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Sample records for al gen env

  1. Optimized Gen-II FeCrAl cladding production in large quantity for campaign testing

    SciTech Connect

    Yamamoto, Yukinori; Sun, Zhiqian; Pint, Bruce A.; Terrani, Kurt A.

    2016-06-03

    There are two major objectives in this report; (1) to optimize microstructure control of ATF FeCrAl alloys during tube drawing processes, and (2) to provide an update on the progress of ATF FeCrAl tube production via commercial manufacturers. Experimental efforts have been made to optimize the process parameters balancing the tube fabricability, especially for tube drawing processes, and microstructure control of the final tube products. Lab-scale sheet materials of Gen II FeCrAl alloys (Mo-containing and Nb-containing FeCrAl alloys) were used in the study, combined with a stepwise warm-rolling process and intermediate annealing, aiming to simulate the tube drawing process in a commercial tube manufacturer. The intermediate annealing at 650ºC for 1h was suggested for the tube-drawing process of Mo-containing FeCrAl alloys because it successfully softened the material by recovering the work hardening introduced through the rolling step, without inducing grain coarsening due to recrystallization. The final tube product is expected to have stabilized deformed microstructure providing the improved tensile properties with sufficient ductility. Optimization efforts on Nb-containing FeCrAl alloys focused on the effect of alloying additions and annealing conditions on the stability of deformed microstructure. Relationships between the second-phase precipitates (Fe2Nb-Laves phase) and microstructure stability are discussed. FeCrAl tube production through commercial tube manufacturers is currently in progress. Three different manufacturers, Century Tubes, Inc. (CTI), Rhenium Alloys, Inc. (RAI), and Superior Tube Company, Inc. (STC), are providing capabilities for cold-drawing, warm-drawing, and HPTR cold-pilgering, respectively. The first two companies are currently working on large quantity tube production (expected 250 ft length) of Gen I model FeCrAl alloy (B136Y3, at CTI) and Gen II (C35M4, at RAI), with the process parameters obtained from the experimental

  2. A proposal to reclassify Nocardia pinensis Blackall et al. as Skermania piniformis gen. nov., comb. nov.

    PubMed

    Chun, J; Blackall, L L; Kang, S O; Hah, Y C; Goodfellow, M

    1997-01-01

    The type strain of Nocardia pinensis was the subject of chemotaxonomic and 16S ribosomal DNA sequencing studies. The resultant nucleotide sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordona, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella, and phylogenetic trees were generated by using the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, and neighbor-joining methods. It was evident from the phylogenetic analyses that N. pinensis represents a distinct phyletic line that is most closely associated with the Gordona clade. This genealogical evidence, together with chemotaxonomic and phenotypic data derived from this and previous studies, indicates that N. pinensis merits generic status within the family Nocardiaceae. Therefore, we propose that N. pinensis Blackall et al. 1989 be reclassified as Skermania piniformis gen. nov., comb. nov. The type strain of Skermania piniformis cleaved an array of conjugated substrates based on the fluorophores 7-amino-4-methylcoumarin and 4-methylumbelliferone.

  3. ALV-J GP37 molecular analysis reveals novel virus-adapted sites and three tyrosine-based Env species.

    PubMed

    Ye, Jianqiang; Fan, Zhonglei; 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.

  4. 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.

  5. Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov.

    PubMed

    Miñana-Galbis, David; Pinzón, Dora L; Lorén, J Gaspar; Manresa, Angels; Oliart-Ros, Rosa M

    2010-07-01

    Although Anoxybacillus and Geobacillus, two genera of thermophilic bacteria close to the genus Bacillus, have only been described recently, the number of species in these genera has increased rapidly. Four thermophilic, lipolytic strains (DR01, DR02, DR03 and DR04) isolated from a hot spring in Veracruz (Mexico), which could not be identified phenotypically, were subjected to 16S rRNA gene sequence analysis. Three strains were identified as belonging to the genus Anoxybacillus, but strain DR03 was identified as Geobacillus pallidus. This result led us to perform a phylogenetic analysis of the genera Anoxybacillus and Geobacillus based on 16S rRNA gene sequences from all the type strains of these genera. Phylogenetic trees showed three major clusters, Anoxybacillus-Geobacillus tepidamans, Geobacillus sensu stricto and Geobacillus pallidus, while the 16S rRNA gene sequences of G. pallidus (DR03 and the type strain) showed low similarity to sequences of Anoxybacillus (92.5-95.1 %) and Geobacillus (92.8-94.5 %) species, as well as to Bacillus subtilis (92.2-92.4 %). In addition, G. pallidus could be differentiated from Anoxybacillus and Geobacillus on the basis of DNA G+C content and fatty acid and polar lipid profiles. From these results, it is proposed that Geobacillus pallidus should be classified in a novel genus, for which we propose the name Aeribacillus, as Aeribacillus pallidus gen. nov., comb. nov. The type strain of Aeribacillus pallidus is H12(T) (=ATCC 51176(T) =DSM 3670(T) =LMG 19006(T)).

  6. Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga and reclassification of Hoeflea suaedae (Chung et al., 2013) as Pseudohoeflea suaedae gen. nov., comb. nov.

    PubMed

    Hyeon, Jong Woo; Jeong, Sang Eun; Baek, Kyunghwa; Jeon, Che Ok

    2016-11-02

    A Gram-staining-negative, strictly aerobic bacterial strain, designated MA7-20T, was isolated from a marine alga, Porphyridium marinum, in Korea. Cells showing oxidase-positive and catalase-positive activities were motile rods with bipolar flagella. Growth of strain MA7-20T was observed at 15-45 C (optimum, 30-37 C), at pH 6.0-10.5 (optimum, pH 7.0-8.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2-3 %). Strain MA7-20T contained summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c) and 11-methyl-C18:1 ω7c and C18:0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. The G+C content of the genomic DNA was 61.5 mol%. Strain MA7-20T was most closely related to Hoeflea suaedae YC6898T, Oricola cellulosilytica CC-AMH-OT and Nitratireductor basaltis J3T with 96.0 %, 95.8 % and 95.8 % 16S rRNA gene sequence similarities, respectively, but the strain formed a distinct phylogenetic lineage from them within the family Phyllobacteriaceae with a low bootstrap value. H. suaedae also formed a clearly distinct phylogenetic lineage from other members of the genus Hoeflea and closely related genera. On the basis of phenotypic, chemotaxonomic and molecular properties, strain MA7-20T represents a novel genus of the family Phyllobacteriaceae, for which the name Roseitalea porphyridii gen. nov., sp. nov. is proposed. The type strain is MA7-20T (=KACC 18807T =JCM 31538T). In addition, H. suaedae is also reclassified as Pseudohoeflea suaedae gen. nov., comb. nov. (type strain YC6898T =KACC 14911T =NBRC 107700T).

  7. Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov.

    PubMed

    Hamada, Moriyuki; Iino, Takao; Iwami, Takahiro; Harayama, Shigeaki; Tamura, Tomohiko; Suzuki, Ken-ichiro

    2010-01-01

    Two Gram-positive bacteria, designated strains Aji5-31(T) and Ngc37-23(T), were isolated from the intestinal tracts of fishes. 16S rRNA gene sequence analysis indicated that both strains were related to the members of the family Dermatophilaceae, with 95.6-96.9% 16S rRNA gene sequence similarities. The family Dermatophilaceae contains 2 genera and 3 species: Dermatophilus congolensis, Dermatophilus chelonae and Kineosphaera limosa. However, it has been suggested that the taxonomic position of D. chelonae should be reinvestigated using a polyphasic approach, because the chemotaxonomic characteristics are not known (Stackebrandt, 2006; Stackebrandt and Schumann, 2000). Our present study revealed that strains Aji5-31(T), Ngc37-23(T) and D. chelonae NBRC 105200(T) should be separated from the other members of the family Dermatophilaceae on the basis of the following characteristics: the predominant menaquinone of strain Aji5-31(T) is MK-8(H(2)), strain Ngc37-23(T) possesses iso- branched fatty acids as major components, and the menaquinone composition of D. chelonae is MK-8(H(4)), MK-8 and MK-8(H(2)) (5 : 3 : 2, respectively). On the basis of these distinctive phenotypic characteristics and phylogenetic analysis results, it is proposed that strains Aji5-31(T) and Ngc37-23(T) be classified as two novel genera and species of the family Dermatophilaceae. The names are Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., and the type strains are Aji5-31(T) (=NBRC 104925(T) =DSM 22762(T)) and Ngc37-23(T) (=NBRC 104926(T) =DSM 22761(T)), respectively. In addition, D. chelonae should be reassigned to a new genus of the family Dermatophilaceae with the name Austwickia chelonae gen. nov., comb. nov.

  8. Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

    PubMed

    Downes, Julia; Dewhirst, Floyd E; Tanner, Anne C R; Wade, William G

    2013-04-01

    Five strains of anaerobic, gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae, and the most closely related species was Prevotella tannerae. P. tannerae and the novel taxon are deeply branched from the genus Prevotella, with sequence identities to the type strain of the type species of Prevotella, Prevotella melaninogenica, of 82.2 and 85.6 %, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12(T) ( = DSM 22548(T)  = CCUG 58091(T)) and the type strain of Alloprevotella tannerae is ATCC 51259(T)  = CCUG 34292(T)  = CIP 104476(T)  = NCTC 13073(T). Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.

  9. Description of Mogibacterium pumilum gen. nov., sp. nov. and Mogibacterium vescum gen. nov., sp. nov., and reclassification of Eubacterium timidum (Holdeman et al. 1980) as Mogibacterium timidum gen. nov., comb. nov.

    PubMed

    Nakazawa, F; Sato, M; Poco, S E; Hashimura, T; Ikeda, T; Kalfas, S; Sundqvist, G; Hoshino, E

    2000-03-01

    A new genus, Mogibacterium, is proposed for anaerobic, non-spore-forming, Gram-positive, rod-shaped bacteria which have been isolated from the periodontal pockets of adult human patients with periodontal disease and infected root canals. The novel isolates, strains D2-18T, BA11a-f and D5-2T, were inert in most of the conventional biochemical tests and phenotypically resemble asaccharolytic Eubacterium species. The protein profiles of whole cells on SDS-PAGE gels and Western immunoblotting reaction analysis distinguished these organisms from type strains belonging to the previously described Eubacterium species. The G + C content of the DNA is 45-46 mol% for Mogibacterium pumilum and 46 mol% for Mogibacterium vescum. The levels of DNA-DNA relatedness of these new species to other Eubacterium species, including Eubacterium limosum, Eubacterium brachy, Eubacterium lentum, Eubacterium nodatum, Eubacterium saphenum, and the more recently proposed Eubacterium minutum and Eubacterium exiguum (reclassified as Slackia exigua), are less than 2%. The DNA-DNA hybridization value between M. pumilum and M. vescum was 30%. Eubacterium timidum exhibited DNA homologies with Mogibacterium species which were low (17 and 18%) but clearly higher than with all the other Eubacterium species. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the closest phylogenetic neighbour of Mogibacterium species was E. timidum, and that these three species represent a novel lineage distinct from the previously described genera of Gram-positive, rod-shaped bacteria. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, it is also proposed that E. timidum is transferred to the genus Mogibacterium gen. nov. as Mogibacterium timidum gen. nov., comb. nov. (type strain ATCC 33093T).

  10. Quantifying CD4/CCR5 Usage Efficiency of HIV-1 Env Using the Affinofile System.

    PubMed

    Webb, Nicholas E; Lee, Benhur

    2016-01-01

    Entry of HIV-1 into target cells involves the interaction of the HIV envelope (Env) with both a primary receptor (CD4) and a coreceptor (CXCR4 or CCR5). The relative efficiency with which a particular Env uses these receptors is a major component of cellular tropism in the context of entry and is related to a variety of pathological Env phenotypes (Chikere et al. Virology 435:81-91, 2013). The protocols outlined in this chapter describe the use of the Affinofile system, a 293-based dual-inducible cell line that expresses up to 25 distinct combinations of CD4 and CCR5, as well as the associated Viral Entry Receptor Sensitivity Assay (VERSA) metrics used to summarize the CD4/CCR5-dependent infectivity results. This system allows for high-resolution profiling of CD4 and CCR5 usage efficiency in the context of unique viral phenotypes.

  11. Retroviral env glycoprotein trafficking and incorporation into virions.

    PubMed

    Murakami, Tsutomu

    2012-01-01

    Together with the Gag protein, the Env glycoprotein is a major retroviral structural protein and is essential for forming infectious virus particles. Env is synthesized, processed, and transported to certain microdomains at the plasma membrane and takes advantage of the same host machinery for its trafficking as that used by cellular glycoproteins. Incorporation of Env into progeny virions is probably mediated by the interaction between Env and Gag, in some cases with the additional involvement of certain host factors. Although several general models have been proposed to explain the incorporation of retroviral Env glycoproteins into virions, the actual mechanism for this process is still unclear, partly because structural data on the Env protein cytoplasmic tail is lacking. This paper presents the current understanding of the synthesis, trafficking, and virion incorporation of retroviral Env proteins.

  12. Nucleotide Sequence of the Akv env Gene

    PubMed Central

    Lenz, Jack; Crowther, Robert; Straceski, Anthony; Haseltine, William

    1982-01-01

    The sequence of 2,191 nucleotides encoding the env gene of murine retrovirus Akv was determined by using a molecular clone of the Akv provirus. Deduction of the encoded amino acid sequence showed that a single open reading frame encodes a 638-amino acid precursor to gp70 and p15E. In addition, there is a typical leader sequence preceding the amino terminus of gp70. The locations of potential glycosylation sites and other structural features indicate that the entire gp70 molecule and most of p15E are located on the outer side of the membrane. Internal cleavage of the env precursor to generate gp70 and p15E occurs immediately adjacent to several basic amino acids at the carboxyl terminus of gp70. This cleavage generates a region of 42 uncharged, relatively hydrophobic amino acids at the amino terminus of p15E, which is located in a position analogous to the hydrophobic membrane fusion sequence of influenza virus hemagglutinin. The mature polypeptides are predicted to associate with the membrane via a region of 30 uncharged, mostly hydrophobic amino acids located near the carboxyl terminus of p15E. Distal to this membrane association region is a sequence of 35 amino acids at the carboxyl terminus of the env precursor, which is predicted to be located on the inner side of the membrane. By analogy to Moloney murine leukemia virus, a proteolytic cleavage in this region removes the terminal 19 amino acids, thus generating the carboxyl terminus of p15E. This leaves 15 amino acids at the carboxyl terminus of p15E on the inner side of the membrane in a position to interact with virion cores during budding. The precise location and order of the large RNase T1-resistant oligonucleotides in the env region were determined and compared with those from several leukemogenic viruses of AKR origin. This permitted a determination of how the differences in the leukemogenic viruses affect the primary structure of the env gene products. PMID:6283170

  13. Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov.

    PubMed

    Jones, Amanda L; Sutcliffe, Iain C; Goodfellow, Michael

    2013-06-01

    Recently we proposed that Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 be transferred to a novel genus, Prescottia, as Prescottia equi comb. nov. However, in accordance with Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision), the bacterial genus name Prescottia Jones et al. 2013 is deemed illegitimate as this name has been used previously for a plant genus within the family Orchidaceae. Consequently, a new genus name, Prescottella gen. nov. is proposed for the bacterial taxon and a new combination Prescottella equi comb. nov. is proposed for the type species.

  14. Proposal to replace the illegitimate genus name Bryantella Wolin et al. 2004VP with the genus name Marvinbryantia gen. nov. and to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004VP with Marvinbryantia formatexigens comb. nov.

    PubMed

    Wolin, Meyer J; Miller, Terry L; Lawson, Paul A

    2008-03-01

    The prokaryote generic name Bryantella Wolin et al. 2004(VP) is illegitimate because it is a later homonym of Bryantella Chickering, 1946 (Animalia, Arthropoda, Arachnida, Araneae, Salticidae, Dendryphantinae, Dendryphantini) and a later homonym of Bryantella Britton, 1957 (Animalia, Arthropoda, Scarabaeoidea, Scarabaeidae, Melolonthinae) [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Bryantella represents a genus of jumping spiders within the family Salticidae and a genus of melolonthine scarab beetles within the family Scarabaeidae. Therefore, a new genus name, Marvinbryantia gen. nov., is proposed for this taxon. As a result, a new combination, Marvinbryantia formatexigens comb. nov., is required for the type species to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004(VP).

  15. Presence of env-like sequences in Quercus suber retrotransposons.

    PubMed

    Carvalho, M; Ribeiro, T; Viegas, W; Morais-Cecilio, L; Rocheta, M

    2010-01-01

    The main difference between LTR retrotransposons and retroviruses is the presence of the envelope (env) gene in the latter, downstream of the pol gene. The env gene is involved in their infectious capacity. Here we report the presence of env-like sequences in the genome of Quercus suber (cork oak), one of the most economically important Portuguese species. These gene sequences were isolated through DNA amplification between RNaseH conserved motifs and 3' LTR, based on the structure of copia retrotransposons. Phylogenetic analysis revealed that almost all the clones isolated are clustered with Cyclops-2, a Ty3-gypsy element identified in Pisum sativum, except one clustered with gypsy and copia retroelements found in different species. This suggests the existence of a potential ancestral sequence of the env gene, prior to the separation of Ty3-gypsy and Ty1-copia retrotransposons. Additionally, the isolated env-like sequences showed 26-39% of homology with env-like sequences characterized in viruses. The origin of env-like sequences in retrotransposons from host plant taxa is discussed.

  16. Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively.

    PubMed

    Salvetti, Elisa; Felis, Giovanna E; Dellaglio, Franco; Castioni, Anna; Torriani, Sandra; Lawson, Paul A

    2011-10-01

    The development of molecular tools and in particular the use of 16S rRNA gene sequencing has had a profound effect on the taxonomy of many bacterial groups. Gram-positive organisms that encompass the genera Lactobacillus and Clostridium within the Firmicutes are examples of taxa that have undergone major revisions based on phylogenetic information. A consequence of these reorganizations is that a number of organisms are now recognized as being misclassified. Previous studies have demonstrated that Lactobacillus catenaformis and Lactobacillus vitulinus are phylogenetically unrelated to Lactobacillus sensu stricto, being placed within the Clostridia rRNA cluster XVII. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, it is proposed that L. catenaformis and L. vitulinus be reclassified in two new genera, named respectively Eggerthia gen. nov., with the type species Eggerthia catenaformis gen. nov., comb. nov. (type strain DSM 20559(T) = ATCC 25536(T) = CCUG 48174(T) = CIP 104817(T) = JCM 1121(T)) and Kandleria gen. nov., with the type species Kandleria vitulina gen. nov., comb. nov. (type strain LMG 18931(T) = ATCC 27783(T) = CCUG 32236(T) = DSM 20405(T) = JCM 1143(T)).

  17. The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.

    PubMed

    Wade, W G; Downes, J; Dymock, D; Hiom, S J; Weightman, A J; Dewhirst, F E; Paster, B J; Tzellas, N; Coleman, B

    1999-04-01

    16S rRNA gene sequences were determined for Eubacterium exiguum and Peptostreptococcus heliotrinreducens. These species were found to be closely related and, together with Eubacterium lentum, to constitute a branch of the Coriobacteriaceae. Two new genera are proposed on the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons: Slackia to include the bile-sensitive species Eubacterium exiguum and P. heliotrinreducens, and Eggerthella to include the bile-resistant Eubacterium lentum. It is proposed that Eubacterium exiguum and Peptostreptococcus heliotrinreducens are transferred to the genus Slackia gen. nov. as Slackia exigua gen. nov., comb. nov. (type strain ATCC 700122T) and Slackia heliotrinireducens gen. nov., comb. nov. (type strain NTCC 11029T), respectively, and Eubacterium lentum is transferred to the genus Eggerthella gen. nov. as Eggerthella lenta gen. nov., comb. nov. with Eggerthella lenta as the type species.

  18. Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae.

    PubMed

    De Maesschalck, Celine; Van Immerseel, Filip; Eeckhaut, Venessa; De Baere, Siegrid; Cnockaert, Margo; Croubels, Siska; Haesebrouck, Freddy; Ducatelle, Richard; Vandamme, Peter

    2014-11-01

    Strains LMG 27428(T) and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428(T) and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734(T). Strain LMG 27428(T) could be distinguished from S. pleomorphus ATCC 29734(T) based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734(T). The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428(T) and LMG 27427. Strain LMG 27428(T) ( =DSM 26963(T)) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( =DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756(T) =ATCC 29734(T) =DSM 20574(T)). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983(T) (94.4% 16S rRNA gene sequence similarity to strain LMG 27428(T)) and Eubacterium biforme DSM 3989(T) (92.7% 16S rRNA gene sequence similarity to strain LMG 27428(T)). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983(T) =ATCC 27803(T) =JCM 10261(T) and that of Holdemanella biformis is DSM 3989(T

  19. 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.

  20. An amphipathic sequence in the cytoplasmic tail of HIV-1 Env alters cell tropism and modulates viral receptor specificity.

    PubMed

    Vzorov, A N; Yang, C; Compans, R W

    2015-09-01

    The human immunodeficiency virus type 1 (HIV-1) 92UG046 Env protein, obtained from a CD4-independent HIV-1 primary isolate (Zerhouni et al., 2004), has the ability to initiate an infection in HeLa cells expressing CD4 when carrying the full-length (FL) Env, but uses CD8 molecules for receptor-mediated entry when carrying a truncated Env (CT84). To determine whether a specific length or structure in the cytoplasmic tail (CT) is responsible for this alteration of tropism, we compared a series of Env constructs with different CT truncations and the presence or absence of an amphipathic alpha- helical sequence. We found that truncated constructs containing the alpha-helical LLP-2 structure in their CT domains conferred a switch from CD4 to CD8 tropism. The results support the conclusion that the structure of the CT domain can play an important role in determining receptor specificity.

  1. 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.

  2. Feline immunodeficiency virus env gene evolution in experimentally infected cats.

    PubMed

    Kraase, Martin; Sloan, Richard; Klein, Dieter; Logan, Nicola; McMonagle, Linda; Biek, Roman; Willett, Brian J; Hosie, Margaret J

    2010-03-15

    Feline immunodeficiency virus (FIV), an immunosuppressive lentivirus found in cats worldwide, is studied to illuminate mechanisms of lentiviral pathogenesis and to identify key components of protective immunity. During replication, lentiviruses accumulate errors of nucleotide mis-incorporation due to the low-fidelity of reverse transcriptase and recombination between viral variants, resulting in the emergence of a complex viral "quasispecies". In patients infected with HIV-1, env sequences may vary by up to 10% and the detection of quasispecies with greater heterogeneity is associated with higher viral loads and reduced CD4+ T cell numbers [1], indicating that transmission of more complex quasispecies may lead to disease progression. However, little is known about how FIV evolves as disease progresses, or why some cats develop AIDS rapidly while disease progression is slow in others. The aim of this study was to determine whether disease progression may be governed by viral evolution and to examine the diversity of viral variants emerging following infection with an infectious molecular clone. The FIV env gene encoding the envelope glycoprotein (Env) was examined at early (12 weeks) and late (322 weeks) stages of FIV infection in two groups of cats infected experimentally with the FIV-GL8 molecular clone. Viral variants were detected within quasispecies in cats in the late stages of FIV infection that contained differing amino acid compositions in several variable loops of Env, some of which were identified as determinants of receptor usage and resistance to neutralization. Therefore these results indicate that the FIV env gene evolves during the course of infection, giving rise to variants that resist neutralization and likely lead to disease progression.

  3. A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability

    PubMed Central

    Ding, Shilei; Tolbert, William D.; Prévost, Jérémie; Pacheco, Beatriz; Coutu, Mathieu; Debbeche, Olfa; Xiang, Shi-Hua

    2016-01-01

    ABSTRACT Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656–667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549–2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697–709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127–2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the

  4. Glycosylation Benchmark Profile for HIV-1 Envelope Glycoprotein Production Based on Eleven Env Trimers.

    PubMed

    Go, Eden P; Ding, Haitao; Zhang, Shijian; Ringe, Rajesh P; Nicely, Nathan; Hua, David; Steinbock, Robert T; Golabek, Michael; Alin, James; Alam, S Munir; Cupo, Albert; Haynes, Barton F; Kappes, John C; Moore, John P; Sodroski, Joseph G; Desaire, Heather

    2017-05-01

    HIV-1 envelope glycoprotein (Env) glycosylation is important because individual glycans are components of multiple broadly neutralizing antibody epitopes, while shielding other sites that might otherwise be immunogenic. The glycosylation on Env is influenced by a variety of factors, including the genotype of the protein, the cell line used for its expression, and the details of the construct design. Here, we used a mass spectrometry (MS)-based approach to map the complete glycosylation profile at every site in multiple HIV-1 Env trimers, accomplishing two goals. (i) We determined which glycosylation sites contain conserved glycan profiles across many trimeric Envs. (ii) We identified the variables that impact Env's glycosylation profile at sites with divergent glycosylation. Over half of the gp120 glycosylation sites on 11 different trimeric Envs have a conserved glycan profile, indicating that a native consensus glycosylation profile does indeed exist among trimers. We showed that some soluble gp120s and gp140s exhibit highly divergent glycosylation profiles compared to trimeric Env. We also assessed the impact of several variables on Env glycosylation: truncating the full-length Env; producing Env, instead of the more virologically relevant T lymphocytes, in CHO cells; and purifying Env with different chromatographic platforms, including nickel-nitrilotriacetic acid (Ni-NTA), 2G12, and PGT151 affinity. This report provides the first consensus glycosylation profile of Env trimers, which should serve as a useful benchmark for HIV-1 vaccine developers. This report also defines the sites where glycosylation may be impacted when Env trimers are truncated or produced in CHO cells.IMPORTANCE A protective HIV-1 vaccine will likely include a recombinant version of the viral envelope glycoprotein (Env). Env is highly glycosylated, and yet vaccine developers have lacked guidance on how to assess whether their immunogens have optimal glycosylation. The following important

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env.

    PubMed

    Scharf, Louise; Wang, Haoqing; Gao, Han; Chen, Songye; McDowall, Alasdair W; Bjorkman, Pamela J

    2015-09-10

    The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal and electron microscopy (EM) structures of bNAb 8ANC195 complexed with monomeric gp120 and trimeric Env, respectively, spans the gp120 and gp41 Env subunits. To investigate 8ANC195's gp41 epitope at higher resolution, we solved a 3.58 Å crystal structure of 8ANC195 complexed with fully glycosylated Env trimer, revealing 8ANC195 insertion into a glycan shield gap to contact gp120 and gp41 glycans and protein residues. To determine whether 8ANC195 recognizes the CD4-bound open Env conformation that leads to co-receptor binding and fusion, one of several known conformations of virion-associated Env, we solved EM structures of an Env/CD4/CD4-induced antibody/8ANC195 complex. 8ANC195 binding partially closed the CD4-bound trimer, confirming structural plasticity of Env by revealing a previously unseen conformation. 8ANC195's ability to bind different Env conformations suggests advantages for potential therapeutic applications.

  10. Wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including Ralstonia eutropha and related species, and proposal of Ralstonia [Pseudomonas] syzygii (Roberts et al. 1990) comb. nov.

    PubMed

    Vaneechoutte, Mario; Kämpfer, Peter; De Baere, Thierry; Falsen, Enevold; Verschraegen, Gerda

    2004-03-01

    Comparative 16S rDNA sequence analysis indicates that two distinct sublineages, with a sequence dissimilarity of >4 % (bootstrap value, 100 %), exist within the genus RALSTONIA: the Ralstonia eutropha lineage, which comprises Ralstonia basilensis, Ralstonia campinensis, R. eutropha, Ralstonia gilardii, Ralstonia metallidurans, Ralstonia oxalatica, Ralstonia paucula, Ralstonia respiraculi and Ralstonia taiwanensis; and the Ralstonia pickettii lineage, which comprises Ralstonia insidiosa, Ralstonia mannitolilytica, R. pickettii, Ralstonia solanacearum and Ralstonia syzygii comb. nov. (previously Pseudomonas syzygii). This phylogenetic discrimination is supported by phenotypic differences. Members of the R. eutropha lineage have peritrichous flagella, do not produce acids from glucose and are susceptible to colistin, in contrast to members of the R. pickettii lineage, which have one or more polar flagella, produce acid from several carbohydrates and are colistin-resistant. Members of the R. pickettii lineage are viable for up to 6 days on tryptic soy agar at 25 degrees C, whereas members of the R. eutropha lineage are viable for longer than 9 days. It is proposed that species of the R. eutropha lineage should be classified in a novel genus, Wautersia gen. nov. Finally, based on the literature and new DNA-DNA hybridization data, it is proposed that Pseudomonas syzygii should be renamed Ralstonia syzygii comb. nov.

  11. Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.

    PubMed

    Carlier, Jean-Philippe; Bedora-Faure, Marie; K'ouas, Guylène; Alauzet, Corentine; Mory, Francine

    2010-03-01

    We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812-826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740(T) and Eubacterium plautii DSM 4000(T). Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799(T) branching off from this line of descent with sequence similarities of 97.1-97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1-93.4, 91.2-91.4, 89.8-90 and 88.7-89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA-DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1(T) (=ATCC 29863(T) =VPI 0310(T) =DSM 4000(T)), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402A(T) (=ATCC 29799(T) =VPI R2-29-1(T)).

  12. Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991.

    PubMed

    Pankratov, Timofey A; Kirsanova, Lilia A; Kaparullina, Elena N; Kevbrin, Vadim V; Dedysh, Svetlana N

    2012-02-01

    A gram-negative, facultatively anaerobic, chemo-organotrophic, non-pigmented, slow-growing bacterium was isolated from acidic Sphagnum peat and designated strain TPB6017(T). Cells of this strain were long rods that multiplied by normal cell division and were motile by means of a single flagellum. Cells grew under reduced oxygen tension and under anoxic conditions and were able to ferment sugars and several polysaccharides, including amorphous and crystalline cellulose. Strain TPB6017(T) was a psychrotolerant acidophile capable of growth between pH 3.0 and 7.5 (optimum 4.5-5.0) and at 4-35 °C (optimum 20-28 °C). It was extremely sensitive to salt stress; growth was inhibited at NaCl concentrations above 0.1 % (w/v). The major fatty acids were iso-C(15 : 0) and iso-C(17 : 1)ω9c; the polar lipids were phosphatidylethanolamine and a number of phospholipids and aminophospholipids with an unknown structure. The quinone was MK-8. The DNA G+C content was 57.6 mol%. Comparative 16S rRNA gene sequence analysis revealed that strain TPB6017(T) was a member of subdivision 1 of the phylum Acidobacteria and belonged to a phylogenetic lineage defined by the acidophilic aerobic chemo-organotroph Acidobacterium capsulatum (92.3 % sequence similarity). However, cell morphology, type of flagellation, the absence of pigment, differences in fatty acid and polar lipid composition, possession of a cellulolytic capability, inability to grow under fully oxic conditions and good growth in anoxic conditions distinguished strain TPB6017(T) from A. capsulatum. Therefore, it is proposed that strain TPB6017(T) represents a novel acidobacterium species in a new genus, Telmatobacter bradus gen. nov., sp. nov.; strain TPB6017(T) ( = DSM 23630(T) = VKM B-2570(T)) is the type strain.

  13. 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…

  14. Nucleotide sequencing of an apparent proviral copy of env mRNA defines determinants of expression of the mouse mammary tumor virus env gene.

    PubMed Central

    Majors, J E; Varmus, H E

    1983-01-01

    To extend our understanding of the organization and expression of the mouse mammary tumor virus genome, we determined the nucleotide sequence of large regions of a cloned mouse mammary tumor virus strain C3H provirus that appears to be a DNA copy of env mRNA. In conjunction with analysis of several additional clones of integrated and unintegrated mouse mammary tumor virus DNAs, we came to the following conclusions: (i) the mRNA for env is generated by splicing mechanisms that recognize conventional eucaryotic signals at donor and acceptor sites with a leader of at least 289 bases in length; (ii) the first of three possible initiation codons for translation of env follows the splice junction by a single nucleotide and produces a signal peptide of 98 amino acids; (iii) the amino terminal sequence of the major virion glycoprotein gp52env is confirmed by nucleotide sequencing and is encoded by a sequence beginning 584 nucleotides from the 5' end of env mRNA; (iv) the final 17 amino acids at the carboxyl terminus of the primary product of env are encoded within the long terminal repeat by the 51 bases at the 5' end of the U3 domain; and (v) bases 2 through 4 at the 5' end of the long terminal repeat constitute an initiation codon that commences an open reading frame capable of directing the synthesis of a 36-kilodalton protein. PMID:6312081

  15. Phenethyl Alcohol as a Suppressor of the EnvA Phenotype Associated with the envA Gene in Escherichia coli K-12

    PubMed Central

    Normark, Staffan

    1971-01-01

    In Escherichia coli K-12 the envA gene was previously shown to mediate chain formation and a decreased tolerance to several antibacterial agents. Phenethyl alcohol at low concentrations has now been found to increase the tolerance to actinomycin D, ampicillin, rifampin, and gentian violet in strains containing envA. The increased tolerance to gentian violet was correlated to a decreased uptake of the dye. A phenotype suppression of chain formation and colony morphology in envA mutants was also obtained. Except for an increase in palmitic acid, chemical analysis revealed no differences between an envA and its wild-type strain in the lipopolysaccharide part of the envelope. However, a decrease in the amount of phosphatidylglycerol and a C18: 1 fatty acid was observed in the extractable lipids of a strain containing envA. Growth in the presence of phenethyl alcohol reversed the changes in fatty acid and the phospholipid composition. Phenethyl alcohol was found to cause an immediate but transient inhibition of ribonucleic acid synthesis. It is suggested that this inhibition affects the penetrability barrier of the outer cell envelope layers in strains containing envA. Images PMID:4941568

  16. 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.

  17. Functional and structural characterization of EnvZ, an osmosensing histidine kinase of E. coli.

    PubMed

    Yoshida, Takeshi; Phadtare, Sangita; Inouye, Masayori

    2007-01-01

    EnvZ is an osmosensing histidine kinase located in the inner membrane, and one of the most extensively studied Escherichia coli histidine kinases. Because of its structural complexity, functional and structural studies have been quite challenging. It is a multidomain transmembrane protein consisting of 450 amino acid residues. In addition, it must form a dimer to function as a histidine kinase like all the other histidine kinases. EnvZ consists of the 115-residue periplasmic domain, two transmembrane domains (TM1 and TM2), and the cytoplasmic domain consisting of the 43-residue linker (HAMP) domain and the 228-residue kinase domain. It has been shown that the kinase domain of EnvZ, responsible for its enzymatic activities, contains all of the conserved regions of histidine kinases such as H, F, N, G1, G2, and G3 boxes. Therefore, the 271-residue cytoplasmic domain of EnvZ (termed EnvZc) has been used as a model system to establish fundamental characteristics of histidine kinases. The DNA fragment encoding EnvZc was cloned in pET vector and EnvZc was expressed and purified. It is highly soluble and retains all the enzymatic activities of EnvZ. We demonstrated that it consists of two functional domains, domain A and domain B. NMR spectroscopic studies of these two domains revealed, for the first time, the structure of a histidine kinase. Domain A is responsible for dimerization of EnvZc forming a four-helical bundle containing two alpha-helical hairpin structures, while domain B is a monomer and has an ATP-binding pocket formed by regions conserved among the histidine kinases. In this chapter, we describe functional and structural studies of EnvZc, which can be applied to characterize other histidine kinases.

  18. Pseudotyping incompatibility between HIV-1 and gibbon ape leukemia virus Env is modulated by Vpu.

    PubMed

    Lucas, Tiffany M; Lyddon, Terri D; Cannon, Paula M; Johnson, Marc C

    2010-03-01

    The Env protein from gibbon ape leukemia virus (GaLV) has been shown to be incompatible with human immunodeficiency virus type 1 (HIV-1) in the production of infectious pseudotyped particles. This incompatibility has been mapped to the C-terminal cytoplasmic tail of GaLV Env. Surprisingly, we found that the HIV-1 accessory protein Vpu modulates this incompatibility. The infectivity of HIV-1 pseudotyped with murine leukemia virus (MLV) Env was not affected by Vpu. However, the infectivity of HIV-1 pseudotyped with an MLV Env with the cytoplasmic tail from GaLV Env (MLV/GaLV Env) was restricted 50- to 100-fold by Vpu. A Vpu mutant containing a scrambled membrane-spanning domain, Vpu(RD), was still able to restrict MLV/GaLV Env, but mutation of the serine residues at positions 52 and 56 completely alleviated the restriction. Loss of infectivity appeared to be caused by reduced MLV/GaLV Env incorporation into viral particles. The mechanism of this downmodulation appears to be distinct from Vpu-mediated CD4 downmodulation because Vpu-expressing cells that failed to produce infectious HIV-1 particles nonetheless continued to display robust surface MLV/GaLV Env expression. In addition, if MLV and HIV-1 were simultaneously introduced into the same cells, only the HIV-1 particle infectivity was restricted by Vpu. Collectively, these data suggest that Vpu modulates the cellular distribution of MLV/GaLV Env, preventing its recruitment to HIV-1 budding sites.

  19. 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

  20. Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

    PubMed

    Horino, Haruka; Fujita, Takashi; Tonouchi, Akio

    2014-04-01

    An obligately anaerobic bacterial strain designated T-1-35(T) was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35(T) stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8-1.0×3.5-15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35(T) exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15-40 °C, with an optimum at 35 °C. The pH range for growth was 5.5-9.0, with an optimum at pH 8.0-8.5 (slightly alkaliphilic). Strain T-1-35(T) fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35(T) belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35(T) was Bacteroides cellulosolvens WM2(T), with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35(T) was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35(T) is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35(T) ( = DSM 27016(T) = NBRC 109520(T)). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified

  1. Effects of modification of the HIV-1 Env cytoplasmic tail on immunogenicity of VLP vaccines.

    PubMed

    Vzorov, Andrei N; Wang, Li; Chen, Jianjun; Wang, Bao-Zhong; Compans, Richard W

    2016-02-01

    We investigated the effects on assembly and antigenic properties of specific modifications of the transmembrane spanning (TMS) and cytoplasmic tail (CT) domains of HIV-1 Env from a transmitted/founder (T/F) ZM53 Env glycoprotein. A construct containing a short version of the TMS domain derived from the mouse mammary tumor virus (MMTV) Env with or without a GCN4 trimerization sequence in the CT exhibited the highest levels of incorporation into VLPs and induced the highest titers of anti-Env IgG immune responses in a VLP context. Sera from guinea pigs immunized by VLPs with high Env content, and containing the CT trimerization sequence, had increased neutralization activity and antibody avidity. A cross-clade prime-boost regimen with clade B SF162 or clade C ZM53 Env DNA priming and boosting with VLPs containing modified ZM53 Env further enhanced these immune responses. The modified VLPs demonstrate improved potential as HIV-1 vaccine antigens.

  2. env Gene of Chicken RNA Tumor Viruses: Extent of Conservation in Cellular and Viral Genomes

    PubMed Central

    Fujita, Donald J.; Tal, Jacov; Varmus, Harold E.; Bishop, J. Michael

    1978-01-01

    The env gene of avian sarcoma-leukosis viruses codes for envelope glycoproteins that determine viral host range, antigenic specificity, and interference patterns. We used molecular hybridization to analyze the natural distribution and possible origins of the nucleotide sequences that encode env; our work exploited the availability of radioactive DNA (cDNAgp) complementary to most or all of env. env sequences were detectable in the DNAs of chickens which synthesized an env gene product (chick helper factor positive) encoded by an endogenous viral gene and also in the DNAs of chickens which synthesized little or no env gene product (chick helper factor negative). env sequences were not detectable in DNAs from Japanese quail, ring-necked pheasant, golden pheasant, duck, squab, salmon sperm, or calf thymus. The detection of sequences closely related to viral env only in chicken DNA contrasts sharply with the demonstration that the transforming gene (src) of avian sarcoma viruses has readily detectable homologues in the DNAs of all avian species tested [D. Stehelin, H. E. Varmus, J. M. Bishop, and P. K. Vogt, Nature (London) 260: 170-173, 1976] and in the DNAs of other vertebrates (D. Spector, personal communication). Thermal denaturation studies on duplexes formed between cDNAgp and chicken DNA and also between cDNAgp and RNAs of subgroup A to E viruses derived from chickens indicated that these duplexes were well matched. In contrast, cDNAgp did not form stable hybrids with RNAs of viruses which were isolated from ring-necked and golden pheasants. We conclude that substantial portions of nucleotide sequences within the env genes of viruses of subgroups A to E are closely related and that these genes probably have a common, perhaps cellular, evolutionary origin. PMID:212576

  3. 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 the env gene of subgroup A FeLV (FeLV-A), the primary virus. We report the isolation and characterization of a novel env gene, 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.

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

    PubMed Central

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

    2016-01-01

    Feline leukemia virus (FeLV) subgroups have emerged in infected cats via the mutation or recombination of the env gene of subgroup A FeLV (FeLV-A), the primary virus. We report the isolation and characterization of a novel env gene, 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

  5. Using GenCade to Create a Sediment Budget in SBAS

    DTIC Science & Technology

    2015-08-01

    change and sand transport model (Frey et al. 2012a), and the Sediment Budget Analysis System (SBAS) (Dopsovic et al. 2003). Two of the main GenCade...GENESIS (Hanson and Kraus 1989) and the regional-scale, planning-level calculations of Cascade (Larson et al. 2003; Connell and Kraus 2006). GenCade...use advanced cards in the GenCade input files for earlier versions of the SMS. A GenCade technical report (Frey et al. 2012a) includes model theory, a

  6. Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution

    PubMed Central

    Zanini, Fabio

    2013-01-01

    Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8+ T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the env gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not. PMID:23986591

  7. 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 .

  8. 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

  9. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

    2008-01-01

    GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing 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 Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, 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 Homepage: www.ncbi.nlm.nih.gov.

  10. GenBank.

    PubMed

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

    2011-01-01

    GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, 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 that 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 Homepage: www.ncbi.nlm.nih.gov.

  11. GenBank.

    PubMed

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

    2010-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, 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 Molecular Biology Laboratory Nucleotide Sequence Database in Europe 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 bi-monthly 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 homepage: www.ncbi.nlm.nih.gov.

  12. Using GenBank.

    PubMed

    Wheeler, David

    2007-01-01

    GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through 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 Homepage at http://www.ncbi.nlm.nih.gov.

  13. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

    2007-01-01

    GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing 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 EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, 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 Homepage (www.ncbi.nlm.nih.gov).

  14. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

    2006-01-01

    GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing 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 EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, 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, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

  15. GenBank.

    PubMed

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

    2009-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe 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 Homepage: www.ncbi.nlm.nih.gov.

  16. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

    2005-01-01

    GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing 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 EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, 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, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

  17. Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer

    PubMed Central

    2016-01-01

    Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI. PMID:27992602

  18. 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.

  19. Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer.

    PubMed

    Khasnis, Mukta D; Halkidis, Konstantine; Bhardwaj, Anshul; Root, Michael J

    2016-12-01

    Structural rearrangements of HIV-1 glycoprotein Env promote viral entry through membrane fusion. Env is a symmetric homotrimer with each protomer composed of surface subunit gp120 and transmembrane subunit gp41. Cellular CD4- and chemokine receptor-binding to gp120 coordinate conformational changes in gp41, first to an extended prehairpin intermediate (PHI) and, ultimately, into a fusogenic trimer-of-hairpins (TOH). HIV-1 fusion inhibitors target gp41 in the PHI and block TOH formation. To characterize structural transformations into and through the PHI, we employed asymmetric Env trimers containing both high and low affinity binding sites for individual fusion inhibitors. Asymmetry was achieved using engineered Env heterotrimers composed of protomers deficient in either CD4- or chemokine receptor-binding. Linking receptor engagement to inhibitor affinity allowed us to assess conformational changes of individual Env protomers in the context of a functioning trimer. We found that the transition into the PHI could occur symmetrically or asymmetrically depending on the stoichiometry of CD4 binding. Sequential engagement of multiple CD4s promoted progressive exposure of individual fusion inhibitor binding sites in a CD4-dependent fashion. By contrast, engagement of only a single CD4 molecule led to a delayed, but symmetric, exposure of the gp41 trimer. This complex coupling between Env-CD4 interaction and gp41 exposure explained the multiphasic fusion-inhibitor titration observed for a mutant Env homotrimer with a naturally asymmetric gp41. Our results suggest that the spatial and temporal exposure of gp41 can proceed in a nonconcerted, asymmetric manner depending on the number of CD4s that engage the Env trimer. The findings have important implications for the mechanism of viral membrane fusion and the development of vaccine candidates designed to elicit neutralizing antibodies targeting gp41 in the PHI.

  20. Diverse antibody genetic and recognition properties revealed following HIV-1 Env immunization

    PubMed Central

    Phad, Ganesh E.; Bernat, Néstor Vázquez; Feng, Yu; Ingale, Jidnyasa; Murillo, Paola Andrea Martinez; O’Dell, Sijy; Li, Yuxing; Mascola, John R.; Sundling, Christopher; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2015-01-01

    Isolation of monoclonal antibodies (MAbs) elicited by vaccination provides opportunities to define the development of effective immunity. Ab responses elicited by current HIV-1 envelope glycoprotein (Env) immunogens display narrow neutralizing activity with limited capacity to block infection by tier 2 viruses. Intense work in the field suggests that improved Env immunogens are forthcoming and it is therefore important to concurrently develop approaches to investigate the quality of vaccine-elicited responses at a higher level of resolution. Here, we cloned a representative set of MAbs elicited by a model Env immunogen in rhesus macaques and comprehensively characterized their genetic and functional properties. The MAbs were genetically diverse, even within groups of Abs targeting the same sub-region of Env, consistent with a highly polyclonal response. MAbs directed against two sub-determinants of Env, the CD4 binding site (CD4bs) and the V3 region, could in part account for the neutralizing activity observed in the plasma of the animal from which they were cloned, demonstrating the power of MAb isolation for a detailed understanding of the elicited response. Finally, through comparative analyses of MAb binding and neutralizing capacity of HIV-1 using matched Envs, we demonstrate complex relationships between epitope recognition and accessibility, highlighting the protective quaternary packing of the HIV-1 spike relative to vaccine-induced MAbs. PMID:25964491

  1. GenBank

    PubMed Central

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

    2017-01-01

    GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 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 the NCBI Submission Portal. GenBank staff assign 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 Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and 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. Recent updates include changes to policies regarding sequence identifiers, an improved 16S submission wizard, targeted loci studies, the ability to submit methylation and BioNano mapping files, and a database of anti-microbial resistance genes. PMID:27899564

  2. Processing and amino acid sequence analysis of the mouse mammary tumor virus env gene product.

    PubMed Central

    Arthur, L O; Copeland, T D; Oroszlan, S; Schochetman, G

    1982-01-01

    The envelope proteins of mouse mammary tumor virus (MMTV) are synthesized from a subgenomic 24S mRNA as a 75,000-dalton glycosylated precursor polyprotein which is eventually processed to the mature glycoproteins gp52 and gp36. In vivo synthesis of this env precursor in the presence of the core glycosylation inhibitor tunicamycin yielded a precursor of approximately 61,000 daltons (P61env). However, a 67,000-dalton protein (P67env) was obtained from cell-free translation with the MMTV 24S mRNA as the template. To determine whether the portion of the protein cleaved from P67env to give P61env was removed from the NH2-terminal end of P67env and as such would represent a leader sequence, the NH2-terminal amino acid sequence of the terminal peptide gp52 was determined. Glutamic acid, and not methionine, was found to be the amino-terminal residue of gp52, indicating that the cleaved portion was derived from the NH2-terminal end of P67env. The NH2-terminal amino acid sequences of gp52's from endogenous and exogenous C3H MMTVs were determined though 46 residues and found to be identical. However, amino acid composition and type-specific gp52 radioimmunoassays from MMTVs grown in heterologous cells indicated primary structure differences between gp52's of the two viruses. The nucleic acid sequence of cloned MMTV DNA fragments (J. Majors and H. E. Varmus, personal communication) in conjunction with the NH2-terminal sequence of gp52 allowed localization of the env gene in the MMTV genome. Nucleotides coding for the NH2 terminus of gp52 begin approximately 0.8 kilobase to the 3' side of the single EcoRI cleavage site. Localization of the env gene at that point agrees with the proposed gene order -gag-pol-env- and also allows sufficient coding potential for the glycoprotein precursor without extending into the long terminal repeat. Images PMID:6281457

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

    PubMed

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

    2014-11-07

    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.

  4. Antibody to gp41 MPER alters functional properties of HIV-1 Env without complete neutralization.

    PubMed

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

    2014-07-01

    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.

  5. 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.

  6. Role of Virus Receptor Hyal2 in Oncogenic Transformation of Rodent Fibroblasts by Sheep Betaretrovirus Env Proteins

    PubMed Central

    Liu, Shan-Lu; Duh, Fuh-Mei; Lerman, Michael I.; Miller, A. Dusty

    2003-01-01

    The ovine betaretroviruses jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV) cause contagious cancers in the lungs and upper airways of sheep and goats. Oncogenic transformation assays using mouse and rat fibroblasts have localized the transforming activity to the Env proteins encoded by these viruses, which require the putative lung and breast cancer tumor suppressor hyaluronidase 2 (Hyal2) to promote virus entry into cells. These results suggested the hypothesis that the JSRV and ENTV Env proteins cause cancer by inhibiting the tumor suppressor activity of Hyal2. Consistent with this hypothesis, we show that human Hyal2 and other Hyal2 orthologs that can promote virus entry, including rat Hyal2, can suppress transformation by the Env proteins of JSRV and ENTV. Furthermore, we provide direct evidence for binding of the surface (SU) region of JSRV Env to human and rat Hyal2. However, mouse Hyal2 did not mediate entry of virions bearing JSRV or ENTV Env proteins, bound JSRV SU poorly if at all, and did not suppress transformation by the JSRV or ENTV Env proteins, indicating that mouse Hyal2 plays no role in transformation of mouse fibroblasts and that the Env proteins can transform at least some cells by a Hyal2-independent mechanism. Expression of human Hyal2 in mouse cells expressing JSRV Env caused a marked reduction in Env protein levels, indicating that human Hyal2 suppresses Env-mediated transformation in mouse cells by increasing Env degradation rather than by exerting a more general Env-independent tumor suppressor activity. PMID:12584308

  7. Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008.

    PubMed

    Dedysh, Svetlana N; Kulichevskaya, Irina S; Serkebaeva, Yulia M; Mityaeva, Maria A; Sorokin, Vladimir V; Suzina, Natalia E; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe

    2012-03-01

    An aerobic, pink-pigmented, chemo-organotrophic bacterium, designated strain SN10(T), was isolated from a methanotrophic enrichment culture obtained from an acidic Sphagnum peat. This isolate was represented by Gram-negative, non-motile rods that multiply by normal cell division and form rosettes. Strain SN10(T) is an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.2-6.6 (with an optimum at pH 4.7-5.2) and at 6-32 °C (with an optimum at 20-24 °C). The preferred growth substrates are sugars and several heteropolysaccharides of plant and microbial origin, such as pectin, lichenan, fucoidan and gellan gum. While not being capable of growth on C(1) compounds, strain SN10(T) can develop in co-culture with exopolysaccharide-producing methanotrophs by utilization of their capsular material. The major fatty acids determined in strain SN10(T) using the conventional lipid extraction procedure are iso-C(15:0) and C(16:1)ω7c. Upon hydrolysis of total cell material, substantial amounts of the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (isodiabolic acid) were also detected. The polar lipids are two phosphohexoses, phosphatidylethanolamine, phosphatidylglycerol and several phospholipids of unknown structure. The major quinone is MK-8. Pigments are carotenoids. The G+C content of the DNA is 60.7 mol%. Strain SN10(T) forms a separate lineage within subdivision 1 of the phylum Acidobacteria and displays 94.0-95.4% 16S rRNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0-93.7% similarity to members of the genus Terriglobus and 92.2-92.3 % similarity to the type strains of Telmatobacter bradus and Acidobacterium capsulatum. Therefore, strain SN10(T) is classified within a novel genus and species, for which the name Bryocella elongata gen. nov., sp. nov. is proposed. Strain SN10(T) (=LMG 25276(T) =DSM 22489(T)) is the type strain of Bryocella elongata. An emended description of Edaphobacter

  8. Intracellular trafficking of Gag and Env proteins and their interactions modulate pseudotyping of retroviruses.

    PubMed

    Sandrin, Virginie; Muriaux, Delphine; Darlix, Jean-Luc; Cosset, François-Loïc

    2004-07-01

    Glycoproteins derived from most retroviruses and from several families of enveloped viruses can form infectious pseudotypes with murine leukemia virus (MLV) and lentiviral core particles, like the MLV envelope glycoproteins (Env) that are incorporated on either virus type. However, coexpression of a given glycoprotein with heterologous core proteins does not always give rise to highly infectious viral particles, and restrictions on pseudotype formation have been reported. To understand the mechanisms that control the recruitment of viral surface glycoproteins on lentiviral and retroviral cores, we exploited the fact that the feline endogenous retrovirus RD114 glycoprotein does not efficiently pseudotype lentiviral cores derived from simian immunodeficiency virus, whereas it is readily incorporated onto MLV particles. Our results indicate that recruitment of glycoproteins by the MLV and lentiviral core proteins occurs in intracellular compartments and not at the cell surface. We found that Env and core protein colocalization in intracytoplasmic vesicles is required for pseudotype formation. By investigating MLV/RD114 Env chimeras, we show that signals in the cytoplasmic tail of either glycoprotein differentially influenced their intracellular localization; that of MLV allows endosomal localization and hence recruitment by both lentiviral and MLV cores. Furthermore, we found that upon membrane binding, MLV core proteins could relocalize Env glycoproteins in late endosomes and allow their incorporation on viral particles. Thus, intracellular colocalization, as well as interactions between Env and core proteins, may influence the recruitment of the glycoprotein onto viral particles and generate infectious pseudotyped viruses.

  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. Mutations in both env and gag genes are required for HIV-1 resistance to the polysulfonic dendrimer SPL2923, as corroborated by chimeric virus technology.

    PubMed

    Hantson, Anke; Fikkert, Valery; Van Remoortel, Barbara; Pannecouque, Chistophe; Cherepanov, Peter; Matthews, Barry; Holan, George; De Clercq, Erik; Vandamme, Anne-Mieke; Debyser, Zeger; Witvrouw, Myriam

    2005-01-01

    A drug-resistant NL4.3/SPL2923 strain has previously been generated by in vitro selection of HIV-1(NL4.3) in the presence of the polysulfonic dendrimer SPL2923 and mutations were reported in its gp120 gene (Witvrouw et al., 2000). Here, we further analysed the (cross) resistance profile of NL4.3/SPL2923. NL4.3/SPL2923 was found to contain additional mutations in gp41 and showed reduced susceptibility to SPL2923, dextran sulfate (DS) and enfuvirtide. To delineate to what extent the mutations in each env gene were accountable for the phenotypic (cross) resistance of NL4.3/SPL2923, the gp120-, gp41- and gp160-sequences derived from this strain were placed into a wild-type background using env chimeric virus technology (CVT). The cross resistance of NL4.3/SPL2923 towards DS was fully reproduced following gp160-recombination, while it was only partially reproduced following gp120- or gp41-recombination. The mutations in gp41 of NL4.3/SPL2923 were sufficient to reproduce the cross resistance to enfuvirtide. Unexpectedly, the reduced sensitivity towards SPL2923 was not fully reproduced after gp160-recombination. The search for mutations in NL4.3/SPL2923 in viral genes other than env revealed several mutations in the gene encoding the HIV p17 matrix protein (MA) and one mutation in the gene encoding the p24 capsid protein (CA). In order to analyse the impact of the gag mutations alone and in combination with the mutations in env on the phenotypic resistance towards SPL2923, we developed a novel p17- and p17/gp160-CVT. Phenotypic analysis of the NL4.3/SPL2923 p17- and p17/gp160-recombined strains indicated that the mutations in both env and gag have to be present to fully reproduce the resistance of NL4.3/SPL2923 towards SPL2923.

  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.

  12. 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

  13. Direct evidence for intracellular anterograde co-transport of M-PMV Gag and Env on microtubules

    PubMed Central

    Pereira, Lara E.; Clark, Jasmine; Grznarova, Petra; Wen, Xiaoyun; LaCasse, Rachel; Ruml, Tomas; Spearman, Paul

    2014-01-01

    The intracellular transport of Mason-Pfizer monkey virus (M-PMV) assembled capsids from the pericentriolar region to the plasma membrane (PM) requires trafficking of envelope glycoprotein (Env) to the assembly site via the recycling endosome. However, it is unclear if Env-containing vesicles play a direct role in trafficking capsids to the PM. Using live cell microscopy, we demonstrate, for the first time, anterograde co-transport of Gag and Env. Nocodazole disruption of microtubules had differential effects on Gag and Env trafficking, with pulse-chase assays showing a delayed release of Env-deficient virions. Particle tracking demonstrated an initial loss of linear movement of GFP-tagged capsids and mCherry-tagged Env, followed by renewed movement of Gag but not Env at 4 h post-treatment. Thus, while delayed capsid trafficking can occur in the absence of microtubules, efficient anterograde transport of capsids appears to be mediated by microtubule-associated Env-containing vesicles. PMID:24418544

  14. 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

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

    PubMed

    Heydarchi, Behnaz; 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

  16. Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C.

    PubMed

    Lin, Nina H; Becerril, Carlos; Giguel, Francoise; Novitsky, Vladimir; Moyo, Sikhulile; Makhema, Joseph; Essex, Myron; Lockman, Shahin; Kuritzkes, Daniel R; Sagar, Manish

    2012-11-25

    HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C.

  17. Env sequence determinants in CXCR4-using human immunodeficiency virus type-1 subtype C

    PubMed Central

    Lin, Nina H.; Becerril, Carlos; Giguel, Francoise; Novitsky, Vladimir; Moyo, Sikhulile; Makhema, Joseph; Essex, Myron; Lockman, Shahin; Kuritzkes, Daniel R.; Sagar, Manish

    2012-01-01

    HIV-1 subtype C (HIV-1C) CXCR4-using virus is isolated infrequently and is poorly characterized. Understanding HIV-1C env characteristics has implications for the clinical use of antiretrovirals that target viral entry. A total of 209 env clones derived from 10 samples with mixed CCR5-(R5), CXCR4-using (X4) or dual-tropic HIV-1C were phenotyped for coreceptor usage. Intra-patient X4 and R5 variants generally formed distinct monophyletic phylogenetic clusters. X4 compared to R5 envs had significantly greater amino acid variability and insertions, higher net positive charge, fewer glycosylation sites and increased basic amino acid substitutions in the GPGQ crown. Basic amino acid substitution and/or insertion prior to the crown are highly sensitive characteristics for predicting X4 viruses. Chimeric env functional studies suggest that the V3 loop is necessary but often not sufficient to impart CXCR4 utilization. Our studies provide insights into the unique genotypic characteristics of X4 variants in HIV-1C. PMID:22954962

  18. 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

  19. 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.

  20. 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

  1. Reclassification of Eubacterium rectale (Prévot et al., 1967) in a new genus Agathobacter gen. nov., as Agathobacter rectalis comb. nov., within the family Lachnospiraceae, and description of Agathobacter ruminis sp. nov., from the rumen.

    PubMed

    Rosero, Jaime A; Killer, Jiří; Sechovcová, Hana; Mrázek, Jakub; Benada, Oldřich; Fliegerová, Kateřina; Havlík, Jaroslav; Kopečný, Jan

    2015-11-30

    Three strains of a Gram-positive, butyrate producing bacteria were isolated from the rumen content of grazing sheep and cow. The strains were anaerobic, Gram-positive cell wall, straight to slightly curved rod-shaped, non-spore-forming and single flagellate. C14:1, C14:0, C16:0 and C16:1 were the predominant fatty acids. The type of cell-wall peptidoglycan is A1γ. The DNA G+C content varied from 41.4 to 42.2 mol%. The 16S rRNA gene sequence similarities between the isolates and Eubacterium rectale, Roseburia hominis and Roseburia intestinalis were found to be 96, 95 and 95%, respectively. The phylogenetic tree showed that the strains constituted a different taxon, separate from other taxa with validly published names and forming a cluster with strains of Eubacterium rectale. On the basis of phenotypic, chemotaxonomic and phylogenetic results (16S RNA, DnaK, GroEL, atpA genes), isolates are considered to represent a novel species of a novel genus of the family Lachnospiraceae for which we propose the name Agathobacter ruminis gen. nov., sp. nov. with the type strain Agathobacter ruminis JK623T (=DSM 29029T =LMG 28559T). We also propose the transfer of Eubacterium rectale to the new genus Agathobacter gen. nov. This genus represents saccharoclastic chemoorganotrophic non-spore forming rods, with Gram-positive membrane, obligatory anaerobic. Main fermentation products on PYG medium were butyrate, acetate, hydrogen and lactate. Peptidoglycan in all species is of A1γ type. Type species is Agathobacter rectalis, gen. nov., comb nov. (Egghert 1935) with type strain ATCC 33656T (==KCTC 5835T). Two species of the new genus, Agathobacter rectalis and Agathobacter ruminis has been defined.

  2. The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm.

    PubMed

    Wang, Loo Chien; Morgan, Leslie K; Godakumbura, Pahan; Kenney, Linda J; Anand, Ganesh S

    2012-05-30

    Two-component systems mediate bacterial signal transduction, employing a membrane sensor kinase and a cytoplasmic response regulator (RR). Environmental sensing is typically coupled to gene regulation. Understanding how input stimuli activate kinase autophosphorylation remains obscure. The EnvZ/OmpR system regulates expression of outer membrane proteins in response to osmotic stress. To identify EnvZ conformational changes associated with osmosensing, we used HDXMS to probe the effects of osmolytes (NaCl, sucrose) on the cytoplasmic domain of EnvZ (EnvZ(c)). Increasing osmolality decreased deuterium exchange localized to the four-helix bundle containing the autophosphorylation site (His(243)). EnvZ(c) exists as an ensemble of multiple conformations and osmolytes favoured increased helicity. High osmolality increased autophosphorylation of His(243), suggesting that these two events are linked. In-vivo analysis showed that the cytoplasmic domain of EnvZ was sufficient for osmosensing, transmembrane domains were not required. Our results challenge existing claims of robustness in EnvZ/OmpR and support a model where osmolytes promote intrahelical H-bonding enhancing helix stabilization, increasing autophosphorylation and downstream signalling. The model provides a conserved mechanism for signalling proteins that respond to diverse physical and mechanical stimuli.

  3. Sequencing of Gag/Env association with HIV genotyping resolution and HIV-related epidemiologic studies of HIV in China.

    PubMed

    Ren, L; Wang, H W; Xu, Y; Feng, Y; Zhang, H F; Wang, K H

    2016-10-24

    HIV genotyping has led to conflicting results between laboratories. Therefore, identifying the most accurate gene combinations to sequence remains a priority. Datasets of Chinese HIV subtypes based on several markers and deposited in PubMed, Metstr, CNKI, and VIP databases between 2000 and 2015 were studied. In total, 9177 cases of amplification-positive samples from 26 provinces of China were collected and used to classify HIV subtypes based on eight individual genes or a combination thereof. CRF01_AE, CRF07_BC, CRF08_BC and B were the prevalent HIV subtypes in China, accounting for 84.07% of all genotypes. Gag/Env sequencing classified a greater number of HIV subtypes compared to other genes or combination of gene fragments. The geographical distribution of Gag and Gag/Env genotypes was similar to that observed with all genetic markers. Further principal component analysis showed a significantly different geographical distribution pattern of HIV in China for HIV genotypes detected with Gag/Env, which was in line with the distribution of all HIV genotypes in China. Gag/Env sequences had the highest diversity of the eight markers studied, followed by Gag and Gag/Pol/Env; Pol/Env polymorphisms were the least divergent. Gag/Env can serve as a high-resolution marker for HIV genotyping.

  4. Analysis of the human env-specific cytotoxic T-lymphocyte (CTL) response in natural human immunodeficiency virus type 1 infection: low prevalence of broadly cross-reactive env-specific CTL.

    PubMed Central

    Carmichael, A; Jin, X; Sissons, P

    1996-01-01

    Major histocompatibility complex-restricted cytotoxic T lymphocytes (CTL) are part of the cellular immune response to persistent virus infections. Candidate vaccines against human immunodeficiency virus type 1 (HIV-1) should elicit broad cross-reactive immunity to confer protection against different strains of HIV-1. As it is likely that candidate vaccines will include the envelope gene product Env, we determined the proportion of CTL clones which recognized variable and conserved determinants in three env variants during natural infection. Limiting dilution analysis was used to characterize numerous short-term CTL clones derived from peripheral blood of HIV-1-infected subjects, using split-well analysis to assay cytotoxicity against target cells expressing gp160env of HIV-1 strains IIIB, MN, and RF. In 9 of 12 HIV-1-infected subjects, at the clonal level most env-specific CTL recognized determinant(s) within one env variant but not in the other variants. In some subjects, CTL recognized multiple nonconserved determinants in different variants. The pattern of recognition of different env variants was relatively stable over time. In most of the patients studied, the proportion of CTL which showed cross-recognition of conserved determinants shared among the three strains was low. Two novel CTL epitopes within gp41 were identified by using 15-mer peptides of the HIV-SF2 sequence. When specific peptide was used to stimulate CTL precursors in vitro, the frequency of peptide-specific CTL precursors was very high, but the CTL elicited by this stimulation were highly strain specific. We conclude that the use of a single HIV env variant to detect CTL activity can underestimate the magnitude and complexity of the env-specific CTL response. The low prevalence of CTL clones which show cross-recognition of conserved determinants may have implications for immunization strategies based solely on env; to elicit broadly cross-reactive CTL other, more conserved viral antigens are

  5. Crystallographic snapshot of the Escherichia coli EnvZ histidine kinase in an active conformation.

    PubMed

    Ferris, Hedda U; Coles, Murray; Lupas, Andrei N; Hartmann, Marcus D

    2014-06-01

    Sensor histidine kinases are important sensors of the extracellular environment and relay signals via conformational changes that trigger autophosphorylation of the kinase and subsequent phosphorylation of a response regulator. The exact mechanism and the regulation of this protein family are a matter of ongoing investigation. Here we present a crystal structure of a functional chimeric protein encompassing the entire catalytic part of the Escherichia coli EnvZ histidine kinase, fused to the HAMP domain of the Archaeoglobus fulgidus Af1503 receptor. The construct is thus equivalent to the full cytosolic part of EnvZ. The structure shows a putatively active conformation of the catalytic domain and gives insight into how this conformation could be brought about in response to sensory input. Our analysis suggests a sequential flip-flop autokinase mechanism.

  6. 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

  7. 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

  8. 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

    2015-09-25

    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.

  9. 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.

  10. Aerobic Biodegradation of N-Nitrosodimethylamine by the Propanotroph Rhodococcus ruber ENV425▿

    PubMed Central

    Fournier, Diane; Hawari, Jalal; Halasz, Annamaria; Streger, Sheryl H.; McClay, Kevin R.; Masuda, Hisako; Hatzinger, Paul B.

    2009-01-01

    The propanotroph Rhodococcus ruber ENV425 was observed to rapidly biodegrade N-nitrosodimethylamine (NDMA) after growth on propane, tryptic soy broth, or glucose. The key degradation intermediates were methylamine, nitric oxide, nitrite, nitrate, and formate. Small quantities of formaldehyde and dimethylamine were also detected. A denitrosation reaction, initiated by hydrogen atom abstraction from one of the two methyl groups, is hypothesized to result in the formation of n-methylformaldimine and nitric oxide, the former of which decomposes in water to methylamine and formaldehyde and the latter of which is then oxidized further to nitrite and then nitrate. Although the strain mineralized more than 60% of the carbon in [14C]NDMA to 14CO2, growth of strain ENV425 on NDMA as a sole carbon and energy source could not be confirmed. The bacterium was capable of utilizing NDMA, as well as the degradation intermediates methylamine and nitrate, as sources of nitrogen during growth on propane. In addition, ENV425 reduced environmentally relevant microgram/liter concentrations of NDMA to <2 ng/liter in batch cultures, suggesting that the bacterium may have applications for groundwater remediation. PMID:19542346

  11. Novel Monoclonal Antibody Directed at the Receptor Binding Site on the Avian Sarcoma and Leukosis Virus Env Complex

    PubMed Central

    Ochsenbauer-Jambor, Christina; Delos, Sue E.; Accavitti, Mary Ann; White, Judith M.; Hunter, Eric

    2002-01-01

    We report here on the generation of a mouse monoclonal antibody directed against Rous sarcoma virus (RSV) subgroup A Env that will be useful in functional and structural analysis of RSV Env, as well as in approaches employing the RCAS/Tva system for gene targeting. BALB/c mice were primed and given boosters twice with EnvA-expressing NIH 3T3 cells. Resulting hybridomas were tested by enzyme-linked immunosorbent assay against RCANBP virions and SU-A-immunoglobulin G immunoadhesin. One highly reactive hybridoma clone, mc8C5, was subcloned and tested in immunofluorescence, immunoprecipitation (IP), and Western blotting assays. In all three assays, mc8C5-4 subgroup-specifically recognizes SR-A Env, through the SU domain, expressed from different vectors in both avian and mammalian cells. This multifunctionality is notable for a mouse monoclonal. We furthermore observed a preference for binding to terminally glycosylated Env over core-glycosylated Env precursor in IPs, suggesting that the epitope is at least partially conformational and dependent on glycosylation. Most importantly, we found mc8C5-4 inhibited Env function: in vitro, the monoclonal not only interferes with binding of the EnvA receptor, Tva, but it also blocks the Tva-induced conformational change required for activation of the fusion peptide, without inducing that change itself. Infection of Tva-expressing avian or mammalian cells by avian sarcoma and leukosis virus (ASLV) or EnvA-pseudotyped murine leukemia virus, respectively, is efficiently inhibited by mc8C5-4. The apparent interference of the monoclonal with the EnvA-Tva complex formation suggests that the epitope seen by mc8C5 overlaps with the receptor binding site. This is supported by the observation that mutations of basic residues in hr2 or of the downstream glycosylation site, which both impair Tva-binding to EnvA, have similar effects on the binding of mc8C5. Thus, anti-ASLV-SU-A mc8C5-4 proves to be a unique new immunoreagent that targets

  12. Study of the HIV-2 Env Cytoplasmic Tail Variability and Its Impact on Tat, Rev and Nef

    PubMed Central

    Bakouche, Nordine; Vandenbroucke, Anne-Thérèse; Goubau, Patrick; Ruelle, Jean

    2013-01-01

    Background The HIV-2 env’s 3’ end encodes the cytoplasmic tail (CT) of the Env protein. This genomic region also encodes the rev, Tat and Nef protein in overlapping reading frames. We studied the variability in the CT coding region in 46 clinical specimens and in 2 reference strains by sequencing and by culturing. The aims were to analyse the variability of Env CT and the evolution of proteins expressed from overlapping coding sequences. Results A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains in vitro due to a premature stop codon in the env gene. In clinical samples this wasn’t observed, but the CT length varied due to insertions and deletions. We noted 3 conserved and 3 variable regions in the CT. The conserved regions were those containing residues involved in Env endocytosis, the potential HIV-2 CT region implicated in the NF-kB activation and the potential end of the lentiviral lytic peptide one. The variable regions were the potential HIV-2 Kennedy region, the potential lentiviral lytic peptide two and the beginning of the potential lentiviral lytic peptide one. A very hydrophobic region was coded downstream of the premature stop codon observed in vitro, suggesting a membrane spanning region. Interestingly, the nucleotides that are responsible for the variability of the CT don’t impact rev and Nef. However, in the Kennedy-like coding region variability resulted only from nucleotide changes that impacted Env and Tat together. Conclusion The HIV-2 Env, Tat and Rev C-terminal part are subject to major length variations in both clinical samples and cultured strains. The HIV-2 Env CT contains variable and conserved regions. These regions don’t affect the rev and Nef amino acids composition which evolves independently. In contrast, Tat co-evolves with the Env CT. PMID:24223892

  13. TrafficGen Architecture Document

    DTIC Science & Technology

    2016-01-01

    v 1. Overview of TrafficGen Application 1 2. Modules 2 3. User Interface 3 3.1 Top-Level MVC Classes 3 3.1.1 TrafficGenView 3 3.1.2...release; distribution unlimited. 3 A key design concept in use here is the model-view-controller ( MVC ) pattern. In general, the MVC design pattern...and easier to manage. MVC facilitates reuse by reducing and formalizing coupling between model components and the user interface. The same TrafficGen

  14. HIV-1 Nef responsiveness is determined by Env variable regions involved in trimer association and correlates with neutralization sensitivity.

    PubMed

    Usami, Yoshiko; Göttlinger, Heinrich

    2013-11-14

    HIV-1 Nef and the unrelated murine leukemia virus glycoGag similarly enhance the infectivity of HIV-1 virions. We now show that the effects of Nef and glycoGag are similarly determined by variable regions of HIV-1 gp120 that control Env trimer association and neutralization sensitivity. Whereas neutralization-sensitive X4-tropic Env proteins conferred high responsiveness to Nef and glycoGag, particles bearing neutralization-resistant R5-tropic Envs were considerably less affected. The profoundly different Nef/glycoGag responsiveness of a neutralization-resistant and a neutralization-sensitive R5-tropic Env could be switched by exchanging their gp120 V1/V2 regions, which also switches their neutralization sensitivity. Within V1/V2, the same determinants governed Nef/glycoGag responsiveness and neutralization sensitivity, indicating that these phenotypes are mechanistically linked. The V1/V2 and V3 regions, which form an apical trimer-association domain, together determined the Nef and glycoGag responsiveness of an X4-tropic Env. Our results suggest that Nef and glycoGag counteract the inactivation of Env spikes with relatively unstable apical trimer-association domains.

  15. 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.

  16. Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996.

    PubMed

    Ntougias, Spyridon; Zervakis, Georgios I; Fasseas, Constantinos

    2007-09-01

    A novel Gram-negative, motile, nonsporulating, rod-shaped bacterium isolated from alkaline sludge-like wastes ('alpeorujo' or 'alperujo') of two-phase olive oil extraction is described. The strain, designated AW-7(T), is an obligate aerobe that is halotolerant (tolerating up to 15 % w/v NaCl), sugar-tolerant (tolerating up to 45 % and 60 % w/v (+)-d-glucose and maltose respectively; these are the highest concentrations tolerated by any known members of the Bacteria domain) and alkalitolerant (growing at a broad pH range of 5-11). Strain AW-7(T) is chemo-organotrophic. Ubiquinone-9 was detected in the respiratory chain of strain AW-7(T). The major fatty acids present are C(18 : 1)omega7c, C(16 : 0), C(19 : 0) cyclo omega8c, C(12 : 0) 3-OH and C(16 : 1)omega7c/iso-C(15 : 0) 2-OH. Based on 16S rRNA gene sequence analysis, strain AW-7(T) showed almost equal phylogenetic distances from Zymobacter palmae (95.6 % similarity) and Carnimonas nigrificans (95.4 % similarity). In addition, low DNA-DNA relatedness values were found for strain AW-7(T) against Carnimonas nigrificans CECT 4437(T) (22.5-25.4 %) and Z. palmae DSM 10491(T) (11.9-14.4 %). The DNA G+C content of strain AW-7(T) is 64.4 mol%. Physiological and chemotaxonomic data further confirmed the differentiation of strain AW-7(T) from the genera Zymobacter and Carnimonas. Thus, strain AW-7(T) represents a novel bacterial genus within the family Halomonadaceae, for which the name Halotalea gen. nov. is proposed. Halotalea alkalilenta sp. nov. (type strain AW-7(T)=DSM 17697(T)=CECT 7134(T)) is proposed as the type species of the genus Halotalea gen. nov. A reassignment of the descriptive 16S rRNA signature characteristics of the family Halomonadaceae permitted the placement of the novel genus Halotalea into the family; in contrast, the genus Halovibrio possessed only 12 out of the 18 signature characteristics proposed, and hence it was excluded from the family Halomonadaceae.

  17. Real-time analysis of human immunodeficiency virus type 1 Env-mediated membrane fusion by fluorescence resonance energy transfer.

    PubMed

    Furuta, Rika A; Nishikawa, Masao; Fujisawa, Jun-ichi

    2006-02-01

    Human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env)-mediated membrane fusion occurs as a sequence of events that is triggered by CD4 binding to the Env gp120 subunit. In this study, we analyzed the dynamics of Env-mediated membrane fusion at the single-cell level using fluorescent fusion proteins and confocal laser fluorescent microscopy. Either enhanced cyan or yellow fluorescent protein (CFP and YFP, respectively) was fused to the end of the cytoplasmic regions of the HIV-1 receptors (CD4 and CCR5) and Env proteins. Real-time imaging of membrane fusion mediated by these recombinant proteins revealed that the kinetics of fusion in our system was faster than that previously reported. Analysis of the receptor interaction by fluorescence resonance energy transfer (FRET) at the single-cell level demonstrated a tendency for oligomerization of CD4-CD4, but not of CD4-CCR5, in the absence of Env-expressing cells. However, when Env-expressing cells attached to the receptor cells, FRET produced by CD4-CCR5 interaction was increased; the FRET intensity began to decline before the formation of the fusion pore. These changes in FRET may represent the temporal association of these receptors, triggered by gp120 binding, and their dissociation during the formation of the fusion pore. In addition, the FRET analysis of receptor interactions in the presence of fusion inhibitors showed that not only inhibitors acting on CCR5 but also the gp41-derived peptide T-20 interfered with CD4-CCR5 interaction during fusion. These data suggest that T-20 could affect the formation of Env-receptors complexes during the membrane fusion.

  18. Safety and Immunogenicity of a rAd35-EnvA Prototype HIV-1 Vaccine in Combination with rAd5-EnvA in Healthy Adults (VRC 012)

    PubMed Central

    Crank, Michelle C.; Wilson, Eleanor M. P.; Novik, Laura; Enama, Mary E.; Hendel, Cynthia S.; Gu, Wenjuan; Nason, Martha C.; Bailer, Robert T.; Nabel, Gary J.; McDermott, Adrian B.; Mascola, John R.; Koup, Richard A.; Ledgerwood, Julie E.; Graham, Barney S.

    2016-01-01

    Background VRC 012 was a Phase I study of a prototype recombinant adenoviral-vector serotype-35 (rAd35) HIV vaccine, the precursor to two recently published clinical trials, HVTN 077 and 083. On the basis of prior evaluation of multiclade rAd5 HIV vaccines, Envelope A (EnvA) was selected as the standard antigen for a series of prototype HIV vaccines to compare various vaccine platforms. In addition, prior studies of rAd5-vectored vaccines suggested pre-existing human immunity may be a confounding factor in vaccine efficacy. rAd35 is less seroprevalent across human populations and was chosen for testing alone and in combination with a rAd5-EnvA vaccine in the present two-part phase I study. Methods First, five subjects each received a single injection of 109, 1010, or 1011 particle units (PU) of rAd35-EnvA in an open-label, dose-escalation study. Next, 20 Ad5/Ad35-seronegative subjects were randomized to blinded, heterologous prime-boost schedules combining rAd5-EnvA and rAd35-EnvA with a three month interval. rAd35-EnvA was given at 1010 or 1011 PU to ten subjects each; all rAd5-EnvA injections were 1010 PU. EnvA-specific immunogenicity was assessed four weeks post-injection. Solicited reactogenicity and clinical safety were followed after each injection. Results Vaccinations were well tolerated at all dosages. Antibody responses measured by ELISA were detected at 4 weeks in 30% and 50% of subjects after single doses of 1010 or 1011 PU rAd35, respectively, and in 89% after a single rAd5-EnvA 1010 PU injection. EnvA-specific IFN-γ ELISpot responses were detected at four weeks in 0%, 70%, and 50% of subjects after the respective rAd35-EnvA dosages compared to 89% of subjects after rAd5. T cell responses were higher after a single rAd5-EnvA 1010 PU injection than after a single rAd35-EnvA 1010 PU injection, and humoral responses were low after a single dose of either vector. Of those completing the vaccine schedule, 100% of rAd5-EnvA recipients and 90% of rAd35-Env

  19. Phylogenetic and structural diversity in the feline leukemia virus env gene.

    PubMed

    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.

  20. Biochem-Env: a platform of biochemistry for research in environmental and agricultural sciences.

    PubMed

    Cheviron, Nathalie; Grondin, Virginie; Mougin, Christian

    2017-04-07

    Biochemical indicators are potent tools to assess ecosystem functioning under anthropic and global pressures. Nevertheless, additional work is needed to improve the methods used for the measurement of these indicators, and for a more relevant interpretation of the obtained results. To face these challenges, the platform Biochem-Env aims at providing innovative and standardized measurement protocols, as well as database and information system favoring result interpretation and opening. Its skills and tools are also offered for expertise, consulting, training, and standardization. In addition, the platform is a service of a French Research Infrastructure for Analysis and Experimentation on Ecosystems, for research in environmental and agricultural sciences.

  1. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov.

    PubMed

    Kwon, Kae Kyoung; Woo, Jung-Hee; Yang, Sung-Hyun; Kang, Ji-Hyun; Kang, Sung Gyun; Kim, Sang-Jin; Sato, Takako; Kato, Chiaki

    2007-10-01

    A novel marine bacterium, strain JCS350(T), was isolated from marine sediment samples collected from a cold-seep area. The 16S rRNA gene sequence of the isolate showed high similarity to that of Erythrobacter luteolus SW-109(T) (95.9 % sequence similarity). Lower 16S rRNA gene sequence similarities were shown to other members of the genus Erythrobacter (94.6-95.4 %) and members of the genus Porphyrobacter (94.5-95.2 %). Phylogenetic analysis with all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a phyletic line with [Erythrobacter] luteolus that was distinct from other members of the family Erythrobacteraceae. The dominant fatty acids of strain JCS350(T) were 18 : 1omega7c, 16 : 1omega7c and cyclopropane 17 : 0. The major respiratory quinone was ubiquinone 10. The DNA G+C content was 54.5 mol%. The isolate did not contain bacteriochlorophyll a. Optimal growth required the presence of 2 % (w/v) NaCl with either 0.18 % CaCl(2) or 0.59 % MgCl(2), at pH 6.5 and at 35 degrees C. On the basis of the evidence of this polyphasic taxonomic study, strain JCS350(T) should be classified in a novel genus and species in the family Erythrobacteraceae, for which the name Altererythrobacter epoxidivorans gen. nov., sp. nov. is proposed. The misclassified species [Erythrobacter] luteolus is transferred to the new genus as Altererythrobacter luteolus comb. nov. The type strain of Altererythrobacter epoxidivorans is JCS350(T) (=KCCM 42314(T) =JCM 13815(T)) and the type strain of Altererythrobacter luteolus is SW-109(T) (=KCTC 12311(T) =JCM 12599(T)).

  2. 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.

  3. 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

  4. Activation of HERV-K Env protein is essential for tumorigenesis and metastasis of breast cancer cells.

    PubMed

    Zhou, Fuling; Li, Ming; Wei, Yongchang; Lin, Kevin; Lu, Yue; Shen, Jianjun; Johanning, Gary L; Wang-Johanning, Feng

    2016-12-20

    Human endogenous retrovirus type K (HERV-K) Env protein was previously demonstrated to be overexpressed in human breast cancer (BC) cells and tissues. However, the molecular pathways driving the specific alterations are unknown. We now show that knockdown of its expression with an shRNA (shRNAenv) blocked BC cell proliferation, migration, and invasion. shRNAenv transduction also attenuated the ability of BC cells to form tumors, and notably prevented metastasis. Mechanistically, downregulation of HERV-K blocked expression of tumor-associated genes that included Ras, p-RSK, and p-ERK. The major upstream regulators influenced by HERV-K knockdown were p53, TGF- β1, and MYC. Of interest, when the HERV-K env gene was overexpressed in shRNAenv-transduced BC cells using an HERV-K env expression vector, Ras/Raf/MEK/ERK pathway signaling was restored. CDK5, which alters p53 phosphorylation in some cancers, was upregulated and p53 was downregulated when HERV-K was overexpressed. CDK5 is also a mediator of TGF-β1-induced epithelial-mesenchymal transition and migration in cancer cells, and is involved in tumor formation. Importantly, reductions in migration, invasion, and transformation of BC cells stably transduced with shRNAenv was reversed after adding back a vector with a synonymous mutation of HERV-K env. Taken together, these results indicate that HERV-K Env protein plays an important role in tumorigenesis and metastasis of BC.

  5. HIV-1 Env associates with HLA-C free-chains at the cell membrane modulating viral infectivity.

    PubMed

    Serena, Michela; Parolini, Francesca; Biswas, Priscilla; Sironi, Francesca; Blanco Miranda, Almudena; Zoratti, Elisa; Scupoli, Maria Teresa; Ziglio, Serena; Valenzuela-Fernandez, Agustin; Gibellini, Davide; Romanelli, Maria Grazia; Siccardi, Antonio; Malnati, Mauro; Beretta, Alberto; Zipeto, Donato

    2017-01-04

    HLA-C has been demonstrated to associate with HIV-1 envelope glycoprotein (Env). Virions lacking HLA-C have reduced infectivity and increased susceptibility to neutralizing antibodies. Like all others MHC-I molecules, HLA-C requires β2-microglobulin (β2m) for appropriate folding and expression on the cell membrane but this association is weaker, thus generating HLA-C free-chains on the cell surface. In this study, we deepen the understanding of HLA-C and Env association by showing that HIV-1 specifically increases the amount of HLA-C free chains, not bound to β2m, on the membrane of infected cells. The association between Env and HLA-C takes place at the cell membrane requiring β2m to occur. We report that the enhanced infectivity conferred to HIV-1 by HLA-C specifically involves HLA-C free chain molecules that have been correctly assembled with β2m. HIV-1 Env-pseudotyped viruses produced in the absence of β2m are less infectious than those produced in the presence of β2m. We hypothesize that the conformation and surface expression of HLA-C molecules could be a discriminant for the association with Env. Binding stability to β2m may confer to HLA-C the ability to preferentially act either as a conventional immune-competent molecule or as an accessory molecule involved in HIV-1 infectivity.

  6. HIV-1 Env associates with HLA-C free-chains at the cell membrane modulating viral infectivity

    PubMed Central

    Serena, Michela; Parolini, Francesca; Biswas, Priscilla; Sironi, Francesca; Blanco Miranda, Almudena; Zoratti, Elisa; Scupoli, Maria Teresa; Ziglio, Serena; Valenzuela-Fernandez, Agustin; Gibellini, Davide; Romanelli, Maria Grazia; Siccardi, Antonio; Malnati, Mauro; Beretta, Alberto; Zipeto, Donato

    2017-01-01

    HLA-C has been demonstrated to associate with HIV-1 envelope glycoprotein (Env). Virions lacking HLA-C have reduced infectivity and increased susceptibility to neutralizing antibodies. Like all others MHC-I molecules, HLA-C requires β2-microglobulin (β2m) for appropriate folding and expression on the cell membrane but this association is weaker, thus generating HLA-C free-chains on the cell surface. In this study, we deepen the understanding of HLA-C and Env association by showing that HIV-1 specifically increases the amount of HLA-C free chains, not bound to β2m, on the membrane of infected cells. The association between Env and HLA-C takes place at the cell membrane requiring β2m to occur. We report that the enhanced infectivity conferred to HIV-1 by HLA-C specifically involves HLA-C free chain molecules that have been correctly assembled with β2m. HIV-1 Env-pseudotyped viruses produced in the absence of β2m are less infectious than those produced in the presence of β2m. We hypothesize that the conformation and surface expression of HLA-C molecules could be a discriminant for the association with Env. Binding stability to β2m may confer to HLA-C the ability to preferentially act either as a conventional immune-competent molecule or as an accessory molecule involved in HIV-1 infectivity. PMID:28051183

  7. 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.

  8. Superiority in Rhesus Macaques of Targeting HIV-1 Env Gp140 to CD40 Versus LOX-1 in Combination with Replication Competent NYVAC-KC for Induction of Env-Specific Antibody and T Cell Responses.

    PubMed

    Zurawski, Gerard; Shen, Xiaoying; Zurawski, Sandra; Tomaras, Georgia D; Montefiori, David C; Roederer, Mario; Ferrari, Guido; Lacabaratz, Christine; Klucar, Peter; Wang, Zhiqing; Foulds, Kathryn E; Kao, Shing-Fen; Yu, Xuesong; Sato, Alicia; Yates, Nicole L; LaBranche, Celia; Stanfield-Oakley, Sherry; Kibler, Karen; Jacobs, Bertram; Salazar, Andres; Self, Steve; Fulp, Jimmy; Gottardo, Raphael; Galmin, Lindsey; Weiss, Deborah; Cristillo, Anthony; Pantaleo, Giuseppe; Levy, Yves

    2017-02-15

    We compared the HIV-1-specific immune responses generated by targeting HIV-1 envelope protein (Env gp140) to either CD40 or LOX-1, two endocytic receptors on dendritic cells (DCs), in Rhesus macaques primed with a poxvirus vector (NYVAC-KC) expressing Env gp140. The DC-targeting vaccines, humanized recombinant monoclonal antibodies fused to Env gp140, were administered as a boost with poly ICLC adjuvant either alone or co-administered with the NYVAC-KC vector. All the DC-targeting vaccine administrations with poly ICLC increased the low-level serum anti-Env IgG responses elicited by NYVAC-KC priming significantly more (up to P =0.01) than a group without poly ICLC. The responses were robust, cross-reactive, and contained antibodies specific to multiple epitopes within gp140 including the C1, C2, V1-3, C4, C5, and gp41 immuno-dominant regions. The DC-targeting vaccines also elicited modest serum Env-specific IgA responses. All groups gave serum neutralization activity limited to Tier 1 viruses and antibody dependent cytotoxicity responses (ADCC) after DC-targeting boosts. Furthermore, CD4(+) and CD8(+) T cell responses specific to multiple Env epitopes were strongly boosted by the DC-targeting vaccines + poly ICLC. Together, these results indicate that prime/boost immunization via NYVAC-KC and either αCD40.Env gp140/poly ICLC or αLOX-1.Env gp140/poly ICLC induced balanced antibody and T cell responses against HIV-1 Env. Co-administration of NYVAC-KC with the DC-targeting vaccines increased T cell responses, but had minimal effects on antibody responses except for suppressing serum IgA responses. Overall, compared to LOX-1, targeting Env to CD40 gave more robust T cell and serum antibody responses with broader epitope representation and greater durability.IMPORTANCE An effective vaccine to prevent HIV-1 infection does not yet exist. An approach to elicit strong protective antibody development is to direct virus protein antigens specifically to dendritic cells

  9. 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.

  10. Ultrastructural evidence of an interaction between Env and Gag proteins during assembly of HIV type 1.

    PubMed

    Bugelski, P J; Maleeff, B E; Klinkner, A M; Ventre, J; Hart, T K

    1995-01-01

    Assembly and budding of retroviruses is believed to involve a complex interaction of envelope and capsid proteins at the host cell membrane. The nature of these interactions is, however, incompletely understood. Studies of the topography of the surface of HIV-1 have shown that the envelope glycoprotein projections (knobs) are arranged in a T = 7 levo rotational symmetry. Similarly, an icosahedral structure has been suggested for the p17 matrix of HIV-1. In an effort to investigate whether there is a structural interaction between these molecules, virions whose maturation was blocked by an inhibitor of HIV protease were studied using cytochemistry, morphometry, and 2D fast Fourier transform image enhancement. Analysis of the relationship between core morphology and the topographic distribution of envelope glycoprotein projections on HIV-1 provided structural evidence of an interaction between Env and Gag proteins. Furthermore, image enhancement revealed a periodic substructure in the Pr55gag plaque. Taken together, the data suggest an interaction between Pr55gag and the gp120-gp41 complex during assembly and budding of HIV-1. This interaction may, in part, contribute to determining the amount of Env glycoprotein that will be incorporated into a virion, and therefore play a role in the biology of HIV-1.

  11. 25 Years of GenBank

    MedlinePlus

    ... of this page please turn Javascript on. Unique DNA database has helped advance scientific discoveries worldwide Since ... GenBank? Basically, GenBank is the biggest database of DNA in the world. Deoxyribonucleic acid (DNA) is the ...

  12. Antidiabetic, antidyslipidemic and toxicity profile of ENV-2: A potent pyrazole derivative against diabetes and related diseases.

    PubMed

    Hernández-Vázquez, Eduardo; Ocampo-Montalban, Hugo; Cerón-Romero, Litzia; Cruz, Miguel; Gómez-Zamudio, Jaime; Hiriart-Valencia, Guadalupe; Villalobos-Molina, Rafael; Flores-Flores, Angelica; Estrada-Soto, Samuel

    2017-03-18

    Diabetes is a major health problem and a predisposition factor for further degenerative complications and, therefore, novel therapies are urgently needed. Currently, cannabinoid receptor 1 (CB1 receptor) antagonists have been considered as promissory entities for metabolic disorders treatment. Accordingly, the purpose of this work was the evaluation of the sub-acute antidiabetic, anti-hyperglycemic, antidyslipidemic and toxicological profile of ENV-2, a potent hypoglycemic and antioxidant CB1 receptor antagonist. In this study, ENV-2 showed a pronounced anti-hyperglycemic effect even at a dose of 5mg/kg (P<0.05) in a glucose tolerance test on normoglycemic rats. Moreover, after administration of ENV-2 (16mg/kg) to diabetic rats, a prominent antidiabetic activity was observed (P<0.05), which was higher than glibenclamide. Sub-acute treatment (10 days) of ENV-2 resulted in a significant reduction of plasma glucose (P<0.05). Also, the levels of peripheral lipids were improved; blood triacylglycerols (TG) and cholesterol (CHOL) were diminished (P<0.05). In addition, it was found that ENV-2 reduced IL-1β and IL-18 mRNA expression in adipose tissue (P<0.05). Due to the satisfactory outcomes, we were interested in evaluating the toxicity of ENV-2 in both acute and sub-chronic approaches. Regarding the acute administration, the compound resulted to be non-toxic and was grouped in category 5 according to OECD. It was also found that sub-chronic administration did not increase the size of the studied organs, while no structural damage was observed in heart, lung, liver and kidney tissues. Finally, neither AST nor ALT damage hepatic markers were augmented.

  13. Introduction to GenCade

    DTIC Science & Technology

    2012-10-01

    16-18 October 2012 5 GenCade Conceptual Processes: Coastal Sediment Dynamics Flood shoal ~150,000 m3/yr D50 = 0.27 (W) 0.38 (E) Moriches...offset • LMOVY 0.0 Leftward shoreline displacement velocity • D50 0.33 Grain size diameter in millimeters • BERMHT 2 Average berm height • DCLOS 8

  14. 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

  15. Impact of antibody quality and anamnestic response on viremia control post-challenge in a combined Tat/Env vaccine regimen in rhesus macaques

    PubMed Central

    Demberg, Thorsten; Brocca-Cofano, Egidio; Kuate, Seraphin; Aladi, Stanley; Vargas-Inchaustegui, Diego A.; Venzon, David; Kalisz, Irene; Kalyanaraman, V.S.; Lee, Eun Mi; Pal, Ranajit; DiPasquale, Janet; Ruprecht, Ruth M.; Montefiori, David C.; Srivastava, Indresh; Barnett, Susan W.; Robert-Guroff, Marjorie

    2013-01-01

    Previously, priming rhesus macaques with Adenovirus type 5 host range mutant-recombinants encoding Tat and Env and boosting with Tat and Env protein in MPL-SE controlled chronic viremia by 4 logs following homologous intravenous SHIV89.6P challenge. Here we evaluated Tat, Env, and Tat/Env regimens for immunogenicity and protective efficacy using clade C Env, alum adjuvant, and a heterologous intrarectal SHIV1157ipd3N4 challenge. Despite induction of strong cellular and humoral immunity, Tat/Env group T and B-cell memory responses were not significantly enhanced over Tat- or Env-only groups. Lack of viremia control post-challenge was attributed to lower avidity Env antibodies and no anamnestic ADCC response or SHIV1157ipd3N4 neutralizing antibody development post-challenge. Poor biologic activity of the Tat immunogen may have impaired Tat immunity. In the absence of sterilizing immunity, strong anamnestic responses to heterologous virus can help control viremia. Both antibody breadth and optimal adjuvanticity are needed to elicit high-quality antibody for protective efficacy. PMID:23528732

  16. Putative Phosphatidylinositol 3-Kinase (PI3K) Binding Motifs in Ovine Betaretrovirus Env Proteins Are Not Essential for Rodent Fibroblast Transformation and PI3K/Akt Activation

    PubMed Central

    Liu, Shan-Lu; Lerman, Michael I.; Miller, A. Dusty

    2003-01-01

    Jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV) are simple betaretroviruses that cause epithelial cell tumors in the lower and upper airways of sheep and goats. The envelope (Env) glycoproteins of both viruses can transform rodent and chicken fibroblasts, indicating that they play an essential role in oncogenesis. Previous studies found that a YXXM motif in the Env cytoplasmic tail, a putative docking site for phosphatidylinositol 3-kinase (PI3K) after tyrosine phosphorylation, was necessary for rodent cell transformation but was not required for transformation of DF-1 chicken fibroblasts. Here we show that JSRV and ENTV Env proteins with tyrosine or methionine mutations in the YXXM motif can still transform rodent fibroblasts, albeit with reduced efficiency. Akt was activated in cells transformed by JSRV or ENTV Env proteins and in cells transformed by the proteins with tyrosine mutations. Furthermore, the PI3K-specific inhibitor LY294002 could inhibit Akt activation and cell transformation in all cases, indicating that Akt activation and transformation is PI3K dependent. However, we could not detect tyrosine phosphorylation of JSRV or ENTV Env proteins or an interaction between the Env proteins and PI3K in the transformed cells. We found no evidence for mitogen-activated protein kinase activation in cells that were transformed by the JSRV or ENTV Env proteins. We conclude that ovine betaretrovirus Env proteins transform the rodent fibroblasts by indirectly activating the PI3K/Akt pathway. PMID:12829832

  17. Distributed Generation Market Demand Model (dGen): Documentation

    SciTech Connect

    Sigrin, Benjamin; Gleason, Michael; Preus, Robert; Baring-Gould, Ian; Margolis, Robert

    2016-02-01

    The Distributed Generation Market Demand model (dGen) is a geospatially rich, bottom-up, market-penetration model that simulates the potential adoption of distributed energy resources (DERs) for residential, commercial, and industrial entities in the continental United States through 2050. The National Renewable Energy Laboratory (NREL) developed dGen to analyze the key factors that will affect future market demand for distributed solar, wind, storage, and other DER technologies in the United States. The new model builds off, extends, and replaces NREL's SolarDS model (Denholm et al. 2009a), which simulates the market penetration of distributed PV only. Unlike the SolarDS model, dGen can model various DER technologies under one platform--it currently can simulate the adoption of distributed solar (the dSolar module) and distributed wind (the dWind module) and link with the ReEDS capacity expansion model (Appendix C). The underlying algorithms and datasets in dGen, which improve the representation of customer decision making as well as the spatial resolution of analyses (Figure ES-1), also are improvements over SolarDS.

  18. 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.

  19. 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

    2016-02-24

    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.

  20. Hypothyroid Graves' disease complicated with elephantiasis nostras verrucosa (ENV): a case report and review of the literature.

    PubMed

    Ukinç, Kubilay; Bayraktar, Miyase; Gedik, Arzu

    2009-08-01

    Thyroid dermopathy is not a frequent feature of hyperthyroid Graves' disease, being present in less than 5% of the patients. Graves' disease has been shown to exist in euthyroid or hypothyroid forms in untreated patients. Here, we describe a case of hypothyroid Graves' disease with elephantiasis nostras verrucosa (ENV), which is an extreme form of thyroid dermopathy (TD). A 58-year-old female patient was admitted to the emergency department with somnolence, hypothermia, and bradycardia. Her mental status gradually worsened, resulting in a deep coma. She was intubated and followed in the intensive care unit, as she needed mechanical ventilatory assistance due to respiratory failure. She also had bilateral non-pitting edema, a cobblestone-like appearance, and hyperkeratotic greenish-brown-colored lesions in the pretibial and dorsal regions of the feet that were compatible with ENV. Hypothyroid Graves' disease is a very rare condition among autoimmune thyroid disorders, and ENV is an extremely rare form of TD. Here, we present a patient with hypothyroid Graves' disease and ENV.

  1. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

    PubMed Central

    West, Anthony P; Schamber, Michael; Gazumyan, Anna; Golijanin, Jovana; Seaman, Michael S; Fätkenheuer, Gerd; Klein, Florian; Nussenzweig, Michel C; Bjorkman, Pamela J

    2016-01-01

    HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46–derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs. PMID:27617431

  2. 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

  3. Structural and functional studies of the HAMP domain of EnvZ, an osmosensing transmembrane histidine kinase in Escherichia coli.

    PubMed

    Kishii, Ryuta; Falzon, Liliana; Yoshida, Takeshi; Kobayashi, Hiroshi; Inouye, Masayori

    2007-09-07

    The HAMP domain plays an essential role in signal transduction not only in histidine kinase but also in a number of other signal-transducing receptor proteins. Here we expressed the EnvZ HAMP domain (Arg(180)-Thr(235)) with the R218K mutation (termed L(RK)) or with L(RK) connected with domain A (Arg(180)-Arg(289)) (termed LA(RK)) of EnvZ, an osmosensing transmembrane histidine kinase in Escherichia coli, by fusing it with protein S. The L(RK) and LA(RK) proteins were purified after removing protein S. The CD analysis of the isolated L protein revealed that it consists of a random structure or is unstructured. This suggests that the EnvZ HAMP domain by itself is unable to form a stable structure and that this structural fragility may be important for its role in signal transduction. Interestingly the substitution of Ala(193) in the EnvZ HAMP domain with valine or leucine in Tez1A1, a chimeric protein of Tar and EnvZ, caused a constitutive OmpC phenotype. The CD analysis of LA(RK)(A193L) revealed that this mutated HAMP domain possesses considerable secondary structures and that the thermostability of this entire LA(RK)(A193L) became substantially lower than that of LA(RK) or just domain A, indicating that the structure of the HAMP domain with the A193L mutation affects the stability of downstream domain A. This results in cooperative thermodenaturation of domain A with the mutated HAMP domain. These results are discussed in light of the recently solved NMR structure of the HAMP domain from a thermophilic bacterium (Hulko, M., Berndt, F., Gruber, M., Linder, J. U., Truffault, V., Schultz, A., Martin, J., Schultz, J. E., Lupas, A. N., and Coles, M. (2006) Cell 126, 929-940).

  4. 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.

  5. Relationship of the env genes and the endonuclease domain of the pol genes of simian foamy virus type 1 and human foamy virus.

    PubMed Central

    Mergia, A; Shaw, K E; Lackner, J E; Luciw, P A

    1990-01-01

    We have molecularly cloned and sequenced a portion of the simian foamy virus type 1 (SFV-1); open reading frames representing the endonuclease domain of the polymerase (pol) and the envelope (env) genes were identified by comparison with the human foamy virus (HFV). Unlike the HFV genomic organization, the SFV-1 pol gene overlaps the env gene; thus, the open reading frames reported for HFV between pol and env is not present in SFV-1. Comparisons of predicted amino acid sequences of HFV and SFV-1 reveal that the endonuclease domains of the pol genes are about 84% related. The region predicted to encode the SFV-1 extracellular env domain is 569 codons; SFV-1 and HFV have 64% amino acid similarity in this env domain. The predicted hydrophobic transmembrane env proteins of both HFV and SFV-1 show about 73% similarity. A total of 16 potential glycosylation sites are found in SFV-1 env, and 15 are found in HFV; 11 are shared. SFV-1 has 25 cysteine residues, and HFV has 23 residues; all 23 cysteine residues of HFV are conserved in SFV-1. This sequence analysis reveals that the human and simian foamy viruses are highly related. PMID:2152825

  6. Identification and characterization of the Escherichia coli envC gene encoding a periplasmic coiled-coil protein with putative peptidase activity.

    PubMed

    Hara, Hiroshi; Narita, Setsuko; Karibian, Doris; Park, James T; Yamamoto, Yoshihiro; Nishimura, Yukinobu

    2002-07-02

    PM61 is a chain-forming envC strain of Escherichia coli with a leaky outer membrane. It was found to have an oversized penicillin-binding protein 3, which was the result of an IS4 insertion in the prc gene. The other properties of PM61 were caused by the envC mutation. We cloned the envC (yibP) gene and identified the mutation site, causing a single residue substitution, H366Y, in the PM61 envC allele. The gene product was predicted to be a periplasmic protein having coiled-coil structure in the N-terminal region and homology to lysostaphin in the C-terminal region. Overexpression of envC inhibited cell growth, and overexpression of the PM61 mutant allele caused cell lysis. Disruption of the chromosomal envC caused the same defects as the envC point mutation, indicating the gene is dispensable for growth but important for normal septation/separation and cell envelope integrity.

  7. 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.

  8. 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

  9. Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies

    PubMed Central

    deCamp, Allan; Hraber, Peter; Bailer, Robert T.; Seaman, Michael S.; Ochsenbauer, Christina; Kappes, John; Gottardo, Raphael; Edlefsen, Paul; Self, Steve; Tang, Haili; Greene, Kelli; Gao, Hongmei; Daniell, Xiaoju; Sarzotti-Kelsoe, Marcella; Gorny, Miroslaw K.; Zolla-Pazner, Susan; LaBranche, Celia C.; Mascola, John R.; Korber, Bette T.

    2014-01-01

    ABSTRACT Standardized assessments of HIV-1 vaccine-elicited neutralizing antibody responses are complicated by the genetic and antigenic variability of the viral envelope glycoproteins (Envs). To address these issues, suitable reference strains are needed that are representative of the global epidemic. Several panels have been recommended previously, but no clear answers have been available on how many and which strains are best suited for this purpose. We used a statistical model selection method to identify a global panel of reference Env clones from among 219 Env-pseudotyped viruses assayed in TZM-bl cells with sera from 205 HIV-1-infected individuals. The Envs and sera were sampled globally from diverse geographic locations and represented all major genetic subtypes and circulating recombinant forms of the virus. Assays with a panel size of only nine viruses adequately represented the spectrum of HIV-1 serum neutralizing activity seen with the larger panel of 219 viruses. An optimal panel of nine viruses was selected and augmented with three additional viruses for greater genetic and antigenic coverage. The spectrum of HIV-1 serum neutralizing activity seen with the final 12-virus panel closely approximated the activity seen with subtype-matched viruses. Moreover, the final panel was highly sensitive for detection of many of the known broadly neutralizing antibodies. For broader assay applications, all 12 Env clones were converted to infectious molecular clones using a proviral backbone carrying a Renilla luciferase reporter gene (Env.IMC.LucR viruses). This global panel should facilitate highly standardized assessments of vaccine-elicited neutralizing antibodies across multiple HIV-1 vaccine platforms in different parts of the world. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary genetic variability of the virus, where most variation occurs in the viral envelope glycoproteins that are the sole targets for neutralizing antibodies

  10. 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.

  11. Isolation and sequencing of infectious clones of feline foamy virus and a human/feline foamy virus Env chimera.

    PubMed

    Hatama, S; Otake, K; Omoto, S; Murase, Y; Ikemoto, A; Mochizuki, M; Takahashi, E; Okuyama, H; Fujii, Y

    2001-12-01

    Full-length DNAs of the Coleman and S7801 strains (pSKY3.0, pSKY5.0) of infectious feline foamy viruses (FFVs) were cloned and sequenced. Parental viruses, designated SKY3.0 and SKY5.0, were secreted following transfection of Crandell feline kidney (CRFK) cells. Production of the rescued parental viruses was enhanced in the presence of trichostatin A. Amino acid sequence similarities between FFV and human foamy virus (HFV) are extremely low for the envelope protein and capsid antigen, as predicted from the two clones. However, a chimeric FFV clone was constructed with the HFV Env substituted for the FFV Env. The chimeric virus (HFFV, SKY4.0) was able to infect and replicate in CRFK cells as well as in peripheral blood mononuclear cells of cats in vivo. Consequently, the chimeric HFFV may be useful for the creation of FV vectors for gene transfer strategies.

  12. Comparing the flammability of fabrics in accordance with EN 531 and ENV 50354.

    PubMed

    Mäkinen, Helena; Mustonen, Suvi Sanna

    2004-01-01

    The purpose of protective clothing and other personal protective equipment (PPE) is to provide escape time, to reduce the burn injury level, and to prevent aggravation of the consequences to workers during exposure to an electric arc. In this study the flammability properties of 12 different types of flame-retardant fabrics were compared with the normally used flame spread test method (EN 532:1994) and electric arc test method (ENV 50354:2001). In the arc test at the lower testing current level of 4 kA, the requirement was passed by materials which did not pass the flame spread test. These materials contained a large amount of melting fibres, and therefore tended to shrink or melt. In order to meet the current level of 7 kA, a rather thick and heavy flame-retardant fabric is needed to pass the requirement. Lighter fabrics tended to break open in the tests. The flame retardancy of the under layer fabric is therefore important to ensure the needed protection.

  13. 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.

  14. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2.

    PubMed

    Rolland, Morgane; Edlefsen, Paul T; Larsen, Brendan B; Tovanabutra, Sodsai; Sanders-Buell, Eric; Hertz, Tomer; deCamp, Allan C; Carrico, Chris; Menis, Sergey; Magaret, Craig A; Ahmed, Hasan; Juraska, Michal; Chen, Lennie; Konopa, Philip; Nariya, Snehal; Stoddard, Julia N; Wong, Kim; Zhao, Hong; Deng, Wenjie; Maust, Brandon S; Bose, Meera; Howell, Shana; Bates, Adam; Lazzaro, Michelle; O'Sullivan, Annemarie; Lei, Esther; Bradfield, Andrea; Ibitamuno, Grace; Assawadarachai, Vatcharain; O'Connell, Robert J; deSouza, Mark S; Nitayaphan, Sorachai; Rerks-Ngarm, Supachai; Robb, Merlin L; McLellan, Jason S; Georgiev, Ivelin; Kwong, Peter D; Carlson, Jonathan M; Michael, Nelson L; Schief, William R; Gilbert, Peter B; Mullins, James I; Kim, Jerome H

    2012-10-18

    The RV144 trial demonstrated 31% vaccine efficacy at preventing human immunodeficiency virus (HIV)-1 infection. Antibodies against the HIV-1 envelope variable loops 1 and 2 (Env V1 and V2) correlated inversely with infection risk. We proposed that vaccine-induced immune responses against V1/V2 would have a selective effect against, or sieve, HIV-1 breakthrough viruses. A total of 936 HIV-1 genome sequences from 44 vaccine and 66 placebo recipients were examined. We show that vaccine-induced immune responses were associated with two signatures in V2 at amino acid positions 169 and 181. Vaccine efficacy against viruses matching the vaccine at position 169 was 48% (confidence interval 18% to 66%; P = 0.0036), whereas vaccine efficacy against viruses mismatching the vaccine at position 181 was 78% (confidence interval 35% to 93%; P = 0.0028). Residue 169 is in a cationic glycosylated region recognized by broadly neutralizing and RV144-derived antibodies. The predicted distance between the two signature sites (21 ± 7 Å) and their match/mismatch dichotomy indicate that multiple factors may be involved in the protection observed in RV144. Genetic signatures of RV144 vaccination in V2 complement the finding of an association between high V1/V2-binding antibodies and reduced risk of HIV-1 acquisition, and provide evidence that vaccine-induced V2 responses plausibly had a role in the partial protection conferred by the RV144 regimen.

  15. 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

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

    PubMed

    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

    2016-02-01

    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.

  17. 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

  18. 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

  19. HIV cell-to-cell transmission requires the production of infectious virus particles and does not proceed through env-mediated fusion pores.

    PubMed

    Monel, Blandine; Beaumont, Elodie; Vendrame, Daniela; Schwartz, Olivier; Brand, Denys; Mammano, Fabrizio

    2012-04-01

    Direct cell-to-cell transmission of human immunodeficiency virus (HIV) is a more potent and efficient means of virus propagation than infection by cell-free virus particles. The aim of this study was to determine whether cell-to-cell transmission requires the assembly of enveloped virus particles or whether nucleic acids with replication potential could translocate directly from donor to target cells through envelope glycoprotein (Env)-induced fusion pores. To this end, we characterized the transmission properties of viruses carrying mutations in the matrix protein (MA) that affect the incorporation of Env into virus particles but do not interfere with Env-mediated cell-cell fusion. By use of cell-free virus, the infectivity of MA mutant viruses was below the detection threshold both in single-cycle and in multiple-cycle assays. Truncation of the cytoplasmic tail (CT) of Env restored the incorporation of Env into MA mutant viruses and rescued their cell-free infectivity to different extents. In cell-to-cell transmission assays, MA mutations prevented HIV transmission from donor to target cells, despite efficient Env-dependent membrane fusion. HIV transmission was blocked at the level of virus core translocation into the cytosol of target cells. As in cell-free assays, rescue of Env incorporation by truncation of the Env CT restored the virus core translocation and cell-to-cell infectivity of MA mutant viruses. These data show that HIV cell-to-cell transmission requires the assembly of enveloped virus particles. The increased efficiency of this infection route may thus be attributed to the high local concentrations of virus particles at sites of cellular contacts rather than to a qualitatively different transmission process.

  20. Human Ubc9 Is Involved in Intracellular HIV-1 Env Stability after Trafficking out of the Trans-Golgi Network in a Gag Dependent Manner

    PubMed Central

    Bohl, Christopher R.; Abrahamyan, Levon G.; Wood, Charles

    2013-01-01

    The cellular E2 Sumo conjugase, Ubc9 interacts with HIV-1 Gag, and is important for the assembly of infectious HIV-1 virions. In the previous study we demonstrated that in the absence of Ubc9, a defect in virion assembly was associated with decreased levels of mature intracellular Envelope (Env) that affected Env incorporation into virions and virion infectivity. We have further characterized the effect of Ubc9 knockdown on HIV Env processing and assembly. We found that gp160 stability in the endoplasmic reticulum (ER) and its trafficking to the trans-Golgi network (TGN) were unaffected, indicating that the decreased intracellular mature Env levels in Ubc9-depleted cells were due to a selective degradation of mature Env gp120 after cleavage from gp160 and trafficked out of the TGN. Decreased levels of Gag and mature Env were found to be associated with the plasma membrane and lipid rafts, which suggest that these viral proteins were not trafficked correctly to the assembly site. Intracellular gp120 were partially rescued when treated with a combination of lysosome inhibitors. Taken together our results suggest that in the absence of Ubc9, gp120 is preferentially degraded in the lysosomes likely before trafficking to assembly sites leading to the production of defective virions. This study provides further insight in the processing and packaging of the HIV-1 gp120 into mature HIV-1 virions. PMID:23861967

  1. Chimeric adenovirus type 5/35 vector encoding SIV gag and HIV env genes affords protective immunity against the simian/human immunodeficiency virus in monkeys.

    PubMed

    Someya, Kenji; Xin, Ke-Qin; Ami, Yasushi; Izumi, Yasuyuki; Mizuguchi, Hiroyuki; Ohta, Shinrai; Yamamoto, Naoki; Honda, Mitsuo; Okuda, Kenji

    2007-10-25

    Replication-defective adenovirus type 5 (Ad5) vector-based vaccines are widely known to induce strong immunity against immunodeficiency viruses. To exploit this immunogenicity while overcoming the potential problem of preexisting immunity against human adenoviruses type 5, we developed a recombinant chimeric adenovirus type 5 with type 35 fiber vector (rAd5/35). We initially produced a simian immunodeficiency virus (SIV) gag DNA plasmid (rDNA-Gag), a human immunodeficiency virus type 1 (HIV-1) 89.6 env DNA plasmid (rDNA-Env) and a recombinant Ad5/35 vector encoding the SIV gag and HIV env gene (rAd5/35-Gag and rAd5/35-Env). Prime-boost vaccination with rDNA-Gag and -Env followed by high doses of rAd5/35-Gag and -Env elicited higher levels of cellular immune responses than did rDNAs or rAd5/35s alone. When challenged with a pathogenic simian human immunodeficiency virus (SHIV), animals receiving a prime-boost regimen or rAd5/35s alone maintained a higher number of CD4(+) T cells and remarkably suppressed plasma viral RNA loads. These findings suggest the clinical promise of an rAd5/35 vector-based vaccine.

  2. Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) Impairs Viral Release and Hampers BST-2 Antagonism.

    PubMed

    Dufrasne, François E; Lombard, Catherine; Goubau, Patrick; Ruelle, Jean

    2016-10-14

    BST-2 or tetherin is a host cell restriction factor that prevents the budding of enveloped viruses at the cell surface, thus impairing the viral spread. Several countermeasures to evade this antiviral factor have been positively selected in retroviruses: the human immunodeficiency virus type 2 (HIV-2) relies on the envelope glycoprotein (Env) to overcome BST-2 restriction. The Env gp36 ectodomain seems involved in this anti-tetherin activity, however residues and regions interacting with BST-2 are not clearly defined. Among 32 HIV-2 ROD Env mutants tested, we demonstrated that the asparagine residue at position 659 located in the gp36 ectodomain is mandatory to exert the anti-tetherin function. Viral release assays in cell lines expressing BST-2 showed a loss of viral release ability for the HIV-2 N659D mutant virus compared to the HIV-2 wild type virus. In bst-2 inactivated H9 cells, those differences were lost. Subtilisin treatment of infected cells demonstrated that the N659D mutant was more tethered at the cell surface. Förster resonance energy transfer (FRET) experiments confirmed a direct molecular link between Env and BST-2 and highlighted an inability of the mutant to bind BST-2. We also tested a virus presenting a truncation of 109 amino acids at the C-terminal part of Env, a cytoplasmic tail partial deletion that is spontaneously selected in vitro. Interestingly, viral release assays and FRET experiments indicated that a full Env cytoplasmic tail was essential in BST-2 antagonism. In HIV-2 infected cells, an efficient Env-mediated antagonism of BST-2 is operated through an intermolecular link involving the asparagine 659 residue as well as the C-terminal part of the cytoplasmic tail.

  3. Identification of a HERV-K env surface peptide highly recognized in RA patients: A cross-sectional case-control study.

    PubMed

    Mameli, G; Erre, G L; Caggiu, E; Mura, S; Cossu, D; Bo, Marco; Cadoni, M L; Piras, A; Mundula, N; Colombo, E; Buscetta, G; Passiu, G; Sechi, L A

    2017-03-21

    Endogenous Retroviruses (HERV) are believed to be pathogenic in several autoimmune diseases. Among them, HERV-K viruses have been recently reported to be involved in the pathogenesis of rheumatoid arthritis (RA). In this study we have explored the role of humoral immune response against HERV-K as a potential pathogenetic mechanism in RA. Four different peptides from the extracellular portion of the env protein of HERV-K (env-su 19-37 , env-su 109-26 , env-su 164-186 , env-su 209-226 ) were selected by bioinformatic analysis on the basis of their putative immunogenicity. Indirect ELISA was then carried out to quantify antibodies against those peptides on blood samples of seventy consecutive RA patients and seventy-one healthy controls (HC). Differences between the two groups were analysed using the Mann-Whitney test. Potential correlations between RA laboratory, clinical descriptors and IgGs levels were explored by bivariate regression analysis. Serum autoantibodies against one out of four tested peptides of HERV-K (env-su 19-37 ) were significantly higher in RA than in HC (19% vs 3%, p=0.0025). Subgroup analysis showed no association between anti-HERV-K peptide humoral response and clinical, serological and clinimetric RA disease descriptors. Serum from RA patients in our series significantly reacted against HERV-K env-su 19-37 peptide in comparison to the general population suggesting a role for the HERV-K related, secondary antigenic driven immune response in the pathogenesis of RA. Further studies are needed to confirm these results and to explore the role of this HERV-K surface peptide as a potential therapeutic target. This article is protected by copyright. All rights reserved.

  4. 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.

  5. 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

  6. 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.

  7. Teleport Generation 3 (Teleport Gen 3)

    DTIC Science & Technology

    2016-03-01

    DAMIR) UNCLASSIFIED Teleport Gen 3 2016 MAR UNCLASSIFIED 2 Table of Contents Common Acronyms and Abbreviations for MAIS Programs 3...Information System MAIS OE - MAIS Original Estimate MAR – MAIS Annual Report MDA - Milestone Decision Authority MDD - Materiel Development Decision...U.S.C- United States Code USD(AT&L) - Under Secretary of Defense for Acquisition, Technology, & Logistics Teleport Gen 3 2016 MAR UNCLASSIFIED 3 Mrs

  8. The V3 Loop of HIV-1 Env Determines Viral Susceptibility to IFITM3 Impairment of Viral Infectivity.

    PubMed

    Wang, Yimeng; Pan, Qinghua; Ding, Shilei; Wang, Zhen; Yu, Jingyou; Finzi, Andrés; Liu, Shan-Lu; Liang, Chen

    2017-04-01

    Interferon-inducible transmembrane proteins (IFITMs) inhibit a broad spectrum of viruses, including HIV-1. IFITM proteins deter HIV-1 entry when expressed in target cells and also impair HIV-1 infectivity when expressed in virus producer cells. However, little is known about how viruses resist IFITM inhibition. In this study, we have investigated the susceptibilities of different primary isolates of HIV-1 to the inhibition of viral infectivity by IFITMs. Our results demonstrate that the infectivity of different HIV-1 primary isolates, including transmitted founder viruses, is diminished by IFITM3 to various levels, with strain AD8-1 exhibiting strong resistance. Further mutagenesis studies revealed that HIV-1 Env, and the V3 loop sequence in particular, determines the extent of inhibition of viral infectivity by IFITM3. IFITM3-sensitive Env proteins are also more susceptible to neutralization by soluble CD4 or the 17b antibody than are IFITM3-resistant Env proteins. Together, data from our study suggest that the propensity of HIV-1 Env to sample CD4-bound-like conformations modulates viral sensitivity to IFITM3 inhibition.IMPORTANCE Results of our study have revealed the key features of the HIV-1 envelope protein that are associated with viral resistance to the IFITM3 protein. IFITM proteins are important effectors in interferon-mediated antiviral defense. A variety of viruses are inhibited by IFITMs at the virus entry step. Although it is known that envelope proteins of several different viruses resist IFITM inhibition, the detailed mechanisms are not fully understood. Taking advantage of the fact that envelope proteins of different HIV-1 strains exhibit different degrees of resistance to IFITM3 and that these HIV-1 envelope proteins share the same domain structure and similar sequences, we performed mutagenesis studies and determined the key role of the V3 loop in this viral resistance phenotype. We were also able to associate viral resistance to IFITM3

  9. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs.

    PubMed

    Swanson, A K; Stoltzfus, C M

    1998-12-18

    Alternative splicing is used to generate more than 30 human immunodeficiency virus type 1 (HIV-1) spliced and unspliced mRNAs from a single primary transcript. The abundance of HIV-1 mRNAs is determined by the efficiencies with which its different 5' and 3' splice sites are used. Three splice sites (A4c, A4a, and A4b) are upstream of the rev initiator AUG. RNAs spliced at A4c, A4a, and A4b are used as mRNAs for Rev. Another 3' splice site (A5) is immediately downstream of the rev initiator. RNAs spliced at A5 are used as mRNAs for Env and Nef. In this report, primer extension analysis of splicing intermediates was used to show that there are eight branch points in this region, all of which map to adenosine residues. In addition, cis elements recognized by the cellular splicing machinery overlap; the two most 3' branch points overlap with the AG dinucleotides at rev 3' splice sites A4a and A4b. Competition of the overlapping cis sites for different splicing factors may play a role in maintaining the appropriate balance of mRNAs in HIV-1-infected cells. In support of this possibility, mutations at rev 3' splice site A4b AG dinucleotide dramatically increased splicing of the env/nef 3' splice site A5. This correlated with increased usage of the four most 3' branch points, which include those within the rev 3' splice site AG dinucleotides. Consistent with these results, analysis of a mutant in which three of the four env/nef branch points were inactivated indicated that use of splice site A5 was inhibited and splicing was shifted predominantly to the most 5' rev 3' splice site A4c with preferential use of the two most 5' branch points. Our results suggest that spliceosomes formed at rev A4a-4b, rev A4c, and env/nef A5 3' splice sites each recognize different subsets of the eight branch point sequences.

  10. Changes in Structure and Antigenicity of HIV-1 Env Trimers Resulting from Removal of a Conserved CD4 Binding Site-Proximal Glycan

    PubMed Central

    Liang, Yu; Guttman, Miklos; Williams, James A.; Verkerke, Hans; Alvarado, Daniel

    2016-01-01

    ABSTRACT The envelope glycoprotein (Env) is the major target for HIV-1 broadly neutralizing antibodies (bNAbs). One of the mechanisms that HIV has evolved to escape the host's immune response is to mask conserved epitopes on Env with dense glycosylation. Previous studies have shown that the removal of a particular conserved glycan at N197 increases the neutralization sensitivity of the virus to antibodies targeting the CD4 binding site (CD4bs), making it a site of significant interest from the perspective of vaccine design. At present, the structural consequences that result from the removal of the N197 glycan have not been characterized. Using native-like SOSIP trimers, we examine the effects on antigenicity and local structural dynamics resulting from the removal of this glycan. A large increase in the binding of CD4bs and V3-targeting antibodies is observed for the N197Q mutant in trimeric Env, while no changes are observed with monomeric gp120. While the overall structure and thermostability are not altered, a subtle increase in the flexibility of the variable loops at the trimeric interface of adjacent protomers is evident in the N197Q mutant by hydrogen-deuterium exchange mass spectrometry. Structural modeling of the glycan chains suggests that the spatial occupancy of the N197 glycan leads to steric clashes with CD4bs antibodies in the Env trimer but not monomeric gp120. Our results indicate that the removal of the N197 glycan enhances the exposure of relevant bNAb epitopes on Env with a minimal impact on the overall trimeric structure. These findings present a simple modification for enhancing trimeric Env immunogens in vaccines. IMPORTANCE The HIV-1 Env glycoprotein presents a dense patchwork of host cell-derived N-linked glycans. This so-called glycan shield is considered to be a major protective mechanism against immune recognition. While the positions of many N-linked glycans are isolate specific, some are highly conserved and are believed to play key

  11. Characterization of Env antigenicity of feline foamy virus (FeFV) using FeFV-infected cat sera and a monoclonal antibody.

    PubMed

    Phung, Hang T T; Tohya, Yukinobu; Miyazawa, Takayuki; Akashi, Hiroomi

    2005-04-10

    To characterize neutralizing antigenicity in relation to env genotypes of feline foamy virus (FeFV), serological analyses were performed using FeFV-infected cat sera and several field isolates including two env genotypes (F17- and FUV-types). Since three cats from which FeFV were isolated were found to have undetectable titers of virus neutralization (VN) antibodies, even to the homologous virus, VN antibodies were further examined with complement supplementation as an enhancement factor. With the presence of complement, the VN titers of FeFV-infected cat sera increased drastically. Although most of serum samples neutralized strains of either env genotype, sera sampled from two cats neutralized all the strains examined at similar titers, suggesting that superinfection with both env genotypes of FeFV might have occurred in the two cats. Further, we produced a monoclonal antibody (mAb) specifically neutralizing FeFV strains of FUV-type. The mAb was shown to have higher affinity to an epitope on Env of FUV-type than that of F17-type by immunoprecipitation assay. This study supplies basic information important for studies on FeFV vector development as well as on the relationship between the virus and the host immune response.

  12. Immunization with an SIV-based IDLV Expressing HIV-1 Env 1086 Clade C Elicits Durable Humoral and Cellular Responses in Rhesus Macaques

    PubMed Central

    Negri, Donatella; Blasi, Maria; LaBranche, Celia; Parks, Robert; Balachandran, Harikrishnan; Lifton, Michelle; Shen, Xiaoying; Denny, Thomas; Ferrari, Guido; Vescio, Maria Fenicia; Andersen, Hanne; Montefiori, David C; Tomaras, Georgia D; Liao, Hua-Xin; Santra, Sampa; Haynes, Barton F; Klotman, Mary E; Cara, Andrea

    2016-01-01

    The design of an effective HIV-1 vaccine remains a major challenge. Several vaccine strategies based on viral vectors have been evaluated in preclinical and clinical trials, with largely disappointing results. Integrase defective lentiviral vectors (IDLV) represent a promising vaccine candidate given their ability to induce durable and protective immune responses in mice after a single immunization. Here, we evaluated the immunogenicity of a SIV-based IDLV in nonhuman primates. Six rhesus monkeys were primed intramuscularly with IDLV-Env and boosted with the same vector after 1 year. A single immunization with IDLV-Env induced broad humoral and cellular immune responses that waned over time but were still detectable at 1 year postprime. The boost with IDLV-Env performed at 1 year from the prime induced a remarkable increase in both antibodies and T-cell responses. Antibody binding specificity showed a predominant cross-clade gp120-directed response. Monkeys' sera efficiently blocked anti-V2 and anti-CD4 binding site antibodies, neutralized the tier 1 MW965.26 pseudovirus and mediated antibody-dependent cellular cytotoxicity (ADCC). Durable polyfunctional Env-specific T-cell responses were also elicited. Our study demonstrates that an IDLV-Env-based vaccine induces functional, comprehensive, and durable immune responses in Rhesus macaques. These results support further evaluation of IDLV as a new HIV-1 vaccine delivery platform. PMID:27455880

  13. 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

  14. 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.

  15. Debroyerella gen. nov. and Ulladulla gen. nov., two new lysianassoid genera (Crustacea, Amphipoda, Lysianassoidea).

    PubMed

    Lowry, J K; Kilgallen, N M

    2015-02-19

    Two new genera and a new species of lysianassoid amphipods are described. Debroyerella gen. nov. is described for three Antarctic species previously assigned to the genus Cheirimedon. Ulladulla gen. nov. is described to accommodate the new species U. selje, from Australian waters. Diagnostic descriptions are given for the genera and all species are described in full.

  16. Variability of the env gene in cynomolgus macaques persistently infected with human immunodeficiency virus type 2 strain ben.

    PubMed Central

    Tolle, T; Petry, H; Bachmann, B; Hunsmann, G; Lüke, W

    1994-01-01

    The sequence variability of distinct regions of the proviral env gene of human immunodeficiency virus type 2 strain ben (HIV-2ben) isolated sequentially over 3 to 4 years from six experimentally infected macaques was studied. The regions investigated were homologous to the V1, V2, V3, V4, V5, and V7 hypervariable regions identified in the env genes of HIV-1 and simian immunodeficiency virus SIVmac, respectively. In contrast to findings with HIV-1 and SIVmac, the V1- and V2-homologous regions were found to be highly conserved during the course of the HIV-2ben infection in macaques. The V3-homologous region showed a degree of variation comparable to that of HIV-1 but not of SIV. In the V4-, V5-, and V7-homologous regions, mutation hot spots were detected in most reisolates of the infected monkeys. Most of these mutations occurred during the first 10 weeks after infection. After 50 weeks, new mutations were rarely detected. At most mutation sites, a dynamic equilibrium between the mutated viral isotype and the infecting predominant wild type was present. This equilibrium might prevent an accumulation of mutations in isolates later in the course of infection. PMID:8139054

  17. Coexpression of the simian immunodeficiency virus Env and Rev proteins by a recombinant human adenovirus host range mutant.

    PubMed Central

    Cheng, S M; Lee, S G; Ronchetti-Blume, M; Virk, K P; Mizutani, S; Eichberg, J W; Davis, A; Hung, P P; Hirsch, V M; Chanock, R M

    1992-01-01

    Recombinant human adenoviruses (Ads) that replicate in the intestinal tract offer a novel, yet practical, means of immunoprophylaxis against a wide variety of viral and bacterial pathogens. For some infectious agents such as human immunodeficiency virus (HIV), the potential for residual infectious material in vaccine preparations must be eliminated. Therefore, recombinant human Ads that express noninfectious HIV or other microbial proteins are attractive vaccine candidates. To test such an approach for HIV, we chose an experimental model of AIDS based on simian immunodeficiency virus (SIV) infection of macaques. Our data demonstrate that the SIV Env gene products are expressed in cultured cells after infection with a recombinant Ad containing both SIV env and rev genes. An E3 deletion vector derived from a mutant of human Ad serotype 5 that efficiently replicates in both human and monkey cells was used to bypass the usual host range restriction of Ad infection. In addition, we show that the SIV rev gene is properly spliced from a single SIV subgenomic DNA fragment and that the Rev protein is expressed in recombinant Ad-SIV-infected human as well as monkey cells. The expression of SIV gene products in suitable live Ad vectors provides an excellent system for studying the regulation of SIV gene expression in cultured cells and evaluating the immunogenicity and protective efficacy of SIV proteins in macaques. Images PMID:1404612

  18. 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

  19. 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

  20. [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.

  1. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy.

    PubMed

    Lee, Jeong Hyun; de Val, Natalia; Lyumkis, Dmitry; Ward, Andrew B

    2015-10-06

    Secretory and membrane proteins from mammalian cells undergo post-translational modifications, including N-linked glycosylation, which can result in a large number of possible glycoforms. This sample heterogeneity can be problematic for structural studies, particularly X-ray crystallography. Thus, crystal structures of heavily glycosylated proteins such as the HIV-1 Env viral spike protein have been determined by removing the majority of glycans. This step is most frequently carried out using Endoglycosidase H (EndoH) and requires that all expressed glycans be in the high-mannose form, which is often not the native glycoform. With significantly improved technologies in single-particle cryoelectron microscopy, we demonstrate that it is now possible to refine and build natively glycosylated HIV-1 Env structures in solution to 4.36 Å resolution. At this resolution we can now analyze the complete epitope of a broadly neutralizing antibody (bnAb), PGT128, in the context of the trimer expressed with native glycans.

  2. 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!

  3. T-Cell Immune Responses Against Env from CRF12_BF and Subtype B HIV-1 Show High Clade-Specificity that Can Be Overridden by Multiclade Immunizations

    PubMed Central

    Mónaco, Daniela C.; Rodríguez, Ana M.; Pascutti, María F.; Carobene, Mauricio; Falivene, Juliana; Gómez, Alejandro; Maeto, Cynthia; Turk, Gabriela; Nájera, José L.; Esteban, Mariano; Gherardi, M. Magdalena

    2011-01-01

    Background The extreme genetic diversity of the human immunodeficiency virus type 1 (HIV-1) poses a daunting challenge to the generation of an effective AIDS vaccine. In Argentina, the epidemic is characterized by the high prevalence of infections caused by subtype B and BF variants. The aim of this study was to characterize in mice the immunogenic and antigenic properties of the Env protein from CRF12_BF in comparison with clade B, employing prime-boost schemes with the combination of recombinant DNA and vaccinia virus (VV) vectors. Methodology/Principal Findings As determined by ELISPOT from splenocytes of animals immunized with either EnvBF or EnvB antigens, the majority of the cellular responses to Env were found to be clade-specific. A detailed peptide mapping of the responses reveal that when there is cross-reactivity, there are no amino acid changes in the peptide sequence or were minimal and located at the peptide ends. In those cases, analysis of T cell polifunctionality and affinity indicated no differences with respect to the cellular responses found against the original homologous sequence. Significantly, application of a mixed immunization combining both clades (B and BF) induced a broader cellular response, in which the majority of the peptides targeted after the single clade vaccinations generated a positive response. In this group we could also find significant cellular and humoral responses against the whole gp120 protein from subtype B. Conclusions/Significance This work has characterized for the first time the immunogenic peptides of certain EnvBF regions, involved in T cell responses. It provides evidence that to improve immune responses to HIV there is a need to combine Env antigens from different clades, highlighting the convenience of the inclusion of BF antigens in future vaccines for geographic regions where these HIV variants circulate. PMID:21364754

  4. Robust antigen-specific humoral immune responses to sublingually delivered adenoviral vectors encoding HIV-1 Env: association with mucoadhesion and efficient penetration of the sublingual barrier.

    PubMed

    Domm, William; Brooks, Lauren; Chung, Hung Li; Feng, Changyong; Bowers, William J; Watson, Gene; McGrath, James L; Dewhurst, Stephen

    2011-09-16

    The efficient induction of virus-specific mucosal antibodies is an important unmet objective in Human Immunodeficiency Virus Type-1 (HIV-1) vaccine research. One promising approach is sublingual (SL) immunization. We examined the effectiveness of SL delivery of two different viral vectors: (i) a recombinant adenovirus (rAd5), and (ii) a Herpes Simplex Virus Type-1 amplicon vector (HSV-1). Initial in vitro videomicroscopy experiments showed that rAd5 particles were trapped in saliva (i.e., that Ad5 was mucoadhesive) - unlike HSV-1 virions, which migrated freely in both saliva and water. In vivo imaging studies in mice revealed that only the rAd5 vector efficiently transduced the SL epithelium. Consistent with this, SL delivery of an rAd5 encoding HIV-1 envelope glycoprotein (Env) resulted in robust antigen-specific antibody responses in plasma and in vaginal washes, whereas SL delivery of a HSV-1 amplicon vector encoding HIV-1 Env failed to elicit Env-specific antibodies. In contrast, both vectors elicited equivalent humoral responses following intramuscular (IM) delivery. Finally, SL delivery of the rAd5:Env vector resulted in elevated levels of Env-specific serum IgA, and vaginal IgA and IgG, when compared to IM delivery of the same vector. These results findings shed light on vector properties (mucoadhesion, penetration of the sublingual barrier) which may be important for the induction of potent humoral immune responses following sublingual vector administration. Our data also show that SL delivery of an Env-encoding rAd5 vector can elicit a potent antigen-specific mucosal antibody response in the absence of adjuvant. Overall, these findings support the further exploration of the SL delivery route for HIV-1 vaccine delivery.

  5. Robust Antigen-Specific Humoral Immune Responses to Sublingually Delivered Adenoviral Vectors Encoding HIV-1 Env: Association with Mucoadhesion and Efficient Penetration of the Sublingual Barrier

    PubMed Central

    Domm, William; Brooks, Lauren; Chung, Hung Li; Feng, Changyong; Bowers, William J.; Watson, Gene; McGrath, James L.; Dewhurst, Stephen

    2011-01-01

    The efficient induction of virus-specific mucosal antibodies is an important unmet objective in Human Immunodeficiency Virus Type-1 (HIV-1) vaccine research. One promising approach is sublingual (SL) immunization. We examined the effectiveness of SL delivery of two different viral vectors: (i) a recombinant adenovirus (rAd5), and (ii) a Herpes Simplex Virus Type-1 amplicon vector (HSV-1). Initial in vitro videomicroscopy experiments showed that rAd5 particles were trapped in saliva (i.e., that Ad5 was mucoadhesive) - unlike HSV-1 virions, which migrated freely in both saliva and water. In vivo imaging studies in mice revealed that only the rAd5 vector efficiently transduced the SL epithelium. Consistent with this, SL delivery of an rAd5 encoding HIV-1 envelope glycoprotein (Env) resulted in robust antigen-specific antibody responses in plasma and in vaginal washes, whereas SL delivery of a HSV-1 amplicon vector encoding HIV-1 Env failed to elicit Env-specific antibodies. In contrast, both vectors elicited equivalent humoral responses following intramuscular (IM) delivery. Finally, SL delivery of the rAd5:Env vector resulted in elevated levels of Env-specific serum IgA, and vaginal IgA and IgG, when compared to IM delivery of the same vector. These results findings shed light on vector properties (mucoadhesion, penetration of the sublingual barrier) which may be important for the induction of potent humoral immune responses following sublingual vector administration. Our data also show that SL delivery of an Env-encoding rAd5 vector can elicit a potent antigen-specific mucosal antibody response in the absence of adjuvant. Overall, these findings support the further exploration of the SL delivery route for HIV-1 vaccine delivery. PMID:21801777

  6. Three new anascosporic genera of the Saccharomycotina: Danielozyma gen. nov., Deakozyma gen. nov. and Middelhovenomyces gen. nov.

    PubMed

    Kurtzman, Cletus P; Robnett, Christie J

    2014-05-01

    Three new non-ascosporic, ascomycetous yeast genera are proposed based on their isolation from currently described species and genera. Phylogenetic placement of the genera was determined from analysis of nuclear gene sequences for D1/D2 large subunit rRNA, small subunit rRNA, translation elongation factor-1α and RNA polymerase II, subunits B1 and B2. The new taxa are: Deakozyma gen. nov., type species Deakozyma indianensis sp. nov. (type strain NRRL YB-1937, CBS 12903); Danielozyma gen. nov., type species Danielozyma ontarioensis comb. nov. (type strain NRRL YB-1246, CBS 8502); D. litseae comb. nov. (type strain NRRL YB-3246, CBS 8799); Middelhovenomyces gen. nov., type species Middelhovenomyces tepae comb. nov. (type strain NRRL Y-17670, CBS 5115) and M. petrohuensis comb. nov. (type strain NRRL Y-17663, CBS 8173).

  7. 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

  8. Colon Cancer on The Rise Among Gen Xers, Millennials

    MedlinePlus

    ... Colon Cancer on the Rise Among Gen Xers, Millennials And an old adversary -- the obesity epidemic -- may ... their early 50s and younger -- Gen Xers and millennials -- are experiencing significant increases in colon and rectal ...

  9. Yersinia pestis requires the 2-component regulatory system OmpR-EnvZ to resist innate immunity during the early and late stages of plague.

    PubMed

    Reboul, Angéline; Lemaître, Nadine; Titecat, Marie; Merchez, Maud; Deloison, Gaspard; Ricard, Isabelle; Pradel, Elizabeth; Marceau, Michaël; Sebbane, Florent

    2014-11-01

    Plague is transmitted by fleas or contaminated aerosols. To successfully produce disease, the causal agent (Yersinia pestis) must rapidly sense and respond to rapid variations in its environment. Here, we investigated the role of 2-component regulatory systems (2CSs) in plague because the latter are known to be key players in bacterial adaptation to environmental change. Along with the previously studied PhoP-PhoQ system, OmpR-EnvZ was the only one of Y. pestis' 23 other 2CSs required for production of bubonic, septicemic, and pneumonic plague. In vitro, OmpR-EnvZ was needed to counter serum complement and leukocytes but was not required for the secretion of antiphagocyte exotoxins. In vivo, Y. pestis lacking OmpR-EnvZ did not induce an early immune response in the skin and was fully virulent in neutropenic mice. We conclude that, throughout the course of Y. pestis infection, OmpR-EnvZ is required to counter toxic effectors secreted by polymorphonuclear leukocytes in the tissues.

  10. 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

  11. Comparison of Antibody-Dependent Cell-Mediated Cytotoxicity and Virus Neutralization by HIV-1 Env-Specific Monoclonal Antibodies

    PubMed Central

    von Bredow, Benjamin; Arias, Juan F.; Heyer, Lisa N.; Moldt, Brian; Le, Khoa; Robinson, James E.; Burton, Dennis R.

    2016-01-01

    ABSTRACT Although antibodies to the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein have been studied extensively for their ability to block viral infectivity, little data are currently available on nonneutralizing functions of these antibodies, such as their ability to eliminate virus-infected cells by antibody-dependent cell-mediated cytotoxicity (ADCC). HIV-1 Env-specific antibodies of diverse specificities, including potent broadly neutralizing and nonneutralizing antibodies, were therefore tested for ADCC against cells infected with a lab-adapted HIV-1 isolate (HIV-1NL4-3), a primary HIV-1 isolate (HIV-1JR-FL), and a simian-human immunodeficiency virus (SHIV) adapted for pathogenic infection of rhesus macaques (SHIVAD8-EO). In accordance with the sensitivity of these viruses to neutralization, HIV-1NL4-3-infected cells were considerably more sensitive to ADCC, both in terms of the number of antibodies and magnitude of responses, than cells infected with HIV-1JR-FL or SHIVAD8-EO. ADCC activity generally correlated with antibody binding to Env on the surfaces of virus-infected cells and with viral neutralization; however, neutralization was not always predictive of ADCC, as instances of ADCC in the absence of detectable neutralization, and vice versa, were observed. These results reveal incomplete overlap in the specificities of antibodies that mediate these antiviral activities and provide insights into the relationship between ADCC and neutralization important for the development of antibody-based vaccines and therapies for combating HIV-1 infection. IMPORTANCE This study provides fundamental insights into the relationship between antibody-dependent cell-mediated cytotoxicity (ADCC) and virus neutralization that may help to guide the development of antibody-based vaccines and immunotherapies for the prevention and treatment of HIV-1 infection. PMID:27122574

  12. 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

  13. A Comparative Phase I Study of Combination, Homologous Subtype-C DNA, MVA, and Env gp140 Protein/Adjuvant HIV Vaccines in Two Immunization Regimes

    PubMed Central

    Joseph, Sarah; Quinn, Killian; Greenwood, Aldona; Cope, Alethea V.; McKay, Paul F.; Hayes, Peter J.; Kopycinski, Jakub T.; Gilmour, Jill; Miller, Aleisha N.; Geldmacher, Christof; Nadai, Yuka; Ahmed, Mohamed I. M.; Montefiori, David C.; Dally, Len; Bouliotis, George; Lewis, David J. M.; Tatoud, Roger; Wagner, Ralf; Esteban, Mariano; Shattock, Robin J.; McCormack, Sheena; Weber, Jonathan

    2017-01-01

    There remains an urgent need for a prophylactic HIV vaccine. We compared combined MVA and adjuvanted gp140 to sequential MVA/gp140 after DNA priming. We expected Env-specific CD4+ T-cells after DNA and MVA priming, and Env-binding antibodies in 100% individuals after boosting with gp140 and that combined vaccines would not compromise safety and might augment immunogenicity. Forty volunteers were primed three times with DNA plasmids encoding (CN54) env and (ZM96) gag-pol-nef at 0, 4 and 8 weeks then boosted with MVA-C (CN54 env and gag-pol-nef) and glucopyranosyl lipid adjuvant—aqueous formulation (GLA-AF) adjuvanted CN54gp140. They were randomised to receive them in combination at the same visit at 16 and 20 weeks (accelerated) or sequentially with MVA-C at 16, 20, and GLA-AF/gp140 at 24 and 28 weeks (standard). All vaccinations were intramuscular. Primary outcomes included ≥grade 3 safety events and the titer of CN54gp140-specific binding IgG. Other outcomes included neutralization, binding antibody specificity and T-cell responses. Two participants experienced asymptomatic ≥grade 3 transaminitis leading to discontinuation of vaccinations, and three had grade 3 solicited local or systemic reactions. A total of 100% made anti-CN54gp140 IgG and combining vaccines did not significantly alter the response; geometric mean titer 6424 (accelerated) and 6578 (standard); neutralization of MW965.2 Tier 1 pseudovirus was superior in the standard group (82 versus 45% responders, p = 0.04). T-cell ELISpot responses were CD4+ and Env-dominant; 85 and 82% responding in the accelerated and standard groups, respectively. Vaccine-induced IgG responses targeted multiple regions within gp120 with the V3 region most immunodominant and no differences between groups detected. Combining MVA and gp140 vaccines did not result in increased adverse events and did not significantly impact upon the titer of Env-specific binding antibodies, which were seen in 100% individuals

  14. 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...

  15. 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

  16. 75 FR 56654 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... 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 published a... public of a meeting of RTCA NextGen Advisory Committee. The Agenda in that notice has been revised....

  17. 75 FR 54221 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

    ...] [FR Doc No: 2010-22098] DEPARTMENT OF TRANSPORTATION Federal Aviation Administration RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of RTCA NextGen... NextGen Advisory Committee (NAC). DATES: The meeting will be held September 23, 2010, from 8:30 a.m....

  18. 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...

  19. VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS ...

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

    VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS TO THE GEN. THOMAS STATUE DOWN VERMONT AVENUE AND THE GEN. SCOTT STATUE DOWN RHODE ISLAND AVENUE IN THE BACKGROUND - Logan Circle, Vermont Avenue, Rhode Island Avenue, & Thirteenth Street, Washington, District of Columbia, DC

  20. HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization

    PubMed Central

    Bale, Shridhar; Phad, Ganesh E.; Guenaga, Javier; Wilson, Richard; Soldemo, Martina; McKee, Krisha; Sundling, Christopher; Mascola, John; Li, Yuxing; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2014-01-01

    Broadly neutralizing antibodies (bNAbs) isolated from chronically HIV-1 infected individuals reveal important information regarding how antibodies target conserved determinants of the envelope glycoprotein (Env) spike such as the primary receptor CD4 binding site (CD4bs). Many CD4bs-directed bNAbs use the same heavy (H) chain variable (V) gene segment, VH1-2*02, suggesting that activation of B cells expressing this allele is linked to the generation of this type of Ab. Here, we identify the rhesus macaque VH1.23 gene segment to be the closest macaque orthologue to the human VH1-2 gene segment, with 92% homology to VH1-2*02. Of the three amino acids in the VH1-2*02 gene segment that define a motif for VRC01-like antibodies (W50, N58, flanking the HCDR2 region, and R71), the two identified macaque VH1.23 alleles described here encode two. We demonstrate that immunization with soluble Env trimers induced CD4bs-specific VH1.23-using Abs with restricted neutralization breadth. Through alanine scanning and structural studies of one such monoclonal Ab (MAb), GE356, we demonstrate that all three HCDRs are involved in neutralization. This contrasts to the highly potent CD4bs-directed VRC01 class of bNAb, which bind Env predominantly through the HCDR2. Also unlike VRC01, GE356 was minimally modified by somatic hypermutation, its light (L) chain CDRs were of average lengths and it displayed a binding footprint proximal to the trimer axis. These results illustrate that the Env trimer immunogen used here activates B cells encoding a VH1-2 gene segment orthologue, but that the resulting Abs interact distinctly differently with the HIV-1 Env spike compared to VRC01. PMID:25166308

  1. A functional interaction between gp41 and gp120 is observed for monomeric but not oligomeric, uncleaved HIV-1 Env gp140.

    PubMed

    Guttman, Miklos; Lee, Kelly K

    2013-11-01

    The envelope glycoprotein (Env) is the sole antigenic feature on the surface of HIV and the target for the humoral immune system. Soluble, uncleaved gp140 Env constructs truncated at the transmembrane domain are being investigated intensively as potential vaccine immunogens by many groups, and understanding their structural properties is essential. We used hydrogen/deuterium-exchange mass spectrometry and small-angle X-ray scattering to probe structural order in a panel of commonly used gp140 constructs and matched gp120 monomers. We observed that oligomeric forms of uncleaved gp140, generally presumed to be trimeric, contain a protease-resistant form of gp41 akin to the postfusion, helical bundle conformation and appear to lack specific interactions between gp120 and gp41. In contrast, the monomeric form of gp140 shows significant stabilization of the gp120 inner domain imparted by the gp41 region, demonstrating excellent agreement with past mutagenesis studies. Moreover, the gp140 monomers respond to CD4 binding in manner that is consistent with the initial stages of Env activation: CD4 binding induces structural ordering throughout gp120 while loosening its association with gp41. The results indicate that uncleaved gp140 oligomers do not represent an authentic prefusion form of Env, whereas gp140 monomers isolated from the same glycoprotein preparations in many ways exhibit function and internal structural order that are consistent with expectations for certain aspects of native Env. gp140 monomers may thus be a useful reagent for advancing structural and functional studies.

  2. Recombinant pro-apoptotic Mycobacterium tuberculosis generates CD8+ T cell responses against human immunodeficiency virus type 1 Env and M. tuberculosis in neonatal mice.

    PubMed

    Ranganathan, Uma Devi K; Larsen, Michelle H; Kim, John; Porcelli, Steven A; Jacobs, William R; Fennelly, Glenn J

    2009-12-10

    Mycobacterium bovis BCG is an attractive vaccine vector against breast milk HIV transmission because it elicits Th1-type responses in newborns. However, BCG causes disease in HIV-infected infants. Genetically attenuated Mycobacterium tuberculosis (Mtb) mutants represent a safer alternative for immunocompromised populations. In the current study, we compared the immunogenicity in mice of three different recombinant attenuated Mtb strains expressing an HIV envelope (Env) antigen construct. Two of these strains (DeltalysA DeltapanCD Mtb and DeltaRD1 DeltapanCD Mtb) failed to induce significant levels of HIV Env-specific CD8(+) T cell responses. In striking contrast, an HIV-1 Env-expressing attenuated DeltalysA Mtb containing a deletion in secA2, which encodes a virulence-related secretion system involved in evading adaptive immunity, generated consistently measurable Env-specific CD8(+) T cell responses that were significantly greater than those observed after immunization with BCG expressing HIV Env. Similarly, another strain of DeltalysA DeltasecA2 Mtb expressing SIV Gag induced Gag- and Mtb-specific CD8(+) T cells producing perforin or IFNgamma, and Gag-specific CD4(+) T cells producing IFNgamma within 3 weeks after immunization in adult mice; in addition, IFNgamma-producing Gag-specific CD8(+) T cells and Mtb-specific CD4(+) T cells were observed in neonatal mice within 1 week of immunization. We conclude that DeltalysA DeltasecA2 Mtb is a promising vaccine platform to construct a safe combination HIV-TB vaccine for use in neonates.

  3. BLyS-mediated modulation of naïve B cell subsets impacts HIV Env-induced antibody responses1

    PubMed Central

    Dosenovic, Pia; Soldemo, Martina; Scholz, Jean L.; O’Dell, Sijy; Grasset, Emilie K.; Pelletier, Nadège; Karlsson, Mikael C. I.; Mascola, John R.; Wyatt, Richard T.; Cancro, Michael P.; Karlsson Hedestam, Gunilla B.

    2012-01-01

    Neutralizing Abs provide the protective effect of the majority of existing human vaccines. For a prophylactic vaccine against HIV-1, broadly neutralizing Abs (bNAbs) targeting conserved epitopes of the viral envelope glycoproteins (Env) are likely required, as the pool of circulating HIV-1 variants is extremely diverse. The failure to efficiently induce bNAbs by vaccination may be due to the use of sub-optimal immunogens or immunization regimens, or it may indicate that B cells specific for broadly neutralizing Env determinants are selected against during peripheral checkpoints, either before or after antigen encounter. To investigate if perturbation of B cell subsets prior to immunization with recombinant Env protein affects the vaccine-induced Ab response in mice, we used B Lymphocyte Stimulator (BLyS), a cytokine that regulates survival and selection of peripheral B cells. We show that the transient BLyS treatment used here substantially affected naïve B cell populations; in particular, it resulted in an increased number of B cells surviving counter-selection at the transitional stages. We also observed an increased number of mature naïve B cells, especially marginal zone B cells, in BLyS-treated mice. Intriguingly, provision of excess BLyS prior to immunization led to a consistent improvement in the frequency and potency of HIV-1 Env vaccine-induced neutralizing Ab responses, without increasing the number of Env-specific Ab-secreting cells or the Ab binding titers measured after boosting. The results presented here suggest that an increased understanding of BLyS-regulated processes may help the design of vaccine regimens aimed at eliciting improved neutralizing Ab responses against HIV-1. PMID:22561155

  4. 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

  5. Diagnosing ALS

    MedlinePlus

    ... that a person diagnosed with ALS seek a second opinion from an ALS "expert" - someone who diagnoses and treats many ALS patients and has training in this medical specialty. The ALS Association maintains a list of recognized experts in the field of ALS. See ALS Association Certified Centers of ...

  6. 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.

  7. GenCade: Introduction, Background, and Formulation

    DTIC Science & Technology

    2012-03-07

    Draft, ft Wood Wood chips Flour Other US Army Corps of Engineers BUILDING STRONG® GenCade Matagorda Ship Channel, TX CMS Shark River Inlet...morphology change Habitat Change • Regional Sediment Management • Beach fills • Inlet bypassing • Channel maintenance • Unifying technology for...to SLR • Habitat evolution (Piping Plover; vegetation) Project Planning & Design 13th Annual CIRP Technology-Transfer Workshop, March 7, 2012 7

  8. GEN3D Ver. 1.37

    SciTech Connect

    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-dimensional 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.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    The lowest-energy structures of neutral and cationic GenM (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. Such 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.

  11. Antibodies against Gag are diagnostic markers for feline foamy virus infections while Env and Bet reactivity is undetectable in a substantial fraction of infected cats.

    PubMed

    Romen, Fabian; Pawlita, Michael; Sehr, Peter; Bachmann, Silke; Schröder, Johannes; Lutz, Hans; Löchelt, Martin

    2006-02-20

    Spumaretroviruses or foamy viruses constitute a distinct subfamily of retroviruses. The biology of foamy viruses within the authentic host, their mode of transmission, and disease potential in the authentic host or after zoonotic transmission into human or other species are almost unknown. Using feline foamy virus (FFV) as model system, we established modular enzyme-linked immunosorbent assays (ELISA) suited to determine feline IgG and IgM antibody responses against structural and non-structural FFV proteins. We validated the ELISAs with standard reference sera. In 99 cats admitted to a Swiss veterinary hospital, overall FFV Gag antibody prevalence was 36%, reactivity against Env and the non-structural protein Bet each was about 25%, and 19% of the sera were directed against all three FFV antigens. With one exception, all Bet- and/or Env-positive sera were also positive for Gag. In this small epidemiological pilot study, FFV antibodies were not significantly associated with clinical disease.

  12. 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

  13. 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.

  14. env Sequences of Simian Immunodeficiency Viruses from Chimpanzees in Cameroon Are Strongly Related to Those of Human Immunodeficiency Virus Group N from the Same Geographic Area

    PubMed Central

    Corbet, Sylvie; Müller-Trutwin, Michaela C.; Versmisse, Pierre; Delarue, Severine; Ayouba, Ahidjo; Lewis, John; Brunak, Soren; Martin, Paul; Brun-Vezinet, Françoise; Simon, François; Barre-Sinoussi, Françoise; Mauclere, Philippe

    2000-01-01

    Human immunodeficiency virus type 1 (HIV-1) group N from Cameroon is phylogenetically close, in env, to the simian immunodeficiency virus (SIV) cpz-gab from Gabon and SIVcpz-US of unknown geographic origin. We screened 29 wild-born Cameroonian chimpanzees and found that three (Cam3, Cam4, and Cam5) were positive for HIV-1 by Western blotting. Mitochondrial DNA sequence analysis demonstrated that Cam3 and Cam5 belonged to Pan troglodytes troglodytes and that Cam4 belonged to P. t. vellerosus. Genetic analyses of the viruses together with serological data demonstrated that at least one of the two P. t. troglodytes chimpanzees (Cam5) was infected in the wild, and revealed a horizontal transmission between Cam3 and Cam4. These data confirm that P. t. troglodytes is a natural host for HIV-1-related viruses. Furthermore, they show that SIVcpz can be transmitted in captivity, from one chimpanzee subspecies to another. All three SIVcpz-cam viruses clustered with HIV-1 N in env. The full Cam3 SIVcpz genome sequence showed a very close phylogenetic relationship with SIVcpz-US, a virus identified in a P. t. troglodytes chimpanzee captured nearly 40 years earlier. Like SIVcpz-US, SIVcpz-cam3 was closely related to HIV-1 N in env, but not in pol, supporting the hypothesis that HIV-1 N results from a recombination event. SIVcpz from chimpanzees born in the wild in Cameroon are thus strongly related in env to HIV-1 N from Cameroon, demonstrating the geographic coincidence of these human and simian viruses and providing a further strong argument in favor of the origin of HIV-1 being in chimpanzees. PMID:10590144

  15. An Gen2 Based Security Authentication Protocol for RFID System

    NASA Astrophysics Data System (ADS)

    Yi, Xiaoluo; Wang, Liangmin; Mao, Dongmei; Zhan, Yongzhao

    EPC Class-1 Generation-2 specification(Gen2 in brief) has been accepted as the standard for RFID tags under grant number ISO18000-6C. However, Gen2 does not pay due attention to security. For this reason, a Gen2 based security authentication protocol is developed in this paper. In details, we study the security requirements presented in the current Gen2 based RFID authentication protocols[7-13]. Then we point out the security flaws of Chien's mutual authentication protocol[7], and improve the protocol based on a 11 security requirements. Our improved protocol merely uses CRC and PRNG operations supported by Gen2 and meets the 11 security requirements. In contrast to the similar work [14,15] on Chien's protocol or other Gen2 based schemes, our protocol is more secure and our security analysis is much more comprehensive and qualitative.

  16. Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo.

    PubMed Central

    Lamers, S L; Sleasman, J W; She, J X; Barrie, K A; Pomeroy, S M; Barrett, D J; Goodenow, M M

    1993-01-01

    Multiple targets for immune recognition and cellular tropism are localized to the V1 and V2 hypervariable regions in the amino portion of human immunodeficiency virus type 1 (HIV-1) gp120env. We have assessed genetic diversity in env V1 and V2 hypervariable domains in vivo within epidemiologically related strains of HIV-1. Our strategy was to analyze longitudinal samples from two seropositive mothers and multiple children infected by perinatal transmission. Although the V1 and V2 domains are closely linked in the HIV-1 genome, nucleotide sequences in V1 and in V2 evolved independently in maternal-infant viruses in vivo. A high proportion of the nucleotide substitutions would introduce amino acid diversity in V1 and in V2. A significant excess of nonsynonymous over synonymous substitutions was identified in HIV-1 env V1 and V2 peptides in the mothers and in two older children but was not generally apparent in HIV-1 sequences in infants. An excess of nonsynonymous over synonymous substitutions indicated that there is positive selection for independent genetic variation in the V1 and V2 domains in vivo. It is likely that there are host responses to complex determinants in the V1 or V2 hypervariable domain of HIV-1 gp120. PMID:8510212

  17. Construction of infectious feline foamy virus genomes: cat antisera do not cross-neutralize feline foamy virus chimera with serotype-specific Env sequences.

    PubMed

    Zemba, M; Alke, A; Bodem, J; Winkler, I G; Flower, R L; Pfrepper, K; Delius, H; Flügel, R M; Löchelt, M

    2000-01-05

    Full-length genomes of the feline foamy virus (FFV or FeFV) isolate FUV were constructed. DNA clone pFeFV-7 stably directed the expression of infectious FFV progeny virus indistinguishable from wild-type, uncloned FFV isolate FUV. The env and bel 1 genes of pFeFV-7 were substituted for by corresponding sequences of the FFV serotype 951 since previous studies implicated a defined part of FFV Env protein as responsible for serotype-specific differences in serum neutralization (I. G. Winkler, R. M. Flügel, M. Löchelt, and R. L. P. Flower, 1998. Virology 247: 144-151). Recombinant virus derived from chimeric plasmid pFeFV-7/951 containing the hybrid env gene and the parental clone pFeFV-7 were used for neutralization studies. By means of a rapid titration assay for FFV infectivity, we show that progeny virus derived from plasmid pFeFV-7 was neutralized by FUV- but not by 951-specific antisera, whereas pFeFV-7/951-derived chimeric virus was neutralized by 951-specific antisera only. Both recombinant proviruses will be useful for repeated delivery of foreign genes for therapeutic gene applications into cats.

  18. ALS Association

    MedlinePlus

    ... toward a world without ALS! Walk to Defeat ALS® Walk to Defeat ALS® draws people of all ... We need your help. I Will Advocate National ALS Registry The National ALS Registry is a congressionally ...

  19. 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

  20. Nedd4-mediated increase in HIV-1 Gag and Env proteins and immunity following DNA-vaccination of BALB/c mice.

    PubMed

    Lewis, Brad; Whitney, Stephen; Hudacik, Lauren; Galmin, Lindsey; Huaman, Maria Cecilia; Cristillo, Anthony D

    2014-01-01

    The late assembly domain of many viruses is critical for budding. Within these domains, encoded in viral structural proteins, are the conserved motifs PTAP, PPxY and YPxL. These sequences are the key determinants for association of viral proteins with intracellular molecules such as Tsg101, Nedd4 and AIP1/ALIX. While roles for Tsg101 and AIP1/ALIX in HIV-1 budding have been well established, less is known about the role of Nedd4. Recent studies, however, have identified a function for Nedd4-like protein in HIV-1 release. In this study, we investigated post-transcriptional changes of Nedd4 following SHIVSF162P3 infection of rhesus macaques, its role on HIV-1 p24 and gp120 levels in vitro and its potential as an immune modulator in HIV vaccination of BALB/c mice. Increased Nedd4 protein levels were noted in both CD4+ and CD8+ T cells following SHIVSF162P3-infection of naïve macaques. Transient co-transfection studies in 293 cells with HXB2 and Nedd4 demonstrated a Nedd4-mediated increase in p24 and gp120 levels. This increase was found to be dependent on the Ca2+/calmodulin-regulated phospholipid binding C2 domain and not ubiquitin ligase activity or HIV LTR activity. Co-transfection of Nedd4 with plasmid DNA expressing Gag or Env was further shown to augment both intracellular and extracellular Gag or Env proteins. To assess the potential of Nedd4 as an immune modulator, BALB/c mice were immunized intramuscularly with plasmid DNA encoding HIV gag, env and Nedd4. Nedd4 co-administration was found to increase serum anti-p24 but not anti-gp120 antibodies. Nedd4 co-injection was found to have no affect on Gag- or Env-specific IFNγ but had a trend of increased Gag-specific IL-6, IL-17A and TNFα that was not seen following Env stimulation. Based on our initial findings, Nedd4-mediated changes in HIV protein levels and its potential use in HIV-1 vaccine development warrants further investigation.

  1. Nedd4-Mediated Increase in HIV-1 Gag and Env Proteins and Immunity following DNA-Vaccination of BALB/c Mice

    PubMed Central

    Lewis, Brad; Whitney, Stephen; Hudacik, Lauren; Galmin, Lindsey; Huaman, Maria Cecilia; Cristillo, Anthony D.

    2014-01-01

    The late assembly domain of many viruses is critical for budding. Within these domains, encoded in viral structural proteins, are the conserved motifs PTAP, PPxY and YPxL. These sequences are the key determinants for association of viral proteins with intracellular molecules such as Tsg101, Nedd4 and AIP1/ALIX. While roles for Tsg101 and AIP1/ALIX in HIV-1 budding have been well established, less is known about the role of Nedd4. Recent studies, however, have identified a function for Nedd4-like protein in HIV-1 release. In this study, we investigated post-transcriptional changes of Nedd4 following SHIVSF162P3 infection of rhesus macaques, its role on HIV-1 p24 and gp120 levels in vitro and its potential as an immune modulator in HIV vaccination of BALB/c mice. Increased Nedd4 protein levels were noted in both CD4+ and CD8+ T cells following SHIVSF162P3-infection of naïve macaques. Transient co-transfection studies in 293 cells with HXB2 and Nedd4 demonstrated a Nedd4-mediated increase in p24 and gp120 levels. This increase was found to be dependent on the Ca2+/calmodulin-regulated phospholipid binding C2 domain and not ubiquitin ligase activity or HIV LTR activity. Co-transfection of Nedd4 with plasmid DNA expressing Gag or Env was further shown to augment both intracellular and extracellular Gag or Env proteins. To assess the potential of Nedd4 as an immune modulator, BALB/c mice were immunized intramuscularly with plasmid DNA encoding HIV gag, env and Nedd4. Nedd4 co-administration was found to increase serum anti-p24 but not anti-gp120 antibodies. Nedd4 co-injection was found to have no affect on Gag- or Env-specific IFNγ but had a trend of increased Gag-specific IL-6, IL-17A and TNFα that was not seen following Env stimulation. Based on our initial findings, Nedd4-mediated changes in HIV protein levels and its potential use in HIV-1 vaccine development warrants further investigation. PMID:24614057

  2. 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.

  3. 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.

  4. 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…

  5. 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

    2016-07-12

    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. 

  6. 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.

  7. Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov.

    PubMed

    Shida, O; Takagi, H; Kadowaki, K; Komagata, K

    1996-10-01

    16S rRNA gene sequences of the type strains of 11 species belonging to the Bacillus brevis and Bacillus aneurinolyticus groups were determined. On the basis of the results of gene sequence analyses, these species were separated into two clusters. The B. brevis cluster included 10 species, namely, Bacillus brevis, Bacillus agri, Bacillus centrosporus, Bacillus choshinensis, Bacillus parabrevis, Bacillus reuszeri, Bacillus formosus, Bacillus borstelensis, Bacillus laterosporus, and Bacillus thermoruber. Bacillus aneurinolyticus and Bacillus migulanus belonged to the B. aneurinolyticus cluster. Moreover, the two clusters were phylogenetically distinct from other Bacillus, Amphibacillus, Sporolactobacillus, Paenibacillus, and Alicyclobacillus species. On the basis of our data, we propose reclassification of the B. brevis cluster as Brevibacillus gen. nov. and reclassification of the B. aneurinolyticus cluster as Aneurinibacillus gen. nov. By using 16S rRNA gene sequence alignments, two specific PCR amplification primers were designed for differentiating the two new genera from each other and from other aerobic, endospore-forming organisms.

  8. 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.

  9. 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.

  10. Pre-existing neutralizing antibody mitigates B cell dysregulation and enhances the Env-specific antibody response in SHIV-infected rhesus macaques

    PubMed Central

    Jaworski, Juan Pablo; Bryk, Peter; Brower, Zachary; Zheng, Bo; Hessell, Ann J.; Rosenberg, Alexander F.; Wu, Tong Tong; Sanz, Ignacio; Keefer, Michael C.; Haigwood, Nancy L.

    2017-01-01

    Our central hypothesis is that protection against HIV infection will be powerfully influenced by the magnitude and quality of the B cell response. Although sterilizing immunity, mediated by pre-formed abundant and potent antibodies is the ultimate goal for B cell-targeted HIV vaccine strategies, scenarios that fall short of this may still confer beneficial defenses against viremia and disease progression. We evaluated the impact of sub-sterilizing pre-existing neutralizing antibody on the B cell response to SHIV infection. Adult male rhesus macaques received passive transfer of a sub-sterilizing amount of polyclonal neutralizing immunoglobulin (Ig) purified from previously infected animals (SHIVIG) or control Ig prior to intra-rectal challenge with SHIVSF162P4 and extensive longitudinal sampling was performed. SHIVIG treated animals exhibited significantly reduced viral load and increased de novo Env-specific plasma antibody. Dysregulation of the B cell profile was grossly apparent soon after infection in untreated animals; exemplified by a ≈50% decrease in total B cells in the blood evident 2–3 weeks post-infection which was not apparent in SHIVIG treated animals. IgD+CD5+CD21+ B cells phenotypically similar to marginal zone-like B cells were highly sensitive to SHIV infection, becoming significantly decreased as early as 3 days post-infection in control animals, while being maintained in SHIVIG treated animals, and were highly correlated with the induction of Env-specific plasma antibody. These results suggest that B cell dysregulation during the early stages of infection likely contributes to suboptimal Env-specific B cell and antibody responses, and strategies that limit this dysregulation may enhance the host’s ability to eliminate HIV. PMID:28222180

  11. CD4 down-modulation during infection of human T cells with human immunodeficiency virus type 1 involves independent activities of vpu, env, and nef.

    PubMed Central

    Chen, B K; Gandhi, R T; Baltimore, D

    1996-01-01

    The human immunodeficiency virus type 1 (HIV-1) genes vpu, env, and nef have all been implicated in modulating the levels of cell surface CD4 on infected cells. To quantitatively assess the relative contribution of each gene product to the regulation of CD4 during HIV infection of Jurkat T cells and peripheral blood mononuclear cells, we have developed an infectious HIV reporter system which expresses different combinations of these genes. To distinguish infected cells in the early or late stages of infection from uninfected cells, these viruses were designed to express human placental alkaline phosphatase with the kinetics of either early or late viral genes. Flow cytometry to detect placental alkaline phosphatase and CD4 in infected cells showed that vpu, env, and nef are independently capable of down-modulation of CD4. As predicted by their respective expression patterns, nef down-modulated CD4 rapidly during the early phase of virus infection whereas vpu and env functioned late in the infection. In both Jurkat cells and peripheral blood mononuclear cells, a combination of the three genes was more efficient than any one or two genes, demonstrating that all three genes are required to achieve maximal CD4 down-modulation. In primary cells, down-modulation of CD4 was less efficient than in Jurkat cells and there was a stronger dependence on nef function for reducing cell surface CD4. HIV therefore has three genes that are able to independently down-modulate CD4; together, they can eliminate the bulk of cell surface CD4. PMID:8709227

  12. An adenovirus-simian immunodeficiency virus env vaccine elicits humoral, cellular, and mucosal immune responses in rhesus macaques and decreases viral burden following vaginal challenge.

    PubMed Central

    Buge, S L; Richardson, E; Alipanah, S; Markham, P; Cheng, S; Kalyan, N; Miller, C J; Lubeck, M; Udem, S; Eldridge, J; Robert-Guroff, M

    1997-01-01

    Six female rhesus macaques were immunized orally and intranasally at 0 weeks and intratracheally at 12 weeks with an adenovirus type 5 host range mutant (Ad5hr)-simian immunodeficiency virus SIVsm env recombinant and at 24 and 36 weeks with native SIVmac251 gp120 in Syntex adjuvant. Four macaques received the Ad5hr vector and adjuvant alone; two additional controls were naive. In vivo replication of the Ad5hr wild-type and recombinant vectors occurred with detection of Ad5 DNA in stool samples and/or nasal secretions in all macaques and increases in Ad5 neutralizing antibody in 9 of 10 macaques following Ad administrations. SIV-specific neutralizing antibodies appeared after the second recombinant immunization and rose to titers > 10,000 following the second subunit boost. Immunoglobulin G (IgG) and IgA antibodies able to bind gp120 developed in nasal and rectal secretions, and SIV-specific IgGs were also observed in vaginal secretions and saliva. T-cell proliferative responses to SIV gp140 and T-helper epitopes were sporadically detected in all immunized macaques. Following vaginal challenge with SIVmac251, transient or persistent infection resulted in both immunized and control monkeys. The mean viral burden in persistently infected immunized macaques was significantly decreased in the primary infection period compared to that of control macaques. These results establish in vivo use of the Ad5hr vector, which overcomes the host range restriction of human Ads for rhesus macaques, thereby providing a new model for evaluation of Ad-based vaccines. In addition, they show that a vaccine regimen using the Ad5hr-SIV env recombinant and gp120 subunit induces strong humoral, cellular, and mucosal immunity in rhesus macaques. The reduced viral burden achieved solely with an env-based vaccine supports further development of Ad-based vaccines comprising additional viral components for immune therapy and AIDS vaccine development. PMID:9343211

  13. 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.

  14. ALS - resources

    MedlinePlus

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

  15. Polymorphisms in the HIV-1 gp41 env gene, natural resistance to enfuvirtide (T-20) and pol resistance among pregnant Brazilian women.

    PubMed

    Reis, Mônica Nogueira da Guarda; de Alcântara, Keila Correa; Cardoso, Ludimila Paula Vaz; Stefani, Mariane Martins Araújo

    2014-01-01

    The selective pressure of antiretroviral drugs (ARVs) targeting HIV-1 pol can promote drug resistance mutations in other genomic regions, such as env. Drug resistance among women should be monitored to avoid horizontal and mother-to-child transmission. To describe natural resistance to T-20 (enfuvirtide), gp41 env polymorphisms, mutations in pol and HIV-1 subtypes, 124 pregnant women were recruited. For 98 patients, the gp41 env, protease (PR) and reverse transcriptase (RT) fragments were sequenced. The patients were ARV naïve (n = 30), taking mother-to-child transmission prophylaxis (n = 50), or being treated with highly active ARV therapy/HAART (n = 18). The Stanford and IAS/USA databases and other sources were used to analyze PR/RT, gp41 env resistance mutations. The HIV-1 genetic diversity was analyzed by REGA/phylogenetic analyses. The patients' median age was 25 years (range, 16-42), 18.4% had AIDS. The frequency of natural resistance to T-20 (N42D, L44M, and R46M-low-impact mutations) was 6.1% (6/98); 20.4% (20/98) had compensatory mutations in HR2. The prevalence of transmitted drug resistance in the pol was 13.3% (4/30), and the prevalence of secondary drug resistance was 33.3% (6/18). Two patients were infected with multidrug resistant/MDR viruses. The analysis of HIV-1 subtypes (PR/RT/gp41) revealed that 61.2% (60/98) were subtype B, 12.2% (12/98) were subtype C, 4.1% (4/98) were subtype F1, and 22.4% (22/98) were possible recombinants (BF1 = 20.4%; BC = 2%). Natural resistance to T-20 was not associated with pol resistance or previous ARV use. The high rate of secondary resistance, including MDR, indicates that the number of women that may need T-20 salvage therapy may be higher than anticipated.

  16. Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env.

    PubMed

    Heydarchi, Behnaz; Center, Rob J; Bebbington, Jonathan; Cuthbertson, Jack; Gonelli, Christopher; Khoury, Georges; Mackenzie, Charlene; Lichtfuss, Marit; Rawlin, Grant; Muller, Brian; Purcell, Damian

    2017-04-01

    We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection.

  17. Trimeric gp120-specific bovine monoclonal antibodies require cysteine and aromatic residues in CDRH3 for high affinity binding to HIV Env

    PubMed Central

    Center, Rob J.; Bebbington, Jonathan; Cuthbertson, Jack; Khoury, Georges; Lichtfuss, Marit; Rawlin, Grant; Purcell, Damian

    2017-01-01

    ABSTRACT We isolated HIV-1 Envelope (Env)-specific memory B cells from a cow that had developed high titer polyclonal immunoglobulin G (IgG) with broad neutralizing activity after a long duration vaccination with HIV-1AD8 Env gp140 trimers. We cloned the bovine IgG matched heavy (H) and light (L) chain variable (V) genes from these memory B cells and constructed IgG monoclonal antibodies (mAbs) with either a human constant (C)-region/bovine V-region chimeric or fully bovine C and V regions. Among 42 selected Ig+ memory B cells, two mAbs (6A and 8C) showed high affinity binding to gp140 Env. Characterization of both the fully bovine and human chimeric isoforms of these two mAbs revealed them as highly type-specific and capable of binding only to soluble AD8 uncleaved gp140 trimers and covalently stabilized AD8 SOSIP gp140 cleaved trimers, but not monomeric gp120. Genomic sequence analysis of the V genes showed the third heavy complementarity-determining region (CDRH3) of 6A mAb was 21 amino acids in length while 8C CDRH3 was 14 amino acids long. The entire V heavy (VH) region was 27% and 25% diverged for 6A and 8C, respectively, from the best matched germline V genes available, and the CDRH3 regions of 6A and 8C were 47.62% and 78.57% somatically mutated, respectively, suggesting a high level of somatic hypermutation compared with CDRH3 of other species. Alanine mutagenesis of the VH genes of 6A and 8C, showed that CDRH3 cysteine and tryptophan amino acids were crucial for antigen binding. Therefore, these bovine vaccine-induced anti-HIV antibodies shared some of the notable structural features of elite human broadly neutralizing antibodies, such as CDRH3 size and somatic mutation during affinity-maturation. However, while the 6A and 8C mAbs inhibited soluble CD4 binding to gp140 Env, they did not recapitulate the neutralizing activity of the polyclonal antibodies against HIV infection. PMID:27996375

  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. Primate immune responses to HIV-1 Env formulated in the saponin-based adjuvant AbISCO-100 in the presence or absence of TLR9 co-stimulation

    PubMed Central

    Martinez, Paola; Sundling, Christopher; O'Dell, Sijy; Mascola, John R.; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2015-01-01

    Protein-based vaccines require adjuvants to achieve optimal responses. Toll-like receptor (TLR) 9 agonists were previously shown to improve responses to protein-based vaccines, such as the Hepatitis B virus vaccine formulated in alum. Here, we used CpG-C together with the clinically relevant saponin-based adjuvant AbISCO-100/Matrix-M (AbISCO), to assess if TLR9 co-stimulation would quantitatively or qualitatively modulate HIV-1 envelope glycoprotein (Env)-specific B and T cell responses in rhesus macaques. The macaques were inoculated with soluble Env trimers in AbISCO, with or without the addition of CpG-C, using an interval similar to the Hepatitis B virus vaccine. Following a comprehensive evaluation of antigen-specific responses in multiple immune compartments, we show that the Env-specific circulating IgG, memory B cells and plasma cells displayed similar kinetics and magnitude in the presence or absence of CpG-C and that there was no apparent difference between the two groups in the elicited HIV-1 neutralizing antibody titers or antigen-specific CD4+ T cell responses. Importantly, the control of SHIV viremia was significantly improved in animals from both Env-immunized groups relative to adjuvant alone controls, demonstrating the potential of AbISCO to act as a stand-alone adjuvant for Env-based vaccines. PMID:25762407

  1. Virion Background and Efficiency of Virion Incorporation Determine Susceptibility of Simian Immunodeficiency Virus Env-Driven Viral Entry to Inhibition by IFITM Proteins

    PubMed Central

    Wrensch, Florian; Hoffmann, Markus; Gärtner, Sabine; Nehlmeier, Inga; Winkler, Michael

    2016-01-01

    ABSTRACT Interferon-induced transmembrane proteins (IFITMs) can inhibit the cellular entry of several enveloped viruses, including simian immunodeficiency virus (SIV). The blockade of SIV by IFITMs is isolate specific, raising the question of which parameters impact sensitivity to IFITM. We show that the virion context in which SIV-Env is presented and the efficiency of virion incorporation determine Env susceptibility to inhibition by IFITMs. Thus, determinants other than the nature of the envelope protein can impact the IFITM sensitivity of viral entry. IMPORTANCE The host cell-encoded IFITM proteins can block viral entry and are an important component of the innate defenses against viral infection. However, the determinants controlling whether a virus is susceptible to blockade by IFITM proteins are incompletely understood. Our study shows that the amount of envelope proteins incorporated into virions as well as the nature of the virion particle itself can impact the sensitivity of viral entry to IFITMs. These results show for the first time that determinants other than the viral envelope protein can impact sensitivity to IFITM and have implications for the interpretation of previously published data on inhibition of viruses by IFITM proteins. Moreover, our findings might help to define the mechanism underlying the antiviral activity of IFITM proteins. PMID:27807233

  2. Peptide Triazole Inactivators of HIV-1 Utilize a Conserved Two-Cavity Binding Site at the Junction of the Inner and Outer Domains of Env gp120

    PubMed Central

    Aneja, Rachna; Rashad, Adel A.; Li, Huiyuan; Sundaram, Ramalingam Venkat Kalyana; Duffy, Caitlin; Bailey, Lauren D.; Chaiken, Irwin

    2015-01-01

    We used coordinated mutagenesis, synthetic design, and flexible docking to investigate the structural mechanism of Env gp120 encounter by peptide triazole (PT) inactivators of HIV-1. Prior results demonstrated that the PT class of inhibitors suppresses binding at both CD4 and coreceptor sites on Env and triggers gp120 shedding, leading to cell-independent irreversible virus inactivation. Despite these enticing anti-HIV-1 phenotypes, structural understanding of the PT–gp120 binding mechanism has been incomplete. Here we found that PT engages two inhibitor ring moieties at the junction between the inner and outer domains of the gp120 protein. The results demonstrate how combined occupancy of two gp120 cavities can coordinately suppress both receptor and coreceptor binding and conformationally entrap the protein in a destabilized state. The two-cavity model has common features with small molecule gp120 inhibitor binding sites and provides a guide for further design of peptidomimetic HIV-1 inactivators based on the PT pharmacophore. PMID:25860784

  3. Cross-talk Suppression between the CpxA-CpxR and EnvZ-OmpR Two-Component Systems in E. coli

    PubMed Central

    Siryaporn, Albert; Goulian, Mark

    2009-01-01

    Many bacteria possess large numbers of two-component signaling systems, which are composed of histidine kinase-response regulator pairs. The high level of sequence similarity between some systems raises the possibility of undesired cross-talk between a histidine kinase and a non-cognate response regulator. Although molecular specificity ensures that phospho-transfer occurs primarily between correct partners, even a low level of inappropriate cross-talk could lead to unacceptable levels of noise or interference in signal transduction. To explore mechanisms that provide insulation against such interference, we have examined cross-talk between the histidine kinase CpxA and non-cognate response regulator OmpR in Escherichia coli. Our results show that there are two mechanisms that suppress cross-talk between these two proteins, which depend on the corresponding cognate partners CpxR and EnvZ and on the bifunctional nature of the histidine kinases CpxA and EnvZ. When cross-talk is detectable, we find it is independent of CpxA stimulus. We also show that cross-talk suppression leads to mutational robustness, i.e. it masks the effects of mutations that would otherwise lead to increased cross-talk. The mechanisms that provide insulation against interference described here may be applicable to many other two-component systems. PMID:18761686

  4. Different HIV-1 env frames: gp120 and ASP (antisense protein) biosynthesis, and theirs co-variation tropic amino acid signatures in X4- and R5-viruses.

    PubMed

    Dimonte, Salvatore

    2017-01-01

    Antisense protein (ASP) is the new actor of viral life of Human Immunodeficiency Virus type 1 (HIV-1) although proposed above 20 years ago. The asp ORF is into complementary strand of the gp120/gp41 junction of env gene. The ASP biological role remains little known. Knowing the Env markers of viral tropism, a dataset of sequences (660 strains) was used to analyze the hypothetical ASP involvement in CCR5 (R5) and/or CXCR4 (X4) co-receptor interaction. Preliminarily, prevalence of ASP and gp120V3 mutations was performed; following association among mutations were elaborate. The classical V3 tropic-signatures were confirmed, and 36 R5- and 22 X4-tropic ASP mutations were found. Moreover, by analyzing the ASP sequences, 36 out of 179 amino acid positions significantly associated with different co-receptor usage were found. Several statistically significant associations between gp120V3 and ASP mutations were observed. The dendrogram showed the existence of a cluster associated with R5-usage and a large cluster associated with X4-usage. These results show that gp120V3 and specific amino acid changes in ASP are associated together with CXCR4 and/or CCR5-usage. These findings implement previous observations on unclear ASP functions. J. Med. Virol. 89:112-122, 2017. © 2016 Wiley Periodicals, Inc.

  5. Fc Receptor-Mediated Activities of Env-Specific Human Monoclonal Antibodies Generated from Volunteers Receiving the DNA Prime-Protein Boost HIV Vaccine DP6-001.

    PubMed

    Costa, Matthew R; Pollara, Justin; Edwards, Regina Whitney; Seaman, Michael S; Gorny, Miroslaw K; Montefiori, David C; Liao, Hua-Xin; Ferrari, Guido; Lu, Shan; Wang, Shixia

    2016-11-15

    HIV-1 is able to elicit broadly potent neutralizing antibodies in a very small subset of individuals only after several years of infection, and therefore, vaccines that elicit these types of antibodies have been difficult to design. The RV144 trial showed that moderate protection is possible and that this protection may correlate with antibody-dependent cellular cytotoxicity (ADCC) activity. Our previous studies demonstrated that in an HIV vaccine phase I trial, the DP6-001 trial, a polyvalent Env DNA prime-protein boost formulation could elicit potent and broadly reactive, gp120-specific antibodies with positive neutralization activities. Here we report on the production and analysis of HIV-1 Env-specific human monoclonal antibodies (hMAbs) isolated from vaccinees in the DP6-001 trial. For this initial report, 13 hMAbs from four vaccinees in the DP6-001 trial showed broad binding to gp120 proteins of diverse subtypes both autologous and heterologous to vaccine immunogens. Equally cross-reactive Fc receptor-mediated functional activities, including ADCC and antibody-dependent cellular phagocytosis (ADCP) activities, were present with both immune sera and isolated MAbs, confirming the induction of nonneutralizing functional hMAbs by the DNA prime-protein boost vaccination. Elicitation of broadly reactive hMAbs by vaccination in healthy human volunteers confirms the value of the polyvalent formulation in this HIV vaccine design.

  6. Molecular phylogeny of Urosomoida agilis, and new combinations: Hemiurosomoida longa gen. nov., comb. nov., and Heterourosomoida lanceolata gen. nov., comb. nov. (Ciliophora, Hypotricha).

    PubMed

    Singh, Jasbir; Kamra, Komal

    2015-02-01

    For years, systematics of three species, Urosomoida agilis (Engelmann, 1862) Hemberger in Foissner, 1982, Urosomoida longa (Gelei and Szabados, 1950) Foissner et al., 1991 and Oxytricha lanceolata Shibuya, 1930, has remained unresolved due to lack of adequate molecular data. Though, it is known since several years that the three species are not very closely related. In the present paper, 18S rRNA gene sequences for two key species, U. agilis and U. longa, and their morphology and morphometry have been analyzed. Molecular phylogeny inferred from maximum likelihood, neighbour joining and maximum parsimony methods has adequately removed ambiguity over their systematics. In phylogenetic trees, U. agilis clustered consistently with non-stylonychine oxytrichids. Both Urosomoida longa and Oxytricha lanceolata clustered consistently away from U. agilis and O. granulifera, the type species of the genera Urosomoida and Oxytricha, respectively. As a result of the current molecular phylogenetic investigation and based on previously inferred morphological and morphogenetic data it is proposed to remove Urosomoida longa and Oxytricha lanceolata from Urosomoida and incertae sedis in Oxytricha, respectively, and establish two new generic combinations, Hemiurosomoida longa gen. nov., comb. nov. and Heterourosomoida lanceolata gen. nov., comb. nov. for them.

  7. 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.

  8. 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

  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. 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

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

    DOE PAGES

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; ...

    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

  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.

  13. Co-regulation of polysaccharide production, motility, and expression of type III secretion genes by EnvZ/OmpR and GrrS/GrrA systems in Erwinia amylovora.

    PubMed

    Li, Wenting; Ancona, Veronica; Zhao, Youfu

    2014-02-01

    The EnvZ/OmpR and GrrS/GrrA systems, two widely distributed two-component systems in gamma-Proteobacteria, negatively control amylovoran biosynthesis in Erwinia amylovora, and the two systems regulate motility in an opposing manner. In this study, we examined the interplay of EnvZ/OmpR and GrrS/GrrA systems in controlling various virulence traits in E. amylovora. Results showed that amylovoran production was significantly higher when both systems were inactivated, indicating that the two systems act as negative regulators and their combined effect on amylovoran production appears to be enhanced. In contrast, reduced motility was observed when both systems were deleted as compared to that of grrA/grrS mutants and WT strain, indicating that the two systems antagonistically regulate motility in E. amylovora. In addition, glycogen accumulation was much higher in envZ/ompR and two triple mutants than that of grrS/grrA mutants and WT strain, suggesting that EnvZ/OmpR plays a dominant role in regulating glycogen accumulation, whereas levan production was significantly lower in the grrS/grrA and two triple mutants as compared with that of WT and envZ/ompR mutants, indicating that GrrS/GrrA system dominantly controls levan production. Furthermore, both systems negatively regulated expression of three type III secretion (T3SS) genes and their combined negative effect on hrp-T3SS gene expression increased when both systems were deleted. These results demonstrated that EnvZ/OmpR and GrrS/GrrA systems co-regulate various virulence factors in E. amylovora by still unknown mechanisms or through different target genes, sRNAs, or proteins, indicating that a complex regulatory network may be involved, which needs to be further explored.

  14. 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.

  15. Marinagarivorans algicola gen. nov., sp. nov., isolated from marine algae.

    PubMed

    Guo, Ling-Yun; Li, Dong-Qi; Sang, Jin; Chen, Guan-Jun; Du, Zong-Jun

    2016-01-27

    Novel agar-degrading, Gram-staining-negative, motile, heterotrophic, facultatively anaerobic and pale yellow-pigmented bacterial strains, designated Z1T and JL1, were isolated from marine algae Gelidium amansii (Lamouroux) and Gracilaria verrucosa, respectively. Growth of the isolates was optimal at 28-30 °C, pH 7.0-7.5 and 1-3% (w/v) NaCl. Both strains contained Q-8 as the sole respiratory quinone. The major cellular fatty acids in strain Z1T were C18:1 ω7c, C16:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH). The predominant polar lipids in strain Z1T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and aminolipid (AL). The genomic DNA G+C content of both strains was 45.1 mol%. Strains Z1T and JL1 were closely related, with 99.9% 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) value between strains Z1T and JL1 was 99.3%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains Z1T and JL1 form a distinct phyletic line within the class Gammaproteobacteria, with less than 92.3% similarity to their closest relatives. Based on data from the current polyphasic study, the isolates are proposed to belong to a new genus and species designated Marinagarivorans algicola gen. nov., sp. nov. The type strain of Marinagarivorans algicola is Z1T (=ATCC BAA-2617T=CICC 10859T).

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

    PubMed

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

    2012-05-01

    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.

  17. Human Endogenous Retrovirus K(HML-2) Gag- and Env-Specific T-Cell Responses Are Infrequently Detected in HIV-1-Infected Subjects Using Standard Peptide Matrix-Based Screening

    PubMed Central

    John, Vivek M.; Hunter, Diana V.; Martin, Eric; Mujib, Shariq; Mihajlovic, Vesna; Burgers, Peter C.; Luider, Theo M.; Gyenes, Gabor; Sheppard, Neil C.; SenGupta, Devi; Tandon, Ravi; Yue, Feng-Yun; Benko, Erika; Kovacs, Colin; Nixon, Douglas F.; Ostrowski, Mario A.

    2012-01-01

    T-cell responses to human endogenous retrovirus (HERV) K(HML-2) Gag and Env were mapped in HIV-1-infected subjects using 15mer peptides. Small peptide pools and high concentrations were used to maximize sensitivity. In the 23 subjects studied, only three bona fide HERV-K(HML-2)-specific responses were detected. At these high peptide concentrations, we detected false-positive responses, three of which were mapped to an HIV-1 Gag peptide contaminant. Thus, HERV-K(HML-2) Gag- and Env-specific T-cell responses are infrequently detected by 15mer peptide mapping. PMID:22205657

  18. Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov.--two new middle Cambrian hyolithids (?Mollusca) from the Czech Republic.

    PubMed

    Valent, Martin; Fatka, Oldřich; Szabad, Michal; Micka, Václav; Marek, Ladislav

    2015-08-28

    Two new endemic genera and species of extinct group of Hyolitha, Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov. are described and illustrated from the Buchava Formation of the Barrandian area (Czech Republic).

  19. Taxonomy and phylogeny of Laburnicola gen. nov. and Paramassariosphaeria gen. nov. (Didymosphaeriaceae, Massarineae, Pleosporales).

    PubMed

    Wanasinghe, Dhanushka N; Jones, Evan Benjamin Gareth; Camporesi, Erio; Dissanayake, Asha J; Kamolhan, Sutakorn; Mortimer, Peter E; Xu, Jianchu; Abd-Elsalam, Kamel A; Hyde, Kevin D

    2016-11-01

    Laburnicola gen. nov., with four new species, Paramassariosphaeria gen. nov., with a new species and Montagnula saikhuensis sp. nov. are introduced in this paper. The phylogeny of these taxa and genera of Didymosphaeriaceae are resolved based on analysis of combined LSU, SSU, and ITS sequence data. Laburnicola is characterized by obpyriform, immersed ascomata, with a peridium fused to the host tissues, long pedicellate asci and ellipsoidal to fusoid ascospores, whose central cells have longitudinal septa and a rugged surface. Paramassariosphaeria is characterized by globose to subglobose ascomata, papillate ostioles, a peridium comprising pseudoparenchymatous cells of textura angularis, cylindric-clavate to clavate, pedicellate asci and brown, curved-fusoid ascospores, with multiple transverse septa and a mucilaginous sheath. Montagnula saikhuensis has immersed ascomata, with a peridium fused to the host tissues, long pedicellate asci and blackish brown, ellipsoidal ascospores with a single septum. The relationship of these taxa with other Didymosphaeriaceae species is discussed based on comparative morphology and phylogenetic analysis. Munkovalsaria appendiculata and Munkovalsaria donacina are transferred to the genus Montagnula.

  20. 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

  1. Recombination between feline leukemia virus subgroup B or C and endogenous env elements alters the in vitro biological activities of the viruses.

    PubMed Central

    Pandey, R; Ghosh, A K; Kumar, D V; Bachman, B A; Shibata, D; Roy-Burman, P

    1991-01-01

    An important question in feline leukemia virus (FeLV) pathogenesis is whether, as in murine leukemia virus infection, homologous recombination between the infecting FeLV and the noninfectious endogenous FeLV-like proviruses serves as a significant base for the generation of proximal pathogens. To begin an analysis of this issue, several recombinant FeLVs were produced by using two different approaches: (i) the regions of the viral envelope (env) gene of a cloned FeLV (subgroup B virus [FeLV-B], Gardner-Arnstein strain) and those of two different endogenous proviral loci were exchanged to create specific FeLV chimeras, and (ii) vectors containing endogenous env and molecularly cloned infectious FeLV-C (Sarma strain) DNA sequences were coexpressed by transfection in nonfeline cells to facilitate recombination. The results of these combined approaches showed that up to three-fourths of the envelope glycoprotein (gp70), beginning from the N-terminal end, could be replaced by endogenous FeLV sequences to produce biologically active chimeric FeLVs. The in vitro replication efficiency or cell tropism of the recombinants appeared to be influenced by the amount of gp70 sequences replaced by the endogenous partner as well as by the locus of origin of the endogenous sequences. Additionally, a characteristic biological effect, aggregation of feline T-lymphoma cells (3201B cell line), was found to be specifically induced by replicating FeLV-C or FeLV-C-based recombinants. Multiple crossover sites in the gp70 protein selected under the conditions used for coexpression were identified. The results of induced coexpression were also supported by rapid generation of FeLV recombinants when FeLV-C was used to infect the feline 3201B cell line that constitutively expresses high levels of endogenous FeLV-specific mRNAs. Furthermore, a large, highly conserved open reading frame in the pol gene of an endogenous FeLV provirus was identified. This observation, particularly in reference to

  2. 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

  3. 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

  4. HIV-specific humoral and cellular immunity in rabbits vaccinated with recombinant human immunodeficiency virus-like gag-env particles

    SciTech Connect

    Haffar, O.K.; Smithgall, M.D.; Moran, P.A.; Travis, B.M.; Zarling, J.M.; Hu, S.L. )

    1991-08-01

    Recombinant human immunodeficiency virus type-1 (HIV-1)-like gag-env particles produced in mammalian cells were inoculated into two New Zealand white rabbits. In parallel, two control rabbits were inoculated with the homologous HIV-1 virions inactivated by ultraviolet light (uv) and psoralen treatments. The humoral and cellular immune responses to HIV-1 were evaluated for both groups of animals. Recombinant particles elicited humoral immunity that was specific for all the viral structural proteins. The antibodies recognized both denatured and nondenatured proteins. Moreover, the sera neutralized the in vitro infectivity of the homologous virus in CEM cells. Importantly, the recombinant particles also generated a T helper response by priming with the HIV proteins. Similar results were observed with inactivated virus immunization. Therefore, the authors results suggest that the recombinant HIV-like particles elicit functional humoral immunity as well as cellular immunity and represent a novel vaccine candidate for AIDS.

  5. Reduced potency and incomplete neutralization of broadly neutralizing antibodies against cell-to-cell transmission of HIV-1 with transmitted founder Envs.

    PubMed

    Li, Hongru; Zony, Chati; Chen, Ping; Chen, Benjamin K

    2017-02-01

    Broadly neutralizing antibodies (bNAbs) have been isolated from HIV-1 patients and can potently block infection of a wide spectrum of HIV-1 subtypes. These antibodies define common epitopes shared by many viral isolates. While bNAbs potently antagonize infection with cell-free virus, inhibition of HIV-1 transmission from infected to uninfected CD4(+) T cells through virological synapses (VS), has been found to require greater amounts of antibody. In this study, we examined two well-studied molecular clones and two transmitted founder (T/F) viruses for their sensitivities to a panel of bNAbs in cell-free and cell-to-cell infection assays. We observed a relative resistance of cell-to-cell transmission to antibody neutralization that is reflected not only by reductions of antibody potency, but also by decreases in maximum neutralization capacity relative to cell-free infections. BNAbs targeting different epitopes exhibited incomplete neutralization against cell-associated virus with T/F Envs, which was not observed with cell-free form of the same virus. We further identified the membrane proximal internal tyrosine-based sorting motif as a determinant that can affect the incomplete neutralization of these T/F clones in cell-to-cell infection. These findings indicate that the signal that affects surface expression and/or internalization of Env from the plasma membrane can modulate the presentation of neutralizing epitopes on infected cells. These findings highlight that a fraction of virus can escape from high concentrations of antibody through cell-to-cell infection while maintaining sensitivity to neutralization in cell-free infection. The ability to fully inhibit cell-to-cell transmission may represent an important consideration in development of antibodies for treatment or prophylaxis.

  6. Mutations of a residue within the polyproline-rich region of Env alter the replication rate and level of cytopathic effects in chimeric avian retroviral vectors.

    PubMed

    Chang, Kevin W; Barsov, Eugene V; Ferris, Andrea L; Hughes, Stephen H

    2005-08-01

    Previous attempts to extend the host range of the avian sarcoma/leukosis virus (ASLV)-based RCASBP vectors produced two viral vectors, RCASBP M2C (4070A) and RCASBP M2C (797-8), which replicate using the amphotropic murine leukemia virus 4070A Env protein (2). Both viruses were adapted to replicate efficiently in the avian cell line DF-1, but RCASBP M2C (4070A) caused extensive cytopathic effects (CPE) in DF-1 cells whereas RCASBP M2C (797-8) induced low levels of CPE. The two viruses differed only at amino acid 242 of the polyproline-rich region in the surface (SU) subunit of the Env protein. In RCASBP M2C (4070A), an isoleucine replaced the wild-type proline residue, whereas a threonine residue was found in RCASBP M2C (797-8). In the present study, we show that other amino acid substitutions at position 242 strongly influence the CPE and replication rate of the chimeric viruses. There was a correlation between the amount of unintegrated linear retroviral DNA present in infected DF-1 cells and the level of CPE. This suggests that there may be a role for superinfection in the CPE. The treatment of RCASBP M2C (4070A)-infected cells with dantrolene, which inhibits the release of calcium from the endoplasmic reticulum (ER), reduced the amount of CPE seen during infection with the highly cytotoxic virus. Dantrolene treatment did not appear to affect virus production, suggesting that Ca2+ release from the ER had a role in the CPE caused by these viruses.

  7. 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.

  8. 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

  9. Introducing AstroGen: the Astronomy Genealogy Project

    NASA Astrophysics Data System (ADS)

    Tenn, Joseph S.

    2016-12-01

    The Astronomy Genealogy Project (AstroGen), a project of the Historical Astronomy Division of the American Astronomical Society (AAS), will soon appear on the AAS website. Ultimately, it will list the world's astronomers with their highest degrees, theses for those who wrote them, academic advisors (supervisors), universities, and links to the astronomers or their obituaries, their theses when online, and more. At present the AstroGen team is working on those who earned doctorates with astronomy-related theses. We show what can be learned already, with just ten countries essentially completed.

  10. Viability of thin wall tube forming of ATF FeCrAl

    SciTech Connect

    Maloy, Stuart Andrew; Aydogan, Eda; Anderoglu, Osman; Lavender, Curt; Yamamoto, Yukinori

    2016-09-16

    Fabrication of thin walled tubing of FeCrAl alloys is critical to its success as a candidate enhanced accident-tolerant fuel cladding material. Alloys that are being investigated are Generation I and Generation II FeCrAl alloys produced at ORNL and an ODS FeCrAl alloy, MA-956 produced by Special Metals. Gen I and Gen II FeCrAl alloys were provided by ORNL and MA-956 was provided by LANL (initially produced by Special Metals). Three tube development efforts were undertaken. ORNL led the FeCrAl Gen I and Gen II alloy development and tube processing studies through drawing tubes at Rhenium Corporation. LANL received alloys from ORNL and led tube processing studies through drawing tubes at Century Tubing. PNNL led the development of tube processing studies on MA-956 through pilger processing working with Sandvik Corporation. A summary of the recent progress on tube development is provided in the following report and a separate ORNL report: ORNL/TM-2015/478, “Development and Quality Assessments of Commercial Heat Production of ATF FeCrAl Tubes”.

  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. GenStar: A method for de novo drug design

    NASA Astrophysics Data System (ADS)

    Rotstein, Sergio H.; Murcko, Mark A.

    1993-02-01

    A novel method, which we call GenStar, has been developed to suggest chemically reasonable structures which fill the active sites of enzymes. The proposed molecules provide good steric contact with the enzyme and exist in low-energy conformations. These structures are composed entirely of sp3 carbons which are grown sequentially, but which can also branch or form rings. User-selected enzyme seed atoms may be used to determine the area in which structure generation begins. Alternatively, GenStar may begin with a predocked `inhibitor core' from which atoms are grown. For each new atom generated by the program, several hundred candidate positions representing a range of reasonable bond lengths, bond angles, and torsion angles are considered. Each of these candidates is scored, based on a simple enzyme contact model. The selected position is chosen at random from among the highest scoring cases. Duplicate structures may be removed using a variety of criteria. The compounds may be energy minimized and displayed using standard modeling programs. Also, it is possible to analyze the collection of all structures created by GenStar and locate binding motifs for common fragments such as benzene and naphthylene. Tests of the method using HIV protease, FK506 binding protein (FKBP-12) and human carbonic anhydrase (HCA-II) demonstrated that structures similar to known potent inhibitors may be generated with GenStar.

  13. 78 FR 8108 - NextGen Solutions Vendors Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE..., Commerce. ACTION: Notice and request for response. SUMMARY: This notice sets forth a request for responses... Transportation System (NextGen) solutions that meet the requirements of the International Civil...

  14. 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…

  15. An electronic flight bag for NextGen avionics

    NASA Astrophysics Data System (ADS)

    Zelazo, D. Eyton

    2012-06-01

    The introduction of the Next Generation Air Transportation System (NextGen) initiative by the Federal Aviation Administration (FAA) will impose new requirements for cockpit avionics. A similar program is also taking place in Europe by the European Organisation for the Safety of Air Navigation (Eurocontrol) called the Single European Sky Air Traffic Management Research (SESAR) initiative. NextGen will require aircraft to utilize Automatic Dependent Surveillance-Broadcast (ADS-B) in/out technology, requiring substantial changes to existing cockpit display systems. There are two ways that aircraft operators can upgrade their aircraft in order to utilize ADS-B technology. The first is to replace existing primary flight displays with new displays that are ADS-B compatible. The second, less costly approach is to install an advanced Class 3 Electronic Flight Bag (EFB) system. The installation of Class 3 EFBs in the cockpit will allow aircraft operators to utilize ADS-B technology in a lesser amount of time with a decreased cost of implementation and will provide additional benefits to the operator. This paper describes a Class 3 EFB, the NexisTM Flight-Intelligence System, which has been designed to allow users a direct interface with NextGen avionics sensors while additionally providing the pilot with all the necessary information to meet NextGen requirements.

  16. 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.

  17. 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…

  18. ORPC RivGen controller performance raw data - Igiugig 2015

    DOE Data Explorer

    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.

  19. 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...

  20. 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...

  1. 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:...

  2. 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,...

  3. 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:...

  4. 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...

  5. 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:...

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Sequence analysis of selected regions of the env (V3 loop and gp41) and gag (p7) reading frames of Ethiopian human immunodeficiency virus type 1 strains.

    PubMed

    Ayehunie, S; Johansson, B; Sönnerborg, A; Zewdie, D W; Britton, S; Strannegård, O

    1993-01-01

    Amplified polymerase chain reaction (PCR) products, corresponding to the V3 loop and gp41 of the env, and p7 of the gag region, from proviral DNA of several Ethiopian and Swedish HIV-1 strains were sequenced. Of the six amino acids (GPGRAF) that constitute the principal neutralizing determinant (PND) within the V3 loop, the Ethiopian isolates all showed two amino acid changes (GPGQTF). Four to five other substitutions were found in the amino acids flanking the PND. Substitution of alanine (A) for threonine (T) should result in a change in the predicted secondary structure, i.e., disappearance of a coil structure. Percentage similarity data on a stretch of 22 amino acids within the V3 loop showed a concordance of the Ethiopian HIV-1 isolates with the sequences of published macrophage-T-cell tropic HIV isolates. Additionally derived protein sequences in two other regions showed two common substitutions in p7 and one to two substitutions in gp41 compared to a recent consensus sequence. These changes are hitherto unique for the Ethiopian strains, and suggest the presence of a clustering of a divergent HIV-1 strain in Addis Ababa, Ethiopia.

  11. 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

    2016-05-03

    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.

  12. 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.

  13. 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.

  14. Cross-Neutralizing Antibodies in HIV-1 Individuals Infected by Subtypes B, F1, C or the B/Bbr Variant in Relation to the Genetics and Biochemical Characteristics of the env Gene

    PubMed Central

    de Almeida, Dalziza Victalina; Macieira, Karine Venegas; Grinsztejn, Beatriz Gilda Jegerhorn; Veloso dos Santos, Valdiléa Gonçalves; Guimarães, Monick Lindenmeyer

    2016-01-01

    Various HIV-1 env genetic and biochemical features impact the elicitation of cross-reactive neutralizing antibodies in natural infections. Thus, we aimed to investigate cross-neutralizing antibodies in individuals infected with HIV-1 env subtypes B, F1, C or the B/Bbr variant as well as env characteristics. Therefore, plasma samples from Brazilian chronically HIV-1 infected individuals were submitted to the TZM-bl neutralization assay. We also analyzed putative N-glycosylation sites (PNGLs) and the size of gp120 variable domains in the context of HIV-1 subtypes prevalent in Brazil. We observed a greater breadth and potency of the anti-Env neutralizing response in individuals infected with the F1 or B HIV-1 subtypes compared with the C subtype and the variant B/Bbr. We observed greater V1 B/Bbr and smaller V4 F1 than those of other subtypes (p<0.005), however neither was there a correlation verified between the variable region length and neutralization potency, nor between PNLG and HIV-1 subtypes. The enrichment of W at top of V3 loop in weak neutralizing response viruses and the P in viruses with higher neutralization susceptibility was statistically significant (p = 0.013). Some other signatures sites were associated to HIV-1 subtype-specific F1 and B/Bbr samples might influence in the distinct neutralizing response. These results indicate that a single amino acid substitution may lead to a distinct conformational exposure or load in the association domain of the trimer of gp120 and interfere with the induction power of the neutralizing response, which affects the sensitivity of the neutralizing antibody and has significant implications for vaccine design. PMID:27936047

  15. Comparison of telogen hair analyses: genRES MPX-2SP kit versus genRES MPX-SP1 and genRES MPX-SP2 kits.

    PubMed

    Schmid, D; Bayer, B; Anslinger, K

    2008-12-01

    STR investigations of telogen hair are invariably difficult due to the small amounts of nuclear DNA and its degradation products. However, in recent years there has been a considerable improvement. This study examined the suitability of a new STR kit with shortened amplicons for the investigation of hair in routine casework. This kit allows the simultaneous amplification of the eight STR-loci D3S1358, VWA, FGA, TH01, SE33, D8S1179, D18S51, and D21S11, and the sex-determining amelogenin system. It was tested against the genRES MPX-SP1 and genRES MPX-SP2 kits. The sensitivity of the new genRES MPX-2SP kit was demonstrated to be inferior to that of the genRES MPX-SP1, but almost equal to that of the genRES MPX-SP2 kit.

  16. Molecular subtypes of env sequences around V3 region of human immunodeficiency virus type 1 in Taiwan.

    PubMed

    Chang, K S; Lin, C I; Ling, P; Lin, K H; Lin, H C; Twu, S J

    1994-06-01

    Samples of peripheral blood mononuclear cells (PBMC) were collected during 1990-91 from seropositive healthy, male HIV-1 carriers visiting Taipei Venereal Disease Control Center, and a male AIDS patient admitted to a general hospital. The V3 and its flanking nucleotide (nt) sequences in their DNA were amplified by polymerase chain reaction (PCR) and compared with those of known HIV-1 prototypes. The nt sequences obtained from 21 individuals (e.g., TW92) clustered as Group A, which were highly homologous (95.6-99.5%) to that of HXB2 virus while those from 6 individuals (TW90, TW91, TW97, TW99, TW102 and TW104) were classified as Group B showing low similarities (73.2-84.2%) to those of HXB2 and moderate similarities (80.7-90.0%) to those of SC and Bangkok (BK) viruses. By comparison of their deduced amino acid sequences with those of consensus sequences for subtypes A-F as defined by Myers et al. (1993), both Groups A and B viruses (except TW102) together with those of HXB2, SC and BK viruses could be identified as members or variants of subtype B, and the TW102 virus as a member of subtype E viruses. Individuals with the Group A viruses included 4 homosexual and 17 heterosexual Taiwanese males, 2 of the latter having a history of i.v. drug abuse. Among individuals with Group B viruses, those with TW97, TW99, TW104 and TW91, who was an AIDS patient, were heterosexual Taiwanese males, whereas both TW90 and TW102 viruses were from individuals who were overseas heterosexual Chinese from Thailand, the former with a history of i.v. drug abuse and the latter without.

  17. Specific sequences commonly found in the V3 domain of HIV-1 subtype C isolates affect the overall conformation of native Env and induce a neutralization-resistant phenotype independent of V1/V2 masking.

    PubMed

    Salomon, Aidy; Krachmarov, Chavdar; Lai, Zhong; Honnen, William; Zingman, Barry S; Sarlo, Julie; Gorny, Miroslaw K; Zolla-Pazner, Susan; Robinson, James E; Pinter, Abraham

    2014-01-05

    Primary HIV-1 isolates are relatively resistant to neutralization by antibodies commonly induced after infection or vaccination. This is generally attributed to masking of sensitive epitopes by the V1/V2 domain and/or glycans situated at various positions in Env. Here we identified a novel masking effect mediated by subtype C-specific V3 sequences that contributes to the V1/V2-independent and glycan-independent neutralization resistance of chimeric and primary Envs to antibodies directed against multiple neutralization domains. Positions at several conserved charged and hydrophobic sites in the V3 crown and stem were also shown to affect neutralization phenotype. These results indicated that substitutions typically present in subtype C and related V3 sequences influence the overall conformation of native Env in a way that occludes multiple neutralization targets located both within and outside of the V3 domain, and may reflect an alternative mechanism for neutralization resistance that is particularly active in subtype C and related isolates.

  18. 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.

  19. SimGen: A General Simulation Method for Large Systems.

    PubMed

    Taylor, William R

    2017-02-03

    SimGen is a stand-alone computer program that reads a script of commands to represent complex macromolecules, including proteins and nucleic acids, in a structural hierarchy that can then be viewed using an integral graphical viewer or animated through a high-level application programming interface in C++. Structural levels in the hierarchy range from α-carbon or phosphate backbones through secondary structure to domains, molecules, and multimers with each level represented in an identical data structure that can be manipulated using the application programming interface. Unlike most coarse-grained simulation approaches, the higher-level objects represented in SimGen can be soft, allowing the lower-level objects that they contain to interact directly. The default motion simulated by SimGen is a Brownian-like diffusion that can be set to occur across all levels of representation in the hierarchy. Links can also be defined between objects, which, when combined with large high-level random movements, result in an effective search strategy for constraint satisfaction, including structure prediction from predicted pairwise distances. The implementation of SimGen makes use of the hierarchic data structure to avoid unnecessary calculation, especially for collision detection, allowing it to be simultaneously run and viewed on a laptop computer while simulating large systems of over 20,000 objects. It has been used previously to model complex molecular interactions including the motion of a myosin-V dimer "walking" on an actin fibre, RNA stem-loop packing, and the simulation of cell motion and aggregation. Several extensions to this original functionality are described.

  20. 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)

  1. 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

  2. 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 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...

  3. GenCade Version 1 Quick-Start Guide: How to Start a Successful GenCade Project

    DTIC Science & Technology

    2015-03-01

    The CIRP has developed GenCade, a one-dimensional (1D) numerical model that calculates shoreline change and wave-induced longshore sand transport...numerical model developed by the CIRP that calculates shoreline change based on differential wave-driven longshore sand transport rates. The model...has the capability to represent sand transport, accretion, and erosion at inlets and beaches and can include engineering activities such as beach

  4. 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.

  5. Xerochrysium gen. nov. and Bettsia, genera encompassing xerophilic species of Chrysosporium.

    PubMed

    Pitt, John I; Lantz, Henrik; Pettersson, Olga Vinnere; Leong, Su-Lin L

    2013-12-01

    On the basis of a study of ITS sequences, Vidal et al. (Rev. Iber. Micol. 17: 22, 2000) recommended that the genus Chrysosporium be restricted to species belonging to Onygenales. Using nrLSU genes, we studied the majority of clades examined by Vidal et al. and showed that currently accepted species in Chrysosporium phylogenetically belong in six clades in three orders. Surprisingly, the xerophilic species of Chrysosporium, long thought to be a single grouping away from the majority of Chrysosporium species, occupy two clades, one in Leotiales, the other in Eurotiales. Species accepted in Leotiales are related to the sexual genus Bettsia. One is the type species B. alvei, and related asexual strains classified as C. farinicola, the second is C. fastidium transferred to Bettsia as B. fastidia. Species in the Eurotiales are transferred to Xerochrysium gen. nov., where the accepted species are X. xerophilum and X. dermatitidis, the correct name for C. inops on transfer to Xerochrysium. All accepted species are extreme xerophiles, found in dried and concentrated foods.

  6. Worldwide genetic features of HIV-1 Env α4β7 binding motif: the Local Dissemination Impact of the LDI tripeptide

    PubMed Central

    Hait, Sabrina H.; Soares, Esmeralda A.; Sprinz, Eduardo; Arthos, James; Machado, Elizabeth S.; Soares, Marcelo A.

    2015-01-01

    Background HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in MAdCAM and VCAM, the natural ligands of α4β7. In this study we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence Database were included in the analyses. Methodology HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos Database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher’s Exact test and Mann Whitney U-test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope. Results We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection towards LDI expansion, an observation also extended to subtype B in the Americas and Western Europe. Conclusions The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness. PMID:26569174

  7. 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.

  8. The Madagascan endemic myrmicine ants related to Eutetramorium (Hymenoptera: Formicidae): taxonomy of the genera Eutetramorium Emery, Malagidris nom. n., Myrmisaraka gen. n., Royidris gen. n., and Vitsika gen. n.

    PubMed

    Bolton, Barry; Fisher, Brian L

    2014-04-24

    The monophyletic group of myrmicine ant genera related to Eutetramorium is described and its taxonomy is documented. The group is endemic in Madagascar and contains five genera: Eutetramorium Emery, 1899 (3 species, 1 of which is new); Malagidris nom. n., a replacement name for Brunella Forel, 1917, junior homonym of Brunella Smith, G.W. 1909 (Crustacea) (6 species, 5 of which are new); Myrmisaraka gen. n. (2 species, both new); Royidris gen. n. (15 species, 11 of which are new); Vitsika gen. n. (14 species, all of which are new). Keys to the worker caste are provided for all genera, and provisional keys to known males are given for Malagidris and Vitsika.

  9. J3Gen: a PRNG for low-cost passive RFID.

    PubMed

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

    2013-03-19

    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.

  10. Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii.

    PubMed

    Brady, Carrie L; Cleenwerck, Ilse; Denman, Sandra; Venter, Stephanus N; Rodríguez-Palenzuela, Pablo; Coutinho, Teresa A; De Vos, Paul

    2012-07-01

    Bacterial isolates from oak trees in Spain and Britain, showing symptoms of bark canker and Acute Oak Decline (AOD), respectively, were examined by a polyphasic approach. Both 16S rRNA gene sequencing and multilocus sequence analysis (MLSA), based on partial sequences of gyrB, rpoB, infB and atpD genes, revealed that the isolates were separated into two genetic groups according to their origin. Their closest phylogenetic relative was Brenneria quercina, the causal agent of drippy nut disease of oak, which clustered distant to the other species of the genus Brenneria. MLSA data for species of the genera Brenneria, Pectobacterium, Dickeya, Erwinia, Pantoea and Samsonia confirmed the polyphyletic nature of the genus Brenneria and indicated synonymy of Dickeya dadantii and Dickeya dieffenbachiae. DNA-DNA hybridization experiments confirmed this synonymy and also revealed DNA-DNA relatedness values of 58-73% between the new oak isolates and B. quercina. Phenotypic and/or chemotaxonomic methods allowed B. quercina and the two genetic groups of new oak isolates to be discriminated from other recognized species of the genus Brenneria and from members of the closely related genera Dickeya, Pectobacterium and Samsonia. Based on the data obtained, the following taxonomic proposals are made: (1) reclassification of B. quercina as the type species of a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov. (type strain LMG 2724(T)=ATCC 29281(T)=CCUG 48867(T)=CFBP 3617(T)=CIP 105201(T)=DSM 4561(T)=ICMP 1845(T)), (2) classification of the oak isolates as Lonsdalea quercina subsp. iberica subsp. nov. (type strain LMG26264(T)=NCPPB 4490(T)) and Lonsdalea quercina subsp. britannica subsp. nov. (type strain LMG 26267(T)=NCPPB 4481(T)) and leading to the automatic creation of Lonsdalea quercina subsp. quercina subsp. nov. (type strain LMG 2724(T)=ATCC 29281(T)), (3) emendation of the description of the genus Brenneria, and (4) reclassification of Dickeya dieffenbachiae as

  11. Arctocypris fuhrmanni, n. gen., n. sp. (Crustacea, Ostracoda, Eucypridinae) from Spitsbergen (Norway).

    PubMed

    Petkovski, Trajan K; Scharf, Burkhard; Keyser, Dietmar

    2016-01-14

    Material from Spitsbergen (Norway) collected by Spitzenberger (1996) was reinvestigated. A new genus Arctocypris and a new species Arctocypris. fuhrmanni n. gen. n. sp. are described in the present paper. A key to the genera of the subfamily Eucypridinae is provided. At the moment Arctocypris n. gen. comprises four species: Arctocypris arctica (Olofsson, 1918) comb. nov.; A. dulcifons (Diebel & Pietrzeniuk, 1969) comb. nov.; A. foveata (Delorme, 1968) comb. nov. and Arctocypris fuhrmanni n. gen., n. sp.

  12. 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.

  13. Recent changes in the GenBank On-line Service.

    PubMed Central

    Benton, D

    1990-01-01

    The GenBank On-line Service provides access to the GenBank and EMBL nucleic acid sequence databases and to the Swiss-Prot and GenPept protein sequence databases. Users can query the databases by sequence similarity and annotation keywords and retrieve entries of interest. This access is available through e-mail servers, anonymous FTP, anonymous interactive login, and login to established, password-protected, individual accounts. PMID:2326192

  14. Phen-Gen: combining phenotype and genotype to analyze rare disorders.

    PubMed

    Javed, Asif; Agrawal, Saloni; Ng, Pauline C

    2014-09-01

    We introduce Phen-Gen, a method that combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders. Simulations revealed that the causal variant was ranked first in 88% of cases when it was a coding variant-a 52% advantage over a genotype-only approach-and Phen-Gen outperformed other existing prediction methods by 13-58%. If disease etiology was unknown, the causal variant was assigned the top rank in 71% of simulations. Phen-Gen is available at http://phen-gen.org/.

  15. Resolvase OsGEN1 Mediates DNA Repair by Homologous Recombination1[OPEN

    PubMed Central

    Lu, Pingli

    2017-01-01

    Yen1/GEN1 are canonical Holliday junction resolvases that belong to the RAD2/XPG family. In eukaryotes, such as budding yeast, mice, worms, and humans, Yen1/GEN1 work together with Mus81-Mms4/MUS81-EME1 and Slx1-Slx4/SLX1-SLX4 in DNA repair by homologous recombination to maintain genome stability. In plants, the biological function of Yen1/GEN1 remains largely unclear. In this study, we characterized the loss of function mutants of OsGEN1 and OsSEND1, a pair of paralogs of Yen1/GEN1 in rice (Oryza sativa). We first investigated the role of OsGEN1 during meiosis and found a reduction in chiasma frequency by ∼6% in osgen1 mutants, compared to the wild type, suggesting a possible involvement of OsGEN1 in the formation of crossovers. Postmeiosis, OsGEN1 foci were detected in wild-type microspore nuclei, but not in the osgen1 mutant concomitant with an increase in double-strand breaks. Persistent double-strand breaks led to programmed cell death of the male gametes and complete male sterility. In contrast, depletion of OsSEND1 had no effects on plant development and did not enhance osgen1 defects. Our results indicate that OsGEN1 is essential for homologous recombinational DNA repair at two stages of microsporogenesis in rice. PMID:28049740

  16. GenCade Application at Onslow Bay, North Carolina

    DTIC Science & Technology

    2012-08-01

    by Ashley E. Frey, Sophie Munger, Greg L. Williams , Michael J. Wutkowski, and Kevin B. Conner PURPOSE: This Coastal and Hydraulics Engineering...Texas A&M University Corpus Christi, and Greg L. Williams , Michael J. Wutkowski, and Kevin B. Conner of the U.S. Army Engineer District, Wilmington. Dr...follows: Frey, A.E., Munger, S., Williams , G.L., Wutkowski, M.J. and Conner, K.B. 2012. GenCade Application at Onslow Bay, North Carolina. Coastal and

  17. 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.

  18. 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).

  19. Potent, Persistent Induction and Modulation of Cellular Immune Responses in Rhesus Macaques Primed with Ad5hr-Simian Immunodeficiency Virus (SIV) env/rev, gag, and/or nef Vaccines and Boosted with SIV gp120

    PubMed Central

    Patterson, L. Jean; Malkevitch, Nina; Pinczewski, Joel; Venzon, David; Lou, Yuanmei; Peng, Bo; Munch, Cindy; Leonard, Melissa; Richardson, Ersell; Aldrich, Kristine; Kalyanaraman, V. S.; Pavlakis, George N.; Robert-Guroff, Marjorie

    2003-01-01

    Immunity elicited by multicomponent vaccines delivered by replication-competent Ad5hr-simian immunodeficiency virus (SIV) recombinants was systematically investigated. Rhesus macaques were immunized mucosally at weeks 0 and 12 with Ad5hr-SIVsmH4 env/rev, with or without Ad5hr-SIVmac239 gag or Ad5hr-SIVmac239 nef, or with all three recombinants. The total Ad5hr dosage was comparably adjusted among all animals with empty Ad5hr-ΔE3 vector. The macaques were boosted with SIV gp120 in monophosphoryl A-stable emulsion adjuvant at 24 and 36 weeks. Controls received Ad5hr-ΔE3 vector or adjuvant only. By ELISPOT analysis, all four SIV gene products elicited potent cellular immune responses that persisted 42 weeks post-initial immunization. Unexpectedly, modulation of this cellular immune response was observed among macaques receiving one, two, or three Ad5hr-SIV recombinants. Env responses were significantly enhanced throughout the immunization period in macaques immunized with Ad5hr-SIV env/rev plus Ad5hr-SIV gag and tended to be higher in macaques that also received Ad5hr-SIV nef. Macaques primed with all three recombinants displayed significant down-modulation in numbers of gamma interferon (IFN-γ)-secreting cells specific for SIV Nef, and the Env- and Gag-specific responses were also diminished. Modulation of antibody responses was not observed. Down-modulation was seen only during the period of Ad5hr-recombinant priming, not during subunit boosting, although SIV-specific IFN-γ-secreting cells persisted. The effect was not attributable to Ad5hr replication differences among immunization groups. Vaccine delivery via replication-competent live vectors, which can persistently infect new cells and continuously present low-level antigen, may be advantageous in overcoming competition among complex immunogens for immune recognition. Effects of current multicomponent vaccines on individual immune responses should be evaluated with regard to future vaccine design. PMID

  20. 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

  1. Hunting for new restriction enzymes in GenBank

    SciTech Connect

    Roberts, R.J.

    1997-12-01

    Restriction enzyme genes are hard to identify unless their surrounding sequences are available. This is because the best definition of a restriction enzyme gene is an open reading frame, that looks like nothing else in GenBank, but lies close to a DNA methylase gene. There are other clues too, such as nearby reading frames that code control proteins or the DNA specificity subunits of Type I restriction enzymes. We are developing software that searches the daily updates of GenBank to find candidate restriction enzyme genes. This is being followed by bench experiments to see of the predictions are correct. More than 50 potential new restriction enzymes have been predicted and it is quite remarkable that the density of restriction enzyme genes in microbial DNA is greater than one system per 200 Kb. The software development is emphasizing the graphic presentation of the search results. The approach could be used for other situations where a molecular biologist is interested to find new examples of their favorite genes.

  2. GenDecoder: genetic code prediction for metazoan mitochondria

    PubMed Central

    Abascal, Federico; Zardoya, Rafael; Posada, David

    2006-01-01

    Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from . PMID:16845034

  3. 77 FR 54648 - Seventh Meeting: RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-05

    ... Meeting: RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Meeting Notice of RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of the seventh meeting of the RTCA...

  4. How is the Xpert MRSA Gen 3 assay (Cepheid) performing on pooled eSwab medium?

    PubMed

    Jonckheere, Stijn; Van Vaerenbergh, Kristien; Boel, An; Vankeerberghen, Anne; De Beenhouwer, Hans

    2015-11-01

    The performance of the Xpert MRSA Gen 3 was compared to the Xpert MRSA on pooled eSwab media from nose, throat, and perineum using broth enriched cultured as gold standard. A lower specificity was found for the Xpert MRSA Gen 3 compared to the Xpert MRSA (91.8% versus 97.9%; P<0.05).

  5. 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...

  6. 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...

  7. What Is ALS?

    MedlinePlus

    ... Javits, actor David Niven, “Sesame Street” creator Jon Stone, boxing champion Ezzard Charles, NBA Hall of Fame ... Help for People with ALS and Caregivers Read stories from families living with ALS Forms of ALS ...

  8. Proteins of Rous-associated virus 61, an avian retrovirus: common precursor for glycoproteins gp85 and gp35 and use of pactamycin to map translational order of proteins in the gag, pol, and env genes.

    PubMed Central

    Shealy, D J; Rueckert, R R

    1978-01-01

    Cells infected by Rous-associated virus 61 (RAV-61) contained a precursor-like protein, pr90, that was specifically precipitated by antiserum directed against envelope glycoproteins, gp85 and gp35. Tryptic peptide mapping showed that pr90 contained tryptic sequences of both gp85 and gp35. Pactamycin mapping experiments indicated that the two glycoproteins are translated from the env-mRNA in the order (5') gp85--gp35. The pactamycin mapping experiments also indicated a translational order of p10--(p27, p12)--p15 for the gag proteins; this agreement with the order previously reported from tryptic mapping studies on precursor pr76 of avian myeloblastosis virus implied that the stoichiometry of the core proteins was unchanged when virions were assembled in the presence of pactamycin. The reverse transcriptase proteins, unlike those of the env and gag genes, fell on the right side of the pactamycin map. This result is in accord with the idea that most, if not all, of the reverse transcriptase protein is translated by read-through of the gag(pol) message rather than by translation of a hypothetical pol-mRNA devoted solely to synthesis of that protein. Images PMID:77910

  9. 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.

  10. 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.

  11. 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.

  12. Abu al-Layth al-Libi

    DTIC Science & Technology

    2015-02-01

    Introduction In the tradition of post-9/11 senior Arab militant figures operating in Khurasan (the Afghanistan-Pakistan region), there is little doubt as to...the standing of Libyan jihadi commander Abu al-Layth al-Libi. If Usama bin Ladin and Ayman al-Zawahiri came to be the most prominent Arab -Afghan...Libi, a longtime leader of the Libyan Islamic Fighting Group (LIFG), who rapidly established himself as the champion of the Arab -Afghan milieu after

  13. 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.

  14. Hand-held optical imager (Gen-2): improved instrumentation and target detectability.

    PubMed

    Gonzalez, Jean; Decerce, Joseph; Erickson, Sarah J; Martinez, Sergio L; Nunez, Annie; Roman, Manuela; Traub, Barbara; Flores, Cecilia A; Roberts, Seigbeh M; Hernandez, Estrella; Aguirre, Wenceslao; Kiszonas, Richard; Godavarty, Anuradha

    2012-08-01

    Hand-held optical imagers are developed by various researchers towards reflectance-based spectroscopic imaging of breast cancer. Recently, a Gen-1 handheld optical imager was developed with capabilities to perform two-dimensional (2-D) spectroscopic as well as three-dimensional (3-D) tomographic imaging studies. However, the imager was bulky with poor surface contact (~30%) along curved tissues, and limited sensitivity to detect targets consistently. Herein, a Gen-2 hand-held optical imager that overcame the above limitations of the Gen-1 imager has been developed and the instrumentation described. The Gen-2 hand-held imager is less bulky, portable, and has improved surface contact (~86%) on curved tissues. Additionally, the forked probe head design is capable of simultaneous bilateral reflectance imaging of both breast tissues, and also transillumination imaging of a single breast tissue. Experimental studies were performed on tissue phantoms to demonstrate the improved sensitivity in detecting targets using the Gen-2 imager. The improved instrumentation of the Gen-2 imager allowed detection of targets independent of their location with respect to the illumination points, unlike in Gen-1 imager. The developed imager has potential for future clinical breast imaging with enhanced sensitivity, via both reflectance and transillumination imaging.

  15. 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

  16. GenASiS: A full GR-RMHD simulation framework: overview, goals, and preliminary tests

    NASA Astrophysics Data System (ADS)

    Tsatsin, Petr; Budiardja, Reuben; Cardall, Christian; Endeve, Eirik; Marronetti, Pedro; Mezzacappa, Anthony

    2011-04-01

    I present an overview of the General Astrophysics Simulation System (GenASiS). GenASiS is currently under development by a collaboration between researchers at the Oak Ridge National Laboratory (ORNL) and Florida Atlantic University (FAU) and features a high-resolution magnetohydrodynamics solver, a full general relativistic description of gravity based on the BSSN formalism, and will feature a two-moment multi-frequency neutrino radiation field evolution. We intend to use GenASiS to study core collapse supernovae, neutron star mergers, and their associated gamma-ray bursts.

  17. The Early Retirement of Gen Ronald R. Fogleman, Chief of Staff, United States Air Force

    DTIC Science & Technology

    2001-01-01

    The Early Retirement of Gen Ronald R. Fogleman, Chief of Staff, United States Air Force *EDITED by DR. RICHARD H. KOHN Editorial Abstract: Air...Force chief of staff Gen Ronald Fogleman’s early retirement in 1997 has caused great speculation. Was this a “resignation in protest”? Here for the...COVERED 00-00-2001 to 00-00-2001 4. TITLE AND SUBTITLE The Early Retirement of Gen Ronald R. Fogleman, Chief of Staff, United States Air Force 5a

  18. 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.

  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. On the new monotypic wolf spider genus Ovia gen. nov. (Araneae: Lycosidae, Lycosinae).

    PubMed

    Sankaran, Pradeep M; Malamel, Jobi J; Sebastian, Pothalil A

    2017-01-17

    A new monotypic wolf spider genus, Ovia gen. nov. is proposed to accommodate a misplaced species: Pardosa procurva Yu & Song, 1988. Ovia procurva comb. nov. is redescribed, illustrated and designated as the type species for the genus. The subfamily placement of the new genus is discussed and it is considered as a member of Lycosinae Sundevall, 1833 and possibly closely related to Alopecosa Simon, 1885. The presence of an apical process (spur) on the median apophysis is proposed as the putative synapomorphy of Ovia gen. nov. The possible sister-taxon relationship of Ovia gen. nov. with Alopecosa is discussed and evidence on the occurrence of sexual dimorphism and mating plug within the genus are presented. Ovia gen. nov. is assumed to be of Holarctic origin, from which it has migrated to the Indomalayan region. Additionally, a current distribution map for the genus is provided.

  1. 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.

  2. Erections of Changa gen. nov. and Songga gen. nov. of Aolina (Hemiptera: Cicadidae: Cicadinae: Dundubiini) with taxonomic notes and a synonymization.

    PubMed

    Lee, Young June

    2016-02-29

    Two new genera, Changa gen. nov. and Songga gen. nov., are erected in the subtribe Aolina Boulard, 2012, with the designations of Cosmopsaltria sita Distant, 1881 and Pomponia scitula Distant, 1888 as the type species, respectively. Khimbya sita (Distant, 1881) becomes Changa sita (Distant, 1881) comb. nov. Haphsa scitula (Distant, 1888) becomes Songga scitula (Distant, 1888) comb. nov. Haphsa jsguillotsi (Boulard, 2005) is transferred to Changa to become Changa jsguillotsi (Boulard, 2005) comb. nov. Haphsa stellata Lee, 2009 syn. nov. is synonymized with Changa sita. Haphsa sulaeyai (Boulard, 2005) is transferred to Macrosemia Kato, 1925 to become Macrosemia sulaeyai (Boulard, 2005) comb. nov. A revised key to the genera of Aolina is provided.

  3. 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.

  4. /Cu-Al System

    NASA Astrophysics Data System (ADS)

    Kish, Orel; Froumin, Natalya; Aizenshtein, Michael; Frage, Nachum

    2014-05-01

    Wettability and interfacial interaction of the Ta2O5/Cu-Al system were studied. Pure Cu does not wet the Ta2O5 substrate, and improved spreading is achieved when relatively a high fraction of the active element (~40 at.% Al) was added. The Al2O3 and AlTaO4 phases were observed at the Ta2O5/Cu-Al interface. A thermodynamic evaluation allowed us to suggest that the lack of wetting bellow 40 at.% Al is due to the presence of a native oxide, which covers the drop. The conditions of the native oxide decomposition and the formation of the volatile Al2O suboxide strongly depend on the vacuum level during sessile drop experiments and the composition of the Cu-Al alloy. In our case, Al contents greater than 40% provides thermodynamic conditions for the formation of Al2O (as a result of Al reaction with Al2O3) and the drop spreading. It was suggested that the final contact angle in the Ta2O5/Cu-Al system (50°) is determined by Ta adsorption on the newly formed alumina interlayer.

  5. 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).

  6. Cleaning the GenBank Arabidopsis thaliana data set.

    PubMed Central

    Korning, P G; Hebsgaard, S M; Rouze, P; Brunak, S

    1996-01-01

    Data driven computational biology relies on the large quantities of genomic data stored in international sequence data banks. However, the possibilities are drastically impaired if the stored data is unreliable. During a project aiming to predict splice sites in the dicot Arabidopsis thaliana, we extracted a data set from the A.thaliana entries in GenBank. A number of simple 'sanity' checks, based on the nature of the data, revealed an alarmingly high error rate. More than 15% of the most important entries extracted did contain erroneous information. In addition, a number of entries had directly conflicting assignments of exons and introns, not stemming from alternative splicing. In a few cases the errors are due to mere typographical misprints, which may be corrected by comparison to the original papers, but errors caused by wrong assignments of splice sites from experimental data are the most common. It is proposed that the level of error correction should be increased and that gene structure sanity checks should be incorporated--also at the submitter level--to avoid or reduce the problem in the future. A non-redundant and error corrected subset of the data for A.thaliana is made available through anonymous FTP. PMID:8628656

  7. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil.

    PubMed

    Lv, Ying-Ying; Wang, Jia; Chen, Mei-Hong; You, Jia; Qiu, Li-Hong

    2016-04-01

    A novel Gram-stain negative, non-motile, rod-shaped, aerobic bacterial strain, designated DHOA34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. Comparative 16S rRNA gene sequence analysis showed that it exhibited highest similarity with Flavisolibacter ginsengiterrae Gsoil 492T and Flavitalea populi HY-50RT, at 90.89 and 90.83%, respectively. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, DHOA34T formed an independent lineage within the family Chitinophagaceae but was distinct from all recognized species and genera of the family. The major cellular fatty acids of DHOA34T included iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The DNA G+C content was 51.6 mol% and the predominant quinone was menaquinone 7 (MK-7). Flexirubin pigments were produced. The phenotypic, chemotaxonomic and phylogenetic data demonstrate consistently that strain DHOA34T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Dinghuibacter silviterrae gen. nov., sp. nov. is proposed. The type strain of Dinghuibacter silviterrae is DHOA34T (=CGMCC 1.15023T=KCTC 42632T).

  8. 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.

  9. Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes.

    PubMed

    Sorokin, Dimitry Yu; Trotsenko, Yuri A; Doronina, Nina V; Tourova, Tatjana P; Galinski, Erwin A; Kolganova, Tatjana V; Muyzer, Gerard

    2007-12-01

    Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride-sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1(T). The bacterium grew with methanol and methylamine within a pH range of 6.8-8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5-4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the family Ectothiorhodospiraceae (Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species, Methylohalomonas lacus gen. nov., sp. nov., with HMT 1(T) (=DSM 15733(T) =NCCB 100208(T) =UNIQEM U237(T)) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na(+) using methanol as a substrate. Strain AMT 1(T) was enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5-4 M total Na(+), with an optimum at 0.5-1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin-Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1(T) possessed a single cbbL gene of the 'green' form I, clustering with members of the family Ectothiorhodospiraceae

  10. Human T-cell leukemia virus type II nucleotide sequences between env and the last exon of tax/rex are not required for viral replication or cellular transformation.

    PubMed

    Green, P L; Ross, T M; Chen, I S; Pettiford, S

    1995-01-01

    Human T-cell leukemia virus types I (HTLV-I) and II (HTLV-II) and bovine leukemia virus contain a region of approximately 600 nucleotides located 3' to the env gene and 5' to the last exon of the tax and rex regulatory genes. This region was originally termed nontranslated or untranslated (UT) since it did not appear to be expressed. Several studies have identified novel mRNAs in HTLV-I-, HTLV-II-, a bovine leukemia virus-infected cells that splice into open reading frames (ORFs) contained in the UT region and, thus, have the potential to produce proteins that might contribute to the biological properties of these viruses. The HTLV-II infectious molecular clone pH6neo has several ORFs in the UT region (nucleotides 6641 to 7213) and a large ORF which overlaps the third exon of tax/rex. To investigate the importance of these ORF-containing sequences on viral replication and transformation in cell culture, proviral clones containing deletions in UT (pH6neo delta UT) or a stop codon insertion mutation (pH6neoST) were constructed. Lymphoid cells were transfected with mutant proviral constructs, and stable cell clones, designated 729pH6neo delta UT and 729pH6neoST, were characterized. Viral protein production, reverse transcriptase activity, and the capacity to induce syncytia were indistinguishable from cells transfected with the wild-type clone. Finally, 729pH6neo delta UT- and 729pH6neoST-producer cells cocultured with primary blood T lymphocytes resulted in cellular transformation characteristic of HTLV. These results indicate that putative protein-coding sequences between env and the last exon of tax/rex are not required for viral replication or transformation in cell culture.

  11. Pseudogracilibacillus auburnensis gen. nov., sp. nov., isolated from the rhizosphere of Zea mays.

    PubMed

    Glaeser, Stefanie P; McInroy, John A; Busse, Hans-Jürgen; Kämpfer, Peter

    2014-07-01

    A Gram-positive-staining, aerobic, endospore-forming bacterium, strain P-207(T), was isolated from a rhizosphere soil sample in Auburn, AL, USA. On the basis of 16S rRNA gene sequence comparisons, strain P-207(T) was grouped in the vicinity of representatives of the genera Virgibacillus, Ornithinibacillus, Cerasibacillus, Lentibacillus and Oceanobacillus, but could not be assigned clearly to any of these genera. The highest similarity was found to the sequence of Virgibacillus carmonensis LMG 20964(T) (94.4%); however, the 16S rRNA gene sequence similarity to the type strain of the type species of Virgibacillus, Virgibacillus pantothenticus, was only 92.9%. The quinone system of strain P-207(T) consisted predominantly of menaquinone MK-7. The polar lipid profile exhibited the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate to minor amounts of several unidentified phospholipids, glycolipids and phosphoglycolipids, an aminophospholipid and an aminolipid. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 34 mol%. Because of the low sequence similarity of strain P-207(T) to all representatives of Virgibacillus, Ornithinibacillus, Cerasibacillus, Lentibacillus and Oceanobacillus, which was always <95%, and its unique lipid pattern, we propose that strain P-207(T) represents a novel species in a new genus, for which the name Pseudogracilibacillus auburnensis gen. nov., sp. nov. is proposed. The type strain of Pseudogracilibacillus auburnensis is P-207(T) ( = CCM 8509(T)  =  LMG 28212(T) = CIP 110797(T)).

  12. Initial Symptoms of ALS

    MedlinePlus

    ... Chapters Certified Centers and Clinics Support Groups About ALS About Us Our Research In Your Community Advocate ... Diagnosis En español Symptoms The initial symptoms of ALS can be quite varied in different people. One ...

  13. Lou Gehrig's Disease (ALS)

    MedlinePlus

    ... 1930s. People in England and Australia call ALS motor neurone disease (MND). The French refer to it ... about ALS in 1869. Lou Gehrig's disease damages motor neurons in the brain and spinal cord. Motor ...

  14. 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

  15. 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

  16. Haloactinomyces albus gen. nov., sp. nov., isolated from Dead Sea.

    PubMed

    Lai, Hangxian; Jiang, Yingying; Chen, Xiu; Li, Qinyuan; Jiang, Chenglin; Jiang, Yi; Wei, Xiaomin

    2017-01-10

    A novel halophilic, filamentous actinomycete strain, designated AFM 10258T, was isolated from a sediment sample collected from Dead Sea of Israel. The isolate grew with 10-35% NaCl and did not grow without NaCl. The isolate formed white aerial mycelium and long spore chains, and two spores were separated by sterile mycelium. The spores were non-motile, spherical and rugose-surfaced. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the major whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were anteiso-C17:0, iso-C16:0 and iso-C15:0. MK-9(H4) was the predominant menaquinone and the DNA G+C content was 62.8 mol%. 16S rRNA gene sequence analysis indicated that strain AFM 10258T shared low sequence similarity with the closely related representatives of the families Pseudonocardiaceae (below 94.47%) and Actinopolysporaceae (below 93.76%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10258T formed a robust clade with members of the family Actinopolysporaceae. On the basis of analysis of phenotypic, chemical and molecular characteristics, strain AFM 10258T is considered to represent a novel species of a new genus , for which the name Haloactinomyces albus gen. nov., sp. nov., is proposed. The type strain is AFM 10258T (=DSM 45977T = CGMCC 4.7115T).

  17. Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater.

    PubMed

    Xing, Defeng; Ren, Nanqi; Li, Qiubo; Lin, Ming; Wang, Aijie; Zhao, Lihua

    2006-04-01

    Two strictly anaerobic bacterial strains (YUAN-3T and X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0.4-0.8 x 1.5-8.0 microm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3T and non-aggregative growth of strain X-29 were observed at 20-44 degrees C and pH 3.5-9.0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C(16 : 0) (44.18 %) and iso-C(12 : 0) (26.67 %). The DNA G+C contents of strains YUAN-3T and X-29 were 47.8 and 49.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within the Clostridium cellulosi rRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species, Ethanoligenens harbinense gen. nov., sp. nov. The type strain of Ethanoligenens harbinense is YUAN-3T (=JCM 12961T = CGMCC 1.5033T).

  18. 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).

  19. Scopulibacillus darangshiensis gen. nov., sp. nov., isolated from rock.

    PubMed

    Lee, Soon Dong; Lee, Dong Wan

    2009-12-01

    A novel, Gram-positive bacterium, designated DLS-06(T), was isolated from scoria (volcanic ash) under rock on the peak of small mountain (300 m above the sea level; known as Darangshi Oreum) in Jeju, Republic of Korea. The cells of the isolate were aerobic, oxidase-negative, catalase-positive, endospore-forming, non-motile rods. The organism grew at 25 approximately 30 degrees C and initial pH 6.1 approximately 9.1. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family "Sporolactobacillaceae" and related taxa. The phylogenetic neighbours were Pullulanibacillus naganoensis (95.2% 16S rRNA gene sequence similarity), Tuberibacillus calidus (95.0%) and Sporolactobacillus (91.8 approximately 94.2%). Levels of 16S rRNA gene sequence similarity of the isolate to representatives of other genera were in the range of 87.2 approximately 93.7%. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, an unknown ninhydrin-positive phospholipid, three unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C(15:0) and anteiso-C(17:0). The G+C content of the DNA was 50.8 mol%. On the basis of the phenotypic and phylogenetic data presented in this study, this organism represents a novel genus and species in the order Bacillales, for which the name Scopulibacillus darangshiensis gen. nov., sp. nov. is proposed. The type strain is DLS-06(T) (=DSM 19377(T) =KCTC 13161(T)).

  20. 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.

  1. Wave Data Processing and Analysis, Part 2: Codes for Coupling GenCade and CMS-Wave

    DTIC Science & Technology

    2013-09-01

    coastal modeling system , Report 2: CMS -Wave. ERDC/CHL-TR-11-10. Vicksburg, MS: US Army Engineer Research and Development Center. Connell, K. J. and...Coupling GenCade and CMS -Wave by Rusty Permenter, Kenneth J. Connell, and Zeki Demirbilek PURPOSE: This Coastal and Hydraulics Engineering...to GenCade. This is the second CHETN in a two‐part series detailing the process of coupling CMS ‐Wave with GenCade. This CHETN focuses on

  2. Paraclostridium benzoelyticum gen. nov. sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii.

    PubMed

    T S, Sasi Jyothsna; L, Tushar; Ch, Sasikala; Ch V, Ramana

    2016-01-05

    Twenty three rod shaped, endospore forming, Gram-stain-positive, obligately anaerobic bacteria were isolated from different marine sediment samples of Gujarat. All the twenty three strains have 16S rRNA gene sequence similarity of ~100%. Strain JC272T was designated as the type strain and has sequence similarity with Clostridium bifermentans ATCC638T (99.8%), Clostridium ghonii JCM1400T (98.0%), Clostridium sordellii ATCC9714T (97.9%) and other members of the genus Clostridium (<96.4%). C16:0, C18:0, C17:0, C16:1ω9C and iso-C16:0 are the major (>5%) fatty acids. Strain JC272T contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified amino lipids (AL1&AL2). However, genome based analysis of ANI and in silico DDH of strain JC272T with C. bifermentans ATCC 638T yielded values of 94.35% and 58.5+2.8%, respectively. G+C mol% of strain JC272T was 28.3%. Strain JC272T together with C. bifermentans fall outside Clostridium rRNA cluster I considered as Clostridium senso stricto. Based on ANI value, in-silico DDH, distinct morphological and physiological differences from the previously described taxa, we propose strain JC272T as a representative of a new genus and species in the family Clostridiaceae, for which the name Paraclostridium benzoelyticum gen. nov., sp. nov. is proposed. Type strain is JC272T (=KCTC15476T =LMG28745T). It is also proposed to transfer C. bifermentans to this new genus, as Paraclostridium bifermentans comb. nov. (type strain is ATCC638T =DSM14991T =JCM1386T). We also propose the genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii as Paeniclostridium sordellii comb. nov. (type strain is ATCC9714T =LMG15708T =JCM3814T) and Paeniclostridium ghonii comb. nov. (type strain is ATCC25757T = DSM15049T =JCM1400T).

  3. 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.

  4. 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.

  5. Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage

    PubMed Central

    Lee, Shun-Hsiao; Princz, Lissa Nicola; Klügel, Maren Felizitas; Habermann, Bianca; Pfander, Boris; Biertümpfel, Christian

    2015-01-01

    Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ resolvase GEN1 complexed with DNA at 3.0 Å resolution. The GEN1 core is similar to other Rad2/XPG nucleases. However, unlike other members of the superfamily, GEN1 contains a chromodomain as an additional DNA interaction site. Chromodomains are known for their chromatin-targeting function in chromatin remodelers and histone(de)acetylases but they have not previously been found in nucleases. The GEN1 chromodomain directly contacts DNA and its truncation severely hampers GEN1’s catalytic activity. Structure-guided mutations in vitro and in vivo in yeast validated our mechanistic findings. Our study provides the missing structure in the Rad2/XPG family and insights how a well-conserved nuclease core acquires versatility in recognizing diverse substrates for DNA repair and maintenance. DOI: http://dx.doi.org/10.7554/eLife.12256.001 PMID:26682650

  6. Mechanism of Holliday junction resolution by the human GEN1 protein

    PubMed Central

    Rass, Ulrich; Compton, Sarah A.; Matos, Joao; Singleton, Martin R.; Ip, Stephen C.Y.; Blanco, Miguel G.; Griffith, Jack D.; West, Stephen C.

    2010-01-01

    Holliday junction (HJ) resolution is essential for chromosome segregation at meiosis and the repair of stalled/collapsed replication forks in mitotic cells. All organisms possess nucleases that promote HJ resolution by the introduction of symmetrically related nicks in two strands at, or close to, the junction point. GEN1, a member of the Rad2/XPG nuclease family, was isolated recently from human cells and shown to promote HJ resolution in vitro and in vivo. Here, we provide the first biochemical/structural characterization of GEN1, showing that, like the Escherichia coli HJ resolvase RuvC, it binds specifically to HJs and resolves them by a dual incision mechanism in which nicks are introduced in the pair of continuous (noncrossing) strands within the lifetime of the GEN1–HJ complex. In contrast to RuvC, but like other Rad2/XPG family members such as FEN1, GEN1 is a monomeric 5′-flap endonuclease. However, the unique feature of GEN1 that distinguishes it from other Rad2/XPG nucleases is its ability to dimerize on HJs. This functional adaptation provides the two symmetrically aligned active sites required for HJ resolution. PMID:20634321

  7. 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

  8. 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

  9. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov.

    PubMed

    Scholz, Christian F P; Kilian, Mogens

    2016-11-01

    The genus Propionibacterium in the family Propionibacteriaceaeconsists of species of various habitats, including mature cheese, cattle rumen and human skin. Traditionally, these species have been grouped as either classical or cutaneous propionibacteria based on characteristic phenotypes and source of isolation. To re-evaluate the taxonomy of the family and to elucidate the interspecies relatedness we compared 162 public whole-genome sequences of strains representing species of the family Propionibacteriaceae. We found substantial discrepancies between the phylogenetic signals of 16S rRNA gene sequence analysis and our high-resolution core-genome analysis. To accommodate these discrepancies, and to address the long-standing issue of the taxonomically problematic Propionibacterium propionicum, we propose three novel genera, Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov., and an amended description of the genus Propionibacterium. Furthermore, our genome-based analyses support the amounting evidence that the subdivision of Propionibacterium freudenreichii into subspecies is not warranted. Our proposals are supported by phylogenetic analyses, DNA G+C content, peptidoglycan composition and patterns of the gene losses and acquisitions in the cutaneous propionibacteria during their adaptation to the human host.

  10. Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae).

    PubMed

    Kanzaki, Natsumi; Ragsdale, Erik J; Susoy, Vladislav; Sommer, Ralf J

    2014-03-01

    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.

  11. 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.

  12. Thalassomermis megamphis n. gen., n. sp. (Mermithidae: Nemata) from the Bathyal South Atlantic Ocean

    PubMed Central

    Tchesunov, A.V.; Hope, W. D.

    1997-01-01

    Thalassomermis megamphis n. gen., n. sp. (Mermithidae: Nemata) was extracted from sediment collected off the coast of Brazil at a depth of approximately 1,000 m. Although the food of this new nematode is unknown, the reduction of the stoma and esophagus and presence of a trophosome indicate that it is parasitic in its juvenile stages. Thalassomermis megaraphis n. gen., n. sp. is assigned to Mermithidae because of its similarity to that family in the appearance of the cephalic sensory receptors, the long and tubular vagina, and copulatory muscles of the male extending posteriorly throughout most of the length of the tail. Thalassomermis megamphis n. gen., n. sp. differs from all other members of Mermithidae by the large, lenticular, intracuticular amphidial fovea with coiled, emergent terminal filaments as well as the small amphidial aperture situated over the center of the fovea. PMID:19274181

  13. Genetic testing in ALS

    PubMed Central

    McLaughlin, Russell L.; Heverin, Mark; Thorpe, Owen; Abrahams, Sharon; Al-Chalabi, Ammar; Hardiman, Orla

    2017-01-01

    Objective: To determine the degree of consensus among clinicians on the clinical use of genetic testing in amyotrophic lateral sclerosis (ALS) and the factors that determine decision-making. Methods: ALS researchers worldwide were invited to participate in a detailed online survey to determine their attitudes and practices relating to genetic testing. Results: Responses from 167 clinicians from 21 different countries were analyzed. The majority of respondents (73.3%) do not consider that there is a consensus definition of familial ALS (FALS). Fifty-seven percent consider a family history of frontotemporal dementia and 48.5% the presence of a known ALS genetic mutation as sufficient for a diagnosis of FALS. Most respondents (90.2%) offer genetic testing to patients they define as having FALS and 49.4% to patients with sporadic ALS. Four main genes (SOD1, C9orf72, TARDBP, and FUS) are commonly tested. A total of 55.2% of respondents would seek genetic testing if they had personally received a diagnosis of ALS. Forty-two percent never offer presymptomatic testing to family members of patients with FALS. Responses varied between ALS specialists and nonspecialists and based on the number of new patients seen per year. Conclusions: There is a lack of consensus among clinicians as to the definition of FALS. Substantial variation exists in attitude and practices related to genetic testing of patients and presymptomatic testing of their relatives across geographic regions and between experienced specialists in ALS and nonspecialists. PMID:28159885

  14. Ventilatory Control in ALS

    PubMed Central

    Nichols, Nicole L.; Van Dyke, J.; Nashold, L.; Satriotomo, I.; Suzuki, M.; Mitchell, G.S.

    2015-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disease. ALS selectively causes degeneration in upper and lower (spinal) motor neurons, leading to muscle weakness, paralysis and death by ventilatory failure. Although ventilatory failure is generally the cause of death in ALS, little is known concerning the impact of this disorder on respiratory motor neurons, the consequences of respiratory motor neuron cell death, or the ability of the respiratory control system to “fight back” via mechanisms of compensatory respiratory plasticity. Here we review known effects of ALS on breathing, including possible effects on rhythm generation, respiratory motor neurons, and their target organs: the respiratory muscles. We consider evidence for spontaneous compensatory plasticity, preserving breathing well into disease progression despite dramatic loss of spinal respiratory motor neurons. Finally, we review current and potential therapeutic approaches directed toward preserving the capacity to breathe in ALS patients. PMID:23692930

  15. 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.

  16. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    PubMed

    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.

  17. Batwanema gen. n. and Chokwenema gen. n. (Oxyurida, Hystrignathidae), new nematode genera as parasites of Passalidae (Coleoptera) from the Democratic Republic of Congo

    PubMed Central

    Morffe, Jans; García, Nayla

    2013-01-01

    Abstract Two new genera and species parasitizing passalid beetles from the Democratic Republic of Congo are described. Batwanema congo gen. n. et sp. n. is characterized by having females with the cervical cuticle armed with scale-like projections, arranged initially in rows of eight elements that gradually divide and form pointed spines toward the end of the spiny region, two cephalic annuli, clavate procorpus and genital tract monodelphic-prodelphic. Two Malagasian species of Artigasia Christie, 1934 were placed in this genus as B. latum (Van Waerebeke, 1973) comb. n. and B. annulatum (Van Waerebeke, 1973) comb. n. Chokwenema lepidophorum gen. n. et sp. n. is characterized by having females with the cervical cuticle armed with scale-like projections, arranged initially in rows of eight elements (similar to Batwanema) that divide gradually, forming spines; a single cephalic annule cone-like, truncated, moderately inflated; procorpus sub-cylindrical and genital tract didelphic-amphidelphic. PMID:24363593

  18. Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov.

    PubMed

    Kämpfer, P; Denger, K; Cook, A M; Lee, S-T; Jäckel, U; Denner, E B M; Busse, H-J

    2006-04-01

    Comparative 16S rRNA gene sequence analysis indicates that two distinct sublineages exist within the genus Alcaligenes: the Alcaligenes faecalis lineage, comprising Alcaligenes aquatilis and A. faecalis (with the three subspecies A. faecalis subsp. faecalis, A. faecalis subsp. parafaecalis and A. faecalis subsp. phenolicus), and the Alcaligenes defragrans lineage, comprising A. defragrans. This phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. It is proposed that the A. defragrans lineage constitutes a distinct genus, for which the name Castellaniella gen. nov. is proposed. The type strain for Castellaniella defragrans gen. nov., comb. nov. is 54PinT (=CCUG 39790T = CIP 105602T = DSM 12141T). Finally, on the basis of data from the literature and new DNA-DNA hybridization and phenotypic data, the novel species Castellaniella denitrificans sp. nov. (type strain NKNTAUT = DSM 11046T = CCUG 39541T) is proposed for two strains previously identified as strains of A. defragrans.

  19. Description of a new genus, Galgoria gen. nov. (Hemiptera: Cicadidae: Cicadinae: Leptopsaltriini: Leptopsaltriina).

    PubMed

    Lee, Young June

    2016-05-10

    A new cicada genus, Galgoria gen. nov., is described with Tanna herzbergi Schmidt, 1932 (from southern China) as its type species, which is placed in the subtribe Leptopsaltriina Moulton, 1923 of the tribe Leptopsaltriini Moulton, 1923 in the subfamily Cicadinae Latreille, 1802 (Hemiptera: Cicadidae). Tanna herzbergi Schmidt, 1932 is transferred from Tanna Distant, 1905 to Galgoria gen. nov. to become Galgoria herzbergi (Schmidt, 1932) comb. nov. Tanna apicalis Chen, 1940 syn. nov. and Tanna pseudocalis Lei & Chou, 1997 syn. nov. are synonymized here with Galgoria herzbergi (Schmidt, 1932) comb. nov.

  20. 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

  1. GenCade Version 1 Model Theory and User’s Guide

    DTIC Science & Technology

    2012-12-01

    scale processes to the smaller ultra scale processes as shown in Figure 1. GenCade is developed and maintained by the U.S. Army Engineer Research and...wavelength in deep water (m). The deepwater wavelength is calculated from linear wave theory as  2 / 2oL gT  , in which g is the acceleration...littoral zone under extreme waves. In the framework of GenCade, DLTo is calculated at each time step from the deepwater wave data and is assumed to

  2. 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...

  3. 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…

  4. 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...

  5. 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...

  6. 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...

  7. Microcenoscelis n. gen. (Coleoptera: Tenebrionidae: Ulomini) from tropical Africa, with description of a blind species from Zimbabwe.

    PubMed

    Schawaller, Wolfgang

    2015-10-05

    Microcenoscelis n. gen. (Coleoptera: Tenebrionidae: Ulomini) caeca n. sp. is described from Zimbabwe, a small and completely blind species. A second known species, however with completely developed eyes, and originally described as Uloma minuscula Ardoin, 1969, was also placed in the new genus. Microcenoscelis n. gen. seems to be mostly related to the genera Cenoscelis Wollaston, 1867, and Cneocnemis Gebien, 1914.

  8. 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...

  9. 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...

  10. 76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-19

    ... rejecting Terra-Gen's proposed OATT provisions that would provide ``an OATT exemption for its existing and...- Gen explains that its OATT has non-conforming provisions that include limiting the applicability of... the pro forma OATT provisions related to the provision of ] network transmission service,...

  11. PZT piezoelectric films on glass for Gen-X imaging

    NASA Astrophysics Data System (ADS)

    Wilke, Rudeger H. T.; Trolier-McKinstry, Susan; Reid, Paul B.; Schwartz, Daniel A.

    2010-09-01

    The proposed adaptive optics system for the Gen-X telescope uses piezoelectric lead zirconate titanate (PZT) films deposited on flexible glass substrates. The low softening transition of the glass substrates imposes several processing challenges that require the development of new approaches to deposit high quality PZT thin films. Synthesis and optimization of chemical solution deposited 1 μm thick films of PbZr0.52Ti0.48O3 on small area (1 in2) and large area (16 in2) Pt/Ti/glass substrates has been performed. In order to avoid warping of the glass at temperatures typically used to crystallize PZT films ({700°C), a lower temperature, two-step crystallization process was employed. An {80 nm thick seed layer of PbZr0.30Ti0.70O3 was deposited to promote the growth of the perovskite phase. After the deposition of the seed layer, the films were annealed in a rapid thermal annealing (RTA) furnace at 550°C for 3 minutes to nucleate the perovskite phase. This was followed by isothermal annealing at 550°C for 1 hour to complete crystallization. For the subsequent PbZr0.52Ti0.48O3 layers, the same RTA protocol was performed, with the isothermal crystallization implemented following the deposition of three PbZr0.52Ti0.48O3 spin-coated layers. Over the frequency range of 1 kHz to 100 kHz, films exhibit relative permittivity values near 800 with loss tangents below 0.07. Hysteresis loops show low levels of imprint with coercive fields of 40-50 kV/cm in the forward direction and 50-70 kV/cm in the reverse direction. The remanent polarization varied from 25-35 μC/cm2 and e31,f values were approximately -5.0 C/m2. In scaling up the growth procedure to large area films, where warping becomes more pronounced due to the increased size of the substrate, the pyrolysis and crystallization conditions were performed in a box furnace to improve the temperature uniformity. By depositing films on both sides of the glass substrate, the tensile stresses are balanced, providing a

  12. Chitinozoan faunas from the Rügen Ordovician (Rügen 5/66 and Binz 1/73 wells), NE Germany.

    PubMed

    Samuelsson, J; Verniers, J; Vecoli, M

    2000-12-01

    The island of Rügen (NE Germany), situated close to the Trans-European Suture Zone (TESZ), in the southern Baltic Sea is underlain by sedimentary rocks of an Early Palaeozoic age, known only from boreholes. The wells, Rügen 5/66 and Binz 1/73, were investigated for their chitinozoan assemblages to improve the earlier biostratigraphic dating (graptolites and acritarchs) and to facilitate comparisons with other chitinozoan assemblages on both sides of the TESZ. In the lower part of the Rügen 5/66 core (3794.7-3615.8m), Lagenochitina destombesi Elaouad-Debbaj is indicative of an early late Tremadoc age. In the upper part of the same well (3287.3-1709.7m), the observed chitinozoan taxa suggest an age spanning the early Llanvirn to the Caradoc. The entire sampled interval of the Binz 1/73 core (5217.6-5041.8m) is interpreted as belonging to the Siphonochitina formosa Biozone (early-early late Abereiddian, corresponding to the early Llanvirn). The chitinozoan data corroborate the earlier suggested biostratigraphic ages, based on acritarchs and graptolites. The chitinozoans from the Binz 1/73 well point to a high latitude provenance of the investigated host sediments at time of deposition.

  13. Morphology and ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and molecular phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia).

    PubMed

    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.

  14. 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

  15. 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).

  16. ALS2 mutations

    PubMed Central

    Schneider, Susanne A.; Carr, Lucinda; Deuschl, Guenther; Hopfner, Franziska; Stamelou, Maria; Wood, Nicholas W.; Bhatia, Kailash P.

    2014-01-01

    Objective: To determine the genetic etiology in 2 consanguineous families who presented a novel phenotype of autosomal recessive juvenile amyotrophic lateral sclerosis associated with generalized dystonia. Methods: A combination of homozygosity mapping and whole-exome sequencing in the first family and Sanger sequencing of candidate genes in the second family were used. Results: Both families were found to have homozygous loss-of-function mutations in the amyotrophic lateral sclerosis 2 (juvenile) (ALS2) gene. Conclusions: We report generalized dystonia and cerebellar signs in association with ALS2-related disease. We suggest that the ALS2 gene should be screened for mutations in patients who present with a similar phenotype. PMID:24562058

  17. Lou Gehrig's Disease (ALS)

    MedlinePlus

    ... when it becomes necessary. For instance, a power wheelchair can enable a paralyzed person with ALS to ... done these things despite being confined to a wheelchair for many years, being able to move only ...

  18. 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 ...

  19. Ag-Al-Ca

    NASA Astrophysics Data System (ADS)

    Carow-Watamura, U.; Louzguine, D. V.; Takeuchi, A.

    This document is part of Part 1 http://dx.doi.org/10.1007/97.etType="URL"/> 'Systems from Ag-Al-Ca to Au-Pd-Si' of Subvolume B 'Physical Properties of Ternary Amorphous Alloys' of Volume 37 'Phase Diagrams and Physical Properties of Nonequilibrium Alloys' of Landolt-Börnstein - Group III 'Condensed Matter'. It contains the Chapter 'Ag-Al-Ca' with the content:

  20. Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively.

    PubMed

    Li, Guangyu; Zeng, Xiang; Liu, Xiupian; Zhang, Xiaobo; Shao, Zongze

    2016-11-01

    An anaerobic, Gram-stain-positive, spore-forming bacterium, designated DY30321T, was isolated from a sample of mixed hydrothermal sulfides collected during cruise DY30 of R/V Da Yang Yi Hao. Cells of strain DY30321T were rod-shaped with rounded ends, and were not motile. Strain DY30321T grew optimally at pH 8.0, at 30 °C and at a salinity (sea salts) of 30-40 g l-1. The principal fatty acids of strain DY30321T were C14 : 0 and summed feature 1 (comprising iso H-C15 : 1/C13 : 0 3-OH). The predominant polar lipids of strain DY30321T were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. No respiratory quinone was detected. The G+C content of the genomic DNA of strain DY30321T was 33.4 mol%. Phylogenetically, strain DY30321T branched within the family Peptostreptococcaceae, with (misclassified) Clostridium halophilum M1T being its closest phylogenetic relative (94.6 % 16S rRNA gene sequence similarity), followed by (misclassified) Clostridium caminithermale DVird3T (92.1 %). These strains showed very low 16S rRNA gene sequence similarity (<84 %) to Clostrdium butyricum ATCC 19398T, the type species of the genus Clostridium sensu stricto. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain DY30321T (=KCTC 15549T=MCCC 1A01532T) is considered as the type strain of a novel species of a new genus in the family Peptostreptococcaceae, for which the name Wukongibacterbaidiensis gen. nov., sp. nov. is proposed. Maledivibacter gen. nov. is proposed to accommodate Clostridium halophilum as Maledivibacter halophilus comb. nov. (type species of the genus), and Paramaledivibacter gen. nov. to accommodate Clostridium caminithermale as Paramaledivibacter caminithermalis comb. nov. (type species of the genus).

  1. Revision of "Phyllobrotica" from Taiwan with description of Jolibrotica gen. n. (Coleoptera, Chrysomelidae, Galerucinae).

    PubMed

    Lee, Chi-Feng; Bezděk, Jan

    2015-01-01

    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.

  2. 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…

  3. Acantholachesilla gen. n. (Psocodea:'Psocoptera': Lachesillidae: Eolachesillinae: Graphocaeciliini) from Valle del Cauca, Colombia.

    PubMed

    Aldrete, Alfonso N García; Manchola, Oscar Fernando Saenz; Obando, Ranulfo González

    2014-06-25

    Acantholachesilla saltoensis gen. et sp. n. is described from Valle del Cauca, Colombia, in the Lachesillidae, tribe Graphocaeciliini (Eolachesillinae). The genus is related to Dagualachesilla and Dagualachesilloides that occur in the same area, differing from them in the male clunial projection, phallosome, and female subgenital plate and gonapophyses.

  4. The Esophageal Glands of Pratylenchus Filipjev and Apratylenchoides belli n. gen. n. sp. (Nematoda: Tylenchoidea)

    PubMed Central

    Sher, S. A.

    1973-01-01

    The esophageal glands in the genus Pratylenchus occur in a large, single ventral lobe except for four populations in which a few specimens had the glands located dorsally. Apratylenchoides belli n. gen. n. sp. in the subfamily Radopholinae is proposed for a species having two esophageal glands in a large dorsal lobe and one gland in a smaller, shorter ventral lobe. PMID:19319335

  5. Gen Otto P. Weyland: Close Air Support in the Korean War

    DTIC Science & Technology

    2007-03-01

    over four years. In 1931, the young bachelor got mar- ried and was assigned to Luke Field, Hawaii, where he flew both observa- tion and bombardment...University Press, 1936. Smith, Brig Gen Dale O. U.S. Military Doctrine, A Study and Appraisal. New York: Duell, Sloan and Pearce, Inc., 1955. Smith

  6. [Morphological and histological studies on the Chinese drug shan-dou-gen].

    PubMed

    Fang, L Q; Guo, J X

    1992-01-01

    The Chinese drug "Shan-Dou-Gen" has been used for removing toxic heat, promoting the subsidence of swelling and soothing the sore throat since the ancient time. The authors made a survey of the drug "Shan-Dou-Gen" available in drug markets as well as the plant origin from the drug producing districts. The results showed that the drug "Shan-Dou-Gen" used in different regions in China at present are the roots or rhizomes derived from 9 species: Sophora tonkinensis Gagnep. (Leguminosae), Menispermum dauricum DC. (Menispermaceae), Indigofera amblyantha Craib (Leguminosae), I. carlesii Carib, I., fortunei Craib, I. decoa Lindl. var. ichangensis Y. Y. Fang et C. Z. Zheng, I. kirilowii Maxim. et Palibin, I. potaninii Craib, and Beesia calthaefolia (Maxim.) Ulbr. (Ranuculaceae). In this paper, the morphological characters of the crude drugs are described, compared and illustrated with photographs. The histological structures of the used parts are described, compared and illustrated with line drawings. The morphological and histological similarities and differences found among the above 9 species are summarized, and the key for the identification of the crude drugs is provided. As the drug "Shan-Dou-Gen" derived from different species has different actions and dosages, it is necessary to give different names to different species and use them correctly.

  7. 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.

  8. 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

  9. 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.

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

    PubMed Central

    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

  11. 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...

  12. Characterization and design of the FutureGen 2.0 carbon storage site

    SciTech Connect

    Gilmore, Tyler; Bonneville, Alain; Sullivan, Charlotte; Kelley, Mark; Appriou, Delphine; Vermeul, Vince; White, Signe; Zhang, Fred; Bjornstad, Bruce; Cornet, Francois; Gerst, Jacqueline; Gupta, Neeraj; Hund, Gretchen; Horner, Jake; Last, George; Lanigan, Dave; Oostrom, Mart; McNeil, Caitlin; Moody, Mark; Rockhold, Mark; Elliott, Mike; Spane, Frank; Strickland, Chris; Swartz, Lucy; Thorne, Paul; Brown, Christopher; Hoffmann, Jeffrey; Humphreys, Kenneth

    2016-10-01

    The objective of the FutureGen 2.0 Project was to demonstrate, at the commercial scale, the technical feasibility of implementing carbon capture and storage (CCS) in a deep saline formation in Illinois, USA. Over approximately 5 years, the FutureGen Alliance conducted a detailed site-selection process and identified a site for carbon sequestration storage in Morgan County, Illinois. The storage site was fully characterized, including the collection of seismic data and the drilling and characterization of a stratigraphic borehole. The characterization data provided critical input for developing a site-specific conceptual model and subsequent numerical modeling simulations. The modeling simulations, coupled with the upstream designs of the pipeline and power plant supported the development of a detailed 90 percent design that included the injection wells and associated control and monitoring infrastructure. Collectively, all these data were used by the FutureGen Alliance to develop the required documentation to support the applications for four underground injection control (UIC) permits (one for each proposed well). In August 2014, the U.S. Environmental Protection Agency issued four, first-of-their-kind, Class VI UIC permits for carbon sequestration in the United States to the FutureGen Alliance. The information and data generated under this project have been made publically available through reports and publications, including this journal and others.

  13. FY13 Annual Report: PHEV Advanced Series Gen-set Development/Demonstration Activity

    SciTech Connect

    Chambon, Paul H.

    2013-12-01

    The objective of this project is to integrate ORNL advancements in vehicle technologies to properly design, and size a gen-set for various vehicle applications and then simulate multiple advanced series hybrid (HEV/PHEV) vehicles with the genset models.

  14. 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

  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. 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.

  17. 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 ...

  18. Oswaldotrema nacinovici gen. nov. sp. nov. (Digenea: Philophthalmidae) from Numenius phaeopus (Aves: Scolopacidae) in Brazil.

    PubMed

    Muniz-Pereira, L C; Pinto, R M

    2000-01-01

    A new genus, Oswaldotrema gen. nov. is proposed. Oswaldotrema nacinovici sp. nov. is descibed from Numenius phaeopus Latham, 1790. Differentiation from the other related genera, namely Philophthalmus, Pygorchis, Proctobium, Parorchis, Echinostephila, Cloacitrema, Pittacium, Ophthalmotrema, Skrjabinovermis and Paratrema, was based on morphological characters, mainly on those referring to the body surface, body shape, head, esophagus, pharynx, acetabulum, vitellaria, vitelline reservoir and seminal vesicle.

  19. 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…

  20. 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…

  1. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

    PubMed Central

    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

  2. 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

  3. Microcetus lappus gen. nov., sp. nov.: new species of ciliated protozoon from the bovine rumen.

    PubMed Central

    Orpin, C G; Mathiesen, S D

    1986-01-01

    A new species of small, ciliated protozoon, Microcetus lappus gen. nov., sp. nov., from the rumen of Norwegian Red cattle is described. M. lappus possesses a novel cytopharyngeal apparatus of two rod-shaped structures, one situated on the dorsal side of the buccal cavity and one on the ventral side, suggesting that it belongs to a previously undescribed taxon. Images PMID:3094449

  4. Statins: Do They Cause ALS?

    MedlinePlus

    Statins: Do they cause ALS? Do statins cause amyotrophic lateral sclerosis (ALS)? Answers from Francisco Lopez-Jimenez, M.D. ... D. References Sorensen HT, et al. Statins and amyotrophic lateral sclerosis: The level of evidence for an association. Journal ...

  5. 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

  6. 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.

  7. ALS superbend magnet system

    SciTech Connect

    Zbasnik, J.; Wang, S.T.; Chen, J.Y.; DeVries, G.J.; DeMarco, R.; Fahmie, M.; Geyer, A.; Green, M.A.; Harkins, J.; Henderson, T.; Hinkson, J.; Hoyer, E.H.; Krupnick, J.; Marks, S.; Ottens, F.; Paterson, J.A.; Pipersky, P.; Portmann, G.; Robin, D.A.; Schlueter, R.D.; Steier, C.; Taylor, C.E.; Wahrer, R.

    2000-09-15

    The Lawrence Berkeley National Laboratory is preparing to upgrade the Advanced Light Source (ALS) with three superconducting dipoles (Superbends). In this paper we present the final magnet system design which incorporates R&D test results and addresses the ALS operational concerns of alignment, availability, and economy. The design incorporates conduction-cooled Nb-Ti windings and HTS current leads, epoxy-glass suspension straps, and a Gifford-McMahon cryocooler to supply steady state refrigeration. We also present the current status of fabrication and testing.

  8. Transfer of Pseudomonas flectens Johnson 1956 to Phaseolibacter gen. nov., in the family Enterobacteriaceae, as Phaseolibacter flectens gen. nov., comb. nov.

    PubMed

    Halpern, Malka; Fridman, Svetlana; Aizenberg-Gershtein, Yana; Izhaki, Ido

    2013-01-01

    Pseudomonas flectens Johnson 1956, a plant-pathogenic bacterium on the pods of the French bean, is no longer considered to be a member of the genus Pseudomonas sensu stricto. A polyphasic approach that included examination of phenotypic properties and phylogenetic analyses based on 16S rRNA, rpoB and atpD gene sequences supported the transfer of Pseudomonas flectens Johnson 1956 to a new genus in the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Two strains of Phaseolibacter flectens were studied (ATCC 12775(T) and LMG 2186); the strains shared 99.8 % sequence similarity in their 16S rRNA genes and the housekeeping gene sequences were identical. Strains of Phaseolibacter flectens shared 96.6 % or less 16S rRNA gene sequence similarity with members of different genera in the family Enterobacteriaceae and only 84.7 % sequence similarity with Pseudomonas aeruginosa LMG 1242(T), demonstrating that they are not related to the genus Pseudomonas. As Phaseolibacter flectens formed an independent phyletic lineage in all of the phylogenetic analyses, it could not be affiliated to any of the recognized genera within the family Enterobacteriaceae and therefore was assigned to a new genus. Cells were Gram-negative, straight rods, motile by means of one or two polar flagella, fermentative, facultative anaerobes, oxidase-negative and catalase-positive. Growth occurred in the presence of 0-60 % sucrose. The DNA G+C content of the type strain was 44.3 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, Pseudomonas flectens Johnson 1956 is transferred to the novel genus Phaseolibacter gen. nov. as Phaseolibacter flectens gen. nov., comb. nov. The type strain of Phaseolibacter flectens is ATCC 12775(T) = CFBP 3281(T) = ICMP 745(T) = LMG 2187(T) = NCPPB 539(T).

  9. Molecular analysis of human T cell lymphotropic virus type 1 and 2 (HTLV-1/2) seroindeterminate blood donors from Northeast Iran: evidence of proviral tax, env, and gag sequences.

    PubMed

    Zanjani, Delaram Sayadpour; Shahabi, Majid; Talaei, Nasim; Afzalaghaee, Monavar; Tehranian, Farahnaz; Bazargani, Reihane

    2011-02-01

    Human T cell lymphotropic virus type 1 and 2 (HTLV-1/2) Western blot indeterminate results are a problem for blood banks in endemic areas. To determine the prevalence of HTLV-1/2 infection among indeterminate donors, we analyzed 130 cases from Mashhad, an HTLV-1/2 endemic area in Northeast Iran. The most frequent Western blot bands were GD21 alone (37.2%) followed by rgp46-2 alone (32.1%). We further tested 40 available DNA samples of these cases by PCR for viral sequences, tax, gag, and pol, and found five cases (12.5%) to be positive for two or three HTLV-1 genes. There were no significant age, sex, and blood group differences between PCR-positive and PCR-negative cases. Among PCR-positive individuals, the most prevalent Western blot bands were variable combinations of rgp46-1, GD21, and gp21. The mean of the optical density (OD) of the enzyme-linked immunosorbent assay (ELISA) test was significantly higher in PCR-positive individuals. The frequency of the rgp46-1 band was also significantly higher in PCR-positive cases compared to PCR-negative ones. In conclusion, the majority of HTLV-indeterminate donors lack the HTLV provirus and therefore are not considered infected. However, in some cases with higher ODs in the ELISA test and seroreactivity to env proteins, rgp46-1 and GD21 in particular may be indicative of infection and need further evaluation by molecular methods.

  10. 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

  11. 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…

  12. Al Partitioning Patterns and Root Growth as Related to Al Sensitivity and Al Tolerance in Wheat.

    PubMed Central

    Samuels, T. D.; Kucukakyuz, K.; Rincon-Zachary, M.

    1997-01-01

    Studies of Al partitioning and accumulation and of the effect of Al on the growth of intact wheat (Triticum aestivum L.) roots of cultivars that show differential Al sensitivity were conducted. The effects of various Al concentrations on root growth and Al accumulation in the tissue were followed for 24 h. At low external Al concentrations, Al accumulation in the root tips was low and root growth was either unaffected or stimulated. Calculations based on regression analysis of growth and Al accumulation in the root tips predicted that 50% root growth inhibition in the Al-tolerant cv Atlas 66 would be attained when the Al concentrations were 105 [mu]M in the nutrient solution and 376.7 [mu]g Al g-1 dry weight in the tissue. In contrast, in the Al-sensitive cv Tam 105, 50% root growth inhibition would be attained when the Al concentrations were 11 [mu]M in the nutrient solution and 546.2 [mu]g Al g-1 dry weight in the tissue. The data support the hypotheses that differential Al sensitivity correlates with differential Al accumulation in the growing root tissue, and that mechanisms of Al tolerance may be based on strategies to exclude Al from the root meristems. PMID:12223623

  13. Al Sumelat Water Network. Village of Al Sumelat, Iraq

    DTIC Science & Technology

    2006-03-15

    OFFICE OF THE SPECIAL INSPECTOR GENERAL FOR IRAQ RECONSTRUCTION AL SUMELAT WATER NETWORK VILLAGE OF AL SUMELAT, IRAQ...Sumelat Water Network Village of Al Sumelat, Iraq 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e...Al Sumelat Water Network Village of Al Sumelat, Iraq Synopsis Introduction. This report was previously provided on a limited distribution basis

  14. Libkindia masarykiana gen. nov. et sp. nov., Yurkovia mendeliana gen. nov. et sp. nov., and Leucosporidium krtinense f.a. sp. nov., isolated from temperate forest soils.

    PubMed

    Mašínová, Tereza; Pontes, Ana; Carvalho, Cláudia; Sampaio, José Paulo; Baldrian, Petr

    2016-11-30

    One hundred and ninety-eight isolates of soil yeasts were isolated from mixed temperate forests in the Czech Republic, and their abundance and distribution in the litter and soil were evaluated using amplicon sequencing of soil fungal communities. Abundant taxa with no close identified hits were selected for further characterization as potential novel species of yeasts. Phylogenetic analyses using sequences of the D1/D2 domains, the ITS region and RPB1 and TEF1 genes support the recognition of the following three new species belonging to the subphylum Pucciniomycotina, class Microbotryomycetes: Leucosporidium krtinense f.a. sp. nov. (type strain CBS 14304T = PYCC 6879T = DSM 101892T), Yurkovia mendeliana sp. nov. (type strain CBS 14273T = PYCC 6884T = DSM 101889T), and Libkindia masarykiana sp. nov. (type strain CBS 14275T = PYCC 6886T = DSM 101891T). Since the later two novel taxa cannot be assigned to existing genera, two new genera, Libkindia gen. nov. and Yurkovia gen. nov. are also described.

  15. Phyllonema aviceniicola gen. et sp. nov. and Foliisarcina bertiogensis gen. et. sp. nov., novel epiphyllic cyanobacteria associated with Avicennia schaueriana leaves.

    PubMed

    Alvarenga, Danillo Oliveira; Rigonato, Janaina; Branco, Luis Henrique Zanini; Melo, Itamar Soares; Fiore, Marli Fatima

    2015-11-17

    Cyanobacteria dwelling on the salt-excreting leaves of the mangrove tree Avicennia schaueriana were isolated and characterized by ecological, morphological, and genetic approaches. Leaves were collected in a mangrove with a history of oil contamination in the coastline of São Paulo state, Brazil, and isolation was achieved by smearing leaves on the surface of solid media or by submerging leaves in liquid media. Twenty-nine strains isolated were shown to belong to four cyanobacterial orders (thirteen Synechococcales, seven Nostocales, seven Pleurocapsales, one Chroococcales, and one Oscillatoriales) according to morphological and 16S rDNA sequence evaluations. More detailed investigations pointed six Rivulariacean and four Xenococcacean strains as novel taxa. These strains were classified as Phyllonema gen. nov. (type-species P. aviceniicola sp. nov.) and Foliisarcina gen. nov. (type-species F. bertiogensis sp. nov.) according to the International Code of Nomenclature for Algae, Fungi, and Plants. This investigation shows some of the unique cyanobacteria inhabiting the phyllosphere of A. schaueriana can be retrieved by culturing techniques, improving current taxonomy and providing new insights into the evolution, ecology, and biogeography of this phylum.

  16. Roseimaritima ulvae gen. nov., sp. nov. and Rubripirellula obstinata gen. nov., sp. nov. two novel planctomycetes isolated from the epiphytic community of macroalgae.

    PubMed

    Bondoso, Joana; Albuquerque, Luciana; Nobre, M Fernanda; Lobo-da-Cunha, Alexandre; da Costa, Milton S; Lage, Olga Maria

    2015-02-01

    Four isolates, belonging to the deep-branching phylum Planctomycetes, were recovered from the biofilm of two marine macroalgae, Ulva sp. and Laminaria sp., from the Northern coast of Portugal. These strains were light pink- or red-pigmented; the cells were variable in shape and usually organized in rosettes. They had a dimorphic cell cycle with budding reproduction. The organisms were chemoheterotrophic, strictly aerobic and mesophilic. The 16S rRNA gene sequence analysis showed that the strains belong to the family Planctomycetaceae with Rhodopirellula as the closest genus. The isolates form two separate branches (strain LF1(T) forms one branch and the strains UC8(T), UF3 and UF42 form a second branch) clearly separated from Rhodopirellula baltica with 94.2% and 93.8% 16S rRNA gene sequence similarity, respectively. Based on differential characteristics that distinguish the novel genera from R. baltica, such as cell size and shape, ultrastructure, enzymatic activities, substrate utilization pattern, fatty acid composition, phospholipid profiles and phylogeny we propose that the isolates represent two novel genera of the order Planctomycetales, Roseimaritima ulvae gen. nov., sp. nov. (type strain is UC8(T)=DSM 25454(T)=LMG 27778(T)) and Rubripirellula obstinata gen. nov., sp. nov. (type strain is LF1(T)=LMG 27779(T)=CECT 8602(T)).

  17. 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.

  18. 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.

  19. Wilsonosiphonia gen. nov. (Rhodomelaceae, Rhodophyta) based on molecular and morpho-anatomical characters.

    PubMed

    Bustamante, Danilo E; Won, Boo Yeon; Miller, Kathy Ann; Cho, Tae Oh

    2017-01-12

    Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot-shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts.

  20. 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.

  1. Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies.

    PubMed

    Chen, Elizabeth S; Sarkar, Indra Neil

    2011-01-01

    Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the "host" and "isolation_source" fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health.

  2. 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.

  3. 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.

  4. A REVIEW PAPER ON AGING EFFECTS IN ALLOY 617 FOR GEN IVNUCLEAR REACTOR APPLICATIONS

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W

    2009-01-01

    To understand the response of Alloy 617 to long-time exposure conditions and determine the supplementary data needs for structural components in Gen IV nuclear reactors, the literature of aging and aging effects in the alloy was reviewed. Most of the reviewed data were produced in connection with the international research effort supporting High Temperature Gas-Cooled Reactor (HTGR) projects in the 1970s and 1980s. Topics considered included microstructural changes, hardness, tensile properties, toughness, creep-rupture, fatigue, and crack growth. It became clear that, for the long-time, very high temperature conditions of the Gen IV reactors, a significant effort would be needed to fully understand and characterize property changes. Several topics for further research were recommended.

  5. 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.

  6. No quenching of magnetic moment for the GenCo (n=1-13) clusters: First-principles calculations

    NASA Astrophysics Data System (ADS)

    Jing, Qun; Tian, Fu-yang; Wang, Yuan-xu

    2008-03-01

    The authors predict that for the GenCo (n=1-13) clusters the magnetic moment does not quench, which is dark contrast to the previous results with transition-metal-doped Sin clusters. It may be due to the unpaired electrons of the Co atom in the clusters. For the ground state structures of the GenCo (n⩾9) clusters, the Co atom completely falls into the center of the Ge outer frame, forming metal-encapsulated Gen cages. The doping of the Co atom enhances the stability of the host Gen clusters. The Ge10Co cluster with the bicapped tetragonal antiprism structure is more stable than others, which agrees very well with the results of the experiment of the Co /Ge binary clusters by the laser vaporization.

  7. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David [Baylor

    2016-07-12

    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.

  8. Squamasnema amazonica n. gen. n. sp. (Heligmonellinae): A new parasite of Proechimys roberti (Rodentia: Echimyidae) in the Brazilian Amazon.

    PubMed

    Cordeiro, Helrik da Costa; Melo, Francisco Tiago de Vasconcelos; Furtado, Adriano Penha; Giese, Elane Guerreiro; Maldonado, Arnaldo; dos Santos, Jeannie Nascimento

    2015-08-01

    A new species of nematode, Squamasnema amazonica n. gen. n. sp., is described based on specimens found parasitizing the small intestine of Proechimys roberti (Rodentia: Echimyidae) collected during a survey of the fauna of Tapirapé-Aquirí National Forest (Brazil, Eastern Brazilian Amazon). The nematodes were fixed and processed for light microscopy and scanning electron microscopy (SEM). These nematodes were classified under the family Heligmonellidae and the subfamily Heligmonellinae. Although several species in the family Heligmonellidae exhibit discontinuous ridges, Squamasnema n. gen. and Trichotravassosia are the only genera with columns of scales along their entire body, as an apomorphy of the synlophe. Squamasnema n. gen. has columns of cuticular cells along its body, except for on the left flank, and exhibits a synlophe with no size gradient or inclination and does not present chitinized structures supporting the synlophe. Therefore, due to these morphological differences of Squamasnema n. gen., the creation of a new genus was necessary.

  9. 78 FR 56263 - HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc... and accurate information concerning the securities of Security Intelligence Technologies, Inc....

  10. 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.

  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. Implementing genetic education in primary care: the Gen-Equip programme.

    PubMed

    Paneque, Milena; Cornel, Martina C; Curtisova, Vaclava; Houwink, Elisa; Jackson, Leigh; Kent, Alastair; Lunt, Peter; Macek, Milan; Stefansdottir, Vigdis; Turchetti, Daniela; Skirton, Heather

    2017-03-13

    Genetics and genomics are increasingly relevant to primary healthcare but training is unavailable to many practitioners. Education that can be accessed by practitioners without cost or travel is essential. The Gen-Equip project was formed to provide effective education in genetics for primary healthcare in Europe and so improve patient care. Partners include patient representatives and specialists in genetics and primary care from six countries. Here, we report the progress and challenges involved in creating a European online educational program in genetics.

  13. Geochemical Monitoring Considerations for the FutureGen 2.0 Project

    SciTech Connect

    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

  14. Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.

    PubMed

    Lyons, Rhonda

    2012-01-01

    According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment.

  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. 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

  17. 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.

  18. Airpower Leadership on the Front Line: Lt Gen George H. Brett and Combat Command

    DTIC Science & Technology

    2006-09-01

    perspective to the project and his amicable encouragement to me personally. Col Larry Thompson receives my thanks for connecting me with his friend, Lt...a major general, Arnold dispatched him to conduct lend-lease discussions with the British and to make a tour of Africa. This trip turned out much...book examines how well Gen George Brett executed the duties he was assigned during his tour in the Far East. The examination will focus on the

  19. 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

  20. Sclerostylus n. gen. from Panama and Other Neotropical Species of LeptonIchoidea (Dorylaimida).

    PubMed

    G Goseco, C; Ferris, V R; Ferris, J M

    1981-01-01

    Leptonchoid species found in soil samples taken in lowland and mid-elevation seasonal forests at four locations in Panama were as follows: Sclerostylus karri n. gen., n. sp., Basirotyleptus saccatus n. sp., B. nemoralis, B. acus, B. penetrans, Doryllium neotropicum n. sp., D. minor, Tyleptus gymnochilus, Gerthus jamesi, Dorylaimoides micoletzkyi, and Tylencholaimellus macrophallus. The discoveries corroborate our earlier suggestion of a Gondwanian origin for Tyleptus and Basirotyleptus and provide data for additional biogeographical study.

  1. 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.

  2. Effects of Ge Gen Decoction on PGE2 content and COX activity in the degenarated cervical intervertebral discs of rats.

    PubMed

    Jun, Zhou; Fang, Suping; Huo, Hairu; Qi, Yun; Guo, Shuying; Jiang, Tingliang; Shi, Qi

    2005-09-01

    After the rat model of cervical spondylosis was developed for 6 months, the PGE2 content and COX activity in the cervical intervertebral discs were determined respectively by radioimmunoassay and catalytic activity assay. The results indicated that the PGE2 content and COX activity in the model rat increased significantly, and that Ge Gen Decoction could down-regulate the PGE2 content and inhibit COX activity. This is possibly one of the mechanisms of Ge Gen Decoction for treating cervical spondylosis.

  3. ALS insertion devices

    NASA Astrophysics Data System (ADS)

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

    1991-08-01

    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.

  4. 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

  5. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases.

    PubMed

    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.

  6. Taxonomy of the Proisotoma complex. V. Sexually dimorphic Ephemerotoma gen. nov. (Collembola: Isotomidae).

    PubMed

    Potapov, Mikhail; Kahrarian, Morteza; Deharveng, Louis; Shayanmehr, Masoumeh

    2015-12-03

    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.

  7. 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

  8. 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.

  9. GenColors-based comparative genome databases for small eukaryotic genomes.

    PubMed

    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.

  10. 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.

  11. 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.

  12. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    DOE PAGES

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; ...

    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

  13. Sensitivity of IceCube-Gen2 Phase I to tau neutrino appearance

    NASA Astrophysics Data System (ADS)

    de André, João Pedro A. M.; IceCube-Gen2 Collaboration Collaboration

    2017-01-01

    Looking towards the future of IceCube we are planning both high-energy and low-energy (PINGU) extensions. The first step towards these upgrade, ``IceCube-Gen2 Phase I'', consists of 7 additional strings inserted in the denser region DeepCore of the IceCube Neutrino Observatory. These additional photo-multipliers will more than double the number of sensors in the DeepCore region and with that significantly improve our ability to reconstruct low-energy events. This will lead to a significant improvement in the sensitivity to measure nutau appearance thanks to improved precision in reconstruction of nutau events. Also along with the additional photo-multipliers, new calibration devices will also be deployed with IceCube-Gen2 Phase I. These new devices will also further improve our understanding of the surrounding ice, and with that reduce the impact of some of our dominant systematics. The reduction of these systematics will also improve the sensitivity of IceCube to high-energy neutrinos through the re-analysis of the archival data with the improved detector systemtatics. We will present status of the tau neutrino appearance analysis using IceCube-Gen2 Phase I, both from thanks to the additional photomultiplier tubes deployed and from the extended calibration capabilities.

  14. Swedish Plectida (Nematoda). Part 6. Neocamacolaimus parasiticus gen. n., sp. n.

    PubMed

    Holovachov, Oleksandr; Boström, Sven

    2014-06-25

    A new genus Neocamacolaimus gen. n., with one new species N. parasiticus gen. n., sp. n. is described from the benthic polychaete Sphaerosyllis cf. hystrix collected in the Skagerrak off the west coast of Sweden. Neocamacolaimus gen. n. is placed in the family Camacolaimidae and is particularly characterised by having annulated cuticle with lateral alae; setiform cephalic sensilla located at level with amphids; amphidial fovea ventrally spiral; buccal cavity without armament; pharynx muscular; nerve ring located at base of pharynx; male reproductive system diorchic with outstretched testes; spicules weakly arcuate with straight manubrium; gubernaculum absent; alveolar supplements located in the pharyngeal region; tubular supplements absent; tail conoid; caudal glands and spinneret present. Juveniles of this genus are particularly characterised by their parasitic lifestyle and the following unique morphological features: lips form a dorso-ventrally elongated perioral disc with internal sclerotizations: one midventral and two dorsosublateral (right and left); cephalic sensilla setiform, subventral sensilla are noticeably longer than the subdorsal ones; intestine extends posterior to rectum and anal opening, forming a post-anal pouch.

  15. 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

  16. 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.

  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. 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

  19. Frequently Asked Questions about ALS and the ALS Registry

    MedlinePlus

    ... Why is it necessary to provide my Social Security Number (SSN) when registering in the National ALS ... Why is it necessary to provide my Social Security Number (SSN) when registering in the National ALS ...

  20. Alkalimonas amylolytica gen. nov., sp. nov., and Alkalimonas delamerensis gen. nov., sp. nov., novel alkaliphilic bacteria from soda lakes in China and East Africa.

    PubMed

    Ma, Yanhe; Xue, Yanfen; Grant, William D; Collins, Nadine C; Duckworth, Andrew W; Van Steenbergen, Robert P; Jones, Brian E

    2004-06-01

    Two related novel alkaliphilic and slightly halophilic bacteria are described. They are strain N10 from Lake Chahannor in China and strain 1E1 from Lake Elmenteita in East Africa. Both strains are strictly aerobic, heterotrophic, alkaliphilic, mesophilic, and require NaCl for growth. The optimal conditions for growth were at pH 10-10.5 and 2-3% (w/v) NaCl. Cells of both strains were Gram-negative, rod-shaped, non-spore-forming, and motile with a single polar flagellum. Cellular fatty acids in both strains were predominantly saturated and mono-unsaturated straight-chain fatty acids (16:0, 16:1omega7c and 18:1omega7c). The major isoprenoid quinone of both strains was Q8. The major polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylglycerol phosphate and phosphatidylethanolamine. The guanine plus cytosine (G + C) content of the DNA was 52.5 mol% and 55.4 mol%, respectively. Phylogenetic analysis revealed that the two strains formed a distinct lineage within the gamma-3 subclass of the Proteobacteria. The strains shared a 16S rDNA sequence similarity of 96.1% and showed less than 93.7% of sequence similarity to any other known species. Based on polyphasic data, the two strains were differentiated from currently recognized genera and represent a new genus, Alkalimonas gen. nov., with two species, Alkalimonas amylolytica sp. nov. (type strain is N10T = AS 1.3430) and Alkalimonas delamerensis sp. nov. ( type strain is 1E1(P, T) = CBS 391.94). The GenBank accession numbers for the 16S rRNA gene sequence of strains N10 and 1E1 are AF250323 and X92130, respectively.

  1. 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.

  2. 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 ...

  3. Al Qaeda as a System

    DTIC Science & Technology

    2006-03-15

    either as welcome guests or parasites . As welcome guests, Al Qaeda members take sanctuary in sponsor states. Sponsor states provide Al Qaeda with...sponsorship, Al Qaeda takes sanctuary as parasites either overtly or covertly. They take overt sanctuary in countries that publicly claim a policy...39 Yehudit Barsky, “Al Qa’ida, Iran, and Hezbollah: A Continuing Symbiosis ,” The American Jewish Committee Series on Terrorism , February 2004, 2-3

  4. 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

  5. GenSalt: rationale, design, methods and baseline characteristics of study participants.

    PubMed

    2007-08-01

    Hypertension is a complex disorder influenced by genetic and environmental determinants and their interactions. The objectives of the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) are to localize and identify genes related to blood pressure (BP) responses to dietary sodium and potassium intervention. GenSalt utilizes a family feeding-study design. Each family was ascertained through a proband with untreated prehypertension or stage-1 hypertension in rural China. A medical history, lifestyle risk factors and responses to cold pressor tests, were obtained at baseline visits while BP, weight, blood and urine specimens were collected at baseline and follow-up visits. The dietary intervention included a 7-day low-sodium feeding (51.3 mmol/day), a 7-day high-sodium feeding (307.8 mmol/day) and a 7-day high-sodium feeding with an oral potassium supplementation (60 mmol/day). Microsatellite markers for genome-wide linkage scan and single nucleotide polymorphism (SNP) markers in candidate genes will be genotyped. Overall, 3153 participants from 658 families were recruited for GenSalt. The mean systolic and diastolic BPs were 128.0 and 80.3, 111.6 and 71.0, 112.6 and 72.6, 106.6 and 65.3 and 136.7 and 75.0 mm Hg for probands, siblings, spouses, offspring and parents, respectively. The mean urinary excretion of sodium and potassium were 232.5 and 38.6, 222.9 and 38.2, 213.1 and 37.8 and 207.3 and 36.0 mmol/24-h for probands, siblings, spouses and offspring, respectively. Our study will identify novel genes that influence significantly the effect of dietary sodium and potassium intake on BP. This information is useful for development of targeted intervention for the prevention and treatment of hypertension.

  6. An evaluation of the metabolic syndrome in the HyperGEN study

    PubMed Central

    Kraja, Aldi T; Hunt, Steven C; Pankow, James S; Myers, Richard H; Heiss, Gerardo; Lewis, Cora E; Rao, DC; Province, Michael A

    2005-01-01

    Background In 2001 the National Cholesterol Education Program (NCEP) provided a categorical definition for metabolic syndrome (c-MetS). We studied the extent to which two ethnic groups, Blacks and Whites were affected by c-MetS. The groups were members of the Hypertension Genetic Epidemiology Network (HyperGEN), a part of the Family Blood Pressure Program, supported by the NHLBI. Although the c-MetS definition is of special interest in particular to the clinicians, the quantitative latent traits of the metabolic syndrome (MetS) are also important in order to gain further understanding of its etiology. In this study, quantitative evaluation of the MetS latent traits (q-MetS) was based on the statistical multivariate method factor analysis (FA). Results The prevalence of the c-MetS was 34% in Blacks and 39% in Whites. c-MetS showed predominance of obesity, hypertension, and dyslipidemia. Three and four factor domains were identified through FA, classified as "Obesity," "Blood pressure," "Lipids," and "Central obesity." They explained approximately 60% of the variance in the 11 original variables. Two factors classified as "Obesity" and "Central Obesity" overlapped when FA was performed without rotation. All four factors in FA with Varimax rotation were consistent between Blacks and Whites, between genders and also after excluding type 2 diabetes (T2D) participants. Fasting insulin (INS) associated mainly with obesity and lipids factors. Conclusions MetS in the HyperGEN study has a compound phenotype with separate domains for obesity, blood pressure, and lipids. Obesity and its relationship to lipids and insulin is clearly the dominant factor in MetS. Linkage analysis on factor scores for components of MetS, in familial studies such as HyperGEN, can assist in understanding the genetic pathways for MetS and their interactions with the environment, as a first step in identifying the underlying pathophysiological causes of this syndrome. PMID:15656912

  7. GenClust: A genetic algorithm for clustering gene expression data

    PubMed Central

    Di Gesú, Vito; Giancarlo, Raffaele; Lo Bosco, Giosué; Raimondi, Alessandra; Scaturro, Davide

    2005-01-01

    Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods. We have experimented with the FOM methodology, specifically conceived for validating clusters of gene expression data. The validity of GenClust has been assessed experimentally on real data sets, both with the use of validation measures and in comparison with other algorithms, i.e., Average Link, Cast, Click and K-means. Conclusion Experiments show that none of the algorithms we have used is markedly superior to the others across data sets and validation measures; i.e., in many cases the observed differences between the worst and best performing algorithm may be statistically insignificant and they could be considered equivalent. However, there are cases in which an algorithm may be better than others and therefore worthwhile. In particular, experiments for GenClust show that, although simple in its data representation, it converges very rapidly to a local optimum and that its ability to identify meaningful clusters is comparable, and sometimes superior, to that of more sophisticated algorithms. In addition, it is well suited for use in conjunction with data driven internal validation measures and, in particular, the FOM methodology. PMID:16336639

  8. 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.

  9. Data-link and surface map traffic intent displays for NextGen 4DT and equivalent visual surface operations

    NASA Astrophysics Data System (ADS)

    Shelton, Kevin J.; Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J., III; Jones, Denise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-05-01

    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.

  10. 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.

  11. Clinical utility of Beckman-Coulter Gen's reticulocyte analysis in the study of anemia of chronic disease (ACD).

    PubMed

    Rodrigues, Ana; Ortega, Carlos; Santos, Luís; Teixeira, Alexandre; Dinis, Maria Joáo; Vasconcelos, Iponina; Lacerda, Jorge; Fonseca, Elisa

    2007-01-01

    The aim of this study is to analyze the reticulocyte parameters (classical and research parameters) acquired by the Beckman Coulter GEN'S blood counter (GEN'S; Brea, CA, USA) to establish the "reticulocyte profile" characteristics of patients with anemia of chronic disease (ACD). The reticulocyte parameters and profile provided by the GEN'S were studied in 38 anemic patients who fulfilled the diagnostic criteria for the ACD, and the results were compared with those of 38 healthy controls in a multivariate statistical analysis using the Student t-test and the receiver operating characteristics (ROC) curve analysis.Statistically significant (P <.05) differences between the 2 population groups were observed in several of the reticulocyte parameters provided by the GEN'S: mean volume of the reticulocyte population (MRV) (high), percentage of high light scatter reticulocytes HLR% (high), mean volume of the whole sphered red cell and reticulocyte population (MSCV) (high) MCV-MSCV (low) with the highest diagnostic value, as measured by the area under the ROC curve (>0.9), for the IRF (high) and the reticulocyte population data: mean channel scatter retics (high) and the mean channel conductivity retics (high). This study establishes the reticulocyte parameters and reticulocyte profile as provided by the GEN'S and characteristic of patients with ACD as compared with normal subjects. This should provide the basis for further studies comparing the reticulocyte profile of patients with ACD with those found in other types of anemia.

  12. Reclassification of Gemmobacter changlensis to a new genus as Cereibacter changlensis gen. nov., comb. nov.

    PubMed

    Suresh, G; Sasikala, Ch; Ramana, Ch V

    2015-03-01

    We propose a new genus to accommodate the phototrophic bacterium Gemmobacter changlensis [Chen W. M., Cho, N. T., Huang, W. C., Young, C. C. & Sheu, S. Y. (2013) Int J Syst Evol Microbiol 63, 470-478] based on multiple strain analysis. Differences in the major diagnostic properties such as ability to grow phototrophically, the presence of internal photosynthetic membranes, the light harvesting complexes, fatty acids, carotenoids, bacterial chlorophylls, polar lipid composition and some other phenotypic properties warrant the creation of a new genus, designated Cereibacter gen. nov., to accommodate the phototrophic members of the genus Gemmobacter, as represented by the type species Cereibacter changlensis comb. nov.

  13. 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).

  14. 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.

  15. 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.

  16. GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS

    PubMed Central

    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

  17. 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.

  18. 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.

  19. Traffic Generator (TrafficGen) Version 1.4.2: Users Guide

    DTIC Science & Technology

    2016-06-01

    TrafficGen Graphical User Interface (GUI) 3 3.1 Anatomy of the User Interface 3 3.2 Scenario Configuration and MGEN Files 4 4. Working with...4.6.1 Node Name Conflict Resolution 11 4.7 Import Existing MGEN Files 12 4.8 Edit an Existing Node 12 4.9 Edit an Existing Flow 13 4.10 Edit an...Save a Scenario 18 4.19.1 Save a Scenario to a Different Name 18 4.20 Export Scenario Data 19 4.20.1 Export SDT File 19 4.20.2 Export MGEN Timeline

  20. Havispora longyearbyenensis gen. et sp. nov.: an arctic marine fungus from Svalbard, Norway.

    PubMed

    Pang, Ka-Lai; Chiang, Michael W L; Vrijmoed, Lilian L P

    2008-01-01

    Information on the diversity and ecology of arctic marine fungi is lacking. During a short visit to Longyearbyen (78 degrees 13'N 15 degrees 33'E), Svalbard, Norway, a new marine fungus growing on driftwood collected at the shore was encountered. This taxon belongs to the Halosphaeriales (Ascomycota), a fungal order of mostly marine species. Havispora longyearbyenensis gen. et sp. nov. is morphologically similar to Nautosphaeria and Nereiospora, all with tufts of appendages at polar and equatorial positions of the ascospore but differing in color and septation of the ascospore and morphology and ontogeny of the ascospore appendage.

  1. Hemichloris antarctica, gen. et sp. nov. (Chlorococcales, Chlorophyta), a cryptoendolithic alga from Antarctica.

    PubMed

    Tschermak-Woess, E; Friedmann, E I

    1984-01-01

    Hemichloris antarctica gen. et sp. nov. (Oocystaceae, Chlorococcales) is characterized by a single, articulated, pyrenoid-less, thick saucer-shaped chloroplast, which generally fills less than half of the cell periphery. Multiplication is only by autospores. The species is psychrophilic and is damaged at temperatures above 20 degree C. Hemichloris antarctica is a member of the cryptoendolithic microbial community living in porous sandstone rocks of the Antarctica cold desert. It inhabits the zone below that of cryptoendolithic lichens and survives at extremely low light intensities. In the natural habitat, morphology is somewhat different from that in culture, as chloroplasts are smaller and without articulation, and the cells develop a gelatinous sheath.

  2. Trematodes of marine fishes from South Australia. I. Paraneocreadium australiense gen. et sp. n. (Lepocreadiidae).

    PubMed

    Kruse, G O

    1978-06-01

    Paraneocreadium australiense gen. et sp. n. (Lepocreadiidae) is described from Psilocranium nigricans (Richardson) from the Aldinga Reef of South Australia. Paraneocreadium is most similar to Neocreadium Howell 1966 from Geniagnus in New Zealand and Neolepocreadium Thomas 1960 from Trachinotus in Ghana. It differs from both genera in being ovoid rather than elongate, in having a coiled rather than saccate internal seminal vesicle, and having no viteline follicles between the gonads. It differs further from Neocreadium in lacking lymphatic vessels and in the position of the genital pore.

  3. Thermal stability study for candidate stainless steels of GEN IV reactors

    NASA Astrophysics Data System (ADS)

    Simeg Veternikova, J.; Degmova, J.; Pekarcikova, M.; Simko, F.; Petriska, M.; Skarba, M.; Mikula, P.; Pupala, M.

    2016-11-01

    Candidate stainless steels for GEN IV reactors were investigated in term of thermal and corrosion stability at high temperatures. New austenitic steel (NF 709), austenitic ODS steel (ODS 316) and two ferritic ODS steels (MA 956 and MA 957) were exposed to around 1000 °C in inert argon atmosphere at pressure of ∼8 MPa. The steels were further studied in a light of vacancy defects presence by positron annihilation spectroscopy and their thermal resistance was confronted to classic AISI steels. The thermal strain supported a creation of oxide layers observed by scanning electron microscopy (SEM).

  4. First Insertions of Carbene Ligands into Ge-N and Si-N Bonds.

    PubMed

    Álvarez-Rodríguez, Lucía; Cabeza, Javier A; García-Álvarez, Pablo; Gómez-Gallego, Mar; Merinero, Alba D; Sierra, Miguel A

    2017-03-28

    The insertion of carbene ligands into Ge-N (three examples) and Si-N (one example) bonds has been achieved for the first time by treating Fischer carbene complexes (M=W, Cr) with bulky amidinatotetrylenes (E=Ge, Si). These reactions, which start with a nucleophilic attack of the amidinatotetrylene heavier group 14 atom to the carbene C atom, proceed through a stereoselective insertion of the carbene fragment into an E-N bond of the amidinatotetrylene ENCN four-membered ring, leading to [M(CO)5 L] derivatives in which L belongs to a novel family of tetrylene ligands comprising an ECNCN five-membered ring.

  5. Growth and Optical Properties of Al rich AlN/AlGaN Quantum Wells

    NASA Astrophysics Data System (ADS)

    Tahtamouni, T. M. Al; Nepal, N.; Nakarmi, M. L.; Lin, J. Y.; Jiang, H. X.

    2006-03-01

    Al rich AlGaN alloys are promising materials for the applications in the optoelectronic devices such as deep ultraviolet (UV) emitters and detectors in the spectral range down to 200 nm. AlGaN based UV emitters (λ<340nm) has applications in bio-chemical agent detection and medical research/ health care. To realize deep UV emission (λ< 280 nm) Al rich AlGaN based quantum wells (QWs) are required. We report here the growth of AlN/AlxGa1-xNQWs (x>0.65) on AlN/sapphire templates by metalorganic chemical vapor deposition (MOCVD). Deep UV photoluminescence (PL) was employed to study the optical properties of the QWs. Well width (Al composition) dependence was studied by varying the QW thickness (Al composition) with fixed x ˜ 0.65 (well width at 3 nm). Optical properties of these QWs such as the effects of alloy fluctuation, temperature, strain and piezoelectric field, carrier and exciton localizations on the quantum efficiency have been studied. Carrier and exciton dynamics were probed. Implications of our findings on the applications of Al rich AlN/AlGaN QWs for UV emitters and detectors will also be discussed.

  6. 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.

  7. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.

    PubMed

    Francis, Isolde M; Jochimsen, Kenneth N; De Vos, Paul; van Bruggen, Ariena H C

    2014-04-01

    The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T) = LMG 17323(T) = ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) ( = LMG 12560(T) = ATCC 51296(T)), WI4(T) ( = LMG 11032(T) = ATCC 51292(T)) and SP1(T) ( = LMG 12581(T) = ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic.

  8. 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

  9. 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.

  10. Morton et al. Reply

    NASA Technical Reports Server (NTRS)

    Morton, Douglas C.; Nagol, Jyoteshwar; Carabajal, Claudia C.; Rosette, Jacqueline; Palace, Michael; Cook, Bruce D.; Vermote, Eric F.; Harding, David J.; North, Peter R. J.

    2016-01-01

    Multiple mechanisms could lead to up-regulation of dry-season photosynthesis in Amazon forests, including canopy phenology and illumination geometry. We specifically tested two mechanisms for phenology-driven changes in Amazon forests during dry-season months, and the combined evidence from passive optical and lidar satellite data was incompatible with large net changes in canopy leaf area or leaf reflectance suggested by previous studies. We therefore hypothesized that seasonal changes in the fraction of sunlit and shaded canopies, one aspect of bidirectional reflectance effects in Moderate Resolution Imaging Spectroradiometer (MODIS) data, could alter light availability for dry-season photosynthesis and the photosynthetic capacity of Amazon forests without large net changes in canopy composition. Subsequent work supports the hypothesis that seasonal changes in illumination geometry and diffuse light regulate light saturation in Amazon forests. These studies clarify the physical mechanisms that govern light availability in Amazon forests from seasonal variability in direct and diffuse illumination. Previously, in the debate over light limitation of Amazon forest productivity, seasonal changes in the distribution of light within complex Amazon forest canopies were confounded with dry-season increases in total incoming photosynthetically active radiation. In the accompanying Comment, Saleska et al. do not fully account for this confounding effect of forest structure on photosynthetic capacity.

  11. Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.

    PubMed

    Morse, Alison M; Carballo, Valentina; Baldwin, Donald A; Taylor, Christopher G; McIntyre, Lauren M

    2010-09-01

    Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser-capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser-capture microdissection. Arabidopsis root cells undergoing giant cell formation as a result of nematode infestation and uninfested control root cells were laser-captured and used to evaluate two amplification systems. One, NuGEN's WT-Ovation Pico (Pico) amplification system, uses total RNA as starting material, and the other, NuGEN's WT-One-Direct (One-Direct) amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The One-Direct system was less reproducible and more variable than the Pico system. The Pico amplification kit resulted in the detection of thousands of differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the One-Direct amplification kit.

  12. Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Kasai, Hiroaki

    2017-01-01

    A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732(T), was isolated from marine sediment in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732(T) were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 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 Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732(T) (= KCTC 52207(T) = NBRC 112211(T)).

  13. IceCube Gen2: The Next Generation of Neutrino Astronomy

    NASA Astrophysics Data System (ADS)

    Blaufuss, Erik; IceCube Collaboration

    2017-01-01

    The observations of an astrophysical flux of neutrinos by the IceCube neutrino observatory signaled the start of the era of neutrino astronomy. While the source of these astrophysical neutrinos remains unclear, many strong constraints have already been made. Unfortunately, the limits of the current detector are becoming clear and the design of the next generation of Antarctic neutrino observatory is well underway. The IceCube-Gen2 high-energy array will instrument a 10km3 volume of clear glacial ice at the South Pole to deliver substantially larger astrophysical samples of all neutrino flavors. This contribution will highlight the science case and detector sensitivity studies performed in the design process. Additionally, astrophysical neutrino sensitivity can be increased by the addition of an extensive surface detector to identify and reject atmospheric backgrounds originating from the southern hemisphere. This large detector, in combination with the existing IceCube neutrino observatory and the rest of the IceCube-Gen2 facility, will be the flagship experiment of the new field of neutrino astronomy.

  14. Molecular phylogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa).

    PubMed

    Karpov, Serguei A; Bass, David; Mylnikov, Alexander P; Cavalier-Smith, Thomas

    2006-06-01

    Cercomonads are among the most abundant and widespread zooflagellates in soil and freshwater. We cultured 22 strains and report their complete 18S rRNA sequences and light microscopic morphology. Phylogenetic analysis of 51 Cercomonas rRNA genes shows in each previously identified major clade (A, B) two very robust, highly divergent, multi-species subclades (A1, A2; B1, B2). We studied kinetid ultrastructure of five clade A representatives by serial sections. All have two closely associated left ventral posterior microtubular roots, an anterior dorsal root, a microtubule-nucleating left anterior root, and a cone of microtubules passing to the nucleus. Anterior centrioles (=basal bodies, kinetosomes) of A1 have cartwheels; the posterior centriole does not, suggesting it is older, and implying flagellar transformation similar to other bikonts. Strain C-80 (subclade A2) differs greatly, having a dorsal posterior microtubule band, but lacking the A1-specific fibrillar striated root, nuclear extension to the centrioles, centriolar diaphragm, extrusomes; both mature centrioles lack cartwheels. For clade A2 we establish Eocercomonas gen. n., with type Eocercomonas ramosa sp. n., and for clade B1 Paracercomonas gen. n. (type Paracercomonas marina sp. n.). We establish Paracercomonas ekelundi sp. n. for culture SCCAP C1 and propose a Cercomonas longicauda neotype and Cercomonas (=Neocercomonas) jutlandica comb. n. and Paracercomonas (=Cercomonas) metabolica comb. n.

  15. 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.

  16. Gen-2 hand-held optical imager towards cancer imaging: reflectance and transillumination phantom studies.

    PubMed

    Gonzalez, Jean; Roman, Manuela; Hall, Michael; Godavarty, Anuradha

    2012-01-01

    Hand-held near-infrared (NIR) optical imagers are developed by various researchers towards non-invasive clinical breast imaging. Unlike these existing imagers that can perform only reflectance imaging, a generation-2 (Gen-2) hand-held optical imager has been recently developed to perform both reflectance and transillumination imaging. The unique forked design of the hand-held probe head(s) allows for reflectance imaging (as in ultrasound) and transillumination or compressed imaging (as in X-ray mammography). Phantom studies were performed to demonstrate two-dimensional (2D) target detection via reflectance and transillumination imaging at various target depths (1-5 cm deep) and using simultaneous multiple point illumination approach. It was observed that 0.45 cc targets were detected up to 5 cm deep during transillumination, but limited to 2.5 cm deep during reflectance imaging. Additionally, implementing appropriate data post-processing techniques along with a polynomial fitting approach, to plot 2D surface contours of the detected signal, yields distinct target detectability and localization. The ability of the gen-2 imager to perform both reflectance and transillumination imaging allows its direct comparison to ultrasound and X-ray mammography results, respectively, in future clinical breast imaging studies.

  17. Paragnomoxyala gen. nov. (Xyalidae, Monhysterida, Nematoda) from the East China Sea.

    PubMed

    Jiang, Weijun; Huang, Yong

    2015-11-05

    A new genus, Paragnomoxyala gen. nov., and a new species, Paragnomoxyala breviseta sp. nov. are described from the East China Sea. Paragnomoxyala gen. nov. is characterized by having large funnel-shaped buccal cavity with cuticularized walls and extended anteriorly; lips very high; striated cuticle; four cephalic setae, absence of outer labial setae; circular amphidial fovea; straight spicules and absence of gubernaculum; tail conico-cylindrical with three terminal setae; female monodelphic with an anterior outstretched ovary. It differs from similar genera by having a large buccal cavity unique in Xyalidae, straight spicules, lacking gubernaculum, and conico-cylindrical tail with terminal setae. Paragnomoxyala breviseta sp. nov. is characterized by having a large funnel-shaped buccal cavity, with cuticularized walls and extended anteriorly, 1.6-1.8 hd long and 63-79% cbd wide; four cephalic setae 3-4 µm long; circular amphids 6-9 µm in diameter; spicules straight but slightly bent at both ends; absence of gubernaculum and precloacal supplement.

  18. 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.

  19. Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems

    PubMed Central

    Morse, Alison M.; Carballo, Valentina; Baldwin, Donald A.; Taylor, Christopher G.; McIntyre, Lauren M.

    2010-01-01

    Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser-capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser-capture microdissection. Arabidopsis root cells undergoing giant cell formation as a result of nematode infestation and uninfested control root cells were laser-captured and used to evaluate two amplification systems. One, NuGEN's WT-Ovation Pico (Pico) amplification system, uses total RNA as starting material, and the other, NuGEN's WT-One-Direct (One-Direct) amplification system, uses lysate containing the captured cells. The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis. The One-Direct system was less reproducible and more variable than the Pico system. The Pico amplification kit resulted in the detection of thousands of differentially expressed genes between giant cells and control cells. This is in marked contrast to the relatively few genes detected after amplification with the One-Direct amplification kit. PMID:20808643

  20. Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.

    PubMed

    Ferbeyre, G; Bourdeau, V; Pageau, M; Miramontes, P; Cedergren, R

    2000-07-01

    Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes from the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster.