglaterra, no início da década de 1960, seguida pela elucidação da estrutura de seus metabólitos tóxicos, as aflatoxinas, deu novo enfoque e prioridade para a pesquisa sobre micotoxinas. Análises de aflatoxinas realizadas no Laboratório de Análises Micotoxicológicas (LAMIC da Universidade Fedaral de Santa Maria, entre os anos de 1986 e janeiro de 2000, em 15.600 amostras de alimentos destinados principalmente ao consumo animal, demonstram que no milho analisado, 41,9% das amostras estavam contaminadas por aflatoxinas. Em surtos de aflatoxicose no campo, uma das características mais marcantes é a má absorção que se manifesta como partículas de ração mal digeridas na excreta das aves. Também observa-se, em frangos e poedeiras que recebem AFL, extrema palidez das mucosas e pernas. Dietas deficientes em riboflavina ou colecalciferol (vit. D tornaram frangos sensíveis, nos índices de desenvolvimento corporal, a concentrações muito baixas de AFL. O efeito aflatoxina nos frangos é maior na fase inicial de crescimento, ou seja, quando as aves ingeriram aflatoxina nos primeiros 21 dias de vida, e quanto maior o nível de stress do lote, menor a quantidade de AFL para afetar negativamente seu desempenho, seja na produção de carne ou de ovos. As principais micotoxinas do grupo dos tricotecenos são: toxina T-2; deoxynivalenol (DON; diacetoxyscirpenol (DAS, todas produzidas através de diversas espécies de fungos do gênero Fusarium. Além dos tricotecenos, o fusarium também pode produzir zearalenona e fumonisinas. Dessas fusarium-toxinas, somente toxina T-2 gera patologias s

  11. Evaluation of FcγRIIIB-NA1/NA2 Polymorphism in Visceral Leishmaniasis.

    Science.gov (United States)

    Abasi, Mohammad; Lotfi, Pegah; Bazmani, Ahad; Matini, Mohamad; Hajilooi, Mehrdad

    2014-04-01

    Several lines of evidence demonstrating that innate and adaptive immunity play important roles in the defense against visceral leishmaniasis (VL). A polymorphism within the FcγRIIIB gene can lead to the expression of three variants of NA1, NA2, and the combined one (NA1/NA2) which alters affinity of IgG to its receptor. The main aim of this study was to evaluate the FcγRIIIB-NA1/NA2 polymorphism in the FcγRIIIB gene of VL patients in comparison to healthy controls. In this cross-sectional study, three groups; 54 seropositive patients with clinical presentation of VL (group 1), 104 seropositive patients without clinical presentation (group 2), and 104 healthy controls (group 3) were evaluated with respect to the FcγRIIIB-NA1/NA2 polymorphism using a PCR-SSP method. The titration of anti-leishmania antibodies was analyzed using an immunoflorescence technique. Our results indicated that polymorphisms within the FcγRIIIB gene (that lead to the expression of the NA1/NA2 isoforms) are significantly associated with VL. The results demonstrated that the genotype heterozygotic for FcγRIIIB-NA1/NA2 expression was significantly increased in VL patients, group 1 when compared to groups 2 and 3. Conversely, there is a decrease in homozygous NA1 and NA2 genotypes in VL patients; however, the overall frequency of NA1 and NA2 alleles appear similar across the three cohorts examined. According to our results, it is likely that the increased frequency of the FcγRIIIB-NA1/NA2 genotype is associated with impaired immune responses against VL and its subsequent clearance from the patient.

  12. Growth of binary organic NLO crystals: m.NA-p.NA and m.NA-CNA system

    Science.gov (United States)

    Singh, N. B.; Henningsen, T.; Hopkins, R. H.; Mazelsky, R.

    1993-01-01

    Experiments were carried out to grow 3.Nitroaniline (m.NA) crystals doped with 4.Nitroaniline (p.NA) and 2.chloro 4.Nitroaniline (CNA). The measured undercooling for m.NA, p.NA, and CNA were 0.21 tm K, 0.23 tm K, and 0.35 tm K respectively, where tm represents the melting temperature of the pure component. Because of the crystals' large heat of fusion and large undercooling, it was not possible to grow good quality crystals with low thermal gradients. In the conventional two-zone Bridgman furnace we had to raise the temperature of the hot zone above the decomposition temperature of CNA, p.NA, and m.NA to achieve the desired thermal gradient. To avoid decomposition, we used an unconventional Bridgman furnace. Two immiscible liquids, silicone oil and ethylene glycol, were used to build a special two-zone Bridgman furnace. A temperature gradient of 18 K/cm was achieved without exceeding the decomposition temperature of the crystal. The binary crystals, m.NA-p.NA and m.NA-CNA, were grown in centimeter size in this furnace. X-ray and optical characterization showed good optical quality.

  13. Fotografia na Imprensa: conflitos na câmara escura

    Directory of Open Access Journals (Sweden)

    José Lúcio da Silva Menezes

    2014-07-01

    Full Text Available Este artigo recupera o teor ideológico do discurso que a Revista Veja elaborou sobre a classe trabalhadora que emergiu no cenário brasileiro, no final da década de 1970. O destaque dado aos trabalhadores como temática central resgatada, deve-se aos movimentos grevistas por eles encetados, após anos de ocultamento de sua resistência sob a repressão da ditadura civil-militar (1964-1985. Com a rebeldia operária, as matérias a respeito deste grupo, na Revista,foram se tornando mais constantes e visíveis, pois já não era mais possível, para a Revista Veja, ignorar a existência da classe operária que, com a força insurgente das greves, ocupava as ruas do Brasil.

  14. Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

    Science.gov (United States)

    Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pwater microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

  15. Relative contributions of Na+/H+ exchange and Na+/HCO3- cotransport to ischemic Na-i(+) overload in isolated rat hearts

    NARCIS (Netherlands)

    Ten Hove, M; Nederhoff, MGJ; Van Echteld, CJA

    The Na+/H+ exchanger (NHE) and/or the Na+/HCO3- cotransporter (NBC) were blocked during ischemia in isolated rat hearts. Intracellular Na+ concentration ([Na+](i)), intracellular pH (pH(i)), and energy-related phosphates were measured by using simultaneous Na-23 and P-31 NMR spectroscopy. Hearts

  16. Structural phase transition and opto-electronic properties of NaZnAs

    Energy Technology Data Exchange (ETDEWEB)

    Djied, A.; Seddik, T.; Merabiha, O. [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 (Algeria); Murtaza, G. [Materials Modeling Lab, Department of Physics, Islamia College University, Peshawar (Pakistan); Khenata, R. [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 (Algeria); Ahmed, R., E-mail: rashidahmed@utm.my [Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor (Malaysia); Bin-Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Uğur, Ş. [Department of Physics, Faculty of Sciences, Gazi University, 06500 Teknikokullar, Ankara (Turkey); Bouhemadou, A. [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University Setif 1, 19000 Setif (Algeria)

    2015-02-15

    Highlights: • First competent characterizations of NaZnAs at the level of FP-LAPW+lo. • NaZnAs, a potential alternative candidate to III-V for photovoltaic applications. • NaZnAs, a cheaper and abundantly available direct band gap semiconductor. • Potential material for solar radiation absorber from infrared to ultraviolet. - Abstract: In this study, we predict the structural phase transitions as well as opto-electronic properties of the filled-tetrahedral (Nowotny-Juza) NaZnAs compound. Calculations employ the full potential (FP) linearized augmented plane wave (LAPW) plus local orbitals (lo) scheme. The exchange-correlation potential is treated within the generalized gradient approximation of Perdew-Burke and Ernzerhof (GGA-PBE). In addition, Tran and Blaha (TB) modified Becke-Johnson (mBJ) potential is also used to obtain more accurate optoelectronic properties. Geometry optimization is performed to obtain reliable total energies and other structural parameters for each NaZnAs phase. In our study, the sequence of the structural phase transition on compression is Cu{sub 2}Sb-type → β → α phase. NaZnAs is a direct (Γ-Γ) band gap semiconductor for all the structural phases. However, compared to PBE-GGA, the mBJ approximation reproduces better fundamental band gaps. Moreover, for insight into its potential for photovoltaic applications, different optical parameters are studied.

  17. Protein sequence analysis using Hewlett-Packard biphasic sequencing cartridges in an applied biosystems 473A protein sequencer.

    Science.gov (United States)

    Tang, S; Mozdzanowski, J; Anumula, K R

    1999-01-01

    Protein sequence analysis using an adsorptive biphasic sequencing cartridge, a set of two coupled columns introduced by Hewlett-Packard for protein sequencing by Edman degradation, in an Applied Biosystems 473A protein sequencer has been demonstrated. Samples containing salts, detergents, excipients, etc. (e.g., formulated protein drugs) can be easily analyzed using the ABI sequencer. Simple modifications to the ABI sequencer to accommodate the cartridge extend its utility in the analysis of difficult samples. The ABI sequencer solvents and reagents were compatible with the HP cartridge for sequencing. Sequence information up to ten residues can be easily generated by this nonoptimized procedure, and it is sufficient for identifying proteins by database search and for preparing a DNA probe for cloning novel proteins.

  18. Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier.

    Science.gov (United States)

    Sheppard, Sarah; Lawson, Nathan D; Zhu, Lihua Julie

    2013-10-15

    3' end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 3' ends, most techniques use an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Although heuristic filters have been applied in these cases, they typically result in a high proportion of both false-positive and -negative classifications. Therefore, there is a need to develop improved algorithms to better identify mis-priming events in oligo-dT primed sequences. By analyzing sequence features flanking 3' ends derived from oligo-dT-based sequencing, we developed a naïve Bayes classifier to classify them as true or false/internally primed. The resulting algorithm is highly accurate, outperforms previous heuristic filters and facilitates identification of novel polyadenylation sites.

  19. O Tempo e o Cuidado na velhice

    Directory of Open Access Journals (Sweden)

    Wanda Pereira Patrocinio

    2016-01-01

    Full Text Available Os temas deste Volume Temático da Revista Kairós Gerontologia versam sobre o multifacetado tema do “Cuidar” na velhice, em diferentes contextos e dentro de uma abordagem multidisciplinar. Com isso, espera-se que os textos aqui apresentados possam contribuir para o campo da pesquisa e da prática na área da Gerontologia, auxiliando profissionais e familiares na complexa tarefa de cuidar de idosos.  

  20. NaLS–ascorbic acid sys

    Indian Academy of Sciences (India)

    Unknown

    Abstract. The photogalvanic effect has been studied in three systems using photogalvanic cells and. NaLS–ascorbic acid–azur A, NaLS–ascorbic acid–azur B, NaLS–ascorbic acid–azur C systems. The pho- topotential and photocurrent generated by these systems are 770⋅0, 971⋅0, 623⋅0 mV and 160⋅0, 185⋅0,. 145⋅0 ...

  1. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  2. Sequence correlations shape protein promiscuity

    Science.gov (United States)

    Lukatsky, David B.; Afek, Ariel; Shakhnovich, Eugene I.

    2011-08-01

    We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term "promiscuity" to describe such nonspecific binding. Diagonal correlations represent statistically significant repeats of sequence patterns where amino acids of the same type are clustered together. The predicted effect is qualitatively robust with respect to the form of the microscopic interaction potentials and the average amino acid composition. Our analytical results provide an explanation for the enhanced diagonal correlations observed in hubs of eukaryotic organismal proteomes [J. Mol. Biol. 409, 439 (2011)], 10.1016/j.jmb.2011.03.056. We suggest experiments that will allow direct testing of the predicted effect.

  3. Genome Sequence of Mycobacteriophage Momo.

    Science.gov (United States)

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F

    2015-06-18

    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages. Copyright © 2015 Pope et al.

  4. VPLIV GRADBENIH DEJAVNIKOV NA EKONOMIKO FOTONAPETOSTNIH SISTEMOV

    OpenAIRE

    Vrečič, Nuša

    2013-01-01

    Relavantne raziskave kažejo, da fotovoltaika postaja konkurenčna preostalim konvencionalnim virom, da bo v prihodnosti bistveno vplivala na proizvodnjo energije v Evropi ter pomembno vpliva na zamnjšanje emisij toplogrednih plinov. V teoretičnem delu so zajete tehnične zasnove in delovanje fotovoltaičnih elektrarn. Pri tehničnih zasnovah so opisani materiali in njihove lastnosti, obremenitve ter načrtovanje in montaža fotonapetostnih sistemov. V nadaljevanju spoznamo osnove fotovoltaike ...

  5. NA-NET numerical analysis net

    Energy Technology Data Exchange (ETDEWEB)

    Dongarra, J. [Tennessee Univ., Knoxville, TN (United States). Dept. of Computer Science]|[Oak Ridge National Lab., TN (United States); Rosener, B. [Tennessee Univ., Knoxville, TN (United States). Dept. of Computer Science

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host ``na-net.ornl.gov`` at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message ``send index`` to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user`s perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  6. NA-NET numerical analysis net

    Energy Technology Data Exchange (ETDEWEB)

    Dongarra, J. (Tennessee Univ., Knoxville, TN (United States). Dept. of Computer Science Oak Ridge National Lab., TN (United States)); Rosener, B. (Tennessee Univ., Knoxville, TN (United States). Dept. of Computer Science)

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host na-net.ornl.gov'' at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message send index'' to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user's perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  7. OGLAŠEVANJE NA FACEBOOKU V SLOVENIJI

    OpenAIRE

    Dobnik, Monja

    2013-01-01

    Danes so zahvaljujoč napredni mobilni tehnologiji družbena omrežja z nami na vsakem koraku. Facebook (FB) se po priljubljenosti uvršča v sam vrh družbenih omrežij in glede na to, da ga uporablja že več kot milijarda zemljanov, ponuja tudi odlične trg za oglaševanje. To so ugotovili tudi slovenski podjetniki. V diplomski nalogi je predstavljeno, kako na FB oglašujejo nekatera slovenska podjetja, s pomočjo spletnega vprašalnika pa je ugotovljeno tudi, kaj o oglasih na FB menijo njegovi uporabni...

  8. Fabrication of implanted $^{22}$Na targets

    CERN Multimedia

    2002-01-01

    A knowledge of the $^{22}$Na(p,$\\gamma$)$^{23}$ Mg reaction rate is of significant astrophysical interest. In order to complete previous studies of this reaction, radioactive $^{22}$Na targets of high purity are required. We ask for support to fabricate these targets via the implantation technique at ISOLDE GPS (off—line mode) using $^{22}$Na nuclides in an Al matrix produced in Nov. 1990 at the PSI (Zürich). The $^{22}$Na nuclides are released and ionized in a surface ionisation source, mass-analyzed at ISOLDE GPS, and implanted in a Ni-Ta backing and a C—foil in a special implantation setup.

  9. Cation and anion sequences in dark-adapted Balanus photoreceptor

    Science.gov (United States)

    1977-01-01

    Anion and cation permeabilities in dark-adapted Balanus photoreceptors were determined by comparing changes in the membrane potential in response to replacement of the dominant anion (Cl-) or cation (Na+) by test anions or cations in the superfusing solution. The anion permeability sequence obtained was PI greater than PSO4 greater than PBr greater than PCl greater than Pisethionate greater than Pmethanesulfonate. Gluconate, glucuronate, and glutamate generally appeared more permeable and propionate less permeable than Cl-. The alkali-metal cation permeability sequence obtained was PK greater than PRb greater than PCx greater than PNa approximately PLi. This corresponds to Eisenman's IV which is the same sequencethat has been obtained for other classes of nerve cells in the resting state. The values obtained for the permeability ratios of the alkali-metal cations are considered to be minimal. The membrane conductance measured by passing inward current pulses in the different test cations followed the sequence, GK greater than GRb greater than GCs greater than GNa greater than GLi. The conductance ratios obtained for a full substitution of the test cation agreed quite well with permeability ratios for all the alkali-metal cations except K+ which was generally higher. PMID:199688

  10. Sequence heterogeneity in Parkinsonian speech.

    Science.gov (United States)

    Ho, A K; Bradshaw, J L; Cunnington, R; Phillips, J G; Iansek, R

    1998-08-01

    Parkinson's disease (PD) is a neurodegenerative movement disorder primarily due to basal ganglia dysfunction. While much research has been conducted on Parkinsonian deficits in the traditional arena of musculoskeletal limb movement, research in other functional motor tasks is lacking. The present study examined articulation in PD with increasingly complex sequences of articulatory movement. Of interest was whether dysfunction would affect articulation in the same manner as in limb-movement impairment. In particular, since very similar (homogeneous) articulatory sequences (the tongue twister effect) are more difficult for healthy individuals to achieve than dissimilar (heterogeneous) gestures, while the reverse may apply for skeletal movements in PD, we asked which factor would dominate when PD patients articulated various grades of artificial tongue twisters: the influence of disease or a possible difference between the two motor systems. Execution was especially impaired when articulation involved a sequence of motor program heterogeneous in terms of place of articulation. The results are suggestive of a hypokinesic tendency in complex sequential articulatory movement as in limb movement. It appears that PD patients do show abnormalities in articulatory movement which are similar to those of the musculoskeletal system. The present study suggests that an underlying disease effect modulates movement impairment across different functional motor systems. Copyright 1998 Academic Press.

  11. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  12. Molecular characterization and functional analysis of a vacuolar Na(+)/H(+) antiporter gene (HcNHX1) from Halostachys caspica.

    Science.gov (United States)

    Guan, Bo; Hu, Youzhen; Zeng, Youling; Wang, Yan; Zhang, Fuchun

    2011-03-01

    According to sequences of several vacuolar Na(+)/H(+) antiporter genes from Xinjiang halophytic plants, a new vacuolar Na(+)/H(+) antiporter gene (HcNHX1) from the halophyte Halostachys caspica was obtained by RACE and RT-PCR using primers corresponding to conserved regions of the coding sequences. The obtained HcNHX1 cDNA was 1,983 bp and contained a 1,656 bp open reading frame encoding a deduced protein of 551 amino acid residues. The deduced amino acid sequence showed high identity with other NHX1 we have cloned previously from halophyte in Xinjiang desert area. The phylogenetic analysis showed that HcNHX1 formed a clade with NHX homologs of Chenopodiaceae. Expression profiles under salt treatment and ABA induction were investigated, and the results revealed that expression of HcNHX1 was induced by NaCl and ABA. To compare the degree of salt tolerance, we over-expressed HcNHX1 in Arabidopsis. Two transgenic lines grew more vigorously than the wild type (WT) under salt stress. The analysis of ion contents indicated that under salt stress, the transgenic plants compartmentalized more Na(+) in the leaves compared with wild-type plants. Together, these results suggest that the products of the novel gene HcNHX1 from halophyte Halostachys caspica is a functional tonoplast Na(+)/H(+) antiporter.

  13. O consumo na vida digital

    Directory of Open Access Journals (Sweden)

    Iuri Yudi Furukita Baptista

    2016-02-01

    Full Text Available O modelo de consumo não possui as mesmas características sempre: suas relações, motivações, formatos, espaços, interesses e atividades são construções sociais que se modificam atreladas ao cenário econômico, político e tecnológico. O presente trabalho repassa o surgimento da sociedade do consumidor para então conjecturar sobre as propriedades distintivas do consumo na vida digital. O que se defende ao final é que o consumidor já não se restringe ao papel de consumir.

  14. Odpowiedź na pytanie

    Directory of Open Access Journals (Sweden)

    Michel Foucault

    2016-12-01

    Full Text Available Prezentowany artykuł Michela Foucaulta został opublikowany w 1963 roku. Foucault rozwija w nim koncepcję archeologii wiedzy – metody analizy historycznych dyskursów, którą zaprezentuje w sześć lat później w książce o tym właśnie tytule. Artykuł powstał na kanwie pytania wybranego przez autora spośród zadanych mu przez redakcję „Esprit”, które dotyczyło możliwości pojęciowego opracowania przymusu systemu dyskursywnego przy jednoczesnym zaakcentowaniu nieciągłości w jego obrębie a tym samym możliwości twórczego działania w historii ducha. A także, czy tak sformułowana aporia zakładałaby z konieczności zgodę na przymus systemu lub afirmację siły zdolnej do przekształcenia go za pomocą zewnętrznej przemocy? Tekst jest wprawką do sformułowania dojrzałej teorii dyskursu, rodzajem autoanalizy, która pozwala Foucaultowi powiązać własną metodę historyczną z „progresywistyczną polityką” myśli i rozwiązać w ten sposób dylemat pełnej determinacji i wolnego sprawstwa obecny w rozważaniach wielu strukturalistów.

  15. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  16. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    OpenAIRE

    Natanaelsson, Christian; Oskarsson, Mattias CR; Angleby, Helen; Lundeberg, Joakim; Kirkness, Ewen; Savolainen, Peter

    2006-01-01

    Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromo...

  17. Diagnostic yield of molecular autopsy in patients with sudden arrhythmic death syndrome using targeted exome sequencing

    DEFF Research Database (Denmark)

    Nunn, Laurence M; Lopes, Luis R; Syrris, Petros

    2016-01-01

    AIMS: The targeted genetic screening of Sudden Arrhythmic Death Syndrome (SADS) probands in a molecular autopsy has a diagnostic yield of up to 35%. Exome sequencing has the potential to improve this yield. The primary aim of this study is to examine the feasibility and diagnostic utility...... of control exomes were prioritized for analysis followed by mutations and 10 probands (17%) had...... previously published rare (0.02-0.5%) candidate mutations-a total yield of 29%. Co-segregation fully confirmed two private SCN5A Na channel mutations. Variants of unknown significance were detected in a further 34% of probands. CONCLUSION: Molecular autopsy using targeted exome sequencing has a relatively...

  18. Analiza utjecaja stabilizatora na određivanje elemenata vanjske orijentacije kamere na bespilotnoj letjelici

    OpenAIRE

    Gašparović, Mateo; Gajski, Dubravko

    2016-01-01

    U radu su prikazani i interpretirani rezultati analize utjecaja stabilizatora kamere na određivanje elemenata vanjske orijentacije na bespilotnim letjelicama. Riječ je o 3-osnom stabilizatoru baziranom na elektromotorima bez četkica. Prikazan je i objašnjen koncept rada stabilizatora kamera na bespilotnim letjelicama. Za potrebe rada stabilizator je unaprijeđen upotrebom drugog inercijalnog mjernog uređaja (IMU). Provedena su dva testiranja stabilizatora upotrebom jednog i dva inercijalna mje...

  19. UTJECAJ SAMOOTKRIVANJA NA FACEBOOKU NA SMANJENJE NESIGURNOSTI, SVIĐANJE I SOCIJALNU ATRAKTIVNOST

    OpenAIRE

    Vuletić, Ana

    2016-01-01

    Cilj ovog istraživanja bio je ispitati utjecaj samootkrivanja na Facebooku na smanjenje nesigurnosti, sviđanje i socijalnu atraktivnost prilikom inicijalnog kontakta. Istraživanje je provedeno na uzorku od 196 studenata u dobi od 18 do 25 godina koji su bili raspoređeni u tri eksperimentalne situacije. Svaka situacija razlikovala se po razini samootkrivanja na Facebook profilu (niska, srednja, visoka). Sudionici su procjene vlastite nesigurnosti, sviđanja i socijalne atraktivnosti prezentiran...

  20. Identification of Nocobactin NA Biosynthetic Gene Clusters in Nocardia farcinica▿ §

    OpenAIRE

    Hoshino, Yasutaka; Chiba, Kazuhiro; Ishino, Keiko; Fukai, Toshio; Igarashi, Yasuhiro; Yazawa, Katsukiyo; Mikami, Yuzuru; Ishikawa, Jun

    2010-01-01

    We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structu...

  1. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  2. On Inclusion Relations between Some Sequence Spaces

    Directory of Open Access Journals (Sweden)

    R. Çolak

    2016-01-01

    Full Text Available We determine the relations between the classes S^λ of almost λ-statistically convergent sequences and the relations between the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ, μ in the class Λ. Furthermore we also give the relations between the classes S^λ of almost λ-statistically convergent sequences and the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ,μ∈Λ.

  3. Capsazepine, a synthetic vanilloid that converts the Na,K-ATPase to Na-ATPase

    DEFF Research Database (Denmark)

    Mahmmoud, Yasser Ahmed

    2008-01-01

    Capsazepine (CPZ), a synthetic capsaicin analogue, inhibits ATP hydrolysis by Na,K-ATPase in the presence, but not in the absence of K+. Studies with purified membranes revealed that CPZ reduced Na+-dependent phosphorylation by interference with Na+ binding from the intracellular side of the memb...

  4. Interaction between Na+/K+-pump and Na+/Ca2+-exchanger modulates intercellular communication

    DEFF Research Database (Denmark)

    Matchkov, Vladimir; Gustafsson, Helena; Rahman, Awahan

    2007-01-01

    Ouabain, a specific inhibitor of the Na(+)/K(+)-pump, has previously been shown to interfere with intercellular communication. Here we test the hypothesis that the communication between vascular smooth muscle cells is regulated through an interaction between the Na(+)/K(+)-pump and the Na(+)/Ca(2...

  5. Regeneration of plantlets under NaCl stress from NaN3 treated ...

    African Journals Online (AJOL)

    use

    2011-11-16

    Nov 16, 2011 ... plant regeneration under NaCl stressed conditions was assessed in some sugarcane (Saccharum officinarum L.) cultivars ... cell is a useful work for the establishment of pure form of species. It can facilitate .... Sub-cultures of NaN3 treated explants on different NaCl stressed cultures a. Callus proliferation ...

  6. Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Gonzalo H Villarino

    Full Text Available Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.

  7. Effector-independent and effector-dependent sequence representations underlie general and specific perceptuomotor sequence learning.

    Science.gov (United States)

    Andresen, David R; Marsolek, Chad J

    2012-01-01

    Perceptuomotor sequence learning could be due to learning of effector-independent sequence information (e.g., response locations), effector-dependent information (e.g., motor movements of a particular effector), or both. Evidence also suggests that learning of statistical regularities in sequences (general-regularity learning) and specific sequences (specific-sequence learning) are dissociable. The authors examined the degree to which general and specific-sequence learning rely on effector-independent and effector-dependent representations. During training, participants typed sequences that followed a construction rule with a subset of sequences repeatedly processed. At test, effector-independent and effector-dependent learning was examined with respect to general-regularity and specific-sequence learning. Results suggest that general-regularity learning is subserved by effector-independent sequence representations, whereas specific-sequence learning is subserved by effector-dependent sequence representations, further dissociating these types of learning.

  8. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics

    NARCIS (Netherlands)

    Sikkema-Raddatz, B.; Johansson, L.F.; de Boer, E.N.; Almomani, R.; Boven, L.G.; van den Berg, M.P.; van Spaendonck-Zwarts, K.Y.; van Tintelen, J.P.; Sijmons, R.H.; Jongbloed, J.D.H.; Sinke, R.J.

    Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted

  9. Structure of Liquid Na-K Alloys

    NARCIS (Netherlands)

    Alblas, B.P.; Lugt, W. van der; Valk, H.J.L. van der; Hosson, J.Th.M. De; Dijk, C. van

    1980-01-01

    X-ray and neutron diffraction data are presented for a number of liquid Na-K alloys covering the whole composition range. Additionally, for the composition 50 at.% Na - 50 at.% K, a computer experiment in molecular dynamics has been carried out. An attempt is made to analyze the results in terms of

  10. Benchmarking short sequence mapping tools.

    Science.gov (United States)

    Hatem, Ayat; Bozdağ, Doruk; Toland, Amanda E; Çatalyürek, Ümit V

    2013-06-07

    The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results.

  11. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  12. Differential correlation for sequencing data.

    Science.gov (United States)

    Siska, Charlotte; Kechris, Katerina

    2017-01-19

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

  13. Razvitak naselja na kvarnerskim otocima - primjer Dobrinja

    Directory of Open Access Journals (Sweden)

    Marijan Bradanović

    2012-12-01

    Full Text Available Na dosad slabo poznatom i sa stajališta povijesti umjetnosti još posve neobrađenom primjeru Dobrinja na otoku Krku, raspravlja se o razvitku naselja na kvarnerskim otocima. Uz isticanje štetnosti dosad prevladavajućih uopćavanja, karakteristični položaj i razvitak Dobrinja tumače se u širem, komparativnom kontekstu. Analiziraju se prostiranje i obilježja pojedinih dijelova ovog naselja, a naglasak je na vremenu kasnog srednjeg i ranijeg novog vijeka. Tada je najuži dio povijesnog središta Dobrinja poprimio čvrstu, na tlorisnoj osnovi i danas, usprkos opsežnim pregradnjama i arhitektonskim preinakama, jasno uočljivu, urbanu fizionomiju.

  14. Regulation of Na+ fluxes in plants

    Directory of Open Access Journals (Sweden)

    Frans eMaathuis

    2014-09-01

    Full Text Available When exposed to salt, every plant takes up Na+ from the environment. Once in the symplast, Na+ is distributed within cells and between different tissues and organs. There it can help to lower the cellular water potential but also exert potentially toxic effects. Control of Na+ fluxes is therefore crucial and indeed, research shows that the divergence between salt tolerant and salt sensitive plants is not due to a variation in transporter types but rather originates in the control of uptake and internal Na+ fluxes. A number of regulatory mechanisms has been identified based on signalling of Ca2+, cyclic nucleotides, reactive oxygen species, hormones, or on transcriptional and post translational changes of gene and protein expression. This review will give an overview of intra- and intercellular movement of Na+ in plants and will summarise our current ideas of how these fluxes are controlled and regulated in the early stages of salt stress.

  15. Bullying na Escola: um sofrimento

    Directory of Open Access Journals (Sweden)

    Marlene Silva Sardinha Gurpilhares

    2014-07-01

    Full Text Available O bullying é uma forma de violência presente nas escolas e o termo é utilizado para caracterizar todas as formas de agressões repetitivas psicológicas e físicas, direta ou indiretamente. Esta violência causa sofrimentos, intimidação e medo, sempre numa relação de poder entre pares. Esta pesquisa trata de um estudo do bullying escolar: o que é, como surgiu, como identificá-lo e sua caracterização, conseqüências, causas, o papel da escola, de professores e pais e uma proposta prática que pode ser adotada para sua prevenção e contenção. O objetivo é organizar materiais para leitura dos atores educacionais para uma possível reflexão, através de pesquisas bibliográficas. Esta violência é grave e deveria ser tratada como saúde pública, devido às conseqüências que traz, como queda na aprendizagem, na autoestima e em casos mais graves, até o suicido e outras tragédias. A escola necessita atentar para esse tipo de violência, revendo suas ações em todos os momentos, tendo um olhar integral e diferenciado em relação aos alunos. É fundamental que o bullying não seja tratado como brincadeira de criança e para ser identificado e combatido é necessária uma ação entre a família e todos da escola, que pode ser desenvolvida através de projetos que ajudem a apontar caminhos para a solução do problema. Tais ações devem ser pautadas por constantes debates e reflexões, nas quais o aluno se torne o protagonista. Não existem fórmulas prontas, pois a intervenção deve ser feita através da realidade de cada escola.

  16. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.

    Directory of Open Access Journals (Sweden)

    Teresita M Porter

    Full Text Available Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1 a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN; 2 a composition-based method (Ribosomal Database Project naïve bayesian classifier, NBC; and, 3 a phylogeny-based method (Statistical Assignment Package, SAP. We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50-100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.

  17. Clues to NaCN formation ⋆

    Science.gov (United States)

    Quintana-Lacaci, G.; Cernicharo, J.; Velilla Prieto, L.; Agúndez, M.; Castro-Carrizo, A.; Fonfría, J.P.; Massalkhi, S.; Pardo, J.R.

    2017-01-01

    Context ALMA is providing us essential information on where certain molecules form. Observing where these molecules emission arises from, the physical conditions of the gas, and how this relates with the presence of other species allows us to understand the formation of many species, and to significantly improve our knowledge of the chemistry that occurs in the space. Aims We studied the molecular distribution of NaCN around IRC +10216, a molecule detected previously, but whose origin is not clear. High angular resolution maps allow us to model the abundance distribution of this molecule and check suggested formation paths. Methods We modeled the emission of NaCN assuming local thermal equilibrium (LTE) conditions. These profiles were fitted to azimuthal averaged intensity profiles to obtain an abundance distribution of NaCN. Results We found that the presence of NaCN seems compatible with the presence of CN, probably as a result of the photodissociation of HCN, in the inner layers of the ejecta of IRC +10216. However, similar as for CH3CN, current photochemical models fail to reproduce this CN reservoir. We also found that the abundance peak of NaCN appears at a radius of 3 × 1015cm, approximately where the abundance of NaCl, suggested to be the parent species, starts to decay. However, the abundance ratio shows that the NaCl abundance is lower than that obtained for NaCN. We expect that the LTE assumption might result in NaCN abundances higher than the real ones. Updated photochemical models, collisional rates, and reaction rates are essential to determine the possible paths of the NaCN formation.

  18. The Genome Sequence of Drosophila melanogaster

    National Research Council Canada - National Science Library

    ...; Mark D. Adams; Susan E. Celniker; Robert A. Holt; Cheryl A. Evans; Jeannine D. Gocayne; Peter G. Amanatides; Steven E. Scherer; Peter W. Li; Roger A. Hoskins; Richard F. Galle; Reed A. George; Suzanna E. Lewis; Stephen Richards; Michael Ashburner; Scott N. Henderson; Granger G. Sutton; Jennifer R. Wortman; Mark D. Yandell; Qing Zhang; Lin X. Chen; Rhonda C. Brandon; Yu-Hui C. Rogers; Robert G. Blazej; Mark Champe; Barret D. Pfeiffer; Kenneth H. Wan; Clare Doyle; Evan G. Baxter; Gregg Helt; Catherine R. Nelson; George L. Gabor; Miklos; Josep F. Abril; Anna Agbayani; Hui-Jin An; Cynthia Andrews-Pfannkoch; Danita Baldwin; Richard M. Ballew; Anand Basu; James Baxendale; Leyla Bayraktaroglu; Ellen M. Beasley; Karen Y. Beeson; P. V. Benos; Benjamin P. Berman; Deepali Bhandari; Slava Bolshakov; Dana Borkova; Michael R. Botchan; John Bouck; Peter Brokstein; Phillipe Brottier; Kenneth C. Burtis; Dana A. Busam; Heather Butler; Edouard Cadieu; Angela Center; Ishwar Chandra; J. Michael Cherry; Simon Cawley; Carl Dahlke; Lionel B. Davenport; Peter Davies; Beatriz de Pablos; Arthur Delcher; Zuoming Deng; Anne Deslattes Mays; Ian Dew; Suzanne M. Dietz; Kristina Dodson; Lisa E. Doup; Michael Downes; Shannon Dugan-Rocha; Boris C. Dunkov; Patrick Dunn; Kenneth J. Durbin; Carlos C. Evangelista; Concepcion Ferraz; Steven Ferriera; Wolfgang Fleischmann; Carl Fosler; Andrei E. Gabrielian; Neha S. Garg; William M. Gelbart; Ken Glasser; Anna Glodek; Fangcheng Gong; J. Harley Gorrell; Zhiping Gu; Ping Guan; Michael Harris; Nomi L. Harris; Damon Harvey; Thomas J. Heiman; Judith R. Hernandez; Jarrett Houck; Damon Hostin; Kathryn A. Houston; Timothy J. Howland; Ming-Hui Wei

    2000-01-01

    ... of the ∼120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map...

  19. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  20. An Assignment Sequence for Underprepared Writers.

    Science.gov (United States)

    Nimmo, Kristi

    2000-01-01

    Presents a sequenced writing assignment on shopping to aid basic writers. Describes a writing assignment focused around online and mail-order shopping. Notes steps in preparing for the assignment, the sequence, and discusses responses to the assignments. (SC)