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Sample records for al gen env

  1. Remarks on Peinado et al.'s Analysis of J3Gen.

    PubMed

    Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi; Melià-Seguí, Joan

    2015-01-01

    Peinado et al. analyzed the security of the J3Gen pseudorandom number generator proposed by Melià-Seguí et al., and claimed weaknesses regarding its security properties. They also presented a deterministic attack based on the decimation of the J3Gen output sequences. We show that the assumptions made by Peinado et al. are not correct and that the proposed deterministic attack against J3Gen does not hold in practice. PMID:25781510

  2. Revision of J3Gen Validity of the Attacks by Peinado et al.

    PubMed Central

    Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

    2015-01-01

    This letter is the reply to: Remarks on Peinado et al.’s Analysis of J3Gen by J. Garcia-Alfaro, J. Herrera-Joancomartí and J. Melià-Seguí published in Sensors 2015, 15, 6217–6220. Peinado et al. cryptanalyzed the pseudorandom number generator proposed by Melià-Seguí et al., describing two possible attacks. Later, Garcia-Alfaro claimed that one of this attack did not hold in practice because the assumptions made by Peinado et al. were not correct. This letter reviews those remarks, showing that J3Gen is anyway flawed and that, without further information, the interpretation made by Peinado et al. seems to be correct. PMID:26007740

  3. ALV-J GP37 Molecular Analysis Reveals Novel Virus-Adapted Sites and Three Tyrosine-Based Env Species

    PubMed Central

    Shang, Jianjun; Tian, Xiaoyan; Yang, Jialiang; Chen, Hongjun; Shao, Hongxia; Qin, Aijian

    2015-01-01

    Compared to other avian leukosis viruses (ALV), ALV-J primarily induces myeloid leukemia and hemangioma and causes significant economic loss for the poultry industry. The ALV-J Env protein is hypothesized to be related to its unique pathogenesis. However, the molecular determinants of Env for ALV-J pathogenesis are unclear. In this study, we compared and analyzed GP37 of ALV-J Env and the EAV-HP sequence, which has high homology to that of ALV-J Env. Phylogenetic analysis revealed five groups of ALV-J GP37 and two novel ALV-J Envs with endemic GP85 and EAV-HP-like GP37. Furthermore, at least 15 virus-adapted mutations were detected in GP37 compared to the EAV-HP sequence. Further analysis demonstrated that three tyrosine-based motifs (YxxM, ITIM (immune tyrosine-based inhibitory motif) and ITAM-like (immune tyrosine-based active motif like)) associated with immune disease and oncogenesis were found in the cytoplasmic tail of GP37. Based on the potential function and distribution of these motifs in GP37, ALV-J Env was grouped into three species, inhibitory Env, bifunctional Env and active Env. Accordingly, 36.91%, 61.74% and 1.34% of ALV-J Env sequences from GenBank are classified as inhibitory, bifunctional and active Env, respectively. Additionally, the Env of the ALV-J prototype strain, HPRS-103, and 17 of 18 EAV-HP sequences belong to the inhibitory Env. And models for signal transduction of the three ALV-J Env species were predicted. Our findings and models provide novel insights for identifying the roles and molecular mechanism of ALV-J Env in the unique pathogenesis of ALV-J. PMID:25849207

  4. Incorporation of chimeric HIV-SIV-Env and modified HIV-Env proteins into HIV pseudovirions

    SciTech Connect

    Devitt, Gerard; Emerson, Vanessa; Holtkotte, Denise; Pfeiffer, Tanya; Pisch, Thorsten; Bosch, Valerie . E-mail: v.bosch@dkfz.de

    2007-05-10

    Low level incorporation of the viral glycoprotein (Env) into human immunodeficiency virus (HIV) particles is a major drawback for vaccine strategies against HIV/AIDS in which HIV particles are used as immunogen. Within this study, we have examined two strategies aimed at achieving higher levels of Env incorporation into non-infectious pseudovirions (PVs). First, we have generated chimeric HIV/SIV Env proteins containing the truncated C-terminal tail region of simian immunodeficiency virus (SIV)mac239-Env767{sup stop}, which mediates strongly increased incorporation of SIV-Env into SIV particles. In a second strategy, we have employed a truncated HIV-Env protein (Env-Tr752{sup N750K}) which we have previously demonstrated to be incorporated into HIV virions, generated in infected T-cells, to a higher level than that of Wt-HIV-Env. Although the chimeric HIV/SIV Env proteins were expressed at the cell surface and induced increased levels of cell-cell fusion in comparison to Wt-HIV-Env, they did not exhibit increased incorporation into either HIV-PVs or SIV-PVs. Only Env-Tr752{sup N750K} exhibited significantly higher (threefold) levels of incorporation into HIV-PVs, an improvement, which, although not dramatic, is worthwhile for the large-scale preparation of non-infectious PVs for vaccine studies aimed at inducing Env humoral responses.

  5. Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.

    PubMed

    Hameed, Asif; Shahina, Mariyam; Lin, Shih-Yao; Nakayan, Phanit; Liu, You-Cheng; Lai, Wei-An; Hsu, Yi-Han

    2014-08-01

    A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-E(T), was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-E(T) shared 95.7 and 93.9% 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera Donghicola (Donghicola eburneus SW-277(T)) and Roseovarius (Roseovarius tolerans EL-172(T)). The predominant (>75% of the total) fatty acid was summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-E(T) represents a novel genus and species of the family Rhodobacteraceae, for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-E(T) ( = JCM 18819(T) = BCRC 80549(T)). In addition, an emended description of the genus Donghicola Yoon et al. 2007 and the reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2(T) = MCCC 1A00107(T) = LMG 24574(T) = CGMCC 1.7081(T)) are proposed. PMID:24844264

  6. Biodegradation of Bis(2-Chloroethyl) Ether by Xanthobacter sp. Strain ENV481▿

    PubMed Central

    McClay, Kevin; Schaefer, Charles E.; Vainberg, Simon; Steffan, Robert J.

    2007-01-01

    Degradation of bis(2-chloroethyl) ether (BCEE) was observed to occur in two bacterial strains. Strain ENV481, a Xanthobacter sp. strain, was isolated by enrichment culturing of samples from a Superfund site located in the northeastern United States. The strain was able to grow on BCEE or 2-chloroethylethyl ether as the sole source of carbon and energy. BCEE degradation in strain ENV481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol and diethylene glycol (DEG), respectively. 2-Hydroxyethoxyacetic acid was detected as a product of DEG catabolism by the strain. Degradation of BCEE by strain ENV481 was independent of oxygen, and the strain was not able to grow on a mixture of benzene, ethylbenzene, toluene, and xylenes, other prevalent contaminants at the site. Another bacterial isolate, Pseudonocardia sp. strain ENV478 (S. Vainberg et al., Appl. Environ. Microbiol. 72:5218-5224, 2006), degraded BCEE after growth on tetrahydrofuran or propane but was not able to grow on BCEE as a sole carbon source. BCEE degradation by strain ENV478 appeared to be facilitated by a monooxygenase-mediated O-dealkylation mechanism, and it resulted in the accumulation of 2-chloroacetic acid that was not readily degraded by the strain. PMID:17873075

  7. HIV-1 Vpr increases Env expression by preventing Env from endoplasmic reticulum-associated protein degradation (ERAD).

    PubMed

    Zhang, Xianfeng; Zhou, Tao; Frabutt, Dylan A; Zheng, Yong-Hui

    2016-09-01

    Vpr enhances HIV-1 replication in macrophages and dendritic cells, as well as the human CD4(+) CEM.NKR T cell line. Recently, Vpr was reported to increase HIV-1 Env expression in macrophages. Here, we report that Vpr also increases HIV-1 Env expression in dendritic cells and CEM.NKR cells. The Vpr activity depends on its N-terminal region, which was disrupted by a single A30L mutation. Env was rapidly degraded in the absence of Vpr, which was blocked by the ERAD pathway inhibitor kifunesine or the lysosome inhibitor Bafilomycin. As2O3 or PK11195, which reportedly enhances HIV-1 Env folding, also blocked the Env degradation in CEM.NKR cells. Thus, these results not only identify Env as a primary target for Vpr to boost HIV-1 replication, but also suggest that Vpr likely promotes Env folding in the ER, which is otherwise misfolded and targeted by the ERAD pathway to lysosomes for degradation. PMID:27343732

  8. RRE-dependent HIV-1 Env RNA effects on Gag protein expression, assembly and release

    SciTech Connect

    López, Claudia S.; Sloan, Rachel; Cylinder, Isabel; Kozak, Susan L.; Kabat, David; Barklis, Eric

    2014-08-15

    The HIV-1 Gag proteins are translated from the full-length HIV-1 viral RNA (vRNA), whereas the envelope (Env) protein is translated from incompletely spliced Env mRNAs. Nuclear export of vRNAs and Env mRNAs is mediated by the Rev accessory protein which binds to the rev-responsive element (RRE) present on these RNAs. Evidence has shown there is a direct or indirect interaction between the Gag protein, and the cytoplasmic tail (CT) of the Env protein. Our current work shows that env gene expression impacts HIV-1 Gag expression and function in two ways. At the protein level, full-length Env expression altered Gag protein expression, while Env CT-deletion proteins did not. At the RNA level, RRE-containing Env mRNA expression reduced Gag expression, processing, and virus particle release from cells. Our results support models in which Gag is influenced by the Env CT, and Env mRNAs compete with vRNAs for nuclear export. - Highlights: • At the protein level, full-length HIV-1 Env alters Gag protein expression. • HIV-1 Env RNA expression reduces Gag levels and virus release. • Env RNA effects on Gag are dependent on the RRE. • RRE-containing Env RNAs compete with vRNAs for nuclear export.

  9. Biodegradation of Ether Pollutants by Pseudonocardia sp. Strain ENV478

    PubMed Central

    Vainberg, Simon; McClay, Kevin; Masuda, Hisako; Root, Duane; Condee, Charles; Zylstra, Gerben J.; Steffan, Robert J.

    2006-01-01

    A bacterium designated Pseudonocardia sp. strain ENV478 was isolated by enrichment culturing on tetrahydrofuran (THF) and was screened to determine its ability to degrade a range of ether pollutants. After growth on THF, strain ENV478 degraded THF (63 mg/h/g total suspended solids [TSS]), 1,4-dioxane (21 mg/h/g TSS), 1,3-dioxolane (19 mg/h/g TSS), bis-2-chloroethylether (BCEE) (12 mg/h/g TSS), and methyl tert-butyl ether (MTBE) (9.1 mg/h/g TSS). Although the highest rates of 1,4-dioxane degradation occurred after growth on THF, strain ENV478 also degraded 1,4-dioxane after growth on sucrose, lactate, yeast extract, 2-propanol, and propane, indicating that there was some level of constitutive degradative activity. The BCEE degradation rates were about threefold higher after growth on propane (32 mg/h/g TSS) than after growth on THF, and MTBE degradation resulted in accumulation of tert-butyl alcohol. Degradation of 1,4-dioxane resulted in accumulation of 2-hydroxyethoxyacetic acid (2HEAA). Despite its inability to grow on 1,4-dioxane, strain ENV478 degraded this compound for >80 days in aquifer microcosms. Our results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1,4-dioxane is related to their inability to efficiently metabolize the 1,4-dioxane degradation product 2HEAA but that strain ENV478 may nonetheless be useful as a biocatalyst for remediating 1,4-dioxane-contaminated aquifers. PMID:16885268

  10. Appreciating HIV-1 diversity: subtypic differences in ENV

    SciTech Connect

    Gnanakaran, S; Shen, Tongye; Lynch, Rebecca M; Derdeyn, Cynthia A

    2008-01-01

    Human immunodeficiency virus type 1 (HIV-1) group M is responsible for the current AIDS pandemic and exhibits exceedingly high levels of viral genetic diversity around the world, necessitating categorization of viruses into distinct lineages, or subtypes. These subtypes can differ by around 35% in the envelope (Env) glycoproteins of the virus, which are displayed on the surface of the virion and are targets for both neutralizing antibody and cell-mediated immune responses. This diversity reflects the remarkable ability of the virus to adapt to selective pressures, the bulk of which is applied by the host immune response, and represents a serious obstacle for developing an effective vaccine with broad coverage. Thus, it is important to understand the underlying biological consequences of inter-subtype diversity. Recent studies have revealed that the HIV-1 subtypes exhibit phenotypic differences that result from subtle differences in Env structure, particularly within the highly immunogenic V3 domain, which participates directly in viral entry. This review will therefore explore current research that describes subtypic differences in Env at the genetic and phenotypic level, focusing in particular on V3, and highlighting recent discoveries about the unique features of subtype C Env, which is the most prevalent subtype globally.

  11. Structure and immune recognition of trimeric prefusion HIV-1 Env

    PubMed Central

    Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr; Georgiev, Ivelin S.; Soto, Cinque; Gorman, Jason; Huang, Jinghe; Acharya, Priyamvada; Chuang, Gwo-Yu; Ofek, Gilad; Stewart-Jones, Guillaume B. E.; Stuckey, Jonathan; Bailer, Robert T.; Joyce, M. Gordon; Louder, Mark K.; Tumba, Nancy; Yang, Yongping; Zhang, Baoshan; Cohen, Myron S.; Haynes, Barton F.; Mascola, John R.; Morris, Lynn; Munro, James B.; Blanchard, Scott C.; Mothes, Walther; Connors, Mark; Kwong, Peter D.

    2015-01-01

    The HIV-1-envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a postfusion state. As the sole viral antigen on the HIV-1-virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5-Å resolution for an HIV-1-Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the prefusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Prefusion gp41 encircles N- and C-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry likely involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the prefusion closed spike: we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation. PMID:25296255

  12. Splicing of Friend Murine Leukemia Virus env-mRNA Enhances Its Ability to Form Polysomes.

    PubMed

    Machinaga, Akihito; Ishihara, Syuhei; Shirai, Akiko; Takase-Yoden, Sayaka

    2016-01-01

    Friend murine leukemia virus (MLV) belongs to the gamma retroviruses of the Retroviridae family. The positive-sense RNA of its genome contains a 5' long terminal repeat (LTR), 5' leader sequence, gag, pol, env, and 3' LTR. Transcription from proviral DNA begins from the R region of the 5' LTR and ends at the polyadenylation signal located at the R region of the other end of the 3' LTR. There is a 5' splice site in the 5' leader sequence and a 3' splice site at the 3' end of the pol region. Both full-length unspliced mRNAs and a singly spliced mRNA (env-mRNA) are produced in MLV-infected cells. The MLV Env protein plays important roles both in viral adsorption to host cells and in neuropathogenic disease in MLV-infected mice and rats. Understanding the regulatory mechanisms controlling Env expression is important for determining the functions of the Env protein. We have previously shown that splicing increases env-mRNA stability and translation efficiency. Generally, mRNA polysome formation correlates with translation efficiency. Therefore, here we investigated the effects of env-mRNA splicing on polysome formation to identify mechanisms for Env up-regulation due to splicing. We performed polysome profile analyses using Env-expression plasmids producing spliced or unspliced env-mRNA and showed that the former formed polysomes more efficiently than the latter. Thus, splicing of env-mRNA facilitated polysome formation, suggesting that this contributes to up-regulation of Env expression. We replaced the env region of the expression plasmids with a luciferase (luc) gene, and found that in this case both unspliced and spliced luc-mRNA formed polysomes to a similar extent. Thus, we conclude that whether mRNA polysome formation is affected by splicing depends on the structure of gene in question. PMID:26909075

  13. Splicing of Friend Murine Leukemia Virus env-mRNA Enhances Its Ability to Form Polysomes

    PubMed Central

    Machinaga, Akihito; Ishihara, Syuhei; Shirai, Akiko; Takase-Yoden, Sayaka

    2016-01-01

    Friend murine leukemia virus (MLV) belongs to the gamma retroviruses of the Retroviridae family. The positive-sense RNA of its genome contains a 5′ long terminal repeat (LTR), 5′ leader sequence, gag, pol, env, and 3′ LTR. Transcription from proviral DNA begins from the R region of the 5′ LTR and ends at the polyadenylation signal located at the R region of the other end of the 3′ LTR. There is a 5′ splice site in the 5′ leader sequence and a 3′ splice site at the 3′ end of the pol region. Both full-length unspliced mRNAs and a singly spliced mRNA (env-mRNA) are produced in MLV-infected cells. The MLV Env protein plays important roles both in viral adsorption to host cells and in neuropathogenic disease in MLV-infected mice and rats. Understanding the regulatory mechanisms controlling Env expression is important for determining the functions of the Env protein. We have previously shown that splicing increases env-mRNA stability and translation efficiency. Generally, mRNA polysome formation correlates with translation efficiency. Therefore, here we investigated the effects of env-mRNA splicing on polysome formation to identify mechanisms for Env up-regulation due to splicing. We performed polysome profile analyses using Env-expression plasmids producing spliced or unspliced env-mRNA and showed that the former formed polysomes more efficiently than the latter. Thus, splicing of env-mRNA facilitated polysome formation, suggesting that this contributes to up-regulation of Env expression. We replaced the env region of the expression plasmids with a luciferase (luc) gene, and found that in this case both unspliced and spliced luc-mRNA formed polysomes to a similar extent. Thus, we conclude that whether mRNA polysome formation is affected by splicing depends on the structure of gene in question. PMID:26909075

  14. Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA.

    PubMed

    Purcell, Maureen K; Pearman-Gillman, Schuyler; Thompson, Rachel L; Gregg, Jacob L; Hart, Lucas M; Winton, James R; Emmenegger, Eveline J; Hershberger, Paul K

    2016-07-01

    Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea. PMID:27154315

  15. Transcriptional and functional studies of Human Endogenous Retrovirus envelope EnvP(b) and EnvV genes in human trophoblasts

    SciTech Connect

    Vargas, Amandine Thiery, Maxime Lafond, Julie Barbeau, Benoit

    2012-03-30

    HERV (Human Endogenous Retrovirus)-encoded envelope proteins are implicated in the development of the placenta. Indeed, Syncytin-1 and -2 play a crucial role in the fusion of human trophoblasts, a key step in placentation. Other studies have identified two other HERV env proteins, namely EnvP(b) and EnvV, both expressed in the placenta. In this study, we have fully characterized both env transcripts and their expression pattern and have assessed their implication in trophoblast fusion. Through RACE analyses, standard spliced transcripts were detected, while EnvV transcripts demonstrated alternative splicing at its 3 Prime end. Promoter activity and expression of both genes were induced in forskolin-stimulated BeWo cells and in primary trophoblasts. Although we have confirmed the fusogenic activity of EnvP(b), overexpression or silencing experiments revealed no impact of this protein on trophoblast fusion. Our results demonstrate that both env genes are expressed in human trophoblasts but are not required for syncytialization.

  16. Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA

    USGS Publications Warehouse

    Purcell, Maureen K.; Pearman-Gillman, Schuyler; Thompson, Rachel L.; Gregg, Jacob L.; Hart, Lucas M.; Winton, James R.; Emmenegger, Eveline J.; Hershberger, Paul K.

    2016-01-01

    Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii. The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.

  17. Expression of Human Endogenous Retrovirus env Genes in the Blood of Breast Cancer Patients

    PubMed Central

    Rhyu, Dong-Won; Kang, Yun-Jeong; Ock, Mee-Sun; Eo, Jung-Woo; Choi, Yung-Hyun; Kim, Wun-Jae; Leem, Sun-Hee; Yi, Joo-Mi; Kim, Heui-Soo; Cha, Hee-Jae

    2014-01-01

    Human endogenous retroviruses (HERV) env proteins have been recently reported to be significantly up-regulated in certain cancers. Specifically, mRNA and protein levels of HERV-K (HML-2) are up-regulated in the blood plasma or serum of breast cancer patients. Here, we collected blood samples of 49 breast cancer patients and analyzed mRNA expressions of various HERVs env genes including HERV-R, HERV-H, HERV-K, and HERV-P by real-time PCR. The expression of env genes were significantly increased in the blood of primary breast cancer patients but were decreased in patients undergoing chemotherapy to a similar level with benign patients. When we compared the group currently undergoing chemotherapy and those patients undergoing chemotherapy simultaneously with radiotherapy, HERVs env genes were reduced more in the chemotherapy only group, suggesting that chemotherapy is more effective in reducing HERV env gene expression than is radiotherapy. Among chemotherapy groups, HERV env gene expression was the lowest in the taxotere- or taxol-treated group, suggesting that taxotere and taxol can reduce HERVs env expression. These data suggest the potential to use HERVs env genes as a diagnosis marker for primary breast cancer, and further studies are needed to identify the mechanism and physiological significance of the reduction of HERV env gene expression during chemotherapy. PMID:24964007

  18. Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov.

    PubMed

    Wen, A; Fegan, M; Hayward, C; Chakraborty, S; Sly, L I

    1999-04-01

    The phylogenetic relationships among members of the family Comamonadaceae and several unclassified strains were studied by direct sequencing of their PCR-amplified 16S rRNA genes. Based on the 16S rRNA gene sequence analysis, members of the family formed a coherent group. The closest relatives are species of the Rubrivivax sub-group: Leptothrix discophora, Ideonella dechloratans and Rubrivivax gelatinosus. The genus Hydrogenophaga formed two subclusters, as did the species of Acidovorax, whereas the five species of the genus [Aquaspirillum] were polyphyletic. Comamonas acidovorans was phylogenetically distant from the type species of Comamonas, Comamonas terrigena. On the basis of this work and previous studies, Comamonas acidovorans is removed from the genus Comamonas and renamed as Delftia acidovorans gen. nov., comb. nov. Descriptions of the new genus Delftia and of the type species Delftia acidovorans, for which the type strain is ATCC 15668T, are presented. PMID:10319477

  19. NMobTec-EnvEdu: M-Learning System for Environmental Education

    ERIC Educational Resources Information Center

    Cavus, Nadire

    2008-01-01

    This paper introduced the implementation of a New Mobile Technologies and Environmental Education System (NMobTec-EnvEdu) designed for m-learning environments. The NMobTec-EnvEdu system has been developed to provide environmental education in a collaborative framework to undergraduate students through the Internet using mobile phones. The study…

  20. Direct Involvement of HERV-W Env Glycoprotein in Human Trophoblast Cell Fusion and Differentiation

    PubMed Central

    Frendo, Jean-Louis; Olivier, Delphine; Cheynet, Valérie; Blond, Jean-Luc; Bouton, Olivier; Vidaud, Michel; Rabreau, Michèle; Evain-Brion, Danièle; Mallet, François

    2003-01-01

    We recently demonstrated that the product of the HERV-W env gene, a retroviral envelope protein also dubbed syncytin, is a highly fusogenic membrane glycoprotein inducing the formation of syncytia on interaction with the type D mammalian retrovirus receptor. In addition, the detection of HERV-W Env protein (Env-W) expression in placental tissue sections led us to propose a role for this fusogenic glycoprotein in placenta formation. To evaluate this hypothesis, we analyzed the involvement of Env-W in the differentiation of primary cultures of human villous cytotrophoblasts that spontaneously differentiate by cell fusion into syncytiotrophoblasts in vitro. First, we observed that HERV-W env mRNA and glycoprotein expression are colinear with primary cytotrophoblast differentiation and with expression of human chorionic gonadotropin (hCG), a marker of syncytiotrophoblast formation. Second, we observed that in vitro stimulation of trophoblast cell fusion and differentiation by cyclic AMP is also associated with a concomitant increase in HERV-W env and hCG mRNA and protein expression. Finally, by using specific antisense oligonucleotides, we demonstrated that inhibition of Env-W protein expression leads to a decrease of trophoblast fusion and differentiation, with the secretion of hCG in culture medium of antisense oligonucleotide-treated cells being decreased by fivefold. Taken together, these results strongly support a direct role for Env-W in human trophoblast cell fusion and differentiation. PMID:12724415

  1. Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques.

    PubMed

    Zurawski, Gerard; Zurawski, Sandra; Flamar, Anne-Laure; Richert, Laura; Wagner, Ralf; Tomaras, Georgia D; Montefiori, David C; Roederer, Mario; Ferrari, Guido; Lacabaratz, Christine; Bonnabau, Henri; Klucar, Peter; Wang, Zhiqing; Foulds, Kathryn E; Kao, Shing-Fen; Yates, Nicole L; LaBranche, Celia; Jacobs, Bertram L; Kibler, Karen; Asbach, Benedikt; Kliche, Alexander; Salazar, Andres; Reed, Steve; Self, Steve; Gottardo, Raphael; Galmin, Lindsey; Weiss, Deborah; Cristillo, Anthony; Thiebaut, Rodolphe; Pantaleo, Giuseppe; Levy, Yves

    2016-01-01

    Improved antigenicity against HIV-1 envelope (Env) protein is needed to elicit vaccine-induced protective immunity in humans. Here we describe the first tests in non-human primates (NHPs) of Env gp140 protein fused to a humanized anti-LOX-1 recombinant antibody for delivering Env directly to LOX-1-bearing antigen presenting cells, especially dendritic cells (DC). LOX-1, or 1ectin-like oxidized low-density lipoprotein (LDL) receptor-1, is expressed on various antigen presenting cells and endothelial cells, and is involved in promoting humoral immune responses. The anti-LOX-1 Env gp140 fusion protein was tested for priming immune responses and boosting responses in animals primed with replication competent NYVAC-KC Env gp140 vaccinia virus. Anti-LOX-1 Env gp140 vaccination elicited robust cellular and humoral responses when used for either priming or boosting immunity. Co-administration with Poly ICLC, a TLR3 agonist, was superior to GLA, a TLR4 agonist. Both CD4+ and CD8+ Env-specific T cell responses were elicited by anti-LOX-1 Env gp140, but in particular the CD4+ T cells were multifunctional and directed to multiple epitopes. Serum IgG and IgA antibody responses induced by anti-LOX-1 Env gp140 against various gp140 domains were cross-reactive across HIV-1 clades; however, the sera neutralized only HIV-1 bearing sequences most similar to the clade C 96ZM651 Env gp140 carried by the anti-LOX-1 vehicle. These data, as well as the safety of this protein vaccine, justify further exploration of this DC-targeting vaccine approach for protective immunity against HIV-1. PMID:27077384

  2. Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques

    PubMed Central

    Zurawski, Sandra; Flamar, Anne-Laure; Richert, Laura; Wagner, Ralf; Tomaras, Georgia D.; Montefiori, David C.; Roederer, Mario; Ferrari, Guido; Lacabaratz, Christine; Bonnabau, Henri; Klucar, Peter; Wang, Zhiqing; Foulds, Kathryn E.; Kao, Shing-Fen; Yates, Nicole L.; LaBranche, Celia; Jacobs, Bertram L.; Kibler, Karen; Asbach, Benedikt; Kliche, Alexander; Salazar, Andres; Reed, Steve; Self, Steve; Gottardo, Raphael; Galmin, Lindsey; Weiss, Deborah; Cristillo, Anthony; Thiebaut, Rodolphe; Pantaleo, Giuseppe; Levy, Yves

    2016-01-01

    Improved antigenicity against HIV-1 envelope (Env) protein is needed to elicit vaccine-induced protective immunity in humans. Here we describe the first tests in non-human primates (NHPs) of Env gp140 protein fused to a humanized anti-LOX-1 recombinant antibody for delivering Env directly to LOX-1-bearing antigen presenting cells, especially dendritic cells (DC). LOX-1, or 1ectin-like oxidized low-density lipoprotein (LDL) receptor-1, is expressed on various antigen presenting cells and endothelial cells, and is involved in promoting humoral immune responses. The anti-LOX-1 Env gp140 fusion protein was tested for priming immune responses and boosting responses in animals primed with replication competent NYVAC-KC Env gp140 vaccinia virus. Anti-LOX-1 Env gp140 vaccination elicited robust cellular and humoral responses when used for either priming or boosting immunity. Co-administration with Poly ICLC, a TLR3 agonist, was superior to GLA, a TLR4 agonist. Both CD4+ and CD8+ Env-specific T cell responses were elicited by anti-LOX-1 Env gp140, but in particular the CD4+ T cells were multifunctional and directed to multiple epitopes. Serum IgG and IgA antibody responses induced by anti-LOX-1 Env gp140 against various gp140 domains were cross-reactive across HIV-1 clades; however, the sera neutralized only HIV-1 bearing sequences most similar to the clade C 96ZM651 Env gp140 carried by the anti-LOX-1 vehicle. These data, as well as the safety of this protein vaccine, justify further exploration of this DC-targeting vaccine approach for protective immunity against HIV-1. PMID:27077384

  3. Clustering and Mobility of HIV-1 Env at Viral Assembly Sites Predict Its Propensity To Induce Cell-Cell Fusion

    PubMed Central

    Roy, Nathan H.; Chan, Jany; Lambelé, Marie

    2013-01-01

    HIV-1 Env mediates virus attachment to and fusion with target cell membranes, and yet, while Env is still situated at the plasma membrane of the producer cell and before its incorporation into newly formed particles, Env already interacts with the viral receptor CD4 on target cells, thus enabling the formation of transient cell contacts that facilitate the transmission of viral particles. During this first encounter with the receptor, Env must not induce membrane fusion, as this would prevent the producer cell and the target cell from separating upon virus transmission, but how Env's fusion activity is controlled remains unclear. To gain a better understanding of the Env regulation that precedes viral transmission, we examined the nanoscale organization of Env at the surface of producer cells. Utilizing superresolution microscopy (stochastic optical reconstruction microscopy [STORM]) and fluorescence recovery after photobleaching (FRAP), we quantitatively assessed the clustering and dynamics of Env upon its arrival at the plasma membrane. We found that Gag assembly induced the aggregation of small Env clusters into larger domains and that these domains were completely immobile. Truncation of the cytoplasmic tail (CT) of Env abrogated Gag's ability to induce Env clustering and restored Env mobility at assembly sites, both of which correlated with increased Env-induced fusion of infected and uninfected cells. Hence, while Env trapping by Gag secures Env incorporation into viral particles, Env clustering and its sequestration at assembly sites likely also leads to the repression of its fusion function, and thus, by preventing the formation of syncytia, Gag helps to secure efficient transfer of viral particles to target cells. PMID:23637402

  4. High throughput functional analysis of HIV-1 env genes without cloning

    PubMed Central

    Kirchherr, Jennifer L; Lu, Xiaozhi; Kasongo, Webster; Chalwe, Victor; Mwananyanda, Lawrence; Musonda, Rosemary M; Xia, Shi-Mao; Scearce, Richard M; Liao, Hua-Xin; Montefiori, David C; Haynes, Barton F; Gao, Feng

    2007-01-01

    Functional human immunodeficiency virus type -1 env clones have been widely used for vaccine design, neutralization assays, and pathogenesis studies. However, obtaining bona fide functional env clones is a time consuming and labor intensive process. A new high throughput method has been developed to characterize HIV-1 env genes. Multiple rev/env gene cassettes were obtained from each of seven HIV-1 strains using single genome amplification (SGA) PCR. The CMV promoter was amplified separately by PCR. A promoter PCR (pPCR) method was developed to link both PCR products using an overlapping PCR method. Pseudovirions were generated by cotransfection of pPCR products and pSG3Δenv backbone into 293T cells. After infecting TZM-bl cells, 75 out of 87 (86%) of the rev/env gene cassettes were functional. Pseudoviruses generated with pPCR products or corresponding plasmid DNA showed similar sensitivity to six HIV-1 positive sera and three monoclonal antibodies, suggesting neutralization properties are not altered in pPCR pseudovirions. Furthermore, sufficient amounts of pseudovirions can be obtained for a large number of neutralization assays. The new pPCR method eliminates cloning, transformation, and plasmid DNA preparation steps in the generation of HIV-1 pseudovirions, this allows for quick analysis of multiple env genes from HIV-1 infected individuals. PMID:17416428

  5. Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, Antarcticimonas flava Yang et al. 2009 and Hoppeia youngheungensis Kwon et al. 2014.

    PubMed

    Hameed, Asif; Shahina, Mariyam; Lai, Wei-An; Lin, Shih-Yao; Liu, You-Cheng; Hsu, Yi-Han; Young, Chiu-Chung

    2015-02-01

    A Gram-staining-negative, strictly aerobic, yellowish-orange, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50(T), was isolated from estuarine water off Pingtung, Taiwan. The strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to Bizionia hallyeonensis T-y7(T) (93.9 %) followed by Corallibacter vietnamensis KMM 6217(T) (93.8 %), Geojedonia litorea YCS-16(T) (93.7 %) and other members of the family Flavobacteriaceae (<93.7 %). Strain CC-PY-50(T) established a distinct phyletic lineage associated with Mangrovimonas yunxiaonensis LYYY01(T) (93.1 % sequence similarity) with poor bootstrap support during neighbour-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50(T) was determined to accommodate large numbers of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, C16 : 0 and C16 : 1ω6c and/or C16 : 1ω7c. The DNA G+C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50(T) is proposed to represent a novel genus and species of the family Flavobacteriaceae, for which the name Hanstruepera neustonica gen. nov., sp. nov. is proposed. The type strain of the type species Hanstruepera neustonica gen. nov., sp. nov. is CC-PY-50(T) ( = JCM 19743(T) = BCRC 80747(T)). Emended descriptions of the species Sediminibacter furfurosus, Mangrovimonas yunxiaonensis, Antarcticimonas flava and Hoppeia

  6. Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus

    PubMed Central

    Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J.; Hosie, Margaret J.

    2015-01-01

    Analysing the evolution of feline immunodeficiency virus (FIV) at the intra-host level is important in order to address whether the diversity and composition of viral quasispecies affect disease progression. We examined the intra-host diversity and the evolutionary rates of the entire env and structural fragments of the env sequences obtained from sequential blood samples in 43 naturally infected domestic cats that displayed different clinical outcomes. We observed in the majority of cats that FIV env showed very low levels of intra-host diversity. We estimated that env evolved at a rate of 1.16×10−3 substitutions per site per year and demonstrated that recombinant sequences evolved faster than non-recombinant sequences. It was evident that the V3–V5 fragment of FIV env displayed higher evolutionary rates in healthy cats than in those with terminal illness. Our study provided the first evidence that the leader sequence of env, rather than the V3–V5 sequence, had the highest intra-host diversity and the highest evolutionary rate of all env fragments, consistent with this region being under a strong selective pressure for genetic variation. Overall, FIV env displayed relatively low intra-host diversity and evolved slowly in naturally infected cats. The maximum evolutionary rate was observed in the leader sequence of env. Although genetic stability is not necessarily a prerequisite for clinical stability, the higher genetic stability of FIV compared with human immunodeficiency virus might explain why many naturally infected cats do not progress rapidly to AIDS. PMID:25535323

  7. Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov.

    PubMed

    Krishnamurthi, S; Bhattacharya, A; Mayilraj, S; Saha, P; Schumann, P; Chakrabarti, T

    2009-06-01

    In the course of a study of the prokaryotic diversity of a landfill site in Chandigarh, India, a strain designated SK 55(T) was isolated and characterized using a polyphasic approach. Its 16S rRNA gene sequence showed closest similarity (98.3 %) to that of Sporosarcina macmurdoensis CMS 21w(T). The sequence similarity to strains of other hitherto described species of Sporosarcina was less than 95.5 %. Strain SK 55(T) contains peptidoglycan of the A4alpha type (l-Lys-d-Asp), MK-8 and MK-7 as the major menaquinones and iso-C(15 : 0) as the major fatty acid. Strain SK 55(T), Sporosarcina macmurdoensis and Sporosarcina ureae, the type species of the genus, had some polar lipids in common (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and an unknown lipid). However, an aminolipid, an aminophospholipid and an unknown lipid found in the former two organisms are similar, though not identical, but quite different from the profile of S. ureae. The genomic DNA G+C contents of strain SK 55(T) (46.0 mol%) and S. macmurdoensis CMS 21w(T) (44.0 mol%) are higher than those reported for the majority of species of Sporosarcina (36-42 mol%). As revealed by 16S rRNA gene sequence analysis, strain SK 55(T) and S. macmurdoensis CMS 21w(T) form a clade which is distinct from the clade occupied by other species of Sporosarcina. On the basis of phenotypic characteristics including chemotaxonomic data and analysis of the 16S rRNA gene sequence, we conclude that strain SK 55(T) should be considered as a member of a novel genus and species, for which the name Paenisporosarcina quisquiliarum gen. nov., sp. nov. is proposed. The type strain of Paenisporosarcina quisquiliarum is SK 55(T) (=MTCC7604(T) =JCM 14041(T)). S. macmurdoensis CMS 21w(T) shows more similarity in its 16S rRNA gene sequence (98.3 %), DNA G+C content and polar lipid profile to strain SK 55(T) than to S. ureae DSM 2281(T). Phylogenetically, it forms a coherent cluster with strain SK 55

  8. Immunization against HTLV-I with chitosan and tri-methylchitosan nanoparticles loaded with recombinant env23 and env13 antigens of envelope protein gp46.

    PubMed

    Amirnasr, Maryam; Fallah Tafti, Tannan; Sankian, Mojtaba; Rezaei, Abdorrahim; Tafaghodi, Mohsen

    2016-08-01

    To prevent the spread of HTLV-I (Human T-lymphotropic virus type 1), a safe and effective vaccine is required. To increase immune responses against the peptide antigens can be potentiated with polymer-based nanoparticles, like chitosan (CHT) and trimethylchitosan (TMC), as delivery system/adjuvant. CHT and TMC nanoparticles loaded with recombinant proteins (env23 & env13) of gp46 were prepared by direct coating of antigens with positively charged polymers. The size of CHT and TMC nanoparticles (NPs) loaded with each antigen was about 400 nm. The physical stability of NPs was followed for 4 weeks. Both formulations showed to be stable for about 15 days. The immunogenicity of NPs loaded with antigens was studied after nasal and subcutaneous immunization in mice. Three immunizations (7.5 μg antigen) were performed with 2 weeks intervals. Two weeks after the last booster dose, sera IgG subtypes were measured. After subcutaneous administration, for both nanoparticulate antigens, serum IgG1 and IgGtotal levels were higher than antigen solution (P < 0.001). After nasal administration, for env23, IgG2a levels and IgG2a/IgG1 ratio was significantly higher than groups with subcutaneous administration (P < 0.001). Both nanoparticles showed good immunoadjuvant potential. Env23 antigen was a better candidate for vaccination against HTLV-I, as it induced higher cellular immune responses, compared with env13. PMID:27235335

  9. Molecular evolution of human immunodeficiency virus env in humans and monkeys: similar patterns occur during natural disease progression or rapid virus passage.

    PubMed

    Hofmann-Lehmann, Regina; Vlasak, Josef; Chenine, Agnès-Laurence; Li, Pei-Lin; Baba, Timothy W; Montefiori, David C; McClure, Harold M; Anderson, Daniel C; Ruprecht, Ruth M

    2002-05-01

    Neonatal rhesus macaque 95-3 was inoculated with nonpassaged simian-human immunodeficiency virus strain SHIV-vpu(+), which encodes env of the laboratory-adapted human immunodeficiency virus (HIV) strain IIIB and is considered nonpathogenic. CD4(+) T-cell counts dropped to <200 cells/microl within 4.6 years, and monkey 95-3 died with opportunistic infections 5.9 years postinoculation. Transfer of blood from 95-3 to two naive adult macaques resulted in high peak viral loads and rapid, persistent T-cell depletion. Progeny virus evolved in 95-3 despite high SHIV-vpu(+) neutralizing antibody titers and still used CXCR4 but, in contrast to parental SHIV-vpu(+), productively infected macrophages and resisted neutralization. Sequence analysis revealed three new potential glycosylation sites in gp120; another two were lost. Strikingly similar mutations were detected in a laboratory worker who progressed to AIDS after accidental HIV-IIIB infection (T. Beaumont et al., J. Virol. 75:2246-2252, 2001), thus supporting the SHIV-vpu(+)/rhesus macaque system as a relevant model. Similar mutations were also described after rapid passage of chimeric viruses encoding IIIB env in rhesus and pig-tailed macaques (M. Cayabyab et al., J. Virol. 73:976-984, 1999; Z. Q. Liu et al., Virology 260:295-307, 1999; S. V. Narayan et al., Virology 256:54-63, 1999; R. Raghavan et al., Brain Pathol. 7:851-861, 1997; E. B. Stephens et al., Virology 231:313-321, 1997). Thus, HIV-IIIB env evolved similarly in three different species; this selection occurred in chronically infected individuals during disease progression as well as after rapid virus passage. We postulate that evolutionary pressure led to the outgrowth of more aggressive viral variants in all three species. PMID:11967343

  10. GenBank

    PubMed Central

    Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2014-01-01

    GenBank® is a comprehensive database that contains publicly available nucleotide sequences for over 280 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:24217914

  11. Using GenBank.

    PubMed

    Sayers, Eric W; Karsch-Mizrachi, Ilene

    2016-01-01

    GenBank(®) is a comprehensive database of publicly available DNA sequences for 300,000 named organisms, more than 110,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure and domain information, as well as the biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. GenBank usage scenarios ranging from local analyses of the data available via FTP to online analyses supported by the NCBI web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at www.ncbi.nlm.nih.gov . PMID:26519398

  12. GenBank

    PubMed Central

    Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2013-01-01

    GenBank® (http://www.ncbi.nlm.nih.gov) is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:23193287

  13. GenBank

    PubMed Central

    Benson, Dennis A.; Karsch-Mizrachi, Ilene; Clark, Karen; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2012-01-01

    GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 250 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:22144687

  14. GenBank

    PubMed Central

    Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2016-01-01

    GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:26590407

  15. Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported.

    PubMed

    Tongo, Marcel; Essomba, René G; Nindo, Frederick; Abrahams, Fatima; Nanfack, Aubin Joseph; Fokam, Joseph; Takou, Desire; Torimiro, Judith N; Mpoudi-Ngole, Eitel; Burgers, Wendy A; Martin, Darren P; Dorfman, Jeffrey R

    2015-10-01

    HIV-1 subtype G has played an early and central role in the emergent complexity of the HIV-1 group M (HIV-1M) epidemic in central/west Africa. Here, we analysed new subtype G env sequences sampled from 8 individuals in Yaoundé, Cameroon during 2007-2010, together with all publically available subtype G-attributed full-length env sequences with known sampling dates and locations. We inferred that the most recent common ancestor (MRCA) of the analysed subtype G env sequences most likely occurred in ∼1953 (95% Highest Posterior Density interval [HPD] 1939-1963): about 15 years earlier than previous estimates. We found that the subtype G env phylogeny has a complex structure including seven distinct lineages, each likely dating back to the late 1960s or early 1970s. Sequences from Angola, Gabon and the Democratic Republic of Congo failed to group consistently in these lineages, possibly because they are related to more ancient sequences that are poorly sampled. The circulating recombinant form (CRF), CRF06_cpx env sequences but not CRF25_cpx env sequences are phylogenetically nested within the subtype G clade. This confirms that the CRF06_cpx env plausibly was derived through recombination from a subtype G parent, and suggests that the CRF25_cpx env was likely derived from an HIV-1M lineage related to the MRCA of subtype G that has remained undiscovered and may be extinct. Overall, this fills important gaps in our knowledge of the early events in the spread of HIV-1M. PMID:26190450

  16. Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium.

    PubMed

    Yoon, J H; Kang, S S; Lee, K C; Lee, E S; Kho, Y H; Kang, K H; Park, Y H

    2001-07-01

    A bacterial strain, JG07T, isolated from the Korean traditional fermented seafood jeotgal, was subjected to a polyphasic taxonomic study. Cells of strain JG07T are cocci or short rods in the early growth phase but change to rods as the cultures age. The peptidoglycan type is A4alpha, based on L-Lys-D-Glu. The menaquinone profile is characterized by the predominance of MK-8 followed by MK-7 and MK-6. The cellular fatty acid profile contains major amounts of saturated, unsaturated and branched fatty acids. The cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol and bisphosphatidylglycerol. The G+C content of the DNA is 47 mol%. Phylogenetic analysis showed that strain JG07T forms a cluster with Planococcus okeanokoites and Planococcus mcmeekinii, and the relationship between this cluster and two other Planococcus species described previously is supported by bootstrap analysis at a confidence level of 100%. The 16S-23S internally transcribed spacer (ITS) sequence similarity and DNA-DNA relatedness values between strain JG07T and the type strains of other Planococcus species are in the range 74.6-83.2% and 10.4-20.5%, respectively. On the basis of the phenotypic and phylogenetic data and the genomic distinctiveness, strain JG07T is considered to represent a new genus and a new species, for which the name Planomicrobium koreense gen. nov., sp. nov. is proposed. It is also proposed that Planococcus okeanokoites and Planococcus mcmeekinii be transferred to the new genus Planomicrobium as Planomicrobium okeanokoites and Planomicrobium mcmeekinii, respectively. PMID:11491353

  17. Dose-dependent inhibition of Gag cellular immunity by Env in SIV/HIV DNA vaccinated macaques

    PubMed Central

    Valentin, Antonio; Li, Jinyao; Rosati, Margherita; Kulkarni, Viraj; Patel, Vainav; Jalah, Rashmi; Alicea, Candido; Reed, Steven; Sardesai, Niranjan; Berkower, Ira; Pavlakis, George N; Felber, Barbara K

    2015-01-01

    The induction of a balanced immune response targeting the major structural proteins, Gag and Env of HIV, is important for the development of an efficacious vaccine. The use of DNA plasmids expressing different antigens offers the opportunity to test in a controlled manner the influence of different vaccine components on the magnitude and distribution of the vaccine-induced cellular and humoral immune responses. Here, we show that increasing amounts of env DNA results in greatly enhanced Env antibody titers without significantly affecting the levels of anti-Env cellular immune responses. Co-immunization with Env protein further increased antibody levels, indicating that vaccination with DNA only is not sufficient for eliciting maximal humoral responses against Env. In contrast, under high env:gag DNA plasmid ratio, the development of Gag cellular responses was significantly reduced by either SIV or HIV Env, whereas Gag humoral responses were not affected. Our data indicate that a balanced ratio of the 2 key HIV/SIV vaccine components, Gag and Env, is important to avoid immunological interference and to achieve both maximal humoral responses against Env to prevent virus acquisition and maximal cytotoxic T cell responses against Gag to prevent virus spread. PMID:26125521

  18. Mucosal Immunization with Newcastle Disease Virus Vector Coexpressing HIV-1 Env and Gag Proteins Elicits Potent Serum, Mucosal, and Cellular Immune Responses That Protect against Vaccinia Virus Env and Gag Challenges

    PubMed Central

    Khattar, Sunil K.; Manoharan, Vinoth; Bhattarai, Bikash; LaBranche, Celia C.; Montefiori, David C.

    2015-01-01

    ABSTRACT Newcastle disease virus (NDV) avirulent strain LaSota was used to coexpress gp160 Env and p55 Gag from a single vector to enhance both Env-specific and Gag-specific immune responses. The optimal transcription position for both Env and Gag genes in the NDV genome was determined by generating recombinant NDV (rNDV)-Env-Gag (gp160 located between the P and M genes and Gag between the HN and L genes), rNDV-Gag-Env (Gag located between the P and M genes and gp160 between the HN and L genes), rNDV-Env/Gag (gp160 followed by Gag located between the P and M genes), and rNDV-Gag/Env (Gag followed by gp160 located between the P and M genes). All the recombinant viruses replicated at levels similar to those seen with parental NDV in embryonated chicken eggs and in chicken fibroblast cells. Both gp160 and Gag proteins were expressed at high levels in cell culture, with gp160 found to be incorporated into the envelope of NDV. The Gag and Env proteins expressed by all the recombinants except rNDV-Env-Gag self-assembled into human immunodeficiency virus type 1 (HIV-1) virus-like particles (VLPs). Immunization of guinea pigs by the intranasal route with these rNDVs produced long-lasting Env- and Gag-specific humoral immune responses. The Env-specific humoral and mucosal immune responses and Gag-specific humoral immune responses were higher in rNDV-Gag/Env and rNDV-Env/Gag than in the other recombinants. rNDV-Gag/Env and rNDV-Env/Gag were also more efficient in inducing cellular as well as protective immune responses to challenge with vaccinia viruses expressing HIV-1 Env and Gag in mice. These results suggest that vaccination with a single rNDV coexpressing Env and Gag represents a promising strategy to enhance immunogenicity and protective efficacy against HIV. PMID:26199332

  19. GenBank

    PubMed Central

    Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2015-01-01

    GenBank® (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:25414350

  20. Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring (Clupea pallasii)

    USGS Publications Warehouse

    Emmenegger, Eveline J.; Glenn, Jolene A.; Winton, James R.; Batts, William N.; Gregg, Jacob L.; Hershberger, Paul K.

    2014-01-01

    Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring (Clupea pallasii) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.

  1. Intersubunit disulfide isomerization controls membrane fusion of human T-cell leukemia virus Env.

    PubMed

    Li, Kejun; Zhang, Shujing; Kronqvist, Malin; Wallin, Michael; Ekström, Maria; Derse, David; Garoff, Henrik

    2008-07-01

    Human T-cell leukemia virus (HTLV-1) Env carries a typical disulfide isomerization motif, C(225)XXC, in the C-terminal domain SU. Here we have tested whether this motif is used for isomerization of the intersubunit disulfide of Env and whether this rearrangement is required for membrane fusion. We introduced the C225A and C228A mutations into Env and found that the former but not the latter mutant matured into covalently linked SU-TM complexes in transfected cells. Next, we constructed a secreted Env ectodomain and showed that it underwent incubation-dependent intersubunit disulfide isomerization on target cells. However, the rearrangement was blocked by the C225A mutation, suggesting that C(225) carried the isomerization-active thiol. Still, it was possible to reduce the intersubunit disulfide of the native C225A ectodomain mutant with dithiothreitol (DTT). The importance of the CXXC-mediated disulfide isomerization for infection was studied using murine leukemia virus vectors pseudotyped with wild-type or C225A HTLV-1 Env. We found that the mutant Env blocked infection, but this could be rescued with DTT. The fusion activity was tested in a fusion-from-within assay using a coculture of rat XC target and transfected BHK-21 effector cells. We found that the mutation blocked polykaryon formation, but this could be reversed with DTT. Similar DTT-reversible inhibition of infection and fusion was observed when a membrane-impermeable alkylator was present during the infection/fusion incubation. We conclude that the fusion activity of HTLV-1 Env is controlled by an SU CXXC-mediated isomerization of the intersubunit disulfide. Thus, this extends the applicability of the isomerization model from gammaretroviruses to deltaretroviruses. PMID:18480461

  2. Antibody to gp41 MPER Alters Functional Properties of HIV-1 Env without Complete Neutralization

    PubMed Central

    Kim, Arthur S.; Leaman, Daniel P.; Zwick, Michael B.

    2014-01-01

    Human antibody 10E8 targets the conserved membrane proximal external region (MPER) of envelope glycoprotein (Env) subunit gp41 and neutralizes HIV-1 with exceptional potency. Remarkably, HIV-1 containing mutations that reportedly knockout 10E8 binding to linear MPER peptides are partially neutralized by 10E8, producing a local plateau in the dose response curve. Here, we found that virus partially neutralized by 10E8 becomes significantly less neutralization sensitive to various MPER antibodies and to soluble CD4 while becoming significantly more sensitive to antibodies and fusion inhibitors against the heptad repeats of gp41. Thus, 10E8 modulates sensitivity of Env to ligands both pre- and post-receptor engagement without complete neutralization. Partial neutralization by 10E8 was influenced at least in part by perturbing Env glycosylation. With unliganded Env, 10E8 bound with lower apparent affinity and lower subunit occupancy to MPER mutant compared to wild type trimers. However, 10E8 decreased functional stability of wild type Env while it had an opposite, stabilizing effect on MPER mutant Envs. Clade C isolates with natural MPER polymorphisms also showed partial neutralization by 10E8 with altered sensitivity to various gp41-targeted ligands. Our findings suggest a novel mechanism of virus neutralization by demonstrating how antibody binding to the base of a trimeric spike cross talks with adjacent subunits to modulate Env structure and function. The ability of an antibody to stabilize, destabilize, partially neutralize as well as alter neutralization sensitivity of a virion spike pre- and post-receptor engagement may have implications for immunotherapy and vaccine design. PMID:25058619

  3. GenBank.

    PubMed

    Benson, D A; Boguski, M; Lipman, D J; Ostell, J

    1994-09-01

    The GenBank sequence database continues to expand its data coverage, quality control, annotation content and retrieval services for the scientific community. Besides handling direct submissions of sequence data from authors, GenBank also incorporates DNA sequences from all available public sources; an integrated retrieval system, known as Entrez, also makes available data from the major protein sequence and structural databases, and from U.S. and European patents. MIDLINE abstracts from published articles describing the sequences are also included as an additional source of biological annotation for sequence entries. GenBank supports distribution of the data via FTP, CD-ROM, and E-mail servers. Network server-client programs provide access to an integrated database for literature retrieval and sequence similarity searching. PMID:7937042

  4. GenBank

    PubMed Central

    Burks, Christian; Cassidy, Maxxwell; Cinkosky, Michael J.; Cumella, Karen E.; Gilna, Paul; Hayden, Jamie E.-D.; Keen, Gifford M.; Kelley, Tom A.; Kelly, Michael; Kristofferson, David; Ryals, Julie

    1991-01-01

    The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:2041806

  5. Cleavage-independent HIV-1 Env trimers engineered as soluble native spike mimetics for vaccine design

    PubMed Central

    Sharma, Shailendra Kumar; de Val, Natalia; Bale, Shridhar; Guenaga, Javier; Tran, Karen; Feng, Yu; Dubrovskaya, Viktoriya; Ward, Andrew B.; Wyatt, Richard T.

    2015-01-01

    Summary Viral glycoproteins mediate entry by pH-activated or receptor-engaged activation and exist in metastable pre-fusogenic states that may be stabilized by directed rational design. As recently reported, the conformationally fixed HIV-1 envelope glycoprotein (Env) trimers in the pre-fusion state (SOSIP) display molecular homogeneity and structural integrity at relatively high levels of resolution. However, the SOSIPs necessitate full Env precursor cleavage, which requires endogenous furin over-expression. Here, we developed an alternative strategy using flexible peptide covalent linkage of Env subdomains to produce soluble, homogeneous and cleavage-independent Env mimics, called native flexibly linked (NFL) trimers, as vaccine candidates. This simplified design avoids the need for furin co-expression and, in one case, antibody affinity purification to accelerate trimer scale-up for preclinical and clinical applications. We have successfully translated the NFL design to multiple HIV-1 subtypes, establishing the potential to become a general method of producing native-like, well-ordered Env trimers for HIV-1 or other viruses. PMID:25892233

  6. Parenteral Administration of Capsule Depolymerase EnvD Prevents Lethal Inhalation Anthrax Infection.

    PubMed

    Negus, David; Vipond, Julia; Hatch, Graham J; Rayner, Emma L; Taylor, Peter W

    2015-12-01

    Left untreated, inhalation anthrax is usually fatal. Vegetative forms of Bacillus anthracis survive in blood and tissues during infection due to elaboration of a protective poly-γ-D-glutamic acid (PDGA) capsule that permits uncontrolled bacterial growth in vivo, eventually leading to overwhelming bacillosis and death. As a measure to counter threats from multidrug-resistant strains, we are evaluating the prophylactic and therapeutic potential of the PDGA depolymerase EnvD, a stable and potent enzyme which rapidly and selectively removes the capsule from the surface of vegetative cells. Repeated intravenous administration of 10 mg/kg recombinant EnvD (rEnvD) to mice infected with lethal doses of B. anthracis Ames spores by inhalation prevented the emergence of symptoms of anthrax and death; all animals survived the 5-day treatment period, and 70% survived to the end of the 14-day observation period. In contrast to results in sham-treated animals, the lungs and spleen of rEnvD-dosed animals were free of gross pathological changes. We conclude that rEnvD has potential as an agent to prevent the emergence of inhalation anthrax in infected animals and is likely to be effective against drug-resistant forms of the pathogen. PMID:26438506

  7. Inside the Envelope: Endogenous Retrovirus-K Env as a Biomarker and Therapeutic Target

    PubMed Central

    Nadeau, Marie-Josée; Manghera, Mamneet; Douville, Renée N.

    2015-01-01

    Due to multiple ancestral human retroviral germ cell infections, the modern human genome is strewn with relics of these infections, termed endogenous retroviruses (ERVs). ERV expression has been silenced due to negative selective pressures and genetic phenomena such as mutations and epigenetic silencing. Nonetheless, select ERVs have retained the capacity to be damaging to their host when reawakened. Much of the current research on the ERVK Env protein strongly suggests a causal or contributive role in the pathogenesis of various cancers, autoimmune and infectious diseases. Additionally, there is a small body of research suggesting that ERVK Env has been domesticated for use in placental development, akin to the ERVW syncytin. Though much is left to ascertain, the innate immune response to ERVK Env expression has been partially characterized and appears to be due to a region located in the transmembrane domain of the Env protein. In this review, we aim to highlight ERVK Env as a biomarker for inflammatory conditions and explore its use as a future therapeutic target for cancers, HIV infection and neurological disease. PMID:26617584

  8. Inside the Envelope: Endogenous Retrovirus-K Env as a Biomarker and Therapeutic Target.

    PubMed

    Nadeau, Marie-Josée; Manghera, Mamneet; Douville, Renée N

    2015-01-01

    Due to multiple ancestral human retroviral germ cell infections, the modern human genome is strewn with relics of these infections, termed endogenous retroviruses (ERVs). ERV expression has been silenced due to negative selective pressures and genetic phenomena such as mutations and epigenetic silencing. Nonetheless, select ERVs have retained the capacity to be damaging to their host when reawakened. Much of the current research on the ERVK Env protein strongly suggests a causal or contributive role in the pathogenesis of various cancers, autoimmune and infectious diseases. Additionally, there is a small body of research suggesting that ERVK Env has been domesticated for use in placental development, akin to the ERVW syncytin. Though much is left to ascertain, the innate immune response to ERVK Env expression has been partially characterized and appears to be due to a region located in the transmembrane domain of the Env protein. In this review, we aim to highlight ERVK Env as a biomarker for inflammatory conditions and explore its use as a future therapeutic target for cancers, HIV infection and neurological disease. PMID:26617584

  9. Parenteral Administration of Capsule Depolymerase EnvD Prevents Lethal Inhalation Anthrax Infection

    PubMed Central

    Negus, David; Vipond, Julia; Hatch, Graham J.; Rayner, Emma L.

    2015-01-01

    Left untreated, inhalation anthrax is usually fatal. Vegetative forms of Bacillus anthracis survive in blood and tissues during infection due to elaboration of a protective poly-γ-d-glutamic acid (PDGA) capsule that permits uncontrolled bacterial growth in vivo, eventually leading to overwhelming bacillosis and death. As a measure to counter threats from multidrug-resistant strains, we are evaluating the prophylactic and therapeutic potential of the PDGA depolymerase EnvD, a stable and potent enzyme which rapidly and selectively removes the capsule from the surface of vegetative cells. Repeated intravenous administration of 10 mg/kg recombinant EnvD (rEnvD) to mice infected with lethal doses of B. anthracis Ames spores by inhalation prevented the emergence of symptoms of anthrax and death; all animals survived the 5-day treatment period, and 70% survived to the end of the 14-day observation period. In contrast to results in sham-treated animals, the lungs and spleen of rEnvD-dosed animals were free of gross pathological changes. We conclude that rEnvD has potential as an agent to prevent the emergence of inhalation anthrax in infected animals and is likely to be effective against drug-resistant forms of the pathogen. PMID:26438506

  10. Role of the long cytoplasmic domain of the SIV Env glycoprotein in early and late stages of infection

    PubMed Central

    Vzorov, Andrei N; Weidmann, Armin; Kozyr, Natalia L; Khaoustov, Vladimir; Yoffe, Boris; Compans, Richard W

    2007-01-01

    Background The Env glycoproteins of retroviruses play an important role in the initial steps of infection involving the binding to cell surface receptors and entry by membrane fusion. The Env glycoprotein also plays an important role in viral assembly at a late step of infection. Although the Env glycoprotein interacts with viral matrix proteins and cellular proteins associated with lipid rafts, its possible role during the early replication events remains unclear. Truncation of the cytoplasmic tail (CT) of the Env glycoprotein is acquired by SIV in the course of adaptation to human cells, and is known to be a determinant of SIV pathogenicity. Results We compared SIV viruses with full length or truncated (T) Env glycoproteins to analyze possible differences in entry and post-entry events, and assembly of virions. We observed that early steps in replication of SIV with full length or T Env were similar in dividing and non-dividing cells. However, the proviral DNA of the pathogenic virus clone SIVmac239 with full length Env was imported to the nucleus about 20-fold more efficiently than proviral DNA of SIVmac239T with T Env, and 100-fold more efficiently than an SIVmac18T variant with a single mutation A239T in the SU subunit and with a truncated cytoplasmic tail (CT). In contrast, proviral DNA of SIVmac18 with a full length CT and with a single mutation A239T in the SU subunit was imported to the nucleus about 50-fold more efficiently than SIVmac18T. SIV particles with full length Env were released from rhesus monkey PBMC, whereas a restriction of release of virus particles was observed from human 293T, CEMx174, HUT78 or macrophages. In contrast, SIV with T Envs were able to overcome the inhibition of release in human HUT78, CEMx174, 293T or growth-arrested CEMx174 cells and macrophages resulting in production of infectious particles. We found that the long CT of the Env glycoprotein was required for association of Env with lipid rafts. An Env mutant C787S which

  11. [VLP vaccines and effects of HIV-1 Env protein modifications on their antigenic properties].

    PubMed

    Vzorov, A N; Compans, R W

    2016-01-01

    An ideal protective HIV-1 vaccine can elicit broadly neutralizing antibodies, capable of preventing HIV transmission. The strategies of designing vaccines include generation of soluble recombinant proteins which mimic the native Env complex and are able to enhance the immunogenicity of gp120. Recent data indicate that the cytoplasmic tail (CT) of the Env protein has multiple functions, which can affect the early steps of infection, as well as viral assembly and antigenic properties. Modifications in the CT can be used to induce conformational changes in functional regions of gp120 and to stabilize the trimeric structure, avoiding immune misdirection and induction of non-neutralizing antibody responses. Env-trimers with modified CTs in virus-like particles (VLPs) are able to induce antibodies with broad spectrum neutralizing activity and high avidity and have the potential for developing an effective vaccine against HIV. PMID:27414779

  12. Increased susceptibility to beta-lactam antibiotics and decreased porin content caused by envB mutations of Salmonella typhimurium.

    PubMed Central

    Oppezzo, O J; Avanzati, B; Antón, D N

    1991-01-01

    Isogenic derivatives carrying envB6, envB9, or envB+ alleles were obtained from a strain of Salmonella typhimurium that was partially resistant to mecillinam, a beta-lactam antibiotic specific for penicillin-binding protein 2 (PBP 2). Testing of the isogenic strains with several antibacterial agents demonstrated that envB mutations either increased resistance (mecillinam) or did not affect the response (imipemen) to beta-lactams that act primarily on PBP 2, while susceptibilities to beta-lactams that act on PBP 1B, PBP 3, or both were increased. Furthermore, the susceptibilities of envB strains to hydrophobic compounds such as rifampin, novobiocin, or chloramphenicol were not modified, even though their susceptibilities to deoxycholate and crystal violet were enhanced. Outer cell membranes of envB mutants presented a 50% reduction in protein content compared with that of the isogenic envB+ strains, and OmpF and OmpD porins were particularly affected by the reduction. No alteration in the amount or pattern of periplasmic proteins was noticed, and lipopolysaccharides from envB mutants appeared to be normal by sodium dodecyl sulfate-urea-polyacrylamide gel electrophoresis. By using derivatives that produced a plasmid-encoded beta-lactamase, it was demonstrated that envB cells are slightly less permeable to cephalothin than envB+ bacteria are. It is concluded that the high susceptibility of envB mutants to beta-lactams is due to the increased effectiveness of the antibiotics on PBP 1B, PBP 3, or both. Images PMID:1656857

  13. SHIV-1157i and passaged progeny viruses encoding R5 HIV-1 clade C env cause AIDS in rhesus monkeys

    PubMed Central

    Humbert, Michael; Rasmussen, Robert A; Song, Ruijiang; Ong, Helena; Sharma, Prachi; Chenine, Agnès L; Kramer, Victor G; Siddappa, Nagadenahalli B; Xu, Weidong; Else, James G; Novembre, Francis J; Strobert, Elizabeth; O'Neil, Shawn P; Ruprecht, Ruth M

    2008-01-01

    Background Infection of nonhuman primates with simian immunodeficiency virus (SIV) or chimeric simian-human immunodeficiency virus (SHIV) strains is widely used to study lentiviral pathogenesis, antiviral immunity and the efficacy of AIDS vaccine candidates. SHIV challenges allow assessment of anti-HIV-1 envelope responses in primates. As such, SHIVs should mimic natural HIV-1 infection in humans and, to address the pandemic, encode HIV-1 Env components representing major viral subtypes worldwide. Results We have developed a panel of clade C R5-tropic SHIVs based upon env of a Zambian pediatric isolate of HIV-1 clade C, the world's most prevalent HIV-1 subtype. The parental infectious proviral clone, SHIV-1157i, was rapidly passaged through five rhesus monkeys. After AIDS developed in the first animal at week 123 post-inoculation, infected blood was infused into a sixth monkey. Virus reisolated at this late stage was still exclusively R5 tropic and mucosally transmissible. Here we describe the long-term follow-up of this initial cohort of six monkeys. Two have remained non-progressors, whereas the other four gradually progressed to AIDS within 123–270 weeks post-exposure. Two progressors succumbed to opportunistic infections, including a case of SV40 encephalitis. Conclusion These data document the disease progression induced by the first mucosally transmissible, pathogenic R5 non-clade B SHIV and suggest that SHIV-1157i-derived viruses, including the late-stage, highly replication-competent SHIV-1157ipd3N4 previously described (Song et al., 2006), display biological characteristics that mirror those of HIV-1 clade C and support their expanded use for AIDS vaccine studies in nonhuman primates. PMID:18928523

  14. Confluentimicrobium lipolyticum gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and emended description of Actibacterium mucosum Lucena et al. 2012.

    PubMed

    Park, Sooyeon; Park, Ji-Min; Kang, Chul-Hyung; Yoon, Jung-Hoon

    2014-11-01

    A Gram-negative, aerobic, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated SSK1-4(T), was isolated from the junction between the ocean and a freshwater spring at Jeju island, South Korea. Strain SSK1-4(T) was found to grow optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. In the neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences, strain SSK1-4(T) was found to form an evolutionary lineage independent of those of other genera within the family Rhodobacteraceae. Strain SSK1-4(T) exhibited the highest 16S rRNA gene sequence similarity values to the type strains of Ruegeria lacuscaerulensis (94.99 %), Ruegeria atlantica (94.98 %) and Rhodovulum marinum (94.97 %). Sequence similarities to the type strains of other recognized species were less than 94.87 %. Strain SSK1-4(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c and cyclo-C19:0 ω8c as the major fatty acids. The polar profile of strain SSK1-4(T) was found to contain phosphatidylglycerol, sulfoquinovosyldiacylglycerol, an unidentified lipid and an unidentified aminolipid as major components, which distinguish it from those of the phylogenetically related taxa. The DNA G+C content of strain SSK1-4(T) was determined to be 58.4 mol%. On the basis of the phylogenetic data and the chemotaxonomic and other phenotypic properties, strain SSK1-4(T) is considered to represent a new genus and species within the class Alphaproteobacteria, for which the name Confluentimicrobium lipolyticum gen. nov., sp. nov. is proposed. The type strain of C. lipolyticum is SSK1-4(T) (=KCTC 42136(T) = CECT 8621(T)). In addition, an emended description of Actibacterium mucosum Lucena et al. 2012 is also proposed. PMID:25150887

  15. Human Antibodies that Recognize Novel Immunodominant Quaternary Epitopes on the HIV-1 Env Protein.

    PubMed

    Hicar, Mark D; Chen, Xuemin; Sulli, Chidananda; Barnes, Trevor; Goodman, Jason; Sojar, Hakimuddin; Briney, Bryan; Willis, Jordan; Chukwuma, Valentine U; Kalams, Spyros A; Doranz, Benjamin J; Spearman, Paul; Crowe, James E

    2016-01-01

    Numerous broadly neutralizing antibodies (Abs) target epitopes that are formed or enhanced during mature HIV envelope formation (i.e. quaternary epitopes). Generally, it is thought that Env epitopes that induce broadly neutralizing Abs are difficult to access and poorly immunogenic because of the characteristic oligomerization, conformational flexibility, sequence diversity and extensive glycosylation of Env protein. To enhance for isolation of quaternary epitope-targeting Abs (QtAbs), we previously used HIV virus-like particles (VLPs) to bind B cells from long-term non-progressor subjects to identify a panel of monoclonal Abs. When expressed as recombinant full-length Abs, a subset of these novel Abs exhibited the binding profiles of QtAbs, as they either failed to bind to monomeric Env protein or showed much higher affinity for Env trimers and VLPs. These QtAbs represented a significant proportion of the B-cell response identified with VLPs. The Ab genes of these clones were highly mutated, but they did not neutralize common HIV strains. We sought to further define the epitopes targeted by these QtAbs. Competition-binding and mapping studies revealed these Abs targeted four separate epitopes; they also failed to compete for binding by Abs to known major neutralizing epitopes. Detailed epitope mapping studies revealed that two of the four epitopes were located in the gp41 subunit of Env. These QtAbs bound pre-fusion forms of antigen and showed differential binding kinetics depending on whether oligomers were produced as recombinant gp140 trimers or as full-length Env incorporated into VLPs. Antigenic regions within gp41 present unexpectedly diverse structural epitopes, including these QtAb epitopes, which may be targeted by the naturally occurring Ab response to HIV infection. PMID:27411063

  16. Human Antibodies that Recognize Novel Immunodominant Quaternary Epitopes on the HIV-1 Env Protein

    PubMed Central

    Hicar, Mark D.; Chen, Xuemin; Sulli, Chidananda; Barnes, Trevor; Goodman, Jason; Sojar, Hakimuddin; Briney, Bryan; Willis, Jordan; Chukwuma, Valentine U.; Kalams, Spyros A.; Doranz, Benjamin J.; Spearman, Paul; Crowe, James E.

    2016-01-01

    Numerous broadly neutralizing antibodies (Abs) target epitopes that are formed or enhanced during mature HIV envelope formation (i.e. quaternary epitopes). Generally, it is thought that Env epitopes that induce broadly neutralizing Abs are difficult to access and poorly immunogenic because of the characteristic oligomerization, conformational flexibility, sequence diversity and extensive glycosylation of Env protein. To enhance for isolation of quaternary epitope-targeting Abs (QtAbs), we previously used HIV virus-like particles (VLPs) to bind B cells from long-term non-progressor subjects to identify a panel of monoclonal Abs. When expressed as recombinant full-length Abs, a subset of these novel Abs exhibited the binding profiles of QtAbs, as they either failed to bind to monomeric Env protein or showed much higher affinity for Env trimers and VLPs. These QtAbs represented a significant proportion of the B-cell response identified with VLPs. The Ab genes of these clones were highly mutated, but they did not neutralize common HIV strains. We sought to further define the epitopes targeted by these QtAbs. Competition-binding and mapping studies revealed these Abs targeted four separate epitopes; they also failed to compete for binding by Abs to known major neutralizing epitopes. Detailed epitope mapping studies revealed that two of the four epitopes were located in the gp41 subunit of Env. These QtAbs bound pre-fusion forms of antigen and showed differential binding kinetics depending on whether oligomers were produced as recombinant gp140 trimers or as full-length Env incorporated into VLPs. Antigenic regions within gp41 present unexpectedly diverse structural epitopes, including these QtAb epitopes, which may be targeted by the naturally occurring Ab response to HIV infection. PMID:27411063

  17. B cells and monocytes from patients with active multiple sclerosis exhibit increased surface expression of both HERV-H Env and HERV-W Env, accompanied by increased seroreactivity

    PubMed Central

    2009-01-01

    Background The etiology of the neurogenerative disease multiple sclerosis (MS) is unknown. The leading hypotheses suggest that MS is the result of exposure of genetically susceptible individuals to certain environmental factor(s). Herpesviruses and human endogenous retroviruses (HERVs) represent potentially important factors in MS development. Herpesviruses can activate HERVs, and HERVs are activated in MS patients. Results Using flow cytometry, we have analyzed HERV-H Env and HERV-W Env epitope expression on the surface of PBMCs from MS patients with active and stable disease, and from control individuals. We have also analyzed serum antibody levels to the expressed HERV-H and HERV-W Env epitopes. We found a significantly higher expression of HERV-H and HERV-W Env epitopes on B cells and monocytes from patients with active MS compared with patients with stable MS or control individuals. Furthermore, patients with active disease had relatively higher numbers of B cells in the PBMC population, and higher antibody reactivities towards HERV-H Env and HERV-W Env epitopes. The higher antibody reactivities in sera from patients with active MS correlate with the higher levels of HERV-H Env and HERV-W Env expression on B cells and monocytes. We did not find such correlations for stable MS patients or for controls. Conclusion These findings indicate that both HERV-H Env and HERV-W Env are expressed in higher quantities on the surface of B cells and monocytes in patients with active MS, and that the expression of these proteins may be associated with exacerbation of the disease. PMID:19917105

  18. GenBank

    PubMed Central

    Burks, Christian; Cinkosky, Michael J.; Fischer, William M.; Gilna, Paul; Hayden, Jamie E.-D.; Keen, Gifford M.; Kelly, Michael; Kristofferson, David; Lawrence, Julie

    1992-01-01

    The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:1598235

  19. Repeated Vaccination of Cows with HIV Env gp140 during Subsequent Pregnancies Elicits and Sustains an Enduring Strong Env-Binding and Neutralising Antibody Response

    PubMed Central

    Center, Rob J.; Gonelli, Christopher; Muller, Brian; Mackenzie, Charlene; Khoury, Georges; Lichtfuss, Marit; Rawlin, Grant; Purcell, Damian F. J.

    2016-01-01

    An important feature of a potential vaccine against HIV is the production of broadly neutralising antibodies (BrNAbs) capable of potentially blocking infectivity of a diverse array of HIV strains. BrNAbs naturally arise in some HIV infected individuals after several years of infection and their serum IgG can neutralise various HIV strains across different subtypes. We previously showed that vaccination of cows with HIV gp140 AD8 trimers resulted in a high titre of serum IgG against HIV envelope (Env) that had strong BrNAb activity. These polyclonal BrNAbs concentrated into the colostrum during the late stage of pregnancy and can be harvested in vast quantities immediately after calving. In this study, we investigated the effect of prolonged HIV gp140 vaccination on bovine colostrum IgG HIV Env-binding and BrNAb activity over subsequent pregnancies. Repeated immunisation led to a maintained high titre of HIV Env specific IgG in the colostrum batches, but this did not increase through repeated cycles. Colostrum IgG from all batches also strongly competed with sCD4 binding to gp140 Env trimer and with human-derived monoclonal VRC01 and b12 BrNAbs that bind the CD4 binding site (CD4bs). Furthermore, competition neutralisation assays using RSC3 Env gp120 protein core and a derivative CD4bs mutant, RSC3 Δ371I/P363N, showed that CD4bs neutralising antibodies contribute to the neutralising activity of all batches of purified bovine colostrum IgG. This result indicates that the high IgG titre/avidity of anti-CD4bs antibodies with BrNAb activity was achieved during the first year of vaccination and was sustained throughout the years of repeated vaccinations in the cow tested. Although IgG of subsequent colostrum batches may have a higher avidity towards the CD4bs, the overall breadth in neutralisation was not enhanced. This implies that the boosting vaccinations over 4 years elicited a polyclonal antibody response that maintained the proportion of both neutralising and non

  20. Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability.

    PubMed

    Mason, Rosemarie D; Welles, Hugh C; Adams, Cameron; Chakrabarti, Bimal K; Gorman, Jason; Zhou, Tongqing; Nguyen, Richard; O'Dell, Sijy; Lusvarghi, Sabrina; Bewley, Carole A; Li, Hui; Shaw, George M; Sheng, Zizhang; Shapiro, Lawrence; Wyatt, Richard; Kwong, Peter D; Mascola, John R; Roederer, Mario

    2016-04-01

    The simian immunodeficiency virus (SIV) challenge model of lentiviral infection is often used as a model to human immunodeficiency virus type 1 (HIV-1) for studying vaccine mediated and immune correlates of protection. However, knowledge of the structure of the SIV envelope (Env) glycoprotein is limited, as is knowledge of binding specificity, function and potential efficacy of SIV antibody responses. In this study we describe the use of a competitive probe binding sort strategy as well as scaffolded probes for targeted isolation of SIV Env-specific monoclonal antibodies (mAbs). We isolated nearly 70 SIV-specific mAbs directed against major sites of SIV Env vulnerability analogous to broadly neutralizing antibody (bnAb) targets of HIV-1, namely, the CD4 binding site (CD4bs), CD4-induced (CD4i)-site, peptide epitopes in variable loops 1, 2 and 3 (V1, V2, V3) and potentially glycan targets of SIV Env. The range of SIV mAbs isolated includes those exhibiting varying degrees of neutralization breadth and potency as well as others that demonstrated binding but not neutralization. Several SIV mAbs displayed broad and potent neutralization of a diverse panel of 20 SIV viral isolates with some also neutralizing HIV-2(7312A). This extensive panel of SIV mAbs will facilitate more effective use of the SIV non-human primate (NHP) model for understanding the variables in development of a HIV vaccine or immunotherapy. PMID:27064278

  1. Identification of HIV-1 Genitourinary Tract Compartmentalization by Analyzing the env Gene Sequences in Urine

    PubMed Central

    BLASI, Maria; CARPENTER, J. Harris; BALAKUMARAN, Bala; CARA, Andrea; GAO, Feng; KLOTMAN, Mary E.

    2015-01-01

    Objective HIV-1 persists indefinitely in memory CD4+ T cells and other long-lived cellular reservoirs despite antiretroviral therapy (ART). Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from twenty-four HIV-1 infected subjects with detectable viremia. Design and Methods Blood and urine samples were obtained from 35 HIV-1 positive subjects. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine derived cell pellets respectively, as well as from plasma and PBMC from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter mode. Results We amplified and sequenced the full-length HIV-1 envelope (env) gene from twelve of the twenty-four individuals, indicating that fifty percent (50%) of the viremic HIV-1 positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four subjects with more than fifteen urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those PBMC and plasma-derived sequences, consistent with viral compartmentalization in the urine. Conclusions Our results suggest the presence of a distinct HIV compartment in the genitourinary tract. PMID:26372275

  2. Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability

    PubMed Central

    Mason, Rosemarie D.; Welles, Hugh C.; Adams, Cameron; Chakrabarti, Bimal K.; Gorman, Jason; Zhou, Tongqing; Nguyen, Richard; O’Dell, Sijy; Lusvarghi, Sabrina; Bewley, Carole A.; Li, Hui; Shaw, George M.; Sheng, Zizhang; Shapiro, Lawrence; Wyatt, Richard; Kwong, Peter D.; Mascola, John R.; Roederer, Mario

    2016-01-01

    The simian immunodeficiency virus (SIV) challenge model of lentiviral infection is often used as a model to human immunodeficiency virus type 1 (HIV-1) for studying vaccine mediated and immune correlates of protection. However, knowledge of the structure of the SIV envelope (Env) glycoprotein is limited, as is knowledge of binding specificity, function and potential efficacy of SIV antibody responses. In this study we describe the use of a competitive probe binding sort strategy as well as scaffolded probes for targeted isolation of SIV Env-specific monoclonal antibodies (mAbs). We isolated nearly 70 SIV-specific mAbs directed against major sites of SIV Env vulnerability analogous to broadly neutralizing antibody (bnAb) targets of HIV-1, namely, the CD4 binding site (CD4bs), CD4-induced (CD4i)-site, peptide epitopes in variable loops 1, 2 and 3 (V1, V2, V3) and potentially glycan targets of SIV Env. The range of SIV mAbs isolated includes those exhibiting varying degrees of neutralization breadth and potency as well as others that demonstrated binding but not neutralization. Several SIV mAbs displayed broad and potent neutralization of a diverse panel of 20 SIV viral isolates with some also neutralizing HIV-27312A. This extensive panel of SIV mAbs will facilitate more effective use of the SIV non-human primate (NHP) model for understanding the variables in development of a HIV vaccine or immunotherapy. PMID:27064278

  3. Env7p Associates with the Golgin Protein Imh1 at the trans-Golgi Network in Candida albicans.

    PubMed

    Rao, Kongara Hanumantha; Ghosh, Swagata; Datta, Asis

    2016-01-01

    Vesicular dynamics is one of the very important aspects of cellular physiology, an imbalance of which leads to the disorders or diseases in higher eukaryotes. We report the functional characterization of a palmitoylated protein kinase from Candida albicans whose homologue in Saccharomyces cerevisiae has been reported to be involved in negative regulation of membrane fusion and was named Env7. However, the downstream target of this protein remains to be identified. Env7 in C. albicans (CaEnv7) could be isolated from the membrane fraction and localized to vesicular structures associated with the Golgi apparatus. Our work reports Env7 in C. albicans as a new player involved in maintaining the functional dynamics at the trans-Golgi network (TGN) by interacting with two other TGN-resident proteins, namely, Imh1p and Arl1p. Direct interaction could be detected between Env7p and the golgin protein Imh1p. Env7 is itself phosphorylated (Env7p) and phosphorylates Imh1 in vivo. An interaction between Env7 and Imh1 is required for the targeted localization of Imh1. CaEnv7 has a putative palmitoylation site toward both N and C termini. An N-terminal palmitoylation-defective strain retains its ability to phosphorylate Imh1 in vitro. An ENV7 homozygous mutant showed compromised filamentation in solid media and attenuated virulence, whereas an overexpressed strain affected cell wall integrity. Thus, Env7 plays a subtle but important role at the level of multitier regulation that exists at the TGN. IMPORTANCE A multitier regulation exists at the trans-Golgi network in all higher organisms. We report a palmitoylated protein kinase, Env7, that functions at the TGN interface by interacting with two more TGN-resident proteins, namely, Imh1 and Arl1. Palmitoylation seems to be important for the specific localization. This study focuses on the involvement of a ubiquitous protein kinase, whose substrates had not yet been reported from any organism, as an upstream signaling component that

  4. Env7p Associates with the Golgin Protein Imh1 at the trans-Golgi Network in Candida albicans

    PubMed Central

    Rao, Kongara Hanumantha; Ghosh, Swagata

    2016-01-01

    ABSTRACT Vesicular dynamics is one of the very important aspects of cellular physiology, an imbalance of which leads to the disorders or diseases in higher eukaryotes. We report the functional characterization of a palmitoylated protein kinase from Candida albicans whose homologue in Saccharomyces cerevisiae has been reported to be involved in negative regulation of membrane fusion and was named Env7. However, the downstream target of this protein remains to be identified. Env7 in C. albicans (CaEnv7) could be isolated from the membrane fraction and localized to vesicular structures associated with the Golgi apparatus. Our work reports Env7 in C. albicans as a new player involved in maintaining the functional dynamics at the trans-Golgi network (TGN) by interacting with two other TGN-resident proteins, namely, Imh1p and Arl1p. Direct interaction could be detected between Env7p and the golgin protein Imh1p. Env7 is itself phosphorylated (Env7p) and phosphorylates Imh1 in vivo. An interaction between Env7 and Imh1 is required for the targeted localization of Imh1. CaEnv7 has a putative palmitoylation site toward both N and C termini. An N-terminal palmitoylation-defective strain retains its ability to phosphorylate Imh1 in vitro. An ENV7 homozygous mutant showed compromised filamentation in solid media and attenuated virulence, whereas an overexpressed strain affected cell wall integrity. Thus, Env7 plays a subtle but important role at the level of multitier regulation that exists at the TGN. IMPORTANCE A multitier regulation exists at the trans-Golgi network in all higher organisms. We report a palmitoylated protein kinase, Env7, that functions at the TGN interface by interacting with two more TGN-resident proteins, namely, Imh1 and Arl1. Palmitoylation seems to be important for the specific localization. This study focuses on the involvement of a ubiquitous protein kinase, whose substrates had not yet been reported from any organism, as an upstream signaling

  5. Antigenic properties of a transport-competent influenza HA/HIV Env chimeric protein

    SciTech Connect

    Ye Ling; Sun Yuliang; Lin Jianguo; Bu Zhigao; Wu Qingyang; Jiang, Shibo; Steinhauer, David A.; Compans, Richard W.; Yang Chinglai . E-mail: chyang@emory.edu

    2006-08-15

    The transmembrane subunit (gp41) of the HIV Env glycoprotein contains conserved neutralizing epitopes which are not well-exposed in wild-type HIV Env proteins. To enhance the exposure of these epitopes, a chimeric protein, HA/gp41, in which the gp41 of HIV-1 89.6 envelope protein was fused to the C-terminus of the HA1 subunit of the influenza HA protein, was constructed. Characterization of protein expression showed that the HA/gp41 chimeric proteins were expressed on cell surfaces and formed trimeric oligomers, as found in the HIV Env as well as influenza HA proteins. In addition, the HA/gp41 chimeric protein expressed on the cell surface can also be cleaved into 2 subunits by trypsin treatment, similar to the influenza HA. Moreover, the HA/gp41 chimeric protein was found to maintain a pre-fusion conformation. Interestingly, the HA/gp41 chimeric proteins on cell surfaces exhibited increased reactivity to monoclonal antibodies against the HIV Env gp41 subunit compared with the HIV-1 envelope protein, including the two broadly neutralizing monoclonal antibodies 2F5 and 4E10. Immunization of mice with a DNA vaccine expressing the HA/gp41 chimeric protein induced antibodies against the HIV gp41 protein and these antibodies exhibit neutralizing activity against infection by an HIV SF162 pseudovirus. These results demonstrate that the construction of such chimeric proteins can provide enhanced exposure of conserved epitopes in the HIV Env gp41 and may represent a novel vaccine design strategy for inducing broadly neutralizing antibodies against HIV.

  6. How Can HIV-Type-1-Env Immunogenicity Be Improved to Facilitate Antibody-Based Vaccine Development?

    PubMed Central

    Sanders, Rogier W.; Cerutti, Andrea; Moore, John P.

    2012-01-01

    Abstract No vaccine candidate has induced antibodies (Abs) that efficiently neutralize multiple primary isolates of HIV-1. Preexisting high titers of neutralizing antibodies (NAbs) are essential, because the virus establishes infection before anamnestic responses could take effect. HIV-1 infection elicits Abs against Env, Gag, and other viral proteins, but of these only a subset of the anti-Env Abs can neutralize the virus. Whereas the corresponding proteins from other viruses form the basis of successful vaccines, multiple large doses of HIV-1 Env elicit low, transient titers of Abs that are not protective in humans. The inaccessibility of neutralization epitopes hinders NAb induction, but Env may also subvert the immune response by interacting with receptors on T cells, B cells, monocytes, macrophages, and dendritic cells. Here, we discuss evidence from immunizations of different species with various modified Env constructs. We also suggest how the divergent Ab responses to Gag and Env during infection may reflect differences in B cell regulation. Drawing on these analyses, we outline strategies for improving Env as a component of a vaccine aimed at inducing strong and sustained NAb responses. PMID:21495876

  7. Identification of EnvC and Its Cognate Amidases as Novel Determinants of Intrinsic Resistance to Cationic Antimicrobial Peptides

    PubMed Central

    Oguri, Tamiko; Yeo, Won-Sik; Bae, Taeok

    2016-01-01

    Cationic antimicrobial peptides (CAMPs) are an essential part of the innate immune system. Some Gram-negative enteric pathogens, such as Salmonella enterica, show intrinsic resistance to CAMPs. However, the molecular basis of intrinsic resistance is poorly understood, largely due to a lack of information about the genes involved. In this study, using a microarray-based genomic technique, we screened the Keio collection of 3,985 Escherichia coli mutants for altered susceptibility to human neutrophil peptide 1 (HNP-1) and identified envC and zapB as novel genetic determinants of intrinsic CAMP resistance. In CAMP killing assays, an E. coli ΔenvCEc or ΔzapBEc mutant displayed a distinct profile of increased susceptibility to both LL-37 and HNP-1. Both mutants, however, displayed wild-type resistance to polymyxin B and human β-defensin 3 (HBD3), suggesting that the intrinsic resistance mediated by EnvC or ZapB is specific to certain CAMPs. A corresponding Salmonella ΔenvCSe mutant showed similarly increased CAMP susceptibility. The envC mutants of both E. coli and S. enterica displayed increased surface negativity and hydrophobicity, which partly explained the increased CAMP susceptibility. However, the ΔenvCEc mutant, but not the ΔenvCSe mutant, was defective in outer membrane permeability, excluding this defect as a common factor contributing to the increased CAMP susceptibility. Animal experiments showed that the Salmonella ΔenvCSe mutant had attenuated virulence. Taken together, our results indicate that the role of envC in intrinsic CAMP resistance is likely conserved among Gram-negative enteric bacteria, demonstrate the importance of intrinsic CAMP resistance for full virulence of S. enterica, and provide insight into distinct mechanisms of action of CAMPs. PMID:26810659

  8. Comprehensive Characterization of the Transmitted/founder env Genes from a Single MSM Cohort in China

    PubMed Central

    Chen, Yue; Li, Ning; Zhang, Tong; Huang, Xiaojie; Cai, Fangping; Vandergrift, Nathan; Xin, Ruolei; Meng, Zhefeng; Zhang, Xiaoyan; Jiang, Chunlai; Xu, Xiaoning; Montefiori, David C; Gao, Feng; Wu, Hao

    2015-01-01

    Background The men having sex with men (MSM) population has become one of major risk groups for HIV-1 infection in China. However, the epidemiological patterns, function of the env genes, and autologous and heterologous neutralization activity in the same MSM population have not been systematically characterized. Methods The env gene sequences were obtained by the single genome amplification (SGA). The time to the most recent common ancestor (tMRCA) was estimated for each genotype using the Bayesian MCMC approach. Coreceptor usage was determined in NP-2 cells. Neutralization was analyzed using Env pseudoviruses in TZM-bl cells. Results We have obtained 547 full-length env gene sequences by SGA from 30 acute/early HIV-1-infected individuals in the Beijing MSM cohort. Three genotypes (Subtype B, CRF01_AE, and CRF07_BC) were identified and 20% of the individuals were infected with multiple transmitted/founder (T/F) viruses. The tight clusters of the MSM sequences regardless of geographic origins indicated nearly exclusive transmission within the MSM population and limited number of introductions. The tMRCA for each genotype was 10-15 years after each was first introduced in China. Disparate preferences for coreceptor usages among three genotypes might lead to the changes in percentage of different genotypes in the MSM population over time. The genotype-matched and -mismatched neutralization activity varied among the three genotypes. Conclusions Identification of unique characteristics for transmission, coreceptor usage, neutralization profile and epidemic patterns of HIV-1 is critical for the better understanding of transmission mechanisms, development of preventive strategies, and evaluation of vaccine efficacy in the MSM population in China. PMID:25886933

  9. EnvMine: A text-mining system for the automatic extraction of contextual information

    PubMed Central

    2010-01-01

    Background For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind. Results EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings. Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations. Conclusion EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus

  10. Construction and characterization of the recombinant Moloney murine leukemia viruses bearing the mouse Fv-4 env gene.

    PubMed Central

    Masuda, M; Yoshikura, H

    1990-01-01

    A nucleotide sequence of the mouse Fv-4 env gene was completed. Structural comparison revealed a close relationship of Fv-4 to the ecotropic Cas-Br-E murine leukemia virus isolated from a wild mouse in southern California. Various portions of the env gene of Moloney murine leukemia virus were replaced by the corresponding Fv-4 env sequence to construct recombinant murine leukemia virus clones. Infectivity of these recombinants was checked by the S+L- cell focus induction assay and the XC cell syncytium formation assay. Recombinants bearing the following Fv-4 env sequence retained ecotropic infectivity; the AccI-BamHI and BamHI-BalI regions coding for the N- and C-terminal halves of Fv-4 gp70SU, respectively; and the BalI-NcoI region encoding the cleavage site between gp70SU and p15(E)TM of the Fv-4 env. However, when the Fv-4 sequence was substituted for the p15(E)TM-coding NcoI-EcoRV region or the AccI-EcoRV region covering almost the entire env gene, infectivity was undetectable in our assays. The recombinant clone containing the Fv-4 AccI-EcoRV region, i.e., almost the entire Fv-4 env sequence, was introduced with pSV2neo into NIH 3T3 cells, and a G418r cell line named NIH(Fv4)-2 was isolated. The NIH(Fv4)-2 cell released viral particles that contained reverse transcriptase, Fv-4 env molecules as well as the other viral proteins, and viral genomic RNA. However, proviral DNA synthesis was not detected upon inoculation of this virus in NIH 3T3 cells. The loss of infectivity of the recombinant virus bearing the Fv-4 AccI-EcoRV region appeared to be caused by failure in an early step of replication. Images PMID:2304138

  11. Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike

    PubMed Central

    Lee, Jeong Hyun; Leaman, Daniel P.; Kim, Arthur S.; Torrents de la Peña, Alba; Sliepen, Kwinten; Yasmeen, Anila; Derking, Ronald; Ramos, Alejandra; de Taeye, Steven W.; Ozorowski, Gabriel; Klein, Florian; Burton, Dennis R.; Nussenzweig, Michel C.; Poignard, Pascal; Moore, John P.; Klasse, Per Johan; Sanders, Rogier W.; Zwick, Michael B.; Wilson, Ian A.; Ward, Andrew B.

    2015-01-01

    The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120–gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120–gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes. PMID:26404402

  12. Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike.

    PubMed

    Lee, Jeong Hyun; Leaman, Daniel P; Kim, Arthur S; Torrents de la Peña, Alba; Sliepen, Kwinten; Yasmeen, Anila; Derking, Ronald; Ramos, Alejandra; de Taeye, Steven W; Ozorowski, Gabriel; Klein, Florian; Burton, Dennis R; Nussenzweig, Michel C; Poignard, Pascal; Moore, John P; Klasse, Per Johan; Sanders, Rogier W; Zwick, Michael B; Wilson, Ian A; Ward, Andrew B

    2015-01-01

    The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes. PMID:26404402

  13. Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike

    NASA Astrophysics Data System (ADS)

    Lee, Jeong Hyun; Leaman, Daniel P.; Kim, Arthur S.; Torrents de La Peña, Alba; Sliepen, Kwinten; Yasmeen, Anila; Derking, Ronald; Ramos, Alejandra; de Taeye, Steven W.; Ozorowski, Gabriel; Klein, Florian; Burton, Dennis R.; Nussenzweig, Michel C.; Poignard, Pascal; Moore, John P.; Klasse, Per Johan; Sanders, Rogier W.; Zwick, Michael B.; Wilson, Ian A.; Ward, Andrew B.

    2015-09-01

    The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes.

  14. Crystal structure, conformational fixation, and entry-related interactions of mature ligand-free HIV-1 Env

    PubMed Central

    Kwon, Young Do; Pancera, Marie; Acharya, Priyamvada; Georgiev, Ivelin S.; Crooks, Emma T.; Gorman, Jason; Joyce, M. Gordon; Guttman, Miklos; Ma, Xiaochu; Narpala, Sandeep; Soto, Cinque; Terry, Daniel S.; Yang, Yongping; Zhou, Tongqing; Ahlsen, Goran; Bailer, Robert T.; Chambers, Michael; Chuang, Gwo-Yu; Doria-Rose, Nicole A.; Druz, Aliaksandr; Hallen, Mark A.; Harned, Adam; Kirys, Tatsiana; Louder, Mark K.; O’Dell, Sijy; Ofek, Gilad; Osawa, Keiko; Prabhakaran, Madhu; Sastry, Mallika; Stewart-Jones, Guillaume B.E.; Stuckey, Jonathan; Thomas, Paul V.; Tittley, Tishina; Williams, Constance; Zhang, Baoshan; Zhao, Hong; Zhou, Zhou; Donald, Bruce R.; Lee, Lawrence K.; Zolla-Pazner, Susan; Baxa, Ulrich; Schön, Arne; Freire, Ernesto; Shapiro, Lawrence; Lee, Kelly K.; Arthos, James; Munro, James B.; Blanchard, Scott C.; Mothes, Walther; Binley, James M.; McDermott, Adrian B.; Mascola, John R.; Kwong, Peter D.

    2016-01-01

    As the sole viral antigen on the HIV-1-virion surface, trimeric Env is a focus of vaccine efforts. Here we present the structure of the ligand-free HIV-1-Env trimer, fix its conformation, and determine its receptor interactions. Epitope analyses revealed trimeric ligand-free Env to be structurally compatible with broadly neutralizing antibodies, but not poorly neutralizing ones. We coupled these compatibility considerations with binding antigenicity to engineer conformationally fixed Envs, including a 201C-433C (DS) variant, specifically recognized by broadly neutralizing antibodies. DS-Env retained nanomolar affinity for the CD4 receptor, with which it formed an asymmetric intermediate: a closed trimer bound by a single CD4 without the typical antigenic hallmarks of CD4 induction. Antigenicity-guided structural design can thus be used both to delineate mechanism and to fix conformation, with DS-Env trimers in virus-like particle and soluble formats providing a new generation of vaccine antigens. PMID:26098315

  15. Expression of the env gene from the avian endogenous retrovirus ALVE and regulation by miR-155.

    PubMed

    Hu, Xuming; Zhu, Wenqi; Chen, Shihao; Liu, Yangyang; Sun, Zhen; Geng, Tuoyu; Wang, Xiaoyan; Gao, Bo; Song, Chengyi; Qin, Aijian; Cui, Hengmi

    2016-06-01

    Endogenous retroviruses (ERVs) are important retroelements that reside in host genomes. However, ERV expression patterns and regulatory mechanisms are poorly understood. In this study, chicken embryo fibroblasts (CEFs) and MSB1 cells infected with Marek's disease virus (MDV) exhibited significantly increased expression of env from the endogenous retrovirus ALVE. In contrast, env expression was significantly lower in CEF and MSB1 cells infected with exogenous avian leukosis virus J (ALVJ) at the early infection stage. Furthermore, env was found to be ubiquitously expressed in various chicken tissues, with high expression in certain tissues at 2 days of age and low levels in most tissues, including immune organs (thymus, spleen and bursa) as well as the brain and heart, at 35 days of age. Sequence analysis revealed miR-155 target sites in env transcripts, which was verified using a firefly luciferase reporter assay, and treatment with miR-155 agomir significantly decreased levels of env transcripts in MSB1 and CEF cells. Together, these findings suggest that the env gene from the endogenous retrovirus ALVE is regulated by miR-155. PMID:27016933

  16. Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env

    NASA Astrophysics Data System (ADS)

    Guttman, Miklos; Cupo, Albert; Julien, Jean-Philippe; Sanders, Rogier W.; Wilson, Ian A.; Moore, John P.; Lee, Kelly K.

    2015-02-01

    HIV’s envelope glycoprotein (Env) is the sole target for neutralizing antibodies. The structures of many broadly neutralizing antibodies (bNAbs) in complex with truncated Env subunits or components have been reported. However, their interaction with the intact Env trimer, and the structural determinants that underlie neutralization resistance in this more native context are less well understood. Here we use hydrogen/deuterium exchange to examine the interactions between a panel of bNAbs and native-like Env trimers (SOSIP.664 trimers). Highly potent bNAbs cause only localized effects at their binding interface, while the binding of less potent antibodies is associated with elaborate changes throughout the trimer. In conjunction with binding kinetics, our results suggest that poorly neutralizing antibodies can only bind when the trimer transiently samples an open state. We propose that the kinetics of such opening motions varies among isolates, with Env from neutralization-sensitive viruses opening more frequently than Env from resistant viruses.

  17. HIV-1 Tat Promotes Integrin-Mediated HIV Transmission to Dendritic Cells by Binding Env Spikes and Competes Neutralization by Anti-HIV Antibodies

    PubMed Central

    Monini, Paolo; Cafaro, Aurelio; Srivastava, Indresh K.; Moretti, Sonia; Sharma, Victoria A.; Andreini, Claudia; Chiozzini, Chiara; Ferrantelli, Flavia; Cossut, Maria R. Pavone.; Tripiciano, Antonella; Nappi, Filomena; Longo, Olimpia; Bellino, Stefania; Picconi, Orietta; Fanales-Belasio, Emanuele; Borsetti, Alessandra; Toschi, Elena; Schiavoni, Ilaria; Bacigalupo, Ilaria; Kan, Elaine; Sernicola, Leonardo; Maggiorella, Maria T.; Montin, Katy; Porcu, Marco; Leone, Patrizia; Leone, Pasqualina; Collacchi, Barbara; Palladino, Clelia; Ridolfi, Barbara; Falchi, Mario; Macchia, Iole; Ulmer, Jeffrey B.; Buttò, Stefano; Sgadari, Cecilia; Magnani, Mauro; Federico, Maurizio P. M.; Titti, Fausto; Banci, Lucia; Dallocchio, Franco; Rappuoli, Rino; Ensoli, Fabrizio; Barnett, Susan W.; Garaci, Enrico; Ensoli, Barbara

    2012-01-01

    Use of Env in HIV vaccine development has been disappointing. Here we show that, in the presence of a biologically active Tat subunit vaccine, a trimeric Env protein prevents in monkeys virus spread from the portal of entry to regional lymph nodes. This appears to be due to specific interactions between Tat and Env spikes that form a novel virus entry complex favoring R5 or X4 virus entry and productive infection of dendritic cells (DCs) via an integrin-mediated pathway. These Tat effects do not require Tat-transactivation activity and are blocked by anti-integrin antibodies (Abs). Productive DC infection promoted by Tat is associated with a highly efficient virus transmission to T cells. In the Tat/Env complex the cysteine-rich region of Tat engages the Env V3 loop, whereas the Tat RGD sequence remains free and directs the virus to integrins present on DCs. V2 loop deletion, which unshields the CCR5 binding region of Env, increases Tat/Env complex stability. Of note, binding of Tat to Env abolishes neutralization of Env entry or infection of DCs by anti-HIV sera lacking anti-Tat Abs, which are seldom present in natural infection. This is reversed, and neutralization further enhanced, by HIV sera containing anti-Tat Abs such as those from asymptomatic or Tat-vaccinated patients, or by sera from the Tat/Env vaccinated monkeys. Thus, both anti-Tat and anti-Env Abs are required for efficient HIV neutralization. These data suggest that the Tat/Env interaction increases HIV acquisition and spreading, as a mechanism evolved by the virus to escape anti-Env neutralizing Abs. This may explain the low effectiveness of Env-based vaccines, which are also unlikely to elicit Abs against new Env epitopes exposed by the Tat/Env interaction. As Tat also binds Envs from different clades, new vaccine strategies should exploit the Tat/Env interaction for both preventative and therapeutic interventions. PMID:23152803

  18. A Native-Like SOSIP.664 Trimer Based on an HIV-1 Subtype B env Gene

    PubMed Central

    Pugach, Pavel; Ozorowski, Gabriel; Cupo, Albert; Ringe, Rajesh; Yasmeen, Anila; de Val, Natalia; Derking, Ronald; Kim, Helen J.; Korzun, Jacob; Golabek, Michael; de los Reyes, Kevin; Ketas, Thomas J.; Julien, Jean-Philippe; Burton, Dennis R.; Wilson, Ian A.; Sanders, Rogier W.; Klasse, P. J.

    2015-01-01

    ABSTRACT Recombinant trimeric mimics of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike should expose as many epitopes as possible for broadly neutralizing antibodies (bNAbs) but few, if any, for nonneutralizing antibodies (non-NAbs). Soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A strain BG505 approach this ideal and are therefore plausible vaccine candidates. Here, we report on the production and in vitro properties of a new SOSIP.664 trimer derived from a subtype B env gene, B41, including how to make this protein in low-serum media without proteolytic damage (clipping) to the V3 region. We also show that nonclipped trimers can be purified successfully via a positive-selection affinity column using the bNAb PGT145, which recognizes a quaternary structure-dependent epitope at the trimer apex. Negative-stain electron microscopy imaging shows that the purified, nonclipped, native-like B41 SOSIP.664 trimers contain two subpopulations, which we propose represent an equilibrium between the fully closed and a more open conformation. The latter is different from the fully open, CD4 receptor-bound conformation and may represent an intermediate state of the trimer. This new subtype B trimer adds to the repertoire of native-like Env proteins that are suitable for immunogenicity and structural studies. IMPORTANCE The cleaved, trimeric envelope protein complex is the only neutralizing antibody target on the HIV-1 surface. Many vaccine strategies are based on inducing neutralizing antibodies. For HIV-1, one approach involves using recombinant, soluble protein mimics of the native trimer. At present, the only reliable way to make native-like, soluble trimers in practical amounts is via the introduction of specific sequence changes that confer stability on the cleaved form of Env. The resulting proteins are known as SOSIP.664 gp140 trimers, and the current paradigm is based on the BG505 subtype A env gene. Here, we describe the

  19. Phylogenetic and Structural Diversity in the Feline Leukemia Virus Env Gene

    PubMed Central

    Watanabe, Shinya; Kawamura, Maki; Odahara, Yuka; Anai, Yukari; Ochi, Haruyo; Nakagawa, So; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

    2013-01-01

    Feline leukemia virus (FeLV) belongs to the genus Gammaretrovirus, and causes a variety of neoplastic and non-neoplastic diseases in cats. Alteration of viral env sequences is thought to be associated with disease specificity, but the way in which genetic diversity of FeLV contributes to the generation of such variants in nature is poorly understood. We isolated FeLV env genes from naturally infected cats in Japan and analyzed the evolutionary dynamics of these genes. Phylogenetic reconstructions separated our FeLV samples into three distinct genetic clusters, termed Genotypes I, II, and III. Genotype I is a major genetic cluster and can be further classified into Clades 1–7 in Japan. Genotypes were correlated with geographical distribution; Genotypes I and II were distributed within Japan, whilst FeLV samples from outside Japan belonged to Genotype III. These results may be due to geographical isolation of FeLVs in Japan. The observed structural diversity of the FeLV env gene appears to be caused primarily by mutation, deletion, insertion and recombination, and these variants may be generated de novo in individual cats. FeLV interference assay revealed that FeLV genotypes did not correlate with known FeLV receptor subgroups. We have identified the genotypes which we consider to be reliable for evaluating phylogenetic relationships of FeLV, which embrace the high structural diversity observed in our sample. Overall, these findings extend our understanding of Gammaretrovirus evolutionary patterns in the field, and may provide a useful basis for assessing the emergence of novel strains and understanding the molecular mechanisms of FeLV transmission in cats. PMID:23593376

  20. Drosophila germline invasion by the endogenous retrovirus gypsy: involvement of the viral env gene.

    PubMed

    Pelisson, A; Mejlumian, L; Robert, V; Terzian, C; Bucheton, A

    2002-10-01

    The endogenous retrovirus gypsy is expressed at high levels in mutant flamenco female flies. Gypsy viral particles extracted from such flies can infect naive flamenco individuals raised in the presence of these extracts mixed into their food. This results in the integration of new proviruses into the germline genome. These proviruses can then increase their copy number by (1) expression in the flamenco female somatic cells, (2) transfer into the oocyte and (3) integration into the genome of the progeny. Surprisingly, unlike the infection observed in the feeding experiments, this strategy of endogenous proviral multiplication does not seem to involve the expression of the viral env gene. PMID:12225916

  1. Novel Feline Leukemia Virus Interference Group Based on the env Gene.

    PubMed

    Miyake, Ariko; Watanabe, Shinya; Hiratsuka, Takahiro; Ito, Jumpei; Ngo, Minh Ha; Makundi, Isaac; Kawasaki, Junna; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

    2016-05-01

    Feline leukemia virus (FeLV) subgroups have emerged in infected cats via the mutation or recombination of theenvgene of subgroup A FeLV (FeLV-A), the primary virus. We report the isolation and characterization of a novelenvgene, TG35-2, and report that the TG35-2 pseudotype can be categorized as a novel FeLV subgroup. The TG35-2 envelope protein displays strong sequence identity to FeLV-A Env, suggesting that selection pressure in cats causes novel FeLV subgroups to emerge. PMID:26889025

  2. λ Light Chain Bias Associated With Enhanced Binding and Function of Anti-HIV Env Glycoprotein Antibodies.

    PubMed

    Sajadi, Mohammad M; Farshidpour, Maham; Brown, Eric P; Ouyang, Xin; Seaman, Michael S; Pazgier, Marzena; Ackerman, Margaret E; Robinson, Harriet; Tomaras, Georgia; Parsons, Matthew S; Charurat, Manhattan; DeVico, Anthony L; Redfield, Robert R; Lewis, George K

    2016-01-01

    The humoral response to human immunodeficiency virus (HIV) remains incompletely understood. In this report, we describe biased λ light chain use during the HIV Env glycoprotein (Env) response in HIV infection and vaccination. We examined HIV Env binding (and neutralization) in the context of light chain use in subjects with acute HIV infection, chronic HIV infection, and among HIV vaccinees. In all populations tested, there was a λ chain bias for HIV Env binding antibodies, compared with other HIV antigens (such as p24) or tetanus toxoid. In subjects with chronic HIV infection, a λ bias was noted for neutralization, with λ antibodies accounting for up to 90% of all neutralization activity observed. This is the first report of antibody function in a human infection being tied to light chain use. In HIV infection, antibodies expressing λ light chains tended to have longer CDRL3s, increased light chain contact with HIV Env, and less hypermutation in the heavy chain, compared with antibodies using the κ light chain. These data also support an evolutionary model for the understanding the various κ to λ light chain ratios observed across species and suggest that the λ light chain bias against HIV provides the host an advantage in developing a more efficient humoral response. PMID:26347575

  3. Avian hemangioma retrovirus induces cell proliferation via the envelope (env) gene.

    PubMed

    Alian, A; Sela-Donenfeld, D; Panet, A; Eldor, A

    2000-10-10

    Several years ago, a field strain retrovirus, avian hemangioma virus (AHV), was isolated from hemangioma tumors in layer hens. Sequence analysis indicated that the AHV genome contains the three prototypic retroviral genes, gag, pol, and env, and is devoid of an oncogene. In cultured endothelial cells, however, AHV induced a significant cytopathic effect through a typical apoptotic cascade. We now demonstrate that AHV also induces cell proliferation and anchorage-independent growth of BSC-1 epithelial cells and NIH-3T3 fibroblasts. This was shown by measurements of (1) cell viability, (2) DNA synthesis, (3) flow cytometry analysis of the cell DNA content, and (4) clonogenic efficiency of the infected cells. Anchorage-independent cell growth was demonstrated by colony formation in soft agar. Moreover, the AHV env gene was cloned into a MuLV-based retroviral vector, and infection of NIH-3T3 cells with this vector induced cell proliferation as well as clonogenic growth. These results suggest that AHV, which is devoid of an oncogene, is a pleiotropic activator capable of inducing either apoptosis or cellular proliferation, depending on the infected cell type. PMID:11022004

  4. Structural insights into key sites of vulnerability on HIV-1 Env and influenza HA.

    PubMed

    Julien, Jean-Philippe; Lee, Peter S; Wilson, Ian A

    2012-11-01

    Human immunodeficiency virus-1 (HIV-1) envelope protein (Env) and influenza hemagglutinin (HA) are the surface glycoproteins responsible for viral entry into host cells, the first step in the virus life cycle necessary to initiate infection. These glycoproteins exhibit a high degree of sequence variability and glycosylation, which are used as strategies to escape host immune responses. Nonetheless, antibodies with broadly neutralizing activity against these viruses have been isolated that have managed to overcome these barriers. Here, we review recent advances in the structural characterization of these antibodies with their viral antigens that defines a few sites of vulnerability on these viral spikes. These broadly neutralizing antibodies tend to focus their recognition on the sites of similar function between the two viruses: the receptor-binding site and membrane fusion machinery. However, some sites of recognition are unique to the virus neutralized, such as the dense shield of oligomannose carbohydrates on HIV-1 Env. These observations are discussed in the context of structure-based design strategies to aid in vaccine design or development of antivirals. PMID:23046130

  5. Bordetella bronchialis sp. nov., Bordetella flabilis sp. nov. and Bordetella sputigena sp. nov., isolated from human respiratory specimens, and reclassification of Achromobacter sediminum Zhang et al. 2014 as Verticia sediminum gen. nov., comb. nov.

    PubMed

    Vandamme, Peter A; Peeters, Charlotte; Cnockaert, Margo; Inganäs, Elisabeth; Falsen, Enevold; Moore, Edward R B; Nunes, Olga C; Manaia, Célia M; Spilker, Theodore; LiPuma, John J

    2015-10-01

    The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile. PMID:26220296

  6. Enteractinococcus coprophilus gen. nov., sp. nov., of the family Micrococcaceae, isolated from Panthera tigris amoyensis faeces, and transfer of Yaniella fodinae Dhanjal et al. 2011 to the genus Enteractinococcus as Enteractinococcus fodinae comb. nov.

    PubMed Central

    Cao, Yan-Ru; Jin, Rong-Xian; Han, Li; Li, You-Long; Huang, Xue-Shi; Xue, Quan-Hong

    2012-01-01

    A novel actinobacterium, designated strain YIM 100590T, was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590T is a member of the family Micrococcaceae. Cells were coccoid to oval (0.7–1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10–37 °C (optimum 28 °C) and at pH 7.0–11.0 (optimum pH 8.0). The major fatty acids were iso-C15 : 0 (32.22 %), anteiso-C15 : 0 (31.64 %) and iso-C16 : 0 (17.38 %). The peptidoglycan was of A4α type (l-Lys–Gly–l-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9 %) and MK-8 (8.3 %). The DNA G+C content of strain YIM 100590T was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae. On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590T is considered to represent a novel species of a new genus within the family Micrococcaceae, for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590T ( = DSM 24083T = JCM 17352T). Yaniella fodinae DSM 22966T was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5T = DSM 22966T = JCM 17931T = MTCC 9846T). PMID:22228667

  7. A Multivalent Clade C HIV-1 Env Trimer Cocktail Elicits a Higher Magnitude of Neutralizing Antibodies than Any Individual Component

    PubMed Central

    Bricault, Christine A.; Kovacs, James M.; Nkolola, Joseph P.; Yusim, Karina; Giorgi, Elena E.; Shields, Jennifer L.; Perry, James; Lavine, Christy L.; Cheung, Ann; Ellingson-Strouss, Katharine; Rademeyer, Cecelia; Gray, Glenda E.; Williamson, Carolyn; Stamatatos, Leonidas; Seaman, Michael S.; Korber, Bette T.; Chen, Bing

    2014-01-01

    ABSTRACT The sequence diversity of human immunodeficiency virus type 1 (HIV-1) presents a formidable challenge to the generation of an HIV-1 vaccine. One strategy to address such sequence diversity and to improve the magnitude of neutralizing antibodies (NAbs) is to utilize multivalent mixtures of HIV-1 envelope (Env) immunogens. Here we report the generation and characterization of three novel, acute clade C HIV-1 Env gp140 trimers (459C, 405C, and 939C), each with unique antigenic properties. Among the single trimers tested, 459C elicited the most potent NAb responses in vaccinated guinea pigs. We evaluated the immunogenicity of various mixtures of clade C Env trimers and found that a quadrivalent cocktail of clade C trimers elicited a greater magnitude of NAbs against a panel of tier 1A and 1B viruses than any single clade C trimer alone, demonstrating that the mixture had an advantage over all individual components of the cocktail. These data suggest that vaccination with a mixture of clade C Env trimers represents a promising strategy to augment vaccine-elicited NAb responses. IMPORTANCE It is currently not known how to generate potent NAbs to the diverse circulating HIV-1 Envs by vaccination. One strategy to address this diversity is to utilize mixtures of different soluble HIV-1 envelope proteins. In this study, we generated and characterized three distinct, novel, acute clade C soluble trimers. We vaccinated guinea pigs with single trimers as well as mixtures of trimers, and we found that a mixture of four trimers elicited a greater magnitude of NAbs than any single trimer within the mixture. The results of this study suggest that further development of Env trimer cocktails is warranted. PMID:25540368

  8. Biodegradation of tetrahydrofuran and 1,4-dioxane by soluble diiron monooxygenase in Pseudonocardia sp. strain ENV478.

    PubMed

    Masuda, Hisako; McClay, Kevin; Steffan, Robert J; Zylstra, Gerben J

    2012-01-01

    1,4-Dioxane is an important groundwater contaminant. Pseudonocardia sp. strain ENV478 degrades 1,4-dioxane via cometabolism after the growth on tetrahydrofuran (THF) and other carbon sources. Here, we have identified a THF monooxygenase (thm) in ENV478. The thm genes are transcribed constitutively and are induced to higher levels by THF. Decreased translation of the thmB gene encoding one of the monooxygenase subunits by antisense RNA resulted in the loss of its ability to degrade THF and 1,4-dioxane. This is the first study to link thm genes to THF degradation, as well as the cometabolic oxidation of 1,4-dioxane. PMID:23147387

  9. Antigenic and 3D structural characterization of soluble X4 and hybrid X4-R5 HIV-1 Env trimers

    PubMed Central

    2014-01-01

    Background HIV-1 is decorated with trimeric glycoprotein spikes that enable infection by engaging CD4 and a chemokine coreceptor, either CCR5 or CXCR4. The variable loop 3 (V3) of the HIV-1 envelope protein (Env) is the main determinant for coreceptor usage. The predominant CCR5 using (R5) HIV-1 Env has been intensively studied in function and structure, whereas the trimeric architecture of the less frequent, but more cytopathic CXCR4 using (X4) HIV-1 Env is largely unknown, as are the consequences of sequence changes in and near V3 on antigenicity and trimeric Env structure. Results Soluble trimeric gp140 Env constructs were used as immunogenic mimics of the native spikes to analyze their antigenic properties in the context of their overall 3D structure. We generated soluble, uncleaved, gp140 trimers from a prototypic T-cell line-adapted (TCLA) X4 HIV-1 strain (NL4-3) and a hybrid (NL4-3/ADA), in which the V3 spanning region was substituted with that from the primary R5 isolate ADA. Compared to an ADA (R5) gp140, the NL4-3 (X4) construct revealed an overall higher antibody accessibility, which was most pronounced for the CD4 binding site (CD4bs), but also observed for mAbs against CD4 induced (CD4i) epitopes and gp41 mAbs. V3 mAbs showed significant binding differences to the three constructs, which were refined by SPR analysis. Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope. We obtained 3D reconstructions of the NL4-3 and the NL4-3/ADA gp140 trimers via electron microscopy and single particle analysis, which indicates that both constructs inherit a propeller-like architecture. The first 3D reconstruction of an Env construct from an X4 TCLA HIV-1 strain reveals an open conformation, in contrast to recently published more closed structures from R5 Env. Exchanging the X4 V3 spanning region for that of R5 ADA did not alter the open

  10. Inhibition of HIV Env binding to cellular receptors by monoclonal antibody 2G12 as probed by Fc-tagged gp120

    PubMed Central

    Binley, James M; Ngo-Abdalla, Stacie; Moore, Penny; Bobardt, Michael; Chatterji, Udayan; Gallay, Philippe; Burton, Dennis R; Wilson, Ian A; Elder, John H; de Parseval, Aymeric

    2006-01-01

    During natural HIV infection, an array of host receptors are thought to influence virus attachment and the kinetics of infection. In this study, to probe the interactions of HIV envelope (Env) with various receptors, we assessed the inhibitory properties of various anti-Env monoclonal antibodies (mAbs) in binding assays. To assist in detecting Env in attachment assays, we generated Fc fusions of full-length wild-type gp120 and several variable loop-deleted gp120s. Through investigation of the inhibition of Env binding to cell lines expressing CD4, CCR5, DC-SIGN, syndecans or combinations thereof, we found that the broadly neutralizing mAb, 2G12, directed to a unique carbohydrate epitope of gp120, inhibited Env-CCR5 binding, partially inhibited Env-DC-SIGN binding, but had no effect on Env-syndecan association. Furthermore, 2G12 inhibited Env attachment to primary monocyte-derived dendritic cells, that expressed CD4 and CCR5 primary HIV receptors, as well as DC-SIGN, and suggested that the dual activities of 2G12 could be valuable in vivo for inhibiting initial virus dissemination and propagation. PMID:16817962

  11. FutureGen Project Report

    SciTech Connect

    Cabe, Jim; Elliott, Mike

    2010-09-30

    This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near zero emissions integrated gasification combined cycle power plant and carbon capture and storage project (IGCC-CCS). With the goal to design, build, and reliably operate the first IGCC-CCS facility, FutureGen would have been the lowest emitting pulverized coal power plant in the world, while providing a timely and relevant basis for coal combustion power plants deploying carbon capture in the future. The content of this report summarizes key findings and results of applicable project evaluations; modeling, design, and engineering assessments; cost estimate reports; and schedule and risk mitigation from initiation of the FutureGen project through final flow sheet analyses including capital and operating reports completed under DOE award DE-FE0000587. This project report necessarily builds upon previously completed siting, design, and development work executed under DOE award DE-FC26- 06NT4207 which included the siting process; environmental permitting, compliance, and mitigation under the National Environmental Policy Act; and development of conceptual and design basis documentation for the FutureGen plant. For completeness, the report includes as attachments the siting and design basis documents, as well as the source documentation for the following: • Site evaluation and selection process and environmental characterization • Underground Injection Control (UIC) Permit Application including well design and subsurface modeling • FutureGen IGCC-CCS Design Basis Document • Process evaluations and technology selection via Illinois Clean Coal Review Board Technical Report • Process flow diagrams and heat/material balance for slurry-fed gasifier configuration • Process flow diagrams and heat/material balance

  12. Summary of CPAS Gen II Parachute Analysis

    NASA Technical Reports Server (NTRS)

    Morris, Aaron L.; Bledsoe, Kristin J.; Fraire, Usbaldo, Jr.; Moore, James W.; Olson, Leah M.; Ray, Eric

    2011-01-01

    The Orion spacecraft is currently under development by NASA and Lockheed Martin. Like Apollo, Orion will use a series of parachutes to slow its descent and splashdown safely. The Orion parachute system, known as the CEV Parachute Assembly System (CPAS), is being designed by NASA, the Engineering and Science Contract Group (ESCG), and Airborne Systems. The first generation (Gen I) of CPAS testing consisted of thirteen tests and was executed in the 2007-2008 timeframe. The Gen I tests provided an initial understanding of the CPAS parachutes. Knowledge gained from Gen I testing was used to plan the second generation of testing (Gen II). Gen II consisted of six tests: three singleparachute tests, designated as Main Development Tests, and three Cluster Development Tests. Gen II required a more thorough investigation into parachute performance than Gen I. Higher fidelity instrumentation, enhanced analysis methods and tools, and advanced test techniques were developed. The results of the Gen II test series are being incorporated into the CPAS design. Further testing and refinement of the design and model of parachute performance will occur during the upcoming third generation of testing (Gen III). This paper will provide an overview of the developments in CPAS analysis following the end of Gen I, including descriptions of new tools and techniques as well as overviews of the Gen II tests.

  13. Preclinical Studies of Human Immunodeficiency Virus/AIDS Vaccines: Inverse Correlation between Avidity of Anti-Env Antibodies and Peak Postchallenge Viremia ▿ †

    PubMed Central

    Zhao, Jun; Lai, Lilin; Amara, Rama Rao; Montefiori, David C.; Villinger, Francois; Chennareddi, Lakshmi; Wyatt, Linda S.; Moss, Bernard; Robinson, Harriet L.

    2009-01-01

    A major challenge for human immunodeficiency virus (HIV)/AIDS vaccines is the elicitation of anti-Env antibodies (Ab) capable of neutralizing the diversity of isolates in the pandemic. Here, we show that high-avidity, but nonneutralizing, Abs can have an inverse correlation with peak postchallenge viremia for a heterologous challenge. Vaccine studies were conducted in rhesus macaques using DNA priming followed by modified vaccinia Ankara boosting with HIV type 1 (HIV-1) immunogens that express virus-like particles displaying CCR5-tropic clade B (strain ADA) or clade C (IN98012) Envs. Rhesus granulocyte-macrophage colony-stimulating factor was used as an adjuvant for enhancing the avidity of anti-Env Ab responses. Challenge was with simian/human immunodeficiency virus (SHIV)-162P3, a CCR5-tropic clade B chimera of SIV and HIV-1. Within the groups receiving the clade B vaccine, a strong inverse correlation was found between the avidity of anti-Env Abs and peak postchallenge viremia. This correlation required the use of native but not gp120 or gp140 forms of Env for avidity assays. The high-avidity Ab elicited by the ADA Env had excellent breadth for the Envs of incident clade B but not clade C isolates, whereas the high-avidity Ab elicited by the IN98012 Env had excellent breadth for incident clade C but not clade B isolates. High-avidity Ab elicited by a SHIV vaccine with a dual-tropic clade B Env (89.6) had limited breadth for incident isolates. Our results suggest that certain Envs can elicit nonneutralizing but high-avidity Ab with broad potential for blunting incident infections of the same clade. PMID:19224993

  14. Preclinical studies of human immunodeficiency virus/AIDS vaccines: inverse correlation between avidity of anti-Env antibodies and peak postchallenge viremia.

    PubMed

    Zhao, Jun; Lai, Lilin; Amara, Rama Rao; Montefiori, David C; Villinger, Francois; Chennareddi, Lakshmi; Wyatt, Linda S; Moss, Bernard; Robinson, Harriet L

    2009-05-01

    A major challenge for human immunodeficiency virus (HIV)/AIDS vaccines is the elicitation of anti-Env antibodies (Ab) capable of neutralizing the diversity of isolates in the pandemic. Here, we show that high-avidity, but nonneutralizing, Abs can have an inverse correlation with peak postchallenge viremia for a heterologous challenge. Vaccine studies were conducted in rhesus macaques using DNA priming followed by modified vaccinia Ankara boosting with HIV type 1 (HIV-1) immunogens that express virus-like particles displaying CCR5-tropic clade B (strain ADA) or clade C (IN98012) Envs. Rhesus granulocyte-macrophage colony-stimulating factor was used as an adjuvant for enhancing the avidity of anti-Env Ab responses. Challenge was with simian/human immunodeficiency virus (SHIV)-162P3, a CCR5-tropic clade B chimera of SIV and HIV-1. Within the groups receiving the clade B vaccine, a strong inverse correlation was found between the avidity of anti-Env Abs and peak postchallenge viremia. This correlation required the use of native but not gp120 or gp140 forms of Env for avidity assays. The high-avidity Ab elicited by the ADA Env had excellent breadth for the Envs of incident clade B but not clade C isolates, whereas the high-avidity Ab elicited by the IN98012 Env had excellent breadth for incident clade C but not clade B isolates. High-avidity Ab elicited by a SHIV vaccine with a dual-tropic clade B Env (89.6) had limited breadth for incident isolates. Our results suggest that certain Envs can elicit nonneutralizing but high-avidity Ab with broad potential for blunting incident infections of the same clade. PMID:19224993

  15. Specifically modified Env immunogens activate B-cell precursors of broadly neutralizing HIV-1 antibodies in transgenic mice

    PubMed Central

    McGuire, Andrew T.; Gray, Matthew D.; Dosenovic, Pia; Gitlin, Alexander D.; Freund, Natalia T.; Petersen, John; Correnti, Colin; Johnsen, William; Kegel, Robert; Stuart, Andrew B.; Glenn, Jolene; Seaman, Michael S.; Schief, William R.; Strong, Roland K.; Nussenzweig, Michel C.; Stamatatos, Leonidas

    2016-01-01

    VRC01-class broadly neutralizing HIV-1 antibodies protect animals from experimental infection and could contribute to an effective vaccine response. Their predicted germline forms (gl) bind Env inefficiently, which may explain why they are not elicited by HIV-1 Env-immunization. Here we show that an optimized Env immunogen can engage multiple glVRC01-class antibodies. Furthermore, this immunogen activates naive B cells expressing the human germline heavy chain of 3BNC60, paired with endogenous mouse light chains in vivo. To address whether it activates B cells expressing the fully humanized gl3BNC60 B-cell receptor (BCR), we immunized mice carrying both the heavy and light chains of gl3BNC60. B cells expressing this BCR display an autoreactive phenotype and fail to respond efficiently to soluble forms of the optimized immunogen, unless it is highly multimerized. Thus, specifically designed Env immunogens can activate naive B cells expressing human BCRs corresponding to precursors of broadly neutralizing HIV-1 antibodies even when the B cells display an autoreactive phenotype. PMID:26907590

  16. Specifically modified Env immunogens activate B-cell precursors of broadly neutralizing HIV-1 antibodies in transgenic mice.

    PubMed

    McGuire, Andrew T; Gray, Matthew D; Dosenovic, Pia; Gitlin, Alexander D; Freund, Natalia T; Petersen, John; Correnti, Colin; Johnsen, William; Kegel, Robert; Stuart, Andrew B; Glenn, Jolene; Seaman, Michael S; Schief, William R; Strong, Roland K; Nussenzweig, Michel C; Stamatatos, Leonidas

    2016-01-01

    VRC01-class broadly neutralizing HIV-1 antibodies protect animals from experimental infection and could contribute to an effective vaccine response. Their predicted germline forms (gl) bind Env inefficiently, which may explain why they are not elicited by HIV-1 Env-immunization. Here we show that an optimized Env immunogen can engage multiple glVRC01-class antibodies. Furthermore, this immunogen activates naive B cells expressing the human germline heavy chain of 3BNC60, paired with endogenous mouse light chains in vivo. To address whether it activates B cells expressing the fully humanized gl3BNC60 B-cell receptor (BCR), we immunized mice carrying both the heavy and light chains of gl3BNC60. B cells expressing this BCR display an autoreactive phenotype and fail to respond efficiently to soluble forms of the optimized immunogen, unless it is highly multimerized. Thus, specifically designed Env immunogens can activate naive B cells expressing human BCRs corresponding to precursors of broadly neutralizing HIV-1 antibodies even when the B cells display an autoreactive phenotype. PMID:26907590

  17. From AWE-GEN to AWE-GEN-2d: a high spatial and temporal resolution weather generator

    NASA Astrophysics Data System (ADS)

    Peleg, Nadav; Fatichi, Simone; Paschalis, Athanasios; Molnar, Peter; Burlando, Paolo

    2016-04-01

    A new weather generator, AWE-GEN-2d (Advanced WEather GENerator for 2-Dimension grid) is developed following the philosophy of combining physical and stochastic approaches to simulate meteorological variables at high spatial and temporal resolution (e.g. 2 km x 2 km and 5 min for precipitation and cloud cover and 100 m x 100 m and 1 h for other variables variable (temperature, solar radiation, vapor pressure, atmospheric pressure and near-surface wind). The model is suitable to investigate the impacts of climate variability, temporal and spatial resolutions of forcing on hydrological, ecological, agricultural and geomorphological impacts studies. Using appropriate parameterization the model can be used in the context of climate change. Here we present the model technical structure of AWE-GEN-2d, which is a substantial evolution of four preceding models (i) the hourly-point scale Advanced WEather GENerator (AWE-GEN) presented by Fatichi et al. (2011, Adv. Water Resour.) (ii) the Space-Time Realizations of Areal Precipitation (STREAP) model introduced by Paschalis et al. (2013, Water Resour. Res.), (iii) the High-Resolution Synoptically conditioned Weather Generator developed by Peleg and Morin (2014, Water Resour. Res.), and (iv) the Wind-field Interpolation by Non Divergent Schemes presented by Burlando et al. (2007, Boundary-Layer Meteorol.). The AWE-GEN-2d is relatively parsimonious in terms of computational demand and allows generating many stochastic realizations of current and projected climates in an efficient way. An example of model application and testing is presented with reference to a case study in the Wallis region, a complex orography terrain in the Swiss Alps.

  18. Design of Lipid Nanocapsule Delivery Vehicles for Multivalent Display of Recombinant Env Trimers in HIV Vaccination

    PubMed Central

    2015-01-01

    Immunization strategies that elicit antibodies capable of neutralizing diverse virus strains will likely be an important part of a successful vaccine against HIV. However, strategies to promote robust humoral responses against the native intact HIV envelope trimer structure are lacking. We recently developed chemically cross-linked lipid nanocapsules as carriers of molecular adjuvants and encapsulated or surface-displayed antigens, which promoted follicular helper T-cell responses and elicited high-avidity, durable antibody responses to a candidate malaria antigen. To apply this system to the delivery of HIV antigens, Env gp140 trimers with terminal his-tags (gp140T-his) were anchored to the surface of lipid nanocapsules via Ni-NTA-functionalized lipids. Initial experiments revealed that the large (409 kDa), heavily glycosylated trimers were capable of extracting fluid phase lipids from the membranes of nanocapsules. Thus, liquid-ordered and/or gel-phase lipid compositions were required to stably anchor trimers to the particle membranes. Trimer-loaded nanocapsules combined with the clinically relevant adjuvant monophosphoryl lipid A primed high-titer antibody responses in mice at antigen doses ranging from 5 μg to as low as 100 ng, whereas titers dropped more than 50-fold over the same dose range when soluble trimer was mixed with a strong oil-in-water adjuvant comparator. Nanocapsule immunization also broadened the number of distinct epitopes on the HIV trimer recognized by the antibody response. These results suggest that nanocapsules displaying HIV trimers in an oriented, multivalent presentation can promote key aspects of the humoral response against Env immunogens. PMID:25020048

  19. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.

    PubMed

    Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

    1995-10-01

    The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

  20. Progressive Truncations C Terminal to the Membrane-Spanning Domain of Simian Immunodeficiency Virus Env Reduce Fusogenicity and Increase Concentration Dependence of Env for Fusion

    PubMed Central

    Lin, Xiaoxu; Derdeyn, Cynthia A.; Blumenthal, Robert; West, John; Hunter, Eric

    2003-01-01

    The simian immunodeficiency virus (SIV) transmembrane (TM) protein, gp41, has multiple functions, which include anchoring the glycoprotein complex in the lipid envelope of the virus and mediating fusion of the virus and host cell membranes. Recently, a series of mutants of the SIVmac239 TM protein that have truncations at the carboxyl terminus of the membrane-spanning domain (MSD) have been characterized (J. T. West, P. Johnston, S. R. Dubay, and E. Hunter, J. Virol. 75:9601-9612, 2001). These mutants retained membrane anchorage but demonstrated reduced fusogenicity and infectivity as the MSD length was shortened. We have established a novel three-color fluorescence assay, which allows qualitative confocal and quantitative flow cytometric analyses, to further characterize the nature of the fusion defect in five of the MSD mutants: TM185, TM186, TM187, TM188, and TM189. Our analysis showed that each mutant could mediate complete lipid and aqueous dye transfer at early time points after effector and target cell mixing. No hemifusion with only lipid dye flux was detected. However, another intermediate fusion stage, which appears to involve small-fusion-pore formation that allowed small aqueous dye transfer but prevented the exchange of large cytoplasmic components, was identified infrequently in mutant-Env-expressing cell and target cell mixtures. Quantitative flow cytometric analysis of these mutants demonstrated that the TM187, TM188, and TM189 mutants were significantly more fusogenic than TM185 and TM186 but remained significantly impaired compared to the wild type. Moreover, fusion efficiency showed an increased dependence on the expression level of glycoproteins, suggesting that, for these mutants, formation of an active fusion complex was an increasingly stochastic event. PMID:12768026

  1. Macrophage entry mediated by HIV Envs from brain and lymphoid tissues is determined by the capacity to use low CD4 levels and overall efficiency of fusion

    SciTech Connect

    Thomas, Elaine R.; Dunfee, Rebecca L.; Stanton, Jennifer; Bogdan, Derek; Taylor, Joann; Kunstman, Kevin; Bell, Jeanne E.; Wolinsky, Steven M.; Gabuzda, Dana . E-mail: dana_gabuzda@dfci.harvard.edu

    2007-03-30

    HIV infects macrophages and microglia in the central nervous system (CNS), which express lower levels of CD4 than CD4+ T cells in peripheral blood. To investigate mechanisms of HIV neurotropism, full-length env genes were cloned from autopsy brain and lymphoid tissues from 4 AIDS patients with HIV-associated dementia (HAD). Characterization of 55 functional Env clones demonstrated that Envs with reduced dependence on CD4 for fusion and viral entry are more frequent in brain compared to lymphoid tissue. Envs that mediated efficient entry into macrophages were frequent in brain but were also present in lymphoid tissue. For most Envs, entry into macrophages correlated with overall fusion activity at all levels of CD4 and CCR5. gp160 nucleotide sequences were compartmentalized in brain versus lymphoid tissue within each patient. Proline at position 308 in the V3 loop of gp120 was associated with brain compartmentalization in 3 patients, but mutagenesis studies suggested that P308 alone does not contribute to reduced CD4 dependence or macrophage-tropism. These results suggest that HIV adaptation to replicate in the CNS selects for Envs with reduced CD4 dependence and increased fusion activity. Macrophage-tropic Envs are frequent in brain but are also present in lymphoid tissues of AIDS patients with HAD, and entry into macrophages in the CNS and other tissues is dependent on the ability to use low receptor levels and overall efficiency of fusion.

  2. Mutation of the Dominant Endocytosis Motif in Human Immunodeficiency Virus Type 1 gp41 Can Complement Matrix Mutations without Increasing Env Incorporation

    PubMed Central

    West, John T.; Weldon, Sally K.; Wyss, Stephanie; Lin, Xiaoxu; Yu, Qin; Thali, Markus; Hunter, Eric

    2002-01-01

    The human immunodeficiency virus type 1 transmembrane glycoprotein (TM) is efficiently endocytosed in a clathrin-dependent manner. Internalization is mediated by a tyrosine-containing motif within the cytoplasmic domain, and replacement of the cytoplasmic tyrosine by cysteine or phenylalanine increased expression of mutant glycoprotein on the surface of transfected cells by as much as 2.5-fold. Because interactions between the cytoplasmic domain of Env and the matrix protein (MA) have been suggested to mediate incorporation of Env in virus particles, we examined whether perturbation of endocytosis would alter incorporation. Proviruses were constructed to contain the wild-type or mutant Env in conjunction with point mutations in MA that had previously been shown to block Env incorporation. These constructs were used to evaluate the effect of glycoprotein endocytosis on incorporation into virus particles and to test the necessity for a specific interaction between Env and MA to mediate incorporation. Viruses produced from transfected 293T cells were used to infect various cell lines, including MAGI, H9, and CEMx174. Viruses encoding both a disrupted endocytosis motif signal and mutations within MA were significantly more infectious in MAGI cells than their counterparts encoding a mutant MA and wild-type Env. This complementation of infectivity for the MA incorporation mutant viruses was not due to increased glycoprotein incorporation into particles but instead reflected an enhanced fusogenicity of the mutated Env proteins. Our findings further support the concept that a specific interaction between the long cytoplasmic domain of TM and MA is required for efficient incorporation of Env into assembling virions. Alteration of the endocytosis signal of Env, and the resulting increase in cell surface glycoprotein, has no effect on incorporation despite demonstrable effects on fusion, virus entry, and infectivity. PMID:11884559

  3. A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays

    SciTech Connect

    Kraus, Matthias H.; Parrish, Nicholas F.; Shaw, Katharina S.; Decker, Julie M.; Keele, Brandon F.; Salazar-Gonzalez, Jesus F.; Grayson, Truman; McPherson, David T.; Ping, Li-Hua; Anderson, Jeffrey A.; Swanstrom, Ronald; Williamson, Carolyn; Shaw, George M.; Hahn, Beatrice H.

    2010-02-20

    Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted/founder HIV-1 that were defective in the pseudotyping assay, although two produced infectious virions when expressed from their cognate proviruses. All of these constructs exhibited an unusual gene arrangement in which the first exon of rev (rev1) and vpu were in the same reading frame without an intervening stop codon. Disruption of the rev1-vpu fusion gene by frameshift mutation, stop codon, or abrogation of the rev initiation codon restored pseudovirion infectivity. Introduction of the fusion gene into wildtype Env cassettes severely compromised their function. The defect was not due to altered env and rev transcription or a dominant negative effect of the expressed fusion protein, but seemed to be caused by inefficient translation at the env initiation codon. Although the rev1-vpu polymorphism affects Env expression only in vitro, it can cause problems in studies requiring Env complementation, such as analyses of co-receptor usage and neutralization properties, since 3% of subtype A, 20% of subtype C and 5% of CRF01{sub A}/E viruses encode the fusion gene. A solution is to eliminate the rev initiation codon when amplifying rev-vpu-env cassettes since this increases Env expression irrespective of the presence of the polymorphism.

  4. Life+ EnvEurope DEIMS - improving access to long-term ecosystem monitoring data in Europe

    NASA Astrophysics Data System (ADS)

    Kliment, Tomas; Peterseil, Johannes; Oggioni, Alessandro; Pugnetti, Alessandra; Blankman, David

    2013-04-01

    Long-term ecological (LTER) studies aim at detecting environmental changes and analysing its related drivers. In this respect LTER Europe provides a network of about 450 sites and platforms. However, data on various types of ecosystems and at a broad geographical scale is still not easily available. Managing data resulting from long-term observations is therefore one of the important tasks not only for an LTER site itself but also on the network level. Exchanging and sharing the information within a wider community is a crucial objective in the upcoming years. Due to the fragmented nature of long-term ecological research and monitoring (LTER) in Europe - and also on the global scale - information management has to face several challenges: distributed data sources, heterogeneous data models, heterogeneous data management solutions and the complex domain of ecosystem monitoring with regard to the resulting data. The Life+ EnvEurope project (2010-2013) provides a case study for a workflow using data from the distributed network of LTER-Europe sites. In order to enhance discovery, evaluation and access to data, the EnvEurope Drupal Ecological Information Management System (DEIMS) has been developed. This is based on the first official release of the Drupal metadata editor developed by US LTER. EnvEurope DEIMS consists of three main components: 1) Metadata editor: a web-based client interface to manage metadata of three information resource types - datasets, persons and research sites. A metadata model describing datasets based on Ecological Metadata Language (EML) was developed within the initial phase of the project. A crosswalk to the INSPIRE metadata model was implemented to convey to the currently on-going European activities. Person and research site metadata models defined within the LTER Europe were adapted for the project needs. The three metadata models are interconnected within the system in order to provide easy way to navigate the user among the related

  5. HIV type 1 genetic diversity in Moyale, Mandera, and Turkana based on env-C2-V3 sequences.

    PubMed

    Khamadi, Samoel A; Lihana, Raphael W; Mwaniki, D L; Kinyua, Joyceline; Lagat, Nancy; Carter, Jane Y; Ichimura, Hiroshi; Oishi, Isao; Okoth, Fredrick A; Ochieng, Washington

    2008-12-01

    The genetic diversity of HIV-1 subtypes circulating in three districts of northern Kenya, i.e., Turkana, Mandera, and Moyale, was studied. DNA sequences encoding a portion of the env-C2-V3 region of the virus were amplified by PCR and sequenced directly. One hundred and fifty-nine samples were successfully sequenced in the env-C2-V3 region and analyzed. From the analysis, 57% were subtype A1, 27% were subtype C, 9% were subtype D, and the remaining 7% were unclassified. This study showed that HIV-1 subtype A1 was the dominant subtype in circulation in this region, though there was a significant percentage of HIV-1 subtype C in circulation there. PMID:19102688

  6. Vaccine Induction of Lymph Node-Resident Simian Immunodeficiency Virus Env-Specific T Follicular Helper Cells in Rhesus Macaques.

    PubMed

    Vargas-Inchaustegui, Diego A; Demers, Andrew; Shaw, Julia M; Kang, Guobin; Ball, David; Tuero, Iskra; Musich, Thomas; Mohanram, Venkatramanan; Demberg, Thorsten; Karpova, Tatiana S; Li, Qingsheng; Robert-Guroff, Marjorie

    2016-02-15

    Measurement of Ag-specific T follicular helper (TFH) cell activity in rhesus macaques has not previously been reported. Given that rhesus macaques are the animal model of choice for evaluating protective efficacy of HIV/SIV vaccine candidates and that TFH cells play a pivotal role in aiding B cell maturation, quantifying vaccine induction of HIV/SIV-specific TFH cells would greatly benefit vaccine development. In this study, we quantified SIV Env-specific IL-21-producing TFH cells for the first time, to our knowledge, in a nonhuman primate vaccine study. Macaques were primed twice mucosally with adenovirus 5 host range mutant recombinants encoding SIV Env, Rev, Gag, and Nef followed by two i.m. boosts with monomeric SIV gp120 or oligomeric SIV gp140 proteins. At 2 wk after the second protein boost, we obtained lymph node biopsy specimens and quantified the frequency of total and SIV Env-specific IL-21(+) TFH cells and total germinal center B cells, the size and number of germinal centers, and the frequency of SIV-specific Ab-secreting cells in B cell zones. Multiple correlation analyses established the importance of TFH for development of B cell responses in systemic and mucosally localized compartments, including blood, bone marrow, and rectum. Our results suggest that the SIV-specific TFH cells, initially induced by replicating adenovirus-recombinant priming, are long lived. The multiple correlations of SIV Env-specific TFH cells with systemic and mucosal SIV-specific B cell responses indicate that this cell population should be further investigated in HIV vaccine development as a novel correlate of immunity. PMID:26773147

  7. Identification of transmembrane helix 1 (TM1) surfaces important for EnvZ dimerisation and signal output.

    PubMed

    Heininger, Annika; Yusuf, Rahmi; Lawrence, Robert J; Draheim, Roger R

    2016-08-01

    The Escherichia coli sensor kinase EnvZ modulates porin expression in response to various stimuli, including extracellular osmolarity, the presence of procaine and interaction with an accessory protein, MzrA. Two major outer membrane porins, OmpF and OmpC, act as passive diffusion-limited pores that allow compounds, including certain classes of antibiotics such as β-lactams and fluoroquinolones, to enter the bacterial cell. Even though the mechanisms by which EnvZ detects and processes the presence of various stimuli are a fundamental component of microbial physiology, they are not yet fully understood. Here, we assess the role of TM1 during signal transduction in response to the presence of extracellular osmolarity. Various mechanisms of transmembrane communication have been proposed including rotation of individual helices within the transmembrane domain, dynamic movement of the membrane-distal portion of the cytoplasmic domain and regulated intra-protein unfolding. To assess these possibilities, we have created a library of single-Cys-containing EnvZ proteins in order to facilitate sulfhydryl-reactivity experimentation. Our results demonstrate that the major TM1-TM1' interface falls along a single surface consisting of residue positions 19, 23, 26, 30 and 34. In addition, we show that Cys substitutions within the N- and C-terminal regions of TM1 result in drastic changes to EnvZ signal output. Finally, we demonstrate that core residues within TM1 are responsible for both TM1 dimerisation and maintenance of steady-state signal output. Overall, our results suggest that no major rearrangement of the TM1-TM1' interface occurs during transmembrane communication in response to extracellular osmolarity. We conclude by discussing these results within the frameworks of several proposed models for transmembrane communication. PMID:27155567

  8. The cytopathicity of a simian immunodeficiency virus Mne variant is determined by mutations in Gag and Env.

    PubMed Central

    Kimata, J T; Overbaugh, J

    1997-01-01

    Previous studies suggested that the rapidly replicating, highly cytopathic, syncytium-inducing (rapid-high/SI) phenotype of simian immunodeficiency virus Mne variants that evolved in macaques inoculated with a slowly replicating, minimally cytopathic, non-syncytium-inducing (slow-low/NSI) molecular clone was not solely the result of changes in the envelope surface protein (Env SU). To define the viral determinants responsible for the change in phenotype, we molecularly cloned a rapid-high/SI variant (designated SIVMne170) derived from the peripheral blood mononuclear cells (PBMCs) of a pig-tailed macaque that was inoculated with a slow-low/NSI molecular clone, SIVMneCL8. SIVMne170 was SI and replicated with faster kinetics and was more cytopathic than the parent SIVMneCL8 in CEMx174 cells. Additionally, SIVMne170 was more cytopathic for the CD4+ T-cell population than SIVMneCL8 in macaque PBMCs. An analysis of chimeric viruses constructed between the variant SIVMne170 and the parent virus SIVMneCL8 demonstrated that there are determinants encoded within both the 5' and 3' halves of SIVMne170 that independently contribute to its rapid-high/SI phenotype. As we previously observed with other SIVMne variants, the Env SU of SIVMne170 was important for syncytium induction but was not a key determinant of cytopathicity. By contrast, the intracellular domain of the envelope transmembrane protein (Env TM) contributed to both the SI and cytopathic properties of SIVMne170. We also found that the minimal determinant within the 5' half of SIVMne170 that conferred its rapid replication kinetics and cytopathicity mapped to the capsid- and nucleocapsid-encoding regions of gag. Together, these data demonstrate that mutations selected in Gag and Env TM intracytoplasmic tail influence the replication and cytopathicity of SIVMne variants that evolve in the host. PMID:9311845

  9. Effects of murine leukemia virus env gene proteins on macrophage-mediated cytotoxicity in vitro

    NASA Technical Reports Server (NTRS)

    Chapes, S. K.; Takemoto, L. J.; Spooner, B. S. (Principal Investigator)

    1991-01-01

    F5b Tumor cells were incubated with concentrated culture supernatants taken from cells resistant (F5m) or sensitive (F5b) to contact-dependent macrophage cytotoxicity. Macrophage cell line B6MP102 and murine peritoneal macrophages killed targets incubated with supernatants taken from sensitive cells but poorly killed cells incubated in supernatants isolated from resistant cells. Membranes from cells resistant to macrophage killing, F5m, were fused into F5b cells. The fused F5b cells were killed significantly less than F5b cells fused with F5b cell membranes or untreated F5b cells. The decreased killing of F5b cells corresponded to increased concentrations of gp70(a) molecules on F5b cells. Affinity purified gp70(a) was added to cytotoxicity assays but failed to inhibit macrophage cytotoxicity. P15E molecules were detectable on both F5b and F5m cells. In addition, a synthetic peptide found to exhibit the inhibitory properties of p15E was added to cytotoxicity assays. P15E synthetic peptide also did not inhibit macrophage cytotoxicity. Therefore, env gene proteins of murine leukemia virus do not appear responsible for inducing tumor cell resistance to activated macrophage contact-dependent cytotoxicity.

  10. Genetic and neutralization sensitivity of diverse HIV-1 env clones from chronically infected patients in China.

    PubMed

    Shang, Hong; Han, Xiaoxu; Shi, Xuanling; Zuo, Teng; Goldin, Mark; Chen, Dan; Han, Bing; Sun, Wei; Wu, Hao; Wang, Xinquan; Zhang, Linqi

    2011-04-22

    As HIV-1 continues to spread in China from traditional high risk populations to the general public, its genetic makeup has become increasingly complex. However, the impact of these genetic changes on the biological and neutralization sensitivity of the virus is unknown. The current study aims to characterize the genetic, biological, and neutralization sensitivity of HIV-1 identified in China between 2004 and 2007. Based on a total of 107 full-length envelope genes obtained directly from the infected patients, we found that those viruses fell into three major genetic groups: CRF01_AE, subtype B', and subtype C/CRF07_BC/CRF08_BC/B'C. Pseudotyped viruses built upon the viable env genes have demonstrated their substantial variability in mediating viral entry and in sensitivity to neutralization by subtype-specific plasma pools and broadly neutralizing monoclonal antibodies (bnmAb). Many viruses are resistant to one or more bnmAb, including those known to have high potency against diverse viruses from outside China. Sequence and structural analysis has revealed several mechanisms by which these resistant viruses escape recognition from bnmAb. We believe that these results will help us to better understand the impact of genetic diversity on the neutralizing sensitivity of the viruses and to facilitate the design of immunogens capable of eliciting antibodies with potency and breadth similar to those of bnmAb. PMID:21325278

  11. Comparison of intradermal and intramuscular delivery followed by in vivo electroporation of SIV Env DNA in macaques

    PubMed Central

    Kulkarni, Viraj; Rosati, Margherita; Bear, Jenifer; Pilkington, Guy R; Jalah, Rashmi; Bergamaschi, Cristina; Singh, Ashish K; Alicea, Candido; Chowdhury, Bhabadeb; Zhang, Gen-Mu; Kim, Eun-Young; Wolinsky, Steven M; Huang, Wensheng; Guan, Yongjun; LaBranche, Celia; Montefiori, David C; Broderick, Kate E; Sardesai, Niranjan Y; Valentin, Antonio; Felber, Barbara K; Pavlakis, George N

    2013-01-01

    A panel of SIVmac251 transmitted Env sequences were tested for expression, function and immunogenicity in mice and macaques. The immunogenicity of a DNA vaccine cocktail expressing SIVmac239 and three transmitted SIVmac251 Env sequences was evaluated upon intradermal or intramuscular injection followed by in vivo electroporation in macaques using sequential vaccination of gp160, gp120 and gp140 expressing DNAs. Both intradermal and intramuscular vaccination regimens using the gp160 expression plasmids induced robust humoral immune responses, which further improved using the gp120 expressing DNAs. The responses showed durability of binding and neutralizing antibody titers and high avidity for > 1 y. The intradermal DNA delivery regimen induced higher cross-reactive responses able to neutralize the heterologous tier 1B-like SIVsmE660_CG7V. Analysis of cellular immune responses showed induction of Env-specific memory responses and cytotoxic granzyme B+ T cells in both vaccine groups, although the magnitude of the responses were ~10x higher in the intramuscular/electroporation group. The cellular responses induced by both regimens were long lasting and could be detected ~1 y after the last vaccination. These data show that both DNA delivery methods are able to induce robust and durable immune responses in macaques. PMID:23811579

  12. Comparison of intradermal and intramuscular delivery followed by in vivo electroporation of SIV Env DNA in macaques.

    PubMed

    Kulkarni, Viraj; Rosati, Margherita; Bear, Jenifer; Pilkington, Guy R; Jalah, Rashmi; Bergamaschi, Cristina; Singh, Ashish K; Alicea, Candido; Chowdhury, Bhabadeb; Zhang, Gen-Mu; Kim, Eun-Young; Wolinsky, Steven M; Huang, Wensheng; Guan, Yongjun; LaBranche, Celia; Montefiori, David C; Broderick, Kate E; Sardesai, Niranjan Y; Valentin, Antonio; Felber, Barbara K; Pavlakis, George N

    2013-10-01

    A panel of SIVmac251 transmitted Env sequences were tested for expression, function and immunogenicity in mice and macaques. The immunogenicity of a DNA vaccine cocktail expressing SIVmac239 and three transmitted SIVmac251 Env sequences was evaluated upon intradermal or intramuscular injection followed by in vivo electroporation in macaques using sequential vaccination of gp160, gp120 and gp140 expressing DNAs. Both intradermal and intramuscular vaccination regimens using the gp160 expression plasmids induced robust humoral immune responses, which further improved using the gp120 expressing DNAs. The responses showed durability of binding and neutralizing antibody titers and high avidity for>1 y. The intradermal DNA delivery regimen induced higher cross-reactive responses able to neutralize the heterologous tier 1B-like SIVsmE660_CG7V. Analysis of cellular immune responses showed induction of Env-specific memory responses and cytotoxic granzyme B(+) T cells in both vaccine groups, although the magnitude of the responses were ~10x higher in the intramuscular/electroporation group. The cellular responses induced by both regimens were long lasting and could be detected ~1 y after the last vaccination. These data show that both DNA delivery methods are able to induce robust and durable immune responses in macaques. PMID:23811579

  13. Proviral amplification of the Gypsy endogenous retrovirus of Drosophila melanogaster involves env-independent invasion of the female germline.

    PubMed

    Chalvet, F; Teysset, L; Terzian, C; Prud'homme, N; Santamaria, P; Bucheton, A; Pélisson, A

    1999-05-01

    Gypsy is an infectious endogenous retrovirus of Drosophila melanogaster. The gypsy proviruses replicate very efficiently in the genome of the progeny of females homozygous for permissive alleles of the flamenco gene. This replicative transposition is correlated with derepression of gypsy expression, specifically in the somatic cells of the ovaries of the permissive mothers. The determinism of this amplification was studied further by making chimeric mothers containing different permissive/restrictive and somatic/germinal lineages. We show here that the derepression of active proviruses in the permissive soma is necessary and sufficient to induce proviral insertions in the progeny, even if the F1 flies derive from restrictive germ cells devoid of active proviruses. Therefore, gypsy endogenous multiplication results from the transfer of some gypsy-encoded genetic material from the soma towards the germen of the mother and its subsequent insertion into the chromosomes of the progeny. This transfer, however, is not likely to result from retroviral infection of the germline. Indeed, we also show here that the insertion of a tagged gypsy element, mutant for the env gene, occurs at high frequency, independently of the production of gypsy Env proteins by any transcomplementing helper. The possible role of the env gene for horizontal transfer to new hosts is discussed. PMID:10228177

  14. Structures of HIV-1-Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design

    PubMed Central

    Gorman, Jason; Soto, Cinque; Yang, Max M.; Davenport, Thaddeus M.; Guttman, Miklos; Bailer, Robert T.; Chambers, Michael; Chuang, Gwo-Yu; DeKosky, Brandon J.; Doria-Rose, Nicole A.; Druz, Aliaksandr; Ernandes, Michael J.; Georgiev, Ivelin S.; Jarosinski, Marissa C.; Joyce, M. Gordon; Lemmin, Thomas M.; Leung, Sherman; Louder, Mark K.; McDaniel, Jonathan R.; Narpala, Sandeep; Pancera, Marie; Stuckey, Jonathan; Wu, Xueling; Yang, Yongping; Zhang, Baoshan; Zhou, Tongqing; Mullikin, James C.; Baxa, Ulrich; Georgiou, George; McDermott, Adrian B.; Bonsignori, Mattia; Haynes, Barton F.; Moore, Penny L.; Morris, Lynn; Lee, Kelly K.; Shapiro, Lawrence; Mascola, John R.; Kwong, Peter D.

    2016-01-01

    Broadly neutralizing antibodies (bNAbs) against HIV-1-Env V1V2 arise in multiple donors. However, atomic-level interactions had only been determined with antibodies from a single donor, making commonalities in recognition uncertain. Here we report the co-crystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third. These V1V2-directed bNAbs utilized strand-strand interactions between a protruding antibody loop and a V1V2 strand, but differed in their N-glycan recognition. Ontogeny analysis indicated protruding loops to develop early, with glycan interactions maturing over time. Altogether, the multidonor information suggested V1V2-directed bNAbs to form an ‘extended class’, for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class. PMID:26689967

  15. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.

    PubMed

    Gorman, Jason; Soto, Cinque; Yang, Max M; Davenport, Thaddeus M; Guttman, Miklos; Bailer, Robert T; Chambers, Michael; Chuang, Gwo-Yu; DeKosky, Brandon J; Doria-Rose, Nicole A; Druz, Aliaksandr; Ernandes, Michael J; Georgiev, Ivelin S; Jarosinski, Marissa C; Joyce, M Gordon; Lemmin, Thomas M; Leung, Sherman; Louder, Mark K; McDaniel, Jonathan R; Narpala, Sandeep; Pancera, Marie; Stuckey, Jonathan; Wu, Xueling; Yang, Yongping; Zhang, Baoshan; Zhou, Tongqing; Mullikin, James C; Baxa, Ulrich; Georgiou, George; McDermott, Adrian B; Bonsignori, Mattia; Haynes, Barton F; Moore, Penny L; Morris, Lynn; Lee, Kelly K; Shapiro, Lawrence; Mascola, John R; Kwong, Peter D

    2016-01-01

    Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class. PMID:26689967

  16. A novel human immunodeficiency virus type 1 protein, tev, shares sequences with tat, env, and rev proteins.

    PubMed Central

    Benko, D M; Schwartz, S; Pavlakis, G N; Felber, B K

    1990-01-01

    We have characterized a novel 28-kilodalton protein, p28tev, detected in human immunodeficiency virus type 1-infected cells. tev is recognized by both tat and rev monospecific antibodies. tev is initiated at the tat AUG and contains the first exon of tat at its amino terminus, a small portion of env in the middle, and the second exon of rev at its carboxy terminus. A cDNA clone producing tev was cloned and expressed in human cells. Sequence analysis revealed that the tev mRNA is generated by splicing to a novel exon located in the env region. This identifies a fourth class of multiply spliced human immunodeficiency virus mRNAs, produced in infected and transfected cells. tev is regulated during the virus life cycle similarly to the other regulatory proteins, tat, rev, and nef, and displays both tat and rev activities in functional assays. Since tev contains important functional domains of tat and rev and is produced very early after transfection, it may be an important regulator in the initial phase of virus expression. Another rev-related protein, p18(6)Drev, containing env and rev sequences, was characterized and was found not to have detectable rev activity. Images PMID:2186172

  17. Production of Mucosally Transmissible SHIV Challenge Stocks from HIV-1 Circulating Recombinant Form 01_AE env Sequences

    PubMed Central

    Tartaglia, Lawrence J.; Chang, Hui-Wen; Lee, Benjamin C.; Abbink, Peter; Ng’ang’a, David; Boyd, Michael; Lavine, Christy L.; Lim, So-Yon; Sanisetty, Srisowmya; Whitney, James B.; Seaman, Michael S.; Rolland, Morgane; Tovanabutra, Sodsai; Ananworanich, Jintanat; Robb, Merlin L.; Kim, Jerome H.; Michael, Nelson L.; Barouch, Dan H.

    2016-01-01

    Simian-human immunodeficiency virus (SHIV) challenge stocks are critical for preclinical testing of vaccines, antibodies, and other interventions aimed to prevent HIV-1. A major unmet need for the field has been the lack of a SHIV challenge stock expressing circulating recombinant form 01_AE (CRF01_AE) env sequences. We therefore sought to develop mucosally transmissible SHIV challenge stocks containing HIV-1 CRF01_AE env derived from acutely HIV-1 infected individuals from Thailand. SHIV-AE6, SHIV-AE6RM, and SHIV-AE16 contained env sequences that were >99% identical to the original HIV-1 isolate and did not require in vivo passaging. These viruses exhibited CCR5 tropism and displayed a tier 2 neutralization phenotype. These challenge stocks efficiently infected rhesus monkeys by the intrarectal route, replicated to high levels during acute infection, and established chronic viremia in a subset of animals. SHIV-AE16 was titrated for use in single, high dose as well as repetitive, low dose intrarectal challenge studies. These SHIV challenge stocks should facilitate the preclinical evaluation of vaccines, monoclonal antibodies, and other interventions targeted at preventing HIV-1 CRF01_AE infection. PMID:26849216

  18. Genomic stability of murine leukemia viruses containing insertions at the Env-3' untranslated region boundary.

    PubMed

    Logg, C R; Logg, A; Tai, C K; Cannon, P M; Kasahara, N

    2001-08-01

    Retroviruses containing inserts of exogenous sequences frequently eliminate the inserted sequences upon spread in susceptible cells. We have constructed replication-competent murine leukemia virus (MLV) vectors containing internal ribosome entry site (IRES)-transgene cassettes at the env-3' untranslated region boundary in order to examine the effects of insert sequence and size on the loss of inserts during viral replication. A virus containing an insertion of 1.6 kb replicated with greatly attenuated kinetics relative to wild-type virus and lost the inserted sequences in a single infection cycle. In contrast, MLVs containing inserts of 1.15 to 1.30 kb replicated with kinetics only slightly attenuated compared to wild-type MLV and exhibited much greater stability, maintaining their genomic integrity over multiple serial infection cycles. Eventually, multiple species of deletion mutants were detected simultaneously in later infection cycles; once detected, these variants rapidly dominated the population and thereafter appeared to be maintained at a relative equilibrium. Sequence analysis of these variants identified preferred sites of recombination in the parental viruses, including both short direct repeats and inverted repeats. One instance of insert deletion through recombination with an endogenous retrovirus was also observed. When specific sequences involved in these recombination events were eliminated, deletion variants still arose with the same kinetics upon virus passage and by apparently similar mechanisms, although at different locations in the vectors. Our results suggest that while lengthened, insert-containing genomes can be maintained over multiple replication cycles, preferential deletions resulting in loss of the inserted sequences confer a strong selective advantage. PMID:11435579

  19. Disulfide Sensitivity in the Env Protein Underlies Lytic Inactivation of HIV-1 by Peptide Triazole Thiols.

    PubMed

    Bailey, Lauren D; Kalyana Sundaram, Ramalingam Venkat; Li, Huiyuan; Duffy, Caitlin; Aneja, Rachna; Rosemary Bastian, Arangassery; Holmes, Andrew P; Kamanna, Kantharaju; Rashad, Adel A; Chaiken, Irwin

    2015-12-18

    We investigated the mode of action underlying lytic inactivation of HIV-1 virions by peptide triazole thiol (PTT), in particular the relationship between gp120 disulfides and the C-terminal cysteine-SH required for virolysis. Obligate PTT dimer obtained by PTT SH cross-linking and PTTs with serially truncated linkers between pharmacophore isoleucine-ferrocenyltriazole-proline-tryptophan and cysteine-SH were synthesized. PTT variants showed loss of lytic activity but not binding and infection inhibition upon SH blockade. A disproportionate loss of lysis activity vs binding and infection inhibition was observed upon linker truncation. Molecular docking of PTT onto gp120 argued that, with sufficient linker length, the peptide SH could approach and disrupt several alternative gp120 disulfides. Inhibition of lysis by gp120 mAb 2G12, which binds at the base of the V3 loop, as well as disulfide mutational effects, argued that PTT-induced disruption of the gp120 disulfide cluster at the base of the V3 loop is an important step in lytic inactivation of HIV-1. Further, PTT-induced lysis was enhanced after treating virus with reducing agents dithiothreitol and tris (2-carboxyethyl)phosphine. Overall, the results are consistent with the view that the binding of PTT positions the peptide SH group to interfere with conserved disulfides clustered proximal to the CD4 binding site in gp120, leading to disulfide exchange in gp120 and possibly gp41, rearrangement of the Env spike, and ultimately disruption of the viral membrane. The dependence of lysis activity on thiol-disulfide interaction may be related to intrinsic disulfide exchange susceptibility in gp120 that has been reported previously to play a role in HIV-1 cell infection. PMID:26458166

  20. An Automated HIV-1 Env-Pseudotyped Virus Production for Global HIV Vaccine Trials

    PubMed Central

    Fuss, Martina; Mazzotta, Angela S.; Sarzotti-Kelsoe, Marcella; Ozaki, Daniel A.; Montefiori, David C.; von Briesen, Hagen; Zimmermann, Heiko; Meyerhans, Andreas

    2012-01-01

    Background Infections with HIV still represent a major human health problem worldwide and a vaccine is the only long-term option to fight efficiently against this virus. Standardized assessments of HIV-specific immune responses in vaccine trials are essential for prioritizing vaccine candidates in preclinical and clinical stages of development. With respect to neutralizing antibodies, assays with HIV-1 Env-pseudotyped viruses are a high priority. To cover the increasing demands of HIV pseudoviruses, a complete cell culture and transfection automation system has been developed. Methodology/Principal Findings The automation system for HIV pseudovirus production comprises a modified Tecan-based Cellerity system. It covers an area of 5×3 meters and includes a robot platform, a cell counting machine, a CO2 incubator for cell cultivation and a media refrigerator. The processes for cell handling, transfection and pseudovirus production have been implemented according to manual standard operating procedures and are controlled and scheduled autonomously by the system. The system is housed in a biosafety level II cabinet that guarantees protection of personnel, environment and the product. HIV pseudovirus stocks in a scale from 140 ml to 1000 ml have been produced on the automated system. Parallel manual production of HIV pseudoviruses and comparisons (bridging assays) confirmed that the automated produced pseudoviruses were of equivalent quality as those produced manually. In addition, the automated method was fully validated according to Good Clinical Laboratory Practice (GCLP) guidelines, including the validation parameters accuracy, precision, robustness and specificity. Conclusions An automated HIV pseudovirus production system has been successfully established. It allows the high quality production of HIV pseudoviruses under GCLP conditions. In its present form, the installed module enables the production of 1000 ml of virus-containing cell culture supernatant per

  1. Enhanced cell surface expression, immunogenicity and genetic stability resulting from a spontaneous truncation of HIV Env expressed by a recombinant MVA

    SciTech Connect

    Wyatt, Linda S. Belyakov, Igor M.; Earl, Patricia L.; Berzofsky, Jay A.; Moss, Bernard

    2008-03-15

    During propagation of modified vaccinia virus Ankara (MVA) encoding HIV 89.6 Env, a few viral foci stained very prominently. Virus cloned from such foci replicated to higher titers than the parent and displayed enhanced genetic stability on passage. Sequence analysis showed a single nucleotide deletion in the 89.6 env gene of the mutant that caused a frame shift and truncation of 115 amino acids from the cytoplasmic domain. The truncated Env was more highly expressed on the cell surface, induced higher antibody responses than the full-length Env, reacted with HIV neutralizing monoclonal antibodies and mediated CD4/co-receptor-dependent fusion. Intramuscular (IM), intradermal (ID) needleless, and intrarectal (IR) catheter inoculations gave comparable serum IgG responses. However, intraoral (IO) needleless injector route gave the highest IgA in lung washings and IR gave the highest IgA and IgG responses in fecal extracts. Induction of CTL responses in the spleens of individual mice as assayed by intracellular cytokine staining was similar with both the full-length and truncated Env constructs. Induction of acute and memory CTL in the spleens of mice immunized with the truncated Env construct by ID, IO, and IR routes was comparable and higher than by the IM route, but only the IR route induced CTL in the gut-associated lymphoid tissue. Thus, truncation of Env enhanced genetic stability as well as serum and mucosal antibody responses, suggesting the desirability of a similar modification in MVA-based candidate HIV vaccines.

  2. A pilot study comparing the development of EIAV Env-specific antibodies induced by DNA/recombinant vaccinia-vectored vaccines and an attenuated Chinese EIAV vaccine.

    PubMed

    Meng, Qinglai; Lin, Yuezhi; Ma, Jian; Ma, Yan; Zhao, Liping; Li, Shenwei; Yang, Kai; Zhou, Jianhua; Shen, Rongxian; Zhang, Xiaoyan; Shao, Yiming

    2012-12-01

    Data from successful attenuated lentiviral vaccine studies indicate that fully mature Env-specific antibodies characterized by high titer, high avidity, and the predominant recognition of conformational epitopes are associated with protective efficacy. Although vaccination with a DNA prime/recombinant vaccinia-vectored vaccine boost strategy has been found to be effective in some trials with non-human primate/simian/human immunodeficiency virus (SHIV) models, it remains unclear whether this vaccination strategy could elicit mature equine infectious anemia virus (EIAV) Env-specific antibodies, thus protecting vaccinated horses against EIAV infection. Therefore, in this pilot study we vaccinated horses using a strategy based on DNA prime/recombinant Tiantan vaccinia (rTTV)-vectored vaccines encoding EIAV env and gag genes, and observed the development of Env-specific antibodies, neutralizing antibodies, and p26-specific antibodies. Vaccination with DNA induced low titer, low avidity, and the predominant recognition of linear epitopes by Env-specific antibodies, which was enhanced by boosting vaccinations with rTTV vaccines. However, the maturation levels of Env-specific antibodies induced by the DNA/rTTV vaccines were significantly lower than those induced by the attenuated vaccine EIAV(FDDV). Additionally, DNA/rTTV vaccines did not elicit broadly neutralizing antibodies. After challenge with a virulent EIAV strain, all of the vaccinees and control horses died from EIAV disease. These data indicate that the regimen of DNA prime/rTTV vaccine boost did not induce mature Env-specific antibodies, which might have contributed to immune protection failure. PMID:23171359

  3. Enhancing Transport of Hydrogenophaga flava ENV735 for Bioaugmentation of Aquifers Contaminated with Methyl tert-Butyl Ether

    PubMed Central

    Streger, Sheryl H.; Vainberg, Simon; Dong, Hailiang; Hatzinger, Paul B.

    2002-01-01

    The gasoline oxygenate methyl tert-butyl ether (MTBE) has become a widespread contaminant in groundwater throughout the United States. Bioaugmentation of aquifers with MTBE-degrading cultures may be necessary to enhance degradation of the oxygenate in some locations. However, poor cell transport has sometimes limited bioaugmentation efforts in the past. The objective of this study was to evaluate the transport characteristics of Hydrogenophaga flava ENV735, a pure culture capable of growth on MTBE, and to improve movement of the strain through aquifer solids. The wild-type culture moved only a few centimeters in columns of aquifer sediment. An adhesion-deficient variant (H. flava ENV735:24) of the wild-type strain that moved more readily through sediments was obtained by sequential passage of cells through columns of sterile sediment. Hydrophobic and electrostatic interaction chromatography revealed that the wild-type strain is much more hydrophobic than the adhesion-deficient variant. Electrophoretic mobility assays and transmission electron microscopy showed that the wild-type bacterium contains two distinct subpopulations, whereas the adhesion-deficient strain has only a single, homogeneous population. Both the wild-type strain and adhesion-deficient variant degraded MTBE, and both were identified by 16S rRNA analysis as pure cultures of H. flava. The effectiveness of surfactants for enhancing transport of the wild-type strain was also evaluated. Many of the surfactants tested were toxic to ENV735; however, one nonionic surfactant, Tween 20, enhanced cell transport in sand columns. Improving microbial transport may lead to a more effective bioaugmentation strategy for MTBE-contaminated sites where indigenous oxygenate degraders are absent. PMID:12406751

  4. AutoGen Version 5.0

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

    2010-01-01

    Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

  5. The conserved His8 of the Moloney murine leukemia virus Env SU subunit directs the activity of the SU-TM disulphide bond isomerase

    SciTech Connect

    Li Kejun; Zhang, Shujing; Kronqvist, Malin; Ekstroem, Maria; Wallin, Michael; Garoff, Henrik . E-mail: henrik.garoff@cbt.ki.se

    2007-04-25

    Murine leukemia virus (MLV) fusion is controlled by isomerization of the disulphide bond between the receptor-binding surface (SU) and fusion-active transmembrane subunits of the Env-complex. The bond is in SU linked to a CXXC motif. This carries a free thiol that upon receptor binding can be activated (ionized) to attack the disulphide and rearrange it into a disulphide isomer within the motif. To find out whether His8 in the conserved SPHQ sequence of Env directs thiol activation, we analyzed its ionization in MLV vectors with wtEnv and Env with His8 deleted or substituted for Tyr or Arg, which partially or completely arrests fusion. The ionization was monitored by following the pH effect on isomerization in vitro by Ca{sup 2+} depletion or in vivo by receptor binding. We found that wtEnv isomerized optimally at slightly basic pH whereas the partially active mutant required higher and the inactive mutants still higher pH. This suggests that His8 directs the ionization of the CXXC thiol.

  6. Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers

    PubMed Central

    Blattner, Claudia; Lee, Jeong Hyun; Sliepen, Kwinten; Derking, Ronald; Falkowska, Emilia; de la Peña, Alba Torrents; Cupo, Albert; Julien, Jean-Philippe; van Gils, Marit; Lee, Peter S.; Peng, Wenjie; Paulson, James C.; Poignard, Pascal; Burton, Dennis R.; Moore, John P.; Sanders, Rogier W.

    2014-01-01

    Summary All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. As PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer. PMID:24768348

  7. Early Steps of Jaagsiekte Sheep Retrovirus-Mediated Cell Transformation Involve the Interaction between Env and the RALBP1 Cellular Protein

    PubMed Central

    Monot, Margaux; Erny, Alexandra; Gineys, Barbara; Desloire, Sophie; Dolmazon, Christine; Aublin-Gex, Anne; Lotteau, Vincent; Archer, Fabienne

    2015-01-01

    ABSTRACT Ovine pulmonary adenocarcinoma is a naturally occurring lung cancer in sheep induced by the Jaagsiekte sheep retrovirus (JSRV). Its envelope glycoprotein (Env) carries oncogenic properties, and its expression is sufficient to induce in vitro cell transformation and in vivo lung adenocarcinoma. The identification of cellular partners of the JSRV envelope remains crucial for deciphering mechanisms leading to cell transformation. We initially identified RALBP1 (RalA binding protein 1; also known as RLIP76 or RIP), a cellular protein implicated in the ras pathway, as a partner of JSRV Env by yeast two-hybrid screening and confirmed formation of RALBP1/Env complexes in mammalian cells. Expression of the RALBP1 protein was repressed in tumoral lungs and in tumor-derived alveolar type II cells. Through its inhibition using specific small interfering RNA (siRNA), we showed that RALBP1 was involved in envelope-induced cell transformation and in modulation of the mTOR (mammalian target of rapamycin)/p70S6K pathway by the retroviral envelope. IMPORTANCE JSRV-induced lung adenocarcinoma is of importance for the sheep industry. While the envelope has been reported as the oncogenic determinant of the virus, the cellular proteins directly interacting with Env are still not known. Our report on the formation of RALBP/Env complexes and the role of this interaction in cell transformation opens up a new hypothesis for the dysregulation observed upon virus infection in sheep. PMID:26041289

  8. N-terminally myristoylated feline foamy virus Gag allows Env-independent budding of sub-viral particles.

    PubMed

    Liu, Yang; Kim, Yong-Boum; Löchelt, Martin

    2011-11-01

    Foamy viruses (FVs) are distinct retroviruses classified as Spumaretrovirinae in contrast to the other retroviruses, the Orthoretrovirinae. As a unique feature of FVs, Gag is not sufficient for sub-viral particle (SVP) release. In primate and feline FVs (PFV and FFV), particle budding completely depends on the cognate FV Env glycoproteins. It was recently shown that an artificially added N-terminal Gag myristoylation signal (myr-signal) overcomes this restriction in PFV inducing an Orthoretrovirus-like budding phenotype. Here we show that engineered, heterologous N-terminal myr-signals also induce budding of the distantly related FFV Gag. The budding efficiency depends on the myr-signal and its location relative to the N-terminus of Gag. When the first nine amino acid residues of FFV Gag were replaced by known myr-signals, the budding efficiency as determined by the detection of extracellular SVPs was low. In contrast, adding myr-signals to the intact N-terminus of FFV Gag resulted in a more efficient SVP release. Importantly, budding of myr-Gag proteins was sensitive towards inhibition of cellular N-myristoyltransferases. As expected, the addition or insertion of myr-signals that allowed Env-independent budding of FFV SVPs also retargeted Gag to plasma membrane-proximal sites and other intracellular membrane compartments. The data confirm that membrane-targeted FV Gag has the capacity of SVP formation. PMID:22163342

  9. In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

    PubMed Central

    Ren, Aiming; Košutić, Marija; Rajashankar, Kanagalaghatta R.; Frener, Marina; Santner, Tobias; Westhof, Eric; Micura, Ronald; Patel, Dinshaw J.

    2015-01-01

    Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modeled 2′-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5′ bond. Both an invariant guanosine and a Mg2+ are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently-reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site. PMID:25410397

  10. Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism

    PubMed Central

    Jeanne, Nicolas; Saliou, Adrien; Carcenac, Romain; Lefebvre, Caroline; Dubois, Martine; Cazabat, Michelle; Nicot, Florence; Loiseau, Claire; Raymond, Stéphanie; Izopet, Jacques; Delobel, Pierre

    2015-01-01

    HIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds. PMID:26585833

  11. Characterization of the env gene and long terminal repeat of molecularly cloned Friend mink cell focus-inducing virus DNA.

    PubMed Central

    Adachi, A; Sakai, K; Kitamura, N; Nakanishi, S; Niwa, O; Matsuyama, M; Ishimoto, A

    1984-01-01

    The highly oncogenic erythroleukemia-inducing Friend mink cell focus-inducing (MCF) virus was molecularly cloned in phage lambda gtWES.lambda B, and the DNA sequences of the env gene and the long terminal repeat were determined. The nucleotide sequences of Friend MCF virus and Friend spleen focus-forming virus were quite homologous, supporting the hypothesis that Friend spleen focus-forming virus might be generated via Friend MCF virus from an ecotropic Friend virus mainly by some deletions. Despite their different pathogenicity, the nucleotide sequences of the env gene of Friend MCF virus and Moloney MCF virus were quite homologous, suggesting that the putative parent sequence for the generation of both MCF viruses and the recombinational mechanism for their generation might be the same. We compare the amino acid sequences in lymphoid leukemia-inducing ecotropic Moloney virus and Moloney MCF virus, and erythroblastic leukemia-inducing ecotropic Friend virus, Friend-MCF virus, and Friend spleen focus-forming virus. The Friend MCF virus long terminal repeat was found to be 550 base pairs long. This contained two copies of the 39-base-pair tandem repeat, whereas the spleen focus-forming virus genome contained a single copy of the same sequence. PMID:6328011

  12. [Functional analysis of Grp and Iris, the gag and env domesticated errantivirus genes, in the Drosophila melanogaster genome].

    PubMed

    Makhnovskii, P A; Kuzmin, I V; Nefedova, L N; Kima, A I

    2016-01-01

    Drosophila melanogaster is the only invertebrate that contains endogenous retroviruses, which are called errantiviruses. Two domesticated genes, Grp and Iris, which originate from errantivirus gag and env, respectively, have been found in the D. melanogaster genome. The functions performed by the genes in Drosophila are still unclear. To identify the functions of domesticated gag and env in the D. melanogaster genome, expression of Iris and Grp was studied in strains differing by the presence or absence of the functional gypsy errantivirus. In addition, the expression levels were measured after injection of gram-positive and gram-negative bacteria, which activate different immune response pathways, and exposure to various abiotic stress factors. The presence of functional D. melanogaster retrovirus gypsy was found to increase the Grp expression level in somatic tissues of the carcass, while exerting no effect on the Iris expression level. Activation of the immune response in D. melanogaster by bacteria Bacillus cereus increased the Grp expression level and did not affect Iris expression. As for the effects of abiotic stress factors (oxidative stress, starvation, and heat and cold stress), the Grp expression level increased in response to starvation in D. melanogaster females, and the Iris expression level was downregulated in heat shock and oxidative stress. Based on the findings, Grp was assumed to play a direct role in the immune response in D. melanogaster; Iris is not involved in immune responses, but and apparently performs a cell function that is inhibited in stress. PMID:27414781

  13. Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors.

    PubMed

    Brown, Richard J P; Peters, Paul J; Caron, Catherine; Gonzalez-Perez, Maria Paz; Stones, Leanne; Ankghuambom, Chiambah; Pondei, Kemebradikumo; McClure, C Patrick; Alemnji, George; Taylor, Stephen; Sharp, Paul M; Clapham, Paul R; Ball, Jonathan K

    2011-06-01

    HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo. PMID:21471230

  14. N-Terminally Myristoylated Feline Foamy Virus Gag Allows Env-Independent Budding of Sub-Viral Particles

    PubMed Central

    Liu, Yang; Kim, Yong-Boum; Löchelt, Martin

    2011-01-01

    Foamy viruses (FVs) are distinct retroviruses classified as Spumaretrovirinae in contrast to the other retroviruses, the Orthoretrovirinae. As a unique feature of FVs, Gag is not sufficient for sub-viral particle (SVP) release. In primate and feline FVs (PFV and FFV), particle budding completely depends on the cognate FV Env glycoproteins. It was recently shown that an artificially added N-terminal Gag myristoylation signal (myr-signal) overcomes this restriction in PFV inducing an Orthoretrovirus-like budding phenotype. Here we show that engineered, heterologous N-terminal myr-signals also induce budding of the distantly related FFV Gag. The budding efficiency depends on the myr-signal and its location relative to the N-terminus of Gag. When the first nine amino acid residues of FFV Gag were replaced by known myr-signals, the budding efficiency as determined by the detection of extracellular SVPs was low. In contrast, adding myr-signals to the intact N-terminus of FFV Gag resulted in a more efficient SVP release. Importantly, budding of myr-Gag proteins was sensitive towards inhibition of cellular N-myristoyltransferases. As expected, the addition or insertion of myr-signals that allowed Env-independent budding of FFV SVPs also retargeted Gag to plasma membrane-proximal sites and other intracellular membrane compartments. The data confirm that membrane-targeted FV Gag has the capacity of SVP formation. PMID:22163342

  15. Surface Exposure of the HIV-1 Env Cytoplasmic Tail LLP2 Domain during the Membrane Fusion Process

    PubMed Central

    Lu, Lu; Zhu, Yun; Huang, Jinghe; Chen, Xi; Yang, Hengwen; Jiang, Shibo; Chen, Ying-Hua

    2008-01-01

    HIV-1 gp41 cytoplasmic tail (CT) is highly conserved among HIV-1 isolates, particularly the region designated lentivirus lytic peptide (LLP1–2), which includes two α-helical domains LLP1 and LLP2. Although the gp41 CT is recognized as a modulator of viral fusogenicity, little is known about the regulatory mechanism of this region in the viral fusion process. Here we report that anti-LLP1–2 and anti-LLP2 antibodies (IgG) inhibited HIV-1 Env-mediated cell fusion and bound to the interface between effector and target cells at a suboptimal temperature (31.5 °C), which slows down the fusion process and prolongs the fusion intermediate state. This suggests that LLP1–2, especially the LLP2 region located inside the viral membrane, is transiently exposed on the membrane surface during the fusion process. Synthetic LLP2 peptide could bind to the gp41 six-helix bundle core with high binding affinity. These results suggest that the gp41 CT may interact with the gp41 core, via the surface-exposed LLP2 domain, to regulate Env-mediated membrane fusion. PMID:18408000

  16. Unleashing Gen Y: Marketing Mars to Millennials

    NASA Technical Reports Server (NTRS)

    Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

    2007-01-01

    Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

  17. ATLAS Versus NextGen Model Atmospheres: A Combined Analysis of Synthetic Spectral Energy Distributions

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.; Chávez, M.; Rodríguez-Merino, L. H.

    2004-08-01

    We carried out a critical appraisal of the two theoretical models, Kurucz' ATLAS9 and PHOENIX/NextGen, for stellar atmosphere synthesis. Our tests relied on the theoretical fit of spectral energy distributions (SEDs) for a sample of 334 target stars along the whole spectral-type sequence, from the classical optical catalogs of Gunn & Stryker and Jacoby et al. The best-fitting physical parameters (Teff, logg) of stars allowed an independent calibration of the temperature and bolometric scale versus empirical classification parameters (i.e., spectral type and MK luminosity class); in addition, the comparison of the synthetic templates from the ATLAS and NextGen grids allowed us to probe the capability of the models to match spectrophotometric properties of real stars and assess the impact of the different input physics. We can sketch the following main conclusions of our analysis: (1) Fitting accuracy of both theoretical libraries drastically degrades at low Teff at which both ATLAS and NextGen models still fail to properly account for the contribution of molecular features in the observed SED of K-M stars. (2) Compared with empirical calibrations, both ATLAS and NextGen fits tend, on average, to predict slightly warmer (by 4%-8%) Teff for both giant and dwarf stars of fixed spectral type, but ATLAS provides, in general, a sensibly better fit (a factor of 2 lower σ of flux residuals) than NextGen. (3) There is a striking tendency of NextGen to label target stars with an effective temperature and surface gravity higher than that of ATLAS. The effect is especially evident for MK I-III objects for which about one in four stars is clearly misclassified by NextGen in logg. This is a consequence of some ``degeneracy'' in the solution space, partly induced by the different input physics and geometry constraints in the computation of the integrated emerging flux (ATLAS model atmospheres assume standard plane-parallel layers, while NextGen adopts, for low-gravity stars, a

  18. Mucosal Immunization of Lactating Female Rhesus Monkeys with a Transmitted/Founder HIV-1 Envelope Induces Strong Env-Specific IgA Antibody Responses in Breast Milk

    PubMed Central

    Fouda, Genevieve G. A.; Amos, Joshua D.; Wilks, Andrew B.; Pollara, Justin; Ray, Caroline A.; Chand, Anjali; Kunz, Erika L.; Liebl, Brooke E.; Whitaker, Kaylan; Carville, Angela; Smith, Shannon; Colvin, Lisa; Pickup, David J.; Staats, Herman F.; Overman, Glenn; Eutsey-Lloyd, Krissey; Parks, Robert; Chen, Haiyan; LaBranche, Celia; Barnett, Susan; Tomaras, Georgia D.; Ferrari, Guido; Montefiori, David C.; Liao, Hua-Xin; Letvin, Norman L.; Haynes, Barton F.

    2013-01-01

    We previously demonstrated that vaccination of lactating rhesus monkeys with a DNA prime/vector boost strategy induces strong T-cell responses but limited envelope (Env)-specific humoral responses in breast milk. To improve vaccine-elicited antibody responses in milk, hormone-induced lactating rhesus monkeys were vaccinated with a transmitted/founder (T/F) HIV Env immunogen in a prime-boost strategy modeled after the moderately protective RV144 HIV vaccine. Lactating rhesus monkeys were intramuscularly primed with either recombinant DNA (n = 4) or modified vaccinia virus Ankara (MVA) poxvirus vector (n = 4) expressing the T/F HIV Env C.1086 and then boosted twice intramuscularly with C.1086 gp120 and the adjuvant MF59. The vaccines induced Env-binding IgG and IgA as well as neutralizing and antibody-dependent cellular cytotoxicity (ADCC) responses in plasma and milk of most vaccinated animals. Importantly, plasma neutralization titers against clade C HIV variants MW965 (P = 0.03) and CAP45 (P = 0.04) were significantly higher in MVA-primed than in DNA-primed animals. The superior systemic prime-boost regimen was then compared to a mucosal-boost regimen, in which animals were boosted twice intranasally with C.1086 gp120 and the TLR 7/8 agonist R848 following the same systemic prime. While the systemic and mucosal vaccine regimens elicited comparable levels of Env-binding IgG antibodies, mucosal immunization induced significantly stronger Env-binding IgA responses in milk (P = 0.03). However, the mucosal regimen was not as potent at inducing functional IgG responses. This study shows that systemic MVA prime followed by either intranasal or systemic protein boosts can elicit strong humoral responses in breast milk and may be a useful strategy to interrupt postnatal HIV-1 transmission. PMID:23596289

  19. Elevation of Ser9 phosphorylation of GSK3β is required for HERV-W env-mediated BDNF signaling in human U251 cells.

    PubMed

    Qin, Chengchen; Li, Shan; Yan, Qiujin; Wang, Xiuling; Chen, Yatang; Zhou, Ping; Lu, Mengxin; Zhu, Fan

    2016-08-01

    Human endogenous retrovirus W family (HERV-W) envelope (env) is known to be associated with neurological and psychiatric disorders, such as multiple sclerosis and schizophrenia. Previous studies showed that overexpression of HERV-W env could induce brain-derived neurotrophic factor (BDNF) gene expression. In human and rat cells, BDNF-mediated signal transduction might be modulated by glycogen synthase kinase 3β (GSK3β). Both BDNF and GSK3β are schizophrenia-related genes. In this paper, we investigated whether GSK3β was involved in the HERV-W env-induced expression of BDNF. We found that HERV-W env increased phosphorylation of GSK3β at Ser9 (p-GSK3β (Ser9)) and the ratio of p-GSK3β (Ser9) to total GSK3β (p<0.05) in U251 cells. Overexpression of HERV-W env led to a 36.2% reduction in GSK3β activity compared to control (p<0.05). The levels of β-catenin, cyclin D1 and TSC2 mRNAs were upregulated (p<0.05). These data suggested that overexpression of HERV-W env might activate the GSK3β signaling pathway in U251 cells. Further, knockdown of GSK3β reduced the expression of total GSK3β, p-GSK3β (Ser9), and the ratio of p-GSK3β (Ser9) to total GSK3β by 28.6%, 50.4%, and 30.2%, respectively (p<0.05). Levels of β-catenin, cyclin D1 and TSC2 mRNAs were also reduced (p<0.05). Interestingly, GSK3β activity increased (p<0.05). Knockdown of GSK3β also decreased mRNA and protein expression of BDNF by 49.9% and 48.5% respectively (p<0.05). These results indicated that phosphorylation of GSK3β at Ser9 might be involved in HERV-W env-induced BDNF expression, and will hopefully improve our understanding of the role of HERV-W env in neurological and psychiatric diseases (schizophrenia, etc). PMID:27235578

  20. Complete sequence of the Rous sarcoma virus env gene: identification of structural and functional regions of its product.

    PubMed Central

    Hunter, E; Hill, E; Hardwick, M; Bhown, A; Schwartz, D E; Tizard, R

    1983-01-01

    The amino-terminal amino acid sequences of gp85 and gp37, the envelope glycoproteins of Rous sarcoma virus (RSV), were determined. Alignment of these sequences with the amino acid sequence predicted from the complete nucleotide sequence of the Prague strain of RSV, subgroup C (PR-C), has allowed us to delineate the env gene-coding region of this virus. The coding sequences for gp85 and gp37 have been placed in an open reading frame that extends from nucleotide 5045 to nucleotide 6862 and predict sizes of 341 amino acids (36,962 molecular weight) for gp85 and 198 amino acids (21,566 molecular weight) for gp37. Carbohydrate makes a significant contribution to the observed molecular weights of these polypeptides--the amino acid sequence contains 14 potential glycosylation sites (Asn-X-Ser/Thr) in gp85 and two in gp37. Experiments aimed at estimating the number of carbohydrate side chains yielded results consistent with most or all of these sites being occupied. Although an initiation codon is located early (codon 4) in the open reading frame, it is likely that splicing yields an mRNA on which translation initiates at the same AUG as that of the gag gene to produce a nascent polypeptide in which gp85 is preceded by a 62-amino-acid-long leader peptide. This leader contains the hydrophobic sequence (signal sequence) necessary for translocation across the endoplasmic reticulum and is completely removed from the env gene product during translation. The polyprotein precursor, Pr95env, is cleaved to gp85 and gp37 at the carboxyl side of the basic sequence:-Arg-Arg-Lys-Arg-. gp85 is attached through a disulphide linkage to gp37, and although the positions of the cysteines involved in this linkage are not known, the presence of a 27-amino-acid-long hydrophobic region at the carboxy-terminus of gp37 is consistent with its role as a membrane anchor for the viral glycoprotein complex. The location of host range variable regions with respect to the possible tertiary structure of

  1. 77 FR 2342 - Fifth Meeting: RTCA, Next Gen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... TRANSPORTATION Federal Aviation Administration Fifth Meeting: RTCA, Next Gen Advisory Committee AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA, NextGen... RTCA, NextGen Advisory Committee. DATES: The meeting will be held February 3, 2012, from 9:30...

  2. 75 FR 54221 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

    ... Federal Aviation Administration RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  3. Pharmacologic Inhibition of Nedd8 Activation Enzyme Exposes CD4-Induced Epitopes within Env on Cells Expressing HIV-1

    PubMed Central

    Tokarev, Andrey; Stoneham, Charlotte; Lewinski, Mary K.; Mukim, Amey; Deshmukh, Savitha; Vollbrecht, Thomas; Spina, Celsa A.

    2015-01-01

    ABSTRACT HIV-1 Vpu decreases the exposure of epitopes within the viral envelope glycoprotein (Env) on the surface of infected cells by downregulating both BST2 and CD4. To test the hypothesis that inhibiting Vpu activity would increase the exposure of these epitopes and sensitize infected cells to antibody-dependent cellular cytotoxicity (ADCC), we treated cells with the Nedd8 activation enzyme (NAE) inhibitor MLN4924, which inhibits the cullin1-based ubiquitin ligase complex coopted by Vpu to degrade cellular targets. Treatment of HeLa cells with MLN4924 or expression of a dominant negative mutant of cullin1 inhibited the Vpu-mediated downregulation of CD4 but not the downregulation of BST2. NAE inhibition also increased the surface exposure of CD4-induced epitopes within Env on HEK293 cells containing an inducible HIV genome, on infected CEM T cells, and on infected primary T cells. In contrast, the Vpu-mediated downregulation of BST2 was substantially inhibited by MLN4924 only when T cells were treated with alpha interferon (IFN-α) to induce high levels of BST2 expression. As reported previously, the absence of vpu or nef and even more so the combined absence of these two genes sensitized infected cells to ADCC. However, NAE inhibition affected ADCC minimally. Paradoxically, even in infected, IFN-treated cells in which NAE inhibition substantially rescued the surface level of BST2, the surface level of Env detected with an antibody recognizing a CD4-independent epitope (2G12) was minimally increased. Mutation of the C-terminal Vpu residue W76, which supports the ability of Vpu to stimulate virion release by displacing BST2 from assembly sites on the plasma membrane by a cullin1-independent mechanism, increased the exposure of Env detected by 2G12 on infected T cells. Thus, inhibiting the displacement function of Vpu together with its ability to degrade CD4 and BST2 may be required to sensitize infected cells to ADCC. IMPORTANCE Pathogenic viruses encode gene

  4. Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa

    PubMed Central

    Richard, Léa; Rua, Réjane; Betsem, Edouard; Mouinga-Ondémé, Augustin; Kazanji, Mirdad; Leroy, Eric; Njouom, Richard; Buseyne, Florence; Afonso, Philippe V.

    2015-01-01

    ABSTRACT Simian foamy virus (SFV) is a ubiquitous retrovirus in nonhuman primates (NHPs) that can be transmitted to humans, mostly through severe bites. In the past few years, our laboratory has identified more than 50 hunters from central Africa infected with zoonotic SFVs. Analysis of the complete sequences of five SFVs obtained from these individuals revealed that env was the most variable gene. Furthermore, recombinant SFV strains, some of which involve sequences in the env gene, were recently identified. Here, we investigated the variability of the env genes of zoonotic SFV strains and searched for possible recombinants. We sequenced the complete env gene or its surface glycoprotein region (SU) from DNA amplified from the blood of (i) a series of 40 individuals from Cameroon or Gabon infected with a gorilla or chimpanzee foamy virus (FV) strain and (ii) 1 gorilla and 3 infected chimpanzees living in the same areas as these hunters. Phylogenetic analyses revealed the existence of two env variants among both the gorilla and chimpanzee FV strains that were present in zoonotic and NHP strains. These variants differ greatly (>30% variability) in a 753-bp-long region located in the receptor-binding domain of SU, whereas the rest of the gene is very conserved. Although the organizations of the Env protein sequences are similar, the potential glycosylation patterns differ between variants. Analysis of recombination suggests that the variants emerged through recombination between different strains, although all parental strains could not be identified. IMPORTANCE SFV infection in humans is a great example of a zoonotic retroviral infection that has not spread among human populations, in contrast to human immunodeficiency viruses (HIVs) and human T-lymphotropic viruses (HTLVs). Recombination was a major mechanism leading to the emergence of HIV. Here, we show that two SFV molecular envelope gene variants circulate among ape populations in Central Africa and that both

  5. Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env

    PubMed Central

    Georgiev, Ivelin S.; Joyce, M. Gordon; Yang, Yongping; Sastry, Mallika; Zhang, Baoshan; Baxa, Ulrich; Chen, Rita E.; Druz, Aliaksandr; Lees, Christopher R.; Narpala, Sandeep; Schön, Arne; Van Galen, Joseph; Chuang, Gwo-Yu; Gorman, Jason; Harned, Adam; Pancera, Marie; Stewart-Jones, Guillaume B. E.; Cheng, Cheng; Freire, Ernesto; McDermott, Adrian B.; Mascola, John R.

    2015-01-01

    ABSTRACT Similar to other type I fusion machines, the HIV-1 envelope glycoprotein (Env) requires proteolytic activation; specifically, cleavage of a gp160 precursor into gp120 and gp41 subunits creates an N-terminal gp41 fusion peptide and permits folding from an immature uncleaved state to a mature closed state. While the atomic-level consequences of cleavage for HIV-1 Env are still being determined, the uncleaved state is antigenically distinct from the mature closed state, and cleavage has been reported to be essential for mimicry of the mature viral spike by soluble versions of Env. Here we report the redesign of a current state-of-the-art soluble Env mimic, BG505.SOSIP, to make it cleavage independent. Specifically, we replaced the furin cleavage site between gp120 and gp41 with Gly-Ser linkers of various lengths. The resultant linked gp120-gp41 constructs, termed single-chain gp140 (sc-gp140), exhibited different levels of structural and antigenic mimicry of the parent cleaved BG505.SOSIP. When constructs were subjected to negative selection to remove subspecies recognized by poorly neutralizing antibodies, trimers of high antigenic mimicry of BG505.SOSIP could be obtained; negative-stain electron microscopy indicated these to resemble the mature closed state. Higher proportions of BG505.SOSIP-trimer mimicry were observed in sc-gp140s with linkers of 6 or more residues, with a linker length of 15 residues exhibiting especially promising traits. Overall, flexible linkages between gp120 and gp41 in BG505.SOSIP can thus substitute for cleavage, and sc-gp140s that closely mimicked the vaccine-preferred mature closed state of Env could be obtained. IMPORTANCE The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41

  6. Inhibition of HIV-1 Env-Mediated Cell-Cell Fusion by Lectins, Peptide T-20, and Neutralizing Antibodies

    PubMed Central

    Yee, Michael; Konopka, Krystyna; Balzarini, Jan; Düzgüneş, Nejat

    2011-01-01

    Background: Broadly cross-reactive, neutralizing human monoclonal antibodies, including 2F5, 2G12, 4E10 and IgG1 b12, can inhibit HIV-1 infection in vitro at very low concentrations. We examined the ability of these antibodies to inhibit cell-cell fusion between Clone69TRevEnv cells induced to express the viral envelope proteins, gp120/gp41 (Env), and highly CD4-positive SupT1 cells. The cells were loaded with green and red-orange cytoplasmic fluorophores, and fusion was monitored by fluorescence microscopy. Results: Cell-cell fusion was inhibited completely by the carbohydrate binding proteins (CBPs), Hippeastrum hybrid (Amaryllis) agglutinin (HHA), and Galanthus nivalis (Snowdrop) agglutinin (GNA), and by the peptide, T-20, at relatively low concentrations. Anti-gp120 and anti-gp41 antibodies, at concentrations much higher than those required for neutralization, were not particularly effective in inhibiting fusion. Monoclonal antibodies b12, m14 IgG and 2G12 had moderate inhibitory activity; the IC50 of 2G12 was about 80 µg/ml. Antibodies 4E10 and 2F5 had no inhibitory activity at the concentrations tested. Conclusions: These observations raise concerns about the ability of neutralizing antibodies to inhibit the spread of viral genetic material from infected cells to uninfected cells via cell-cell fusion. The interaction of gp120/gp41 with cell membrane CD4 may be different in cell-cell and virus-cell membrane fusion reactions, and may explain the differential effects of antibodies in these two systems. The fluorescence assay described here may be useful in high throughput screening of potential HIV fusion inhibitors. PMID:21660189

  7. VitisGen: accelerating grape cultivar improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    VitisGen is a multiple institute collaborative project funded by the USDA SCRI program, with a long term goal to accelerate grape cultivar improvement by using cutting-edge molecular marker technologies, rigorous centralized facilities to characterize traits, and molecular breeding expertise. The ge...

  8. High-Resolution Longitudinal Study of HIV-1 Env Vaccine-Elicited B Cell Responses to the Virus Primary Receptor Binding Site Reveals Affinity Maturation and Clonal Persistence.

    PubMed

    Wang, Yimeng; Sundling, Christopher; Wilson, Richard; O'Dell, Sijy; Chen, Yajing; Dai, Kaifan; Phad, Ganesh E; Zhu, Jiang; Xiao, Yongli; Mascola, John R; Karlsson Hedestam, Gunilla B; Wyatt, Richard T; Li, Yuxing

    2016-05-01

    Because of the genetic variability of the HIV-1 envelope glycoproteins (Env), the elicitation of neutralizing Abs to conserved neutralization determinants including the primary receptor binding site, CD4 binding site (CD4bs), is a major focus of vaccine development. To gain insight into the evolution of Env-elicited Ab responses, we used single B cell analysis to interrogate the memory B cell Ig repertoires from two rhesus macaques after five serial immunizations with Env/adjuvant. We observed that the CD4bs-specific repertoire displayed unique features in the third CDR of Ig H chains with minor alterations along the immunization course. Progressive affinity maturation occurred as evidenced by elevated levels of somatic hypermutation (SHM) in Ab sequences isolated at the late immunization time point compared with the early time point. Abs with higher SHM were associated with increased binding affinity and virus neutralization capacity. Moreover, a notable portion of the CD4bs-specific repertoire was maintained between early and late immunization time points, suggesting that persistent clonal lineages were induced by Env vaccination. Furthermore, we found that the predominant persistent CD4bs-specific clonal lineages had larger population sizes and higher affinities than that from the rest of the repertoires, underscoring the critical role of Ag affinity selection in Ab maturation and clonal expansion. Genetic and functional analyses revealed that the accumulation of SHM in both framework regions and CDRs contributed to the clonal affinity and antigenicity evolution. Our longitudinal study provides high-resolution understanding of the dynamically evolving CD4bs-specific B cell response after Env immunization in primates. PMID:27001953

  9. Regulation of Gag- and Env-Specific CD8+ T Cell Responses in ART-Naïve HIV-Infected Patients: Potential Implications for Individualized Immunotherapy

    PubMed Central

    Prebensen, Christian; Lind, Andreas; Dyrhol-Riise, Anne-Ma; Kvale, Dag

    2016-01-01

    Strategies to develop a functional cure for HIV infection will likely require boosting of effector T cell responses to eliminate reactivated, latently infected cells. We have recently explored an assay for assessing antigen-specific regulation of T cell proliferation, which was related to clinical progression in untreated patients and to vaccine efficacy in two trials of therapeutic Gag-based vaccines. We here expand the same assay to further investigate regulation mediated by various inhibitory pathways. Peripheral blood mononuclear cells from 26 asymptomatic HIV-infected, antiretroviral therapy-naïve patients were stimulated with Gag and Env overlapping peptide panels for 5 days. Monoclonal antibodies (mAbs) blocking inhibitory mediators interleukin (IL) 10, transforming growth factor (TGF) β, programmed death ligand (PD–L) 1 and herpes virus entry mediator (HVEM) were added to parallel cultures. Functional T cell regulation (FTR) was defined as the difference in proliferation between stimulated cultures with and without blocking mAbs. FTR was detected in 54% of patients. Blockade of IL-10/PD-L1 and IL10/TGF-β detected all cases with Gag- and Env-associated FTR, respectively. In accordance with previous findings, isolated Env FTR was associated with higher plasma HIV RNA and lower CD4 counts, while patients with both Gag and Env FTR also had higher Gag- and Env-specific proliferative CD8+ T cell responses. There was no association between FTR and frequencies of activated regulatory T cells. In conclusion, we observed substantial heterogeneity in FTR between patients, inhibitory pathways and HIV antigens. FTR may help to individualize immunomodulation and warrants further assessment in clinical immunotherapy trials. PMID:27128502

  10. The sequence complementarity between HIV-1 5' splice site SD4 and U1 snRNA determines the steady-state level of an unstable env pre-mRNA.

    PubMed Central

    Kammler, S; Leurs, C; Freund, M; Krummheuer, J; Seidel, K; Tange, T O; Lund, M K; Kjems, J; Scheid, A; Schaal, H

    2001-01-01

    HIV-1 env expression from certain subgenomic vectors requires the viral regulatory protein Rev, its target sequence RRE, and a 5' splice site upstream of the env open reading frame. To determine the role of this splice site in the 5'-splice-site-dependent Rev-mediated env gene expression, we have subjected the HIV-1 5' splice site, SD4, to a mutational analysis and have analyzed the effect of those mutations on env expression. The results demonstrate that the overall strength of hydrogen bonding between the 5' splice site, SD4, and the free 5' end of the U1 snRNA correlates with env expression efficiency, as long as env expression is suboptimal, and that a continuous stretch of 14 hydrogen bonds can lead to full env expression, as a result of stabilizing the pre-mRNA. The U1 snRNA-mediated stabilization is independent of functional splicing, as a mismatch in position +1 of the 5' splice site that led to loss of detectable amounts of spliced transcripts did not preclude stabilization and expression of the unspliced env mRNA, provided that Rev enables its nuclear export. The nucleotides capable of participating in U1 snRNA:pre-mRNA interaction include positions -3 to +8 of the 5' splice site and all 11 nt constituting the single-stranded 5' end of U1 snRNA. Moreover, env gene expression is significantly decreased upon the introduction of point mutations in several upstream GAR nucleotide motifs, which are mediating SF2/ASF responsiveness in an in vitro splicing assay. This suggests that the GAR sequences may play a role in stabilizing the pre-mRNA by sequestering U1 snRNP to SD4. PMID:11333022

  11. Gen IV Materials Handbook Implementation Plan

    SciTech Connect

    Rittenhouse, P.; Ren, W.

    2005-03-29

    A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product

  12. Safety Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    HarrisonFleming, Cody; Spencer, Melissa; Leveson, Nancy; Wilkinson, Chris

    2012-01-01

    The generation of minimum operational, safety, performance, and interoperability requirements is an important aspect of safely integrating new NextGen components into the Communication Navigation Surveillance and Air Traffic Management (CNS/ATM) system. These requirements are used as part of the implementation and approval processes. In addition, they provide guidance to determine the levels of design assurance and performance that are needed for each element of the new NextGen procedures, including aircraft, operator, and Air Navigation and Service Provider. Using the enhanced Airborne Traffic Situational Awareness for InTrail Procedure (ATSA-ITP) as an example, this report describes some limitations of the current process used for generating safety requirements and levels of required design assurance. An alternative process is described, as well as the argument for why the alternative can generate more comprehensive requirements and greater safety assurance than the current approach.

  13. GEN3D Ver. 1.37

    Energy Science and Technology Software Center (ESTSC)

    2012-01-04

    GEN3D is a three-dimensional mesh generation program. The three-dimensional mesh is generated by mapping a two-dimensional mesh into threedimensions according to one of four types of transformations: translating, rotating, mapping onto a spherical surface, and mapping onto a cylindrical surface. The generated three-dimensional mesh can then be reoriented by offsetting, reflecting about an axis, and revolving about an axis. GEN3D can be used to mesh geometries that are axisymmetric or planar, but, due to three-dimensionalmore » loading or boundary conditions, require a three-dimensional finite element mesh and analysis. More importantly, it can be used to mesh complex three-dimensional geometries composed of several sections when the sections can be defined in terms of transformations of two dimensional geometries. The code GJOIN is then used to join the separate sections into a single body. GEN3D reads and writes twodimensional and threedimensional mesh databases in the GENESIS database format; therefore, it is compatible with the preprocessing, postprocessing, and analysis codes used by the Engineering Analysis Department at Sandia National Laboratories, Albuquerque, NM.« less

  14. Generic classification of the Archiborborinae (Diptera: Sphaeroceridae), with a revision of Antrops Enderlein, Coloantrops gen. nov., Maculantrops gen. nov., Photoantrops gen. nov., and Poecilantrops gen. nov.

    PubMed

    Kits, Joel H; Marshall, Stephen A

    2013-01-01

    The Archiborborinae comprise a diverse clade of flies in the family Sphaeroceridae. We here revise the generic classification, redefining the genus Antrops Enderlein and naming 5 new genera: Boreantrops gen. nov., Coloantrops gen. nov., Maculantrops gen. nov., Photoantrops gen. nov., and Poecilantrops gen. nov. The genus Archiborborus, until recently a paraphyletic assemblage including most of the described species in the subfamily, is treated as a junior synonym of Antrops (syn. nov.) We revise the genera Antrops (53 species, including 40 sp. nov.: Antrops anovariegatus, Antrops aurantifemur, Antrops baeza, Antrops bellavista, Antrops biflavus, Antrops bucki, Antrops carpishensis, Antrops cochabamba, Antrops cochinoca, Antrops coniobaptos, Antrops coroico, Antrops cotopaxi, Antrops didactylos, Antrops diversipennis, Antrops eurus, Antrops fulgiceps, Antrops fuliginosus, Antrops guandera, Antrops guaramacalensis, Antrops inca, Antrops juninensis, Antrops mucarensis, Antrops niger, Antrops papallacta, Antrops pecki, Antrops podocarpus, Antrops quadrilobus, Antrops siberia, Antrops sierrazulensis, Antrops tachira, Antrops tequendama, Antrops tetrastichus, Antrops tumbrensis, Antrops unduavi, Antrops variegatus, Antrops versabilis, Antrops vittatus, Antrops yungas, and Antrops zongo and the following comb. nov.: Antrops annulatus (Richards), Antrops chaetosus (Richards), Antrops femoralis (Blanchard), Antrops hirtus (Bigot), Antrops maculipennis (Duda), Antrops maximus (Richards), Antrops microphthalmus (Richards), Antrops quadrinotus (Bigot), Antrops setosus (Duda), Antrops simplicimanus (Richards), Antrops nitidicollis (Becker), and Antrops orbitalis (Duda)), Coloantrops (1 species: Coloantrops daedalus, sp. nov.), Maculantrops (2 species, Maculantrops hirtipes (Macquart) comb. nov. and Maculantrops altiplanus, sp. nov.), Photoantrops (1 species: Pho-toantrops echinus sp. nov.), and Poecilantrops (10 species: Poecilantrops baorucensis, Poecilantrops boraceiensis

  15. [Identification of Env-specific monoclonal antibodies from Chinese HIV-1 infected person by B cell activation and RT-PCR cloning].

    PubMed

    Wang, Hui-Min; Xu, Ke; Yu, Shuang-Qing; Ding, Lin-Lin; Luo, Hai-Yan; Flinko, Robin; Lewis, George K; Feng, Xia; Shao, Ji-Rong; Guan, Yong-Jun; Zeng, Yi

    2012-06-01

    To obtain protective human monoclonal antibody from HIV-1 infected person, we adapted a technology for isolating antigen specific monoclonal antibody from human memory B cells through in vitro B cell activation coupled with RT-PCT and expression cloning. Human B cells were purified by negative sorting from PBMCs of HIV-1 infected individuals and memory B cells were further enriched using anti-CD27 microbeads. Two hundred memory B cells per well were cultured in 96-well round-bottom plates Env-specific antibodies in supernatants were with feeder cells in medium containing EBV and CpG. screened by ELISA after 1-2 weeks' culture. Cells from positive wells of Env-specific antibody were harvested and total RNA was isolated. Human VH and Vkappa or Vlambda genes were amplified by RT-PCR and cloned into IgG1 and kappa or lambda expressing vectors. Functional VH and Vkappa or Vlambda were identified by cotransfecting 293T cells with individual heavy chain and light chain clones followed by analysis of culture supernatants by ELISA for Env-specific antibodies. Finally, corresponding mAb was produced by transient transfection of 293T cells with the identified VH and Vkappa/lambda pair and purified by protein A affinity chromatography. Purified monocolonal antibodies were used for HIV-1 specific antibody-dependent cell-mediated cytotoxicity (ADCC) and neutralizing activity assay. Four monocolonal Env-specific antibodies were isolated from one HIV-1 subtype B' infected individual. Two of them showed strong ADCC activity and one showed weak neutralizing activity against HIV-1. Its further studies on their application in therapeutic or prophylactic vaccines against HIV-1 should be grounded. PMID:22978159

  16. DNA prime-protein boost using subtype consensus Env was effective in eliciting neutralizing antibody responses against subtype BC HIV-1 viruses circulating in China

    PubMed Central

    Zhang, Mingshun; Zhang, Lu; Zhang, Chunhua; Hong, Kunxue; Shao, Yiming; Huang, Zuhu; Wang, Shixia; Lu, Shan

    2012-01-01

    Previously, we have shown that DNA prime-protein boost is effective in eliciting neutralizing antibodies (NAb) against randomly selected HIV-1 isolates. Given the genetic diversity of HIV-1 viruses and the unique predominant subtypes in different geographic regions, it is critical to test the DNA prime-protein boost approach against circulating viral isolates in key HIV endemic areas. In the current study, the same DNA prime-protein boost vaccine was used as in previous studies to investigate the induction of NAb responses against HIV-1 clade BC, a major subtype circulating in China. A codon optimized gp120-BC DNA vaccine, based on the consensus envelope (Env) antigen sequence of clade BC, was constructed and a stable CHO cell line expressing the same consensus BC gp120 protein was produced. The immunogenicity of this consensus gp120-BC was examined in New Zealand White rabbits by either DNA prime-protein boost or protein alone vaccination approaches. High levels of Env-specific antibody responses were elicited by both approaches. However, DNA prime-protein boost but not the protein alone immune sera contained significant levels of NAb against pseudotyped viruses expressing HIV-1 BC Env antigens. Furthermore, high frequencies of CD4 binding site-targeted antibodies were found in the DNA prime- protein boost rabbit sera indicating that the positive NAb may be the result of antibodies against conformationally sensitive epitopes on HIV-1 Env. The findings support that DNA prime-protein boost was effective in eliciting NAb against a key HIV-1 virus subtype in China. This result may lead to the development of regional HIV vaccines through this approach. PMID:23111170

  17. The Environmental-Data Automated Track Annotation (Env-DATA) System: Linking Animal Tracks with Environmental Data

    NASA Astrophysics Data System (ADS)

    Bohrer, G.; Dodge, S.; Weinzierl, R.; Davidson, S. C.; Kays, R.; Douglas, D. C.; Brandes, D.; Bildstein, K.; Wikelski, M.

    2013-12-01

    The movement of animals is strongly influenced by external factors in their surrounding environment such as weather, habitat types, and human land use. With the advances in positioning and sensor technologies, it is now possible to capture data of animal locations at high spatial and temporal granularities. Likewise, modern technology provides us with an increasing access to large volumes of environmental data, some of which changes on an hourly basis. Although there have been strong developments in computational methods for the analysis of movement in its environmental context, there remain challenges in efficiently linking the spatiotemporal locations of animals with the appropriate environmental conditions along their trajectories. To this end, our new Environmental-Data Automated Track Annotation (Env-DATA) system enhances Movebank, an open portal of animal tracking data, by automating access to environmental variables from global remote sensing, weather, and ecosystem products. The system automates the download and decryption of the data from open web resources of remote sensing and weather data, and provides several interpolation methods from the native grid resolution and structure to a global regular grid linked with the movement tracks in space and time. The system is open and free to any user with movement data. The aim is to facilitate new understanding and predictive capabilities of spatiotemporal patterns of animal movement in response to dynamic and changing environments from local to global scales. The system is illustrated with a series of case studies of pan-American migrations of turkey vultures, and foraging flights of Galapagos Albatross.

  18. Level of education and multiple sclerosis risk after adjustment for known risk factors: The EnvIMS study

    PubMed Central

    Bjørnevik, Kjetil; Riise, Trond; Cortese, Marianna; Holmøy, Trygve; Kampman, Margitta T; Magalhaes, Sandra; Myhr, Kjell-Morten; Wolfson, Christina; Pugliatti, Maura

    2016-01-01

    Background: Several recent studies have found a higher risk of multiple sclerosis (MS) among people with a low level of education. This has been suggested to reflect an effect of smoking and lower vitamin D status in the social class associated with lower levels of education. Objective: The objective of this paper is to investigate the association between level of education and MS risk adjusting for the known risk factors smoking, infectious mononucleosis, indicators of vitamin D levels and body size. Methods: Within the case-control study on Environmental Factors In MS (EnvIMS), 953 MS patients and 1717 healthy controls from Norway reported educational level and history of exposure to putative environmental risk factors. Results: Higher level of education were associated with decreased MS risk (p trend = 0.001) with an OR of 0.53 (95% CI 0.41–0.68) when comparing those with the highest and lowest level of education. This association was only moderately reduced after adjusting for known risk factors (OR 0.61, 95% CI 0.44–0.83). The estimates remained similar when cases with disease onset before age 28 were excluded. Conclusion: These findings suggest that factors related to lower socioeconomic status other than established risk factors are associated with MS risk. PMID:26014605

  19. Functional Analysis of the env Open Reading Frame in Human Endogenous Retrovirus IDDMK1,222 Encoding Superantigen Activity

    PubMed Central

    Lapatschek, Matthias; Dürr, Susanne; Löwer, Roswitha; Magin, Christine; Wagner, Hermann; Miethke, Thomas

    2000-01-01

    Mice harbor a family of endogenous retroviruses, the mouse mammary tumor viruses (MMTV), which encode superantigens. These superantigens are responsible for the deletion of T cells expressing certain Vβ chains of the T-cell receptor in the thymus. Human T cells are able to recognize MMTV-encoded superantigens presented by human major histocompatibility complex class II-positive cells. Owing to this and to the similarity of the human and murine immune systems, it was speculated that human endogenous retroviruses might also code for superantigens. Recently, it was reported that a proviral clone (IDDMK1,222) of the human endogenous retrovirus family HTDV/HERV-K encodes a superantigen. The putative superantigen gene was located within the env region of the virus. Stimulated by these findings, we amplified by PCR and cloned into eucaryotic expression vectors open reading frames (ORFs) which were identical or very similar to IDDMK1,222. When we transfected these vectors into A20 cells, a murine B-cell lymphoma, we were able to demonstrate mRNA expression and protein production. However, we did not find any evidence that the ORF stimulated human or murine T cells in a Vβ-specific fashion, the most prominent feature of superantigens. PMID:10864649

  20. Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch.

    PubMed

    MacLeod, Daniel T; Choi, Nancy M; Briney, Bryan; Garces, Fernando; Ver, Lorena S; Landais, Elise; Murrell, Ben; Wrin, Terri; Kilembe, William; Liang, Chi-Hui; Ramos, Alejandra; Bian, Chaoran B; Wickramasinghe, Lalinda; Kong, Leopold; Eren, Kemal; Wu, Chung-Yi; Wong, Chi-Huey; Kosakovsky Pond, Sergei L; Wilson, Ian A; Burton, Dennis R; Poignard, Pascal

    2016-05-17

    The high-mannose patch on HIV Env is a preferred target for broadly neutralizing antibodies (bnAbs), but to date, no vaccination regimen has elicited bnAbs against this region. Here, we present the development of a bnAb lineage targeting the high-mannose patch in an HIV-1 subtype-C-infected donor from sub-Saharan Africa. The Abs first acquired autologous neutralization, then gradually matured to achieve breadth. One Ab neutralized >47% of HIV-1 strains with only ∼11% somatic hypermutation and no insertions or deletions. By sequencing autologous env, we determined key residues that triggered the lineage and participated in Ab-Env coevolution. Next-generation sequencing of the Ab repertoire showed an early expansive diversification of the lineage followed by independent maturation of individual limbs, several of them developing notable breadth and potency. Overall, the findings are encouraging from a vaccine standpoint and suggest immunization strategies mimicking the evolution of the entire high-mannose patch and promoting maturation of multiple diverse Ab pathways. PMID:27192579

  1. A Bidirectional SF2/ASF- and SRp40-Dependent Splicing Enhancer Regulates Human Immunodeficiency Virus Type 1 rev, env, vpu, and nef Gene Expression

    PubMed Central

    Caputi, Massimo; Freund, Marcel; Kammler, Susanne; Asang, Corinna; Schaal, Heiner

    2004-01-01

    The integrated human immunodeficiency virus type 1 (HIV-1) genome is transcribed in a single pre-mRNA that is alternatively spliced into more than 40 mRNAs. We characterized a novel bidirectional exonic splicing enhancer (ESE) that regulates the expression of the HIV-1 env, vpu, rev, and nef mRNAs. The ESE is localized downstream of the vpu-, env-, and nef-specific 3′ splice site no. 5. SF2/ASF and SRp40 activate the ESE and are required for efficient 3′ splice site usage and binding of the U1 snRNP to the downstream 5′ splice site no. 4. U1 snRNP binding to the 5′ splice site no. 4 is required for splicing of the rev and nef mRNAs and to increase expression of the partially spliced env mRNA. Finally, our results indicate that this ESE is necessary for the recruitment of the U1 snRNP to the 5′ splice site no. 4, even when the 5′ splice site and the U1 snRNA have been mutated to obtain a perfect complementary match. The ESE characterized here is highly conserved in most viral subtypes. PMID:15163745

  2. Serological evaluation of Escherichia coli-expressed human T-cell leukemia virus type I env, gag p24, and tax proteins.

    PubMed Central

    Coates, S R; Harris, A J; Parkes, D L; Smith, C M; Liu, H L; Akita, R W; Ferrer, M M; Sampson, E K; Brandis, J W; Sliwkowski, M X

    1990-01-01

    Three proteins (env, gag, and tax) encoded by the human T-cell leukemia virus type I (HTLV-I) genome were cloned and expressed in Escherichia coli. The env protein contained a substantial part of the gp46 domain and a majority of the p21e domain. The gag protein contained all of p24 and portions of p19 and p15. In addition to these two structural proteins, a full-length tax (p40X) construct was obtained. All three recombinant proteins were purified to near homogeneity. When used in an immunoblot assay, the three recombinant proteins detected antibodies in more HTLV-I antibody-positive patient sera than did the corresponding native proteins. Antibodies to at least two of these three different gene products were detected in 98.4% of adult T-cell leukemia patients, 100% of HTLV-I-associated myelopathy patients, 97.4% of asymptomatic carriers, and 94% of uncharacterized HTLV-I-positive patients. Antibody to recombinant tax was found in 4.9% of adult T-cell leukemia patients, whereas antibody to recombinant env could not be detected. These recombinant proteins from three different gene products may be useful in detecting or confirming the presence of antibodies to HTLV-I. Images PMID:2199486

  3. Differential repositioning of the second transmembrane helices from E. coli Tar and EnvZ upon moving the flanking aromatic residues

    PubMed Central

    Botelho, Salomé C.; Enquist, Karl; von Heijne, Gunnar; Draheim, Roger R.

    2014-01-01

    Aromatic tuning, i.e. repositioning aromatic residues found at the cytoplasmic end of transmembrane (TM) domains within bacterial receptors, has been previously shown to be an efficient way to modulate signal output from the aspartate chemoreceptor (Tar) and the major osmosensor EnvZ of Escherichia coli. In the case of Tar, changes in signal output consistent with the vertical position of the native Trp-Tyr aromatic tandem within TM2 were observed. In contrast, within EnvZ, where a Trp-Leu-Phe aromatic triplet was repositioned, the surface that the triplet resided upon was shown to be the major determinant governing signal output. However, these previous studies failed to determine whether moving the aromatic residues within TM2 of Tar or EnvZ was sufficient to physically reposition the TM helix within a membrane. Recent coarse-grained molecular dynamics (CG-MD) simulations predicted displacement of Tar TM2 upon moving the aromatic residues at the cytoplasmic end of TM2. Here, we have employed a glycosylation-mapping technique to demonstrate that repositioning the Trp-Tyr tandem within Tar TM2 is sufficient to displace the C-terminal boundary of the helix relative to the membrane. In a similar analysis of EnvZ, an abrupt initial displacement of TM2 was observed but no subsequent movement was seen, suggesting that the vertical position of TM2 is not governed by the location of the Trp-Leu-Phe triplet. In summary, our results support recent CG-MD simulations with aromatically tuned Tar segments that demonstrated the Trp-Tyr tandem is sufficient to displace TM2 within a membrane. Our results also provide another set of experimental data, i.e. the resistance of EnvZ TM2 to being displaced upon aromatic tuning, which could be useful for subsequent refinement of the initial CG-MD simulations. We suggest that differences observed between the behavior of helices is due to the inherently different properties of the residues being repositioned (i.e. Trp or Tyr versus Phe

  4. R5 Clade C SHIV Strains with Tier 1 or 2 Neutralization Sensitivity: Tools to Dissect Env Evolution and to Develop AIDS Vaccines in Primate Models

    PubMed Central

    Siddappa, Nagadenahalli B.; Watkins, Jennifer D.; Wassermann, Klemens J.; Song, Ruijiang; Wang, Wendy; Kramer, Victor G.; Lakhashe, Samir; Santosuosso, Michael; Poznansky, Mark C.; Novembre, Francis J.; Villinger, François; Else, James G.; Montefiori, David C.; Rasmussen, Robert A.; Ruprecht, Ruth M.

    2010-01-01

    Background HIV-1 clade C (HIV-C) predominates worldwide, and anti-HIV-C vaccines are urgently needed. Neutralizing antibody (nAb) responses are considered important but have proved difficult to elicit. Although some current immunogens elicit antibodies that neutralize highly neutralization-sensitive (tier 1) HIV strains, most circulating HIVs exhibiting a less sensitive (tier 2) phenotype are not neutralized. Thus, both tier 1 and 2 viruses are needed for vaccine discovery in nonhuman primate models. Methodology/Principal Findings We constructed a tier 1 simian-human immunodeficiency virus, SHIV-1157ipEL, by inserting an “early,” recently transmitted HIV-C env into the SHIV-1157ipd3N4 backbone [1] encoding a “late” form of the same env, which had evolved in a SHIV-infected rhesus monkey (RM) with AIDS. SHIV-1157ipEL was rapidly passaged to yield SHIV-1157ipEL-p, which remained exclusively R5-tropic and had a tier 1 phenotype, in contrast to “late” SHIV-1157ipd3N4 (tier 2). After 5 weekly low-dose intrarectal exposures, SHIV-1157ipEL-p systemically infected 16 out of 17 RM with high peak viral RNA loads and depleted gut CD4+ T cells. SHIV-1157ipEL-p and SHIV-1157ipd3N4 env genes diverge mostly in V1/V2. Molecular modeling revealed a possible mechanism for the increased neutralization resistance of SHIV-1157ipd3N4 Env: V2 loops hindering access to the CD4 binding site, shown experimentally with nAb b12. Similar mutations have been linked to decreased neutralization sensitivity in HIV-C strains isolated from humans over time, indicating parallel HIV-C Env evolution in humans and RM. Conclusions/Significance SHIV-1157ipEL-p, the first tier 1 R5 clade C SHIV, and SHIV-1157ipd3N4, its tier 2 counterpart, represent biologically relevant tools for anti-HIV-C vaccine development in primates. PMID:20657739

  5. TidGen Power System Commercialization Project

    SciTech Connect

    Sauer, Christopher R.; McEntee, Jarlath

    2013-12-30

    ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric

  6. Gen IV Materials Handbook Functionalities and Operation

    SciTech Connect

    Ren, Weiju

    2009-12-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  7. Timing of use of cod liver oil, a vitamin D source, and multiple sclerosis risk: The EnvIMS study

    PubMed Central

    Cortese, Marianna; Riise, Trond; Bjørnevik, Kjetil; Holmøy, Trygve; Kampman, Margitta T; Magalhaes, Sandra; Pugliatti, Maura; Wolfson, Christina; Myhr, Kjell-Morten

    2015-01-01

    Background: Low vitamin D levels have been associated with an increased risk of multiple sclerosis (MS), although it remains unknown whether this relationship varies by age. Objective: The objective of this paper is to investigate the association between vitamin D3 supplementation through cod liver oil at different postnatal ages and MS risk. Methods: In the Norwegian component of the multinational case-control study Environmental Factors In Multiple Sclerosis (EnvIMS), a total of 953 MS patients with maximum disease duration of 10 years and 1717 controls reported their cod liver oil use from childhood to adulthood. Results: Self-reported supplement use at ages 13–18 was associated with a reduced risk of MS (OR 0.67, 95% CI 0.52–0.86), whereas supplementation during childhood was not found to alter MS risk (OR 1.01, 95% CI 0.81–1.26), each compared to non-use during the respective period. An inverse association was found between MS risk and the dose of cod liver oil during adolescence, suggesting a dose-response relationship (p trend = 0.001) with the strongest effect for an estimated vitamin D3 intake of 600–800 IU/d (OR 0.46, 95% CI 0.31–0.70). Conclusions: These findings not only support the hypothesis relating to low vitamin D as a risk factor for MS, but further point to adolescence as an important susceptibility period for adult-onset MS. PMID:25948625

  8. Towards an International Culture: Gen Y Students and SNS?

    ERIC Educational Resources Information Center

    Lichy, Jessica

    2012-01-01

    This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of…

  9. Hoja informativa de pruebas genéticas

    Cancer.gov

    Trata de pruebas genéticas para riesgos heredados de cáncer; incluye tipos de pruebas, para quién son, explicación y confidencialidad de los resultados. Ofrece información de pruebas genéticas a domicilio o pruebas para el consumidor.

  10. Back to the FutureGen?

    SciTech Connect

    Buchsbaum, L.

    2009-04-15

    After years of political wrangling, Democrats may green-light the experimental clean coal power plants. The article relates how the project came to be curtailed, how Senator Dick Durbin managed to protect $134 million in funding for FutureGen in Mattoon, and how once Obama was in office a $2 billion line item to fund a 'near zero emissions power plant(s)' was placed in the Senate version of the Stimulus Bill. The final version of the legislation cut the funding to $1 billion for 'fossil energy research and development'. In December 2008 the FutureGen Alliance and the City of Mattoon spent $6.5 billion to purchase the plants eventual 440 acre site. A report by the Government Accountability Office (GAO) said that Bush's inaction may have set back clean coal technology in the US by as much as a decade. If additional funding comes through construction of the plant could start in 2010. 1 fig., 1 photo.

  11. The Integrated Airport: Building a Successful NextGen Testbed

    ScienceCinema

    Frederick-Recascino, Christina [Embry-Riddle Aeronautical University, Daytona Beach, Florida, United States]; Sweigard, Doug [Lockheed Martin Corporation]; Lester, Wade [ERAU

    2010-01-08

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  12. The Integrated Airport: Building a Successful NextGen Testbed

    SciTech Connect

    Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

    2009-02-18

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  13. Env-2dCD4 S60C complexes act as super immunogens and elicit potent, broadly neutralizing antibodies against clinically relevant human immunodeficiency virus type 1 (HIV-1).

    PubMed

    Killick, Mark A; Grant, Michelle L; Cerutti, Nichole M; Capovilla, Alexio; Papathanasopoulos, Maria A

    2015-11-17

    The ability to induce a broadly neutralizing antibody (bNAb) response following vaccination is regarded as a crucial aspect in developing an effective vaccine against human immunodeficiency virus type 1 (HIV-1). The bNAbs target the HIV-1 envelope glycoprotein (Env) which is exposed on the virus surface, thereby preventing cell entry. To date, conventional vaccine approaches such as the use of Env-based immunogens have been unsuccessful. We expressed, purified, characterized and evaluated the immunogenicity of several unique HIV-1 subtype C Env immunogens in small animals. Here we report that vaccine immunogens based on Env liganded to a two domain CD4 variant, 2dCD4(S60C) are capable of consistently eliciting potent, broadly neutralizing antibody responses in New Zealand white rabbits against a panel of clinically relevant HIV-1 pseudoviruses. This was irrespective of the Env protein subtype and context. Importantly, depletion of the anti-CD4 antibodies appeared to abrogate the neutralization activity in the rabbit sera. Taken together, this data suggests that the Env-2dCD4(S60C) complexes described here are "super" immunogens, and potentially immunofocus antibody responses to a unique epitope spanning the 2dCD4(60C). Recent data from the two available anti-CD4 monoclonal antibodies, Ibalizumab and CD4-Ig (and bispecific variants thereof) have highlighted that the use of these broad and potent entry inhibitors could circumvent the need for a conventional vaccine targeting HIV-1. Overall, the ability of the unique Env-2dCD4(S60C) complexes to elicit potent bNAb responses has not been described previously, reinforcing that further investigation for their utility in preventing and controlling HIV-1/SIV infection is warranted. PMID:26432912

  14. EarthEnv-DEM90: A nearly-global, void-free, multi-scale smoothed, 90m digital elevation model from fused ASTER and SRTM data

    NASA Astrophysics Data System (ADS)

    Robinson, Natalie; Regetz, James; Guralnick, Robert P.

    2014-01-01

    A variety of DEM products are available to the public at no cost, though all are characterized by trade-offs in spatial coverage, data resolution, and quality. The absence of a high-resolution, high-quality, well-described and vetted, free, global consensus product was the impetus for the creation of a new DEM product described here, 'EarthEnv-DEM90'. This new DEM is a compilation dataset constructed via rigorous techniques by which ASTER GDEM2 and CGIAR-CSI v4.1 products were fused into a quality-enhanced, consistent grid of elevation estimates that spans ∼91% of the globe. EarthEnv-DEM90 was assembled using methods for seamlessly merging input datasets, thoroughly filling voids, and smoothing data irregularities (e.g. those caused by DEM noise) from the approximated surface. The result is a DEM product in which elevational artifacts are strongly mitigated from the input data fusion zone, substantial voids are filled in the northern-most regions of the globe, and the entire DEM exhibits reduced terrain noise. As important as the final product is a well defined methodology, along with new processing techniques and careful attention to final outputs, that extends the value and usability of the work beyond just this single product. Finally, we outline EarthEnv-DEM90 acquisition instructions and metadata availability, so that researchers can obtain this high-resolution, high-quality, nearly-global new DEM product for the study of wide-ranging global phenomena.

  15. A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies

    PubMed Central

    Sanders, Rogier W.; Derking, Ronald; Cupo, Albert; Julien, Jean-Philippe; Yasmeen, Anila; de Val, Natalia; Kim, Helen J.; Blattner, Claudia; de la Peña, Alba Torrents; Korzun, Jacob; Golabek, Michael; de los Reyes, Kevin; Ketas, Thomas J.; van Gils, Marit J.; King, C. Richter; Wilson, Ian A.; Ward, Andrew B.; Klasse, P. J.; Moore, John P.

    2013-01-01

    A desirable but as yet unachieved property of a human immunodeficiency virus type 1 (HIV-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bNAbs). One approach to the problem is to create trimeric mimics of the native envelope glycoprotein (Env) spike that expose as many bNAb epitopes as possible, while occluding those for non-neutralizing antibodies (non-NAbs). Here, we describe the design and properties of soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A transmitted/founder strain, BG505. These trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. They are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (EM). We used several techniques, including ELISA and surface plasmon resonance (SPR), to determine the relationship between the ability of monoclonal antibodies (MAbs) to bind the soluble trimers and neutralize the corresponding virus. In general, the concordance was excellent, in that virtually all bNAbs against multiple neutralizing epitopes on HIV-1 Env were highly reactive with the BG505 SOSIP.664 gp140 trimers, including quaternary epitopes (CH01, PG9, PG16 and PGT145). Conversely, non-NAbs to the CD4-binding site, CD4-induced epitopes or gp41ECTO did not react with the trimers, even when their epitopes were present on simpler forms of Env (e.g. gp120 monomers or dissociated gp41 subunits). Three non-neutralizing MAbs to V3 epitopes did, however, react strongly with the trimers but only by ELISA, and not at all by SPR and to only a limited extent by EM. These new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens. PMID:24068931

  16. Polyvalent HIV-1 Env vaccine formulations delivered by the DNA priming plus protein boosting approach are effective in generating neutralizing antibodies against primary human immunodeficiency virus type 1 isolates from subtypes A, B, C, D and E.

    PubMed

    Wang, Shixia; Pal, Ranajit; Mascola, John R; Chou, Te-Hui W; Mboudjeka, Innocent; Shen, Siyuan; Liu, Qin; Whitney, Stephen; Keen, Timothy; Nair, B C; Kalyanaraman, V S; Markham, Philip; Lu, Shan

    2006-06-20

    A major challenge in developing an HIV-1 vaccine is to identify immunogens and their delivery methods that can elicit broad neutralizing antibodies against primary isolates of different genetic subtypes. Recently, we demonstrated that priming with DNA vaccines expressing primary HIV-1 envelope glycoprotein (Env) followed by recombinant Env protein boosting was successful in generating positive neutralizing antibody responses against a clade B primary HIV-1 isolate, JR-FL, that was not easily neutralized. In the current study, we examined whether the DNA priming plus recombinant protein boosting approach delivering a polyvalent primary Env formulation was able to generate neutralizing antibodies against primary HIV-1 viral isolates from various genetic subtypes. New Zealand White rabbits were first immunized with DNA vaccines expressing one, three or eight primary HIV-1 gp120 antigens delivered by a gene gun followed by recombinant gp120 protein boosting. Neutralizing antibody responses were examined by two independently executed neutralization assays: the first one was a single round infection neutralization assay against a panel of 10 primary HIV-1 isolates of subtypes A, B, C and E and the second one used the PhenoSense assay against a panel of 12 pseudovirues expressing primary HIV-1 Env antigens from subtypes A, B, C, D and E as well as 2 pseudoviruses expressing the Env antigens from MN and NL4-3 viruses. Rabbit sera immunized with the DNA priming plus protein boosting approach, but not DNA vaccine alone or Env protein alone, were capable of neutralizing 7 of 10 viruses in the first assay and 12 of 14 viruses in the second assay. More importantly, sera immunized with the polyvalent Env antigens were able to neutralize a significantly higher percentage of viruses than the sera immunized with the monovalent antigens. Our results suggest that DNA priming followed by recombinant Env protein boosting can be used to deliver polyvalent Env-antigen-based HIV-1

  17. Neutralization-Sensitive R5-Tropic Simian-Human Immunodeficiency Virus SHIV-2873Nip, Which Carries env Isolated from an Infant with a Recent HIV Clade C Infection▿

    PubMed Central

    Siddappa, Nagadenahalli B.; Song, Ruijiang; Kramer, Victor G.; Chenine, Agnès-Laurence; Velu, Vijayakumar; Ong, Helena; Rasmussen, Robert A.; Grisson, Ricky D.; Wood, Charles; Zhang, Hong; Kankasa, Chipeppo; Amara, Rama Rao; Else, James G.; Novembre, Francis J.; Montefiori, David C.; Ruprecht, Ruth M.

    2009-01-01

    Human immunodeficiency virus clade C (HIV-C) accounts for >56% of all HIV infections worldwide. To investigate vaccine safety and efficacy in nonhuman primates, a pathogenic, R5-tropic, neutralization-sensitive simian-human immunodeficiency virus (SHIV) carrying HIV-C env would be desirable. We have constructed SHIV-2873Ni, an R5-tropic SHIV carrying a primary pediatric HIV-C env gene isolated from a 2-month-old Zambian infant, who died within 1 year of birth. SHIV-2873Ni was constructed using SHIV-1157ipd3N4 (R. J. Song, A. L. Chenine, R. A. Rasmussen, C. R. Ruprecht, S. Mirshahidi, R. D. Grisson, W. Xu, J. B. Whitney, L. M. Goins, H. Ong, P. L. Li, E. Shai-Kobiler, T. Wang, C. M. McCann, H. Zhang, C. Wood, C. Kankasa, W. E. Secor, H. M. McClure, E. Strobert, J. G. Else, and R. M. Ruprecht. J. Virol. 80:8729-8738, 2006) as the backbone, since the latter contains additional NF-κB sites in the long terminal repeats to enhance viral replicative capacity. The parental virus, SHIV-2873Ni, was serially passaged through five rhesus monkeys (RMs); SHIV-2873Nip, the resulting passaged virus, was reisolated from the fourth recipient about 1 year postinoculation. SHIV-2873Nip was replication competent in RM peripheral blood mononuclear cells of all random donors tested and was exclusively R5 tropic, and its env gene clustered with HIV-C by phylogenetic analysis; its high sensitivity to neutralization led to classification as a tier 1 virus. Indian-origin RMs were inoculated by different mucosal routes, resulting in high peak viral RNA loads. Signs of virus-induced disease include depletion of gut CD4+ T lymphocytes, loss of memory T cells in blood, and thrombocytopenia that resulted in fatal cerebral hemorrhage. SHIV-2873Nip is a highly replication-competent, mucosally transmissible, pathogenic R5-tropic virus that will be useful to study viral pathogenesis and to assess the efficacy of immunogens targeting HIV-C Env. PMID:19019970

  18. Head-Worn Displays for NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

    2011-01-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  19. RxGen General Optical Model Prescription Generator

    NASA Technical Reports Server (NTRS)

    Sigrist, Norbert

    2012-01-01

    RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

  20. NextGen Future Safety Assessment Game

    NASA Technical Reports Server (NTRS)

    Ancel, Ersin; Gheorghe, Adian; Jones, Sharon Monica

    2010-01-01

    The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

  1. NextGen Future Safety Assessment Game

    NASA Technical Reports Server (NTRS)

    Ancel, Ersin; Gheorghe, Adrian; Jones, Sharon Monica

    2011-01-01

    The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

  2. A new genus and species of isanthid sea anemone (Cnidaria: Anthozoa: Actiniaria) from Chilean Patagonia, Anthoparactis fossii n. gen. et sp

    NASA Astrophysics Data System (ADS)

    Häussermann, Verena; Rodríguez, Estefanía

    2014-09-01

    We describe a new genus and species of sea anemone from Chilean Patagonia. Anthoparactis fossii n. gen. et sp. adds another acontiate genus and species to the family Isanthidae Carlgren, 1938. Anthoparactis n. gen. differs from the other isanthid genera in having the same number of mesenteries distally and proximally, acontia with basitrichs only, and a column with verrucae distally. Anthoparactis fossii n. sp. differs from the most similar species, Isoparactis fionae Lauretta et al., 2013, in the number of cycles of mesenteries and tentacles, structures of the column, colour pattern of the oral disc, cnidae, and geographical distribution. Isanthidae now includes seven genera and 11 species.

  3. Genetic analysis of the Rous sarcoma virus subgroup D env gene: mammal tropism correlates with temperature sensitivity of gp85.

    PubMed Central

    Bova-Hill, C; Olsen, J C; Swanstrom, R

    1991-01-01

    Subgroup D avian sarcoma and leukosis viruses can penetrate a variety of mammalian cells in addition to cells from their natural host, chickens. Sequences derived from the gp85-coding domain within the env gene of a mammal-tropic subgroup D virus (Schmidt-Ruppin D strain of Rous sarcoma virus [SR-D RSV]) and a non-mammal-tropic subgroup B virus (Rous-associated virus type 2) were recombined to map genetic determinants that allow penetration of mammalian cells. The following conclusions were based on host range analysis of the recombinant viruses. (i) The determinants of gp85 that result in the mammal tropism phenotype of SR-D RSV are encoded within the 160 codons that lie 3' of codon 121 from the corresponding amino terminus of the gp85 protein. (ii) Small linear domains of the SR-D RSV gp85-coding domain placed in the subgroup B background did not yield viruses with titers equal to that of the subgroup D virus in a human cell line. (iii) Recombinant viruses that contained subgroup D sequences within the hr1 variable domain of gp85 showed modest-to-significant increases in infectivity on human cells relative to chicken cells. A recombinant virus that contained three fortuitous amino acid substitutions in the gp85-coding domain was found to penetrate the human cell line and give a titer similar to that of the subgroup D virus. In addition, we found that the subgroup D virus, the mutant virus, and recombinant viruses with an increased mammal tropism phenotype were unstable at 42 degrees C. These results suggest that the mammal tropism of the SR-D strain is not related to altered receptor specificity but rather to an unstable and fusogenic viral glycoprotein. A temperature sensitivity phenotype for infectivity of mammalian cells was also observed for another mammal-tropic avian retrovirus, the Bratislava 77 strain of RSV, a subgroup C virus, but was not seen for any other avian retrovirus tested, strengthening the correlation between mammal tropism and temperature

  4. The GenDev Curriculum Development Workshop.

    PubMed

    D'cunha, J

    1997-01-01

    This article describes the second Curriculum Development Workshop held in May 1997 at the Asian Institute of Technology (AIT) in Bangkok, Thailand. The workshop aimed to review critically and restructure the Gender and Development Studies (GenDev) curriculum and to assess AIT's role in training gender experts for the region. Participants included 22 people from 16 countries in Asia, Europe, and the US who were teaching graduate students about gender issues and who were activists with nongovernmental organizations working on gender issues. It was determined that the following were required courses: Culture, Knowledge and Gender Relations; Gender, Technology, and Development; Principles of Gender Research and Methodology in Science and Technology; and Gender Analysis and Field Methods. Other suggested core courses included: Gender and Natural Resource Management; Enterprise Management, Technology, and Gender; Gender and Agrarian Reform; Urbanization: A Gender Perspective; Gender-Responsive Development Planning; and Gender and Economic Change: Past and Present Concerns. Participants distinguished between GenDev courses offered to anyone attending AIT and training courses designed to produce gender experts in the region. The aim of training courses for AIT graduate students was to sensitize potential managers, technologists, and others on gender issues and to create awareness of the importance of including gender perspectives within decision-making, policy formation, and implementation. Training courses to produce gender experts should be directed to those with a prior background in gender studies and include gender analysis in field methods. Participants agreed that there should be an independent and autonomous field of gender and development studies. Participants made six recommendations for such a field of study. PMID:12179927

  5. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    DOE PAGESBeta

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-26

    The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Suchmore » cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

  6. Intercompartmental Recombination of HIV-1 Contributes to env Intrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors▿†‡

    PubMed Central

    Brown, Richard J. P.; Peters, Paul J.; Caron, Catherine; Gonzalez-Perez, Maria Paz; Stones, Leanne; Ankghuambom, Chiambah; Pondei, Kemebradikumo; McClure, C. Patrick; Alemnji, George; Taylor, Stephen; Sharp, Paul M.; Clapham, Paul R.; Ball, Jonathan K.

    2011-01-01

    HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo. PMID:21471230

  7. 98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW ...

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

    98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW OF OPPOSITE SIDE FROM HAER No. PA-505-97 - Delaware County Electric Company, Chester Station, Delaware River at South end of Ward Street, Chester, Delaware County, PA

  8. EPCGen2 Pseudorandom Number Generators: Analysis of J3Gen

    PubMed Central

    Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

    2014-01-01

    This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues. PMID:24721767

  9. 1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...

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

    1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

  10. Combivena gen.n (Hymenoptera: Ichneumonidae: Acaenitinae) from China.

    PubMed

    Sheng, Mao-Ling; Sun, Shu-Ping

    2014-01-01

    Combivena Sheng & Sun, gen.n. and Combivena sulcata Sheng & Sun, sp.n. belonging to Acaenitinae of family Ichneumonidae (Hymenoptera), collected from Qinghai Province, China, are described and illustrated. PMID:25347843

  11. The haemosporidian parasites of bats with description of Sprattiella alecto gen. nov., sp. nov.

    PubMed Central

    Landau, I.; Chavatte, J.M.; Karadjian, G.; Chabaud, A.; Beveridge, I.

    2012-01-01

    Four species of Haemoproteidae were found in Pteropus alecto Temminck, 1837 in Queensland, Australia: i) Johnsprentia copemani, Landau et al., 2012; ii) Sprattiella alecto gen. nov., sp. nov., characterised by schizonts in the renal vessels; iii) Hepatocystis levinei, Landau et al., 1985, originally described from Pteropus poliocephalus Temminck, 1825 and, experimentally from Culicoides nubeculosus and found in this new host and for which features of the hepatic schizonts are reported; iv) gametocytes of Hepatocystis sp. which are illustrated but cannot be assigned to a known species. A tentative interpretation of phylogenetic characters of haemosporidians of bats is provided from the morphology of the gametocytes and localisation of the tissue stages with respect to recent data on the phylogeny of bats. PMID:22550624

  12. Viable but non-culturable state (VBNC) of Escherichia coli related to EnvZ under the effect of pH, starvation and osmotic stress in sea water.

    PubMed

    Darcan, Cihan; Ozkanca, Reşit; Idil, Onder; Flint, Ken P

    2009-01-01

    When exposed extreme environmental conditions such as sea water, bacteria have been shown different survival strategy for continue their life. One of this strategy known as viable but nonculturable (VBNC) state which is very important for nondifferiation bacteria. VBNC cells cause serious human health problems. Little is known, however, about the genetic mechanisms underlying the VBNC state. Under different environmental conditions, porins are important in the survival strategy of bacteria. EnvZ/OmpR work together as regulators of ompF and ompC gene expression. It is known that the EnvZ system has a role in VBNC state. In this study we tried to find out the viability of EnvZ, OmpC and OmpF mutant E. coli under stress effect of osmolarity, pH and starvation. Bacteria were suspended in filtered-autoclaved sea water microcosms and numbers determined over 25 day incubation periods by plate count (PC), direct viable count (DVC) and count of cells capable of respiration (RCC). As regard to results, alkaline pH affected E. coli more than acidic pH, which led to decline in number. On the contrary glycine betaine addition to sea water protected E. coli porin mutants and also reduced the death rate of bacteria. Under the effect of pH, osmotic stress and starvation stress, wild type E. coli and porin mutants entered a dormant state or became VBNC with the exception of MSZ31 (envZ mutant) E. coli cells which did not enter the VBNC state under the three tested stress conditions. This study is the first report to demonstrate that E. coli could not enter the VBNC state in the lack of EnvZ product under the stress of osmolarity, pH and starvation and the relationship between EnvZ and VBNC state are not affected by pH, osmolarity and starvation. PMID:20380141

  13. ALS - resources

    MedlinePlus

    Resources - ALS ... The following organizations are good resources for information on amyotrophic lateral sclerosis : Muscular Dystrophy Association -- mda.org/disease/amyotrophic-lateral-sclerosis National Amyotrophic Lateral Sclerosis (ALS) Registry -- ...

  14. ALS Association

    MedlinePlus

    ... ALS. Find Out How Our Mission Leading the fight to treat and cure ALS through global research ... you participate, advocate, and donate, you advance the fight to find the cure and lead us toward ...

  15. New sequestrate fungi from Guyana: Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. (Boletaceae, Boletales).

    PubMed

    Smith, Matthew E; Amses, Kevin R; Elliott, Todd F; Obase, Keisuke; Aime, M Catherine; Henkel, Terry W

    2015-12-01

    Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. are described as new to science. These sequestrate, hypogeous fungi were collected in Guyana under closed canopy tropical forests in association with ectomycorrhizal (ECM) host tree genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae), and Pakaraimaea (Dipterocarpaceae). Molecular data place these fungi in Boletaceae (Boletales, Agaricomycetes, Basidiomycota) and inform their relationships to other known epigeous and sequestrate taxa within that family. Macro- and micromorphological characters, habitat, and multi-locus DNA sequence data are provided for each new taxon. Unique morphological features and a molecular phylogenetic analysis of 185 taxa across the order Boletales justify the recognition of the three new genera. PMID:26732137

  16. Reflexión bioética sobre el uso de organismos genéticamente modificados

    PubMed Central

    Yunta, Eduardo Rodríguez

    2011-01-01

    El presente artículo reflexiona desde los 4 principios de la bioética el uso comercial de organismos genéticamente modificados. Se cuestiona fundamentalmente la falta de transferencia de tecnología entre el mundo desarrollado y en desarrollo y el que el presente sistema de patentamiento de organismos vivos modificados fomenta intereses comerciales y no da debida importancia al desarrollo sostenible de la agricultura y ganadería en los países en desarrollo, donde más se necesita. Se reflexiona sobre la importancia que tiene evaluar los riesgos antes de introducirse en el mercado organismos genéticamente modificados y la necesidad de regulación en los países. PMID:21927675

  17. SEQ-GEN: A comprehensive multimission sequencing system

    NASA Technical Reports Server (NTRS)

    Salcedo, Jose; Starbird, Thomas J.

    1994-01-01

    SEQ-GEN is a user-interactive computer program used to plan and generate a sequence of commands for spacecraft. Desired activities are specified by the user of SEQ-GEN; SEQ-GEN in turn expands these activities, deriving the spacecraft commands necessary to accomplish the desired activities. SEQ-GEN models the effects on the spacecraft of the commands, predicting the state as a function of time, flagging any conflicts and rule violations. These states, conflicts, and violations are viewable both graphically and textually at the user's request. SEQ-GEN also displays the entire sequence graphically, showing each requested activity as a bar on its graphical timeline. SEQ-GEN immediately revalidates the sequence, updating its models and calculations along with its displays based on these changes. Because it has the ability to recalculate spacecraft states immediately, the user is able to perform 'what-if' sessions easily. SEQ-GEN, a multimission tool, is adaptable to any flight project. A flight project writes its adaptation files containing project unique information including in its simplest form, only spacecraft commands. For more involved projects the adaptation files may also contain flight and mission rules, description of the spacecraft and ground models, and the definition of activities. SEQ-GEN operates at whatever level of detail the adaptation files imply. Simple adaptations are straight forward to do. There is, however, no limit to the complexity of activity definitions or of spacecraft models: both may involve unlimited logical decision points. Commands and activities may involve any number of parameters of a wide variety of data types, including integer, float, time, boolean, and character strings. SEQ-GEN will be used by the Mars Pathfinder, Cassini, and VIM (Voyager Interstellar Mission) project in an effort to speed up adaptation time and to keep sequence generation costs down. SEQ-GEN is hosted on UNIX workstations. It uses MOTIF and X for windowing

  18. Identification of three feline immunodeficiency virus (FIV) env gene subtypes and comparison of the FIV and human immunodeficiency virus type 1 evolutionary patterns.

    PubMed Central

    Sodora, D L; Shpaer, E G; Kitchell, B E; Dow, S W; Hoover, E A; Mullins, J I

    1994-01-01

    Feline immunodeficiency virus (FIV) is a lentivirus associated with AIDS-like illnesses in cats. As such, FIV appears to be a feline analog of human immunodeficiency virus (HIV). A hallmark of HIV infection is the large degree of viral genetic diversity that can develop within an infected individual and the even greater and continually increasing level of diversity among virus isolates from different individuals. Our goal in this study was to determine patterns of FIV genetic diversity by focusing on a 684-nucleotide region encompassing variable regions V3, V4, and V5 of the FIV env gene in order to establish parallels and distinctions between FIV and HIV type 1 (HIV-1). Our data demonstrate that, like HIV-1, FIV can be separated into distinct envelope sequence subtypes (three are described here). Similar to that found for HIV-1, the pairwise sequence divergence within an FIV subtype ranged from 2.5 to 15.0%, whereas that between subtypes ranged from 17.8 to 26.2%. However, the high number of synonymous nucleotide changes among FIV V3 to V5 env sequences may also include a significant number of back mutations and suggests that the evolutionary distances among FIV subtypes are underestimated. Although only a few subtype B viruses were available for examination, the pattern of diversity between the FIV A and B subtypes was found to be significantly distinct; subtype B sequences had proportionally fewer mutations that changed amino acids, compared with silent changes, suggesting a more advanced state of adaptation to the host. No similar distinction was evident for HIV-1 subtypes. The diversity of FIV genomes within individual infected cats was found to be as high as 3.7% yet twofold lower than that within HIV-1-infected people over a comparable region of the env gene. Despite these differences, significant parallels between patterns of FIV evolution and HIV-1 evolution exist, indicating that a wide array of potentially divergent virus challenges need to be considered

  19. Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov.

    PubMed

    Johansen, J E; Nielsen, P; Sjøholm, C

    1999-07-01

    Phenotypic data indicate that gliding, yellow/orange-pigmented, agar-digesting bacterial strains were members of the Cytophaga-Flavobacterium-Bacteroides (CFB) group. The strains were isolated from the surface of the marine benthic macroalga Fucus serratus L. and the surrounding seawater at three localities in Danish waters. The bacteria were Gram-negative, flexirubin-negative, aerobic, catalase-positive and oxidase-negative and were psychrophilic and halophilic. All strains utilized D-fructose, L-fucose and alpha-ketobutyric acid and degraded alginic acid, carrageenan, starch and autoclaved yeast cells. Amplification with primers specific for repetitive extragenic palindromic elements by PCR divided the strains of this study into two groups. Both groups showed unique PCR amplification patterns compared to reference strains of the CFB group. Phylogenetic analysis of 16S rDNA sequences showed association of these organisms and [Cytophaga] lytica at the genus level. Hybridization of total chromosomal DNA revealed that the new strains and [Cytophaga] lytica ATCC 23178T were clearly distinct from each other and other previously described species of the CFB group. A new genus is described, Cellulophaga gen. nov. comprising two new species, Cellulophaga baltica gen. nov., sp. nov. (NN015840T = LMG 18535T) and Cellulophaga fucicola gen. nov., sp. nov. (NN015860T = LMG 18536T), as well as the emendation of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. PMID:10425785

  20. Friend strain of spleen focus-forming virus is a recombinant between ecotropic murine type C virus and the env gene region of xenotropic type C virus.

    PubMed Central

    Troxler, D H; Lowy, D; Howk, R; Young, H; Scolnick, E M

    1977-01-01

    The spleen focus-forming virus (SFFV), a replication-defective murine leukemia virus that causes the rapid transformation of certain hematopoietic target cells, has acquired specific xenotropic viral genetic information not contained in Friend helper virus. In the current studies, it is shown that a cDNA that represents a xenotropic virus portion of SFFV detects genetic sequences derived from the env gene region of murine xenotropic virus. The significance of the acquisition of these xenotropic viral sequences by SFFV is discussed with regard to their possible role in the rapid leukemogenicity of SFFV, and an analogy is drawn between the formation of SFFV and the formation of the Kirsten and Harvey sarcoma viruses. PMID:200927

  1. The MuLV 4070A G541R Env mutation decreases the stability and alters the conformation of the TM ectodomain

    SciTech Connect

    Schneider, William M. Zheng, Haiyan Cote, Marie L. Roth, Monica J.

    2008-02-05

    Virus-cell and cell-cell fusion events are affected by various properties of the fusogenic Env protein on the cell surface. The G541R mutation within the TM ectodomain of murine leukemia virus (MuLV) 4070A arose by positive selection in viral passage and results in a reduction of cell-cell fusion events while maintaining viral titer. Size exclusion chromatography shows that the multimerization properties are similar among expressed wild-type and mutant ectodomain peptides. Circular dichroism measurements reveal decreased thermal stability of the G541R mutant as compared to wild type. The G541R mutant also renders the peptide more susceptible to Lys-C protease cleavage. The 42-114 monoclonal antibody does not bind to the G541R mutant peptides, suggesting a structural difference from wild type. These altered physical properties result in productive viral infection of G541R bearing virus with decreased syncytia.

  2. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens

    PubMed Central

    Julien, Jean-Philippe; Lee, Jeong Hyun; Ozorowski, Gabriel; Hua, Yuanzi; Torrents de la Peña, Alba; de Taeye, Steven W.; Nieusma, Travis; Cupo, Albert; Yasmeen, Anila; Golabek, Michael; Pugach, Pavel; Klasse, P. J.; Moore, John P.; Sanders, Rogier W.; Ward, Andrew B.; Wilson, Ian A.

    2015-01-01

    A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

  3. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens.

    PubMed

    Julien, Jean-Philippe; Lee, Jeong Hyun; Ozorowski, Gabriel; Hua, Yuanzi; Torrents de la Peña, Alba; de Taeye, Steven W; Nieusma, Travis; Cupo, Albert; Yasmeen, Anila; Golabek, Michael; Pugach, Pavel; Klasse, P J; Moore, John P; Sanders, Rogier W; Ward, Andrew B; Wilson, Ian A

    2015-09-22

    A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. PMID:26372963

  4. ENV-specific cytotoxic T lymphocyte responses in HIV seronegative health care workers occupationally exposed to HIV-contaminated body fluids.

    PubMed Central

    Pinto, L A; Sullivan, J; Berzofsky, J A; Clerici, M; Kessler, H A; Landay, A L; Shearer, G M

    1995-01-01

    Identification of the components of protective immunity are crucial for the development of effective prophylactic and therapeutic vaccine strategies. Analysis of HIV-specific responses in exposed but uninfected individuals might thus provide a unique resource to elucidate the components and correlates of protective immunity to HIV. In the present study we analyzed HIV-specific cytotoxic and helper T lymphocyte responses in health care workers (HCW) exposed to body fluids from HIV-positive individuals. HCW exposed to blood from HIV-negative individuals as well as healthy donors served as controls. Cytotoxic T lymphocyte (CTL) responses to HIV envelope (env) peptides were detected in 7/20 (35%) HCW exposed to HIV-positive blood and in none of the 20 health care workers exposed to uninfected blood or the seven healthy blood donors studied. HIV-specific CTL responses were detected only after in vitro stimulation, and were MHC class I restricted. No MHC class I restriction elements were uniformly identified among the different responders. 21/28 (75%) HCW exposed to contaminated blood responded to env as measured by IL-2 production to the peptides, in contrast to only 9/38 (24%) HCW exposed to HIV seronegative blood and 3/35 (9%) healthy blood donors. All the HIV exposed individuals were seronegative on repeated ELISA tests, and no evidence of infection was obtained by PCR analysis. These findings indicate that a single exposure to HIV can induce CTL immunity to HIV antigens, in the absence of other evidence of infection. Images PMID:7635981

  5. Defective herpes simplex virus type 1 vectors harboring gag, pol, and env genes can be used to rescue defective retrovirus vectors.

    PubMed Central

    Savard, N; Cosset, F L; Epstein, A L

    1997-01-01

    A retroviral packaging transcription unit was constructed in which the Moloney murine leukemia virus (MoMLV) gag-pol and env genes are expressed under the control of herpesvirus regulatory sequences. This transcription unit, lacking long terminal repeats, primer binding sites, and most of the retrovirus packaging signal but retaining both retroviral donor and acceptor splice sites, was cloned into a herpes simplex virus type 1 (HSV-1) amplicon plasmid, and amplicon vectors (the gag-pol-env [GPE] vectors) were generated by using a defective HSV-1 vector as helper virus. The GPE vector population was used to infect human TE671 cells (ATCC CRL 8805), harboring a lacZ provirus (TE-lac2 cells), and supernatants of infected cells were collected and filtered at different times after infection. These supernatants were found to contain infectious ecotropic lacZ retroviral particles, as shown both by reverse transcription-PCR and by their ability to transduce a beta-galactosidase activity to murine NIH 3T3 cells but not to human TE671 cells. The titer of retroviral vectors released by GPE vector-infected TE-lac2 cells increased with the dose of infectious amplicon particles. Retrovirus vector production was inhibited by superinfection with helper virus, indicating that helper virus coinfection negatively interfered with retrovirus production. Induction of retrovirus vectors by GPE vectors was neutralized by anti-HSV-1 but not by anti-MoMLV antiserum, while transduction of beta-galactosidase activity to NIH 3T3 cells by supernatants of GPE vector-infected TE-lac2 cells was neutralized by anti-MoMLV antiserum. These results demonstrate that HSV-1 GPE amplicon vectors can rescue defective lacZ retrovirus vectors and suggest that they could be used as a sort of launching ramp to fire defective retrovirus vectors from within virtually any in vitro or in vivo cell type containing defective retroviral vectors. PMID:9094692

  6. Retrovirus Vectors Bearing Jaagsiekte Sheep Retrovirus Env Transduce Human Cells by Using a New Receptor Localized to Chromosome 3p21.3

    PubMed Central

    Rai, Sharath K.; DeMartini, James C.; Miller, A. Dusty

    2000-01-01

    Jaagsiekte sheep retrovirus (JSRV) is a type D retrovirus associated with a contagious lung tumor of sheep, ovine pulmonary carcinoma. Other than sheep, JSRV is known to infect goats, but there is no evidence of human infection. Until now it has not been possible to study the host range for JSRV because of the inability to grow this virus in culture. Here we show that the JSRV envelope protein (Env) can be used to pseudotype Moloney murine leukemia virus (MoMLV)-based retrovirus vectors and that such vectors can transduce human cells in culture. We constructed hybrid retrovirus packaging cells that express the JSRV Env and the MoMLV Gag-Pol proteins and can produce JSRV-pseudotype vectors at titers of up to 106 alkaline phosphatase-positive focus-forming units/ml. Using this high-titer virus, we have studied the host range for JSRV, which includes sheep, human, monkey, bovine, dog, and rabbit cells but not mouse, rat, or hamster cells. Considering the inability of the JSRV-pseudotype vector to transduce hamster cells, we used the hamster cell line-based Stanford G3 panel of whole human genome radiation hybrids to phenotypically map the JSRV receptor (JVR) gene within the p21.3 region of human chromosome 3. JVR is likely a new retrovirus receptor, as none of the previously identified retrovirus receptors localizes to the same position. Several chemokine receptors that have been shown to serve as coreceptors for lentivirus infection are clustered in the same region of chromosome 3; however, careful examination shows that the JSRV receptor does not colocalize with any of these genes. PMID:10775607

  7. GenAnneal: Genetically modified Simulated Annealing

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-05-01

    A modification of the standard Simulated Annealing (SA) algorithm is presented for finding the global minimum of a continuous multidimensional, multimodal function. We report results of computational experiments with a set of test functions and we compare to methods of similar structure. The accompanying software accepts objective functions coded both in Fortran 77 and C++. Program summaryTitle of program:GenAnneal Catalogue identifier:ADXI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXI_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The tool is designed to be portable in all systems running the GNU C++ compiler Installation: University of Ioannina, Greece on Linux based machines Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data: 200 KB No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of bytes in distributed program, including test data, etc.:84 885 No. of lines in distributed program, including test data, etc.:14 896 Distribution format: tar.gz Nature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Typical running time: Depending on the objective function. Method of solution: We modified the process of step selection that the traditional Simulated

  8. Collapse of the Cretaceous Helvetiafjellet Formation due to tectonic activity at Kvalvågen, eastern Spitsbergen

    NASA Astrophysics Data System (ADS)

    Onderdonk, N.; Midtkandal, I.; Ahokas, J.

    2008-12-01

    A variety of features recording disturbance of Mid-Cretaceous sediments are exposed in coastal cliffs at Kvalvågen, east Spitsbergen. The most striking of these features are large displaced blocks of Helvetiafjellet Formation sandstone (ranging from 5 to 25 meters across) that were dropped down into underlying shale- dominated sediments along normal faults. In addition to the displaced blocks much of the sandstone unit is missing along a 2 km stretch of coastal exposure and must have been slipped out of the plane of exposure. Several hypotheses have been proposed to explain the style and cause of the Cretaceous collapse at Kvalvågen including delta front collapse (Nemec et al., 1988), landslides into a submarine canyon (Steel et al., 2001), and collapse related to magmatic activity (Midtkandal et al., 2007). New structural data and field observations show that the orientations and style of deformation are not entirely consistent with the previous hypotheses and are better explained as the direct result of tectonically produced topography (i.e., a fault scarp). The deformation at Kvalvågen is the result of west-side-down displacement along a north-striking fault that crops out at the southern end of the cliff exposure. Tectonic disturbance in the area began in Hauterivian time and was over by the early Aptian. These outcrops are the only evidence of tectonic activity in the area during the Mid-Cretaceous and may be the result of displacement along a previously unrecognized extension of the Lomfjorden fault zone or related to regional stresses imposed by extensive sill intrusions during the formation of the High Arctic Large Igneous Province.

  9. Genes and proteins of Escherichia coli (GenProtEc).

    PubMed

    Riley, M; Space, D B

    1996-01-01

    GenProtEc is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. The database is available as a PKZip file by ftp from mbl.edu/pub/ecoli.exe. The program runs under MS-DOS on IMB-compatible machines. GenProtEc can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html. PMID:8594596

  10. History of the Juliusruh ionospheric observatory on Rügen

    NASA Astrophysics Data System (ADS)

    Weiß, J.

    2016-02-01

    The history of the Juliusruh ionospheric observatory on Rügen is closely connected to the history of ground-based ionospheric sounding. After a short introduction to the ionospheric research and the sounding technique, the founding of the Juliusruh station in 1954 and its development until today are described. The different methods of ground-based sounding - as far as they apply to Juliusruh - are briefly discussed. The condition of life and work in a small team on the island of Rügen, remote from the respective parent institute, is also the subject of this article, whose author headed Juliusruh Station from 1965 to 2004.

  11. A Virtual Reality Framework to Optimize Design, Operation and Refueling of GEN-IV Reactors.

    SciTech Connect

    Rizwan-uddin; Nick Karancevic; Stefano Markidis; Joel Dixon; Cheng Luo; Jared Reynolds

    2008-04-23

    many GEN-IV candidate designs are currently under investigation. Technical issues related to material, safety and economics are being addressed at research laboratories, industry and in academia. After safety, economic feasibility is likely to be the most important crterion in the success of GEN-IV design(s). Lessons learned from the designers and operators of GEN-II (and GEN-III) reactors must play a vital role in achieving both safety and economic feasibility goals.

  12. 77 FR 54648 - Seventh Meeting: RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-05

    ... Federal Aviation Administration Seventh Meeting: RTCA NextGen Advisory Committee (NAC) AGENCY: Federal...Gen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of the seventh meeting of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held October...

  13. 77 FR 25524 - Sixth Meeting: RTCA, NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-30

    ... Federal Aviation Administration Sixth Meeting: RTCA, NextGen Advisory Committee AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of a meeting of RTCA, NextGen... RTCA, NextGen Advisory Committee. DATES: The meeting will be held May 24, 2012, from 9:00 a.m.-3:00...

  14. 78 FR 5860 - Eighth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ... Federal Aviation Administration Eighth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... meeting of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held February 7,...

  15. 78 FR 54509 - Tenth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... Federal Aviation Administration Tenth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held September 19, 2013...

  16. 76 FR 3931 - Second Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ... Federal Aviation Administration Second Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  17. 76 FR 22162 - Third Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-20

    ... Federal Aviation Administration Third Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  18. 76 FR 54526 - Fourth Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-01

    ... Federal Aviation Administration Fourth Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  19. 78 FR 28940 - Ninth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-16

    ... Federal Aviation Administration Ninth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held June 4, 2013 from...

  20. ORPC RivGen controller performance raw data - Igiugig 2015

    SciTech Connect

    Jarlath McEntee

    2015-12-18

    Contains raw data for operations of Ocean Renewable Power Company (ORPC) RivGen Power System in Igiugig 2015 in Matlab data file format. Two data files capture the data and timestamps for data, including power in, voltage, rotation rate, and velocity.

  1. Meet Mr. and Mrs. Gen X: A New Parent Generation

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over…

  2. 75 FR 56654 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... Notice in the Federal Register on September 3, 2010 (75-FR-54221), concerning a Notice to advise the... the Federal Register Notice on September 3, 2010, (75-FR-54221) is revised to read as follows: Opening... Federal Aviation Administration RTCA NextGen Advisory Committee (NAC) AGENCY: Federal...

  3. Safer Systems: A NextGen Aviation Safety Strategic Goal

    NASA Technical Reports Server (NTRS)

    Darr, Stephen T.; Ricks, Wendell R.; Lemos, Katherine A.

    2008-01-01

    The Joint Planning and Development Office (JPDO), is charged by Congress with developing the concepts and plans for the Next Generation Air Transportation System (NextGen). The National Aviation Safety Strategic Plan (NASSP), developed by the Safety Working Group of the JPDO, focuses on establishing the goals, objectives, and strategies needed to realize the safety objectives of the NextGen Integrated Plan. The three goal areas of the NASSP are Safer Practices, Safer Systems, and Safer Worldwide. Safer Practices emphasizes an integrated, systematic approach to safety risk management through implementation of formalized Safety Management Systems (SMS) that incorporate safety data analysis processes, and the enhancement of methods for ensuring safety is an inherent characteristic of NextGen. Safer Systems emphasizes implementation of safety-enhancing technologies, which will improve safety for human-centered interfaces and enhance the safety of airborne and ground-based systems. Safer Worldwide encourages coordinating the adoption of the safer practices and safer systems technologies, policies and procedures worldwide, such that the maximum level of safety is achieved across air transportation system boundaries. This paper introduces the NASSP and its development, and focuses on the Safer Systems elements of the NASSP, which incorporates three objectives for NextGen systems: 1) provide risk reducing system interfaces, 2) provide safety enhancements for airborne systems, and 3) provide safety enhancements for ground-based systems. The goal of this paper is to expose avionics and air traffic management system developers to NASSP objectives and Safer Systems strategies.

  4. A New Parent Generation: Meet Mr. and Mrs. Gen X

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in…

  5. DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond

    SciTech Connect

    Pan, Paul Y

    2010-12-10

    An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

  6. Detection of HIV type 1 env subtypes A, B, C, and E in Asia using dried blood spots: a new surveillance tool for molecular epidemiology.

    PubMed

    Cassol, S; Weniger, B G; Babu, P G; Salminen, M O; Zheng, X; Htoon, M T; Delaney, A; O'Shaughnessy, M; Ou, C Y

    1996-10-10

    Global surveillance of HIV-1 subtypes for genetic characterization is hampered by the biohazard of processing and the difficulties of shipping whole blood or cells from many developing country regions. We developed a technique for the direct automated sequencing of viral DNA from dried blood spot (DBS) specimens collected on absorbent paper, which can be mailed unrefrigerated in sturdy paper envelopes with low biohazard risk. DBS were collected nonrandomly from HIV-1-infected, mostly asymptomatic, patients in five Asian countries in 1991, and shipped via airmail or hand carried without refrigeration to Bangkok, and then transshipped to North America for processing. After more than 2 years of storage, including 6 months at ambient temperatures, proviral DNA in the DBS was amplified by nested PCR, and a 389-nucleotide segment of the C2-V3 env gene region was sequenced, from which 287 base pairs were aligned and subtyped by phylogenetic analysis with neighbor-joining and other methods. From southern India, there were 25 infections with subtype C and 2 with subtype A. From Myanmar (Burma), we identified the first subtype E infection, as well as six subtype BB, a distinct cluster within subtype B that was first discovered in Thailand and that has now appeared in China, Malaysia, and Japan. From southwest China, one BB was identified, while a "classical" B typical of North American and European strains was found in Indonesia. From Thailand, five DBS of ambiguous serotype were identified as three B, one BB, and one E. A blinded control serotype E specimen was correctly identified, but a serotype BB control was not tested. Most HIV-1 in southern India appears to be env subtype C, with rare A, as others have reported in western and northern India. The subtypes BB and E in Myanmar, and the BB in China, suggest epidemiological linkage with these subtypes in neighboring Thailand. DBS are a practical, economical technique for conducting large-scale molecular epidemiological

  7. Equine Viperin Restricts Equine Infectious Anemia Virus Replication by Inhibiting the Production and/or Release of Viral Gag, Env, and Receptor via Distortion of the Endoplasmic Reticulum

    PubMed Central

    Tang, Yan-Dong; Na, Lei; Zhu, Chun-Hui; Shen, Nan; Yang, Fei; Fu, Xian-Qiu; Wang, Yu-Hong; Fu, Li-Hua; Wang, Jia-Yi; Lin, Yue-Zhi; Wang, Xue-Feng; Wang, Xiaojun

    2014-01-01

    ABSTRACT Viperin is an endoplasmic reticulum (ER)-associated multifunctional protein that regulates virus replication and possesses broad antiviral activity. In many cases, viperin interferes with the trafficking and budding of viral structural proteins by distorting the membrane transportation system. The lentivirus equine infectious anemia virus (EIAV) has been studied extensively. In this study, we examined the restrictive effect of equine viperin (eViperin) on EIAV replication and investigated the possible molecular basis of this restriction to obtain insights into the effect of this cellular factor on retroviruses. We demonstrated that EIAV infection of primary equine monocyte-derived macrophages (eMDMs) upregulated the expression of eViperin. The overexpression of eViperin significantly inhibited the replication of EIAV in eMDMs, and knockdown of eViperin transcription enhanced the replication of EIAV in eMDMs by approximately 45.8%. Further experiments indicated that eViperin restricts EIAV at multiple steps of viral replication. The overexpression of eViperin inhibited EIAV Gag release. Both the α-helix domain and radical S-adenosylmethionine (SAM) domain were required for this activity. However, the essential motifs in SAM were different from those reported for the inhibition of HIV-1 Gag by human viperin. Furthermore, eViperin disrupted the synthesis of both EIAV Env and receptor, which consequently inhibited viral production and entry, respectively, and this disruption was dependent on the eViperin α-helix domain. Using immunofluorescence assays and electron microscopy, we demonstrated that the α-helix domain is responsible for the distortion of the endoplasmic reticulum (ER). Finally, EIAV did not exhibit counteracting eViperin at the protein level. IMPORTANCE In previous studies, viperin was indicated as restricting virus replications primarily by the inhibition of virus budding. Here, we show that viperin may have multiple antiviral mechanisms

  8. Identification of the Escherichia coli cell division gene sep and organization of the cell division-cell envelope genes in the sep-mur-ftsA-envA cluster as determined with specialized transducing lambda bacteriophages.

    PubMed Central

    Fletcher, G; Irwin, C A; Henson, J M; Fillingim, C; Malone, M M; Walker, J R

    1978-01-01

    From a lysogen with lambda integrated in the leu operon, specialized transducing phages that carry the cell division, murein biosynthesis, and envelope permeability genes located about 0.5 min to the right of leu were isolated. These phages were used to identify the previously undiscovered cell division gene sep. A genetic map proves that sep is located in the sequence leuA sep murE murF murC ddl ftsA envA. A physical map of this region was prepared by heteroduplex analysis of the phage DNAs. Overlapping segments of host DNA extended rightward for as much as 26.4 kilobase pairs from the prophage insertion point (thought to be in leuA) to include all the genes through envA. Images PMID:338600

  9. Potential impact of viral load and genetic makeup of HIV type 1 on mother-to-child transmission: characterization of env-C2V3C3 and nef sequences.

    PubMed

    Pádua, Elizabeth; Parreira, Ricardo; Tendeiro, Rita; Nunes, Baltazar; Castela, João; Soares, Isabel; Mouzinho, Ana; Reis, Eduarda; Paixão, Maria Teresa

    2009-11-01

    HIV-1 mother-to-child transmission (MTCT) was evaluated in terms of the molecular characterization of the env and nef genomic regions and quantification of maternal RNA viral loads. Assignment of viral subtype was achieved by direct sequencing of PCR 1172 products amplified from proviral DNA in 45 HIV-1-nontransmitting mothers (NTM), along with 13 pairs of HIV-1-transmitting mothers (TM) and their infected children (C). Analysis of the env C2V3C3 and nef sequences revealed that subtypes G and B, and their genetic combinations (AG, BG), accounted for over 84.5% of all viruses identified. The genetic structure form envA-nefG was the most commonly observed, with a lower frequency in the NTM (13.3%) compared to the TM (23.1%) group. A greater number of genetic forms was observed among NTM, namely the presence of sequences assigned to subtypes D and F, as well as the intergenetic A/J, and C/U, recombinant forms, along with a mosaic provirus with a complex putative envA-nefEGE genetic structure. No significant differences were found when RNA viral loads were evaluated as a function of the viral subtypes. Nevertheless, a relatively high quantification of HIV-1 RNA was obtained in the NTM group, emphasizing the importance of the compliance and effectiveness of therapeutic schemes to control viral replication and reduce the risk of HIV vertical transmission. V3 sequences displaying features associated with the R5 phenotype dominated in both groups. Both C2V3C3 and Nef's functional domains were conserved during HIV-1 vertical transmission. PMID:19886833

  10. Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer.

    PubMed

    Kong, Leopold; Torrents de la Peña, Alba; Deller, Marc C; Garces, Fernando; Sliepen, Kwinten; Hua, Yuanzi; Stanfield, Robyn L; Sanders, Rogier W; Wilson, Ian A

    2015-10-01

    The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer. Here, a crystal structure of the soluble BG505 SOSIP gp140 trimer at 4.6 Å resolution with the bNAbs 8ANC195 and PGT128 reveals additional interactions in comparison to previous antibody-gp120 structures. For 8ANC195, in addition to previously documented interactions with gp120, a substantial interface with gp41 is now elucidated that includes extensive interactions with the N637 glycan. Surprisingly, removal of the N637 glycan did not impact 8ANC195 affinity, suggesting that the antibody has evolved to accommodate this glycan without loss of binding energy. PGT128 indirectly affects the N262 glycan by a domino effect, in which PGT128 binds to the N301 glycan, which in turn interacts with and repositions the N262 glycan, thereby illustrating the important role of neighboring glycans on epitope conformation and stability. Comparisons with other Env trimer and gp120 structures support an induced conformation for glycan N262, suggesting that the glycan shield is allosterically modified upon PGT128 binding. These complete epitopes of two broadly neutralizing antibodies on the Env trimer can now be exploited for HIV-1 vaccine design. PMID:26457433

  11. The opgC gene is required for OPGs succinylation and is osmoregulated through RcsCDB and EnvZ/OmpR in the phytopathogen Dickeya dadantii

    PubMed Central

    Bontemps-Gallo, Sébastien; Madec, Edwige; Robbe-Masselot, Catherine; Souche, Erika; Dondeyne, Jacqueline; Lacroix, Jean-Marie

    2016-01-01

    Osmoregulated periplasmic glucans (OPGs) are a family of periplasmic oligosaccharides found in the envelope of most Proteobacteria. They are required for virulence of zoo- and phyto-pathogens. The glucose backbone of OPGs is substituted by various kinds of molecules depending on the species, O-succinyl residues being the most widely distributed. In our model, Dickeya dadantii, a phytopathogenic bacteria causing soft rot disease in a wide range of plant species, the backbone of OPGs is substituted by O-succinyl residues in media of high osmolarity and by O-acetyl residues whatever the osmolarity. The opgC gene encoding a transmembrane protein required for the succinylation of the OPGs in D. dadantii was found after an in silico search of a gene encoding a protein with the main characteristics recovered in the two previously characterized OpgC of E. coli and R. sphaeroides, i.e. 10 transmembrane segments and one acyl-transferase domain. Characterization of the opgC gene revealed that high osmolarity expression of the succinyl transferase is controlled by both the EnvZ-OmpR and RcsCDB phosphorelay systems. The loss of O-succinyl residue did not affect the virulence of D. dadantii, suggesting that only the glucose backbone of OPGs is required for virulence. PMID:26790533

  12. Rapid, Transient Changes at the env Locus of Plasma Human Immunodeficiency Virus Type 1 Populations during the Emergence of Protease Inhibitor Resistance

    PubMed Central

    Delwart, Eric L.; Pan, Heng; Neumann, Avidan; Markowitz, Martin

    1998-01-01

    Plasma human immunodeficiency virus type 1 (HIV-1) populations were genetically analyzed at their most variable locus, the envelope gene, during the rapid emergence of resistance to protease inhibitor monotherapy. Plasma virus populations remained genetically constant prior to drug treatment and during the 1 to 2 weeks following initiation of therapy, while viremia fell 10- to 100-fold. Concomitant with rapid plasma viremia rebounds associated with the emergence of drug-resistant virus, marked alterations were then detected at the env locus. Plasma population changes lasted only a few weeks before the reappearance of the pretreatment envelope variants. The emergence of resistance to single protease inhibitors was therefore associated with major but transient changes at a nonselected locus. Selection for resistance to single protease inhibitors thus appears to be more complex than the continued replication of a large, random, and therefore genetically representative sampling of the pretreatment plasma population. The possibility that drug-privileged anatomical sites containing distinct envelope variants and/or a small effective HIV-1 population size account for these results is discussed. PMID:9499102

  13. Phylogenetic analysis of env, gag, and tat genes of HIV type 1 detected among the injecting drug users in West Bengal, India.

    PubMed

    Mullick, Ranajoy; Sengupta, Satarupa; Sarkar, Kamalesh; Saha, M K; Chakrabarti, Sekhar

    2006-12-01

    A recent occurrence of HIV-1 seropositivity among a group of injecting drug users (IDUs) in Darjeeling, a hilly district in northern West Bengal, revealed overall 11.8% HIV seroprevalence. Our study based on env (C2-V3), gag (p24-p7), and tat (exon-1) genomic regions of HIV-1 detected among this population showed that Darjeeling IDU sequences belonged to subtype C. Interestingly, the IDU sequences from Darjeeling were again found to be closer to the C strains from Manipur, a northeastern state in India, which is linked to the Golden Triangle via the Manipur-Myanmar border, rather than the IDU C sequences from Nepal, a neighboring country of India. The outgroup reference strains from different sites of IDU-driven epidemics in the world like Russia, Vietnam, Thailand, and Spain belonged to the nonsubtype C group and formed separate clusters from the subtype C cluster in our analysis. These results indicate a rapid spread of HIV-1 by possible drug trafficking along international boundaries, which might also help in the invasion of HIV-1 among IDUs of Darjeeling through the Manipur-Myanmar border of India. PMID:17209773

  14. Use of a High Resolution Melting (HRM) Assay to Compare Gag, Pol, and Env Diversity in Adults with Different Stages of HIV Infection

    PubMed Central

    Cousins, Matthew M.; Laeyendecker, Oliver; Beauchamp, Geetha; Brookmeyer, Ronald; Towler, William I.; Hudelson, Sarah E.; Khaki, Leila; Koblin, Beryl; Chesney, Margaret; Moore, Richard D.; Kelen, Gabor D.; Coates, Thomas; Celum, Connie; Buchbinder, Susan P.; Seage, George R.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

    2011-01-01

    Background Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual. Methods HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14–540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env. Results Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection. Conclusions The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined. PMID:22073290

  15. HIV-1 Env DNA vaccine plus protein boost delivered by EP expands B- and T-cell responses and neutralizing phenotype in vivo.

    PubMed

    Muthumani, Kar; Wise, Megan C; Broderick, Kate E; Hutnick, Natalie; Goodman, Jonathan; Flingai, Seleeke; Yan, Jian; Bian, Chaoran B; Mendoza, Janess; Tingey, Colleen; Wilson, Christine; Wojtak, Krzysztof; Sardesai, Niranjan Y; Weiner, David B

    2013-01-01

    An effective HIV vaccine will most likely require the induction of strong T-cell responses, broadly neutralizing antibodies (bNAbs), and the elicitation of antibody-dependent cellular cytotoxicity (ADCC). Previously, we demonstrated the induction of strong HIV/SIV cellular immune responses in macaques and humans using synthetic consensus DNA immunogens delivered via adaptive electroporation (EP). However, the ability of this improved DNA approach to prime for relevant antibody responses has not been previously studied. Here, we investigate the immunogenicity of consensus DNA constructs encoding gp140 sequences from HIV-1 subtypes A, B, C and D in a DNA prime-protein boost vaccine regimen. Mice and guinea pigs were primed with single- and multi-clade DNA via EP and boosted with recombinant gp120 protein. Sera were analyzed for gp120 binding and induction of neutralizing antibody activity. Immunization with recombinant Env protein alone induced low-titer binding antibodies with limited neutralization breath. In contrast, the synthetic DNA prime-protein boost protocol induced significantly higher antibody binding titers. Furthermore, sera from DNA prime-protein boost groups were able to neutralize a broader range of viruses in a panel of tier 1 clade B viruses as well as multiple tier 1 clade A and clade C viruses. Further investigation of synthetic DNA prime plus adaptive EP plus protein boost appears warranted. PMID:24391921

  16. HIV-1 Env DNA Vaccine plus Protein Boost Delivered by EP Expands B- and T-Cell Responses and Neutralizing Phenotype In Vivo

    PubMed Central

    Muthumani, Kar; Wise, Megan C.; Broderick, Kate E.; Hutnick, Natalie; Goodman, Jonathan; Flingai, Seleeke; Yan, Jian; Bian, Chaoran B.; Mendoza, Janess; Tingey, Colleen; Wilson, Christine; Wojtak, Krzysztof; Sardesai, Niranjan Y.; Weiner, David B.

    2013-01-01

    An effective HIV vaccine will most likely require the induction of strong T-cell responses, broadly neutralizing antibodies (bNAbs), and the elicitation of antibody-dependent cellular cytotoxicity (ADCC). Previously, we demonstrated the induction of strong HIV/SIV cellular immune responses in macaques and humans using synthetic consensus DNA immunogens delivered via adaptive electroporation (EP). However, the ability of this improved DNA approach to prime for relevant antibody responses has not been previously studied. Here, we investigate the immunogenicity of consensus DNA constructs encoding gp140 sequences from HIV-1 subtypes A, B, C and D in a DNA prime-protein boost vaccine regimen. Mice and guinea pigs were primed with single- and multi-clade DNA via EP and boosted with recombinant gp120 protein. Sera were analyzed for gp120 binding and induction of neutralizing antibody activity. Immunization with recombinant Env protein alone induced low-titer binding antibodies with limited neutralization breath. In contrast, the synthetic DNA prime-protein boost protocol induced significantly higher antibody binding titers. Furthermore, sera from DNA prime-protein boost groups were able to neutralize a broader range of viruses in a panel of tier 1 clade B viruses as well as multiple tier 1 clade A and clade C viruses. Further investigation of synthetic DNA prime plus adaptive EP plus protein boost appears warranted. PMID:24391921

  17. Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region.

    PubMed

    Tolbert, William D; Gohain, Neelakshi; Veillette, Maxime; Chapleau, Jean-Philippe; Orlandi, Chiara; Visciano, Maria L; Ebadi, Maryam; DeVico, Anthony L; Fouts, Timothy R; Finzi, Andrés; Lewis, George K; Pazgier, Marzena

    2016-05-01

    Evidence supports a role of antibody-dependent cellular cytotoxicity (ADCC) toward transitional epitopes in the first and second constant (C1-C2) regions of gp120 (A32-like epitopes) in preventing HIV-1 infection and in vaccine-induced protection. Here, we describe the first successful attempt at isolating the inner domain (ID) of gp120 as an independent molecule that encapsulates the A32-like region within a minimal structural unit of the HIV-1 Env. Through structure-based design, we developed ID2, which consists of the ID expressed independently of the outer domain and stabilized in the CD4-bound conformation by an inter-layer disulfide bond. ID2 expresses C1-C2 epitopes in the context of CD4-triggered full-length gp120 but without any known neutralizing epitope present. Thus, ID2 represents a novel probe for the analysis and/or selective induction of antibody responses to the A32 epitope region. We also present the crystal structure of ID2 complexed with mAb A32, which defines its epitope. PMID:27041594

  18. The Receptor Complex Associated with Human T-Cell Lymphotropic Virus Type 3 (HTLV-3) Env-Mediated Binding and Entry Is Distinct from, but Overlaps with, the Receptor Complexes of HTLV-1 and HTLV-2▿

    PubMed Central

    Jones, Kathryn S.; Huang, Ying K.; Chevalier, Sébastien A.; Afonso, Philippe V.; Petrow-Sadowski, Cari; Bertolette, Daniel C.; Gessain, Antoine; Ruscetti, Francis W.; Mahieux, Renaud

    2009-01-01

    Little is known about the transmission or tropism of the newly discovered human retrovirus, human T-cell lymphotropic virus type 3 (HTLV-3). Here, we examine the entry requirements of HTLV-3 using independently expressed Env proteins. We observed that HTLV-3 surface glycoprotein (SU) binds efficiently to both activated CD4+ and CD8+ T cells. This contrasts with both HTLV-1 SU, which primarily binds to activated CD4+ T cells, and HTLV-2 SU, which primarily binds to activated CD8+ T cells. Binding studies with heparan sulfate proteoglycans (HSPGs) and neuropilin-1 (NRP-1), two molecules important for HTLV-1 entry, revealed that these molecules also enhance HTLV-3 SU binding. However, unlike HTLV-1 SU, HTLV-3 SU can bind efficiently in the absence of both HSPGs and NRP-1. Studies of entry performed with HTLV-3 Env-pseudotyped viruses together with SU binding studies revealed that, for HTLV-1, glucose transporter 1 (GLUT-1) functions at a postbinding step during HTLV-3 Env-mediated entry. Further studies revealed that HTLV-3 SU binds efficiently to naïve CD4+ T cells, which do not bind either HTLV-1 or HTLV-2 SU and do not express detectable levels of HSPGs, NRP-1, and GLUT-1. These results indicate that the complex of receptor molecules used by HTLV-3 to bind to primary T lymphocytes differs from that of both HTLV-1 and HTLV-2. PMID:19279090

  19. Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA sequence analysis has shown that species of the Candida kruisii clade and species of the Candida tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T. kruisii, and Suhomyces gen. nov., type species S. tanzawaensis. Many o...

  20. Al Composites

    NASA Astrophysics Data System (ADS)

    Chandanayaka, Tharaka; Azarmi, Fardad

    2014-05-01

    In the present study, cold spraying technique was used to fabricate a metal matrix composite (MMC) that consists of Ni matrix and 20 vol.% Ni3Al particles at two different particle sizes as reinforcement. This study intends to investigate the effect of reinforcement particle size on microstructural and mechanical properties of cold sprayed MMCs. Two different Ni3Al powders with nominal particle size of -45 to +5 and +45 to 100 μm were used as reinforcement in this study. Cold sprayed Ni-Ni3Al samples were subjected to the microstructural observation and characterization prior to any mechanical testing. Then, samples were tested using nano-indentation, Knoop hardness, Vickers hardness, and Resonance frequency to evaluate their mechanical properties. No significant changes were observed in microstructural characteristics due to different particle sizes. The results obtained from a variety of mechanical testings indicated that the increasing reinforcement particle size resulted in the slight reduction of mechanical properties such as elastic modulus and hardness in cold sprayed MMCs. The mechanical interlock between deposited particles defines the bonding strength in cold sprayed samples. Small size particles have a higher velocity and impact resulting in stronger interlock between deformed particles.

  1. Advanced Vehicle Concepts and Implications for NextGen

    NASA Technical Reports Server (NTRS)

    Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

    2010-01-01

    This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

  2. Technology evaluation: C242-DM1, ImmunoGen Inc.

    PubMed

    Smith, S

    2001-04-01

    C242-DM1 is a tumor-activated immunotoxin under development by GlaxoSmithKline plc (formerly SmithKline Beecham plc), under licence from ImmunoGen Inc, as a potential treatment for colon tumor. It consists of a colon cancer-specific humanized antibody, C242, conjugated to the maytansine derivative DM1. In preclinical studies, C242-DM1 caused complete tumor regression in animal models of both human pancreatic and non-small cell lung cancer (NSCLC) at non-toxic doses. C242-DM1 has also been evaluated in an immunoconjugate combination with J-591 (Cornell University). The J591-DM1 immunoconjugate demonstrated effective, antigen-specific delivery of a highly cytotoxic drug to PSMA-positive Pca cells in vitro and in vivo with low systemic toxicity. Results from studies in monkeys showed that C242-DM1 had no significant toxicity or side effects, when administered at doses higher than those that were previously shown to completely eradicate human colon tumors in mice [271420]. ImmunoGen acquired the right to evaluate, and an option to license, technology related to maytansines from Takeda. In February 1999, ImmunoGen and SmithKline Beecham signed a US $45 million development and commercialization agreement for C242-DM1 [313493]. In August 1997, Immunogen received an SBIR grant to advance development of huC242-DM1 [258356]. EP-00425235, held by ImmunoGen, covers conjugated forms of ansamitocin (maytansine) derivatives. Takeda holds several patents for the production of ansamitocin and its analogs, the first one being JP-53124692. PMID:11338934

  3. Coal-Gen attendees hear there's no magic bullet

    SciTech Connect

    2007-09-15

    Those attending COAL-GEN 2007 in August heard that there is no magic bullet for meeting the energy and infrastructure needs facing the USA. The article reports on the conference which addressed topics including development of supercritical circulating fluidized bed coal unit; IGCC projects, the importance of including carbon capture and sequestration, and the need to attract and train personnel to work in the power industry. 3 photos.

  4. Vaccination of Rhesus Macaques with Recombinant Mycobacterium bovis Bacillus Calmette-Guérin Env V3 Elicits Neutralizing Antibody-Mediated Protection against Simian-Human Immunodeficiency Virus with a Homologous but Not a Heterologous V3 Motif

    PubMed Central

    Someya, Kenji; Cecilia, Dayaraj; Ami, Yasushi; Nakasone, Tadashi; Matsuo, Kazuhiro; Burda, Sherri; Yamamoto, Hiroshi; Yoshino, Naoto; Kaizu, Masahiko; Ando, Shuji; Okuda, Kenji; Zolla-Pazner, Susan; Yamazaki, Shudo; Yamamoto, Naoki; Honda, Mitsuo

    2005-01-01

    Although the correlates of vaccine-induced protection against human immunodeficiency virus type 1 (HIV-1) are not fully known, it is presumed that neutralizing antibodies (NAb) play a role in controlling virus infection. In this study, we examined immune responses elicited in rhesus macaques following vaccination with recombinant Mycobacterium bovis bacillus Calmette-Guérin expressing an HIV-1 Env V3 antigen (rBCG Env V3). We also determined the effect of vaccination on protection against challenge with either a simian-human immunodeficiency virus (SHIV-MN) or a highly pathogenic SHIV strain (SHIV-89.6PD). Immunization with rBCG Env V3 elicited significant levels of NAb for the 24 weeks tested that were predominantly HIV-1 type specific. Sera from the immunized macaques neutralized primary HIV-1 isolates in vitro, including HIV-1BZ167/X4, HIV-1SF2/X4, HIV-1CI2/X4, and, to a lesser extent, HIV-1MNp/X4, all of which contain a V3 sequence homologous to that of rBCG Env V3. In contrast, neutralization was not observed against HIV-1SF33/X4, which has a heterologous V3 sequence, nor was it found against primary HIV-1 R5 isolates from either clade A or B. Furthermore, the viral load in the vaccinated macaques was significantly reduced following low-dose challenge with SHIV-MN, and early plasma viremia was markedly decreased after high-dose SHIV-MN challenge. In contrast, replication of pathogenic SHIV-89.6PD was not affected by vaccination in any of the macaques. Thus, we have shown that immunization with an rBCG Env V3 vaccine elicits a strong, type-specific V3 NAb response in rhesus macaques. While this response was not sufficient to provide protection against a pathogenic SHIV challenge, it was able to significantly reduce the viral load in macaques following challenge with a nonpathogenic SHIV. These observations suggest that rBCG vectors have the potential to deliver an appropriate virus immunogen for desirable immune elicitations. PMID:15650171

  5. AL Amyloidosis

    PubMed Central

    2012-01-01

    Definition of the disease AL amyloidosis results from extra-cellular deposition of fibril-forming monoclonal immunoglobulin (Ig) light chains (LC) (most commonly of lambda isotype) usually secreted by a small plasma cell clone. Most patients have evidence of isolated monoclonal gammopathy or smoldering myeloma, and the occurrence of AL amyloidosis in patients with symptomatic multiple myeloma or other B-cell lymphoproliferative disorders is unusual. The key event in the development of AL amyloidosis is the change in the secondary or tertiary structure of an abnormal monoclonal LC, which results in instable conformation. This conformational change is responsible for abnormal folding of the LC, rich in β leaves, which assemble into monomers that stack together to form amyloid fibrils. Epidemiology AL amyloidosis is the most common type of systemic amyloidois in developed countries with an estimated incidence of 9 cases/million inhabitant/year. The average age of diagnosed patients is 65 years and less than 10% of patients are under 50. Clinical description The clinical presentation is protean, because of the wide number of tissues or organs that may be affected. The most common presenting symptoms are asthenia and dyspnoea, which are poorly specific and may account for delayed diagnosis. Renal manifestations are the most frequent, affecting two thirds of patients at presentation. They are characterized by heavy proteinuria, with nephrotic syndrome and impaired renal function in half of the patients. Heart involvement, which is present at diagnosis in more than 50% of patients, leading to restrictive cardiopathy, is the most serious complication and engages prognosis. Diagnostic methods The diagnosis relies on pathological examination of an involved site showing Congo red-positive amyloid deposits, with typical apple-green birefringence under polarized light, that stain positive with an anti-LC antibody by immunohistochemistry and/or immunofluorescence. Due to the

  6. GEN IV reactors: Where we are, where we should go

    SciTech Connect

    Locatelli, G.; Mancini, M.; Todeschini, N.

    2012-07-01

    GEN IV power plants represent the mid-long term option of the nuclear sector. International literature proposes many papers and reports dealing with these reactors, but there is an evident difference of type and shape of information making impossible each kind of detailed comparison. Moreover, authors are often strongly involved in some particular design; this creates many difficulties in their super-partes position. Therefore it is necessary to put order in the most relevant information to understand strengths and weaknesses of each design and derive an overview useful for technicians and policy makers. This paper presents the state-of the art for GEN IV nuclear reactors providing a comprehensive literature review of the different designs with a relate taxonomy. It presents the more relevant references, data, advantages, disadvantages and barriers to the adoptions. In order to promote an efficient and wide adoption of GEN IV reactors the paper provides the pre-conditions that must be accomplished, enabling factors promoting the implementation and barriers limiting the extent and intensity of its implementation. It concludes outlying the state of the art of the most important R and D areas and the future achievements that must be accomplished for a wide adoption of these technologies. (authors)

  7. The GenABEL Project for statistical genomics.

    PubMed

    Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

    2016-01-01

    Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

  8. The GenABEL Project for statistical genomics

    PubMed Central

    Karssen, Lennart C.; van Duijn, Cornelia M.; Aulchenko, Yurii S.

    2016-01-01

    Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination. PMID:27347381

  9. Cosmosperma polyloba gen. et sp. nov., a seed plant from the Upper Devonian of South China

    NASA Astrophysics Data System (ADS)

    Wang, Deming; Liu, Le; Meng, Meicen; Xue, Jinzhuang; Liu, Tuo; Guo, Yun

    2014-08-01

    Seed plants with ovules were abundant in the Late Devonian of Euramerica and they contribute significantly to our understanding of their early history. However, coeval ovules have been scarce in other regions of the world. Specimens of the seed plant Cosmosperma polyloba gen. et sp. nov. Wang et al. were recently obtained from the Upper Devonian (Famennian) Wutong Formation, at Fanwan Village, Changxing County, Zhejiang Province, China. This new seed plant has cupulate ovules, the uniovulate cupules with up to 16 distal segments and with minute spines on the outer surface, synangiate pollen organs bearing six to eight microsporangia fused only at the base, and planate and highly dissected pinnules in alternate arrangement. It differs from other Devonian seed plants mainly in the organization and position of the uniovulate and ornamented cupule, and in the highly dissected pinnules. Cosmosperma Wang et al. represents the first Devonian ovules recovered from China or eastern Asia and further illustrates the diversity of early spermatophytes. As for the Late Devonian seed plants, it is suggested that the pollen organs are synangiate and simple in organization, and the branches and leaves are generally planate.

  10. Cosmosperma polyloba gen. et sp. nov., a seed plant from the Upper Devonian of South China.

    PubMed

    Wang, Deming; Liu, Le; Meng, Meicen; Xue, Jinzhuang; Liu, Tuo; Guo, Yun

    2014-08-01

    Seed plants with ovules were abundant in the Late Devonian of Euramerica and they contribute significantly to our understanding of their early history. However, coeval ovules have been scarce in other regions of the world. Specimens of the seed plant Cosmosperma polyloba gen. et sp. nov. Wang et al. were recently obtained from the Upper Devonian (Famennian) Wutong Formation, at Fanwan Village, Changxing County, Zhejiang Province, China. This new seed plant has cupulate ovules, the uniovulate cupules with up to 16 distal segments and with minute spines on the outer surface, synangiate pollen organs bearing six to eight microsporangia fused only at the base, and planate and highly dissected pinnules in alternate arrangement. It differs from other Devonian seed plants mainly in the organization and position of the uniovulate and ornamented cupule, and in the highly dissected pinnules. Cosmosperma Wang et al. represents the first Devonian ovules recovered from China or eastern Asia and further illustrates the diversity of early spermatophytes. As for the Late Devonian seed plants, it is suggested that the pollen organs are synangiate and simple in organization, and the branches and leaves are generally planate. PMID:24965709

  11. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    PubMed

    Vieira Vaz, Marcelo Gomes Marçal; Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Célia Leite; Barbiero, Laurent; Fiore, Marli Fátima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (≤91.6 %) and to other sequences from known pseudanabaenacean genera (≤94.3 and 93.7 %, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99 % bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa. PMID:25351877

  12. J3Gen: A PRNG for Low-Cost Passive RFID

    PubMed Central

    Melià-Seguí, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi

    2013-01-01

    Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal. PMID:23519344

  13. Measurement of the neutron electric form factor GEn in quasielastic scattering

    SciTech Connect

    Donal Day

    2003-07-15

    We have measured the electric form factor of the neutron, GEn, at two momentum transfers (Q2= 0.5 and Q2= 1.0 GeV/c2) through quasielastic scattering in Jefferson Lab's Hall C. Longitudinally polarized electrons scattered from polarized deuterated ammonia and GEn was extracted from the beam-target asymmetry AVed which, in quasielastic kinematics, is particularly sensitive to GEn and insensitive to MEC and FSI.

  14. Evaluation of moisture and heat transport in the fast-response building-resolving urban transport code QUIC EnvSim

    NASA Astrophysics Data System (ADS)

    Briggs, Kevin A.

    QUIC EnvSim (QES) is a complete building-resolving urban microclimate modeling system developed to rapidly compute mass, momentum, and heat transport for the design of sustainable cities. One of the more computationally intensive components of this type of modeling system is the transport and dispersion of scalars. In this paper, we describe and evaluate QESTransport, a Reynolds-averaged Navier-Stokes (RANS) scalar transport model. QESTransport makes use of light-weight methods and modeling techniques. It is parallelized for Graphics Processing Units (GPUs), utilizing NVIDIA's OptiX application programming interfaces (APIs). QESTransport is coupled with the well-validated QUIC Dispersion Modeling system. To couple the models, a new methodology was implemented to efficiently prescribe surface flux boundary conditions on both vertical walls and flat surfaces. In addition, a new internal boundary layer parameterization was introduced into QUIC to enable the representation of momentum advection across changing surface conditions. QESTransport is validated against the following three experimental test cases designed to evaluate the model's performance under idealized conditions: (i) flow over a step change in moisture, roughness, and temperature, (ii) flow over an isolated heated building, and (iii) flow through an array of heated buildings. For all three cases, the model is compared against published simulation results. QESTransport produces velocity, temperature, and moisture fields that are comparable to much more complex numerical models for each case. The code execution time performance is evaluated and demonstrates linear scaling on a single GPU for problem sizes up to 4.5 x 4.5 km at 5 m grid resolution, and is found to produce results at much better than real time for a 1.2 x 1.2 km section of downtown Salt Lake City, Utah.

  15. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus.

    PubMed

    Busse, Hans-Jürgen

    2016-01-01

    In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen. nov. (ten species). PMID:26486726

  16. GRAIL and GenQuest Sequence Annotation Tools

    SciTech Connect

    Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.

    1997-12-31

    Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.

  17. An env gene derived from a primary human immunodeficiency virus type 1 isolate confers high in vivo replicative capacity to a chimeric simian/human immunodeficiency virus in rhesus monkeys.

    PubMed Central

    Reimann, K A; Li, J T; Voss, G; Lekutis, C; Tenner-Racz, K; Racz, P; Lin, W; Montefiori, D C; Lee-Parritz, D E; Lu, Y; Collman, R G; Sodroski, J; Letvin, N L

    1996-01-01

    To explore the roles played by specific human immunodeficiency virus type 1 (HIV-1) genes in determining the in vivo replicative capacity of AIDS viruses, we have examined the replication kinetics and virus-specific immune responses in rhesus monkeys following infection with two chimeric simian/human immunodeficiency viruses (SHIVs). These viruses were composed of simian immunodeficiency virus SIVmac239 expressing HIV-1 env and the associated auxiliary HIV-1 genes tat, vpu, and rep. Virus replication was assessed during primary infection of rhesus monkeys by measuring plasma SIVmac p27 levels and by quantifying virus replication in lymph nodes using in situ hybridization. SHIV-HXBc2, which expresses the HIV-1 env of a T-cell-tropic, laboratory-adapted strain of HIV-1 (HXBc2), replicated well in rhesus monkey peripheral blood leukocytes (PBL) in vitro but replicated only to low levels when inoculated in rhesus monkeys. In contrast, SHIV-89.6 was constructed with the HIV-1 env gene of a T-cell- and macrophage-tropic clone of a patient isolate of HIV-1 (89.6). This virus replicated to a lower level in monkey PBL in vitro but replicated to a higher degree in monkeys during primary infection. Moreover, monkeys infected with SHIV-89.6 developed an inversion in the PBL CD4/CD8 ratio coincident with the clearance of primary viremia. The differences in the in vivo consequences of infection by these two SHIVs could not be explained by differences in the immune responses elicited by these viruses, since infected animals had comparable type-specific neutralizing antibody titers, proliferative responses to recombinant HIV-1 gp120, and virus-specific cytolytic effector T-cell responses. With the demonstration that a chimeric SHIV can replicate to high levels during primary infection in rhesus monkeys, this model can now be used to define genetic determinants of HIV-1 pathogenicity. PMID:8627800

  18. CottonGen: a genomics, genetics and breeding database for cotton research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

  19. 76 FR 15039 - RTCA Government/Industry NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration RTCA Government/Industry NextGen Advisory Committee AGENCY: Federal...-9434; Web site http://www.rtca.org or the FAA Business Operations Group, NextGen and...

  20. VitisGen on the road: mapping the way to the next generation of grapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project (Award No. 2011-51181-30635) aims to optimize grape cultivar improvement through the integration of grape breeding, cutting edge genomics technology, precision phenotyping, socioeconomic research, and extension. VitisGen is a five-year project involving 25 co-PIs at 11...

  1. ALVAC-SIV-gag-pol-env-Based Vaccination and Macaque Major Histocompatibility Complex Class I (A*01) Delay Simian Immunodeficiency Virus SIVmac-Induced Immunodeficiency

    PubMed Central

    Pal, R.; Venzon, D.; Letvin, N. L.; Santra, S.; Montefiori, D. C.; Miller, N. R.; Tryniszewska, E.; Lewis, M. G.; VanCott, T. C.; Hirsch, V.; Woodward, R.; Gibson, A.; Grace, M.; Dobratz, E.; Markham, P. D.; Hel, Z.; Nacsa, J.; Klein, M.; Tartaglia, J.; Franchini, G.

    2002-01-01

    T-cell-mediated immune effector mechanisms play an important role in the containment of human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) replication after infection. Both vaccination- and infection-induced T-cell responses are dependent on the host major histocompatibility complex classes I and II (MHC-I and MHC-II) antigens. Here we report that both inherent, host-dependent immune responses to SIVmac251 infection and vaccination-induced immune responses to viral antigens were able to reduce virus replication and/or CD4+ T-cell loss. Both the presence of the MHC-I Mamu-A*01 genotype and vaccination of rhesus macaques with ALVAC-SIV-gag-pol-env (ALVAC-SIV-gpe) contributed to the restriction of SIVmac251 replication during primary infection, preservation of CD4+ T cells, and delayed disease progression following intrarectal challenge exposure of the animals to SIVmac251 (561). ALVAC-SIV-gpe immunization induced cytotoxic T-lymphocyte (CTL) responses cumulatively in 67% of the immunized animals. Following viral challenge, a significant secondary virus-specific CD8+ T-cell response was observed in the vaccinated macaques. In the same immunized macaques, a decrease in virus load during primary infection (P = 0.0078) and protection from CD4 loss during both acute and chronic phases of infection (P = 0.0099 and P = 0.03, respectively) were observed. A trend for enhanced survival of the vaccinated macaques was also observed. Neither boosting the ALVAC-SIV-gpe with gp120 immunizations nor administering the vaccine by the combination of mucosal and systemic immunization routes increased significantly the protective effect of the ALVAC-SIV-gpe vaccine. While assessing the role of MHC-I Mamu-A*01 alone in the restriction of viremia following challenge of nonvaccinated animals with other SIV isolates, we observed that the virus load was not significantly lower in Mamu-A*01-positive macaques following intravenous challenge with either SIVmac251 (561) or

  2. Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

    PubMed Central

    Lamers, Susanna L.; Nolan, David J.; Rife, Brittany D.; Fogel, Gary B.; McGrath, Michael S.; Burdo, Tricia H.; Autissier, Patrick; Williams, Kenneth C.; Goodenow, Maureen M.

    2015-01-01

    ABSTRACT While a clear understanding of the events leading to successful establishment of host-specific viral populations and productive infection in the central nervous system (CNS) has not yet been reached, the simian immunodeficiency virus (SIV)-infected rhesus macaque provides a powerful model for the study of human immunodeficiency virus (HIV) intrahost evolution and neuropathogenesis. The evolution of the gp120 and nef genes, which encode two key proteins required for the establishment and maintenance of infection, was assessed in macaques that were intravenously inoculated with the same viral swarm and allowed to naturally progress to simian AIDS and potential SIV-associated encephalitis (SIVE). Longitudinal plasma samples and immune markers were monitored until terminal illness. Single-genome sequencing was employed to amplify full-length env through nef transcripts from plasma over time and from brain tissues at necropsy. nef sequences diverged from the founder virus faster than gp120 diverged. Host-specific sequence populations were detected in nef (∼92 days) before they were detected in gp120 (∼182 days). At necropsy, similar brain nef sequences were found in different macaques, indicating convergent evolution, while gp120 brain sequences remained largely host specific. Molecular clock and selection analyses showed weaker clock-like behavior and stronger selection pressure in nef than in gp120, with the strongest nef selection in the macaque with SIVE. Rapid nef diversification, occurring prior to gp120 diversification, indicates that early adaptation of nef in the new host is essential for successful infection. Moreover, the convergent evolution of nef sequences in the CNS suggests a significant role for nef in establishing neurotropic strains. IMPORTANCE The SIV-infected rhesus macaque model closely resembles HIV-1 immunopathogenesis, neuropathogenesis, and disease progression in humans. Macaques were intravenously infected with identical viral

  3. GenGIS: A geospatial information system for genomic data

    PubMed Central

    Parks, Donovan H.; Porter, Michael; Churcher, Sylvia; Wang, Suwen; Blouin, Christian; Whalley, Jacqueline; Brooks, Stephen; Beiko, Robert G.

    2009-01-01

    The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets. PMID:19635847

  4. Next gen wavelets down-sampling preserving statistics

    NASA Astrophysics Data System (ADS)

    Szu, Harold; Miao, Lidan; Chanyagon, Pornchai; Cader, Masud

    2007-04-01

    We extend the 2 nd Gen Discrete Wavelet Transform (DWT) of Swelden to the Next Generations (NG) Digital Wavelet Transform (DWT) preserving the statistical salient features. The lossless NG DWT accomplishes the data compression of "wellness baseline profiles (WBP)" of aging population at homes. For medical monitoring system at home fronts we translate the military experience to dual usage of veterans & civilian alike with the following three requirements: (i) Data Compression: The necessary down sampling reduces the immense amount of data of individual WBP from hours to days and to weeks for primary caretakers in terms of moments, e.g. mean value, variance, etc., without the artifacts caused by FFT arbitrary windowing. (ii) Lossless: our new NG_DWT must preserve the original data sets. (iii) Phase Transition: NG_DWT must capture the critical phase transition of the wellness toward the sickness with simultaneous display of local statistical moments. According to the Nyquist sampling theory, assuming a band-limited wellness physiology, we must sample the WBP at least twice per day since it is changing diurnally and seasonally. Since NG_DWT, like the 2 nd Gen, is lossless, we can reconstruct the original time series for the physicians' second looks. This technique of NG_DWT can also help stock market day-traders monitoring the volatility of multiple portfolios without artificial horizon artifacts.

  5. TAXONOMIC STUDY OF TWO NEW GENERA OF FUSIFORM GREEN FLAGELLATES, TABRIS GEN. NOV. AND HAMAKKO GEN. NOV. (VOLVOCALES, CHLOROPHYCEAE)(1).

    PubMed

    Nakada, Takashi; Nozaki, Hisayoshi

    2009-04-01

    On the basis of LM, we isolated strains of two species of fusiform green flagellates that could be assigned to former Chlorogonium (Cg.) Ehrenb. One species, "Cg."heimii Bourr., lacked a pyrenoid in its vegetative cells and required organic compounds for growth. The other was similar to Cg. elongatum (P. A. Dang.) Francé and "Cg."acus Nayal, but with slightly smaller vegetative cells. Their molecular phylogeny was also studied based on combined 18S rRNA, RUBISCO LSU (rbcL), and P700 chl a-apoprotein A2 (psaB) gene sequences. Both species were separated from Chlorogonium emend., Gungnir Nakada and Rusalka Nakada, which were formerly assigned to Chlorogonium. They were accordingly assigned to new genera, Tabris Nakada gen. nov. and Hamakko (Hk.) Nakada gen. nov. as T. heimii (Bourr.) Nakada comb. nov. and Hk. caudatus Nakada sp. nov., respectively. Tabris is differentiated from other genera of fusiform green flagellates by its vegetative cells, which only have two apical contractile vacuoles and lack a pyrenoid in the chloroplast. Hamakko, on the other hand, is distinguishable by the fact that its pyrenoids in vegetative cells are penetrated by flattened thylakoid lamellae. PMID:27033826

  6. Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design

    PubMed Central

    Ping, Li-Hua; Joseph, Sarah B.; Anderson, Jeffrey A.; Abrahams, Melissa-Rose; Salazar-Gonzalez, Jesus F.; Kincer, Laura P.; Treurnicht, Florette K.; Arney, Leslie; Ojeda, Suany; Zhang, Ming; Keys, Jessica; Potter, E. Lake; Chu, Haitao; Moore, Penny; Salazar, Maria G.; Iyer, Shilpa; Jabara, Cassandra; Kirchherr, Jennifer; Mapanje, Clement; Ngandu, Nobubelo; Seoighe, Cathal; Hoffman, Irving; Gao, Feng; Tang, Yuyang; Labranche, Celia; Lee, Benhur; Saville, Andrew; Vermeulen, Marion; Fiscus, Susan; Morris, Lynn; Karim, Salim Abdool; Haynes, Barton F.; Shaw, George M.; Korber, Bette T.; Hahn, Beatrice H.; Cohen, Myron S.; Montefiori, David; Williamson, Carolyn

    2013-01-01

    Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets. PMID:23616655

  7. What Can a Historian Do with AstroGen?

    NASA Astrophysics Data System (ADS)

    Tenn, Joseph S.

    2015-01-01

    "Astrogen", the Astronomy Genealogy Project, is in the development stage. Patterned after the Mathematics Genealogy Project at http://genealogy.math.ndsu.nodak.edu, it will eventually include most of the world's astronomers, past and present, and provide information about their years of life, highest degrees, universities, and thesis titles. There will also be links to online theses, home pages, and obituaries when these are available. Although a few details remain to be worked out before it becomes public, it is possible to make some use of what has already been compiled. I will give an example, comparing graduates of Harvard University, the University of California at Berkeley, and the University of Chicago from different decades, with information about their professional careers and publication records. The author welcomes queries about AstroGen and is seeking more participants.

  8. Commissioning and Performance Analysis of WhisperGen Stirling Engine

    NASA Astrophysics Data System (ADS)

    Pradip, Prashant Kaliram

    Stirling engine based cogeneration systems have potential to reduce energy consumption and greenhouse gas emission, due to their high cogeneration efficiency and emission control due to steady external combustion. To date, most studies on this unit have focused on performance based on both experimentation and computer models, and lack experimental data for diversified operating ranges. This thesis starts with the commissioning of a WhisperGen Stirling engine with components and instrumentation to evaluate power and thermal performance of the system. Next, a parametric study on primary engine variables, including air, diesel, and coolant flowrate and temperature were carried out to further understand their effect on engine power and efficiency. Then, this trend was validated with the thermodynamic model developed for the energy analysis of a Stirling cycle. Finally, the energy balance of the Stirling engine was compared without and with heat recovery from the engine block and the combustion chamber exhaust.

  9. Two-dimensional MHD generator model. [GEN code

    SciTech Connect

    Geyer, H. K.; Ahluwalia, R. K.; Doss, E. D.

    1980-09-01

    A steady state, two-dimensional MHD generator code, GEN, is presented. The code solves the equations of conservation of mass, momentum, and energy, using a Von Mises transformation and a local linearization of the equations. By splitting the source terms into a part proportional to the axial pressure gradient and a part independent of the gradient, the pressure distribution along the channel is easily obtained to satisfy various criteria. Thus, the code can run effectively in both design modes, where the channel geometry is determined, and analysis modes, where the geometry is previously known. The code also employs a mixing length concept for turbulent flows, Cebeci and Chang's wall roughness model, and an extension of that model to the effective thermal diffusities. Results on code validation, as well as comparisons of skin friction and Stanton number calculations with experimental results, are presented.

  10. Decay heat removal in GEN IV gas cooled fast reactors.

    SciTech Connect

    Cheng, L. Y.; Wei, T. Y. C.

    2009-08-01

    The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow were evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.

  11. Mutation and association analysis of GEN1 in breast cancer susceptibility

    PubMed Central

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Evans, D. Gareth; Eccles, Diana; Stratton, Michael R.

    2013-01-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519del-AAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case–control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  12. New Boletaceae taxa from Guyana: Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov., Singerocomus rubriflavus gen. and sp. nov., and a new combination for Xerocomus inundabilis.

    PubMed

    Henkel, Terry W; Obase, Keisuke; Husbands, Dillon; Uehling, Jessie K; Bonito, Gregory; Aime, M Catherine; Smith, Matthew E

    2016-01-01

    Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov. and Singerocomus rubriflavus gen. and sp. nov. (Boletaceae, Boletales, Basidiomycota) are described from the Pakaraima Mountains and adjacent lowlands of Guyana. Xerocomus inundabilis, originally described from the central Brazilian Amazon and based solely on the type collection, is redescribed from numerous collections from Guyana and transferred into Singerocomus. These boletes occur in Neotropical forests dominated by ectomycorrhizal trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae) and Pakaraimaea (Dipterocarpaceae). Three of the species were repeatedly found in a multiyear sporocarp survey in Dicymbe corymbosa-monodominant forest. Macromorphological, micromorphological, habitat and multilocus DNA sequence data are provided for each species. A molecular phylogenetic analysis based on a large taxon set across the Boletaceae justifies erection of the new genera. PMID:26490700

  13. Multi-PMT Optical Module Designs for IceCube-Gen2

    NASA Astrophysics Data System (ADS)

    Kappes, Alexander

    2016-04-01

    IceCube-Gen2 is the planned next generation neutrino telescope at the South Pole incorporating a high-energy array for neutrino astronomy and a dense array (PINGU) aimed at the determination of the neutrino mass hierarchy. Here, we present alternative designs to IceCube-Gen2's single-PMT baseline optical module which are currently being developed. These designs feature up to 24 smaller photomultipliers and use glass and gel with enhanced UV transparency to increase the number of detected photons and provide additional information. Thereby, they have the potential to significantly enhance the performance of IceCube-Gen2.

  14. gSeaGen: A GENIE-based code for neutrino telescopes

    NASA Astrophysics Data System (ADS)

    Distefano, Carla

    2016-04-01

    The gSeaGen code is a GENIE based application to generate neutrino-induced events in an underwater neutrino detector. The gSeaGen code is able to generate events induced by all neutrino flavours, taking into account topological differences between track-type and shower-like events. The neutrino interaction is simulated taking into account the density and the composition of the media surrounding the detector. The main features of gSeaGen will be presented together with some examples of its application within ANTARES and KM3NeT.

  15. Can natural levels of Al influence Cu speciation and toxicity to Daphnia magna in a Swedish soft water lake?

    PubMed

    Hoppe, S; Gustafsson, J-P; Borg, H; Breitholtz, M

    2015-11-01

    It is well known that chemical parameters, such as natural organic matter (NOM), cation content and pH may influence speciation and toxicity of metals in freshwaters. Advanced bioavailability models, e.g. Biotic Ligand Models (BLMs), can use these and other chemical parameters to calculate site specific recommendations for metals in the aquatic environment. However, since Al is not an input parameter in the BLM v.2.2.3, used in this study, there could be a discrepancy between calculated and measured results in Al rich waters. The aim of this study was to evaluate if the presence of Al in a circumneutral (pH ∼6) soft humic freshwater, Lake St. Envättern, will affect the Cu speciation and thereby the toxicity to the cladoceran Daphnia magna. The results show a statistically significant increase in the free Cu(2+) concentration with Al additions and that measured levels of Cu(2+) significantly differed from BLM calculated levels of Cu(2+). Furthermore, there was also a statistically significant elevated acute toxic response to D. magna at low additions of Al (10 μg/L). However, since the large difference between calculated and measured Cu(2+) resulted in a significant but minor (factor of 2.3) difference between calculated and measured toxicity, further studies should be conducted in Al rich soft waters to evaluate the importance of adding Al as an input parameter into the BLM software. PMID:26073589

  16. Characterizing changes in the immune repertoire of cattle using next-gen sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Next-gen sequencing permits characterization of expressed antibody repertoires at previously unattainable depths of coverage and accuracy. We examined the bovine immunoglobul...

  17. Revision of the East Mediterranean Orthomus (Coleoptera, Carabidae, Pterostichini), with description of Parorthomus gen. n. socotranus sp. n. from Socotra Island and key to the Old World genera of subtribe Euchroina.

    PubMed

    Guéorguiev, Borislav; Wrase, David W; Farkač, Jan

    2014-01-01

    The East Mediterranean species of Orthomus Chaudoir, 1838 are revised. The type series of Feronia longula Reiche & Saulcy, 1855, F. berytensis Reiche & Saulcy, 1855, F. proelonga Reiche & Saulcy, 1855, Orthomus longior Chaudoir, 1873, O. sidonicus Chaudoir, 1873, and O. berytensis akbensis Mateu, 1955 were studied and lectotypes for the first four are designated. Also, the following nomenclatural acts are proposed: Feronia proelonga Reiche & Saulcy, 1855, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Feronia elongata Chaudoir, 1859, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Orthomus sidonicus Chaudoir, 1873, syn. n. of Orthomus longior Chaudoir, 1873; Orthomus velocissimus andalusiacus Mateu, 1957, syn. n. of Orthomus velocissimus akbensis Mateu, 1955, new assignment for Orthomus berytensis akbensis Mateu, 1955. As a result, three species of the genus inhabit the East Mediterranean biogeographical region: O. berytensis, O. longior, and O. longulus. A key to these three species is given. O. longior is recorded for Turkey and Syria for the first time. In addition, a new synonymy of two West Mediterranean taxa is proposed: O. szekessyi (Jedlička, 1956), syn. n. of O. balearicus (Piochard de la Brûlerie, 1868), and a new genus and a species are described: Parorthomus gen. n. socotranus sp. n. (type locality: Republic of Yemen, Socotra Archipelago, Socotra Island, Fimihin env., 530 m.a.s.l.). Illustrations of the species dealt with here are provided including external characters, habitus, mentum and submentum, and genitalia are provided. Nine genera of the "African Series" of subtribe Euchroina Chaudoir, 1874 are keyed for the first time. Checklists of the species of Orthomus and of the Old World euchroine genera are given. PMID:25147463

  18. Revision of the East Mediterranean Orthomus (Coleoptera, Carabidae, Pterostichini), with description of Parorthomus gen. n. socotranus sp. n. from Socotra Island and key to the Old World genera of subtribe Euchroina

    PubMed Central

    Guéorguiev, Borislav; Wrase, David W.; Farkač, Jan

    2014-01-01

    Abstract The East Mediterranean species of Orthomus Chaudoir, 1838 are revised. The type series of Feronia longula Reiche & Saulcy, 1855, F. berytensis Reiche & Saulcy, 1855, F. proelonga Reiche & Saulcy, 1855, Orthomus longior Chaudoir, 1873, O. sidonicus Chaudoir, 1873, and O. berytensis akbensis Mateu, 1955 were studied and lectotypes for the first four are designated. Also, the following nomenclatural acts are proposed: Feronia proelonga Reiche & Saulcy, 1855, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Feronia elongata Chaudoir, 1859, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Orthomus sidonicus Chaudoir, 1873, syn. n. of Orthomus longior Chaudoir, 1873; Orthomus velocissimus andalusiacus Mateu, 1957, syn. n. of Orthomus velocissimus akbensis Mateu, 1955, new assignment for Orthomus berytensis akbensis Mateu, 1955. As a result, three species of the genus inhabit the East Mediterranean biogeographical region: O. berytensis, O. longior, and O. longulus. A key to these three species is given. O. longior is recorded for Turkey and Syria for the first time. In addition, a new synonymy of two West Mediterranean taxa is proposed: O. szekessyi (Jedlička, 1956), syn. n. of O. balearicus (Piochard de la Brûlerie, 1868), and a new genus and a species are described: Parorthomus gen. n. socotranus sp. n. (type locality: Republic of Yemen, Socotra Archipelago, Socotra Island, Fimihin env., 530 m.a.s.l.). Illustrations of the species dealt with here are provided including external characters, habitus, mentum and submentum, and genitalia are provided. Nine genera of the “African Series” of subtribe Euchroina Chaudoir, 1874 are keyed for the first time. Checklists of the species of Orthomus and of the Old World euchroine genera are given. PMID:25147463

  19. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

    PubMed

    Gerritsen, Jacoline; Fuentes, Susana; Grievink, Wieke; van Niftrik, Laura; Tindall, Brian J; Timmerman, Harro M; Rijkers, Ger T; Smidt, Hauke

    2014-05-01

    A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1σ lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C

  20. Genes and proteins of Escherichia coli K-12 (GenProtEC).

    PubMed

    Riley, M

    1997-01-01

    GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities amongE.coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html . PMID:9016503

  1. Integrated Design and Production Reference Integration with ArchGenXML V1.00

    SciTech Connect

    Barter, R H

    2004-07-20

    ArchGenXML is a tool that allows easy creation of Zope products through the use of Archetypes. The Integrated Design and Production Reference (IDPR) should be highly configurable in order to meet the needs of a diverse engineering community. Ease of configuration is key to the success of IDPR. The purpose of this paper is to describe a method of using a UML diagram editor to configure IDPR through ArchGenXML and Archetypes.

  2. Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

    PubMed

    Kurtzman, Cletus P; Robnett, Christie J; Blackwell, Meredith

    2016-08-01

    DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA. PMID:27188882

  3. Regulation of the aprX-lipA operon of Pseudomonas fluorescens B52: differential regulation of the proximal and distal genes, encoding protease and lipase, by ompR-envZ.

    PubMed

    McCarthy, Conor N; Woods, Rick G; Beacham, Ifor R

    2004-12-15

    The production of lipase and protease from psychrotrophic strains of Pseudomonas fluorescens may result in spoilage of dairy products. The lipase (lipA) and alkaline metalloprotease (aprX) genes of P. fluorescens B52 are regulated by temperature and are located at opposite ends of an operon which contains eight genes and spans 14 kb. In this report, we show that lipase activity in the supernatant of cultures of P. fluorescens strain B52 is also regulated by the homologue of the Escherichia coli EnvZ-OmpR two-component regulatory system. Differences in the regulation of lipase and protease may be related to the proximal and distal locations of aprX and lipA within the operon. PMID:15598539

  4. Association of lymph-node antigens with lower Gag-specific central-memory and higher Env-specific effector-memory CD8+ T-cell frequencies in a macaque AIDS model

    PubMed Central

    Ishii, Hiroshi; Matsuoka, Saori; Nomura, Takushi; Nakamura, Midori; Shiino, Teiichiro; Sato, Yuko; Iwata-Yoshikawa, Naoko; Hasegawa, Hideki; Mizuta, Kazuta; Sakawaki, Hiromi; Miura, Tomoyuki; Koyanagi, Yoshio; Naruse, Taeko K.; Kimura, Akinori; Matano, Tetsuro

    2016-01-01

    Virus-specific CD8+ T cells exert strong suppressive pressure on human/simian immunodeficiency virus (HIV/SIV) replication. These responses have been intensively examined in peripheral blood mononuclear cells (PBMCs) but not fully analyzed in lymph nodes (LNs), where interaction between CD8+ T cells and HIV/SIV-infected cells occurs. Here, we investigated target antigen specificity of CD8+ T cells in LNs in a macaque AIDS model. Analysis of virus antigen-specific CD8+ T-cell responses in the inguinal LNs obtained from twenty rhesus macaques in the chronic phase of SIV infection showed an inverse correlation between viral loads and frequencies of CD8+ T cells with CD28+ CD95+ central memory phenotype targeting the N-terminal half of SIV core antigen (Gag-N). In contrast, analysis of LNs but not PBMCs revealed a positive correlation between viral loads and frequencies of CD8+ T cells with CD28−CD95+ effector memory phenotype targeting the N-terminal half of SIV envelope (Env-N), soluble antigen. Indeed, LNs with detectable SIV capsid p27 antigen in the germinal center exhibited significantly lower Gag-N-specific CD28+ CD95+ CD8+ T-cell and higher Env-N-specific CD28−CD95+ CD8+ T-cell responses than those without detectable p27. These results imply that core and envelope antigen-specific CD8+ T cells show different patterns of interactions with HIV/SIV-infected cells. PMID:27452272

  5. Association of lymph-node antigens with lower Gag-specific central-memory and higher Env-specific effector-memory CD8(+) T-cell frequencies in a macaque AIDS model.

    PubMed

    Ishii, Hiroshi; Matsuoka, Saori; Nomura, Takushi; Nakamura, Midori; Shiino, Teiichiro; Sato, Yuko; Iwata-Yoshikawa, Naoko; Hasegawa, Hideki; Mizuta, Kazuta; Sakawaki, Hiromi; Miura, Tomoyuki; Koyanagi, Yoshio; Naruse, Taeko K; Kimura, Akinori; Matano, Tetsuro

    2016-01-01

    Virus-specific CD8(+) T cells exert strong suppressive pressure on human/simian immunodeficiency virus (HIV/SIV) replication. These responses have been intensively examined in peripheral blood mononuclear cells (PBMCs) but not fully analyzed in lymph nodes (LNs), where interaction between CD8(+) T cells and HIV/SIV-infected cells occurs. Here, we investigated target antigen specificity of CD8(+) T cells in LNs in a macaque AIDS model. Analysis of virus antigen-specific CD8(+) T-cell responses in the inguinal LNs obtained from twenty rhesus macaques in the chronic phase of SIV infection showed an inverse correlation between viral loads and frequencies of CD8(+) T cells with CD28(+) CD95(+) central memory phenotype targeting the N-terminal half of SIV core antigen (Gag-N). In contrast, analysis of LNs but not PBMCs revealed a positive correlation between viral loads and frequencies of CD8(+) T cells with CD28(-)CD95(+) effector memory phenotype targeting the N-terminal half of SIV envelope (Env-N), soluble antigen. Indeed, LNs with detectable SIV capsid p27 antigen in the germinal center exhibited significantly lower Gag-N-specific CD28(+) CD95(+) CD8(+) T-cell and higher Env-N-specific CD28(-)CD95(+) CD8(+) T-cell responses than those without detectable p27. These results imply that core and envelope antigen-specific CD8(+) T cells show different patterns of interactions with HIV/SIV-infected cells. PMID:27452272

  6. Saccharibacillus sacchari gen. nov., sp. nov., isolated from sugar cane.

    PubMed

    Rivas, Raúl; García-Fraile, Paula; Zurdo-Piñeiro, José Luis; Mateos, Pedro F; Martínez-Molina, Eustoquio; Bedmar, Eulogio J; Sánchez-Raya, Juan; Velázquez, Encarna

    2008-08-01

    A bacterial strain designated GR21T was isolated from apoplastic fluid of Saccharum officinarum (sugar cane). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate forms a separate branch within the family 'Paenibacillaceae', with Paenibacillus as the closest related genus. Within this genus, the closest related species is Paenibacillus xylanilyticus, with 93.4 % similarity to the sequence of the type strain. The isolate has Gram-variable, facultatively anaerobic, rod-shaped cells, motile by polar and subpolar flagella. Round, non-ornamented, central or subterminal spores are formed in unswollen sporangia. The strain is catalase-positive and oxidase-negative on nutrient agar medium. Cellulose and aesculin were hydrolysed, whereas xylan, starch and gelatin were not. Growth was supported by many carbohydrates as carbon sources. Strain GR21T displayed a lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone and anteiso-C15: 0 was the major fatty acid. The DNA G+C content was 57.8 mol%. Phylogenetic and phenotypic analyses, including assimilation of carbon sources and exoenzyme production commonly used for classification within the family 'Paenibacillaceae', showed that strain GR21T belongs to a new genus within this family, for which the name Saccharibacillus sacchari gen. nov., sp. nov. is proposed. The type strain of Saccharibacillus sacchari is GR21T (=LMG 24085T =DSM 19268T). PMID:18676467

  7. Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater.

    PubMed

    Teramoto, Maki; Nishijima, Miyuki

    2014-12-01

    A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, designated strain 2-3(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. This strain grew well with starch. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Rhodobacteraceae and that the strain was related most closely to the genus Pacificibacter (94.0 % sequence similarity to the type strain). The DNA G+C content was 52.4 mol%. The major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The major isoprenoid quinone was Q-10. Strain 2-3(T) did not grow at 4 or 35 °C, while the type strain of the type species of the genus Pacificibacter grows at both temperatures. From the taxonomic data obtained in this study, it is proposed that strain 2-3(T) be placed into a novel genus and species named Amylibacter marinus gen. nov., sp. nov. in the family Rhodobacteraceae. The type strain of Amylibacter marinus is 2-3(T) ( = NBRC 110140(T) = LMG 28364(T)). PMID:25225261

  8. Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment.

    PubMed

    Wang, Yun-xiang; Huang, Fa-qi; Nogi, Yuichi; Pang, Shou-Ji; Wang, Ping-kang; Lv, Jie

    2015-07-01

    A Gram-reaction-negative bacterial strain, designated fig4(T), was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4(T )was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8-96.2% sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1 ω7c, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4(T) is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4(T) ( = CGMCC 1.12719(T) = JCM 19854(T)). PMID:25829329

  9. Preliminary Investigation of Civil Tiltrotor in NextGen Airspace

    NASA Technical Reports Server (NTRS)

    Young, Larry A.; Salvano, Dan; Wright, Ken; Chung, William; Young, Ray; Miller, David; Paris, Alfanso; Gao, Huina; Cheng, Victor

    2010-01-01

    Presentation intro: Tiltrotor aircraft have long been envisioned as being a potentially viable means of commercial aviation transport. Preliminary results from an ongoing study into the operational and technological considerations of Civil Tiltrotor (CTR) operation in the Next Generation airspace, circa the 2025 time-frame, are presented and discussed. In particular, a fleet of CTR aircraft has been conceptually designed. The performance characteristics of this CTR fleet was subsequently translated into BADA (Base of Aircraft DAta) models that could be used as input to emulate CTR aircraft operations in the ACES and AvTerminal airspace and terminal area simulation tools. A network of nine North-Eastern corridor airports is the focus of the airspace simulation effort; the results from this airport network viII then be extrapolated to provide insights into systemic impact of CTRs on the National Airspace System (NAS). Future work will also be detailed as to attempts to model the systemic effects of noise and emissions from this fleet of new aircraft as well as assess their leveraged impact on public service missions, in time of need, such as major regional/national disaster relief efforts. The ideal outcome of this study is a set of results whereby Next Gen airspace CONOPs can be refined to reflect potential CTR capabilities and, conversely, CTR technology development efforts can be better informed as to key performance requirement thresholds needed to be met in order to successfully introduce these aircraft into civilian aviation operation.

  10. Electronic and magnetic properties of CrGen (15 ⩽ n ⩽ 29) clusters: A DFT study

    NASA Astrophysics Data System (ADS)

    Mahtout, Sofiane; Tariket, Yacine

    2016-06-01

    We report ab initio calculations of electronic and magnetic properties of medium-sized CrGen (15 ⩽ n ⩽ 29) clusters using density functional theory. The encapsulation of Cr atoms within Gen clusters leads to stable Cr encapsulated Gen clusters. The binding energies generally increase while the differences between the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) generally decrease with the increasing of cluster size. The clusters of CrGen at size 16, 17, 19, 22, 24 and 29 exhibit high stabilities when compared to their neighbors. This has been discussed in terms of their structures, energies and the effect of the position of doping atom. Doping of Gen clusters with one Cr atom leads to CrGen clusters with magnetic moment depending on the structure of the clusters and the position of Cr atom in the clusters. Moreover, vertical ionization potential, vertical electronic affinity, and chemical hardness are also analyzed.

  11. 78 FR 26004 - Notice of Availability; Draft Environmental Impact Statement for the FutureGen 2.0 Project

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-03

    ...The U.S. Department of Energy (DOE) announces the availability of the Draft Environmental Impact Statement for the FutureGen 2.0 Project (DOE/EIS-0460D) for public review and comment, as well as the date, location, and time for a public hearing. The draft environmental impact statement (EIS) analyzes the potential impacts associated with the FutureGen 2.0 Project (FutureGen 2.0), which would......

  12. Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State

    PubMed Central

    Rasheed, Muhibur; Bettadapura, Radhakrishna; Bajaj, Chandrajit

    2015-01-01

    Summary Envelope glycoprotein gp120 of HIV-1 possesses several variable regions whose precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol which uses cryo-electron microscopy (EM) maps, atomic-resolution structures of the core, and information of binding interactions. Our model has excellent fit with EMD5020 (Liu et al., 2008), is stereochemically and energetically favorable, and has the expected binding interfaces. Comparison of the ternary arrangement of the loops in this model with those bound to PGT122 (Julien et al., 2013a) and PGV04 (Lyumkis et al., 2013) suggested a possible motion of the V1V2 away from the CCR5 binding site and towards CD4. Our study also revealed that the CD4-bound state of the V1V2 loop is not optimal for gp120 bound with several neutralizing antibodies. PMID:26039348

  13. Critical Issues on Materials for Gen-IV Reactors

    SciTech Connect

    Caro, M; Marian, J; Martinez, E; Erhart, P

    2009-02-27

    Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and

  14. Cutaneous hyalohyphomycosis due to Parengyodontium album gen. et comb. nov.

    PubMed

    Tsang, Chi-Ching; Chan, Jasper F W; Pong, Wai-Mei; Chen, Jonathan H K; Ngan, Antonio H Y; Cheung, Mei; Lai, Christopher K C; Tsang, Dominic N C; Lau, Susanna K P; Woo, Patrick C Y

    2016-10-01

    "Engyodontium album" is an environmental saprobic mould and an emerging opportunistic pathogen able to cause both superficial and systemic infections. In this study, we isolated a mould from the skin lesion biopsy specimen of the right shin in a patient who received renal transplantation for end-stage renal failure with prednisolone, tacrolimus, and azathioprine immunosuppressant therapy. Histology of the skin biopsy showed mild squamous hyperplasia and neutrophilic infiltrate in the epidermis, active chronic inflammation in the dermis, and fat necrosis in the subcutis, with numerous fungal elements within the serum crusts. On Sabouraud glucose agar, the fungus grew as white, cobweb-like, floccose colonies. Microscopically, conidiogenous cells were arranged in whorls of one to seven at wide angles, with zigzag-shaped terminal fertile regions and smooth, hyaline, oval, apiculate conidia. DNA sequencing showed the mould isolate belonged to "E. album" but matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate. Phylogenetic analyses based on the internal transcribed spacer region, 28S nuclear ribosomal DNA, and β-tubulin gene and MALDI-TOF MS coupled with hierarchical cluster analysis showed that "E. album" is distantly related to other Engyodontium species and should be transferred to a novel genus within the family Cordycipitaceae, for which the name Parengyodontium album gen. et comb. nov. is proposed. Three potential cryptic species within this species complex were also revealed. Antifungal susceptibility testing showed posaconazole and voriconazole had high activities against all clinical P. album isolates and may be better drug options for treating P. album infections. PMID:27161787

  15. Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water.

    PubMed

    Kämpfer, Peter; Rosselló-Mora, Ramon; Hermansson, Malte; Persson, Frank; Huber, Birgit; Falsen, Enevold; Busse, Hans-Jürgen

    2007-07-01

    Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains CCUG 49009(T) and CCUG 49012), both isolated from drinking water, were characterized. On the basis of chemotaxonomic data [major ubiquinone, Q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, C(16 : 0) and summed feature 3 (C(16 : 1) omega 7c/C(15 : 0) iso 2-OH)] and 16S rRNA gene sequence similarities, both strains clearly belong to the family Oxalobacteraceae of the Betaproteobacteria. 16S rRNA gene sequence similarities with members of the most closely related genera of this group (Herminiimonas, Massilia, Duganella, Telluria, Herbaspirillum, Janthinobacterium, Naxibacter and Paucimonas) were less than 96.5 % for both strains. The two strains also shared a relatively low 16S rRNA gene sequence similarity (96.8 %). Although phylogenetic analysis based on 16S rRNA gene sequence similarities clearly showed that the two organisms formed a separate branch, their phenotypes (including chemotaxonomic features) were hardly distinguishable and showed high similarities to those reported for the most closely related genera. On the basis of DNA-DNA hybridization results, the two strains were shown to represent separate species (sharing only 20 % DNA-DNA relatedness), but they could not be clearly differentiated phenotypically from each other. It is evident that these organisms represent a new genus, Undibacterium gen. nov., with one species, Undibacterium pigrum sp. nov. The type strain of Undibacterium pigrum is strain CCUG 49009(T) (=CIP 109318(T)). Strain CCUG 49012 (=CIP 108976) probably represents a second species of this genus, but is described here as a second genomovar of this species because of the lack of differentiating characters. PMID:17625185

  16. Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil.

    PubMed

    Kim, Soo-Jin; Lim, Jun-Muk; Hamada, Moriyuki; Ahn, Jae-Hyung; Weon, Hang-Yeon; Suzuki, Ken-ichiro; Ahn, Tae-Young; Kwon, Soon-Wo

    2015-09-01

    A bacterial strain, PSGM2-16(T), was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16(T) revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4%), Fodinibacter luteus YIM C003(T) (97.2%) and Lapillicoccus jejuensis R-Ac013(T) (97.0%), and the phylogenetic tree showed that strain PSGM2-16(T) formed a subgroup with Ornithinibacter aureus HB09001(T) and F. luteus YIM C003(T) within the family Intrasporangiaceae. The major fatty acids (>10% of the total fatty acids) of strain PSGM2-16(T) were iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with meso-diaminopimelic acid as the diagnostic diamino acid. DNA-DNA hybridization values between strain PSGM2-16(T) and closely related taxa were much less than 70%. The genomic DNA G+C content of strain PSGM2-16(T) was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16(T) represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16(T) ( = KACC 17299(T)= DSM 27137(T)= NBRC 109598(T)). PMID:26297674

  17. Terrilactibacillus laevilacticus gen. nov., sp. nov., isolated from soil.

    PubMed

    Prasirtsak, Budsabathip; Thongchul, Nuttha; Tolieng, Vasana; Tanasupawat, Somboon

    2016-03-01

    A Gram-stain-positive, catalase-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium, strain NK26-11T, was isolated from soil in Thailand. This strain produced d-lactic acid from glucose homofermentatively, and grew at 20-45 °C and pH 5-8.5. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major respiratory quinone was menaquinone 7 (MK-7), the DNA G+C content was 42.6 mol%, and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of 16S rRNA gene sequences analysis, strain NK26-11T was closely related to Bacillus solimangrovi JCM 18994T (93.89 % 16S rRNA gene sequence similarity), Pullulanibacillus naganoensis LMG 12887T (93.32 %), Sporolactobacillus inulinus NRIC 1133T (92.99 %), Tuberibacillus calidus JCM 13397T (92.98 %) and Thalassobacillus devorans DSM 16966T ( < 90.93 %). Strain NK26-11T could be clearly distinguished from the closely related genera based on phenotypic characteristics and DNA G+C content, and thus represents a novel species of a new genus between the Bacillus and Sporolactobacillus cluster, for which the name Terrilactibacillus laevilacticus gen. nov., sp. nov. is proposed. The type strain of the type species is NK26-11T ( = LMG 27803T = TISTR 2241T = PCU 335T). PMID:26843374

  18. Parasediminibacterium paludis gen. nov., sp. nov., isolated from wetland.

    PubMed

    Kang, Heeyoung; Kim, Haneul; Joung, Yochan; Joh, Kiseong

    2016-01-01

    A novel orange-pigmented bacterial strain, designated HME6815T, was isolated from wetland in Jeju Island, Republic of Korea. The cells were Gram stain-negative, non-motile, strictly aerobic and rod-shaped. Optimal growth occurred at 30 °C and pH 7.0 on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HME6815T formed a distinct phyletic lineage within the family Chitinophagaceae and was most closely related to members of the genera Sediminibacterium, Vibrionimonas, Hydrobacter, Hydrotalea and Asinibacterium with 92.3-94.3 % 16S rRNA gene sequence similarity. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C13 : 0. The only respiratory quinone was MK-7. Polar lipid analysis revealed the presence of phosphatidylethanolamine, four unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content was 38.4 mol%. On the basis of the evidence presented in this study, strain HME6815T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Parasediminibacterium paludis gen. nov., sp. nov. is proposed. The type strain of the type species is HME6815T ( = KCTC 23736T = CECT 8010T). PMID:26514371

  19. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil.

    PubMed

    Dahal, Ram Hari; Kim, Jaisoo

    2016-01-01

    An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium, designated strain R49T, was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R49T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes that was distinct from the most closely related genera Dyadobacter (91.98-93.85 % sequence similarity), Persicitalea (88.69 %) and Runella (84.79-85.81 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain R49T was 53.9 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R49T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhabdobacter roseus gen. nov., sp. nov. is proposed. The type strain of Rhabdobacter roseus is R49T ( = KEMB 9005-318T = KACC 18395T = JCM 30685T). PMID:26508300

  20. Electricity Generation Cost Simulation Model (GenSim)

    SciTech Connect

    DRENNEN, THOMAS E.; KAMERY, WILLIAM

    2002-11-01

    The Electricity Generation Cost Simulation Model (GenSim) is a user-friendly, high-level dynamic simulation model that calculates electricity production costs for variety of electricity generation technologies, including: pulverized coal, gas combustion turbine, gas combined cycle, nuclear, solar (PV and thermal), and wind. The model allows the user to quickly conduct sensitivity analysis on key variables, including: capital, O&M, and fuel costs; interest rates; construction time; heat rates; and capacity factors. The model also includes consideration of a wide range of externality costs and pollution control options for carbon dioxide, nitrogen oxides, sulfur dioxide, and mercury. Two different data sets are included in the model; one from the US. Department of Energy (DOE) and the other from Platt's Research Group. Likely users of this model include executives and staff in the Congress, the Administration and private industry (power plant builders, industrial electricity users and electric utilities). The model seeks to improve understanding of the economic viability of various generating technologies and their emissions trade-offs. The base case results, using the DOE data, indicate that in the absence of externality costs, or renewable tax credits, pulverized coal and gas combined cycle plants are the least cost alternatives at 3.7 and 3.5 cents/kwhr, respectively. A complete sensitivity analysis on fuel, capital, and construction time shows that these results coal and gas are much more sensitive to assumption about fuel prices than they are to capital costs or construction times. The results also show that making nuclear competitive with coal or gas requires significant reductions in capital costs, to the $1000/kW level, if no other changes are made. For renewables, the results indicate that wind is now competitive with the nuclear option and is only competitive with coal and gas for grid connected applications if one includes the federal production tax credit

  1. Electricity Generation Cost Simulation Model (GenSim).

    SciTech Connect

    Kamery, William; Baker, Arnold Barry; Drennen, Thomas E.

    2003-07-01

    The Electricity Generation Cost Simulation Model (GenSim) is a user-friendly, high-level dynamic simulation model that calculates electricity production costs for variety of electricity generation technologies, including: pulverized coal, gas combustion turbine, gas combined cycle, nuclear, solar (PV and thermal), and wind. The model allows the user to quickly conduct sensitivity analysis on key variables, including: capital, O&M, and fuel costs; interest rates; construction time; heat rates; and capacity factors. The model also includes consideration of a wide range of externality costs and pollution control options for carbon dioxide, nitrogen oxides, sulfur dioxide, and mercuty. Two different data sets are included in the model; one from the US. Department of Energy (DOE) and the other from Platt's Research Group. Likely users of this model include executives and staff in the Congress, the Administration and private industry (power plant builders, industrial electricity users and electric utilities). The model seeks to improve understanding of the economic viability of various generating technologies and their emissions trade-offs. The base case results, using the DOE data, indicate that in the absence of externality costs, or renewable tax credits, pulverized coal and gas combined cycle plants are the least cost alternatives at 3.7 and 3.5 cents/kwhr, respectively. A complete sensitivity analysis on fuel, capital, and construction time shows that these results coal and gas are much more sensitive to assumption about fuel prices than they are to capital costs or construction times. The results also show that making nuclear competitive with coal or gas requires significant reductions in capital costs, to the $1000/kW level, if no other changes are made. For renewables, the results indicate that wind is now competitive with the nuclear option and is only competitive with coal and gas for grid connected applications if one includes the federal production tax credit

  2. Tamlicoccus marinus gen. nov., sp. nov., isolated from seawater.

    PubMed

    Lee, Soon Dong

    2013-06-01

    A novel actinobacterial strain was isolated from a seawater sample collected on Mara Island, Jeju, Republic of Korea. Cells of this organism were aerobic, Gram-positive, non-spore-forming, non-motile cocci that occurred singly or in pairs. Colonies were circular, smooth, convex and white-cream in colour. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Dermacoccaceae and formed a monophyletic clade between the type strains of Demetria terragena (96.8% similarity) and Branchiibius hedensis (95.2% similarity). The cell-wall peptidoglycan contained L-lysine, alanine, aspartic acid, glutamic acid, glycine and serine, indicating that the isolate possessed peptidoglycan type A4α. The whole-cell sugars were galactose, glucose, mannose, xylose, arabinose, ribose and rhamnose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and five unknown lipids. The cellular fatty acid profile was represented by large amounts of iso-methyl branched and monounsaturated iso- and anteiso-methyl branched acids, along with the presence of a diagnostic 10-methyl acid. The G+C content of the DNA was 71 mol%. On the basis of data from polyphasic analyses presented here, strain MSW-24(T) is considered to represent a novel species of a new genus in the family Dermacoccaceae, for which the name Tamlicoccus marinus gen. nov., sp. nov. is proposed. The type strain of Tamlicoccus marinus is MSW-24(T) (=KCTC 19485(T)=DSM 21415(T)). PMID:23041643

  3. Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil.

    PubMed

    Kim, Soo-Jin; Park, Joo-Hyeon; Lim, Jun-Muk; Ahn, Jae-Hyung; Anandham, Rangasamy; Weon, Hang-Yeon; Kwon, Soon-Wo

    2014-09-01

    A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2(T), was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2(T) indicated that the isolate belonged to the family Chitinophagaceae, and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2-92.6 %), Sediminibacterium (90.8-91.4 %) and Chitinophaga (89.2-91.7 %), Filimonas lacunae YT21(T) (91.7 %), members of the genus Segetibacter (90.2-91.6 %), Parasegetibacter luojiensis RHYL-37(T) (90.9 %) and Flavihumibacter petaseus T41(T) (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2(T) was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2(T) represents a novel species of a new genus in the family Chitinophagaceae, for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2(T) ( = KACC 17343(T) = DSM 28286(T)). PMID:24925599

  4. Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research

    NASA Technical Reports Server (NTRS)

    Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

    2009-01-01

    The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

  5. Safety Sufficiency for NextGen: Assessment of Selected Existing Safety Methods, Tools, Processes, and Regulations

    NASA Technical Reports Server (NTRS)

    Xu, Xidong; Ulrey, Mike L.; Brown, John A.; Mast, James; Lapis, Mary B.

    2013-01-01

    NextGen is a complex socio-technical system and, in many ways, it is expected to be more complex than the current system. It is vital to assess the safety impact of the NextGen elements (technologies, systems, and procedures) in a rigorous and systematic way and to ensure that they do not compromise safety. In this study, the NextGen elements in the form of Operational Improvements (OIs), Enablers, Research Activities, Development Activities, and Policy Issues were identified. The overall hazard situation in NextGen was outlined; a high-level hazard analysis was conducted with respect to multiple elements in a representative NextGen OI known as OI-0349 (Automation Support for Separation Management); and the hazards resulting from the highly dynamic complexity involved in an OI-0349 scenario were illustrated. A selected but representative set of the existing safety methods, tools, processes, and regulations was then reviewed and analyzed regarding whether they are sufficient to assess safety in the elements of that OI and ensure that safety will not be compromised and whether they might incur intolerably high costs.

  6. Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.

    2011-01-01

    Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change. The approach taken by this NASA Ames team is to build a collaborative systems assessment template (CSAT) based on detailed task descriptions within each system to establish a baseline of the current operations. The collaborative content and context are delineated through the review of regulatory and advisory materials, policies, procedures and documented practices as augmented by field observations and interviews. The CSAT is developed to aid the assessment of key human factors and performance tradeoffs that result from considering different collaborative arrangements under NextGen system changes. In theory, the CSAT product may be applied to any NextGen application (such as Trajectory Based Operations) with specified ground and aircraft capabilities.

  7. HIV gp120 vaccine - VaxGen: AIDSVAX, AIDSVAX B/B, AIDSVAX B/E, HIV gp120 vaccine - Genentech, HIV gp120 vaccine AIDSVAX - VaxGen, HIV vaccine AIDSVAX - VaxGen.

    PubMed

    2003-01-01

    VaxGen is developing prophylactic vaccines against HIV-1 consisting of two recombinant gp120 surface proteins from different HIV-1 strains.This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. The bivalent vaccines [AIDSVAX B/B and AIDSVAX B/E] are being evaluated in two phase III trials. The first multicentre phase III trial of AIDSVAX B/B, was conducted principally in Canada and the US but also at some sites in the Netherlands and Puerto Rico. The trial was completed at the end of 2002. The second phase III trial is being conducted in Thailand with the AIDSVAX B/E vaccine. VaxGen announced in July 2002 that it would be delaying its Biologics License Application (BLA) for AIDSVAX until 2004 to enable the company to fulfil pre-approval manufacturing requirements. AIDSVAX is based on an earlier monovalent gp120 vaccine developed by Genentech that was shown to be safe in humans. VaxGen (formerly Genenvax) was formed as a spin-off company from Genentech with the sole purpose of developing the gp120 vaccine. VaxGen announced in July 2002 that the original License and Supply agreement with Genentech, signed in May 1997, had been amended. Under the revised agreement, Genentech maintains its right to market and sell AIDSVAX in North America, but has relinquished its options to commercialise the vaccine candidate in the rest of the world. Genentech's earlier decision to waive its option to manufacture AIDSVAX has also been formalised in this agreement. Additionally, VaxGen's royalty payments to Genentech for sales to the WHO or UN for underdeveloped nations have also been reduced by up to 50% and Genentech has extended the milestone date associated with VaxGen submitting an NDA. A $US120 million joint venture (Celltrion) has been formed between VaxGen and South Korean investors to manufacture more than 200 million doses of AIDSVAX a year. Celltrion will build and operate two biotechnology manufacturing

  8. SIPSMetGen: It's Not Just For Aircraft Data and ECS Anymore.

    NASA Astrophysics Data System (ADS)

    Schwab, M.

    2015-12-01

    The SIPSMetGen utility, developed for the NASA EOSDIS project, under the EED contract, simplified the creation of file level metadata for the ECS System. The utility has been enhanced for ease of use, efficiency, speed and increased flexibility. The SIPSMetGen utility was originally created as a means of generating file level spatial metadata for Operation IceBridge. The first version created only ODL metadata, specific for ingest into ECS. The core strength of the utility was, and continues to be, its ability to take complex shapes and patterns of data collection point clouds from aircraft flights and simplify them to a relatively simple concave hull geo-polygon. It has been found to be a useful and easy to use tool for creating file level metadata for many other missions, both aircraft and satellite. While the original version was useful it had its limitations. In 2014 Raytheon was tasked to make enhancements to SIPSMetGen, this resulted a new version of SIPSMetGen which can create ISO Compliant XML metadata; provides optimization and streamlining of the algorithm for creating the spatial metadata; a quicker runtime with more consistent results; a utility that can be configured to run multi-threaded on systems with multiple processors. The utility comes with a java based graphical user interface to aid in configuration and running of the utility. The enhanced SIPSMetGen allows more diverse data sets to be archived with file level metadata. The advantage of archiving data with file level metadata is that it makes it easier for data users, and scientists to find relevant data. File level metadata unlocks the power of existing archives and metadata repositories such as ECS and CMR and search and discovery utilities like Reverb and Earth Data Search. Current missions now using SIPSMetGen include: Aquarius, Measures, ARISE, and Nimbus.

  9. GenMin: An enhanced genetic algorithm for global optimization

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, I. E.

    2008-06-01

    A new method that employs grammatical evolution and a stopping rule for finding the global minimum of a continuous multidimensional, multimodal function is considered. The genetic algorithm used is a hybrid genetic algorithm in conjunction with a local search procedure. We list results from numerical experiments with a series of test functions and we compare with other established global optimization methods. The accompanying software accepts objective functions coded either in Fortran 77 or in C++. Program summaryProgram title: GenMin Catalogue identifier: AEAR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 810 No. of bytes in distributed program, including test data, etc.: 436 613 Distribution format: tar.gz Programming language: GNU-C++, GNU-C, GNU Fortran 77 Computer: The tool is designed to be portable in all systems running the GNU C++ compiler Operating system: The tool is designed to be portable in all systems running the GNU C++ compiler RAM: 200 KB Word size: 32 bits Classification: 4.9 Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a nonlinear system of equations via optimization, employing a least squares type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Solution method: Grammatical evolution and a stopping rule. Running time: Depending on the

  10. NextGen Operations in a Simulated NY Area Airspace

    NASA Technical Reports Server (NTRS)

    Smith, Nancy M.; Parke, Bonny; Lee, Paul; Homola, Jeff; Brasil, Connie; Buckley, Nathan; Cabrall, Chris; Chevalley, Eric; Lin, Cindy; Morey, Susan; Omar, Faisal; Rein-Weston, Daphne; Yoo, Hyo-Sang

    2013-01-01

    A human-in-the-loop simulation conducted in the Airspace Operations Laboratory (AOL) at NASA Ames Research Center explored the feasibility of a Next Generation Air Transportation System (NextGen) solution to address airspace and airport capacity limitations in and around the New York metropolitan area. A week-long study explored the feasibility of a new Optimal Profile Descent (OPD) arrival into the airspace as well as a novel application of a Terminal Area Precision Scheduling and Spacing (TAPSS) enhancement to the Traffic Management Advisor (TMA) arrival scheduling tool to coordinate high volume arrival traffic to intersecting runways. In the simulation, four en route sector controllers and four terminal radar approach control (TRACON) controllers managed traffic inbound to Newark International Airport's primary runway, 22L, and its intersecting overflow runway, 11. TAPSS was used to generate independent arrival schedules for each runway and a traffic management coordinator participant adjusted the arrival schedule for each runway 11 aircraft to follow one of the 22L aircraft. TAPSS also provided controller-managed spacing tools (slot markers with speed advisories and timelines) to assist the TRACON controllers in managing the arrivals that were descending on OPDs. Results showed that the tools significantly decreased the occurrence of runway violations (potential go-arounds) when compared with a Baseline condition with no tools. Further, the combined use of the tools with the new OPD produced a peak arrival rate of over 65 aircraft per hour using instrument flight rules (IFR), exceeding the current maximum arrival rate at Newark Liberty International Airport (EWR) of 52 per hour under visual flight rules (VFR). Although the participants rated the workload as relatively low and acceptable both with and without the tools, they rated the tools as reducing their workload further. Safety and coordination were rated by most participants as acceptable in both

  11. Alkalimarinus sediminis gen. nov., sp. nov., isolated from marine sediment.

    PubMed

    Zhao, Jin-Xin; Liu, Qian-Qian; Zhou, Yan-Xia; Chen, Guan-Jun; Du, Zong-Jun

    2015-10-01

    Strain FA028T, a beige-pigmented, facultatively anaerobic, heterotrophic, catalase-negative and oxidase-positive, Gram-stain-negative bacterium, was isolated from marine sediment of the coast of Weihai, China. Cells of strain FA028T were rod-shaped, 1–3 μm in length and 0.5 μm in width. The strain was able to grow at 13–37 °C, at pH 7.0–9.5 and in the presence of 1.0–4.0 % (w/v) NaCl. Optimal growth was observed at 28 °C, with 3.0 % NaCl and at pH 7.5–8.0. Nitrate was not reduced. The G+C content of the DNA was 43.4 mol%. The isoprenoid quinone was Q-9 and the main cellular fatty acids (>10 %) were C16 : 0, C16 : 1ω9c and iso-C15 : 0 2-OH/C16 : 1ω7c. The major polar lipids in strain FA028T were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol; phospholipid was present in moderate to minor amounts in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA028T was affiliated with the phylum Proteobacteria. 16S rRNA gene sequence comparisons showed that this isolate is unique, sharing < 93 % similarity with species of the families Alteromonadaceae and Oceanospirillaceae. On the basis of the phenotypic and phylogenetic data, strain FA028T should be classified as representing a novel species of a new genus within the family Alteromonadaceae, for which the name Alkalimarinus sediminis gen. nov., sp. nov. is proposed. The type strain of Alkalimarinus sediminis is FA028T ( = CICC 10906T = KCTC 42258T). PMID:26297022

  12. Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater.

    PubMed

    Kim, Min-Kyeong; Kim, Tae-Woon; Kim, Tae-Su; Joung, Yochan; Han, Ji-Hye; Kim, Seung Bum

    2016-01-01

    A Gram-stain-negative, non-spore-forming and coccus-shaped bacterial strain, designated 4DR5T, was isolated from freshwater and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-40 °C (optimum 30 °C), at pH 6-9 (optimum pH 7) and in the presence of 0-0.4 % (w/v) NaCl (optimum 0 %) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain 4DR5T was assigned to the family Moraxellaceae of the class Gammaproteobacteria, and its closest related taxa were species of the genera Perlucidibaca (93.67 % sequence similarity), Agitococcus (93.07 %), Paraperlucidibaca (92.31-92.38 %), Alkanindiges (91.79 %) and Acinetobacter (90.24-91.23 %). The predominant isoprenoid quinone detected in strain 4DR5T was Q-10. The major cellular fatty acids were a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c, one consisting of C18 : 1ω7c and/or C18 : 1ω6c, and C16 : 0. The major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of the strain was 61.2 mol%. The phylogenetic, chemotaxonomic and biochemical data not only supported the affiliation of strain 4DR5T to the family Moraxellaceae, but also separated it from other established genera within the family. Therefore, the novel isolate evidently represents a novel species of a new genus of Moraxellaceae, for which the name Fluviicoccus keumensis gen. nov., sp. nov. is proposed. The type strain of Fluviicoccus keumensis is 4DR5T ( = KCTC 32475T = JCM 19370T). PMID:26498187

  13. Complete cDNAs from Nylanderia cf. pubens (Hymenoptera: Formicidae). --GenBank accession numbers: JF815100-JF815104

    Technology Transfer Automated Retrieval System (TEKTRAN)

    5 new gene sequences were identified from workers of Caribbean crazy ant, Nylanderia cf. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are JF815100-JF815104. This information will provide scientists with genetic tools to study the popu...

  14. 75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-08

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of Filing December 30, 2009. Take notice that on December 24, 2009, Terra-Gen...

  15. 78 FR 49507 - OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding of OriGen Energy LLC's application for market-based rate authority, with...

  16. 77 FR 56839 - GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of GenOn Marsh Landing, LLC's application for market-based rate authority, with...

  17. 75 FR 80487 - Cambria CoGen Company; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Cambria CoGen Company; Supplemental Notice That Initial Market- Based Rate... notice in the above-referenced proceeding of Cambria CoGen Company's application for market-based...

  18. 75 FR 35018 - GenConn Energy LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission GenConn Energy LLC; Supplemental Notice That Initial Market-Based Rate... notice in the above-referenced proceeding of GenConn Energy LLC's application for market-based...

  19. 78 FR 77670 - AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of AlphaGen Power LLC's application for market-based rate authority, with...

  20. Discourses in Conflict: The Relationship between Gen Y Pre-Service Teachers, Digital Technologies and Lifelong Learning

    ERIC Educational Resources Information Center

    Donnison, Sharn

    2009-01-01

    This paper analyses Gen Y pre-service primary school teachers' conceptualisations of lifelong learning. It is situated within a context of improving the provision and delivery of pre-service teacher education. This paper argues that Gen Y's understanding of lifelong learning has been influenced by their engagements with digital technologies and…

  1. Complete cDNAs from Brachymyrmex patagonicus (Hymenoptera: Formicidae). --GenBank accession numbers: GU582126-GU582140.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    15 new gene sequences were identified from workers of Brachymyrmex patagonicus, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU582126-GU582140. This information will provide scientists with genetic tools to study the development and the p...

  2. Complete cDNAs from Solenopsis invicta (Hymenoptera: Formicidae). --GenBank accession numbers: HM130684-HM130685.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    2 new gene sequences were identified from workers of Solenopsis invicta, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are HM130684-HM130685. This information will provide scientists with genetic tools to study the populations of this ant....

  3. Complete cDNAs from Nylanderia sp. nr. pubens (Hymenoptera: Formicidae). GenBank GU980916-GU980928.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    13 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU980916-GU980928. This information will provide scientists with genetic tools to study the p...

  4. Descriptions of Kashmira dimorphicauda gen. n., sp. n. and Aphelenchoides hypotris sp. n. from Kashmir Valley, India

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Kashmira dimorphicauda gen. n., sp. n. and Aphelenchoides hypotris sp. n. are described and illustrated from freshwater stream soil in Kashmir Valley, India. Kashmira gen. n. is characterized by having dimorphic tails: coinoid-spicate tail in female and subcylindroid with rounded, non-spicate tip wi...

  5. Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut

    PubMed Central

    Tidjani Alou, M.; Rathored, J.; Lagier, J.-C.; Khelaifia, S.; Labas, N.; Sokhna, C.; Diallo, A.; Raoult, D.; Dubourg, G.

    2016-01-01

    Massilibacterium senegalense gen. nov., sp. nov., strain mt8T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes. PMID:26933503

  6. Cerasibacillus quisquiliarum gen. nov., sp. nov., isolated from a semi-continuous decomposing system of kitchen refuse.

    PubMed

    Nakamura, Kohei; Haruta, Shin; Ueno, Shintaro; Ishii, Masaharu; Yokota, Akira; Igarashi, Yasuo

    2004-07-01

    A moderately thermophilic and alkaliphilic bacillus, which had been reported and designated BLx (Haruta et al., 2002), was isolated from a semi-continuous decomposing system of kitchen refuse. Cells of strain BLxT were strictly aerobic, rod-shaped, motile and spore forming. The optimum temperature and pH for growth were approximately 50 degrees C and pH 8-9. Strain BLxT was able to grow at NaCl concentrations from 0.5 to 7.5%, with optimum growth at 0.5% NaCl. The predominant menaquinone was MK-7, and the major fatty acid was iso-C(15 : 0). Phylogenetic analysis showed that strain BLxT was positioned in an independent lineage within the cluster that includes the genera Virgibacillus and Lentibacillus in Bacillus rRNA group 1. Strain BLxT exhibited 16S rDNA similarity of 92.8-94.8% to Virgibacillus species and 92.3% to Lentibacillus salicampi. Phenotypic, chemotaxonomic and phylogenetic analyses supported the classification of strain BLxT in a novel genus and species. Cerasibacillus quisquiliarum gen. nov., sp. nov. is proposed on the basis of phenotypic, chemotaxonomic and phylogenetic data. The type strain is BLxT (DSM 15825T=IAM15044T=KCTC 3815T). PMID:15280270

  7. Morphology and Ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and Molecular Phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia)

    PubMed Central

    Heber, Domingo; Stoeck, Thorsten; Foissner, Wilhelm

    2014-01-01

    The Psilotrichidae are a family of middle-sized hypotrichs with unique morphological and ontogenetic features (e.g. the oral primordium develops in a deep pouch) that, however, did not provide a definite phylogenetic signal. Thus, we studied the 18S rRNA gene of Urospinula succisa (Müller 1786) Esteban et al., 2001 as well as the morphology and ontogenesis of Psilotrichides hawaiiensis, a new genus and species from an ephemeral swamp on Oahu Island, Hawaii. The molecular data classify the psilotrichids into the oxytrichids but without clear branching position. A brief revision, using the structure of the oral apparatus, the location of the contractile vacuole, and three ontogenetic features, showed four distinct genera: Psilotricha Stein, 1859; Urospinula Corliss, 1960; Hemiholosticha Gelei, 1954; and Psilotrichides nov. gen., which differs from the confamilials mainly by the obliquely oriented buccal cavity and the shape of the undulating membranes as well as by a distinct ridge along the right buccal margin. The pyriform species, P. hawaiiensis, is about 65 × 45 μm in size and is easily recognized by the table tennis racket-shaped appearance due to the elongated last cirrus of the left marginal row. Refined diagnoses are provided for the family Psilotrichidae Bütschli, 1889 and the genera contained. PMID:24498929

  8. 75 FR 27332 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources, LLC; Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources... Comments and Motions To Intervene May 7, 2010. On April 30, 2010, AER NY-Gen, LLC (transferor) and Eagle.... Joseph Klimaszewski, AER NY- Gen, LLC, 613 Plank Road, Forestburgh, New York, 12777; phone (845)...

  9. 77 FR 13592 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-07

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources... Comments and Motions To Intervene On February 24, 2012, AER NY-Gen, LLC (transferor), Eagle Creek Hydro...' Contact: Transferor: Mr. Joseph Klimaszewski, AER NY- Gen, LLC, P.O. Box 876, East Aurora, NY 14052,...

  10. ALS - The cost cutter

    NASA Astrophysics Data System (ADS)

    Colucci, Frank

    1987-10-01

    The Advanced Launch System (ALS) development program will avail itself of existing technologies in the short term in order to produce an interim 'core' vehicle that may be operational by 1993; the full, booster-incorporating system objective will then be achieved in 1998. This programmatic 'decoupling' of booster and core vehicle development efforts will separate their funding peaks. The ALS program will cut costs by colocating manufacturing and launch facilities, using Al-Li alloys in booster primary structures, and aggressively applying 'paperless' CIM. The ALS launch vehicle configuration will be primarily determined by both payload requirements and flight frequency.

  11. Litorilituus sediminis gen. nov. sp. nov., isolated from coastal sediment of an amphioxus breeding zone in Qingdao, China.

    PubMed

    Wang, Yan; Zhao, Rui; Ji, Shiqi; Li, Zhao; Yu, Tong; Li, Bingyu; Shi, Xiaochong; Zhang, Xiao-Hua

    2013-09-01

    A Gram-negative, non-spore-forming, catalase- and oxidase-positive, aerobic, curved-rod shaped bacterium with polar or subpolar flagellum, designated strain JYr2(T), was isolated from a sediment sample collected from an amphioxus breeding zone in the coastal region of Qingdao, China. The organism grew optimally at 37 °C, pH 8-9 and in the presence of 3 % (w/v) NaCl or 3-4 % sea salts (w/v; Sigma). Salt was required for growth. The strain contained isoprenoid quinone 8 (Q-8, 100 %) as the predominant isoprenoid quinone and C16:0 (24.1 %) and C16:1 ω7c and/or C16:1 ω6c (35.8 %) as major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid (PN) and two aminolipid (AL1, AL2) were the major constituents of the phospholipids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JYr2(T) formed a distinct evolutionary lineage within the family Colwelliaceae. It showed <95.0 % sequence similarities to all validly published species in the family Colwelliaceae, except 95.2 % to Thalassomonas viridans DSM 13754(T) and 95.0 % to Colwellia polaris JCM 537(T). The G+C content of the DNA was 42.7 mol%. On the basis of the polyphasic taxonomic study, strain JYr2(T) (= CGMCC 1.10794(T) = JCM 17549(T)) was considered to represent a novel genus and species in Gammaproteobacteria, for which the name Litorilituus sediminis gen. nov. sp. nov. was proposed. PMID:23839057

  12. Effect of GEN1 interference on the chemosensitivity of the breast cancer MCF-7 and SKBR3 cell lines

    PubMed Central

    WU, YUNLU; QIAN, YING; ZHOU, GUOZHONG; LV, JUAN; YAN, QIUYUE; DONG, XUEJUN

    2016-01-01

    Chemotherapy is a notable method for the treatment of breast cancer. Numerous genes associated with the sensitivity of cancer to chemotherapy have been found. In recent years, evidence has suggested that a particular structure termed Holliday junction (HJ) plays a crucial role in cancer chemosensitivity. Targeting HJ resolvases, such as structure-specific endonuclease subunit SLX4 (Slx4) and MUS81 structure-specific endonuclease subunit (Mus81), significantly increases the chemosensitivity of tumor cells. Flap endonuclease GEN homolog 1 (GEN1) is a HJ resolvase that belongs to the Rad2/xeroderma pigmentosum complementation group G nuclease family. Whether GEN1 affects the chemosensitivity of tumor cells in a similar manner to Slx4 and Mus81 remains unknown. The aim of the present study was to determine the effect of GEN1 interference on the chemosensitivity of breast cancer cell lines. The investigation of the function of GEN1 was performed using MCF-7 and SKBR3 cells. Short hairpin RNA was used to suppress the expression of GEN1, and western blot analysis and reverse transcription-quantitative polymerase chain reaction were used to detect gene expression. In addition, a cell counting kit-8 assay was performed to detect the viability of cells and flow cytometry was performed to test apoptosis levels. Suppression of GEN1 in SKBR3 cells effectively increased the sensitivity to the chemotherapeutic drug 5-fluorouracil (5-FU), while MCF-7 cells showed no significant change in sensitivity following GEN1 suppression. However, when GEN1 was targeted in addition to Mus81, the MCF-7 cells also demonstrated a significantly increased sensitivity to 5-FU. In addition, when the level of Mus81 was low, GEN1 expression was increased under a low concentration of 5-FU. The present results suggest that GEN1 may play different roles in different breast cancer cell lines. The function of GEN1 may be affected by the level of Mus81 in the cell line. In addition, GEN1 interference may

  13. Macrostylopyga gen. nov., a new genus of cockroaches (Dictyoptera: Blattidae), with descriptions of two new species.

    PubMed

    Anisyutkin, Leonid N; Anichkin, Alexandr E; Thinh, Nguyen Van

    2013-01-01

    The genus Macrostylopyga gen. nov. and two species (M. grandis sp. nov. and M. bidupi sp. nov.) are described. A detailed morphological description with special attention to the male genitalic structures is provided. Some aspects of the evolution of wingless cockroaches are briefly discussed. PMID:26097964

  14. A gilled mushroom, Gerontomyces lepidotus gen. et sp. nov. (Basidiomycota: Agaricales), in Baltic amber.

    PubMed

    Poinar, George

    2016-09-01

    A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. PMID:27567715

  15. List of Predicted Simple Sequence Repeats from Sugar Beet GenBank Accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta vulgaris ESTs from GenBank as of January 2005 collapsed into 13,618 unique clusters (4,023 Tentative Consensus sequences, 9,595 singletons), and 35% were contributed via work partially supported through the BSDF. These sequences were parsed through SSR-Primer software for discovering potential...

  16. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism

    PubMed Central

    Chan, Ying Wai; West, Stephen

    2015-01-01

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  17. Builders Challenge High Performance Builder Spotlight - NextGen Home, Las Vegas, Nevada

    SciTech Connect

    2009-01-01

    Building America Builders Challenge fact sheet on the NextGen demo home built in Las Vegas. The home has a Home Energy Rating System (HERS) index score of 44 with R-40 spray foam attic insulation, R-40 insulated concrete walls, and a 4kW DC solar laminate

  18. Working with Gen Y Teachers: Dealing with a Changing Teacher Workforce

    ERIC Educational Resources Information Center

    Williamson, Ronald; Meyer-Looze, Catherine

    2010-01-01

    A significant change is coming to American classrooms. As Baby Boomer teachers retire and are replaced by members of Generation Y (born between 1977 and 1995) there is growing evidence that they come from a far different set of experiences, experiences that will shape their lives and their careers (Coggins, 2008). Members of Gen Y share several…

  19. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

    PubMed

    Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A

    2011-01-01

    Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach. PMID:22002916

  20. Two new Stratiomyinae, including Panamamyia gen. nov., from the Neotropical Region (Diptera: Stratiomyidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Hoplitimyia James, H. inbioensis sp. nov., is described from Costa Rica. A new genus, Panamamyia gen. nov., with type species P. silbergliedi sp. nov., is described from Panama. Both taxa are very rare in collections, not having been taken during extensive Malaise trap surveys in ...

  1. Gen Y Recruitment: Understanding Graduate Intentions to Join an Organisation Using the Theory of Planned Behaviour

    ERIC Educational Resources Information Center

    Warmerdam, Amanda; Lewis, Ioni; Banks, Tamara

    2015-01-01

    Purpose: Using the Theory of Planned Behaviour (TPB) framework, the purpose of this paper is to explore whether the standard TPB constructs explained variance in Generation Y (Gen Y) individuals' intentions to join their ideal organisation. Design/methodology/approach: A mixed methods approach was used featuring qualitative and quantitative…

  2. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    PubMed Central

    Liu, Yijin; Freeman, Alasdair D.J.; Déclais, Anne-Cécile; Wilson, Timothy J.; Gartner, Anton; Lilley, David M.J.

    2015-01-01

    Summary We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. PMID:26686639

  3. CottonGen: a genomics, genetics and breeding database for cotton research.

    PubMed

    Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G; Main, Dorrie

    2014-01-01

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. PMID:24203703

  4. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    PubMed Central

    Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  5. Revision of “Phyllobrotica” from Taiwan with description of Jolibrotica gen. n. (Coleoptera, Chrysomelidae, Galerucinae)

    PubMed Central

    Lee, Chi-Feng; Bezděk, Jan

    2015-01-01

    Abstract All Taiwanese species formerly classified the genus Phyllobrotica Chevrolat, 1836 are revised. Jolibrotica Lee & Bezděk, gen. n., is described for Phyllobrotica sauteri (Chûjô, 1935) (Taiwan, China: Guangxi) and Phyllobrotica chujoi Kimoto, 1969 (Taiwan). Phyllobrotica shirozui Kimoto, 1969 is transferred to the genus Haplosomoides. All species are redescribed and their diagnostic characters illustrated. PMID:26798315

  6. FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy

    SciTech Connect

    Zitney, S E; Sarkus, T A

    2007-11-04

    This presentation will highlight the U.S. Department of Energy’s (DOE) FutureGen project - a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen initiative is the National Energy Technology Laboratory (NETL), a multi-purpose laboratory operated by the U.S. DOE’s Office of Fossil Energy. NETL has a mission to conduct R&D from fundamental science to technology demonstration for resolving the environmental, supply, and reliability constraints of producing and using fossil energy resources. The commercial-scale FutureGen R&D facility is a pathway toward future fossil-energy power plants that will produce hydrogen and electricity while nearly eliminating emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. Low carbon emissions would be achieved by integrating CO2 capture and sequestration operations with the power plant.

  7. pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

    PubMed Central

    Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

    2015-01-01

    Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

  8. The GenTechnique Project: Developing an Open Environment for Learning Molecular Genetics.

    ERIC Educational Resources Information Center

    Calza, R. E.; Meade, J. T.

    1998-01-01

    The GenTechnique project at Washington State University uses a networked learning environment for molecular genetics learning. The project is developing courseware featuring animation, hyper-link controls, and interactive self-assessment exercises focusing on fundamental concepts. The first pilot course featured a Web-based module on DNA…

  9. Extending Validated Human Performance Models to Explore NextGen Concepts

    NASA Technical Reports Server (NTRS)

    Gore, Brian Francis; Hooey, Becky Lee; Mahlstedt, Eric; Foyle, David C.

    2012-01-01

    To meet the expected increases in air traffic demands, NASA and FAA are researching and developing Next Generation Air Transportation System (NextGen) concepts. NextGen will require substantial increases in the data available to pilots on the flight deck (e.g., weather,wake, traffic trajectory predictions, etc.) to support more precise and closely coordinated operations (e.g., self-separation, RNAV/RNP, and closely spaced parallel operations, CSPOs). These NextGen procedures and operations, along with the pilot's roles and responsibilities, must be designed with consideration of the pilot's capabilities and limitations. Failure to do so will leave the pilots, and thus the entire aviation system, vulnerable to error. A validated Man-machine Integration and design Analysis System (MIDAS) v5 model was extended to evaluate anticipated changes to flight deck and controller roles and responsibilities in NextGen approach and Land operations. Compared to conditions when the controllers are responsible for separation on decent to land phase of flight, the output from these model predictions suggest that the flight deck response time to detect the lead aircraft blunder will decrease, pilot scans to the navigation display will increase, and workload will increase.

  10. Balancing Formative and Summative Science Assessment Practices: Year One of the GenScope Assessment Project.

    ERIC Educational Resources Information Center

    Hickey, Daniel T.; Kruger, Ann Cale; Fredrick, Laura D.; Schafer, Nancy Jo; Kindfield, Ann C. H.

    This paper describes the GenScope Assessment Project, a project that is exploring ways of using multimedia computers to teach complex science content, refining sociocultural views of assessment and motivation, and considering different ways of reconciling the differences between these newer views and prior behavioral and cognitive views. The…

  11. Visualizing and Sharing Results in Bioinformatics Projects: GBrowse and GenBank Exports

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined ...

  12. DmGEN, a novel RAD2 family endo-exonuclease from Drosophila melanogaster.

    PubMed

    Ishikawa, Gen; Kanai, Yoshihiro; Takata, Kei-ichi; Takeuchi, Ryo; Shimanouchi, Kaori; Ruike, Tatsushi; Furukawa, Tomoyuki; Kimura, Seisuke; Sakaguchi, Kengo

    2004-01-01

    A novel endo-exonuclease, DmGEN (Drosophila Melanogaster XPG-like endonuclease), was identified in D.melanogaster. DmGEN is composed of five exons and four introns, and the open reading frame encodes a predicted product of 726 amino acid residues with a molecular weight of 82.5 kDa and a pI of 5.36. The gene locus on Drosophila polytene chromosomes was detected at 64C9 on the left arm of chromosome 3 as a single site. The encoded protein showed a relatively high degree of sequence homology with the RAD2 nucleases, especially XPG. Although the XPG-N- and XPG-I-domains are highly conserved in sequence, locations of the domains are similar to those of FEN-1 and EXO-1, and the molecular weight of the protein is close to that of EXO-1. In vitro, DmGEN showed endonuclease and 3'-5' exonuclease activities with both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), but the endonuclease action with dsDNA was quite specific: 5'-3' exonuclease activity was found to occur with nicked DNA, while dsDNA was endonucleolytically cut at 3-4 bp from the 5' end. Homologs are widely found in mammals and higher plants. The data suggest that DmGEN belongs to a new class of RAD2 nuclease. PMID:15576351

  13. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  14. Plant MetGenMAP: an integrative analysis system for plant systems biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

  15. Overview of NASA's Next Generation Air Transportation System (NextGen) Research

    NASA Technical Reports Server (NTRS)

    Swenson, Harry N.

    2009-01-01

    This slide presentation is an overview of the research for the Next Generation Air Transportation System (NextGen). Included is a review of the current air transportation system and the challenges of air transportation research. Also included is a review of the current research highlights and significant accomplishments.

  16. Sinolatindia petila gen. n. and sp. n. from China (Blattodea, Corydiidae, Latindiinae)

    PubMed Central

    Qiu, Lu; Che, Yanli; Wang, Zongqing

    2016-01-01

    Abstract Sinolatindia petila gen. n. and sp. n. (Blattodea: Corydiidae: Latindiinae) is reported from Yunnan Province, China. Description, illustrations and a distribution map of the new taxon are provided. Comparisons with the type genus Latindia Stål, 1860 and the genus Homopteroidea Shelford, 1906 are given. PMID:27408574

  17. Al-Anon/Alateen

    MedlinePlus

    Find an Al-Anon meeting Español | Français 2018 Int'l Convention Home About Group Meetings What If I'm not ready ... a meeting? What can I expect at an Al-Anon meeting? What was my first meeting like? ...

  18. Geraldocossus gen. nov. (Lepidoptera, Cossidae) from Mount Cameroon (West Africa).

    PubMed

    Yakovlev, Roman V; Sáfián, Szabolcs

    2016-01-01

    The cossid or the Carpenter Moths (Lepidoptera, Cossidae) include about 1000 species worldwide (van Nieukerken et al., 2011), of which 750 species belong to five subfamilies that occur in the Old World (Yakovlev 2011). The Cossidae are still relatively poorly known from vast areas of the African continent, despite recent reports on the fauna of Malawi (Yakovlev & Murphey 2014), Zimbabwe (Yakovlev & Lenz 2014), and Zambia (Yakovlev 2014). The first results of an ongoing revision of the South African Cossidae have also been published (Mey 2015). PMID:27395152

  19. Environmental Information for the U.S. Next Generation Air Transportation System (NextGen)

    NASA Astrophysics Data System (ADS)

    Murray, J.; Miner, C.; Pace, D.; Minnis, P.; Mecikalski, J.; Feltz, W.; Johnson, D.; Iskendarian, H.; Haynes, J.

    2009-09-01

    It is estimated that weather is responsible for approximately 70% of all air traffic delays and cancellations in the United States. Annually, this produces an overall economic loss of nearly 40B. The FAA and NASA have determined that weather impacts and other environmental constraints on the U.S. National Airspace System (NAS) will increase to the point of system unsustainability unless the NAS is radically transformed. A Next Generation Air Transportation System (NextGen) is planned to accommodate the anticipated demand for increased system capacity and the super-density operations that this transformation will entail. The heart of the environmental information component that is being developed for NextGen will be a 4-dimensional data cube which will include a single authoritative source comprising probabilistic weather information for NextGen Air Traffic Management (ATM) systems. Aviation weather constraints and safety hazards typically comprise meso-scale, storm-scale and microscale observables that can significantly impact both terminal and enroute aviation operations. With these operational impacts in mind, functional and performance requirements for the NextGen weather system were established which require significant improvements in observation and forecasting capabilities. This will include satellite observations from geostationary and/or polar-orbiting hyperspectral sounders, multi-spectral imagers, lightning mappers, space weather monitors and other environmental observing systems. It will also require improved in situ and remotely sensed observations from ground-based and airborne systems. These observations will be used to better understand and to develop forecasting applications for convective weather, in-flight icing, turbulence, ceilings and visibility, volcanic ash, space weather and the environmental impacts of aviation. Cutting-edge collaborative research efforts and results from NASA, NOAA and the FAA which address these phenomena are summarized

  20. GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

    PubMed Central

    Parks, Donovan H.; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S.; Armanini, David G.; Baird, Donald J.; Langille, Morgan G. I.; Beiko, Robert G.

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  1. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

    PubMed

    Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  2. [Environmental factors in ALS].

    PubMed

    Juntas-Morales, Raul; Pageot, Nicolas; Corcia, Philippe; Camu, William

    2014-05-01

    ALS is likely to be a disorder of multifactorial origin. Among all the factors that may increase the risk of ALS, environmental ones are being studied for many years, but in the recent years, several advances have pointed to a new interest in their potential involvement in the disease process, especially for the cyanotoxin BMAA. Food containing BMAA has been found on Guam, a well-known focus of ALS/parkinsonism/dementia and high levels of BMAA have been identified into the brain of these patients. The BMAA cyanotoxin is potentially ubiquitous and have also been found into the food of patients who died from ALS both in Europe and USA. BMAA can be wrongly integrated into the protein structure during mRNA traduction, competing with serine. This may induce abnormal protein folding and a subsequent cell death. Heavy metals, such as lead or mercury may be directly toxic for neuronal cells. Several works have suggested an increased risk of ALS in individuals chronically exposed to these metals. Exposure to pesticides has been suggested to be linked to an increased risk of developing ALS. The mechanism of their toxicity is likely to be mediated by paraoxonases. These proteins are in charge of detoxifying the organism from toxins, and particularly organophosphates. To date, there are insufficient scientific data to suggest that exposure to electromagnetic fields may increase the risk of having ALS. We are particularly missing longitudinal cohorts to demonstrate that risk. PMID:24703731

  3. All About ALS

    MedlinePlus

    ... External link, please review our exit disclaimer . Subscribe All About ALS Understanding a Devastating Disorder In the ... a coffee pot, or button a shirt. Eventually, all muscles under voluntary control are affected, and people ...

  4. Amyotrophic Lateral Sclerosis (ALS)

    MedlinePlus

    ... Pictures of ALS Mutant Proteins Support Two Major Theories About How the Disease is Caused May 2003 ... All NINDS-prepared information is in the public domain and may be freely copied. Credit to the ...

  5. Genetic Testing for ALS

    MedlinePlus

    ... Involved Donate Familial Amyotrophic Lateral Sclerosis (FALS) and Genetic Testing By Deborah Hartzfeld, MS, CGC, Certified Genetic ... guarantee a person will develop symptoms of ALS. Genetic Counseling If there is more than one person ...

  6. ALS synchrotron radiation shielding

    SciTech Connect

    Donahue, R.J.

    1995-10-01

    This note discusses the assumptions and results of synchrotron radiation shielding estimates for ALS bend magnet and wiggler beamlines. Estimates of gas bremsstrahlung production are not included and are dealt with elsewhere.

  7. What Is ALS?

    MedlinePlus

    ... scarring or hardening ("sclerosis") in the region. Motor neurons reach from the brain to the spinal cord ... the body. The progressive degeneration of the motor neurons in ALS eventually leads to their demise. When ...

  8. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David [Baylor

    2013-01-25

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  9. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    Sexton, David

    2012-06-01

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  10. Parametric Modeling of the Safety Effects of NextGen Terminal Maneuvering Area Conflict Scenarios

    NASA Technical Reports Server (NTRS)

    Rogers, William H.; Waldron, Timothy P.; Stroiney, Steven R.

    2011-01-01

    The goal of this work was to analytically identify and quantify the issues, challenges, technical hurdles, and pilot-vehicle interface issues associated with conflict detection and resolution (CD&R)in emerging operational concepts for a NextGen terminal aneuvering area, including surface operations. To this end, the work entailed analytical and trade studies focused on modeling the achievable safety benefits of different CD&R strategies and concepts in the current and future airport environment. In addition, crew-vehicle interface and pilot performance enhancements and potential issues were analyzed based on review of envisioned NextGen operations, expected equipage advances, and human factors expertise. The results of perturbation analysis, which quantify the high-level performance impact of changes to key parameters such as median response time and surveillance position error, show that the analytical model developed could be useful in making technology investment decisions.

  11. Hanford Meteorological Station computer codes: Volume 1, The GEN computer code

    SciTech Connect

    Buck, J.W.; Andrews, G.L.

    1987-07-01

    The Hanford Meteorological Station, operated by Pacific Northwest Laboratory, issues general weather forecasts twice a day. The GEN computer code is used to archive the 24-hour forecasts and apply quality assurance checks to the forecast data. This code accesses an input file, which contains the date and hour of the previous forecast, and an output file, which contains 24-hour forecasts for the current month. As part of the program, a data entry form consisting of 14 fields that describe various weather conditions must be filled in. The information on the form is appended to the current 24-hour monthly forecast file, which provides an archive for the 24-hour general weather forecasts. This report consists of several volumes documenting the various computer codes used at the Hanford Meteorological Station. This volume describes the implementation and operation of the GEN computer code at the station.

  12. Fracture of the polyethylene tibial post in a NexGen posterior-stabilized knee prosthesis.

    PubMed

    Chiu, Yen-Shuo; Chen, Wei-Ming; Huang, Ching-Kuei; Chiang, Chao-Ching; Chen, Tain-Hsiung

    2004-12-01

    We reported a case of fracture of a polyethylene tibial post in a 44-year-old woman after 3 years of NexGen posterior-stabilized total knee arthroplasty (Zimmer, Warsaw, IN). Burnishing and delamination of the polyethylene was found around the breakage site of the post, especially over the anterior aspect of the post base. It indicated that the possible failure mechanism was the repeated anterior impingement between the metal femoral cam and polyethylene tibial post. After replacement of the broken insert, the patient obtained complete relief of previous symptoms. To our knowledge, this is the first report of post breakage of a NexGen posterior-stabilized knee prosthesis. PMID:15586342

  13. Developing a Nuclear Grade of Alloy 617 for Gen IV Nuclear Energy Systems

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W; Santella, Michael L

    2010-01-01

    Alloy 617, an attractive material not particularly developed for nuclear use, is now being considered as a leading candidate alloy by several countries for applications in the Gen IV Nuclear Energy Systems. An extensive review of its existing data suggests that it would be beneficial to refine the alloy s specification to a nuclear grade for the intended Gen IV systems. In this paper, rationale for developing a nuclear grade of the alloy is first discussed through an analysis on existing data from various countries. Then initial experiments for refining the alloy specification are described. Preliminary results have suggested the feasibility of the refinement approach, as well as the possibility for achieving a desirable nuclear grade. Based on the results, further research activities are recommended.

  14. Internal combustion engine report: Spark ignited ICE GenSet optimization and novel concept development

    SciTech Connect

    Keller, J.; Blarigan, P. Van

    1998-08-01

    In this manuscript the authors report on two projects each of which the goal is to produce cost effective hydrogen utilization technologies. These projects are: (1) the development of an electrical generation system using a conventional four-stroke spark-ignited internal combustion engine generator combination (SI-GenSet) optimized for maximum efficiency and minimum emissions, and (2) the development of a novel internal combustion engine concept. The SI-GenSet will be optimized to run on either hydrogen or hydrogen-blends. The novel concept seeks to develop an engine that optimizes the Otto cycle in a free piston configuration while minimizing all emissions. To this end the authors are developing a rapid combustion homogeneous charge compression ignition (HCCI) engine using a linear alternator for both power take-off and engine control. Targeted applications include stationary electrical power generation, stationary shaft power generation, hybrid vehicles, and nearly any other application now being accomplished with internal combustion engines.

  15. Gen 2.0 Mixer/Ejector Nozzle Test at LSAF June 1995 to July 1996

    NASA Technical Reports Server (NTRS)

    Arney, L. D.; Sandquist, D. L.; Forsyth, D. W.; Lidstone, G. L.; Long-Davis, Mary Jo (Technical Monitor)

    2005-01-01

    Testing of the HSCT Generation 2.0 nozzle model hardware was conducted at the Boeing Low Speed Aeroacoustic Facility, LSAF. Concurrent measurements of noise and thrust were made at critical takeoff design conditions for a variety of mixer/ejector model hardware. Design variables such as suppressor area ratio, mixer area ratio, liner type and thickness, ejector length, lobe penetration, and mixer chute shape were tested. Parallel testing was conducted at G.E.'s Cell 41 acoustic free jet facility to augment the LSAF test. The results from the Gen 2.0 testing are being used to help shape the current nozzle baseline configuration and guide the efforts in the upcoming Generation 2.5 and 3.0 nozzle tests. The Gen 2.0 results have been included in the total airplane system studies conducted at MDC and Boeing to provide updated noise and thrust performance estimates.

  16. Neutron Arm Study and Calibration for the GEn Experiment at Thomas Jefferson National Laboratory

    SciTech Connect

    Timothy Ngo

    2007-07-01

    The measurement of the neutron electric form factor, GEn, will allow us to solve indirectly for the quark charge distribution inside of the neutron. With the equipment at Jefferson Lab we have measured GEn at four momentum transfer values of Q**2 at 1.3, 2.4 and 3.4 (GeV/c)**2 using a polarized electron beam and polarized Helium target. The scattered electrons off of the Helium target are detected in the BigBite spectrometer and the recoiling neutrons from the Helium are detected in the Neutron Arm, which is composed of an array of scintillators. The main focus of this thesis will be devoted to the geometry, timing and energy calibrations of the Neutron Arm.

  17. Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  18. Rapidly solidified NiAl and FeAl

    NASA Technical Reports Server (NTRS)

    Gaydosh, D. J.; Crimp, M. A.

    1984-01-01

    Melt spinning was used to produce rapidly solidified ribbons of the B2 intermetallics NiAl and FeAl. Both Fe-40Al and Fe-45Al possessed some bend ductility in the as spun condition. The bend ductility of Fe-40Al, Fe-45Al, and equiatomic NiAl increased with subsequent heat treatment. Heat treatment at approximately 0.85 T (sub m) resulted in significant grain growth in equiatomic FeAl and in all the NiAl compositions. Low bend ductility in both FeAl and NiAl generally coincided with intergranular failure, while increased bend ductility was characterized by increasing amounts of transgranular cleavage fracture.

  19. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    PubMed Central

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended. PMID:25157246

  20. Two New Freshwater Woloszynskioids Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov. (Suessiaceae, Dinophyceae) Lacking an Apical Furrow Apparatus.

    PubMed

    Takahashi, Kazuya; Moestrup, Øjvind; Jordan, Richard W; Iwataki, Mitsunori

    2015-12-01

    Two new woloszynskioid dinoflagellates, Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov., are described from Japanese freshwater ponds on the basis of bright field and fluorescence light microscopy, scanning and transmission electron microscopy, and molecular phylogeny inferred from rDNA sequences. Asulcocephalium miricentonis has a spherical anterior nucleus and chloroplast with a pyrenoid penetrated by the cytoplasm. This species has 9-12 latitudinal series of amphiesmal vesicles (AVs), including an apparently large AV on the right ventral side of the epicone. Leiocephalium pseudosanguineum has a U-shaped nucleus in the epicone and chloroplasts without a pyrenoid. This species has at least 24 latitudinal series of AVs. The characteristic features of both species were brick-like material (type E) in the eyespot and the lack of an apical furrow. These features coincide with those of Polarella glacialis, but the two species differ in cell shape, number and arrangement of AVs, shape of resting cysts, and habitats; i.e., P. glacialis has been reported only from marine cold waters. Molecular phylogeny revealed that A. miricentonis and L. pseudosanguineum were positioned in the Suessiaceae and closely related to Piscinoodinium sp., but their relationship to Polarella and other reported taxa was not supported. PMID:26599726

  1. Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.

    PubMed

    Nakada, Takashi; Tomita, Masaru; Wu, Jiunn-Tzong; Nozaki, Hisayoshi

    2016-04-01

    Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400-600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy-in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria-and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup "Pleiochloris," was included in the genus Ixipapillifera as I. deasonii comb. nov. PMID:27037593

  2. MOLECULAR PHYLOGENY, ULTRASTRUCTURE, AND TAXONOMIC REVISION OF CHLOROGONIUM (CHLOROPHYTA): EMENDATION OF CHLOROGONIUM AND DESCRIPTION OF GUNGNIR GEN. NOV. AND RUSALKA GEN. NOV.(1).

    PubMed

    Nakada, Takashi; Nozaki, Hisayoshi; Pröschold, Thomas

    2008-06-01

    We examined the molecular phylogeny and ultrastructure of Chlorogonium and related species to establish the natural taxonomy at the generic level. Phylogenetic analyses of 18S rRNA and RUBISCO LSU (rbcL) gene sequences revealed two separate clades of Chlorogonium from which Chlorogonium (Cg.) fusiforme Matv. was robustly separated. One clade comprised Cg. neglectum Pascher and Cg. kasakii Nozaki, whereas the other clade included the type species Cg. euchlorum (Ehrenb.) Ehrenb., Cg. elongatum (P. A. Dang.) Francé, and Cg. capillatum Nozaki, M. Watanabe et Aizawa. On the basis of unique ultrastructural characteristics, we described Gungnir Nakada gen. nov. comprising three species: G. neglectum (Pascher) Nakada comb. nov., G. mantoniae (H. Ettl) Nakada comb. nov., and G. kasakii (Nozaki) Nakada comb. nov. We also emended Chlorogonium as a monophyletic genus composed of Cg. euchlorum, Cg. elongatum, and Cg. capillatum. Because Cg. fusiforme was distinguished from the redefined Chlorogonium and Gungnir by the structure of its starch plate, which is associated with pyrenoids, we reclassified this species as Rusalka fusiformis (Matv.) Nakada gen. et comb. nov. PMID:27041433

  3. New Particle Formation Events During 2013 in Hada Al Sham, Saudi-Arabia

    NASA Astrophysics Data System (ADS)

    Neitola, K.; Hyvärinen, A.; Lihavainen, H.; Alghamdi, M.; Hussein, T.; Khodeir, M.; Shehata, A.; Laaksonen, A. J.; Kulmala, M. T.

    2014-12-01

    clear growth, S is clear shrinkage, G + S is both growth and shrinkage and unclear is not clear in either way.ReferencesM. Dal Maso, et al. (2005). Bor. Env. Res., 10, 323-336.M. Kulmala, et al. (2006). Atmos. Chem. Phys., 6, 787-793. M. Kulmala, et al. (2013). Science, 336, 943-946.

  4. Yamaguchia toyensis n. sp., n. gen. (Annelida, Clitellata, Lumbriculidae) from profundal lake habitat in Japan

    USGS Publications Warehouse

    Fend, S.V.; Ohtaka, A.

    2004-01-01

    Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.

  5. Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China

    PubMed Central

    Zhao, Zhe; Li, Shuqiang

    2016-01-01

    Abstract One new genus of the spider subfamily Coelotinae, Papiliocoelotes gen. n., with five new species is described for both sexes: Papiliocoelotes guanyinensis sp. n., Papiliocoelotes guitangensis sp. n., Papiliocoelotes jiepingensis sp. n., Papiliocoelotes meiyuensis sp. n., Papiliocoelotes yezhouensis sp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use. PMID:27199603

  6. Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China.

    PubMed

    Zhao, Zhe; Li, Shuqiang

    2016-01-01

    One new genus of the spider subfamily Coelotinae, Papiliocoelotes gen. n., with five new species is described for both sexes: Papiliocoelotes guanyinensis sp. n., Papiliocoelotes guitangensis sp. n., Papiliocoelotes jiepingensis sp. n., Papiliocoelotes meiyuensis sp. n., Papiliocoelotes yezhouensis sp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use. PMID:27199603

  7. Geochemical Monitoring Considerations for the FutureGen 2.0 Project

    DOE PAGESBeta

    Amonette, James E.; Johnson, Timothy A.; Spencer, Clayton F.; Zhong, Lirong; Szecsody, James E.; Vermeul, Vince R.

    2014-12-31

    Geochemical monitoring is an essential component of a suite of monitoring technologies designed to evaluate CO2 mass balance and detect possible loss of containment at the FutureGen 2.0 geologic sequestration site near Jacksonville, IL. This presentation gives an overview of the potential geochemical approaches and tracer technologies that were considered, and describes the evaluation process by which the most cost-effective and robust of these were selected for implementation

  8. Rahiolisaurus gujaratensis, n. gen. n. sp., A New Abelisaurid Theropod from the Late Cretaceous of India

    NASA Astrophysics Data System (ADS)

    Novas, Fernando E.; Chatterjee, Sankar; Rudra, Dhiraj K.; Datta, P. M.

    Systematic excavations in the fluvial mudstone unit of the Upper Cretaceous Lameta Formation near Rahioli village in Kheda District, Gujarat, have yielded a large-bodied (~8 m long) abelisaurid theropod, Rahiolisaurus gujaratensis, gen. et sp. nov. Abundant skeletal remains represent this new genus and species. Rahiolisaurus provides novel information on foot morphology, hitherto little known in other abelisaurids. Rahiolisaurus gujaratensis is a gracile and slender-limbed abelisaurid that appears to be a distinctive taxon from the sympatric species Rajasaurus narmadensis.

  9. A mechanism for maintaining an up-to-date GenBank database via Usenet.

    PubMed

    Smith, R H; Gottesman, S; Hobbs, B; Lear, E; Kristofferson, D; Benton, D; Smith, P R

    1991-01-01

    In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems. PMID:2004268

  10. NQRS Data for C8H20Br3GeN (Subst. No. 1129)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C8H20Br3GeN (Subst. No. 1129)

  11. Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System

    SciTech Connect

    Schatz, Joe E.

    2009-03-12

    Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

  12. Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois

    USGS Publications Warehouse

    Hund, G.; Greenberg, S.E.

    2011-01-01

    FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

  13. MicroGen: a MIAME compliant web system for microarray experiment information and workflow management

    PubMed Central

    Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

    2005-01-01

    Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production. PMID:16351755

  14. Description of Distorhabditis poonchiana n. gen., n. sp. (Nematoda: Rhabditidae) from Jammu and Kashmir, India

    PubMed Central

    Shah, Ali Asghar; Vaid, Shavish; Hussain, Abid; Ahmad, Rakeeb

    2015-01-01

    Distorhabditis poonchiana n. gen., n. sp. from humus in Jammu and Kashmir, India, is described and illustrated. The new genus is characterized by a small body; slightly setoff labial region; long tubular gymnostom; prominently cuticularized cheilostom; absence of glottoid apparatus; monoprodelphic reproductive system; vulva (V) = 81 to 84; spicules with trifurcated distal ends, simple gubernaculum, peloderan bursa with eight pairs of bursal papillae arranged in 1 + 1 + 1 + 2 + 1 + 2 arrangement. PMID:26941466

  15. Gen IV Materials Handbook Beta Release for Structural and Functional Evaluation

    SciTech Connect

    Ren, Weiju; Luttrell, Claire

    2006-09-12

    Development of the Gen IV Materials Handbook is briefly summarized up to date. Current status of the Handbook website construction is described. The developed Handbook components and access control of the beta version are discussed for the present evaluation release. Detailed instructions and examples are given to provide guidance for evaluators to browse the constructed parts and use all the currently developed functionalities of the Handbook in evaluation.

  16. MORPHOLOGY AND MOLECULAR PHYLOGENY OF AUREOPHYCUS ALEUTICUS GEN. ET SP. NOV. (LAMINARIALES, PHAEOPHYCEAE) FROM THE ALEUTIAN ISLANDS(1).

    PubMed

    Kawai, Hiroshi; Hanyuda, Takeaki; Lindeberg, Mandy; Lindstrom, Sandra C

    2008-08-01

    A previously unknown species of kelp was collected on Kagamil Island, Aleutian Islands. The species can be easily distinguished from any known laminarialean alga: the erect sporophytic thallus is composed of a thin lanceolate blade attaining ∼2 m in height and ∼0.50 m in width, without midrib, and the edge of the blade at the transition zone is thickened to form a V-shape; the stipe is solid and flattened, slightly translucent, attaining ∼1 m in length; the holdfast is semidiscoidal and up to 0.15 m in diameter. Anatomically, the blade has the typical trumpet-shaped hyphae characteristic of the Chordaceae and derived foliose laminarialean species (i.e., Alariaceae/Laminariaceae/Lessoniaceae). No hair pits or mucilaginous structures were observed on the blade or stipe. No fertile sporophytes were collected, but abundant juvenile sporophytes were observed in the field. In the molecular phylogenetic analyses using chloroplast rbcL gene, nuclear ITS1-5.8S-ITS2 rDNA, and mitochondria nad6 DNA sequences, the new species (Aureophycus aleuticus gen. et sp. nov.) showed a closer relationship with Alariaceae of conventional taxonomy, or the "Group 1" clade of Lane et al. (2006) including Alaria and related taxa than with other groups, although the species was not clearly included in the group. Aureophycus may be a key species in elucidating the evolution of the Alariaceae within the Laminariales. Because of the lack of information on reproductive organs and insufficient resolution of the molecular analyses, we refrain from assigning the new species to a family, but we place the new species in a new genus in the Laminariales. PMID:27041620

  17. Taxonomy of the Proisotoma complex. V. Sexually dimorphic Ephemerotoma gen. nov. (Collembola: Isotomidae).

    PubMed

    Potapov, Mikhail; Kahrarian, Morteza; Deharveng, Louis; Shayanmehr, Masoumeh

    2015-01-01

    A new genus is proposed based on a new species from Iran, Ephemerotoma skarzynskii gen. et sp. nov., and three known species: E. huadongensis (Chen, 1985) comb. nov., E. multituberculata (Martynova, 1971) comb. nov. and E. porcella (Ellis, 1976) comb. nov. The genus shares the characters of Subisotoma Stach and Proctostephanus Börner and is distributed in southern areas of Eurasia (Eastern Mediterranean, Iran, Tajikistan, China). Ephemerotoma gen. nov. belongs to the Proisotoma-complex and is characterized by a simple maxillary palp, only 4 guards on labial papilla E and 2 prelabral chaetae. Four s-chaetae on Abd.V are arranged in two rows, two anterior and two posterior chaetae. All members of Ephemerotoma gen. nov. are redescribed or discussed based on type or fresh material, and a key to species of the genus is given. Scutisotoma potapovi Xie & Chen, 2008 is considered a synonym of E. huadongensis, while Proisotoma anopolitana is moved to the genus Proctostephanus. Sexual dimorphism is described for three species. PMID:26701434

  18. ConfGen: a conformational search method for efficient generation of bioactive conformers.

    PubMed

    Watts, K Shawn; Dalal, Pranav; Murphy, Robert B; Sherman, Woody; Friesner, Rich A; Shelley, John C

    2010-04-26

    We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. We define efficiency as the ability to generate a bioactive conformation within a small total number of conformations using a reasonable amount of computer time. The method combines physics-based force field calculations with empirically derived heuristics designed to achieve efficient searching and prioritization of the ligand's conformational space. While many parameter settings are supported, four modes spanning a range of speed and quality trades-offs are defined and characterized. The validation set used to test the method is composed of ligands from 667 crystal structures covering a broad array of target and ligand classes. With the fastest mode, ConfGen uses an average of 0.5 s per ligand and generates only 14.3 conformers per ligand, at least one of which lies within 2.0 A root-mean-squared deviation of the crystal structure for 96% of the ligands. The most computationally intensive mode raises this recovery rate to 99%, while taking 8 s per ligand. Combining multiple search modes to "fill-in" holes in the conformation space or energy minimizing using an all-atom force field each lead to improvements in the recovery rates at higher resolutions. Overall, ConfGen is at least as good as competing programs at high resolution and demonstrates higher efficiency at resolutions sufficient for many downstream applications, such as pharmacophore modeling. PMID:20373803

  19. GenColors-based comparative genome databases for small eukaryotic genomes

    PubMed Central

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. PMID:23193285

  20. Enhanced and synthetic vision for terminal maneuvering area NextGen operations

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-06-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  1. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    DOE PAGESBeta

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; et al

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number ofmore » geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.« less

  2. Transitioning Resolution Responsibility between the Controller and Automation Team in Simulated NextGen Separation Assurance

    NASA Technical Reports Server (NTRS)

    Cabrall, C.; Gomez, A.; Homola, J.; Hunt, S..; Martin, L.; Merccer, J.; Prevott, T.

    2013-01-01

    As part of an ongoing research effort on separation assurance and functional allocation in NextGen, a controller- in-the-loop study with ground-based automation was conducted at NASA Ames' Airspace Operations Laboratory in August 2012 to investigate the potential impact of introducing self-separating aircraft in progressively advanced NextGen timeframes. From this larger study, the current exploratory analysis of controller-automation interaction styles focuses on the last and most far-term time frame. Measurements were recorded that firstly verified the continued operational validity of this iteration of the ground-based functional allocation automation concept in forecast traffic densities up to 2x that of current day high altitude en-route sectors. Additionally, with greater levels of fully automated conflict detection and resolution as well as the introduction of intervention functionality, objective and subjective analyses showed a range of passive to active controller- automation interaction styles between the participants. Not only did the controllers work with the automation to meet their safety and capacity goals in the simulated future NextGen timeframe, they did so in different ways and with different attitudes of trust/use of the automation. Taken as a whole, the results showed that the prototyped controller-automation functional allocation framework was very flexible and successful overall.

  3. Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae)

    PubMed Central

    Kanzaki, Natsumi; Ragsdale, Erik J.; Susoy, Vladislav; Sommer, Ralf J.

    2014-01-01

    A new species of diplogastrid nematode, Leptojacobus dorci n. gen., n. sp., was isolated from adults of the stag beetle Dorcus ritsemae (Coleoptera: Lucanidae) that were purchased from a pet shop in Japan. Leptojacobus n. gen. is circumscribed by a very thin, delicate body and by a small stoma with minute armature. A combination of other stomatal characters, namely the division of the cheilostom into adradial plates, the symmetry of the subventral stegostomatal sectors, and the presence of a thin, conical dorsal tooth, further distinguishes Leptojacobus n. gen. from other genera of Diplogastridae. Phylogenetic analysis of nearly full-length SSU rRNA sequences support the new species, together with an isolate identified previously as Koerneria luziae, to be excluded from a clade including all other molecularly characterized diplogastrids with teeth and stomatal dimorphism. Therefore, the new species will be of importance for reconstruction of ancestral character histories in Diplogastridae, a family circumscribed by a suite of feeding-related novelties. PMID:24644371

  4. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    SciTech Connect

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; Spane, Frank A.; USA, Richland Washington; Gilmore, Tyler J.; USA, Richland Washington

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number of geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.

  5. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases

    PubMed Central

    V, Alexandar; Nayar, Pradeep G.; Murugesan, R.; Mary, Beaulah; P, Darshana; Ahmed, Shiek S. S. J.

    2015-01-01

    Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies. PMID:26624015

  6. Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  7. Modulus measurements in ordered Co-Al, Fe-Al, and Ni-Al alloys

    NASA Technical Reports Server (NTRS)

    Harmouche, M. R.; Wolfenden, A.

    1985-01-01

    The composition and/or temperature dependence of the dynamic Young's modulus for the ordered B2 Co-Al, Fe-Al, and Ni-Al aluminides has been investigated using the piezoelectric ultrasonic composite oscillator technique (PUCOT). The modulus has been measured in the composition interval 48.49 to 52.58 at. pct Co, 50.87 to 60.2 at. pct Fe, and 49.22 to 55.95 at. pct Ni for Co-Al, Fe-Al, and Ni-Al, respectively. The measured values for Co-Al are in the temperature interval 300 to 1300 K, while those for the other systems are for ambient temperature only. The data points show that Co-Al is stiffer than Fe-Al, which is stiffer than Ni-Al. The data points for Fe-Al and Ni-Al are slightly higher than those reported in the literature.

  8. FutureGen: Stepping-Stone to Sustainable Fossil-Fuel Power Generation

    SciTech Connect

    Zitney, S.E.

    2006-11-01

    This presentation will highlight the U.S. Department of Energy's FutureGen Initiative. The nearly $1 billion government-industry project is a stepping-stone toward future coal-fired power plants that will produce hydrogen and electricity with zero-emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. The initiative is a response to a presidential directive to develop a hydrogen economy by drawing upon the best scientific research to address the issue of global climate change. The FutureGen plant will be based on cutting-edge power generation technology as well as advanced carbon capture and sequestration systems. The centerpiece of the project will be coal gasification technology that can eliminate common air pollutants such as sulfur dioxide and nitrogen oxides and convert them to useable by-products. Gasification will convert coal into a highly enriched hydrogen gas, which can be burned much more cleanly than directly burning the coal itself. Alternatively, the hydrogen can be used in a fuel cell to produce ultra-clean electricity, or fed to a refinery to help upgrade petroleum products. Carbon sequestration will also be a key feature that will set the Futuregen plant apart from other electric power plant projects. The initial goal will be to capture 90 percent of the plant's carbon dioxide, but capture of nearly 100 percent may be possible with advanced technologies. Once captured, the carbon dioxide will be injected as a compressed fluid deep underground, perhaps into saline reservoirs. It could even be injected into oil or gas reservoirs, or into unmineable coal seams, to enhance petroleum or coalbed methane recovery. The ultimate goal for the FutureGen plant is to show how new technology can eliminate environmental concerns over the future use of

  9. Processing the loblolly pine PtGen2 cDNA microarray.

    PubMed

    Lorenz, W Walter; Yu, Yuan-Sheng; Simões, Marta; Dean, Jeffrey F D

    2009-01-01

    PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root tissues, but also from needle and stem. PtGen2 has been tested by hybridizing different Cy-dye labeled conifer target cDNAs, using both amplified and non-amplified indirect labeling methods, and also tested with a number of hybridization and washing conditions. This video focuses on the handling and processing of slides before and after pre-hybridization, as well as after hybridization, using some modifications to procedures developed previously. Also included, in text form only, are the protocols used for the generation, labeling and clean up of target cDNA s, as well as information on software used for downstream data processing. PtGen2 is printed with a proprietary print buffer that contains high concentrations of salt that can be difficult to remove completely. The slides are washed first in a warm SDS solution prior to pre-hybridization. After pre-hybridization, the slides are washed vigorously in several changes of water to complete removal of remaining salts. LifterSlips are then cleaned and positioned on the slides and labeled cDNA is carefully loaded onto the microarray by way of capillary action which provides for even distribution of the sample across the slide, and reduces the chance of bubble incorporation. Hybridization of targets to the array is done at 48 degrees C in high humidity conditions. After hybridization, a series of standard washes are done at 53 degrees C and room temperature for extended times. Processing PtGen2 slides using this technique reduces salt and SDS-derived artifacts often seen when the array is processed less rigorously. Hybridizing targets derived from several different conifer RNA

  10. Al Shanker Remembers.

    ERIC Educational Resources Information Center

    American Educator, 2000

    2000-01-01

    In a 1996 interview shortly before his death, Al Shanker, longtime president of the American Federation of Teachers, discussed such topics as: his own educational experiences; how he learned about political fighting in the Boy Scouts; the appeal of socialism; multinational corporations and the nation state; teaching tough students; and John Dewey…

  11. ALS renewal moves forward

    NASA Astrophysics Data System (ADS)

    Falcone, R. W.; Feinberg, B.; Hussain, Z.; Kirz, J.; Krebs, G. F.; Padmore, H. A.; Robin, D. S.; Robinson, A. L.

    2007-11-01

    As the result of an extensive long-term planning process involving all its stakeholders—management, staff, and users—the ALS has seen its future and is aggressively moving ahead to implement its vision for keeping the facility at the cutting edge for the next 2-3 decades. The evolving strategic plan now in place aims to renew the ALS so it can address a new generation of fundamental questions about size dependent and dimensional-confinement phenomena at the nanoscale; correlation and complexity in physical, biological, and environmental systems; and temporal evolution, assembly, dynamics and ultrafast phenomena. The renewal spans three areas: (1) increased staffing at beamlines to support the growing user community and safety professionals to keep an increasingly complex facility hazard free; (2) implementing advances in accelerator, insertion device, beamline, and detector technology that will make it possible for ALS users to address emerging grand scientific and technological challenges with incisive world-class tools; and (3) construction of a user support building and guest housing that will increase the safety and user friendliness of the ALS by providing users office, meeting, experiment staging, and laboratory space for their work and on-site accommodations at reasonable rates.

  12. Fosetyl-al

    Integrated Risk Information System (IRIS)

    Fosetyl - al ; CASRN 39148 - 24 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Ef

  13. Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup.

    PubMed

    Overby, C L; Heale, B; Aronson, S; Cherry, J M; Dwight, S; Milosavljevic, A; Nelson, T; Niehaus, A; Weaver, M A; Ramos, E M; Williams, M S

    2016-02-01

    The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded collaborative program that brings together a variety of projects designed to provide high-quality, curated information on clinically relevant genes and variants. ClinGen's EHR (Electronic Health Record) Workgroup aims to ensure that ClinGen is accessible to providers and patients through EHR and related systems. This article describes the current scope of these efforts and progress to date. The ClinGen public portal can be accessed at www.clinicalgenome.org. PMID:26418054

  14. Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.

    PubMed

    Kaur, Sukhpreet; Yawar, Mir; Kumar, P Anil; Suresh, K

    2014-03-01

    A Gram-stain-positive, rod-shaped, spore-forming and strictly anaerobic bacterium, designated UB-B.2(T), was isolated from an industrial effluent anaerobic digester sample. It grew optimally at 30 °C and pH 7.0. Comparative analysis of the 16S rRNA gene sequence confirmed that strain UB-B.2(T) was closely related to Clostridium hathewayi DSM 13479(T) (97.84% similarity), a member of rRNA gene cluster XIVa of the genus Clostridium, and formed a coherent cluster with other related members of the Blautia (Clostridium) coccoides rRNA group in phylogenetic analyses. The end products of glucose fermentation by strain UB-B.2(T) were acetate and propionate. The G+C content of the DNA was 51.4 mol%. Although strain UB-B.2(T) showed 97.8% 16S rRNA gene sequence identity to the type strain of C. hathewayi, it exhibited only 38.4% relatedness at the whole-genome level. It also showed differences from its closest phylogenetic relative, C. hathewayi DSM 13479(T), in phenotypic characteristics such as hydrolysis of aesculin, starch and urea and fermentation end products. Both strains showed phenotypic differences from the members of rRNA gene cluster XIVa of the genus Clostridium. Based on these differences, C. hathewayi DSM 13479(T) and strain UB-B.2(T) were identified as representatives of a new genus of the family Clostridiaceae. Thus, we propose the reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov., the type species of the new genus (type strain DSM 13479(T) = CCUG 43506(T) = MTCC 10951(T)). Strain UB-B.2(T) ( = MTCC 11101(T) = DSM 24995(T)) is assigned to the novel species Hungatella effluvii gen. nov., sp. nov as the type strain. PMID:24186873

  15. ALS Project Management Manual

    SciTech Connect

    Krupnick, Jim; Harkins, Joe

    2000-05-01

    This manual has been prepared to help establish a consistent baseline of management practices across all ALS projects. It describes the initial process of planning a project, with a specific focus on the production of a formal project plan. We feel that the primary weakness in ALS project management efforts to date stems from a failure to appreciate the importance of ''up-front'' project planning. In this document, we present a guide (with examples) to preparing the documents necessary to properly plan, monitor, and control a project's activities. While following the manual will certainly not guarantee good project management, failure to address the issues we raise will dramatically reduce the chance of success. Here we define success as meeting the technical goals on schedule and within the prescribed budget.

  16. ALS insertion devices

    SciTech Connect

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

    1990-11-01

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

  17. Ausbildung als zentrale Aufgabe

    NASA Astrophysics Data System (ADS)

    Krämer, Walter; Schmerbach, Sibylle

    Anders als Lesen und Schreiben zählen Grundkenntnisse in Statistik heute noch nicht zu den Voraussetzungen einer sinnvollen Teilhabe am Sozialgeschehen. Und auch in der akademischen Statistik-Ausbildung gibt es noch einiges zu tun. Das vorliegende Kapitel zeichnet die Geschichte dieser akademischen Ausbildung an deutschen Universitäten nach dem zweiten Weltkrieg nach, stellt aktuelle Defizite vor und weist auf mögliche Verbesserungen hin.

  18. Normally-ON/OFF AlN/GaN High Electron Mobility Transistors

    SciTech Connect

    Chang, C. Y.; Lo, C. F.; Ren, F.; Pearton, S. J.; Kravchenko, Ivan I; Dabiran, A. M.; Cui, B.; Chow, P. P.

    2010-01-01

    We report on the novel normally-on/off AlN/GaN high electron mobility transistors (HEMTs) grown by plasma-assisted molecular beam epitaxy. With simple oxygen plasma exposure, the threshold voltage can be tuned from -2.76 V to +1.13 V depending on the treatment time. The gate current was reduced and gate current-voltage curve show metal-oxide semiconductor diode-like characteris-tics after oxygen plasma exposure. The extrinsic trans-conductance of HEMTs decreased with increasing oxy-gen plasma exposure time due to the thicker Al oxide formed on the gate area. The unity current gain cut-off frequency, fT, and the maximum frequency of oscillation, fmax, were 20.4 GHz and 36.5 GHz, respectively, for a enhancement-mode HEMT with the gate dimension of 0.4 100 m2.

  19. iGen 0.1: the automated generation of a parameterisation of entrainment in marine stratocumulus

    NASA Astrophysics Data System (ADS)

    Tang, D. F.; Dobbie, S.

    2011-09-01

    In a previous paper we described a new technique for automatically generating parameterisations using a program called iGen. iGen generates parameterisations by analysing the source code of a~high resolution model that resolves the physics to be parameterised. In order to demonstrate that this technique scales up to deal with models of realistic complexity we have used iGen to generate a parameterisation of entrainment in marine stratocumulus. We describe how iGen was used to analyse the source code of an eddy resolving model (ERM) and generate a parameterisation of entrainment velocity in marine stratocumulus in terms of the large-scale state of the boundary layer. The parameterisation was tested against results from the DYCOMS-II intercomparison of ERM models and iGen's parameterisation of mean entrainment velocity was found to be 5.27 × 10-3 ± 0.62 × 10-3 m s-1 compared to 5.2 × 10-3 ± 0.8 × 10-3 m s-1 for the DYCOMS-II ensemble of large eddy simulation (LES) models.

  20. GEN1 from a Thermophilic Fungus Is Functionally Closely Similar to Non-Eukaryotic Junction-Resolving Enzymes

    PubMed Central

    Freeman, Alasdair D.J.; Liu, Yijin; Déclais, Anne-Cécile; Gartner, Anton; Lilley, David M.J.

    2014-01-01

    Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1 nt 3′ to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. PMID:25315822

  1. Data-Link and Surface Map Traffic Intent Displays for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Arthur, Jarvis J., III; Jones, Deise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  2. Next Gen NEAR: Near Earth Asteroid Human Robotic Precursor Mission Concept

    NASA Technical Reports Server (NTRS)

    Rivkin, Andrew S.; Kirby, Karen; Cheng, Andrew F.; Gold, Robert; Kelly, Daniel; Reed, Cheryl; Abell, Paul; Garvin, James; Landis, Rob

    2012-01-01

    Asteroids have long held the attention of the planetary science community. In particular, asteroids that evolve into orbits near that of Earth, called near-Earth objects (NEO), are of high interest as potential targets for exploration due to the relative ease (in terms of delta V) to reach them. NASA's Flexible Path calls for missions and experiments to be conducted as intermediate steps towards the eventual goal of human exploration of Mars; piloted missions to NEOs are such example. A human NEO mission is a valuable exploratory step beyond the Earth-Moon system enhancing capabilities that surpass our current experience, while also developing infrastructure for future mars exploration capabilities. To prepare for a human rendezvous with an NEO, NASA is interested in pursuing a responsible program of robotic NEO precursor missions. Next Gen NEAR is such a mission, building on the NEAR Shoemaker mission experience at the JHU/APL Space Department, to provide an affordable, low risk solution with quick data return. Next Gen NEAR proposes to make measurements needed for human exploration to asteroids: to demonstrate proximity operations, to quantify hazards for human exploration and to characterize an environment at a near-Earth asteroid representative of those that may be future human destinations. The Johns Hopkins University Applied Physics Laboratory has demonstrated exploration-driven mission feasibility by developing a versatile spacecraft design concept using conventional technologies that satisfies a set of science, exploration and mission objectives defined by a concept development team in the summer of 2010. We will describe the mission concept and spacecraft architecture in detail. Configuration options were compared with the mission goals and objectives in order to select the spacecraft design concept that provides the lowest cost, lowest implementation risk, simplest operation and the most benefit for the mission implementation. The Next Gen NEAR

  3. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  4. Electromagnetic Interactions GenERalized (EIGER): Applications at Johnson Space Center

    NASA Technical Reports Server (NTRS)

    Dobbins, Justin A.; Fink, Patrick W.; Scully, Robert C.

    2003-01-01

    This slide presentation reviews the software framework for the analysis and design of complex electromagnetic systems. The system called Electromagnetic Interactions GenERalized (EIGER) is a hybrid finite element solution for wave equations and deru=ives boundary element solutions for integral equation formulations. Written in Fortran 90 Eiger uses object-oriented design methods to abstract key analysis components. EIGER has been applied to higher order modeling for analysis of antennas to assist in the design of the antennas of a mini-AERCam. EIGER might also be used to model the Ion Cyclotron Resonant heating stage for the VAriable Specific Impulse Magnetoplasma Rocket (VASIMR).

  5. Drancourtella massiliensis gen. nov., sp. nov. isolated from fresh healthy human faecal sample from South France.

    PubMed

    Durand, G A; Lagier, J-C; Khelaifia, S; Armstrong, N; Robert, C; Rathored, J; Fournier, P-E; Raoult, D

    2016-05-01

    Strain GD1(T) gen. nov., sp. nov., is the type strain of the newly proposed genus and species Drancourtella massiliensis, belonging to the Clostridiales order. This strain, isolated from the stool of a healthy person, is a Gram-positive rod, oxygen intolerant and nonmotile, with spore-forming activity. The features of this organism and its genome sequence are described. The draft genome is 3 057 334 bp long with 45.24% G + C content; it contains 2861 protein-coding genes and 64 RNA genes. PMID:27257490

  6. Gen IV Materials Handbook Functionalities and Operation (2B) Handbook Version 2.0

    SciTech Connect

    Ren, Weiju

    2011-08-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  7. Gen IV Materials Handbook Functionalities and Operation (4A) Handbook Version 4.0

    SciTech Connect

    Ren, Weiju

    2013-09-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  8. Cyathoshiva amaleshi gen. n. sp. n. (Nematoda: Cyatholaimidae) from the coast of India.

    PubMed

    Datta, Tridip Kumar; Miljutin, Dmitry M; Chakraborty, Susanta Kumar; Mohapatra, Anil

    2016-01-01

    A new genus, Cyathoshiva, of free-living marine nematodes from the subfamily Cyatholaiminae (family Cyatholaimidae, order Chromadorida), is described from the Indian coast. The new genus differs from other known Cyatholaiminae genera in having a unique combination of morphological characters: buccal cavity with well-developed dorsal tooth and two subventral teeth, proximally unpaired gubernaculum and non-cup shaped supplements. The type species Cyathoshiva amaleshi gen. n. sp. n. is characterized by having multispiral amphids with 4.5 turns, punctated cuticle with a weak lateral differentiation, a conical tail, three supplements possessing both tubular and setoid parts, and a gubernaculum with a serrated and dentate distal end. PMID:27395607

  9. Irradiation effects in oxide dispersion strengthened (ODS) Ni-base alloys for Gen. IV nuclear reactors

    NASA Astrophysics Data System (ADS)

    Oono, Naoko; Ukai, Shigeharu; Kondo, Sosuke; Hashitomi, Okinobu; Kimura, Akihiko

    2015-10-01

    Oxide particle dispersion strengthened (ODS) Ni-base alloys are irradiated by using simulation technique (Fe/He dual-ion irradiation) to investigate the reliability to Gen. IV high-temperature reactors. The fine oxide particles with less than 10 nm in average size and approximately 8.0 × 1022 m-3 in number density remained after 101 dpa irradiation. The tiny helium bubbles were inside grains, not at grain-boundaries; it is advantageous effect of oxide particles which trap the helium atoms at the particle-matrix interface. Ni-base ODS alloys demonstrated their great ability to overcome He embrittlement.

  10. Modeling Off-Nominal Recovery in NextGen Terminal-Area Operations

    NASA Technical Reports Server (NTRS)

    Callantine, Todd J.

    2011-01-01

    Robust schedule-based arrival management requires efficient recovery from off-nominal situations. This paper presents research on modeling off-nominal situations and plans for recovering from them using TRAC, a route/airspace design, fast-time simulation, and analysis tool for studying NextGen trajectory-based operations. The paper provides an overview of a schedule-based arrival-management concept and supporting controller tools, then describes TRAC implementations of methods for constructing off-nominal scenarios, generating trajectory options to meet scheduling constraints, and automatically producing recovery plans.

  11. Eonandeva gen. nov., a new distinctive genus from Eocene Baltic amber (Diptera: Chironomidae).

    PubMed

    Zakrzewska, Marta; Giłka, Wojciech

    2015-01-01

    A new fossil genus, Eonandeva gen. nov., with two new species: E. helva sp. nov. (type for the genus) and E. latistyla sp. nov., is described from Eocene Baltic amber (~45-40 Ma). Adult males of both new species show the wing venation pattern, shape and chaetotaxy typical for the tribe Tanytarsini. The characters defined as prior apomorphies for the new genus--the gonostylus with a subapical flattened lobe and the stout, strongly elongated superior volsella--separate Eonandeva from the closely related extant genus Nandeva Wiedenbrug, Reiss et Fittkau, 1998. PMID:26624727

  12. GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS.

    PubMed

    Hoppmann, Anselm S; Schlosser, Pascal; Backofen, Rolf; Lausch, Ekkehart; Köttgen, Anna

    2016-01-01

    Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS). For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and systematically phenotyped mice. Based on selected murine phenotypes for which human GWAS data for corresponding traits were publicly available, several candidate gene input lists were derived. Using GenToS for the investigation of candidate genes underlying murine skeletal phenotypes in data from a large human discovery GWAS meta-analysis of bone mineral density resulted in the identification of significantly associated variants in 29 genes. Index variants in 28 of these loci were subsequently replicated in an independent GWAS replication step, highlighting that they are true positive associations. One signal, COL11A1, has not been discovered through GWAS so far and represents a novel human candidate gene for altered bone mineral density. The number of observed genes that contained significant SNP associations in human GWAS based on murine candidate gene input lists was much greater than the number expected by chance across several complex human traits (enrichment p-value as low as 10-10). Gen

  13. Optical gain characteristics in Al-rich AlGaN/AlN quantum wells

    SciTech Connect

    Oto, Takao; Banal, Ryan G.; Funato, Mitsuru; Kawakami, Yoichi

    2014-05-05

    The optical gain characteristics of Al-rich AlGaN/AlN quantum wells (QWs) were assessed by the variable stripe length method at room temperature. An Al{sub 0.79}Ga{sub 0.21}N/AlN QW with a well width of 5 nm had a large optical gain of 140 cm{sup −1}. Increasing the excitation length induced a redshift due to the gain consumption and the consequent saturation of the amplified spontaneous emission. Moreover, a change in the dominant gain polarization with Al composition, which was attributed to switching of the valence band ordering of strained AlGaN/AlN QWs at Al compositions of ∼0.8, was experimentally demonstrated.

  14. 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung.

    PubMed

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-11-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. PMID:26130332

  15. AL Amyloidosis and Agent Orange

    MedlinePlus

    ... for survivors' benefits . Research on AL amyloidosis and herbicides The Health and Medicine Division (formally known as ... to the compounds of interest found in the herbicide Agent Orange and AL amyloidosis." VA made a ...

  16. Al(+)-ligand binding energies

    NASA Technical Reports Server (NTRS)

    Sodupe, M.; Bauschlicher, Charles W., Jr.

    1991-01-01

    Ab initio calculations are used to optimize the structure and determine the binding energies of Al(+) to a series of ligands. For Al(+)-CN, the bonding was found to have a large covalent component. For the remaining ligands, the bonding is shown to be electrostatic in origin. The results obtained for Al(+) are compared with those previously reported for Mg(+).

  17. Interleukin-1- and Type I Interferon-Dependent Enhanced Immunogenicity of an NYVAC-HIV-1 Env-Gag-Pol-Nef Vaccine Vector with Dual Deletions of Type I and Type II Interferon-Binding Proteins

    PubMed Central

    Delaloye, Julie; Filali-Mouhim, Abdelali; Cameron, Mark J.; Haddad, Elias K.; Harari, Alexandre; Goulet, Jean-Pierre; Gomez, Carmen E.; Perdiguero, Beatriz; Esteban, Mariano; Pantaleo, Giuseppe; Roger, Thierry; Sékaly, Rafick-Pierre

    2015-01-01

    ABSTRACT NYVAC, a highly attenuated, replication-restricted poxvirus, is a safe and immunogenic vaccine vector. Deletion of immune evasion genes from the poxvirus genome is an attractive strategy for improving the immunogenic properties of poxviruses. Using systems biology approaches, we describe herein the enhanced immunological profile of NYVAC vectors expressing the HIV-1 clade C env, gag, pol, and nef genes (NYVAC-C) with single or double deletions of genes encoding type I (ΔB19R) or type II (ΔB8R) interferon (IFN)-binding proteins. Transcriptomic analyses of human monocytes infected with NYVAC-C, NYVAC-C with the B19R deletion (NYVAC-C-ΔB19R), or NYVAC-C with B8R and B19R deletions (NYVAC-C-ΔB8RB19R) revealed a concerted upregulation of innate immune pathways (IFN-stimulated genes [ISGs]) of increasing magnitude with NYVAC-C-ΔB19R and NYVAC-C-ΔB8RB19R than with NYVAC-C. Deletion of B8R and B19R resulted in an enhanced activation of IRF3, IRF7, and STAT1 and the robust production of type I IFNs and of ISGs, whose expression was inhibited by anti-type I IFN antibodies. Interestingly, NYVAC-C-ΔB8RB19R induced the production of much higher levels of proinflammatory cytokines (tumor necrosis factor [TNF], interleukin-6 [IL-6], and IL-8) than NYVAC-C or NYVAC-C-ΔB19R as well as a strong inflammasome response (caspase-1 and IL-1β) in infected monocytes. Top network analyses showed that this broad response mediated by the deletion of B8R and B19R was organized around two upregulated gene expression nodes (TNF and IRF7). Consistent with these findings, monocytes infected with NYVAC-C-ΔB8RB19R induced a stronger type I IFN-dependent and IL-1-dependent allogeneic CD4+ T cell response than monocytes infected with NYVAC-C or NYVAC-C-ΔB19R. Dual deletion of type I and type II IFN immune evasion genes in NYVAC markedly enhanced its immunogenic properties via its induction of the increased expression of type I IFNs and IL-1β and make it an attractive candidate HIV

  18. Al Jazirah, Sudan

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Al Jazirah (also Gezira) is one of the 26 states of Sudan. The state lies between the Blue Nile and the White Nile in the east-central region of the country. It is a well populated area suitable for agriculture. The area was at the southern end of Nubia and little is known about its ancient history and only limited archaeological work has been conducted in this area. The region has benefited from the Gezira Scheme, a program to foster cotton farming begun in 1925. At that time the Sennar Dam and numerous irrigation canals were built. Al Jazirah became the Sudan's major agricultural region with more than 2.5 million acres (10,000 km) under cultivation. The initial development project was semi-private, but the government nationalized it in 1950. Cotton production increased in the 1970s but by the 1990s increased wheat production has supplanted a third of the land formerly seeded with cotton.

    The image was acquired December 25, 2006, covers an area of 56 x 36.4 km, and is located near 14.5 degrees north latitude, 33.1 degrees east longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  19. Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut.

    PubMed

    Tidjani Alou, M; Nguyen, T-T; Armstrong, N; Rathored, J; Khelaifia, S; Raoult, D; Fournier, P-E; Lagier, J-C

    2016-07-01

    Numidum massiliense gen. nov., sp. nov., strain mt3(T) is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3 755 739 bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes. PMID:27354918

  20. A REVIEW ON CURRENT STATUS OF ALLOYS 617 AND 230 FOR GEN IV NUCLEAR REACTOR INTERNALS AND HEAT EXCHANGERS

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W

    2009-01-01

    Alloys 617 and 230 are currently identified as two leading candidate metallic materials in the down selection for applications at temperatures above 760 C in the Gen IV Nuclear Reactor Systems. Qualifying the materials requires significant information related to Codification, mechanical behavior modeling, metallurgical stability, environmental resistance, and many other aspects. In the present paper, material requirements for the Gen IV Nuclear Reactor Systems are discussed; certain available information regarding the two alloys under consideration for the intended applications are reviewed and analyzed. Suggestions are presented for further R&D activities for the materials selection.

  1. Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2013-01-01

    Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

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

    PubMed

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

    2016-09-01

    Two Cyanobacteria isolated from South Atlantic Ocean continental shelf deep water and from a marine green algae inhabiting the Admiralty Bay, King George Island, Antarctica were investigated based on morphological and ultrastructural traits, phylogeny of 16S rRNA gene sequences, secondary structure of the 16S-23S internal transcribed spacer regions and phylogenomic analyses. The majority of these evaluations demonstrated that both strains differ from the genera of cyanobacteria with validly published names and, therefore, supported the description of the novel genus as Aliterella gen. nov. The identity and phylogeny of 16S rRNA gene sequences, together with the secondary structure of D1D1' and BoxB intergenic regions, further supported the two strains representing distinct species: Aliterella atlantica gen. nov., sp. nov. (type SP469036, strain CENA595T) and Aliterella antarctica sp. nov. (type SP469035, strain CENA408T). The phylogenomic analysis of A. atlantica sp. nov. CENA595T, based on 21 protein sequences, revealed that this genus belongs to the cyanobacterial order Chroococcidiopsidales. The isolation and cultivation of two geographically distant unicellular members of a novel cyanobacterial genus and the sequenced genome of the type strain bring new insights into the current classification of the coccoid group, and into the reconstruction of their evolutionary history. PMID:27054834

  3. Aircraft deconfliction responsibility across en-route sectors in NextGen separation assurance

    NASA Astrophysics Data System (ADS)

    Cabrall, Christopher D.

    The subject of the current research is a Next Generation Air Transportation System (NextGen) concept that involves automated separation assurance developed to enable controllers to provide both safe and efficient air traffic services at much higher traffic densities than possible today. The study investigated the issue of how responsibility should be handled between controllers for the resolution of a conflict that is predicted to occur in a sector other than where it was detected. Two possibilities, a De-Conflicting AirPlanes procedure (DCAP) versus a De-Conflicting AirSpace procedure (DCAS), were examined under human-in-the-loop simulations with scripted aircraft conflicts. Results showed that the DCAS procedure was preferred and that participants experienced less verbal coordination and took less time to resolve conflicts. The results, however, did not reveal significant differences among other plane performance metrics between DCAP and DCAS. These results indicate that the demands of NextGen separation assurance might still be met with ownership and coordination procedures (e.g., DCAP) similar to today. Reducing verbal coordination requirements, however, and allowing separation assurance responsibilities to extend more seamlessly across sector boundaries (e.g., DCAS) would evidently be more acceptable to controllers.

  4. The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

    PubMed Central

    Adler, Priit; Aksoy, Irène; Anastassiadis, Konstantinos; Bader, Michael; Billon, Nathalie; Boeuf, Hélène; Bourillot, Pierre-Yves; Buchholz, Frank; Dani, Christian; Doss, Michael Xavier; Forrester, Lesley; Gitton, Murielle; Henrique, Domingos; Hescheler, Jürgen; Himmelbauer, Heinz; Hübner, Norbert; Karantzali, Efthimia; Kretsovali, Androniki; Lubitz, Sandra; Pradier, Laurent; Rai, Meena; Reimand, Jüri; Rolletschek, Alexandra; Sachinidis, Agapios; Savatier, Pierre; Stewart, Francis; Storm, Mike P.; Trouillas, Marina; Vilo, Jaak; Welham, Melanie J.; Winkler, Johannes; Wobus, Anna M.; Hatzopoulos, Antonis K.

    2009-01-01

    Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the “Functional Genomics in Embryonic Stem Cells” consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in “Expression Waves” and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells. PMID:19727443

  5. GenSSI: a software toolbox for structural identifiability analysis of biological models

    PubMed Central

    Chiş, Oana; Banga, Julio R.; Balsa-Canto, Eva

    2011-01-01

    Summary: Mathematical modeling has a key role in systems biology. Model building is often regarded as an iterative loop involving several tasks, among which the estimation of unknown parameters of the model from a certain set of experimental data is of central importance. This problem of parameter estimation has many possible pitfalls, and modelers should be very careful to avoid them. Many of such difficulties arise from a fundamental (yet often overlooked) property: the so-called structural (or a priori) identifiability, which considers the uniqueness of the estimated parameters. Obviously, the structural identifiability of any tentative model should be checked at the beginning of the model building loop. However, checking this property for arbitrary non-linear dynamic models is not an easy task. Here we present a software toolbox, GenSSI (Generating Series for testing Structural Identifiability), which enables non-expert users to carry out such analysis. The toolbox runs under the popular MATLAB environment and is accompanied by detailed documentation and relevant examples. Availability: The GenSSI toolbox and the related documentation are available at http://www.iim.csic.es/%7Egenssi. Contact: ebalsa@iim.csic.es PMID:21784792

  6. Structural materials for Gen-IV nuclear reactors: Challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Murty, K. L.; Charit, I.

    2008-12-01

    Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

  7. Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 Performance Evaluation Final Report

    SciTech Connect

    Jon P. Christophersen; Ira Bloom; Edward V. Thomas; Kevin L. Gering; Gary L. Henriksen; Vincent S. Battaglia; David Howell

    2006-07-01

    The Advanced Technology Development Program has completed performance testing of the second generation of lithium-ion cells (i.e., Gen 2 cells). The 18650-size Gen 2 cells, with a baseline and variant chemistry, were distributed over a matrix consisting of three states-of-charge (SOCs) (60, 80, and 100% SOC), four temperatures (25, 35, 45, and 55°C), and three life tests (calendar-, cycle-, and accelerated-life). The calendar- and accelerated-life cells were clamped at an open-circuit voltage corresponding to the designated SOC and were subjected to a once-per-day pulse profile. The cycle-life cells were continuously pulsed using a profile that was centered around 60% SOC. Life testing was interrupted every four weeks for reference performance tests (RPTs), which were used to quantify changes in cell degradation as a function of aging. The RPTs generally consisted of C1/1 and C1/25 static capacity tests, a low-current hybrid pulse power characterization test, and electrochemical impedance spectroscopy. The rate of cell degradation generally increased with increasing test temperature, and SOC. It was also usually slowest for the calendar-life cells and fastest for the accelerated-life cells. Detailed capacity-, power-, and impedance-based performance results are reported.

  8. Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 GDR Performance Evaluation Report

    SciTech Connect

    Jon P. Christophersen; Chinh D. Ho; Gary L. Henriksen; David Howell

    2006-07-01

    The Advanced Technology Development Program has completed the performance evaluation of the second generation of lithium-ion cells (i.e., Gen 2 cells). This report documents the testing and analysis of the Gen 2 GDR cells, which were used to learn and debug the newly developed Technology Life Verification Test Manual. The purpose of the manual is to project a 15-year, 150,000 mile battery life capability with a 90% confidence interval using predictive models and short-term testing. The GDR cells were divided into two different matrices. The core-life test matrix consisted of calendar- and cycle-life cells with various changes to the four major acceleration factors (temperature, state-of-charge, throughput, and power rating). The supplemental-life test matrix consisted of cells subjected either to a path dependence study, or a comparison between the standard hybrid pulse power characterization test and the newly-developed minimum pulse power characterization test. Resistance and capacity results are reported.

  9. The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

    PubMed

    Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

    2015-12-01

    Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. PMID:26192091

  10. A Precision Optical Calibration Module (POCAM) for IceCube-Gen2

    NASA Astrophysics Data System (ADS)

    Jurkovič, M.; Abraham, K.; Holzapfel, K.; Krings, K.; Resconi, E.; Veenkamp, J.

    2016-04-01

    We present here a new concept of an in-situ self-calibrated isotropic light source for the future IceCube-Gen2 neutrino detector called the Precision Optical Calibration Module (POCAM). IceCube-Gen2 will be a matrix of light sensors buried deep in the ice at the geographic South Pole. The timing, the location, and the amount of Cherenkov light deposited by the secondary charged particles are used to reconstruct the properties of the incident neutrinos. The reconstruction relies on a detailed detector model that includes the response of optical modules to the Cherenkov light, as well as the optical properties of the detector medium - the natural Antarctic ice. To understand these properties, both natural, and artificial light sources are already used for calibration. New calibration devices are being developed in order to improve the precision of these measurements, and reduce systematic errors. The POCAM concept is based on the principle of an inverted integrating sphere. The main components are LEDs emitting light at several wavelengths and solid-state light sensors e.g. calibrated photodiode or silicon photomultipliers to monitor the emitted light intensity. We report on the current status of the POCAM R&D.

  11. Studies of 27Al NMR in EuAl4

    NASA Astrophysics Data System (ADS)

    Niki, H.; Nakamura, S.; Higa, N.; Kuroshima, H.; Toji, T.; Yogi, M.; Nakamura, A.; Hedo, M.; Nakama, T.; Ōnuki, Y.; Harima, H.

    2015-03-01

    EuAl4 orders antiferromagnetically at TN ≈ 16 K with an effective magnetic moment of 8.02 μB. In the paramagnetic phase, the magnetic susceptibility of EuAl4 follows the Curie-Weiss law with a positive Curie-Weiss temperature θP = +14 K. The antiferromagnetic state is changed into the field induced ferromagnetic state at a critical field Hc of approximately 2 T. In order to microscopically investigate the magnetic and electronic properties in EuAl4, the NMR measurements of EuAl4 have been carried out at temperatures between 2 and 300 K, applying an external magnetic field of approximately 6.5 T. The 27Al NMR spectra corresponding to Al(I) and Al(II) sites are obtained. From the 27Al NMR spectra, the isotropic part Kiso and anisotropic part Kaniso of Knight shift, and nuclear quadrupole frequncy νQ are obtained. The Kiso and Kaniso shift to negative side with decreasing temperature due to the RKKY interaction. These temperature dependences follow the Curie-Weiss law with θP = +14 K, which is consistent with that of the magnetic susceptibility. From the K - χ plot, the values of the hyperfine fields Hhf_iso and Hhf_aniso are -3.231 and -0.162 kOe/μB for Al(I) site, and -1.823 and -0.264 kOe/μB for Al(II) site, respectively. The values of νQ of 27Al nucleus for Al(I) and Al(II) sites are approximately 0.865 and 0.409 MHz, respectively. The nuclear relaxation time T1 of 27Al NMR for both sites is almost constant in the paramagnetic phase, while the value of 1/T1 is abruptly decreased in the ordered ferromagnetic state.

  12. Interfacial characterization of Al-Al thermocompression bonds

    NASA Astrophysics Data System (ADS)

    Malik, N.; Carvalho, P. A.; Poppe, E.; Finstad, T. G.

    2016-05-01

    Interfaces formed by Al-Al thermocompression bonding were studied by the transmission electron microscopy. Si wafer pairs having patterned bonding frames were bonded using Al films deposited on Si or SiO2 as intermediate bonding media. A bond force of 36 or 60 kN at bonding temperatures ranging from 400-550 °C was applied for a duration of 60 min. Differences in the bonded interfaces of 200 μm wide sealing frames were investigated. It was observed that the interface had voids for bonding with 36 kN at 400 °C for Al deposited both on Si and on SiO2. However, the dicing yield was 33% for Al on Si and 98% for Al on SiO2, attesting for the higher quality of the latter bonds. Both a bond force of 60 kN applied at 400 °C and a bond force of 36 kN applied at 550 °C resulted in completely bonded frames with dicing yields of, respectively, 100% and 96%. A high density of long dislocations in the Al grains was observed for the 60 kN case, while the higher temperature resulted in grain boundary rotation away from the original Al-Al interface towards more stable configurations. Possible bonding mechanisms and reasons for the large difference in bonding quality of the Al films deposited on Si or SiO2 are discussed.

  13. Proposal for Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological...

  14. Studies of 27Al NMR in SrAl4

    NASA Astrophysics Data System (ADS)

    Niki, Haruo; Higa, Nonoka; Kuroshima, Hiroko; Toji, Tatsuki; Morishima, Mach; Minei, Motofumi; Yogi, Mamoru; Nakamura, Ai; Hedo, Masato; Nakama, Takao; Ōnuki, Yoshichika; Harima, Hisatomo

    A charge density wave (CDW) transition at TCDW = 243 K and a structural phase (SP) transition at approximately 100 K occur in SrAl4 with the BaAl4-type body center tetragonal structure, which is the divalent and non-4f electron reference compound of EuAl4. To understand the behaviors of the CDW and SP transitions, the 27Al NMR measurements using a single crystal and a powder sample of SrAl4 have been carried out. The line width below TCDW is modulated by an electrical quadruple interaction between 27Al nucleus and CDW charge modulation. The incommensurate CDW state below TCDW changes into a different structure below TSP. The temperature dependences of Knight shifts of 27Al(I) and 27Al(II) show the different behaviors. The temperature variation of 27Al(I) Knight shift shows anomalies at the CDW and SP transition temperatures, revealing the shift to negative side below TCDW, which is attributable to the core polarization of the d-electrons. However, 27Al(II) Knight shift keeps almost constant except for the small shift due to the SP transition. The 1/T1T of 27Al(I) indicates the obvious changes due to the CDW and SP transitions, while that of 27Al(II) takes a constant value. The density of state at the Fermi level at Al(I) site below 60 K would be about 0.9 times less than that above TCDW.

  15. ALS Performance Summary - Update

    SciTech Connect

    Waters, A M; Brown, W D; Martz, Jr., H E

    2004-09-30

    High Energy Density Physics (HEDP) experiments play an important role in corroborating the improved physics codes that underlie LLNL's Stockpile Stewardship mission. Conducting these experiments, whether on the National Ignition Facility (NIF) or another national facility such as Omega, will require not only improvement in the diagnostics for measuring the experiment, but also detailed knowledge of the as-built target components and assemblies themselves. To assist in this effort, a defined set of well-known reference standards designed to represent a range of HEDP targets have been built and are being used to quantify the performance of different characterization techniques [Hibbard, et al. 2004]. Without the critical step of using reference standards for qualifying characterization tools there can be no verification of either commercial or internally-developed characterization techniques and thus an uncertainty in the input to the physics code models would exist.

  16. Doppelthydrophile Blockcopolymere als Mineralisationstemplate

    NASA Astrophysics Data System (ADS)

    Kasparova, Pavla

    2002-07-01

    Die vorliegende Arbeit beschäftigt sich mit der Synthese und den Eigenschaften von doppelthydrophilen Blockcopolymeren und ihrer Anwendung in einem biomimetischen Mineralisationsprozeß von Calciumcarbonat und Bariumsulfat. Doppelthydrophile Blockcopolymere bestehen aus einem hydrophilen Block, der nicht mit Mineralien wechselwirkt und einem zweiten Polyelektrolyt-Block, der stark mit Mineraloberflächen wechselwirkt. Diese Blockcopolymere wurden durch ringöffnende Polymerisation von N-carboxyanhydriden (NCA's) und a-methoxy-ω-amino[poly(ethylene glycol)] PEG-NH2 als Initiator hergestellt. Die hergestellten Blockcopolymere wurden als effektive Wachstumsmodifikatoren für die Kristallisation von Calciumcarbonat und Bariumsulfat Mineralien eingesetzt. Die so erhaltenen Mineralpartikel (Kugeln, Hantel, eiförmige Partikel) wurden durch Lichtmikroskopie in Lösung, SEM und TEM charakterisiert. Röntgenweitwinkelstreuung (WAXS) wurde verwendet, um die Modifikation von Calciumcarbonat zu ermitteln und die Größe der Calciumcarbonat- und Bariumsulfat-Nanopartikel zu ermitteln. This work describes the synthesis and characterization of double hydrophilic block copolymers and their use in a biomimetic mineralization process of Calcium Carbonate and Barium Sulfate. Double hydrophilic block copolymers consist of a hydrophilic block that does not interact with minerals and another hydrophilic polyelectrolyte block that strongly interacts with mineral surfaces. These polymers were synthesised via ring opening polymerisation of N-carboxyanhydride (NCA), and the first hydrophilic block a-methoxy-ω-amino[poly(ethylene glycol)] PEG-NH2 was used as an initiator. The prepared block copolymers were used as effective crystal growth modifiers to control the crystallization of Calcium Carbonate and Barium Sulfate minerals. The resulting mineral particles (spheres, dumbbells, egg-like particles) were characterised by light microscopy in solution, by SEM, and by TEM. X-Ray scattering

  17. Microstructural evolution and mechanical properties of an Fe-18Ni-16Cr-4Al base alloy during aging at 950°C

    NASA Astrophysics Data System (ADS)

    Wang, Man; Sun, Yong-duo; Feng, Jing-kai; Zhang, Rui-qian; Tang, Rui; Zhou, Zhang-jian

    2016-03-01

    The development of Gen-IV nuclear systems and ultra-supercritical power plants proposes greater demands on structural materials used for key components. An Fe-18Ni-16Cr-4Al (316-base) alumina-forming austenitic steel was developed in our laboratory. Its microstructural evolution and mechanical properties during aging at 950°C were investigated subsequently. Micro-structural changes were characterized by scanning electron microscopy, electron backscatter diffraction, and transmission electron microscopy. Needle-shaped NiAl particles begin to precipitate in austenite after ageing for 10 h, whereas round NiAl particles in ferrite are coarsened during aging. Precipitates of NiAl with different shapes in different matrices result from differences in lattice misfits. The tensile plasticity increases by 32.4% after aging because of the improvement in the percentage of coincidence site lattice grain boundaries, whereas the tensile strength remains relatively high at approximately 790 MPa.

  18. Protosclerogibba australis gen. et sp. nov., new genus and species of sclerogibbid wasps (Hymenoptera: Sclerogibbidae) from South Africa.

    PubMed

    Olmi, Massimo; Marletta, Alessandro; Guglielmino, Adalgisa; Speranza, Stefano

    2016-01-01

    Protosclerogibba australis Olmi, Marletta, Guglielmino & Speranza, gen. et sp. nov. is described and illustrated from specimens collected in Kimberley (Northern Cape Province, South Africa). The female of the new taxon is the first micropterous sclerogibbid. Females of other extant Sclerogibbidae are always apterous, whereas fossil females can be apterous or macropterous. PMID:27394292

  19. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  20. 77 FR 52352 - Notice of Intent To Prepare an Environmental Impact Statement for the Rio Mesa Gen-Tie Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... Gen-Tie Project and Possible Land Use Plan Amendment, Riverside County, CA AGENCY: Bureau of Land..., special management areas, land use, noise, paleontological resources, public health, socioeconomic, soils.... If a land use plan amendment is necessary, the BLM will integrate the land use planning process...

  1. Stoibocephalum n. gen. (Cestoda: Lecanicephalidea) from the sharkray, Rhina ancylostoma Bloch & Schneider (Elasmobranchii: Rhinopristiformes), from northern Australia.

    PubMed

    Cielocha, Joanna J; Jensen, Kirsten

    2013-01-01

    A new genus and species of lecanicephalidean cestode, Stoibocephalum arafurense n. gen., n. sp., is described from the sharkray, Rhina ancylostoma Bloch & Schneider, off northern Australia. Stoibocephalum arafurense n. gen., n. sp. is apolytic, and possesses a large, muscular, retractable apical organ, 3 pairs of excretory vessels, and testes in several columns and layers. The presence of 3 pairs of excretory vessels distinguishes this new genus from all other valid lecanicephalidean genera, except Hexacanalis Perrenoud, 1931, from which it can be distinguished based on ovary shape and egg morphology. Stoibocephalum n. gen. most closely resembles Tylocephalum Linton, 1890 but differs from that genus in its ability to completely retract its apical organ into the scolex proper. Scolex microthrix pattern and histological sections of scoleces attached in situ suggest S. arafurense n. gen., n. sp. to attach to the host's intestinal mucosa with apical organ and scolex proper surfaces, rather than just the apical organ surface. This is the third lecanicephalidean species described from the sharkray. PMID:26176156

  2. A Phocus on Phenotyping: opportunities and challenges in local and centralized trait evaluation from the VitisGen experience

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The integration of relevant genetic resources, robust phenotypes, and cutting-edge genotypic data is a challenge that individual scientists rarely overcome successfully. In the USDA-NIFA VitisGen project ( www.vitisgen.org ) for grapevine cultivar improvement, our research team has pursued a shared ...

  3. The Pselaphinae (Coleoptera: Staphylinidae) of Madagascar. V. Description of Squamiger elegans gen. et sp. nov. from Central Madagascar.

    PubMed

    Hlaváč, Peter; Baňař, Petr

    2016-01-01

    Squamiger elegans, gen. and sp. nov., is described based on a series of specimens collected by sifting of leaf-litter in Ambohitantely Special Reserve, Central Madagascar. The genus is a member of the tribe Clavigerini (Pselaphinae: Clavigeritae) and it is placed into the subtribe Clavigerodina. PMID:27395632

  4. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

  5. Bottom-up synthesis of Zn1.7GeN1.8O nanoparticles for photocatalytic application

    NASA Astrophysics Data System (ADS)

    Schliehe, Constanze; Giordano, Cristina

    2013-03-01

    Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes.Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes. Electronic supplementary information (ESI) available: SEM of the particles; absorption spectra; BET plot; TEM and XRD of the particles of the up-scaled synthesis; TEM of particles synthesized in the absence of ammonium chloride; IR-spectra; TGA plot; TEM of particles synthesized at 600 °C elemental analysis. See DOI: 10.1039/c3nr33561e

  6. Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Shelton, Kevin J.; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis, J., III; Bailey, Randall E.

    2010-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

  7. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of Complaint January 28, 2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed...

  8. An update on VitisGen: recent advances in using DNA marker technologies in U.S. grape breeding programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project involves a multidisciplinary team of 25 co-PIs at 11 institutions aiming to optimize grape cultivar improvement. To this end, an impressive collection of phenotypic data and high-resolution genetic maps has been developed for seventeen F1 families. Here, we will prese...

  9. Interfacial reactions and oxidation behavior of Al 2O 3 and Al 2O 3/Al coatings on an orthorhombic Ti 2AlNb alloy

    NASA Astrophysics Data System (ADS)

    Li, H. Q.; Wang, Q. M.; Gong, J.; Sun, C.

    2011-02-01

    The uniform and dense Al2O3 and Al2O3/Al coatings were deposited on an orthorhombic Ti2AlNb alloy by filtered arc ion plating. The interfacial reactions of the Al2O3/Ti2AlNb and Al2O3/Al/Ti2AlNb specimens after vacuum annealing at 750 °C were studied. In the Al2O3/Ti2AlNb specimens, the Al2O3 coating decomposed significantly due to reaction between the Al2O3 coating and the O-Ti2AlNb substrate. In the Al2O3/Al/Ti2AlNb specimens, a γ-TiAl layer and an Nb-rich zone came into being by interdiffusion between the Al layer and the O-Ti2AlNb substrate. The γ-TiAl layer is chemically compatible with Al2O3, with no decomposition of Al2O3 being detected. No internal oxidation or oxygen and nitrogen dissolution zone was observed in the O-Ti2AlNb alloy. The Al2O3/Al/Ti2AlNb specimens exhibited excellent oxidation resistance at 750 °C.

  10. Preliminary Results From High Temperature Scoping Irradiation Experiments Of Selected Gen IV Structural Metallic Materials

    SciTech Connect

    Nanstad, Randy K; McClintock, David A; Hoelzer, David T

    2007-01-01

    The performance of Generation IV reactors as a class will be determined by the behavior of advanced engineering materials. In the case of materials utilized for reactor internals and pressure vessels, the effects of irradiation are major issues. The environmental conditions for most of the Gen IV reactors are generally beyond present day reactor technology, especially as regards the combinations of operating temperatures, reactor coolant characteristics, and neutron spectra. In some of the applications, the conditions lay well beyond advanced research programs in radiation effects on materials. Therefore, new experimental data as well as analytical predictions of expected behavior of candidate materials at conditions for which there are no experimental data will be required. In the Gen IV Materials Program cross-cutting task, plans are being developed and irradiations and testing are being carried out to address the issues described above. This paper provides preliminary results for the first series of scoping irradiation experiments with selected metallic alloys, some of which are considered candidate materials for current Gen IV reactor applications, while others are considered as potential future candidate materials. The material classes represented are (1) nickel-base alloys (alloy 800H and Inconel 617; (2) advanced oxide-dispersion strengthened steels (14WT and 14YWT); and (3) commercial ferritic-martensitic steels (9Cr-1MoV). The results presented are from tensile tests using small flat tensile specimens (SS-3) in both the unirradiated and irradiated conditions. Specimens were irradiated in so-called rabbit capsules in the High-Flux Isotope Reactor (HFIR) at temperatures from 550 to 750 C and to irradiation doses from about 1.28 to 1.61 dpa. For the preliminary results from the first phase of this study, the annealed 9Cr-1MoV shows small amounts of irradiation-induced hardening. For the Alloy 800H, however, the hardening resulting from the 580 C irradiation

  11. Environmental fatigue of an Al-Li-Cu alloy. Part 3: Modeling of crack tip hydrogen damage

    NASA Technical Reports Server (NTRS)

    Piascik, Robert S.; Gangloff, Richard P.

    1992-01-01

    Environmental fatigue crack propagation rates and microscopic damage modes in Al-Li-Cu alloy 2090 (Parts 1 and 2) are described by a crack tip process zone model based on hydrogen embrittlement. Da/dN sub ENV equates to discontinuous crack advance over a distance, delta a, determined by dislocation transport of dissolved hydrogen at plastic strains above a critical value; and to the number of load cycles, delta N, required to hydrogenate process zone trap sites that fracture according to a local hydrogen concentration-tensile stress criterion. Transgranular (100) cracking occurs for process zones smaller than the subgrain size, and due to lattice decohesion or hydride formation. Intersubgranular cracking dominates when the process zone encompasses one or more subgrains so that dislocation transport provides hydrogen to strong boundary trapping sites. Multi-sloped log da/dN-log delta K behavior is produced by process zone plastic strain-hydrogen-microstructure interactions, and is determined by the DK dependent rates and proportions of each parallel cracking mode. Absolute values of the exponents and the preexponential coefficients are not predictable; however, fractographic measurements theta sub i coupled with fatigue crack propagation data for alloy 2090 established that the process zone model correctly describes fatigue crack propagation kinetics. Crack surface films hinder hydrogen uptake and reduce da/dN and alter the proportions of each fatigue crack propagation mode.

  12. Morphology and phylogenies of two hypotrichous brackish-water ciliates from China, Neourostylopsis orientalis n. sp. and Protogastrostyla sterkii (Wallengren, 1900) n. comb., with establishment of a new genus Neourostylopsis n. gen. (Protista, Ciliophora, Hypotrichia).

    PubMed

    Chen, Xiangrui; Shao, Chen; Liu, Xihan; Huang, Jie; Al-Rasheid, Khaled A S

    2013-03-01

    This paper investigates the morphology, infraciliature and small-subunit (SSU) rRNA gene sequences of two hypotrichous ciliates, Neourostylopsis orientalis n. sp., and Protogastrostyla sterkii (Wallengren, 1900) n. comb. (basionym Gastrostyla sterkii), collected from coastal waters in southern China. Neourostylopsis orientalis n. sp. is diagnosed mainly by the arrangement of brownish cortical granules, the numbers of adoral membranelles and frontal and transverse cirri and the characteristics of its midventral cirral pairs. The SSU rRNA gene phylogeny strongly supports the establishment of the new genus Neourostylopsis n. gen., which is characterized mainly by the following features: frontal and transverse cirri clearly differentiated, buccal cirri present, two frontoterminal cirri, midventral complex composed of midventral pairs only and not exceeding the halfway point of the cell, more than one row of marginal cirri on each side which derive from individual anlagen within each parental row, caudal cirri lacking. Thus, two new combinations are required: Neourostylopsis songi (Lei et al., 2005) n. comb., and Neourostylopsis flavicana (Wang et al., 2011) n. comb. Additionally, improved diagnoses for both Metaurostylopsis and Apourostylopsis are supplied in this study. Protogastrostyla sterkii (Wallengren, 1900) n. comb. differs from the similar congener Protogastrostyla pulchra mainly in body shape, ratio of buccal field to body length in vivo and molecular data. Based on the present studies, we conclude that the estuarine population of P. pulchra collected by J. Gong and others [Gong et al., J Eukaryot Microbiol (2007) 54, 468-478] is a population of P. sterkii. PMID:23355699

  13. Rub' al Khali, Arabia

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Rub' al Khali is one of the largest sand deserts in the world, encompassing most of the southern third of the Arabian Peninsula. It includes parts of Oman, United Arab Emirates, and Yemen. The desert covers 650,000 square kilometers, more than the area of France. Largely unexplored until recently, the desert is 1000 km long and 500 km wide. The first documented journeys made by Westerners were those of Bertram Thomas in 1931 and St. John Philby in 1932. With daytime temperatures reaching 55 degrees Celsius, and dunes taller than 330 meters, the desert may be one of the most forbidding places on Earth.

    The image was acquired December 2, 2005, covers an area of 54.8 x 61.9 km, and is located near 20.7 degrees north latitude, 53.6 degrees east longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  14. Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.

    PubMed

    Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

    2008-09-01

    Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph. PMID:18692373

  15. Metulocladosporiella gen. nov. for the causal organism of Cladosporium speckle disease of banana.

    PubMed

    Crous, Pedro W; Schroers, Hans-Josef; Groenewald, Johannes Z; Braun, Uwe; Schubert, Konstanze

    2006-03-01

    Cladosporium musae, a widespread leaf-spotting hyphomycete on Musa spp., is genetically and morphologically distinct from Cladosporium s. str. (Davidiella anamorphs, Mycosphaerellaceae, Dothideales). DNA sequence data derived from the ITS and LSU gene regions of C. musae isolates show that this species is part of a large group of hyphomycetes in the Chaetothyriales with dematiaceous blastoconidia in acropetal chains. Cladosporium adianticola, a foliicolous hyphomycete known from leaf litter in Cuba is also a member of this clade and is closely related to C. musae. A comparison with other genera in the Cladosporium complex revealed that C. musae belongs to a lineage for which no generic name is currently available, and for which the genus Metulocladosporiella gen. nov. is proposed. Two species of Metulocladosporiella are currently known, namely M. musae, which is widely distributed, and M. musicola sp. nov., which is currently known from Africa. PMID:16483752

  16. Macuahuitloides inexpectans n. gen., n. sp. (Molineidae: Anoplostrongylinae) from Mormoops megalophylla (Chiroptera: Mormoopidae).

    PubMed

    Jiménez, F Agustín; Peralta-Rodríguez, Jorge Luis; Caspeta-Mandujano, Juan; Ramírez-Díaz, Silvia Edith

    2014-10-01

    Macuahuitloides inexpectans n. gen., n. sp. (Molineidae: Anoplostrongylinae) is herein described. The description is based on specimens removed from the small intestine of ghost-faced bats, Mormoops megalophylla, from central Mexico. The monotypic genus is unique in featuring sexual dimorphism on the cuticular ornamentation, which consists of the presence of spines on the anterior quarter of females, and of the presence of rugosities on the surface of the cephalic vesicle of males. The cuticular spines are arranged in spiral rings on the anterior quarter of the body, and there is no trace of said structures on the cuticle of males. The synlophe of the males possess 12 ridges, whereas there is no synlophe in females. Finally, females show a prominent caudal terminus (spine) and 3 subterminal tubercles, whereas males show bursal rays in a 3-2 arrangement, with a relatively prominent dorsal ray. PMID:24919089

  17. GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations

    SciTech Connect

    Cardall, Christian Y.; Budiardja, Reuben D.

    2015-06-11

    Aside from numerical algorithms and problem setup, large-scale physics simulations on distributed-memory supercomputers require more basic utilitarian functionality, such as physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Here we describe and make available Fortran 2003 classes furnishing extensible object-oriented implementations of this sort of rudimentary functionality, along with individual `unit test' programs and larger example problems demonstrating their use. Lastly, these classes compose the Basics division of our developing astrophysics simulation code GenASiS (General Astrophysical Simulation System), but their fundamental nature makes them useful for physics simulations in many fields.

  18. GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations

    DOE PAGESBeta

    Cardall, Christian Y.; Budiardja, Reuben D.

    2015-06-11

    Aside from numerical algorithms and problem setup, large-scale physics simulations on distributed-memory supercomputers require more basic utilitarian functionality, such as physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Here we describe and make available Fortran 2003 classes furnishing extensible object-oriented implementations of this sort of rudimentary functionality, along with individual `unit test' programs and larger example problems demonstrating their use. Lastly, these classes compose the Basics division of our developing astrophysics simulation code GenASiS (General Astrophysical Simulation System), but their fundamental nature makes themmore » useful for physics simulations in many fields.« less

  19. Application of constitutive model considering nonlinear unloading behavior for Gen.3 AHSS

    NASA Astrophysics Data System (ADS)

    Sun, Li; Wagoner, R. H.

    2013-05-01

    Nonlinear unloading behavior has been reported as an important factor for accurate springback prediction. In this study, a newly proposed special component of strain: "Quasi-Plastic-Elastic" ("QPE") strain was utilized to study the springback behavior of Advanced High Strength Steels (AHSS). Several types of steels, including IF steel, DP780, TRIP780, DP980, TWIP980 and QP980 were considered in this research. The results showed that all the tested steels have following behavior: 1) QPE strain is recoverable, like elastic deformation. 2) It dissipates work, like plastic deformation. A 3-D constitutive model considering QPE behavior was implemented in Abaqus/Standard with shell element and applied to draw-bend springback test for Gen. 3 AHSS, QP980. Predictions for springback using the QPE model were more accurate compared with standard elastic-plastic models.

  20. NASA System-Level Design, Analysis and Simulation Tools Research on NextGen

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge

    2011-01-01

    A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

  1. Petrosaltator gen. nov., a new genus replacement for the North African sengi Elephantulus rozeti (Macroscelidea; Macroscelididae).

    PubMed

    Dumbacher, John P

    2016-01-01

    In 2003, a molecular phylogeny was published that examined the role of the Sahara Desert as a vicariant event in the evolution of sengis (also known as elephant-shrews.) The phylogeny included a single sample from the North African sengi, Elephantulus rozeti (Duvernoy, 1833), which was found to be more closely related to the sengi genus Petrodromus Peters, 1846 than to other Elephantulus. Here we independently test the monophyly of Elephantulus using an additional specimen of E. rozeti and similar phylogenetic analyses, and discuss additional morphological and behavioral data that support the phylogeny. We propose a revised taxonomy that reflects the current paraphyly of Elephantulus and the sister relationship of E. rozeti and Petrodromus, including a new genus name for the North African sengi, Petrosaltator rozeti gen. nov., nov. comb. We additionally define two tribes within the subfamily Macroscelidinae, the Macroscelidini (including Macroscelides, Petrodromus, and Petrosaltator), and the Elephantulini (including all other members of Elephantulus). PMID:27395734

  2. Coynema gen. n., a new genus of nematode (Thelastomatoidea, Hystrignathidae) parasites of Passalidae (Coleoptera) from Cuba

    PubMed Central

    Rodríguez, Jans Morffe; Rodríguez, Nayla García

    2011-01-01

    Abstract The new genus Coynema gen. n. is described as parasite of the two passalid beetles from Cuba: Passalus interstitialis Escholtz, 1829 (type host) and Passalus pertyi Kaup, 1869. Females are characterized by the shape of their cephalic end, cervical cuticle unarmed, a sub-cylindrical procorpus with its base abruptly dilated, fore region of intestine dilated as a sac-like structure, genital system didelphic-amphidelphic and eggs markedly ovoid and smooth-shelled. Males have a digestive system similar to females, tail sharply pointed, bearing a Y-like thickening of the dorsal cuticle. They also present a big, median, mammiform pre-cloacal papillae and a pair of small, sub-dorsal pre-cloacal papillae anterior to the cuticular thickening of the tail. PMID:21594137

  3. Sandrewia, n. gen., a problematical plant from the Lower Permian of Texas and Kansas

    USGS Publications Warehouse

    Mamay, S.H.

    1975-01-01

    Sandrewia, n. gen., monotypified by S. texana, n. sp., is a plant from Lower Permian beds of north-central Texas and east-central Kansas. It is characterized by stout axes with spirally disposed, laxly inserted, petiolate leaves; the laminae are broadly flabelliform with coarse, open venation. The leaves are reminiscent of the vojnovskyalean Nephropsis, of the Permian Petchora Basin, U.S.S.R., but biologic relationships are only speculative because of limited material. However, leaf characteristics render Sandrewia easily identifiable. Its presently limited stratigraphic range, along with floristic associations, indicates it may be a useful guide fossil and supports the author's beliefs regarding important times and places in Paleozoic plant evolution. ?? 1975.

  4. Development of Distributed Generic Simulator (GenSim) through Invention of Simulated Network (simNetwork)

    NASA Astrophysics Data System (ADS)

    Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

    2011-09-01

    A simulated network protocol provides the capability of distributed simulation to a generic simulator. Through this, full coverage of management of data and service handling among separated simulators is achieved. The distributed simulation environment is much more conducive to handling simulation load balancing and hazard treatment than a standalone computer. According to the simulated network protocol, one simulator takes on the role of server and the other simulators take on the role of client, and client is controlled by server. The purpose of the simulated network protocol is to seamlessly connect multiple simulator instances into a single simulation environment. This paper presents the development of a simulated network (simNetwork) that provides the capability of distributed simulation to a generic simulator (GenSim), which is a software simulator of satellites that has been developed by the Korea Aerospace Research Institute since 2010, to use as a flight software! validation bench for future satellite development.

  5. Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Agogué, Hélène; Intertaglia, Laurent; Lesongeur, Françoise; Lebaron, Philippe

    2008-11-01

    A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131(T), was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/131(T) represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131(T) (=DSM 19753(T) =CIP 109757(T) =MOLA 225(T)). PMID:18984680

  6. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Intertaglia, Laurent; Lesongeur, Françoise; Lebaron, Philippe

    2008-05-01

    A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T). PMID:18450719

  7. Life cycle of Schizochytriodinium calani nov. gen. nov. spec., a dinoflagellate parasitizing copepod eggs

    NASA Astrophysics Data System (ADS)

    Elbrächter, Malte

    1988-09-01

    During the Polarstern-cruise ARK IV/2 June 1987, in the Fram Strait, dinophytes parasitizing copepod eggs were observed. In the laboratory on board, vegetative reproduction was documented and re-infection of Calanus glacialis and C. hyperboreus eggs was experimentally established. During food uptake, a primary cyst produces successively several secondary cysts, all separating immediately after formation from the primary cyst. In every one of these free floating secondary cysts up to 256 dinospores are formed by palintomy. Re-infection only occurred after a “maturation time” of at least 2 days after formation of the dinospores. The life cycle is compared to that of other similar parasitic dinophyte genera: Apodinium Chatton, Chytriodinium Chatton, Dissodinium Klebs in Pascher and Myxodinium Cachon, Cachon & Bouquaheux. As the taxon under discussion does not fit in with any species or genus known so far, it is described as Schizochytriodinium calani nov. gen. nov. spec.

  8. Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae)

    PubMed Central

    Aguila, Rayner Núñez

    2013-01-01

    Abstract A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe–Sagua–Baracoa. The species inhabits low elevations (300–400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the “Pico Cristal” National Park in the West and the “Alexander von Humbolt” National Park in the East. PMID:24146561

  9. Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays

    NASA Technical Reports Server (NTRS)

    Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

    2012-01-01

    Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

  10. Enhanced Vision for All-Weather Operations Under NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

    2010-01-01

    Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

  11. Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans.

    PubMed

    Kurtzman, Cletus P

    2016-07-01

    DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribed genera. From phylogenetic analysis of gene sequences from nuclear large subunit rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II, Candida auringiensis (NRRL Y-17674(T), CBS 6913(T)), Candida salmanticensis (NRRL Y-17090(T), CBS 5121(T)), and Candida tartarivorans (NRRL Y-27291(T), CBS 7955(T)) were shown to be members of an isolated clade and are proposed for reclassification in the genus Groenewaldozyma gen. nov. (MycoBank MB 815817). Neighbouring taxa include species of the Wickerhamiella clade and Candida blankii. PMID:27142089

  12. Modified CelliGen-packed bed bioreactors for hybridoma cell cultures.

    PubMed

    Wang, G; Zhang, W; Jacklin, C; Freedman, D; Eppstein, L; Kadouri, A

    1992-01-01

    This study describes two packed bed bioreactor configurations which were used to culture a mouse-mouse hybridoma cell line (ATCC HB-57) which produces an IgG1 monoclonal antibody. The first configuration consists of a packed column which is continuously perfused by recirculating oxygenated media through the column. In the second configuration, the packed bed is contained within a stationary basket which is suspended in the vessel of a CelliGen bioreactor. In this configuration, recirculation of the oxygenated media is provided by the CelliGen Cell Lift impeller. Both configurations are packed with disk carriers made from a non-woven polyester fabric. During the steady-state phase of continuous operation, a cell density of 10(8) cells per cm3 of bed volume was obtained in both bioreactor configurations. The high levels of productivity (0.5 gram MAb per 1 of packed bed per day) obtained in these systems demonstrates that the culture conditions achieved in these packed bed bioreactors are excellent for the continuous propagation of hybridomas using media which contains low levels (1%) of serum as well as serum-free media. These packed bed bioreactors allow good control of pH, dissolved oxygen and temperature. The media flows evenly over the cells and produces very low shear forces. These systems are easy to set up and operate for prolonged periods of time. The potential for scale-up using Fibra-cel carriers is enhanced due to the low pressure drop and low mass transfer resistance, which creates high void fraction approaching 90% in the packed bed. PMID:1369180

  13. Tucunarella n. Gen. and other dactylogyrids (Monogenoidea) from cichlid fish (Perciformes) from Peruvian Amazonia.

    PubMed

    Mendoza-Franco, Edgar F; Scholz, T; Rozkosná, P

    2010-06-01

    During parasitological research on cichlid fish from the tributaries of the Amazon River around Iquitos, Peru, the following gill monogenoidean species were found: Tucunarella cichlae n. gen. and n. sp. from Cichla monoculus Spix and Agassiz; Gussevia alioides Kritsky, Thatcher, and Boeger, 1986 from Heros severus Heckel; Gussevia asota Kritsky, Thatcher, and Boeger, 1989 from Astronotus ocellatus (Agassiz); Gussevia disparoides Kritsky, Thatcher, and Boeger, 1986 from H. severus (all new geographical records) and Cichlasoma amazonarum Kullander (new host record); Gussevia longihaptor (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1986 and Gussevia undulata Kritsky, Thatcher, and Boeger, 1986 from C. monoculus ; Sciadicleithrum satanopercae Yamada, Takemoto, Bellay, and Pavanelli, 2008 from Satanoperca jurupari Heckel; and Sciadicleithrum variabilum (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1989 from C. amazonarum (new host and geographical records). Tucunarella n. gen. is proposed to accommodate a new species, Tucunarella cichlae , which is its type and only known species in the genus. The new genus is characterized by, besides a very large body size (about 1.5 mm vs. much less than 1 mm in other ancyrocephaline genera in Amazonia), a thickened tegument, 1 pair of eyes, overlapping gonads (testis dorsal to the germarium), nonarticulated male copulatory organ (MCO) and accessory piece, a coiled (counterclockwise) MCO, a dextral vaginal aperture, a haptor armed with 2 pairs of anchors (each with broad base and subequal roots, which are marginally folded), and dorsal and ventral bars and 14 hooks with protruding blunt thumbs and 2 different shapes (slender vs. slightly expanded shanks). Illustrations and data on morphological and biometric variability of individual species from different hosts are provided. The present data provide evidence of a relatively wide host specificity of gill monogenoideans parasitic in South American cichlids

  14. Evaluating SoilGen2 as a tool for projecting soil evolution induced by global change.

    PubMed

    Keyvanshokouhi, Saba; Cornu, Sophie; Samouëlian, Anatja; Finke, Peter

    2016-11-15

    To protect soils against threats, it is necessary to predict the consequences of human activities and global change on their evolution on a ten to hundred year time scale. Mechanistic modelling of soil evolution is then a useful tool. We analysed the ability of the SoilGen model to be used for projections of soil characteristics associated to various soil threats: vertical distributions of <2μm fraction, organic carbon content (OC), bulk density and pH. This analysis took the form of a functional sensitivity analysis in which we varied the initial conditions (parent material properties) and boundary conditions (co-evolution of precipitation and temperature; type and amount of fertilization and tillage as well as duration of agriculture). The simulated scenario variants comprised anthroposequences in Luvisols at two sites with one default scenario, six variants for initial conditions and 12 variants for boundary conditions. The variants reflect the uncertainties to our knowledge of parent material properties or reconstructed boundary conditions. We demonstrated a sensitivity of the model to climate and agricultural practices for all properties. We also conclude that final model results are not significantly affected by the uncertainties of boundary conditions for long simulations runs, although influenced by uncertainties on initial conditions. The best results were for organic carbon, although improvements can be reached through calibration or by incorporating a dynamic vegetation growth module in SoilGen. Results were poor for bulk density due to a fixed-volume assumption in the model, which is not easily modified. The <2μm fraction depth patterns are reasonable but the process of clay new formation needs to be added to obtain the belly shape of the Bt horizon. After calibration for organic carbon under agriculture, the model is suitable for producing soil projections due to global change. PMID:27470670

  15. Pseudochelatococcus lubricantis gen. nov., sp. nov. and Pseudochelatococcus contaminans sp. nov. from coolant lubricants.

    PubMed

    Kämpfer, Peter; Glaeser, Stefanie P; Gräber, Marco; Rabenstein, Andreas; Kuever, Jan; Busse, Hans-Jürgen

    2015-01-01

    Two Gram-negative, rod-shaped, non-spore-forming bacteria, isolated from metal working fluids were investigated to determine their taxonomic positions. On the basis of 16S rRNA gene sequence phylogeny, both strains (MPA 1113(T) and MPA 1105(T)) formed a distinct cluster with 97.7 % sequence similarity between them, which was in the vicinity of members of the genera Methylobacterium, Camelimonas, Chelatococcus, Bosea, Salinarimonas and Microvirga to which they showed low sequence similarities (below 94 %). The predominant compounds in the polyamine pattern and in the quinone system of the two strains were spermidine and ubiquinone Q-10, respectively. The polar lipid profiles were composed of the major compounds: phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine, major or moderate amounts of diphosphatidylglycerol, two unidentified glycolipids and three unidentified aminolipids. Several minor lipids were also detected. The major fatty acids were either C19 : 0 cyclo ω8c or C18 : 1ω7c. The results of fatty acid analysis and physiological and biochemical tests allowed both, the genotypic and phenotypic differentiation of the isolates from each other, while the chemotaxonomic traits allowed them to be differentiated from the most closely related genera. In summary, low 16S rRNA gene sequence similarities and marked differences in polar lipid profiles, as well as in polyamine patterns, is suggestive of a novel genus for which the name Pseudochelatococcus gen. nov. is proposed. MPA 1113(T) ( = CCM 8528(T) = LMG 28286(T) = CIP 110802(T)) and MPA 1105(T) ( = CCM 8527(T) = LMG 28285(T)) are proposed to be the type strains representing two novel species within the novel genus, Pseudochelatococcus gen. nov., for which the names Pseudochelatococcus lubricantis sp. nov. and Pseudochelatococcus contaminans sp. nov. are suggested, respectively. PMID:25301542

  16. Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.

    PubMed

    Ren, Lvzhi; Chang, Xulu; Jiang, Fan; Kan, Wenjing; Qu, Zhihao; Qiu, Xia; Fang, Chengxiang; Peng, Fang

    2015-01-01

    A pale yellow, aerobic bacterium, strain M0-2(T), was isolated from a till sample. Its taxonomic position was investigated by using a polyphasic approach. Cells were Gram-stain-negative, rod-shaped and motile. Cells reproduced by budding or asymmetrical cell division. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M0-2(T) belonged to the family Sphingomonadaceae and was closely related to species of the genera Novosphingobium (96.4-92.0%) and Blastomonas (94.6%), Sphingopyxis witflariensis W-50(T) (94.0%), Sphingosinicella soli KSL-125(T) (93.6%) and Sphingomonas astaxanthinifaciens TDMA-17(T) (93.5%). Ubiquinone-10 (Q-10) was the predominant respiratory quinone. The major fatty acids were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c, 31.9%), summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c, 19.8%) and C14:0 2-OH (8.9%). Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. Spermidine was the major polyamine observed in the cell. The genomic DNA G+C content was 47.5 mol%. On the basis of phylogenetic relationships and the low DNA G+C content compared with most other genera of the family Sphingomonadaceae, combined with phenotypic and chemotaxonomic data, strain M0-2(T) is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Parablastomonas arctica gen. nov., sp. nov. is proposed. The type strain of Parablastomonas arctica gen. nov., sp. nov. is M0-2(T) ( =CCTCC AB 2012968(T) = NRRL B-59110(T)). PMID:25336722

  17. Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands.

    PubMed

    Zepeda, Vanessa K; Busse, Hans-Jürgen; Golke, Jan; Saw, Jimmy H W; Alam, Maqsudul; Donachie, Stuart P

    2015-10-01

    A Gram-negative, helical bacterium designated PH27AT was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain was motile by bipolar tufts of flagella and grew optimally at pH 7, and microaerobically or aerobically. Closest neighbours based on 16S rRNA gene nucleotide sequence identity are Marinospirillum celere v1c_Sn-redT (93.31 %) and M. alkaliphilum Z4T (92.10 %) in the family Oceanospirillaceae, class Gammaproteobacteria. PH27AT is distinguished phenotypically from members of the genus Marinospirillum by its hydrolysis of gelatin, the absence of growth in media containing ≤ 1 % (w/v) NaCl and the ranges of temperature (12–40 °C) and pH (5–8) for growth. The major compound ubiquinone Q-9 distinguishes the quinone system of strain PH27AT from those in members of the genus Marinospirillum and other members of the Oceanospirillaceae, in which the major quinone is Q-8. Major polar lipids in PH27AT were phosphatidylethanolamine and phosphatidylglycerol, with moderate amounts of diphosphatidylglycerol and phosphatidylserine. Spermidine and cadaverine dominated the polyamine pattern; large proportions of cadaverine have not been reported in members of the genus Marinospirillum. Genotypic and chemotaxonomic data show that PH27AT does not belong in the genus Marinospirillum or other genera of the family Oceanospirillaceae or the Halomonadaceae. We propose a new genus, Terasakiispira gen. nov., be created to accommodate Terasakiispira papahanaumokuakeensis gen. nov., sp. nov. as the type species, with PH27AT ( = ATCC BAA-995T = DSM 16455T = DSM 23961T) as the type strain. PMID:26297573

  18. Gymnoxanthella radiolariae gen. et sp. nov. (Dinophyceae), a dinoflagellate symbiont from solitary polycystine radiolarians.

    PubMed

    Yuasa, Tomoko; Horiguchi, Takeo; Mayama, Shigeki; Takahashi, Osamu

    2016-02-01

    The symbiotic dinoflagellate Gymnoxanthella radiolariae T. Yuasa et T. Horiguchi gen. et sp. nov. isolated from polycystine radiolarians is described herein based on light, scanning and transmission electron microscopy as well as molecular phylogenetic analyses of SSU and LSU rDNA sequences. Motile cells of G. radiolariae were obtained in culture, and appeared to be unarmored. The cells were 9.1-11.4 μm long and 5.7-9.4 μm wide, and oval to elongate oval in the ventral view. They possessed an counterclockwise horseshoe-shaped apical groove, a nuclear envelope with vesicular chambers, cingulum displacement with one cingulum width, and the nuclear fibrous connective; all of these are characteristics of Gymnodinium sensu stricto (Gymnodinium s.s.). Molecular phylogenetic analyses also indicated that G. radiolariae belongs to the clade of Gymnodinium s.s. However, in our molecular phylogenetic trees, G. radiolariae was distantly related to Gymnodinium fuscum, the type species of Gymnodinium. Based on the consistent morphological, genetic, and ecological divergence of our species with the other genera and species of Gymnodinium s.s., we considered it justified to erect a new, separate genus and species G. radiolariae gen. et sp. nov. As for the peridinioid symbiont of radiolarians, Brandtodinium has been erected as a new genus instead of Zooxanthella, but the name Zooxanthella is still valid. Brandtodinium is a junior synonym of Zooxanthella. Our results suggest that at least two dinoflagellate symbiont species, peridinioid Zooxanthella nutricula and gymnodinioid G. radiolariae, exist in radiolarians, and that they may have been mixed and reported as "Z. nutricula" since the 19th century. PMID:26987091

  19. GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments.

    PubMed

    Groß, Lynn; Herrmann, Carmen

    2016-09-30

    Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc. PMID:27416879

  20. Ascidiimonas aurantiaca gen. nov., sp. nov., a member of Flavobacteriaceae isolated from a sea squirt.

    PubMed

    Yoon, Jaewoo; Oku, Naoya; Kasai, Hiroaki

    2016-04-01

    A Gram-stain negative, strictly aerobic, chemoheterotrophic, tangerine orange pigmented, curved-rod shaped bacterium, designated N5DA8-2C(T), was isolated from a sea squirt by use of a bait-streaked agar technique. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared high (92.6 %) sequence similarity with Frondibacter aureus A5Q-67(T). The strain could be differentiated phenotypically from the related members of the family Flavobacteriaceae. The major fatty acids of strain N5DA8-2C(T) were iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 and C16:1 ω7c and/or C16:1 ω6c. A polar lipid profile was present consisting of phosphatidylethanolamine and three unidentified amino lipids. The DNA G+C content of the strain was determined to be 41 mol% and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Ascidiimonas aurantiaca gen. nov., sp. nov. is proposed. The type strain of A. aurantiaca gen. nov., sp. nov. is N5DA8-2C(T) (= KCTC 32992(T) = NBRC 110020(T)). PMID:26800666